diff --git a/data/covid/preprints-summary.csv b/data/covid/preprints-summary.csv
index 113f88a6..c80ea7e8 100644
--- a/data/covid/preprints-summary.csv
+++ b/data/covid/preprints-summary.csv
@@ -1,47 +1,47 @@
-neurology,infectious diseases,pharmacology and therapeutics,molecular biology,health systems and quality improvement,oncology,Total,psychiatry and clinical psychology,microbiology,geriatric medicine,systems biology,primary care research,health economics,dentistry and oral medicine,dermatology,scientific communication and education,evolutionary biology,occupational and environmental health,health informatics,health policy,biophysics,biochemistry,pediatrics,orthopedics,epidemiology,respiratory medicine,month,radiology and imaging,public and global health,genetic and genomic medicine,intensive care and critical care medicine,hiv aids,pathology,genomics,bioinformatics,immunology,surgery,cardiovascular medicine,allergy and immunology,obstetrics and gynecology,emergency medicine
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-1,4,,,,,12,,,,,,,,,,,,,,,,,,6,,Feb-22,,1,,,,,,,,,,,,
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-1,8,,,,,21,,1,,,1,,,,,,,,,,,1,,7,,Dec-21,,1,,,,,,,,,1,,,
-1,5,,,2,,25,1,,,,1,,,,,,,,,1,,,,9,,Nov-21,,3,,1,,,1,,,,,,,
-,3,,,,,11,2,,1,,,,,,,,,,,,,1,,4,,Oct-21,,,,,,,,,,,,,,
-,5,1,,,,17,,,,,,,,,,,,1,,,,,,6,,Sep-21,,2,,1,,,,,,,1,,,
-,3,,,,,13,,,,,,,,,,,1,1,,,,,,2,1,Aug-21,,3,,1,,,,,,,1,,,
-,11,,,,1,25,,,,,,,,,,,,,,,,1,,3,2,Jul-21,,4,1,1,,,,,,,,,,1
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-,8,,,,,23,1,,,,,,,1,,,,1,,,,,,11,,May-21,,,1,,,,,,,,,,,
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-1,17,,,,,38,1,,2,,,,,,,,,2,,,1,1,,6,,Mar-21,1,5,1,,,,,,,,,,,
-,9,,,1,,23,,,,,,1,,,,,,1,,,,,,8,,Feb-21,,1,,,,,,,,1,1,,,
-,7,,,1,,22,1,,1,,1,,1,,,,,,1,,,,,4,,Jan-21,,3,,1,,,,,1,,,,,
-,4,,,1,,23,2,1,,,1,,,,,,,3,,,,,,4,,Dec-20,,3,,,,,2,,,,2,,,
-,13,,,,,28,,,,,,,,,,,,1,1,,,,,6,,Nov-20,,5,,,,,,1,1,,,,,
-,12,,,,1,29,3,,1,1,1,,,,,,,1,,,,,,6,,Oct-20,,,,1,,,,1,1,,,,,
-,8,,,,,26,2,1,,,1,,,,,,,1,,,,,,5,,Sep-20,,3,,1,1,,,,,,,,,3
-,12,,1,1,,26,,,,,,,,,,,1,,,,,,,6,,Aug-20,,2,1,,,,,,,,,,1,1
-,8,,,,,27,1,,,,,,,,,,,,,,,,,9,1,Jul-20,,4,,1,,,1,,1,,1,,,
-,10,,,1,1,34,3,,1,,,,,,,,,1,1,,,,,7,1,Jun-20,,2,,3,,,,1,1,,1,,,
-,10,,,,1,36,,,1,,,1,,,,,1,1,,,,,,7,1,May-20,,9,,1,,,,1,,,2,,,
-,6,,,1,,18,,,,,,,,,,,,,,,,,,7,,Apr-20,,1,2,,,,1,,,,,,,
-,1,,,,,8,,,,,,,,,,,,,,,,,,4,,Mar-20,,3,,,,,,,,,,,,
-,1,,,,,7,,,,,,,,,,,,,,,,,,4,,Feb-20,,2,,,,,,,,,,,,
+pediatrics,primary care research,public and global health,scientific communication and education,oncology,evolutionary biology,surgery,allergy and immunology,genetic and genomic medicine,Total,obstetrics and gynecology,infectious diseases,emergency medicine,respiratory medicine,ophthalmology,biochemistry,geriatric medicine,psychiatry and clinical psychology,hiv aids,pharmacology and therapeutics,health economics,systems biology,immunology,health policy,epidemiology,neurology,molecular biology,dentistry and oral medicine,genomics,cardiovascular medicine,intensive care and critical care medicine,health informatics,microbiology,orthopedics,bioinformatics,radiology and imaging,month,health systems and quality improvement,occupational and environmental health
+,,,,1,,,,,3,,1,,,,,,,,,,,,,1,,,,,,,,,,,,Nov-23,,
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+,,,,,,,,,1,,1,,,,,,,,,,,,,,,,,,,,,,,,,Sep-23,,
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+,,1,,,,,,1,7,,,,,,,,,,,,,,,3,,,,,,,,,,,,Jul-23,2,
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+,,1,,,,,,,6,,1,,1,,,,,,,,,1,,2,,,,,,,,,,,,May-23,,
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+,,2,,,,,,,8,,,,1,,,,,,,,,,,4,1,,,,,,,,,,,Feb-23,,
+,,,,,,,,,6,,1,,,,,,,,,,,,,5,,,,,,,,,,,,Jan-23,,
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+,,2,,,,,,,6,,2,,,,,,,,,,,,,1,,,,,1,,,,,,,Oct-22,,
+1,,1,,,,,,,8,,2,,1,,,,,,,,,,,1,,,,,,,,1,,,,Sep-22,,1
+,,3,,,,,,,9,,3,,,,,,,,,,,,,3,,,,,,,,,,,,Aug-22,,
+1,,,,,,,,,8,,3,,,,,,,,,,,1,,2,,,,,,,1,,,,,Jul-22,,
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+,,1,,,,,,,14,,2,,,,,,,,,1,,,,5,,,,,1,,,1,,,,Apr-22,2,1
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+,,1,,,,,,,12,,4,,,,,,,,,,,,,6,1,,,,,,,,,,,Feb-22,,
+,,1,,,,,,,14,,3,,,,,,,,,,,1,,5,,,,,1,,2,,,,,Jan-22,,1
+1,1,1,,,,,,,23,,8,,,,,,,,,,,,,9,1,,,,1,,,1,,,,Dec-21,,
+,1,3,,,,,,,22,,5,,,,,,1,,,,,,,7,1,,,1,,1,,,,,,Nov-21,2,
+,,,,,,,,,10,,3,,,,,1,2,,,,,,,4,,,,,,,,,,,,Oct-21,,
+,,2,,,,,,,16,,4,,,,,,,,1,,,,,6,,,,,1,1,1,,,,,Sep-21,,
+,,3,,,,,,,13,,3,,1,,,,,,,,,,,2,,,,,1,1,1,,,,,Aug-21,,1
+1,,4,,1,,,,,25,,12,1,2,,,,,,,,,,,3,,,,,,1,,,,,,Jul-21,,
+1,1,4,,,,,1,,27,,6,,,,,,1,,,,,1,,7,1,,,,,1,1,,,,,Jun-21,1,1
+,,1,,,,,,1,22,,8,,,,,,1,,,,,,,10,,,,,,,1,,,,,May-21,,
+,1,1,,,,,1,,18,,6,,,,,,1,,,,,,,3,,,,,,,1,1,,,,Apr-21,1,2
+1,,5,,,,1,,1,38,,16,,,,1,2,1,,,,,,,6,1,,,,,,2,,,,1,Mar-21,,
+,,1,,,,1,,,23,,8,,,,,,,,,1,,,,9,,,,,1,,1,,,,,Feb-21,1,
+,1,3,,,,,,,21,,6,,,,,1,1,,,,,1,1,4,,,1,,,1,,,,,,Jan-21,1,
+,1,3,,,,,,,23,,4,,,,,,2,,,,,,,4,,,,2,2,,3,1,,,,Dec-20,1,
+,,5,,,,,,,28,,13,,,,,,,,,,,1,1,6,,,,,,,1,,,1,,Nov-20,,
+,1,,,,,,,,28,,12,,,,,1,3,,,,1,1,1,5,,,,,,1,1,,,1,,Oct-20,,
+,1,3,,,,,,,26,,8,3,,,,,2,1,,,,,,5,,,,,,1,1,1,,,,Sep-20,,
+,,2,,,,,,1,26,1,12,2,,,,,,,,,,,,5,,1,,,,,,,,,,Aug-20,1,1
+,,4,,,,,,,28,,8,,1,,,,1,,,,,1,,10,,,,1,1,1,,,,,,Jul-20,,
+,,3,,1,,,,,36,,9,,1,1,,1,4,,,,,1,1,7,,,,,1,3,1,,,1,,Jun-20,1,
+,,9,,1,,,,,36,,9,,1,,,1,,,,1,,,,8,,,,,2,1,1,,,1,,May-20,,1
+,,1,,,,,,2,19,,7,,,,,,,,,,,,,7,,,,1,,,,,,,,Apr-20,1,
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diff --git a/data/covid/preprints.csv b/data/covid/preprints.csv
index 4c459c92..e00d7a2d 100644
--- a/data/covid/preprints.csv
+++ b/data/covid/preprints.csv
@@ -376,13 +376,6 @@ ResultsOf 3,670,455 people, those with CRD had a modest higher risk of cardiovas
 ConclusionsHigher risk of cardiovascular events following COVID-19 might be explained at least in part by the underlying CRD and severity of that condition. In addition, COVID-19 vaccines were beneficial to both people with and without CRD with regards to CV events.
 
 Key MessagesPre-existing chronic respiratory disease, asthma and COPD severity were associated with a higher risk of various types of cardiovascular outcomes following COVID-19. Regardless of having pre-existing chronic respiratory disease, COVID-19 vaccination reduced the risk of cardiovascular events following COVID-19.",epidemiology,fuzzy,100,100
-medRxiv,10.1101/2023.02.28.23286559,2023-03-01,https://medrxiv.org/cgi/content/short/2023.02.28.23286559,Elevated symptoms of depression and anxiety among family members and friends of critically ill COVID-19 patients - An observational study of five cohorts across four countries,Anikó Lovik; Juan González-Hijón; Asle Hoffart; Chloe Fawns-Ritchie; Ingibjörg Magnúsdóttir; Li Lu; Anna Bára Unnarsdóttir; Anna K. Kähler; Archie Campbell; Arna Hauksdóttir; Charilaos Chourpiliadis; Daniel L McCartney; Edda Björk Thordardóttir; Emily E. Joyce; Emma M. Frans; Jóhanna Jakobsdóttir; Lill Trogstad; Ole A. Andreassen; Per Magnus; Sverre Urnes Johnson; Patrick F. Sullivan; Thor Aspelund; David J. Porteous; Helga Ask; Omid V. Ebrahimi; Unnur Anna Valdimarsdóttir; Fang Fang,Karolinska Institutet and Leiden University; Karolinska Institutet; University of Oslo; University of Edinburgh; University of Iceland; University of Oslo; University of Iceland; Karolinska Institutet; University of Edinburgh; University of Iceland; Karolinska Institutet; University of Edinburgh; University of Iceland; Karolinska Institutet; Karolinska Institutet; University of Iceland; Norwegian Institute of Public Health; University of Oslo; Norwegian Institute of Public Health; University of Oslo; Karolinska Institutet; University of Iceland; University of Edinburgh; University of Oslo; University of Oslo; Karolinska Institutet; Karolinska Institutet,"BackgroundLittle is known regarding the mental health impact of having a significant person (family member and/or close friend) with COVID-19 of different severity.
-
-MethodsThe study included five prospective cohorts from four countries (Iceland, Norway, Sweden, and the UK) with self-reported data on COVID-19 and symptoms of depression and anxiety during March 2020-March 2022. We calculated the prevalence ratio (PR) of depression and anxiety in relation to having a significant person with COVID-19 and performed a longitudinal analysis in the Swedish cohort to describe the temporal patterns of the results.
-
-Results162,237 and 168,783 individuals were included in the analysis of depression and anxiety, respectively, of whom 24,718 and 27,003 reported a significant person with COVID-19. Overall, the PR was 1.07 (95% CI: 1.05-1.10) for depression and 1.08 (95% CI: 1.03-1.13) for anxiety among significant others of COVID-19 patients. The respective PRs for depression and anxiety were 1.04 (95% CI: 1.01-1.07) and 1.03 (95% CI: 0.98-1.07) if the significant person was never hospitalized, 1.15 (95% CI: 1.08-1.23) and 1.24 (95% CI: 1.14-1.34) if the patient was hospitalized, 1.42 (95% CI: 1.27-1.57) and 1.45 (95% CI: 1.31-1.60) if admitted to the ICU, and 1.34 (95% CI: 1.22-1.46) and 1.36 (95% CI: 1.22-1.51) if the significant person died. Individuals of hospitalized, ICU admitted, or deceased patients showed higher prevalence of depression and anxiety during the entire 12 months after the COVID-19 diagnosis of the significant person.
-
-ConclusionsClose friends and family members of critically ill COVID-19 patients show elevated prevalence of depression and anxiety throughout the first year after the diagnosis.",public and global health,fuzzy,100,100
 medRxiv,10.1101/2023.02.17.23286079,2023-02-23,https://medrxiv.org/cgi/content/short/2023.02.17.23286079,"Surface sampling for SARS-CoV-2 in workplace outbreak settings in the UK, 2021-22.",Ian George Nicholls; Antony Spencer; Yiqun Chen; Allan Bennett; Barry Atkinson,UK Health Security Agency; UK Health Security Agency; Health and Safety Executive; UK Health Security Agency; UK Health Security Agency,"AimsTo utilise environmental surface sampling to evaluate areas of SARS-CoV-2 contamination within workplaces to identify trends and improve local COVID-control measures.
 
 Methods and ResultsSurface sampling was undertaken at 12 workplaces that experienced a cluster of COVID-19 cases in the workforce between March 2021 and March 2022. 7.4% (61/829) of samples collected were positive for SARS-CoV-2 RNA by qPCR with only 1.8% (15/829) of samples identified with crossing threshold (Ct) values below 35.0. No sample returned whole genome sequence inferring RNA detected was degraded.
@@ -571,7 +564,6 @@ Findings64% (456/714) of participants reported poor sleep quality; 56% felt thei
 InterpretationSleep disturbance is associated with dyspnoea, anxiety and muscle weakness following COVID-19 hospitalisation. It could have similar effects for other causes of hospitalisation where sleep disturbance is prevalent.
 
 FundingUK Research and Innovation, National Institute for Health Research, and Engineering and Physical Sciences Research Council.",respiratory medicine,fuzzy,100,100
-medRxiv,10.1101/2022.12.09.22283280,2022-12-13,https://medrxiv.org/cgi/content/short/2022.12.09.22283280,Identification of a protein expression signature distinguishing early from organising diffuse alveolar damage in COVID-19 patients.,Helen Ashwin; Luke Milross; Julie Wilson; Joaquim Majo; Jimmy T. H. Lee; Grant Calder; Bethany Hunter; Sally James; Dimitris Lagos; Nathalie Signoret; Andrew Filby; Omer Ali Bayraktar; Andrew J Fisher; Paul M Kaye,University of York; Newcastle University; University of York; Newcastle upon Tyne Hospitals NHS Foundation Trust; Sanger Institute; University of York; Newcastle University; University of York; University of York; University of York; Newcastle University; Sanger Institute; Newcastle University; University of York,"Diffuse alveolar damage (DAD) is a histopathological finding associated with severe viral infections, including SARS-CoV-2. However, the mechanisms mediating progression of DAD are poorly understood. Applying protein digital spatial profiling to lung tissue obtained from a cohort of 27 COVID-19 autopsy cases from the UK, we identified a protein signature (ARG1, CD127, GZMB, IDO1, Ki67, phospho-PRAS40 (T246), and VISTA that distinguishes early / exudative DAD from late / organising DAD with good predictive accuracy. These proteins warrant further investigation as potential immunotherapeutic targets to modulate DAD progression and improve patient outcome.",pathology,fuzzy,92,100
 medRxiv,10.1101/2022.11.29.22282883,2022-12-12,https://medrxiv.org/cgi/content/short/2022.11.29.22282883,"The protection gap under a social health protection initiative in the COVID-19 pandemic: A case study from Khyber Pakhtunkhwa, Pakistan.",Sheraz  Ahmad Khan; Kathrin Cresswell; Aziz Sheikh,The University of Edinburgh; The University of Edinburgh College of Medicine and Veterinary Medicine; The University of Edinburgh College of Medicine and Veterinary Medicine,"BackgroundSehat Sahulat Programme (SSP) is a Social Health Protection (SHP) initiative by the Government of Khyber Pakhtunkhwa (GoKP), covering inpatient services for 100% of the provinces population. In this paper, we describe SSPs role in GoKPs COVID-19 response and draw inferences for similar programmes in Pakistan.
 
 Methodology and methodsWe conceptualised SSP as an instrumental case study and collected three complementary data sources. First, we studied GoKPs official documents to understand SSPs benefits package. Then we undertook in-depth interviews and collected non-participant observations at the SSP policy and implementation levels. We recruited participants through direct (verbal and email) and indirect (invitation posters) methods.
@@ -770,13 +762,6 @@ C_LIO_LIWe used a novel approach and linked multiple datasets to identify a coho
 C_LIO_LIThere was heterogeneity within the Shielded Patient List that was used to create the cohorts of children identified as CEV or living with a CEV person, in terms of the type and severity of individuals underlying conditions; the manner in which people were added to the list; the time point that people were added to the list; and the extent to which people followed the shielding guidance
 C_LIO_LIRoutinely collected healthcare data does not capture self-reported health, and is likely to underestimate the burden of common mental disorders in the population
 C_LI",pediatrics,fuzzy,100,100
-medRxiv,10.1101/2022.09.09.22279754,2022-09-09,https://medrxiv.org/cgi/content/short/2022.09.09.22279754,Contact patterns of UK home delivery drivers and their use of protective measures during the COVID-19 pandemic: a cross-sectional study,Jessica R E Bridgen; Hua Wei; Carl A Whitfield; Yang Han; Ian Hall; Chris Jewell; Martie JA van Tongeren; Jonathan M Read,Lancaster University; The University of Manchester; University of Manchester; University of Manchester; University of Manchester; Lancaster University; University of Manchester; Lancaster University,"ObjectivesTo quantify contact patterns of UK home delivery drivers and identify protective measures adopted during the pandemic.
-
-MethodsWe conducted a cross-sectional online survey to measure the interactions of 170 UK delivery drivers during a working shift between 7 December 2020 and 31 March 2021.
-
-ResultsDelivery drivers had a mean number of 71.6 (95% Confidence Interval (CI) 61.0 to 84.1) customer contacts per shift and 15.0 (95%CI 11.19 to 19.20) depot contacts per shift. Maintaining physical distancing with customers was more common than at delivery depots. Prolonged contact (more than 5 minutes) with customers was reported by 5.4% of drivers on their last shift. We found 3.0% of drivers had tested positive for SARS-CoV-2 since the start of the pandemic and 16.8% of drivers had self-isolated due to a suspected or confirmed case of COVID-19. Additionally, 5.3% (95%CI 2.3% to 10.2%) of participants reported having worked whilst ill with COVID-19 symptoms, or with a member of their household having a suspected or confirmed case of COVID-19.
-
-ConclusionDelivery drivers had a large number of face-to-face customer and depot contacts per shift compared to other working adults during this time. However, transmission risk may be curtailed as contact with customers was of short duration. Most drivers were unable to maintain physical distance with customers and at depots at all times. Usage of protective items such as face masks and hand sanitizer was widespread.",occupational and environmental health,fuzzy,100,100
 medRxiv,10.1101/2022.09.01.22279473,2022-09-02,https://medrxiv.org/cgi/content/short/2022.09.01.22279473,Rebound in asthma exacerbations following relaxation of COVID-19 restrictions: a longitudinal population-based study (COVIDENCE UK),Florence Tydeman; Paul Pfeffer; Giulia Vivaldi; Hayley Holt; Mohammad Talaei; David Jolliffe; Gwyneth Davies; Ronan Lyons; Chris Griffiths; Frank Kee; Aziz Sheikh; Seif Shaheen; Adrian R Martineau,Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Swansea University; Swansea University; Queen Mary University of London; Queen's University Belfast; Edinburgh University; Queen Mary University of London; Queen Mary University of London,"BackgroundThe imposition of restrictions on social mixing early in the COVID-19 pandemic was followed by a reduction in asthma exacerbations in multiple settings internationally. Temporal trends in social mixing, incident acute respiratory infections (ARI) and asthma exacerbations following relaxation of COVID-19 restrictions have not yet been described.
 
 MethodsWe conducted a population-based longitudinal study in 2,312 UK adults with asthma between November 2020 and April 2022. Details of face covering use, social mixing, incident ARI and moderate/severe asthma exacerbations were collected via monthly on-line questionnaires. Temporal changes in these parameters were visualised using Poisson generalised additive models. Multilevel logistic regression was used to test for associations between incident ARI and risk of asthma exacerbations, adjusting for potential confounders.
@@ -822,37 +807,9 @@ MethodsThis protocol and study materials were co-produced with a Community Advis
 
 Ethics and disseminationEthical approval has been obtained from the Faculty of Medicine Ethics Committee and Research Integrity and Governance, University of Southampton. (reference number 72400). Findings will be reported in a report and submitted for peer-reviewed publication. Definitive methods of dissemination will be decided by the CAB. Summaries of the findings will also be shared on the STIMULATE-ICP website, locally in the study area and through social media. We will specifically target policy makers and those responsible for shaping and commissioning Long Covid healthcare services and social support such as NHSE England Long Covid Group.",public and global health,fuzzy,100,100
 medRxiv,10.1101/2022.08.22.22278973,2022-08-24,https://medrxiv.org/cgi/content/short/2022.08.22.22278973,The Impact of SARS-CoV-2 Vaccine Dose Separation and Dose Targeting on Hospital Admissions and Deaths from COVID-19 in England,Matt J Keeling; Sam Moore; Bridget Penman; Edward M Hill,University of Warwick; University of Warwick; University of Warwick; University of Warwick,"In late 2020, the JCVI (the Joint Committee on Vaccination and Immunisation, which provides advice to the Department of Health and Social Care, England) made two important recommendations for the initial roll-out of the COVID-19 vaccine. The first was that vaccines should be targeted to the elderly and vulnerable, with the aim of maximally preventing disease rather than infection. The second was to increase the interval between first and second doses from 3 to 12 weeks. Here, we re-examine these recommendations through a mathematical model of SARS-CoV-2 infection in England. We show that targeting the most vulnerable had the biggest immediate impact (compared to targeting younger individuals who may be more responsible for transmission). The 12-week delay was also highly beneficial, estimated to have averted between 32-72 thousand hospital admissions and 4-9 thousand deaths over the first ten months of the campaign (December 2020 - September 2021) depending on the assumed interaction between dose interval and efficacy.",infectious diseases,fuzzy,100,100
-medRxiv,10.1101/2022.08.13.22278733,2022-08-16,https://medrxiv.org/cgi/content/short/2022.08.13.22278733,QCovid 4 - Predicting risk of death or hospitalisation from COVID-19 in adults testing positive for SARS-CoV-2 infection during the Omicron wave in England,Julia Hippisley-Cox; Kamlesh Khunti; Aziz Sheikh; Jonathan Nguyen-Van-Tam; Carol Coupland,University of Oxford; University of Leicester; University of Edinburgh; University of Nottingham; University of Oxford,"ObjectivesTo (a) derive and validate risk prediction algorithms (QCovid4) to estimate risk of COVID-19 mortality and hospitalisation in UK adults with a SARS-CoV-2 positive test during the  Omicron pandemic wave in England and (b) evaluate performance with earlier versions of algorithms developed in previous pandemic waves and the high-risk cohort identified by NHS Digital in England.
-
-DesignPopulation-based cohort study using the QResearch database linked to national data on COVID-19 vaccination, high risk patients prioritised for COVID-19 therapeutics, SARS-CoV-2 results, hospitalisation, cancer registry, systemic anticancer treatment, radiotherapy and the national death registry.
-
-Settings and study period1.3 million adults in the derivation cohort and 0.15 million adults in the validation cohort aged 18-100 years with a SARS-CoV-2 positive test between 11th December 2021 and 31st March 2022 with follow up to 30th June 2022.
-
-Main outcome measuresOur primary outcome was COVID-19 death. The secondary outcome of interest was COVID-19 hospital admission. Models fitted in the derivation cohort to derive risk equations using a range of predictor variables. Performance evaluated in a separate validation cohort.
-
-ResultsOf 1,297,984 people with a SARS-CoV-2 positive test in the derivation cohort, 18,756 (1.45%) had a COVID-19 related hospital admission and 3,878 (0.3%) had a COVID-19 death during follow-up. Of the 145,404 people in the validation cohort, there were 2,124 (1.46%) COVID-19 admissions and 461 (0.3%) COVID-19 deaths.
-
-The COVID-19 mortality rate in men increased with age and deprivation. In the QCovid4 model in men hazard ratios were highest for those with the following conditions (for 95% CI see Figure 1): kidney transplant (6.1-fold increase); Downs syndrome (4.9-fold); radiotherapy (3.1-fold); type 1 diabetes (3.4-fold); chemotherapy grade A (3.8-fold), grade B (5.8-fold); grade C (10.9-fold); solid organ transplant ever (2.4-fold); dementia (1.62-fold); Parkinsons disease (2.2-fold); liver cirrhosis (2.5-fold). Other conditions associated with increased COVID-19 mortality included learning disability, chronic kidney disease (stages 4 and 5), blood cancer, respiratory cancer, immunosuppressants, oral steroids, COPD, coronary heart disease, stroke, atrial fibrillation, heart failure, thromboembolism, rheumatoid/SLE, schizophrenia/bipolar disease sickle cell/HIV/SCID; type 2 diabetes. Results were similar in the model in women.
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-O_FIG O_LINKSMALLFIG WIDTH=100 HEIGHT=200 SRC=""FIGDIR/small/22278733v1_fig1.gif"" ALT=""Figure 1"">
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-org.highwire.dtl.DTLVardef@4e93b7org.highwire.dtl.DTLVardef@c3e600org.highwire.dtl.DTLVardef@1311bd4org.highwire.dtl.DTLVardef@11a3246_HPS_FORMAT_FIGEXP  M_FIG O_FLOATNOFigure 1C_FLOATNO QCOVID4 (mortality): Adjusted hazard ratios for COVID-19 death in men mutually adjusted and also adjusted for fractional polynomial terms for age and BMI
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-C_FIG COVID-19 mortality risk was lower among those who had received COVID-19 vaccination compared with unvaccinated individuals with evidence of a dose response relationship. The reduced mortality rates associated with prior SARS-CoV-2 infection were similar in men (adjusted hazard ratio (HR) 0.51 (95% CI 0.40, 0.64)) and women (adjusted HR 0.55 (95%CI 0.45, 0.67)).
+medRxiv,10.1101/2022.08.17.22278893,2022-08-18,https://medrxiv.org/cgi/content/short/2022.08.17.22278893,Uptake of Sotrovimab for prevention of severe COVID-19 and its safety in the community in England,Martina Patone; Holly Tibble; Andrew JHL Snelling; Carol Coupland; Aziz Sheikh; Julia Hippisley-Cox,University of Oxford; University of Edinburgh; University of Oxford; University of Oxford; University of Edinburgh; University of Oxford,"Sotrovimab is a neutralising monoclonal antibody (nMAB), currently administrated in England to treat extremely clinically vulnerable COVID-19 patients. Trials have shown it to have mild or moderate side effects, however safety in real-world settings has not been yet evaluated. We used national databases to investigate its uptake and safety in community patients across England. We used a cohort study to describe uptake and a self-controlled case series design to evaluate the risks of 49 pre-specified suspected adverse events in the 2-28 days post-treatment. Between December 11, 2021 and May 24, 2022, there were 172,860 COVID-19 patients eligible for treatment. Of the 22,815 people who received Sotrovimab, 21,487 (94.2%) had a positive SARS-CoV-2 test and 5,999 (26.3%) were not on the eligible list. Between treated and untreated eligible individuals, the mean age (54.6, SD: 16.1 vs 54.1, SD: 18.3) and sex distribution (women: 60.9% vs 58.1%; men: 38.9% vs 41.1%) were similar. There were marked variations in uptake between ethnic groups, which was higher amongst Indian (15.0%; 95%CI 13.8, 16.3), Other Asian (13.7%; 95%CI 11.9, 15.8), White (13.4%; 95%CI 13.3, 13.6), and Bangladeshi (11.4%; 95%CI 8.8, 14.6); and lower amongst Black Caribbean individuals (6.4%; 95%CI 5.4, 7.5) and Black Africans (4.7%; 95%CI 4.1, 5.4). We found no increased risk of any of the suspected adverse events in the overall period of 2-28 days post-treatment, but an increased risk of rheumatoid arthritis (IRR 3.08, 95% CI 1.44, 6.58) and of systematic lupus erythematosus (IRR 5.15, 95% CI 1.60, 16.60) in the 2-3 days post-treatment, when we narrowed the risk period.
 
-The QCOVID4 algorithm explained 76.6% (95%CI 74.4 to 78.8) of the variation in time to COVID-19 death (R2) in women. The D statistic was 3.70 (95%CI 3.48 to 3.93) and the Harrells C statistic was 0.965 (95%CI 0.951 to 0.978). The corresponding results for COVID-19 death in men were similar with R2 76.0% (95% 73.9 to 78.2); D statistic 3.65 (95%CI 3.43 to 3.86) and C statistic of 0.970 (95%CI 0.962 to 0.979). QCOVID4 discrimination for mortality was slightly higher than that for QCOVID1 and QCOVID2, but calibration was much improved.
-
-ConclusionThe QCovid4 risk algorithm modelled from data during the UKs Omicron wave now includes vaccination dose and prior SARS-CoV-2 infection and predicts COVID-19 mortality among people with a positive test. It has excellent performance and could be used for targeting COVID-19 vaccination and therapeutics. Although large disparities in risks of severe COVID-19 outcomes among ethnic minority groups were observed during the early waves of the pandemic, these are much reduced now with no increased risk of mortality by ethnic group.
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-What is knownO_LIThe QCOVID risk assessment algorithm for predicting risk of COVID-19 death or hospital admission based on individual characteristics has been used in England to identify people at high risk of severe COVID-19 outcomes, adding an additional 1.5 million people to the national shielded patient list in England and in the UK for prioritising people for COVID-19 vaccination.
-C_LIO_LIThere are ethnic disparities in severe COVID-19 outcomes which were most marked in the first pandemic wave in 2020.
-C_LIO_LICOVID-19 vaccinations and therapeutics (monoclonal antibodies and antivirals) are available but need to be targeted to those at highest risk of severe outcomes.
-C_LI
-
-What this study addsO_LIThe QCOVID4 risk algorithm using data from the Omicron wave now includes number of vaccination doses and prior SARS-CoV-2 infection. It has excellent performance both for ranking individuals (discrimination) and predicting levels of absolute risk (calibration) and can be used for targeting COVID-19 vaccination and therapeutics as well as individualised risk assessment.
-C_LIO_LIQCOVID4 more accurately identifies individuals at highest levels of absolute risk for targeted interventions than the  conditions-based approach adopted by NHS Digital based on relative risk of a list of medical conditions.
-C_LIO_LIAlthough large disparities in risks of severe COVID-19 outcomes among ethnic minority groups were observed during the early waves of the pandemic, these are much reduced now with no increased risk of mortality by ethnic group.
-C_LI",epidemiology,fuzzy,100,100
+FundingNational Institute of Health Research (Grant reference 135561)",epidemiology,fuzzy,100,100
 medRxiv,10.1101/2022.08.08.22278532,2022-08-09,https://medrxiv.org/cgi/content/short/2022.08.08.22278532,Clinical effectiveness of SARS-CoV-2 booster vaccine against Omicron infection in residents and staff of Long-Term Care Facilities: a prospective cohort study (VIVALDI),Oliver Stirrup; Madhumita Shrotri; Natalie L Adams; Maria Krutikov; Hadjer Nacer-Laidi; Borscha Azmi; Tom Palmer; Christopher Fuller; Aidan Irwin-Singer; Verity Baynton; Gokhan Tut; Paul Moss; Andrew Hayward; Andrew Copas; Laura Shallcross,University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; Department of Health and Social Care; Department of Health and Social Care; University of Birmingham; University of Birmingham; University College London; University College London; University College London,"BackgroundSuccessive SARS-CoV-2 variants have caused severe disease in long-term care facility (LTCF) residents. Primary vaccination provides strong short-term protection, but data are limited on duration of protection following booster vaccines, particularly against the Omicron variant. We investigated effectiveness of booster vaccination against infections, hospitalisations and deaths among LTCF residents and staff in England.
 
 MethodsWe included residents and staff of LTCFs within the VIVALDI study (ISRCTN 14447421) who underwent routine, asymptomatic testing (December 12 2021-March 31 2022). Cox regression was used to estimate relative hazards of SARS-CoV-2 infection, and associated hospitalisation and death at 0-13, 14-48, 49-83 and 84 days after dose 3 of SARS-CoV-2 vaccination compared to 2 doses (after 84+ days), stratified by previous SARS-CoV-2 infection and adjusting for age, sex, LTCF capacity and local SARS-CoV-2 incidence.
@@ -862,6 +819,13 @@ Results14175 residents and 19973 staff were included. In residents without prior
 ConclusionsBooster vaccination provides sustained protection against severe outcomes following infection with the Omicron variant, but no protection against infection from 3 months onwards. Ongoing surveillance for SARS-CoV-2 in LTCFs is crucial.
 
 SummaryThe COVID-19 pandemic has severely impacted residents in long-term care facilities (LTCFs). Booster vaccination provides sustained moderate protection against severe outcomes, but no protection against infection was apparent from around 3 months onwards. Ongoing surveillance in LTCFs is crucial.",infectious diseases,fuzzy,100,100
+medRxiv,10.1101/2022.08.07.22278510,2022-08-09,https://medrxiv.org/cgi/content/short/2022.08.07.22278510,Metabolomic and gut microbiome profiles across the spectrum of community-based COVID and non-COVID disease: A COVID-19 Biobank study.,Marc F Österdahl; Ronan Whiston; Carole H Sudre; Francesco Asnicar; Nathan J Cheetham; Aitor Blanco Miguez; Vicky Bowyer; Michela Antonelli; Olivia Snell; Liane dos Santos Canas; Christina Hu; Jonathan Wolf; Cristina Menni; Michael Malim; Deborah Hart; Tim Spector; Sarah Berry; Nicola Segata; Katie Doores; Sebastien Ourselin; Emma L Duncan; Claire J Steves,King's College London; King's College London; King's College London; University of Trento; King's College London; University of Trento; King's College London; King's College London; King's College London; King's College London; ZOE Global Ltd.; ZOE Global Ltd.; King's College London; King's College London; King's College London; King's College London; King's College London; University of Trento; King's College London; King's College London; King's College London; King's College London,"Whilst many with SARS-CoV-2 infection have mild disease, managed in the community, individuals with cardiovascular risk factors experienced often more severe acute disease, requiring hospitalisation. Increasing concern has also developed over long symptom duration in many individuals, including the majority who managed acutely in the community. Risk factors for long symptom duration, including biological variables, are still poorly defined.
+
+We examine post-illness metabolomic and gut-microbiome profiles, in community-dwelling participants with SARS-CoV-2, ranging from asymptomatic illness to Post-COVID Syndrome, and participants with prolonged non-COVID-19 illnesses. We also assess a pre-established metabolomic biomarker score for its association with illness duration.
+
+We found an atherogenic-dyslipidaemic metabolic profile, and greater biomarker scores, associated with longer illness, both in individuals with and without SARS-CoV-2 infection. We found no association between illness duration and gut microbiome in convalescence.
+
+Findings highlight the potential role of cardiometabolic dysfunction to the experience of long illness duration, including after COVID-19.",epidemiology,fuzzy,100,100
 medRxiv,10.1101/2022.08.08.22278493,2022-08-09,https://medrxiv.org/cgi/content/short/2022.08.08.22278493,Inequalities in colorectal cancer screening uptake in Wales: examination of the impact of the temporary suspension of the screening programme during the COVID-19 pandemic,Diana Bright; Sharon Hillier; Jiao Song; Dyfed W Huws; Giles Greene; Karen Hodgson; Ashley Akbari; Rowena Griffiths; Alisha R Davies,"Public Health Wales; Public Health Wales; Public Health Wales; Public Health Wales; Population Data Science, Swansea University Medical School, Faculty of Medicine, Health & Life Science, Swansea University, Swansea, Wales; Public Health Wales; Public Health Wales; Population Data Science, Swansea University Medical School, Faculty of Medicine, Health & Life Science, Swansea University, Swansea, Wales; Population Data Science, Swansea University Medical School, Faculty of Medicine, Health & Life Science, Swansea University, Swansea, Wales; Public Health Wales","BackgroundResponse to the early stages of the COVID-19 pandemic resulted in the temporary disruption of cancer screening in the UK, and strong public messaging to stay safe and to protect NHS capacity. Following reintroduction in services, we explored the impact on inequalities in uptake of the Bowel Screening Wales (BSW) programme to identify groups who may benefit from tailored interventions.
 
 MethodsRecords within the BSW were linked to electronic health records (EHR) and administrative data within the Secured Anonymised Information Linkage (SAIL) Databank. Ethnic group was obtained from a linked data method available within SAIL. We examined uptake for the first 3 months of invitations (August to October) following the reintroduction of BSW programme in 2020, compared to the same period in the preceding 3 years. Uptake was measured across a 6 month follow-up period. Logistic models were conducted to analyse variations in uptake by sex, age group, income deprivation quintile, urban/rural location, ethnic group, and clinically extremely vulnerable (CEV) status in each period; and to compare uptake within sociodemographic groups between different periods.
@@ -934,6 +898,13 @@ Results1,528,431 people were matched in each group, contributing a total 23,150,
 
 ConclusionBooster vaccination with mRNA-1273 COVID-19 vaccine was more effective than BNT162b2 in preventing SARS-CoV-2 infection and COVID-19 hospitalisation during the first 12 weeks after vaccination, during a period of Delta followed by Omicron variant dominance.",epidemiology,fuzzy,100,100
 bioRxiv,10.1101/2022.07.26.501570,2022-07-26,https://biorxiv.org/cgi/content/short/2022.07.26.501570,Primary Omicron infection elicits weak antibody response but robust cellularimmunity in children,Alexander C Dowell; Tara Lancaster; Rachel Bruton; Georgina Ireland; Christopher Bentley; Panagiota Sylla; Jianmin Zuo; Sam Scott; Azar Jardin; Jusnara Begum; Thomas Roberts; Christine Stephens; Shabana Ditta; Rebecca Shepherdson; Annable Powell; Andrew Brent; Bernadette Brent; Frances Baawuah; Ifeanyichukwu Okike; Joanna Beckmann; Shazaad Ahmad; Felicity Aiano; Joanna Garstang; Mary Ramsay; Rafaq Azad; Dagmar Waiblinger; Brian Willet; John Wright; Shamez Ladhani; Paul Moss,"Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Immunisation Department, UK Health Security Agency, 61 Colindale Avenue, London, United Kingdom; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61-1QH, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, BD9 6RJ, UK.; Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, BD9 6RJ, UK.; Immunisation Department, UK Health Security Agency, 61 Colindale Avenue, London, United Kingdom; Oxford University Hospitals NHS Foundation Trust, Old Road, Oxford OX3 7HE; Oxford University Hospitals NHS Foundation Trust, Old Road, Oxford OX3 7HE; Immunisation Department, UK Health Security Agency, 61 Colindale Avenue, London, United Kingdom; Immunisation Department, UK Health Security Agency, 61 Colindale Avenue, London, United Kingdom; East London NHS Foundation Trust, 9 Allie Street, London E1 8DE, UK; Manchester University NHS Foundation Trust, Oxford Road, Manchester M13 9WL, UK; Immunisation Department, UK Health Security Agency, 61 Colindale Avenue, London, United Kingdom; Birmingham Community Healthcare NHS Trust, Holt Street, Aston B7 4BN, UK; Immunisation Department, UK Health Security Agency, 61 Colindale Avenue, London, United Kingdom; Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, BD9 6RJ, UK.; Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, BD9 6RJ, UK.; MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61-1QH, UK; Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, BD9 6RJ, UK.; Immunisation Department, UK Health Security Agency, 61 Colindale Avenue, London, United Kingdom; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK","Omicron variants of SARS-CoV-2 are globally dominant and infection rates are very high in children. We determined immune responses following Omicron BA.1/2 infection in children aged 6-14 years and related this to prior and subsequent SARS-CoV-2 infection or vaccination. Primary Omicron infection elicited a weak antibody response with poor functional neutralizing antibodies. Subsequent Omicron reinfection or COVID-19 vaccination elicited increased antibody titres with broad neutralisation of Omicron subvariants. Prior pre-Omicron SARS-CoV-2 virus infection or vaccination primed for robust antibody responses following Omicron infection but these remained primarily focussed against ancestral variants. Primary Omicron infection thus elicits a weak antibody response in children which is boosted after reinfection or vaccination. Cellular responses were robust and broadly equivalent in all groups, providing protection against severe disease irrespective of SARS-CoV-2 variant. Immunological imprinting is likely to act as an important determinant of long-term humoral immunity, the future clinical importance of which is unknown.",immunology,fuzzy,100,100
+medRxiv,10.1101/2022.07.20.22277838,2022-07-21,https://medrxiv.org/cgi/content/short/2022.07.20.22277838,"National and regional prevalence of SARS-CoV-2 antibodies in primary and secondary school children in England: the School Infection Survey, a national open cohort study, November 2021",Annabel A Powell; Georgina Ireland; Rebecca Leeson; Andrea Lacey; Ben Ford; John Poh; Samreen Ijaz; Justin Shute; Peter Cherepanov; Richard Tedder; Christian Bottomley; Fiona Dawe; Punam Mangtani; Peter Jones; Patrick Nguipdop-Djomo; Shamez Ladhani,UK Health Security Agency; UK Health Security Agency; Office for National Statistics; Office for National Statistics; Office for National Statistics; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; Imperial College London; Francis Crick Institute; London School of Hygiene & Tropical Medicine; Office for National Statistics; London School of Hygiene & Tropical Medicine; Office for National Statistics; London School of Hygiene & Tropical Medicine; UK Health Security Agency,"BackgroundRisk factors for infection and, therefore, antibody positivity rates will be different in children compared to adults. We aim to estimate national and regional prevalence of SARS-CoV-2 antibodies in primary (4-11-year-olds) and secondary (11-15-year-olds) school children between 10 November and 10 December 2021.
+
+MethodsCross-sectional surveillance in England using two stage sampling, firstly stratifying into regions and selecting local authorities, then selecting schools according to a stratified sample within selected local authorities. Participants were sampled using a novel oral fluid validated assay for SARS-CoV-2 spike and nucleocapsid IgG antibodies.
+
+Results4,980 students from 117 state-funded schools (2,706 from 83 primary schools, 2,274 from 34 secondary schools) provided a valid sample. After weighting for age, sex and ethnicity, and adjusting for assay accuracy, the national prevalence of SARS-CoV-2 antibodies in primary school students, who were all unvaccinated, was 40.1% (95%CI; 37.3-43.0). Antibody prevalence increased with age (p<0.001) and were higher in urban than rural schools (p=0.01). In secondary school students, the adjusted, weighted national prevalence of SARS-CoV-2 antibodies was 82.4% (95%CI; 79.5-85.1); including 57.5% (95%CI; 53.9-61.1) in unvaccinated and 97.5% (95%CI; 96.1-98.5) in vaccinated students. Antibody prevalence increased with age (p<0.001), and was not significantly different in urban versus rural students (p=0.1).
+
+ConclusionsUsing a validated oral fluid assay, we estimated national and regional seroprevalence of SARS-CoV-2 antibodies in primary and secondary school students. In November 2021, 40% of primary school students and nearly all secondary school students in England had SARS-CoV2 antibodies through a combination of natural infection and vaccination.",epidemiology,fuzzy,92,100
 medRxiv,10.1101/2022.07.21.22277893,2022-07-21,https://medrxiv.org/cgi/content/short/2022.07.21.22277893,"STIMULATE-ICP: A pragmatic, multi-centre, cluster randomised trial of an integrated care pathway with a nested, Phase III, open label, adaptive platform randomised drug trial in individuals with Long COVID: a structured protocol",Denise Forshaw; Emma  C Wall; Gordon Prescott; Hakim-Moulay Dehbi; Angela Green; Emily Attree; Lyth Hismeh; William  D Strain; Michael  G Crooks; Caroline Watkins; Chris Robson; Rajarshi Banerjee; Paula Lorgelly; Melissa Heightman; Amitava Banerjee; - the STIMULATE-ICP trial team,University of Central Lancashire; The Francis Crick Institute; University of Central Lancashire; University College London; Hull University Teaching Hospitals NHS Trust; STIMULATE-ICP study; STIMULATE-ICP study; University of Exeter; University of Hull; University of Central Lancashire; Living with; Perspectum Ltd; The University of Auckland; University College London Hospitals NHS Foundation Trust; University College London; -,"IntroductionLong COVID (LC), the persistent symptoms [&ge;]12 weeks following acute COVID-19, presents major threats to individual and public health across countries, affecting over 1.5 million people in the UK alone. Evidence-based interventions are urgently required and an integrated care pathway (ICP) approach in pragmatic trials, which include investigations, treatments and rehabilitation for LC, could provide scalable and generalisable solutions at pace.
 
 Methods and analysisThis is a pragmatic, multi-centre, cluster-randomised clinical trial of two components of an ICP (Coverscan, a multi-organ MRI, and Living with COVID Recovery, a digitally enabled rehabilitation platform) with a nested, Phase III, open label, platform randomised drug trial in individuals with LC. Cluster randomisation is at level of primary care networks so that ICP interventions are delivered as ""standard of care"" in that area. The drug trial randomisation is at individual level and initial arms are rivaroxaban, colchicine, famotidine/loratadine, compared with no drugs, with potential to add in further drug arms. The trial is being carried out in 6-10 NHS LC clinics in the UK and is evaluating the effectiveness of a pathway of care for adults with LC in reducing fatigue and other physical, psychological and functional outcomes (e.g. EQ-5D-5L, GAD-7, PHQ-9, WSAS, PDQ-5, CFQ, SF-12, MRC Dyspnoea score) at 3 months. The trial also includes an economic evaluation which will be described separately.
@@ -1032,7 +1003,17 @@ MethodsObservational HCU data between 30th-December-2019 and 1st-August-2021 wer
 ResultsThe first national lockdown was associated with reductions in all primary HCU measures, ranging from 24.7% (24.0% to 25.5%) for incident prescribing to 84.9% (84.2% to 85.5%) for cholesterol monitoring. Secondary HCU also dropped significantly for planned (47% (42.9% to 51.5%)) and unplanned admissions (35.0% (28.3% to 41.6%)). Only secondary care had significant reductions in HCU during the second national lockdown. Primary HCU measures had not recovered to pre-pandemic levels by the end of the study. The secondary admission rate ratio between multi-morbid patients and those without LTCs increased during the first lockdown by a factor of 2.4 (2.0 to 2.9;p<0.001) for planned admissions and by 1.3 (1.1 to 1.5;p=0.006) for unplanned admissions. No significant changes in this ratio were observed in primary HCU. Different patterns in secondary care HCU were observed by LTC group.
 
 ConclusionMajor changes in primary and secondary HCU have been observed during the COVID-19 pandemic. Secondary HCU reduced more in those without LTCs and the ratio of utilisation between the most and least deprived increased for the majority of HCU measures. Overall primary HCU measures and secondary care HCU for some LTC groups had not returned to pre-pandemic levels by the end of the study.",epidemiology,fuzzy,100,92
-medRxiv,10.1101/2022.06.09.22276196,2022-06-14,https://medrxiv.org/cgi/content/short/2022.06.09.22276196,Accelerated waning of the humoral response to SARS-CoV-2 vaccines in obesity,"Agatha A. van der Klaauw MD, PhD; Emily C. Horner BSc; Pehuen Pereyra-Gerber PhD; Utkarsh Agrawal PhD; William S. Foster BSc, MRes,; Sarah Spencer MD, BSc; Bensi Vergese BSc Hons.; Miriam E. Smith BSc PhD; Elana Henning B.Soc.Sc; Isobel D. Ramsay MA BM BCh; Jack A. Smith BSc MBiol; Stephane M. Guillaume BSc; Hayley J. Sharpe BSc, PhD; Iain M. Hay BSc, PhD; Sam Thompson BSc; Silvia Innocentin BSc., Ph.D; Lucy H Booth BSc; Chris Robertson Ph.D.; Colin McCowan Ph.D.; Thomas E Mulroney PhD; Martin J O'Reilly; Thevinya P Guragama; Lihinya P Guragama; Maria A Rust BSc; Alex Ferreira; Soraya Ebrahimi MSc; Lourdes Ceron-Gutierrez MSc.; Jacopo Scotucci MD; Barbara Kronsteiner Ph.D.; Susanna J. Dunachie MD., Ph.D.; Paul Klenerman MD., Ph.D.; - PITCH Consortium; Adrian J. Park MD PhD; Francesco Rubino MD.,; Hannah Stark BSc; Nathalie Kingson PhD; Rainer Doffinger PhD; Michelle A. Linterman BBmedSc (H; Nicholas J. Matheson MA BM BCh; Aziz Sheikh MD; I. Sadaf Farooqi MD, PhD; James E. Thaventhiran MD, PhD","University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Meta; Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR; Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, UK; Department of Medi; School of Medicine, University of St. Andrews; Immunology, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT; Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR; University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Meta; University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Meta; University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Meta; 1. Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, UK 2. Department of; 1. Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, UK 2. Department of; Immunology, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT; Signalling, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT; Signalling, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT; Cambridge Institute for Medical Research, Cambridge UK.; Flow cytometry core, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT; Babraham Institute, Babraham Research Campus, Cambridge; Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR; Department of Mathematics and Statistics, University of Strathclyde; School of Medicine, University of St. Andrews; Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR; Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR; Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR; Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR; Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR; Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR; NIHR Cambridge Clinical Research Facility, Departments of Immunology and Clinical Biochemistry; NIHR Cambridge Clinical Research Facility, Departments of Immunology and Clinical Biochemistry; University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Meta; Nuffield Department of Clinical Medicine, University of Oxford; Nuffield Department of Clinical Medicine, University of Oxford; Nuffield Department of Clinical Medicine, University of Oxford; ; Cambridge University Hospitals NHS Foundation Trust, Department of Clinical Biochemistry, Cambridge, United Kingdom; Kings College London, Department of Diabetes, School of Life Course Science, London; NIHR BioResource; NIHR BioResource; NIHR Cambridge Clinical Research Facility, Departments of Immunology, Clinical Biochemistry; Immunology, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT; 1. Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, UK 2. Department of; Usher Institute, University of Edinburgh; University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Meta; Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR","Obesity is associated with an increased risk of severe Covid-19. However, the effectiveness of SARS-CoV-2 vaccines in people with obesity is unknown. Here we studied the relationship between body mass index (BMI), hospitalization and mortality due to Covid-19 amongst 3.5 million people in Scotland. Vaccinated people with severe obesity (BMI>40 kg/m2) were significantly more likely to experience hospitalization or death from Covid-19. Excess risk increased with time since vaccination. To investigate the underlying mechanisms, we conducted a prospective longitudinal study of the immune response in a clinical cohort of vaccinated people with severe obesity. Compared with normal weight people, six months after their second vaccine dose, significantly more people with severe obesity had unquantifiable titres of neutralizing antibody against authentic SARS-CoV-2 virus, reduced frequencies of antigen-experienced SARS-CoV-2 Spike-binding B cells, and a dissociation between anti-Spike antibody levels and neutralizing capacity. Neutralizing capacity was restored by a third dose of vaccine, but again declined more rapidly in people with severe obesity. We demonstrate that waning of SARS-CoV-2 vaccine-induced humoral immunity is accelerated in people with severe obesity and associated with increased hospitalization and mortality from breakthrough infections. Given the prevalence of obesity, our findings have significant implications for global public health.",infectious diseases,fuzzy,100,100
+medRxiv,10.1101/2022.06.08.22276134,2022-06-14,https://medrxiv.org/cgi/content/short/2022.06.08.22276134,Implementation of a digital early warning score (NEWS2) in a cardiac specialist and general hospital settings in the COVID-19 pandemic: A qualitative study.,Baneen Alhmoud; Timothy Bonicci; Riyaz Patel; Daniel Melley; Louise Hicks; Amitava Banerjee,"University College London, University College London Hospital, Barts Health Trust.; University College London, University College London Hospital; University College London, University College London Hospital.; Barts Health Trust; Barts Health Trust; University College London, University College London Hospital, Barts Health Trust.","ObjectivesTo evaluate implementation of EHR-integrated NEWS2 in a cardiac care setting and a general hospital setting in the COVID-19 pandemic.
+
+DesignThematic analysis of qualitative semi-structured interviews with purposefully sampled nurses and managers, as well as online surveys.
+
+SettingsSpecialist cardiac hospital (St Bartholomews Hospital) and General teaching hospital (University College London Hospital).
+
+ParticipantsEleven nurses and managers from cardiology, cardiac surgery, oncology, and intensive care wards (St Bartholomews) and medical, haematology and intensive care wards (UCLH) were interviewed and sixty-seven were surveyed online.
+
+ResultsThree main themes emerged: (i) Implementing NEWS2 challenges and supports; (ii) Value of NEWS2 to alarm, escalate, particularly during the pandemic; and (iii) Digitalisation: EHR integration and automation. The value of NEWS2 was partly positive in escalation, yet there were concerns by nurses who undervalued NEWS2 particularly in cardiac care. Challenges, like clinicians behaviours, lack of resources and training and the perception of NEWS2 value, limit the success of this implementation. Changes in guidelines in the pandemic have led to overlooking NEWS2. EHR integration and automated monitoring are improvement solutions that are not fully employed yet.
+
+ConclusionWhether in specialist or general medical settings, the health professionals implementing EWS in healthcare face cultural and systems related challenges to adopting NEWS2 and digital solutions. The validity of NEWS2 in specialised settings and complex conditions is not yet apparent and requires comprehensive validation. EHRs integration and automation are powerful tools to facilitate NEWS2 if its principles are reviewed and rectified, and resources and training are accessible. Further examination of implementation from the cultural and automation domains are needed.",health informatics,fuzzy,100,100
 medRxiv,10.1101/2022.06.13.22276316,2022-06-13,https://medrxiv.org/cgi/content/short/2022.06.13.22276316,Patterns of Reported Infection and Reinfection of SARS-CoV-2 in England,Matt J Keeling,University of Warwick,"One of the key features of any infectious disease is whether infection generates long-lasting immunity or whether repeated reinfection is common. In the former, the long-term dynamics are driven by the birth of susceptible individuals while in the latter the dynamics are governed by the speed of waning immunity. Between these two extremes a range of scenarios is possible. During the early waves of SARS-CoV-2, the underlying paradigm was for long-lasting immunity, but more recent data and in particular the 2022 Omicron waves have shown that reinfection can be relatively common. Here we investigate reported SARS-CoV-2 cases in England, partitioning the data into four main waves, and consider the temporal distribution of first and second reports of infection. We show that a simple low-dimensional statistical model of random (but scaled) reinfection captures much of the observed dynamics, with the value of this scaling, k, providing information of underlying epidemiological patterns. We conclude that there is considerable heterogeneity in risk of reporting reinfection by wave, age-group and location. The high levels of reinfection in the Omicron wave (we estimate that 18% of all Omicron cases had been previously infected, although not necessarily previously reported infection) point to reinfection events dominating future COVID-19 dynamics.",epidemiology,fuzzy,100,100
 medRxiv,10.1101/2022.06.12.22276307,2022-06-13,https://medrxiv.org/cgi/content/short/2022.06.12.22276307,"Occupation, Worker Vulnerability, and COVID-19 Vaccination Uptake: Analysis of the Virus Watch prospective cohort study",Sarah Beale; Rachel Burns; Isobel Braithwaite; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Susan J Hoskins; Jana Kovar; Annalan Mathew Dwight Navaratnam; Parth Patel; Alexei Yavlinsky; Martie J Van Tongeren; Robert W Aldridge; Andrew Hayward,University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University of Manchester; University College London; University College London,"BackgroundOccupational disparities in COVID-19 vaccine uptake can impact the effectiveness of vaccination programmes and introduce particular risk for vulnerable workers and those with high workplace exposure. This study aimed to investigate COVID-19 vaccine uptake by occupation, including for vulnerable groups and by occupational exposure status.
 
@@ -1125,15 +1106,6 @@ MethodsData were collected as a part of the RADAR-CNS (Remote Assessment of Dise
 ResultsParticipants with MDD (N=255) and MS (N=214) were included in the analyses. Overall, depressive symptoms remained stable across the three periods in both groups. Lower mean HR and HR variation were observed between pre and during lockdown during the day for MDD and during the night for MS. HR variation during rest periods also decreased between pre-and post-lockdown in both clinical conditions. We observed a reduction of physical activity for MDD and MS upon the introduction of lockdowns. The group with MDD exhibited a net increase in social interaction via social network apps over the three periods.
 
 ConclusionsBehavioral response to the lockdown measured by social activity, physical activity and HR may reflect changes in stress in people with MDD and MS.",psychiatry and clinical psychology,fuzzy,100,100
-medRxiv,10.1101/2022.05.09.22274846,2022-05-10,https://medrxiv.org/cgi/content/short/2022.05.09.22274846,"Assessing the impacts of timing on the health benefits, cost-effectiveness and relative affordability of COVID-19 vaccination programmes in 27 African Countries",Yang Liu; Carl AB Pearson; Andres Madriz Montero; Sergio Torres-Rueda; Elias Asfaw; Benjamin Uzochukwu; Tom Drake; Eleanor Bergren; Rosalind M Eggo; Francis Ruiz; Nicaise Ndembi; Justice Nonvignon; Mark Jit; Anna Vassall,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Africa Centres for Disease Control and Prevention; University of Nigeria Nsukka; Centre for Global Development; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Institute of Human Virology Nigeria; Africa Centres for Disease Control and Prevention; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine,"BackgroundThe COVID-19 vaccine supply shortage in 2021 constrained rollout efforts in Africa while populations experienced waves of epidemics. As supply picks up, a key question becomes if vaccination remains an impactful and cost-effective strategy given changes in the timing of implementation.
-
-MethodsWe assessed the impact of timing using an epidemiological and economic model. We fitted our mathematical epidemiological model to reported COVID-19 deaths in 27 African countries to estimate the existing immunity (resulting from infection) before substantial vaccine rollout. We then projected health outcomes for different programme start dates (2021-01-01 to 2021-12-01, n = 12) and roll-out rates (slow, medium, fast; 275, 826, and 2066 doses/ million population-day, respectively) for viral vector and mRNA vaccines. Rollout rates used were derived from observed uptake trajectories. We collected data on vaccine delivery costs by country income group. Lastly, we calculated incremental cost-effectiveness ratios and relative affordability.
-
-FindingsVaccination programmes with early start dates incur the most health benefits and are most cost-effective. While incurring the most health benefits, fast vaccine roll-outs are not always the most cost-effective. At a willingness-to-pay threshold of 0.5xGDP per capita, vaccine programmes starting in August 2021 using mRNA and viral vector vaccines were cost-effective in 6-10 and 17-18 of 27 countries, respectively.
-
-InterpretationAfrican countries with large proportions of their populations unvaccinated by late 2021 may find vaccination programmes less cost-effective than they could have been earlier in 2021. Lower vaccine purchasing costs and/or the emergence of new variants may improve cost-effectiveness.
-
-FundingBill and Melinda Gates Foundation, World Health Organization, National Institute of Health Research (UK), Health Data Research (UK)",health economics,fuzzy,100,100
 medRxiv,10.1101/2022.05.06.22274658,2022-05-07,https://medrxiv.org/cgi/content/short/2022.05.06.22274658,"STIMULATE-ICP-CAREINEQUAL - Defining usual care and examining inequalities in Long Covid support: protocol for a mixed-methods study (part of STIMULATE-ICP: Symptoms, Trajectory, Inequalities and Management: Understanding Long-COVID to Address and Transform Existing Integrated Care Pathways).",Mel Ramasawmy; Yi Mu; Donna Clutterbuck; Marija Pantelic; Gregory Y.H. Lip; Christina Van der Feltz-Cornelis; Dan Wootton; Nefyn H Williams; Hugh Montgomery; Rita Mallinson Cookson; Emily Attree; Mark Gabbay; Melissa J Heightman; Nisreen A Alwan; Amitava Banerjee; Paula Lorgelly; - STIMULATE-ICP consortium,"Institute of Health Informatics, University College London; Institute of Health Informatics, University College London; School of Primary Care, Population Sciences and Medical Education, University of Southampton; Brighton and Sussex Medical School, University of Sussex; Liverpool Centre for Cardiovascular Science, University of Liverpool and Liverpool Heart & Chest Hospital, Liverpool, United Kingdom; and Department of Clinical; Department of Health Sciences, HYMS, University of York, and Institute of Health Informatics, University College London; Institute of Infection Veterinary and Ecological Sciences, University of Liverpool; Department of Primary Care and Mental Health, University of Liverpool; Centre for Human Health and Performance, Department of Medicine, University College London; PPIE Representative; PPIE Representative; Department of Primary Care and Mental Health, University of Liverpool; University College London Hospitals NHS Trust; School of Primary Care, Population Sciences and Medical Education, University of Southampton; NIHR Southampton Biomedical Research Centre, University of Southam; Institute of Health Informatics, University College London; School of Population Health and Department of Economics, University of Auckland; ","IntroductionIndividuals with Long Covid represent a new and growing patient population. In England, fewer than 90 Long Covid clinics deliver assessment and treatment informed by NICE guidelines. However, a paucity of clinical trials or longitudinal cohort studies means that the epidemiology, clinical trajectory, healthcare utilisation and effectiveness of current Long Covid care are poorly documented, and that neither evidence-based treatments nor rehabilitation strategies exist. In addition, and in part due to pre-pandemic health inequalities, access to referral and care varies, and patient experience of the Long Covid care pathways can be poor.
 
 In a mixed methods study, we therefore aim to: (1) describe the usual healthcare, outcomes and resource utilisation of individuals with Long Covid; (2) assess the extent of inequalities in access to Long Covid care, and specifically to understand Long Covid patients experiences of stigma and discrimination.
@@ -1238,7 +1210,6 @@ Analysis of national datasets for 25 countries shows that care home deaths were,
 Several reported interventions or factors suggest the potential to mitigate the risk in care homes substantially. Interventions that could reduce mortality include improving the care home quality, increasing staffing levels, reducing the number of beds in the facility, employing staff confinement strategies with residents, and improving clinical care such as implementing daily examinations. Some care home solutions like US  Green House homes, which usually have fewer than 12 beds, may provide crucial insights into the care home problem compared with larger homes. Furthermore, care home residents faced barriers accessing emergency treatments during the pandemic waves. Finally, interventions targeting care homes should be subject to smaller trials given large effect sizes in some studies.
 
 Approximately one per cent of the global population resides in care homes, while care home residents account for nearly one-third of deaths attributed to COVID-19 in the 25 countries studied. Reducing this ratio requires analysing current care home infrastructures, funding models, and incentives for providing high-quality care. The scale of the problem in care homes requires robust evaluation and coordinated strategies to improve outcomes for those most vulnerable to COVID-19. Failure to address these systemic problems could mean global care home populations will be similarly affected by future crises and pandemics.",public and global health,fuzzy,90,100
-medRxiv,10.1101/2022.04.11.22273690,2022-04-17,https://medrxiv.org/cgi/content/short/2022.04.11.22273690,Evaluation of isotype specific salivary antibody assays for detecting previous SARS-CoV-2 infection in children and adults,Amy C Thomas; Elizabeth Oliver; Holly Baum; Kapil Gupter; Kathryn Shelley; Anna Long; Hayley Jones; Joyce Smith; Benjamin Hitchings; Natalie di Bartolo; Kate Vasileiou; Fruzsina Rabi; Hanin Alamir; Malak Eghleilib; Ore Francis; Jennifer Oliver; Begonia Morales-Aza; Ulrike Obst; Debbie Shattock; Rachael Barr; Lucy Collingwood; Kaltun Duale; Niall Grace; Guillaume Gonnage Livera; Lindsay Bishop; Harriet Downing; Fernanda Rodrigues; Nicholas J Timpson; Caroline J Relton; Ashley Mark Toye; Derek N Woolfson; Imre Berger; Anu Goenka; Andrew  D. Mark Davidson; Kathleen M Gillespie; Alistair JK Williams; Mick Bailey; Ellen Brooks-Pollock; Adam Finn; Alice Halliday; - CoMMinS Study Team,University of Bristol; University of Bristol; University of Bristol; University of Bristol and Imophoron Ltd.; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; Universidade de Coimbra; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; -,"Saliva is easily obtainable non-invasively and potentially suitable for detecting both current and previous SARS-CoV-2 infection. We established 6 standardised enzyme linked immunosorbent assays (ELISA) capable of detecting IgA and IgG antibodies to whole SARS-CoV-2 spike protein, to its receptor binding domain region and to nucleocapsid protein in saliva. In test accuracy (n=320), we found that spike IgG performed best (ROC AUC: 95.0%, 92.8-97.3%), followed by spike IgA (ROC AUC: 89.9%, 86.5-93.2%) for discriminating between pre-pandemic and post COVID-19 saliva samples. Using machine learning, diagnostic performance was improved when a combination of tests was used. As expected, salivary IgA was poorly correlated with serum, indicating an oral mucosal response whereas salivary IgG responses were predictive of those in serum. When deployed to 20 household outbreaks undergoing Delta and Omicron infection, antibody responses were heterogeneous but remained a reliable indicator of recent infection. Intriguingly, unvaccinated children showed evidence of exposure almost exclusively through specific IgA responses in the absence of evidence of viral infection. We have provided robust standardisation, evaluation, and field-testing of salivary antibody assays as tools for monitoring SARS-CoV-2 immune responses. Future work should focus on investigating salivary antibody responses following infection and vaccination to understand patterns of SARS-CoV-2 transmission and inform ongoing vaccination strategies.",infectious diseases,fuzzy,100,100
 medRxiv,10.1101/2022.04.14.22272888,2022-04-14,https://medrxiv.org/cgi/content/short/2022.04.14.22272888,Anti-inflammatory therapy with nebulised dornase alfa in patients with severe COVID-19 pneumonia,Joanna Porter; Jamie Inshaw; Vincente Joel Solis; Emma Denneny; Rebecca Evans; Mia I. Temkin; Nathalia De Vasconcelos; Iker Valle Aramburu; Dennis Hoving; Donna Basire; Tracey Crissell; Jesusa Guinto; Alison Webb; Hanif Esmail; Victoria Johnston; Anna Last; Thomas Rampling; Elisa Theresa Helbig; Lena Lippert; Florian Kurth; Bryan Williams; Aiden Flynn; Pauline Lukey; Veronique Birault; Venizelos Papayannopoulos,"UCL Respiratory, University College London, UK; Exploristics, Belfast, N. Ireland; University College London Hospitals NHS Trust, London, UK; University College London Hospitals NHS Trust, London, UK; University College London Hospitals NHS Trust, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK; UCL Respiratory, University College London, UK; University College London Hospitals NHS Trust, London, UK; University College London Hospitals NHS Trust, London, UK; University College London Hospitals NHS Trust, London, UK; National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK; National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK; Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK; National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK; Charite Universitatsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany; Charite Universitatsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany; Charite Universitatsmedizin Berlin, Department of Infectious Diseases and Respiratory Medicine, Berlin, Germany; National Institute for Health Research, University College London Hospital Biomedical Research Centre, UK; Exploristics, Belfast, N. Ireland; Target to Treatment Consulting Ltd, Stevenage, UK; Translation, The Francis Crick Institute, London, UK; Antimicrobial Defence lab, The Francis Crick Institute, London, UK","BackgroundCell-free (cf)-DNA, from cellular sources, including Neutrophil Extracellular Traps (NETs), is found in the circulation of COVID-19 patients and may contribute to immune dysregulation. This study determined whether pulmonary administration of the endonuclease, dornase alfa, reduced systemic inflammation by degrading local and systemic cf-DNA.
 
 MethodsEligible patients were randomized (3:1) to receive twice-daily nebulised dornase alfa in addition to best available care (BAC) or BAC alone for seven days or until discharge. A 2:1 ratio of matched contemporary controls (CC) provided additional comparators. The primary endpoint was improvement in C-reactive protein (CRP) over time, analysed using a repeated-measures mixed model, adjusted for baseline factors.
@@ -1263,21 +1234,13 @@ Methods and analysisThis study aims to evaluate health services requirements for
 Ethics and disseminationEthical approval for this Delphi study has been obtained (Research Governance Board of the University of York) as have approvals for the other STIMULATE-ICP studies. Study outcomes are likely to inform policy for ICPs across LTCs. Results will be disseminated through scientific publication, conference presentation and communications with patients and stakeholders involved in care of other LTCs and Long COVID.
 
 RegistrationResearchregistry: https://www.researchregistry.com/browse-the-registry#home/registrationdetails/6246bfeeeaaed6001f08dadc/.",health systems and quality improvement,fuzzy,100,100
-medRxiv,10.1101/2022.04.04.22273427,2022-04-05,https://medrxiv.org/cgi/content/short/2022.04.04.22273427,Sustained patient use and improved outcomes with digital transformation of a COPD service: RECEIVER trial and DYNAMIC-SCOT COVID-19 scale-up response.,Anna Taylor; Andrew Cushing; Morgan Dow; Jacqueline Anderson; Grace McDowell; Maureen Manthe; Sandosh Padmanabhan; Shane Burns; Paul McGineess; David J Lowe; Christopher M Carlin,"Queen Elizabeth University Hospital, Glasgow; LenusHealth, Edinburgh; LenusHealth, Edinburgh; Queen Elizabeth University Hospital, Glasgow; Queen Elizabeth University Hospital, Glasgow; Queen Elizabeth University Hospital, Glasgow; Institute of Cardiovascular and Medical Sciences, University of Glasgow; LenusHealth, Edinburgh; LenusHealth, Edinburgh; Queen Elizabeth University Hospital, Glasgow; Queen Elizabeth University Hospital, Glasgow","IntroductionLenusCOPD has been co-designed to enable digital transformation of COPD services for proactive preventative care. Patient-facing progressive web application, clinician dashboard and support website integrate patient-reported outcomes (PROs), self-management resources, structured clinical summary, wearable and home NIV data with asynchronous patient-clinician messaging. We commenced the implementation-effectiveness observational cohort RECEIVER trial in September 2019, with the primary endpoint of sustained patient usage and secondary endpoints including admissions, mortality, exacerbations, service workload and quality of life. We paused recruitment in March 2021 and provided LenusCOPD as routine care in the ""DYNAMIC-SCOT"" COVID-19 response service scale-up.
-
-Methods83 RECEIVER trial participants and 142 DYNAMIC-SCOT participants had completed minimum 1 year follow-up when we censored data on 31st August 2021. We established a control cohort with 5 patients matched per RECEIVER participant from de-identified contemporary routine clinical data.
-
-ResultsSustained patient app utilisation was noted in both cohorts. Median time to admission or death was 43 days in control, 338 days in RECEIVER and 400 days in DYNAMIC-SCOT participants who had had a respiratory-related admission in the preceding year. The 12-month risk of admission or death was 74% in control patients, 53% in RECEIVER and 47% in the DYNAMIC-SCOT sub-cohort participants. There was a median of 2.5 COPD exacerbations per patient per year with stable quality of life across follow up and a manageable workload for clinical users.
-
-ConclusionsA high proportion of people continued to use the co-designed LenusCOPD application during extended follow-up. Outcome data supports scale-up of this digital service transformation.
-
-Key messages
+medRxiv,10.1101/2022.04.03.22272610,2022-04-04,https://medrxiv.org/cgi/content/short/2022.04.03.22272610,Cardiac impairment in Long Covid 1-year post-SARS-CoV-2 infection,Adriana Roca-Fernandez; Malgorzata Wamil; Alison Telford; Valentina Carapella; Alessandra Borlotti; David Monteiro; Helena Thomaides-Brears; Matthew D Kelly; Andrea Dennis; Rajarshi Banerjee; Matthew Robson; Michael Brady; Gregory Lip; Sacha Bull; Melissa J Heightman; Ntobeko Ntusi; Amitava Banerjee,"Perspectum Diagnostics; Great Western Hospital Foundation NHS Trust, Swindon, UK; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; University of Liverpool; Royal Berkshire Hospital, Reading; UCLH; University of Cape Town, Cape Town, South Africa; University College London","BackgroundLong Covid is associated with multiple symptoms and impairment in multiple organs. Cardiac impairment has been reported to varying degrees by varying methodologies in cross-sectional studies. Using cardiac magnetic resonance (CMR), we investigated the 12-month trajectory of cardiac impairment in individuals with Long Covid.
 
-What is the key question?Can sustained patient interaction and improved patient outcomes be achieved with digital transformation of a COPD service?
+Methods534 individuals with Long Covid underwent baseline CMR (T1 and T2 mapping, cardiac mass, volumes, function, and strain) and multi-organ MRI at 6 months (IQR 4.3,7.3) since first post-COVID-19 symptoms and 330 were rescanned at 12.6 (IQR 11.4, 14.2) months if abnormal findings were reported at baseline. Symptoms, standardised questionnaires, and blood samples were collected at both timepoints. Cardiac impairment was defined as one or more of: low left or right ventricular ejection fraction (LVEF and RVEF), high left or right ventricular end diastolic volume (LVEDV and RVEDV), low 3D left ventricular global longitudinal strain (GLS), or elevated native T1 in [&ge;]3 cardiac segments. A significant change over time was reported by comparison with 92 healthy controls.
 
-What is the bottom line?Participants continue to use the LenusCOPD patient app, with an average of 3-3.5 interactions per person per week sustained >1-year post-onboarding. COPD- related hospital admissions and occupied bed days were reduced following LenusCOPD onboarding in participants with a history of a severe exacerbation in the previous year, with a median time to readmission of 380 days compared with 50 days in a contemporary matched control patient cohort.
+ResultsThe technical success of this multiorgan assessment in non-acute settings was 99.1% at baseline, and 98.3% at follow up, with 99.6% and 98.8% for CMR respectively. Of individuals with Long Covid, 102/534 [19%] had cardiac impairment at baseline; 71/102 had complete paired data at 12 months. Of those, 58% presented with ongoing cardiac impairment at 12 months. High sensitivity cardiac troponin I and B-type natriuretic peptide were not predictive of CMR findings, symptoms, or clinical outcomes. At baseline, low LVEF, high RVEDV and low GLS were associated with cardiac impairment. Low LVEF at baseline was associated with persistent cardiac impairment at 12 months.
 
-Why read on?Feasibility and utility results support scale-up adoption of these digital tools, to support optimised co-management of COPD and other long-term conditions within a continuous implementation-evaluation framework. This will establish a test-bed infrastructure for additional innovations including artificial intelligence-insights for MDT decision support.",respiratory medicine,fuzzy,100,91
+ConclusionCardiac impairment, other than myocarditis, is present in 1 in 5 individuals with Long Covid at 6 months, persisting in over half of those at 12 months. Cardiac-related blood biomarkers are unable to identify cardiac impairment in Long COVID. Subtypes of disease (based on symptoms, examination, and investigations) and predictive biomarkers are yet to be established. Interventional trials with pre-specified subgroup analyses are required to inform therapeutic options.",cardiovascular medicine,fuzzy,100,100
 medRxiv,10.1101/2022.03.29.22272997,2022-04-04,https://medrxiv.org/cgi/content/short/2022.03.29.22272997,Glasses and risk of COVID-19 transmission - analysis of the Virus Watch Community Cohort study.,Annalan Mathew Dwight Navaratnam; Chris O'Callaghan; Sarah Beale; Vincent Nguyen; Anna Aryee; Isobel Braithwaite; Thomas E Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Susan Hoskins; Jana Kovar; Parth Patel; Madhumita Shrotri; Sophie Weber; Alexei Yavlinsky; Robert W Aldridge; Andrew C Hayward,University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London,"BackgroundRespiratory viruses, including SARS-CoV-2, can infect the eyes or pass into the nose via the nasolacrimal duct. The importance of transmission via the eyes is unknown but might plausibly be reduced in those who wear glasses. Previous studies have mainly focussed on protective eyewear in healthcare settings.
 
 MethodsParticipants from the Virus Watch prospective community cohort study in England and Wales responded to a questionnaire on the use of glasses and contact lenses. This included frequency of use, purpose, and likelihood of wearing a mask with glasses. Infection was confirmed through data linkage with Second Generation Surveillance System (Pillar 1 and Pillar 2), weekly questionnaires to self-report positive polymerase chain reaction or lateral flow results, and, for a subgroup, monthly capillary blood testing for antibodies (nucleocapsid and spike). A multivariable logistic regression model, controlling for age, sex, income and occupation, was used to identify odds of infection depending on the frequency and purpose of using glasses or contact lenses.
@@ -1439,6 +1402,13 @@ Added value of this studyWe assessed multiple components of the UK vaccination c
 Implications of all the available evidenceOur data confirm that first dose BNT162b2 vaccination in CYP reduces risk of infection by SARS-CoV-2 variants, with generally local and brief side-effects. If infected after vaccination, COVID-19 is milder, if manifest at all. The study aims to contribute quantitative evidence to the risk-benefit evaluation of vaccination in CYP to inform discussion regarding rationale for their vaccination and the designing of national immunisation campaigns for this age group; and applies citizen-science approaches in the conduct of epidemiological surveillance and data collection in the UK community.
 
 Importantly, this study was conducted during Delta and Omicron predominance in UK; specificity of vaccine efficacy to variants is also illustrated; and results may not be generalizable to future SARS-CoV-2 strains.",epidemiology,fuzzy,94,100
+medRxiv,10.1101/2022.03.10.22272081,2022-03-12,https://medrxiv.org/cgi/content/short/2022.03.10.22272081,Interstitial lung damage following COVID-19 hospitalisation: an interim analysis of the UKILD Post-COVID study.,I Stewart; J Jacob; PM George; PL Molyneaux; JC Porter; RJ Allen; JK Baillie; SL Barratt; P Beirne; SM Bianchi; JF Blaikley; J Chalmers; RC Chambers; N Chadhuri; C Coleman; G Collier; EK Denneny; A Docherty; O Elneima; RA Evans; L Fabbri; MA Gibbons; FV Gleeson; B Gooptu; NJ Greening; B Guillen Guio; IP Hall; NA Hanley; V Harris; E Harrison; M Heightman; TE Hillman; A Horsley; L Houchen-Wolloff; I Jarrold; SR Johnson; MG Jones; F Khan; R Lawson; OC Leavy; N Lone; M Marks; H McAuley; P Mehta; E Omer; D Parekh; K Piper Hanley; M Plate; J Pearl; K Poinasamy; JK Quint; B Raman; M Richardson; P Rivera-Ortega; L Saunders; R Saunders; MG Semple; M Sereno; A Shikotra; AJ Simpson; A Singapuri; DJF Smith; M Spears; LG Spencer; S Stanel; D Thickett; AAR Thompson; M Thorpe; R Thwaites; SLF Walsh; S Walker; ND Weatherley; M Weeks; JM Wild; DG Wootton; CE Brightling; LP Ho; LV Wain; RG Jenkins,"National Heart & Lung Institute, Imperial College London; Respiratory Medicine, University College London; Royal Brompton and Harefield NHS Foundation Trust; National Heart & Lung Institute, Imperial College London; University College London; University of Leicester; University of Edinburgh; North Bristol NHS Trust; Leeds Teaching Hospitals & University of Leeds; Sheffield Teaching Hospitals NHS Foundation Trust; University of Manchester; University of Dundee; Respiratory Medicine, University College London; University of Manchester; University of Nottingham; University of Sheffield; University College London; University of Edinburgh; University Hospitals of Leicester NHS Trust; University Hospitals of Leicester NHS Trust; National Heart & Lung Institute, Imperial College London; Royal Devon and Exeter NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; University of Leicester; University of Leicester; University of Leicester; University of Nottingham; University of Manchester; University Hospitals of Leicester NHS Trust; University of Edinburgh; University College London Hospital; University College London Hospital; University of Manchester; University Hospitals of Leicester NHS Trust; Asthma UK British Lung Foundation; University of Nottingham; Faculty of Medicine, University of Southampton; University of Nottingham; Sheffield Teaching Hospitals NHS Foundation Trust; University of Leicester; Usher Institute, University of Edinburgh; University College London Hospital; University of Leicester; University College London Hospital; University of Leicester; University of Birmingham; University of Manchester; University College London Hospital; University of Leicester; British Lung Foundation; National Heart & Lung Institute, Imperial College London; University of Oxford; University of Leicester; University of Manchester; University of Sheffield; University of Leicester; Liverpool University; University of Leicester; University Hospitals of Leicester NHS Trust; Newcastle University; University of Leicester; Royal Brompton and Harefield NHS Foundation Trust; Perth Royal Infirmary, NHS Tayside; Liverpool University Hospitals NHS Foundation Trust; University of Manchester; University of Birmingham; University of Sheffield; University of Edinburgh; National Heart & Lung Institute, Imperial College London; National Heart & Lung Institute, Imperial College London; Sheffield Teaching NHS Foundation Trust; Sheffield Teaching NHS Foundation Trust; National Heart & Lung Institute, Imperial College London; Sheffield Teaching NHS Foundation Trust; University of Liverpool; University Hospitals of Leicester NHS Trust; University of Oxford; University of Leicester; National Heart & Lung Institute, Imperial College London","IntroductionShared characteristics between COVID-19 and pulmonary fibrosis, including symptoms, genetic architecture, and circulating biomarkers, suggests interstitial lung disease (ILD) development may be associated with SARS-CoV-2 infection.
+
+MethodsThe UKILD Post-COVID study planned interim analysis was designed to stratify risk groups and estimate the prevalence of Post-COVID Interstitial Lung Damage (ILDam) using the Post-HOSPitalisation COVID-19 (PHOSP-COVID) Study. Demographics, radiological patterns and missing data were assessed descriptively. Bayes binomial regression was used to estimate the risk ratio of persistent lung damage >10% involvement in linked, clinically indicated CT scans. Indexing thresholds of percent predicted DLco, chest X-ray findings and severity of admission were used to generate risk strata. Number of cases within strata were used to estimate the amount of suspected Post-COVID ILDam.
+
+ResultsA total 3702 people were included in the UKILD interim cohort, 2406 completed an early follow-up research visit within 240 days of discharge and 1296 had follow-up through routine clinical review. We linked the cohort to 87 clinically indicated CTs with visually scored radiological patterns (median 119 days from discharge; interquartile range 83 to 155, max 240), of which 74 people had ILDam. ILDam was associated with abnormal chest X-ray (RR 1.21 95%CrI 1.05; 1.40), percent predicted DLco<80% (RR 1.25 95%CrI 1.00; 1.56) and severe admission (RR 1.27 95%CrI 1.07; 1.55). A risk index based on these features suggested 6.9% of the interim cohort had moderate to very-high risk of Post-COVID ILDam. Comparable radiological patterns were observed in repeat scans >90 days in a subset of participants.
+
+ConclusionThese interim data highlight that ILDam was not uncommon in clinically indicated thoracic CT up to 8 months following SARS-CoV-2 hospitalisation. Whether the ILDam will progress to ILD is currently unknown, however health services should radiologically and physiologically monitor individuals who have Post-COVID ILDam risk factors.",respiratory medicine,fuzzy,91,100
 medRxiv,10.1101/2022.03.09.22272098,2022-03-12,https://medrxiv.org/cgi/content/short/2022.03.09.22272098,"Duration of vaccine effectiveness against SARS-CoV2 infection, hospitalisation, and death in residents and staff of Long-Term Care Facilities (VIVALDI): a prospective cohort study, England, Dec 2020-Dec 2021",Madhumita Shrotri; Maria Krutikov; Hadjer Nacer-Laidi; Borscha Azmi; Tom Palmer; Rebecca Giddings; Chris Fuller; Aidan Irwin-Singer; Verity Baynton; Gokhan Tut; Paul Moss; Andrew Hayward; Andrew Copas; Laura Shallcross,"University College London; University College London; University College London; University College London; University College London; University College London; University College London; UK Government Department of Health & Social Care; UK Government Department of Health & Social Care; University of Birmingham, Medical School; University of Birmingham; UCL; University College London; UCL","BackgroundLong-term care facilities (LTCF) have been prioritised for vaccination, but data on potential waning of vaccine effectiveness (VE) and the impact of booster doses in this vulnerable population remains scarce.
 
 MethodsWe included residents and staff from 331 LTCFs enrolled in VIVALDI (ISRCTN 14447421), who underwent routine PCR testing between Dec 8, 2020 - Dec 11, 2021 in a Cox proportional hazards regression, estimating VE against SARS-CoV2 infection, COVID-19-related hospitalisation, and COVID-19-related death after 1-3 vaccine doses, stratifying by previous SARS-CoV2 exposure.
@@ -1463,7 +1433,6 @@ This is the first study to examine and describe waning of immunity over a one-ye
 
 Implications of all the available evidenceTaken together, our findings indicate high short-term immunity against SARS-CoV2 infection and very high immunity against severe clinical outcomes of COVID-19 for LTCF residents and staff following vaccination. However substantial waning in vaccine-derived immunity is seen beyond 3 months, irrespective of vaccine type, suggesting the need for regular boosting to maintain protection in this vulnerable cohort. Although this analysis took place in the pre-Omicron period, these trends of waning immunity over time are likely to be generalisable across variants, carrying important implications for long-term vaccination policy in LTCFs. Ongoing surveillance in this vulnerable cohort remains crucial, in order to describe further changes in vaccine-induced immunity, particularly in the context of new variants.",infectious diseases,fuzzy,100,100
 bioRxiv,10.1101/2022.03.08.481609,2022-03-08,https://biorxiv.org/cgi/content/short/2022.03.08.481609,The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK,Verity Hill; Louis du Plessis; Thomas P Alexander Peacock; Dinesh Aggarwal; Alessandro Carabelli; Rachel Colquhoun; Nicholas Ellaby; Eileen Gallagher; Natalie Groves; Ben Jackson; JT McCrone; Anna Price; Theo Sanderson; Emily Scher; Joel Alexander Southgate; Erik Volz; - The COVID-19 genomics UK (COG-UK) consortium; Wendy S Barclay; Jeffrey Barrett; Meera Chand; Thomas R Connor; Ian G. Goodfellow; Ravindra K Gupta; Ewan Harrison; Nicholas Loman; Richard Myers; David L Robertson; Oliver Pybus; Andrew Rambaut,The University of Edinburgh; University of Oxford; University College London (UCL); University of Cambridge; University of Cambridge; University of Edinburgh; UK Health Security Agency; Uk Health Security Agency; UK Health Security Agency; University of Edinburgh; University of Edinburgh; Cardiff University; Sanger Institute; University of Edinburgh; Cardiff University; Imperial College London; -; Imperial College London; Sanger Institute; UK Health Security Agency; Cardiff University; University of Cambridge; University of Cambridge; Sanger Institute; University of Birmingham; UK Health Security Agency; University of Glasgow; University of Oxford; University of Edinburgh,"The first SARS-CoV-2 variant of concern (VOC) to be designated was lineage B.1.1.7, later labelled by the World Health Organisation (WHO) as Alpha. Originating in early Autumn but discovered in December 2020, it spread rapidly and caused large waves of infections worldwide. The Alpha variant is notable for being defined by a long ancestral phylogenetic branch with an increased evolutionary rate, along which only two sequences have been sampled. Alpha genomes comprise a well-supported monophyletic clade within which the evolutionary rate is more typical of SARS-CoV-2. The Alpha epidemic continued to grow despite the continued restrictions on social mixing across the UK, and the imposition of new restrictions, in particular the English national lockdown in November 2020. While these interventions succeeded in reducing the absolute number of cases, the impact of these non-pharmaceutical interventions was predominantly to drive the decline of the SARS-CoV-2 lineages which preceded Alpha. We investigate the only two sampled sequences that fall on the branch ancestral to Alpha. We find that one is likely to be a true intermediate sequence, providing information about the order of mutational events that led to Alpha. We explore alternate hypotheses that can explain how Alpha acquired a large number of mutations yet remained largely unobserved in a region of high genomic surveillance: an under-sampled geographical location, a non-human animal population, or a chronically-infected individual. We conclude that the last hypothesis provides the best explanation of the observed behaviour and dynamics of the variant, although we find that the individual need not be immunocompromised, as persistently-infected immunocompetent hosts also display a higher within-host rate of evolution. Finally, we compare the ancestral branches and mutation profiles of other VOCs to each other, and identify that Delta appears to be an outlier both in terms of the genomic locations of its defining mutations, and its lack of rapid evolutionary rate on the ancestral branch. As new variants, such as Omicron, continue to evolve (potentially through similar mechanisms) it remains important to investigate the origins of other variants to identify ways to potentially disrupt their evolution and emergence.",evolutionary biology,fuzzy,100,100
-medRxiv,10.1101/2022.03.06.21267462,2022-03-08,https://medrxiv.org/cgi/content/short/2022.03.06.21267462,Risk of myocarditis and pericarditis following COVID-19 vaccination in England and Wales,Samanatha Ip; Fatemeh Torabi; Spiros Denaxas; Ashley Akbari; Hoda Abbasizanjani; Rochelle Knight; Jennifer Anne Cooper; Rachel Denholm; Spencer Keene; Thomas Bolton; Sam Hollings; Efosa Omigi; Teri-Louise North; Arun Karthikeyan Suseeladevi; Emanuele Di Angelantonio; Kamlesh Khunti; Jonathan A C Sterne; Cathie Sudlow; William Whiteley; Angela Wood; Venexia Walker; - British Heart Foundation Data Science Centre (HDR UK) CVD-COVID-UK/COVID-IMPACT Consortium; - UK Covid-19 Longitudinal Health and Wellbeing National Core Study; - UK Covid-19 Data and Connectivity National Core Study,University of Cambridge; Swansea University; University College London; Swansea University; Swansea University; University of Bristol; University of Bristol; University of Bristol; University of Cambridge; Health Data Research UK; NHS Digital; NHS Digital; University of Bristol; University of Bristol; University of Cambridge; University of Leicester; University of Bristol; Health Data Research UK; University of Edinburgh; University of Cambridge; University of Bristol; ; ; ,"We describe our analyses of data from over 49.7 million people in England, representing near-complete coverage of the relevant population, to assess the risk of myocarditis and pericarditis following BNT162b2 and ChAdOx1 COVID-19 vaccination. A self-controlled case series (SCCS) design has previously reported increased risk of myocarditis after first ChAdOx1, BNT162b2, and mRNA-1273 dose and after second doses of mRNA COVID-19 vaccines in England. Here, we use a cohort design to estimate hazard ratios for hospitalised or fatal myocarditis/pericarditis after first and second doses of BNT162b2 and ChAdOx1 vaccinations. SCCS and cohort designs are subject to different assumptions and biases and therefore provide the opportunity for triangulation of evidence. In contrast to the findings from the SCCS approach previously reported for England, we found evidence for lower incidence of hospitalised or fatal myocarditis/pericarditis after first ChAdOx1 and BNT162b2 vaccination, as well as little evidence to suggest higher incidence of these events after second dose of either vaccination.",epidemiology,fuzzy,100,100
 medRxiv,10.1101/2022.03.02.22271762,2022-03-04,https://medrxiv.org/cgi/content/short/2022.03.02.22271762,"Disparities in SARS-CoV-2 case rates by ethnicity, religion, measures of socio-economic position, English proficiency, and self-reported disability: cohort study of 39 million people in England during the Alpha and Delta waves",Tim Larsen; Matthew L Bosworth; Daniel Ayoubkhani; Ryan Schofield; Raghib Ali; Kamlesh Khunti; Ann Sarah Walker; Myer Glickman; Vahe Nafilyan,Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Cambridge; University of Leicester; University of Oxford; Office for National Statistics; Office for National Statistics,"ObjectiveTo examine socio-demographic disparities in SARS-CoV-2 case rates during the second (Alpha) and third (Delta) waves of the COVID-19 pandemic.
 
 DesignRetrospective, population-based cohort study.
@@ -1709,6 +1678,9 @@ RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed,
 Added value of this studyWe used national databases of COVID-19 case surveillance, laboratory testing, and vaccination from Brazil to investigate effectiveness of CoronaVac, ChAdOx1, Ad26.COV2.S and BNT162b2 among individuals with a prior, laboratory-confirmed SARS-CoV-2 infection. We matched >22,000 RT-PCR-confirmed re-infections with >145,000 RT-PCR-negative controls using a test-negative design. All four vaccines were effective against symptomatic SARS-CoV-2 infections, with effectiveness from 14 days after series completion ranging from 39-65%. For vaccines with two-dose regimens, the second dose provided significantly increased effectiveness compared with one dose. Effectiveness against COVID-19-associated hospitalization or death from 14 days after series completion was >80% for CoronaVac, ChAdOx1and BNT162b2.
 
 Implications of all the available evidenceWe find evidence that four vaccines, using three different platforms, all provide protection to previously infected individuals against symptomatic SARS-CoV-2 infection and severe outcomes, with a second dose conferring significant additional benefits. These results support the provision of a full vaccine series among individuals with prior SARS-CoV-2 infection.",infectious diseases,fuzzy,100,100
+medRxiv,10.1101/2021.12.23.21268276,2021-12-25,https://medrxiv.org/cgi/content/short/2021.12.23.21268276,Risk of myocarditis following sequential COVID-19 vaccinations by age and sex,Martina Patone; Winnie Xue Mei; Lahiru Handunnetthi; Sharon Dixon; Francesco Zaccardi; Manu Shankar-Hari; Peter Watkinson; Kamlesh Khunti; Anthony Harnden; Carol AC Coupland; Keith M. Channon; Nicholas L Mills; Aziz Sheikh; Julia Hippisley-Cox,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Leicester; University of Edinburgh; University of Oxford; University of Leicester; University of Oxford; University of Oxford; University of Oxford; University of Edinburgh; University of Edinburgh; University of Oxford,"In an updated self-controlled case series analysis of 42,200,614 people aged 13 years or more, we evaluate the association between COVID-19 vaccination and myocarditis, stratified by age and sex, including 10,978,507 people receiving a third vaccine dose. Myocarditis risk was increased during 1-28 days following a third dose of BNT162b2 (IRR 2.02, 95%CI 1.40, 2.91). Associations were strongest in males younger than 40 years for all vaccine types with an additional 3 (95%CI 1, 5) and 12 (95% CI 1,17) events per million estimated in the 1-28 days following a first dose of BNT162b2 and mRNA-1273, respectively; 14 (95%CI 8, 17), 12 (95%CI 1, 7) and 101 (95%CI 95, 104) additional events following a second dose of ChAdOx1, BNT162b2 and mRNA-1273, respectively; and 13 (95%CI 7, 15) additional events following a third dose of BNT162b2, compared with 7 (95%CI 2, 11) additional events following COVID-19 infection. An association between COVID-19 infection and myocarditis was observed in all ages for both sexes but was substantially higher in those older than 40 years. These findings have important implications for public health and vaccination policy.
+
+FundingHealth Data Research UK.",epidemiology,fuzzy,100,100
 medRxiv,10.1101/2021.12.23.21268279,2021-12-25,https://medrxiv.org/cgi/content/short/2021.12.23.21268279,Remote Covid Assessment in Primary Care (RECAP) risk prediction tool: derivation and real-world validation studies.,Ana B Espinosa-Gonzalez; Denys Prociuk; Francesca Fiorentino; Christian Ramtale; Ella Mi; Emma Mi; Ben Glampson; Cecilia Okusi; Jack Macartney; Laiba Husain; Martina Brown; Ben Browne; Caroline Warren; Rachna Chowla; Jonty Heaversedge; Trisha Greenhalgh; Simon de Lusignan; Brendan C Delaney,"Institute of Global Health Innovation, Dept of Surgery and Cancer, Imperial College London, UK; Institute of Global Health Innovation, Dept of Surgery and Cancer, Imperial College London, UK; Nightingale-Saunders Clinical Trials & Epidemiology Unit, King's Clinical Trials Unit, King's College London; Institute of Global Health Innovation, Dept of Surgery and Cancer, Imperial College London, UK; Institute of Global Health Innovation, Dept of Surgery and Cancer, Imperial College London, UK; Institute of Global Health Innovation, Dept of Surgery and Cancer, Imperial College London, UK; Imperial College Healthcare NHS Trust, London, UK; Nuffield Dept of Primary Care, University of Oxford, UK; Nuffield Dept of Primary Care, University of Oxford, UK; Nuffield Dept of Primary Care, University of Oxford, UK; South Central Ambulance Service NHS Trust, UK; South Central Ambulance Service NHS Trust, UK; South Central Ambulance Service NHS Trust, UK; Kings Health Partners, London, UK; South East London NHS Clinical Commissioning Group, London UK; Nuffield Dept of Primary Care, University of Oxford, UK; Nuffield Dept of Primary Care, University of Oxford, UK; Institute of Global Health Innovation, Dept of Surgery and Cancer, Imperial College London, UK","BackgroundAccurate assessment of COVID-19 severity in the community is essential for best patient care and efficient use of services and requires a risk prediction score that is COVID-19 specific and adequately validated in a community setting. Following a qualitative phase to identify signs, symptoms and risk factors, we sought to develop and validate two COVID-19-specific risk prediction scores RECAP-GP (without peripheral oxygen saturation (SpO2)) and RECAP-O2 (with SpO2).
 
 MethodsProspective cohort study using multivariable logistic regression for model development. Data on signs and symptoms (model predictors) were collected on community-based patients with suspected COVID-19 via primary care electronic health records systems and linked with secondary data on hospital admission (primary outcome) within 28 days of symptom onset. Data sources: RECAP-GP: Oxford-Royal College of General Practitioners Research and Surveillance Centre (RSC) primary care practices (development), Northwest London (NWL) primary care practices, NHS COVID-19 Clinical Assessment Service (CCAS) (validation). RECAP-O2: Doctaly Assist platform (development, and validation in subsequent sample). Estimated sample size was 2,880 per model.
@@ -1731,13 +1703,6 @@ ResultsWe observed a high overall prevalence of 1.41% (1.33%, 1.51%) in the comm
 ConclusionA large fall in swab positivity from round 15 to round 16 among 12 to 17 year olds, most of whom have been vaccinated, contrasts with the continuing high prevalence among 5 to 11 year olds who have largely not been vaccinated. Likewise there were large falls in swab positivity among people aged 65 years and over, the vast majority of whom have had a third (booster) vaccine dose; these results reinforce the importance of the vaccine and booster campaign. However, the rapidly increasing prevalence of SARS-CoV-2 infections in England during December 2021, coincident with the rapid rise of Omicron infections, may lead to renewed pressure on health services. Additional measures beyond vaccination may be needed to control the current wave of infections and prevent health services (in England and other countries) from being overwhelmed.
 
 SummaryThe unprecedented rise in SARS-CoV-2 infections is concurrent with rapid spread of the Omicron variant in England and globally. We analysed prevalence of SARS-CoV-2 and its dynamics in England from end of November to mid-December 2021 among almost 100,000 participants from the REACT-1 study. Prevalence was high during December 2021 with rapid growth nationally and in London, and of the proportion of infections due to Omicron. We observed a large fall in swab positivity among mostly vaccinated older children (12-17 years) compared with unvaccinated younger children (5-11 years), and in adults who received a third vs. two doses of vaccine. Our results reiterate the importance of vaccination and booster campaigns; however, additional measures may be needed to control the rapid growth of the Omicron variant.",epidemiology,fuzzy,100,100
-medRxiv,10.1101/2021.12.21.21268214,2021-12-23,https://medrxiv.org/cgi/content/short/2021.12.21.21268214,Comparative effectiveness of ChAdOx1 versus BNT162b2 vaccines against SARS-CoV-2 infections in England and Wales: A cohort analysis using trial emulation in the Virus Watch community data,Vincent Grigori Nguyen; Alexei Yavlinsky; Sarah Beale; Susan J Hoskins; Vasileios Lampos; Isobel Braithwaite; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Annalan M D Navaratnam; Parth Patel; Madhumita Shrotri; Sophie Weber; Andrew Hayward; Robert W Aldridge,University College London; University College London; University College London; Univerity College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London,"IntroductionInfections of SARS-CoV-2 in vaccinated individuals have been increasing globally. Understanding the associations between vaccine type and a post-vaccination infection could help prevent further COVID-19 waves. In this paper, we use trial emulation to understand the impact of a phased introduction of the vaccine in the UK driven by vulnerability and exposure status. We estimate the comparative effectiveness of COVID-19 vaccines (ChAdOx1 versus BNT162b2) against post-vaccination infections of SARS-CoV-2 in a community setting in England and Wales.
-
-MethodTrial emulation was conducted by pooling results from six cohorts whose recruitment was staggered between 1st January 2021 and 31st March 2021 and followed until 12th November 2021. Eligibility for each trial was based upon age (18+ at the time of vaccination), without prior signs of infection or an infection within the first 14 days of the first dose. Time from vaccination of ChAdOx1 or BNT162b2 until SARS-CoV-2 infection (positive polymerase chain reaction or lateral flow test after 14 of the vaccination) was modelled using Cox proportional hazards model for each cohort and adjusted for age at vaccination, gender, minority ethnic status, clinically vulnerable status and index of multiple deprivation quintile. For those without SARS-CoV-2 infection during the study period, follow-up was until loss-of-follow-up or end of study (12th November 2021). Pooled hazard ratios were generated using random-effects meta-analysis.
-
-ResultsAcross six cohorts, there were a total of 21,283 participants who were eligible and vaccinated with either ChAdOx1 (n = 13,813) or BNT162b2 (n = 7,470) with a median follow-up time of 266 days (IQR: 235 - 282). By November 12th 2021, 750 (5.4%) adults who had ChAdOx1 as their vaccine experienced a SARS-CoV-2 infection, compared to 296 (4.0%) who had BNT162b2. We found that people who received ChAdOx1 vaccinations had 10.54 per 1000 people higher cumulative incidence for SARS-CoV-2 infection compared to BNT162b2 for infections during a maximum of 315 days of follow-up. When adjusted for age at vaccination, sex, minority ethnic status, index of multiple deprivation, and clinical vulnerability status, we found a pooled adjusted hazard ratio of 1.35 [HR: 1.35, 95%CI: 1.15 - 1.58], demonstrating a 35% increase in SARS-CoV-2 infections in people who received ChAdOx1 compared to BNT162b2.
-
-DiscussionWe found evidence of greater effectiveness of receiving BNT162b2 compared to ChAdOx1 vaccines against SARS-CoV-2 infection in England and Wales during a time period when Delta became the most prevalent variant of concern. Our findings demonstrate the importance of booster (third) doses to maintain protection and suggest that these should be prioritised to those who received ChAdOx1 as their primary course.",epidemiology,fuzzy,100,100
 bioRxiv,10.1101/2021.12.17.473248,2021-12-21,https://biorxiv.org/cgi/content/short/2021.12.17.473248,"SARS-CoV-2 Omicron spike mediated immune escape, infectivity and cell-cell fusion",Bo Meng; Isabella Ferreira; Adam Abdullahi; Niluka Goonawardane; Akatsuki Saito; Izumi Kimura; Daichi Yamasoba; Steven A Kemp; Guido Papa; Saman Fatihi; Surabhi Rathore; Pehuen Perera Gerba; Terumasa Ikeda; Mako Toyoda; Toong Seng Tan; Jin Kuramochi; Shigeki Mitsunaga; Takamasa Ueno; Oscar Charles; Dami Collier; - CITIID-NIHR BioResource COVID-19 Collaboration; - The Genotype to Phenotype Japan (G2P-Japan) Consortium; - Ecuador-COVID19 Consortium; John Bradley; Jinwook Choi; Kenneth Smith; Elo Madissoon; Kerstin Meyer; Petra Mlcochova; Rainer Doffinger; Sarah A Teichmann; Leo James; Joo Hyeon Lee; Teresa Brevini; Matteo Pizzuto; Myra Hosmillo; Donna Mallery; Samantha Zepeda; Alexandra Walls; Anshu Joshi; John Bowen; John Briggs; Alex Sigal; Laurelle Jackson; Sandile Cele; Anna De Marco; Fotios Sampaziotis; Davide Corti; David Veesler; Nicholas Matheson; Ian Goodfellow; Lipi Thukral; Kei Sato; Ravindra K Gupta,"University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Miyazaki; The University of Tokyo; Kumamoto University; University of Cambridge; LMB Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; CSIR Institute of Genomics and Integrative Biology, Delhi, India; University of Cambridge; Kumamoto Univ; Kumamoto University, Kumamoto; Kuramochi Clinic Interpark; Kuramochi Clinic Interpark; National Institute of Genetics, Mishima, Shizuoka; Kumamoto University, Kumamoto; University College London; University of Cambridge; -; -; -; University of Cambridge; University of Cambridge; University of Cambridge; Wellcome Sanger Institute; Wellcome Sanger Institute; University of Cambridge; Cambridge University Hospitals NHS Trust; Cambridge University; MRC LMB; University of Cambridge; University of Cambridge; Humabs Biomed SA; University of Cambridge; MRC LMB Cambridge; University of Washington; University of Washington; University of Washington; University of Washington; University of Heidelberg; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Humabs Biomed SA; University of Cambridge; Humabs Biomed SA; University of Washington; University of Cambridge; University of Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; The University of Tokyo; University of Cambridge","The SARS-CoV-2 Omicron BA.1 variant emerged in late 2021 and is characterised by multiple spike mutations across all spike domains. Here we show that Omicron BA.1 has higher affinity for ACE2 compared to Delta, and confers very significant evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralising antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralisation. Importantly, antiviral drugs remdesevir and molnupiravir retain efficacy against Omicron BA.1. We found that in human nasal epithelial 3D cultures replication was similar for both Omicron and Delta. However, in lower airway organoids, Calu-3 lung cells and gut adenocarcinoma cell lines live Omicron virus demonstrated significantly lower replication in comparison to Delta. We noted that despite presence of mutations predicted to favour spike S1/S2 cleavage, the spike protein is less efficiently cleaved in live Omicron virions compared to Delta virions. We mapped the replication differences between the variants to entry efficiency using spike pseudotyped virus (PV) entry assays. The defect for Omicron PV in specific cell types correlated with higher cellular RNA expression of TMPRSS2, and accordingly knock down of TMPRSS2 impacted Delta entry to a greater extent as compared to Omicron. Furthermore, drug inhibitors targeting specific entry pathways demonstrated that the Omicron spike inefficiently utilises the cellular protease TMPRSS2 that mediates cell entry via plasma membrane fusion. Instead, we demonstrate that Omicron spike has greater dependency on cell entry via the endocytic pathway requiring the activity of endosomal cathepsins to cleave spike. Consistent with suboptimal S1/S2 cleavage and inability to utilise TMPRSS2, syncytium formation by the Omicron spike was dramatically impaired compared to the Delta spike. Overall, Omicron appears to have gained significant evasion from neutralising antibodies whilst maintaining sensitivity to antiviral drugs targeting the polymerase. Omicron has shifted cellular tropism away from TMPRSS2 expressing cells that are enriched in cells found in the lower respiratory and GI tracts, with implications for altered pathogenesis.",microbiology,fuzzy,100,100
 medRxiv,10.1101/2021.12.20.21268098,2021-12-21,https://medrxiv.org/cgi/content/short/2021.12.20.21268098,"Therapies for Long COVID in non-hospitalised individuals - from symptoms, patient-reported outcomes, and immunology to targeted therapies (The TLC Study): Study protocol",Shamil Haroon; Krishnarajah Nirantharakumar; Sarah Hughes; Anuradhaa Subramanian; Olalekan Lee Aiyegbusi; Elin Haf Davies; Puja Myles; Tim Williams; Grace Turner; Joht Singh Chandan; Christel McMullan; Janet Lord; David Wraith; Kirsty McGee; Alastair Denniston; Tom Taverner; Louise Jackson; Elizabeth Sapey; Georgios Gkoutos; Krishna Gokhale; Edward Leggett; Clare Iles; Christopher Frost; Gary McNamara; Amy Bamford; Tom Marshall; Dawit Zemedikun; Gary Price; Steven Marwaha; Nikita Simms-Williams; Kirsty Brown; Anita Walker; Karen Jones; Karen Matthews; Jennifer Camaradou; Michael Saint-Cricq; Sumita Kumar; Yvonne Alder; David Stanton; Lisa Agyen; Megan Baber; Hannah Blaize; Melanie Calvert,University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Aparito; Medicines and Healthcare Products Regulatory Agency; Medicines and Healthcare Products Regulatory Agency; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; University of Birmingham; University ofBirmingham; University of Birmingham; Medicines and Healthcare Products Regulatory Agency; Medicines and Healthcare Products Regulatory Agency; Aparito; Aparito; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; N/A; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; University ofBirmingham,"IntroductionIndividuals with COVID-19 frequently experience symptoms and impaired quality of life beyond 4-12 weeks, commonly referred to as Long COVID. Whether Long COVID is one or several distinct syndromes is unknown. Establishing the evidence base for appropriate therapies is needed. We aim to evaluate the symptom burden and underlying pathophysiology of Long COVID syndromes in non-hospitalised individuals and evaluate potential therapies.
 
@@ -1830,6 +1795,13 @@ METHODSParticipants consisted of 247 249 individuals from seven cohorts across s
 FINDINGSA total of 9979 individuals (4%) were diagnosed with COVID-19 during the study period and presented overall with a higher symptom burden of depression (prevalence ratio [PR] 1{middle dot}18, 95% confidence interval [95% CI] 1{middle dot}03-1{middle dot}36) and poorer sleep quality (1{middle dot}13, 1{middle dot}03-1{middle dot}24) but not with higher levels of symptoms of anxiety or COVID-19 related distress compared with individuals without a COVID-19 diagnosis. While the prevalence of depression and COVID-19 related distress attenuated with time, the trajectories varied significantly by COVID-19 acute infection severity. Individuals diagnosed with COVID-19 but never bedridden due to their illness were consistently at lower risks of depression and anxiety (PR 0{middle dot}83, 95% CI 0{middle dot}75-0{middle dot}91 and 0{middle dot}77, 0{middle dot}63-0{middle dot}94, respectively), while patients bedridden for more than 7 days were persistently at higher risks of symptoms of depression and anxiety (PR 1{middle dot}61, 95% CI 1{middle dot}27-2{middle dot}05 and 1{middle dot}43, 1{middle dot}26-1{middle dot}63, respectively) throughout the 16-month study period.
 
 CONCLUSIONAcute infection severity is a key determinant of long-term mental morbidity among COVID-19 patients.",public and global health,fuzzy,100,92
+medRxiv,10.1101/2021.12.14.21267460,2021-12-15,https://medrxiv.org/cgi/content/short/2021.12.14.21267460,Differential Risk of SARS-CoV-2 Infection by Occupation: Evidence from the Virus Watch prospective cohort study in England and Wales,Sarah Beale; Susan J Hoskins; Thomas Edward Byrne; Erica Wing Lam Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Annalan MD Navaratnam; Vincent Nguyen; Parth Patel; Alexei Yavlinsky; Anne Johnson; Martie Van Tongeren; Robert W Aldridge; Andrew Hayward,University College London; Univerity College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University of Manchester; University College London; University College London,"BackgroundWorkers differ in their risk of SARS-CoV-2 infection according to their occupation, but the direct contribution of occupation to this relationship is unclear. This study aimed to investigate how infection risk differed across occupational groups in England and Wales up to April 2022, after adjustment for potential confounding and stratification by pandemic phase.
+
+MethodsData from 15,190 employed/self-employed participants in the Virus Watch prospective cohort study were used to generate risk ratios for virologically- or serologically-confirmed SARS-CoV-2 infection using robust Poisson regression, adjusting for socio-demographic and health-related factors and non-work public activities. We calculated attributable fractions (AF) amongst the exposed for belonging to each occupational group based on adjusted risk ratios (aRR).
+
+FindingsIncreased risk was seen in nurses (aRR=1.44, 1.25-1.65; AF=30%, 20-39%), doctors (aRR=1.33, 1.08-1.65; AF=25%, 7-39%), carers (1.45, 1.19-1.76; AF=31%, 16-43%), primary school teachers (aRR=1.67, 1.42-1.96; AF=40%, 30-49%), secondary school teachers (aRR=1.48, 1.26-1.72; AF=32%, 21-42%), and teaching support occupations (aRR=1.42, 1.23-1.64; AF=29%, 18-39%) compared to office-based professional occupations. Differential risk was apparent in the earlier phases (Feb 2020 - May 2021) and attenuated later (June - October 2021) for most groups, although teachers and teaching support workers demonstrated persistently elevated risk across waves.
+
+InterpretationOccupational differentials in SARS-CoV-2 infection risk vary over time and are robust to adjustment for socio-demographic, health-related, and non-workplace activity-related potential confounders. Direct investigation into workplace factors underlying elevated risk and how these change over time is needed to inform occupational health interventions.",epidemiology,fuzzy,100,100
 medRxiv,10.1101/2021.12.13.21267723,2021-12-14,https://medrxiv.org/cgi/content/short/2021.12.13.21267723,"Differential impact of Covid-19 on incidence of diabetes mellitus and cardiovascular diseases in acute, post-acute and long Covid-19: population-based cohort study in the United Kingdom",Emma Rezel-Potts; Abdel Douiri; Xiaohui Sun; Phillip J Chowienczyk; Ajay M Shah; Martin C Gulliford,King's College London; King's College London; King's College London; King's College London; King's College London; King's College London,"ObjectiveThis study aimed to estimate the incidence of new diabetes mellitus (DM) and cardiovascular diseases (CVD) up to one year after Covid-19 compared with matched controls.
 
 MethodsA cohort study was conducted using electronic records for 1,473 family practices with a population of 14.9 million. Covid-19 patients without DM or CVD were individually matched with controls and followed up to October 2021. A difference-in-difference analysis estimated the net effect of Covid-19 allowing for baseline differences and covariates.
@@ -1837,6 +1809,32 @@ MethodsA cohort study was conducted using electronic records for 1,473 family pr
 ResultsThere were 372,816 Covid-19 patients, with 2,935 CVD and 3,139 DM events, and 372,816 matched controls with 1,193 CVD and 1,861 DM events following the index date. Net incidence of DM increased in acute Covid-19 up to four weeks from index date (adjusted rate ratio, RR 1.71, 1.40 to 2.10) and remained elevated in post-acute (five to 12 weeks from index date; RR 1.17, 1.01 to 1.36) and long-Covid-19 (13 to 52 weeks, 1.20, 1.09 to 1.31). Acute Covid-19 was associated with net increased CVD incidence (RR 6.02, 95% confidence interval 4.84 to 7.47) including pulmonary embolism (RR 14.5, 7.72 to 27.4), atrial arrythmias (6.58, 3.78 to 11.4) and venous thromboses (5.44, 3.22 to 9.17). CVD incidence declined in post-acute Covid-19 (1.68, 1.41 to 2.01) and showed no net increase in long Covid-19 (0.95, 0.85 to 1.06).
 
 ConclusionsDM incidence remains elevated up to one year following Covid-19. CVD is increased early after Covid-19 mainly from pulmonary embolism, atrial arrhythmias and venous thromboses.",epidemiology,fuzzy,100,100
+medRxiv,10.1101/2021.12.09.21267516,2021-12-09,https://medrxiv.org/cgi/content/short/2021.12.09.21267516,Changes in the trajectory of Long Covid symptoms following COVID-19 vaccination: community-based cohort study,Daniel Ayoubkhani; Charlotte Bermingham; Koen B Pouwels; Myer Glickman; Vahe Nafilyan; Francesco Zaccardi; Kamlesh Khunti; Nisreen A Alwan; Ann Sarah Walker,Office for National Statistics; Office for National Statistics; University of Oxford; Office for National Statistics; Office for National Statistics; University of Leicester; University of Leicester; University of Southampton; University of Oxford,"ObjectiveTo estimate associations between COVID-19 vaccination and Long Covid symptoms in adults who were infected with SARS-CoV-2 prior to vaccination.
+
+DesignObservational cohort study using individual-level interrupted time series analysis.
+
+SettingRandom sample from the community population of the UK.
+
+Participants28,356 COVID-19 Infection Survey participants (mean age 46 years, 56% female, 89% white) aged 18 to 69 years who received at least their first vaccination after test-confirmed infection.
+
+Main outcome measuresPresence of long Covid symptoms at least 12 weeks after infection over the follow-up period 3 February to 5 September 2021.
+
+ResultsMedian follow-up was 141 days from first vaccination (among all participants) and 67 days from second vaccination (84% of participants). First vaccination was associated with an initial 12.8% decrease (95% confidence interval: -18.6% to -6.6%) in the odds of Long Covid, but increasing by 0.3% (-0.6% to +1.2%) per week after the first dose. Second vaccination was associated with an 8.8% decrease (-14.1% to -3.1%) in the odds of Long Covid, with the odds subsequently decreasing by 0.8% (-1.2% to -0.4%) per week. There was no statistical evidence of heterogeneity in associations between vaccination and Long Covid by socio-demographic characteristics, health status, whether hospitalised with acute COVID-19, vaccine type (adenovirus vector or mRNA), or duration from infection to vaccination.
+
+ConclusionsThe likelihood of Long Covid symptoms reduced after COVID-19 vaccination, and the improvement was sustained over the follow-up period after the second dose. Vaccination may contribute to a reduction in the population health burden of Long Covid, though longer follow-up time is needed.
+
+Summary boxWhat is already known on this topic
+
+O_LICOVID-19 vaccines are effective at reducing rates of SARS-CoV-2 infection, transmission, hospitalisation, and death
+C_LIO_LIThe incidence of Long Covid may be reduced if infected after vaccination, but the relationship between vaccination and pre-existing long COVID symptoms is unclear, as published studies are generally small and with self-selected participants
+C_LI
+
+What this study adds
+
+O_LIThe likelihood of Long Covid symptoms reduced after COVID-19 vaccination, and the improvement was sustained over the follow-up period after the second dose
+C_LIO_LIThere was no evidence of differences in this relationship by socio-demographic characteristics, health-related factors, vaccine type, or duration from infection to vaccination
+C_LIO_LIAlthough causality cannot be inferred from this observational evidence, vaccination may contribute to a reduction in the population health burden of Long Covid; further research is needed to understand the biological mechanisms that may ultimately contribute to the development of therapeutics for Long Covid
+C_LI",epidemiology,fuzzy,100,100
 medRxiv,10.1101/2021.12.08.21267458,2021-12-08,https://medrxiv.org/cgi/content/short/2021.12.08.21267458,"Relative contribution of leaving home for work or education, transport, shopping and other activities on risk of acquiring COVID-19 infection outside the household in the second wave of the pandemic in England and Wales",Susan J Hoskins; Sarah Beale; Robert W Aldridge; Colette Smith; Clare French; Alex Yavlinksky; Vincent Nguyen; Thomas Edward Byrne; Jana Kovar; Ellen Fragaszy; W Fong; Cyril Geismar; Parth Patel; Ann Johnson; Andrew Edward Hayward,Univerity College London; University College London; UCL; University College London; University of Bristol; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; UCL,"BackgroundWith the potential for and emergence of new COVID-19 variants, such as the reportedly more infectious Omicron, and their potential to escape the existing vaccines, understanding the relative importance of which non-household activities increase risk of acquisition of COVID-19 infection is vital to inform mitigation strategies.
 
 MethodsWithin an adult subset of the Virus Watch community cohort study, we sought to identify which non-household activities increased risk of acquisition of COVID-19 infection and which accounted for the greatest proportion of non-household acquired COVID-19 infections during the second wave of the pandemic. Among participants who were undertaking antibody tests and self-reporting PCR and lateral flow tests taken through the national testing programme, we identified those who were thought to be infected outside the household during the second wave of the pandemic. We used exposure data on attending work, using public or shared transport, using shops and other non-household activities taken from monthly surveys during the second wave of the pandemic. We used multivariable logistic regression models to assess the relative independent contribution of these exposures on risk of acquiring infection outside the household. We calculated Adjusted Population Attributable Fractions (APAF - the proportion of non-household transmission in the cohort thought to be attributable to each exposure) based on odds ratios and frequency of exposure in cases.
@@ -1934,21 +1932,6 @@ Key pointsO_ST_ABSQuestionC_ST_ABSIs COVID-19 associated with higher long-term i
 FindingsIn this cohort study of 48 million adults in England and Wales, COVID-19 was associated with higher incidence, that declined with time since diagnosis, of both arterial thromboses [week 1: adjusted HR [aHR] 21.7 (95% CI 21.0-22.4) weeks 27-49: aHR 1.34 (1.21-1.48)] and venous thromboembolism [week 1: aHR 33.2 (31.3-35.2), weeks 27-49 1.80 (1.50-2.17)]. aHRs were higher, for longer, after hospitalised than non-hospitalised COVID-19. The estimated excess number of arterial thromboses and venous thromboembolisms was 10,500.
 
 MeaningAvoidance of COVID-19 infection through vaccination, and use of secondary preventive agents after infection in high-risk patients, may reduce post-COVID-19 acute vascular diseases.",infectious diseases,fuzzy,100,100
-medRxiv,10.1101/2021.11.23.21266574,2021-11-24,https://medrxiv.org/cgi/content/short/2021.11.23.21266574,"Reinfection with SARS-CoV-2: outcome, risk factors and vaccine efficacy in a Scottish cohort",Paul M McKeigue; David McAllister; Chris Robertson; Diane Stockton; Helen Colhoun,University of Edinburgh; University of Glasgow; University of Strathclyde; Public Health Scotland; University of Edinburgh,"BackgroundThe objective of this study was to investigate how protection against COVID-19 conferred by previous infection is modified by vaccination.
-
-MethodsIn a cohort of all 152655 individuals in Scotland alive at 90 days after a positive test for SARS-CoV-2 (confirmed by cycle threshold < 30, or two tests) followed till 22 September 2021, rate ratios for reinfection were estimated with calendar time or tests as timescale.
-
-FindingsRates of detected and hospitalised reinfection with COVID-19 while unvaccinated were respectively 6.8 (95% CI 6.4 to 7.2) and 0.18 (95% CI 0.12 to 0.25) per 1000 person-months. These rates were respectively 68% and 74% lower than in a matched cohort of individuals who had not previously tested positive. Efficacy of two doses of vaccine in those with previous infection was estimated as as 84% (95 percent CI 81% to 86%) against detected reinfection and 71% (95 percent CI 29% to 88%) against hospitalised or fatal reinfection. The rate of detected reinfection after two doses of vaccine was 1.35 (95% CI 1.02 to 1.78) times higher in those vaccinated before first infection than in those unvaccinated at first infection.
-
-InterpretationThe combination of natural infection and vaccination provides maximal protection against new infection with SARS-CoV-2: prior vaccination does not impair this protection.
-
-FundingNo specific funding was received for this work.
-
-Research in contextO_ST_ABSEvidence before this studyC_ST_ABSIn a recent systematic review of cohort studies reported up to July 2021, the average reduction in COVID-19 infection rates in those with previous infection compared with those without evidence of previous infection was 90%. There is little information about the protective effect of previous infection against severe COVID-19, or about how the protective effects of previous infection against reinfection and severe disease are modified by vaccination.
-
-What this paper addsIn unvaccinated individuals the protection against hospitalised COVID-19 conferred by previous infection is similar to that induced by vaccination. In those with previous infection, vaccination reduces the rates of reinfection and hospitalised COVID-19 by about 70%.
-
-Implications of all the available evidenceThe combination of natural infection and vaccination provides maximal protection against COVID-19: prior vaccination does not seriously impair this protection.",epidemiology,fuzzy,100,100
 medRxiv,10.1101/2021.11.19.21266529,2021-11-19,https://medrxiv.org/cgi/content/short/2021.11.19.21266529,Impact of the COVID-19 pandemic on community antibiotic prescribing and stewardship: a qualitative interview study with general practitioners in England,Aleksandra J Borek; Katherine Maitland; Monsey Mcleod; Anne Campbell; Benedict Hayhoe; Christopher C Butler; Liz Morrell; Laurence Roope; Alison Holmes; Ann Sarah Walker; Sarah Tonkin-Crine; - the STEP-UP study team,University of Oxford; University of Oxford; Imperial College London; Imperia College London; Imperial College London; University of Oxford; University of Oxford; University of Oxford; Imperial College London; University of Oxford; University of Oxford; ,"The COVID-19 pandemic has had a profound impact on the delivery of primary care services. We aimed to identify general practitioners (GPs) perceptions and experiences of how the COVID-19 pandemic influenced antibiotic prescribing and antimicrobial stewardship (AMS) in general practice in England. Twenty-four semi-structured interviews were conducted with 18 GPs at two time-points: autumn 2020 (14 interviews) and spring 2021 (10 interviews). Interviews were audio-recorded, transcribed and analysed thematically, taking a longitudinal approach. Participants reported a lower threshold for antibiotic prescribing (and fewer consultations) for respiratory infections and COVID-19 symptoms early in the pandemic, then returning to more usual (pre-pandemic) prescribing. They perceived less impact on antibiotic prescribing for urinary and skin infections. Participants perceived the changing ways of working and consulting (e.g., proportions of remote and in-person consultations), and the changing patient presentations and GP workload as influencing the fluctuations in antibiotic prescribing. This was compounded by decreased engagement with, and priority of, AMS due to COVID-19-related urgent priorities. Re-engagement with AMS is needed, e.g., through reviving antibiotic prescribing feedback and targets/incentives. While the pandemic disrupted the usual ways of working, it also produced opportunities, e.g., for re-organising ways of managing infections and AMS in the future.",primary care research,fuzzy,100,100
 medRxiv,10.1101/2021.11.15.21266264,2021-11-16,https://medrxiv.org/cgi/content/short/2021.11.15.21266264,Association of COVID-19 employment disruption with mental and social wellbeing: evidence from nine UK longitudinal studies,Jacques Wels; Charlotte Booth; Bozena Wielgoszewska; Michael J Green; Giorgio Di Gessa; Charlotte F Huggins; Gareth J Griffith; Alex Siu Fung Kwong; Ruth C E Bowyer; Jane Maddock; Praveetha Patalay; Richard J Silverwood; Emla Fitzsimons; Richard John Shaw; Ellen J Thompson; Andrew Steptoe; Alun Hughes; Nishi Chaturvedi; Claire J Steves; Srinivasa Vittal Katikireddi; George B Ploubidis,University College London; University College London; University College London; University of Glasgow; University College London; University of Edinburgh; University of Bristol; University of Bristol; King's College London; University College London; University College London; University College London; University College London; University of Glasgow; Kings College London; University College London; University College London; University College London; King's College London; University of Glasgow; University College London,"BackgroundThe COVID-19 pandemic has led to major economic disruptions. In March 2020, the UK implemented the Coronavirus Job Retention Scheme - known as furlough - to minimize the impact of job losses. We investigate associations between change in employment status and mental and social wellbeing during the early stages of the pandemic.
 
@@ -2022,7 +2005,6 @@ MethodWith the approval of NHS England we conducted a retrospective cohort study
 ResultsAs of 01st November 2021, a total of 15,436,455 individuals were identified as being fully vaccinated against COVID-19, with a median follow-up time of 149 days (IQR: 107-179). From within this population, a total of 577245 (<4%) individuals reported a positive SARS-CoV-2 test. For every 1000 years of patient follow-up time, the corresponding incidence rate was 98.02 (95% CI 97.9-98.15). There were 16,120 COVID-19-related hospital admissions, 1,100 COVID-19 critical care admission patients and 3,925 COVID-19-related deaths; corresponding incidence rates of 2.72 (95% C 2.7-2.74), 0.19 (95% C 0.18-0.19) and 0.66 (95% C 0.65-0.67), respectively. When broken down by the initial priority group, higher rates of hospitalisation and death were seen in those in care homes and those over 80 years of age. Comorbidities with the highest rates of breakthrough COVID-19 included chronic kidney disease, dialysis, transplant, haematological malignancy, and immunocompromised.
 
 ConclusionThe majority of COVID-19 vaccine breakthrough cases in England were mild with relatively few fully vaccinated individuals being hospitalised or dying as a result. However, some concerning differences in rates of breakthrough cases were identified in several clinical and demographic groups. While it is important to note that these findings are simply descriptive and cannot be used to answer why certain groups have higher rates of COVID-19 breakthrough than others, the emergence of the Omicron variant of COVID-19 coupled with the continued increase in numbers of positive SARS-CoV-2 tests are concerning. As numbers of fully vaccinated individuals increases and follow-up time lengthens, so too will the number of COVID-19 breakthrough cases. Additional analyses, aimed at identifying individuals at higher risk, are therefore required.",epidemiology,fuzzy,100,100
-bioRxiv,10.1101/2021.11.05.467529,2021-11-08,https://biorxiv.org/cgi/content/short/2021.11.05.467529,Structural basis of main proteases of coronavirus bound to drug candidate PF-07321332,Jian Li; Cheng Lin; Xuelan Zhou; Fanglin Zhong; Pei Zeng; Haihai Jiang; Yang Yang; Peter McCormick; Yang Fu; Jin Zhang,"College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China.; School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China.; Shenzhen Crystalo Biopharmaceutical Co., Ltd, Shenzhen 518118, China.; Jiangxi Jmerry Biopharmaceutical Co., Ltd, Ganzhou 341000, China.; Jiangxi Jmerry Biopharmaceutical Co., Ltd, Ganzhou 341000, China.; School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China.; Shenzhen Crystalo Biopharmaceutical Co., Ltd, Shenzhen 518118, China.; William Harvey Research Institute, Queen Mary University of London; School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China 518055; School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China.","The high mutation rate of COVID-19 and the prevalence of multiple variants strongly support the need for pharmacological options to complement vaccine strategies. One region that appears highly conserved among different genus of coronaviruses is the substrate binding site of the main protease (Mpro or 3CLpro), making it an attractive target for the development of broad-spectrum drugs for multiple coronaviruses. PF-07321332 developed by Pfizer is the first orally administered inhibitor targeting the main protease of SARS-CoV-2, which also has shown potency against other coronaviruses. Here we report three crystal structures of main protease of SARS-CoV-2, SARS-CoV and MERS-CoV bound to the inhibitor PF-07321332. The structures reveal a ligand-binding site that is conserved among SARS-CoV-2, SARS-CoV and MERS-CoV, providing insights into the mechanism of inhibition of viral replication. The long and narrow cavity in the cleft between domains I and II of main protease harbors multiple inhibitor binding sites, where PF-07321332 occupies subsites S1, S2 and S4 and appears more restricted compared with other inhibitors. A detailed analysis of these structures illuminated key structural determinants essential for inhibition and elucidated the binding mode of action of main proteases from different coronaviruses. Given the importance of main protease for the treatment of SARS-CoV-2 infection, insights derived from this study should accelerate the design of safer and more effective antivirals.",biophysics,fuzzy,100,100
 medRxiv,10.1101/2021.11.04.21265918,2021-11-05,https://medrxiv.org/cgi/content/short/2021.11.04.21265918,Longitudinal Changes of Cardiac and Aortic Imaging Phenotypes Following COVID-19 in the UK Biobank Cohort,Wenjia Bai; Betty Raman; Steffen E Peterson; Stefan Neubauer; Zahra Raisi-Estabragh; Nay Aung; Nicholas C Harvey; Naomi Allen; Rory Collins; Paul M Matthews,"Department of Brain Sciences, Imperial College London and British Heart Foundation Centre for Research Excellence, Imperial College London, London, UK; University of Oxford; William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford and British Heart Foundation; William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London; William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London; MRC Lifecourse Epidemiology Centre, University of Southampton and NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital; Nuffield Department of Population Health, University of Oxford, Oxford, UK and UK Biobank, Stockport, UK; Nuffield Department of Population Health, University of Oxford, Oxford, UK and UK Biobank, Stockport, UK; Imperial College, London","Case studies conducted after recovery from acute infection with SARS-CoV-2 have frequently identified abnormalities on CMR imaging, suggesting the possibility that SARS-CoV-2 infection commonly leads to cardiac pathology. However, these observations have not been able to distinguish between associations that reflect pre-existing cardiac abnormalities (that might confer a greater likelihood of more severe infection) from those that arise as consequences of infection. To address this question, UK Biobank volunteers (n=1285; 54.5% women; mean age at baseline, 59.8 years old; 96.3% white) who attended an imaging assessment including cardiac magnetic resonance (CMR) before the start of the COVID-19 pandemic were invited to attend a second imaging assessment in 2021. Cases with evidence of previous SARS-CoV-2 infection were identified through linkage to PCR-testing or other medical records, or a positive antibody lateral flow test; n=640 in data available on 22 Sep 2021) and were matched to controls with no evidence of previous infection (n=645). The majority of these infections were milder and did not involve hospitalisation. Measures of cardiac and aortic structure and function were derived from the CMR images obtained on the cases before and after SARS-CoV-2 infection from images for the controls obtained over the same time interval using a previously validated, automated algorithm. Cases and controls had similar cardiac and aortic imaging phenotypes at their first imaging assessment. Changes between CMR imaging measures in cases before and after infection were not significantly different from those in the matched control group. Additional adjustment for comorbidities made no material difference to the results. While these results are preliminary and limited to imaging metrics derived from automated analyses, they do not suggest clinically significant persistent cardiac pathology in the UK Biobank population after generally milder (non-hospitalised) SARS-CoV-2 infection.",neurology,fuzzy,100,100
 medRxiv,10.1101/2021.11.02.21265767,2021-11-03,https://medrxiv.org/cgi/content/short/2021.11.02.21265767,Determinants of pre-vaccination antibody responses to SARS-CoV-2: a population-based longitudinal study (COVIDENCE UK),Mohammad Talaei; Sian Faustini; Hayley Holt; David A. Jolliffe; Giulia Vivaldi; Matthew Greenig; Natalia Perdek; Sheena Maltby; Carola M Bigogno; Jane Symons; Gwyneth A. Davies; Ronan A. Lyons; Christopher J Griffiths; Frank Kee; Aziz Sheikh; Alex G. Richter; Seif O. Shaheen; Adrian R Martineau,Queen Mary University of London; University of Birmingham; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Jane Symons Media; Swansea University Medical School; Swansea University Medical School; Queen Mary University of London; Queens University Belfast; University of Edinburgh; University of Birminghan; Queen Mary University of London; Queen Mary University of London,"BackgroundProspective population-based studies investigating multiple determinants of pre-vaccination antibody responses to SARS-CoV-2 are lacking.
 
@@ -2033,13 +2015,6 @@ Results1696 (15.2%) of 11,130 participants were seropositive. Factors independen
 ConclusionsHigher alcohol consumption and reduced light physical exercise represent new modifiable risk factors for SARS-CoV-2 infection. Recognised associations between Asian/Asian British ethnic origin and obesity and increased risk of SARS-CoV-2 seropositivity were independent of other sociodemographic, behavioural, nutritional, clinical and pharmacological factors investigated. Among seropositive participants, higher titres of anti-Spike antibodies in people of Asian ancestry and in obese people were not explained by greater COVID-19 disease severity in these groups.
 
 FundingBarts Charity, Health Data Research UK.",epidemiology,fuzzy,100,100
-medRxiv,10.1101/2021.11.03.21265877,2021-11-03,https://medrxiv.org/cgi/content/short/2021.11.03.21265877,REACT-1 round 15 interim report: High and rising prevalence of SARS-CoV-2 infection in England from end of September 2021 followed by a fall in late October 2021,Marc Chadeau-Hyam; Oliver Eales; Barbara Bodinier; Haowei Wang; David J Haw; Matthew Whitaker; Caroline E Walters; Christina J Atchison; Peter J Diggle; Andrew J Page; Deborah Ashby; Wendy Barclay; Graham P Taylor; Graham Cooke; Helen Ward; Ara Darzi; Christl A. Donnelly; Paul Elliott,Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Quadram Institute; Imperial College London; Imperial College London; Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London School of Public Health,"BackgroundThe third wave of COVID-19 in England coincided with the rapid spread of the Delta variant of SARS-CoV-2 from the end of May 2021. Case incidence data from the national testing programme (Pillar 2) in England may be affected by changes in testing behaviour and other biases. Community surveys may provide important contextual information to inform policy and the public health response.
-
-MethodsWe estimated patterns of community prevalence of SARS-CoV-2 infection in England using RT-PCR swab-positivity, demographic and other risk factor data from round 15 (interim) of the REal-time Assessment of Community Transmission-1 (REACT-1) study (round 15a, carried out from 19 to 29 October 2021). We compared these findings with those from round 14 (9 to 27 September 2021).
-
-ResultsDuring mid- to late-October 2021 (round 15a) weighted prevalence was 1.72% (1.61%, 1.84%) compared to 0.83% (0.76%, 0.89%) in September 2021 (round 14). The overall reproduction number (R) from round 14 to round 15a was 1.12 (1.11, 1.14) with increases in prevalence over this period (September to October) across age groups and regions except Yorkshire and The Humber. However, within round 15a (mid- to late-October) there was evidence of a fall in prevalence with R of 0.76 (0.65, 0.88). The highest weighted prevalence was observed among children aged 5 to 12 years at 5.85% (5.10%, 6.70%) and 13 to 17 years at 5.75% (5.02%, 6.57%). At regional level, there was an almost four-fold increase in weighted prevalence in South West from round 14 at 0.59% (0.43%,0.80%) to round 15a at 2.18% (1.84%, 2.58%), with highest smoothed prevalence at subregional level also found in South West in round 15a. Age, sex, key worker status, and presence of children in the home jointly contributed to the risk of swab-positivity. Among the 126 sequenced positive swabs obtained up until 23 October, all were Delta variant; 13 (10.3%) were identified as the AY.4.2 sub-lineage.
-
-DiscussionWe observed the highest overall prevalence of swab-positivity seen in the REACT-1 study in England to date in round 15a (October 2021), with a two-fold rise in swab-positivity from round 14 (September 2021). Despite evidence of a fall in prevalence from mid- to late-October 2021, prevalence remains high, particularly in school-aged children, with evidence also of higher prevalence in households with one or more children. Thus, vaccination of children aged 12 and over remains a high priority (with possible extension to children aged 5-12) to help reduce within-household transmission and disruptions to education, as well as among adults, to lessen the risk of serious disease among those infected.",epidemiology,fuzzy,100,100
 medRxiv,10.1101/2021.10.28.21265593,2021-11-02,https://medrxiv.org/cgi/content/short/2021.10.28.21265593,"The UK COVID-19 furlough scheme and associations with smoking, alcohol consumption and vaping: evidence from 8 UK longitudinal population surveys.",Michael J Green PhD; Jane Maddock PhD; Giorgio Di Gessa PhD; Bożena Wielgoszewska PhD; Sam Parsons PhD; Gareth J Griffith PhD; Jazz Croft PhD; Anna J Stevenson PhD; Charlotte F Huggins PhD; Charlotte Booth PhD; Jacques Wels; Richard J Silverwood PhD; Praveetha Patalay PhD; Alun D Hughes PhD; Nishi Chaturvedi MD; Laura D Howe PhD; Emla Fitzsimons PhD; Srinivasa Vittal Katikireddi PhD; George B Ploubidis PhD,"MRC/CSO Social & Public Health Sciences Unit, University of Glasgow; MRC Unit for Lifelong Health and Ageing, University College London; Institute of Epidemiology and Health Care, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC Integrative Epidemiology Unit, University of Bristol; MRC Integrative Epidemiology Unit, University of Bristol; Centre for Genomic and Experimental Medicine, University of Edinburgh; Centre for Genomic and Experimental Medicine, University of Edinburgh; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC Unit for Lifelong Health and Ageing, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College; MRC Unit for Lifelong Health and Ageing, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC Unit for Lifelong Health and Ageing, University College London; MRC Unit for Lifelong Health and Ageing, University College London; MRC Integrative Epidemiology Unit, University of Bristol; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC/CSO Social & Public Health Sciences Unit, University of Glasgow; Centre for Longitudinal Studies, UCL Social Research Institute, University College London","BackgroundDisruptions to employment status can impact smoking and alcohol consumption. During the COVID-19 pandemic, the UK implemented a furlough scheme to prevent job loss. We examine how furlough was associated with participants smoking, vaping and alcohol consumption behaviours in the early stages of the pandemic.
 
 MethodsData were from 27,841 participants in eight UK adult longitudinal surveys. Participants self-reported employment status and current smoking, current vaping and drinking alcohol (>4 days/week or 5+ drinks per typical occasion) both before and during the pandemic (April-July 2020). Risk ratios were estimated within each study using modified Poisson regression, adjusting for a range of potential confounders, including pre-pandemic behaviour. Findings were synthesised using random effects meta-analysis. Sub-group analyses were used to identify whether associations differed by gender, age or education.
@@ -2113,23 +2088,6 @@ MethodsData on paediatric Emergency Department (ED) attendances (0-15 years incl
 ResultsBetween 1-March-2016 and 30-July-2021, 155,056 ED attendances occurred and 7,195 respiratory virus PCRs were performed. Detection of all pathogens was suppressed during the first national lockdown. Rhinovirus and adenovirus rates increased when schools reopened September-December 2020, then fell, before rising in March-May 2021. The usual winter RSV peak did not occur in 2020/21, with an inter-seasonal rise (32/1,000 attendances in 0-3yr olds) in July 2021. Influenza remained suppressed throughout. A higher Paediatric Early Warning Score (PEWS) was seen for attendees with adenovirus during the pandemic compared to pre-pandemic (p=0.04, Mann-Witney U test), no other differences in PEWS were seen.
 
 ConclusionsSARS-CoV-2 caused major changes in the incidence of paediatric respiratory viral infection in Oxfordshire, with implications for clinical service demand, testing strategies, timing of palivizumab RSV prophylaxis, and highlighting the need to understand which public health interventions are most effective for preventing respiratory virus infections.",infectious diseases,fuzzy,100,100
-medRxiv,10.1101/2021.10.06.21264467,2021-10-07,https://medrxiv.org/cgi/content/short/2021.10.06.21264467,Illness characteristics of COVID-19 in children infected with the SARS-CoV-2 Delta variant,Erika Molteni; Carole Helene Sudre; Liane S Canas; Sunil S Bhopal; Robert C Hughes; Liyuan Chen; Jie Deng; Benjamin Murray; Eric Kerfoot; Michela S Antonelli; Mark S Graham; Kerstin Klaser; Anna May; Christina Hu; Joan Capdevila Pujol; Jonathan Wolf; Alexander Hammers; Timothy D Spector; Sebastien Ourselin; Marc Modat; Claire Steves; Michael Absoud; Emma L Duncan,"King's College London; School of Biomedical Engineering & Imaging Sciences, Kings College London, London, UK.; King's College London; Newcastle University; Department of Population Health, Faculty of Epidemiology & Population Health, London School of Hygiene & Tropical Medicine, Keppel Street, London, UK.; School of Biomedical Engineering & Imaging Sciences, Kings College London, London, UK.; School of Biomedical Engineering & Imaging Sciences, Kings College London, London, UK.; School of Biomedical Engineering & Imaging Sciences, Kings College London, London, UK.; School of Biomedical Engineering & Imaging Sciences, Kings College London, London, UK.; King's College London; King's College London; King's College London; ZOE Limited London, UK; ZOE Limited London, UK.; ZOE Limited London, UK.; ZOE Limited London, UK.; School of Biomedical Engineering & Imaging Sciences, Kings College London, London, UK.; King's College London; School of Biomedical Engineering & Imaging Sciences, Kings College London, London, UK.; School of Biomedical Engineering & Imaging Sciences, Kings College London, London, UK.; King's College London; Childrens Neurosciences, Evelina London Childrens Hospital, St Thomas Hospital, Kings Health Partners, Academic Health Science Centre, London, UK.; Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK.","BackgroundThe Delta (B.1.617.2) SARS-CoV-2 variant became the predominant UK circulating strain in May 2021. Whether COVID-19 from Delta infection differs to infection with other variants in children is unknown.
-
-MethodsThrough the prospective COVID Symptom Study, 109,626 UK school-aged children were proxy-reported between December 28, 2020 and July 8, 2021. We selected all symptomatic children who tested positive for SARS-CoV-2 and were proxy-reported at least weekly, within two timeframes: December 28, 2020 to May 6, 2021 (Alpha (B.1.1.7) the main UK circulating variant); and May 26 to July 8, 2021 (Delta the main UK circulating variant). We assessed illness profiles (symptom prevalence, duration, and burden), hospital presentation, and presence of long ([&ge;]28 day) illness; and calculated odds ratios for symptoms presenting within the first 28 days of illness.
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-Findings694 (276 younger [5-11 years], 418 older [12-17 years]) symptomatic children tested positive for SARS-CoV-2 with Alpha infection and 706 (227 younger and 479 older) children with Delta infection. Median illness duration was short with either variant (overall cohort: 5 days (IQR 2-9.75) with Alpha, 5 days (IQR 2-9) with Delta). The seven most prevalent symptoms were common to both variants. Symptom burden over the first 28 days was slightly greater with Delta compared with Alpha infection (in younger children, 3 (IQR 2-5) with Alpha, 4 (IQR 2-7) with Delta; in older children 5 (IQR 3-8) with Alpha and 6 (IQR 3-9) with Delta infection in older children). The odds of several symptoms were higher with Delta than Alpha infection, including headache and fever. Few children presented to hospital, and long illness duration was uncommon, with either variant.
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-InterpretationCOVID-19 in UK school-aged children due to SARS-CoV-2 Delta strain B.1.617.2 resembles illness due to the Alpha variant B.1.1.7., with short duration and similar symptom burden.
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-FundingZOE Limited, UK Government Department of Health and Social Care, Wellcome Trust, UK Engineering and Physical Sciences Research Council, UK Research and Innovation London Medical Imaging & Artificial Intelligence Centre for Value Based Healthcare, UK National Institute for Health Research, UK Medical Research Council, British Heart Foundation and Alzheimers Society.
-
-EthicsEthics approval was granted by KCL Ethics Committee (reference LRS-19/20-18210).
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-Research in contextO_ST_ABSEvidence before this studyC_ST_ABSTo identify existing evidence for differences in COVID-19 due to infection with Alpha (B.1.1.7) or Delta (B.1.617.2) SARS-CoV-2 variants, we searched PubMed for peer-reviewed articles and medRxiv for preprint publications between March 1, and September 17, 2021 using keywords (""SARS-CoV-2"" OR ""COVID-19"") AND (children OR p?ediatric*) AND (""delta variant"" OR ""B.1.617.2""). We did not restrict our search by language. Of twenty published articles identified in PubMed, we found one case study describing disease presentation associated with Delta variant infection in a child. Another study examining the increase in hospitalization rates of paediatric cases in USA from August 1, 2020 to August 27, 2021 stated that ""It is not known whether the B.1.617.2 (Delta) variant [...] causes different clinical outcomes in children and adolescents compared with variants that circulated earlier."" Four studies reported cases of transmission of the Delta variant in school and community contexts; and two discussed screening testing in school-aged children (thus not directly relevant to the research question here). Remaining papers did not target paediatric age specifically. We found no studies investigating differences in COVID-19 presentation (e.g., duration, burden, individual symptoms) in school-aged children either in the UK or world-wide.
-
-Added value of this studyWe describe and compare illness profiles in symptomatic UK school-aged children (aged 5-17 years) with COVID-19 when either Alpha or Delta strains were the predominant circulating SARS-CoV-2 variant. Our data, collected through one of the largest UK citizen science epidemiological initiatives, show that symptom profile and illness duration of COVID-19 are broadly similar between the strains. Although there were slightly more symptoms with Delta than with Alpha, particularly in older children, this was offset by similar symptom duration (whether considered for symptoms individually or for illness overall). Our study adds quantitative information to the debate on whether there are meaningful clinical differences in COVID-19 due to Alpha vs. Delta variants; and contributes to the discussion regarding rationale for vaccinating children (particularly younger children) against SARS-CoV-2.
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-Implications of all the available evidenceOur data confirm that COVID-19 in UK school-aged children is usually of short duration and similar symptom burden, whether due to Delta or Alpha. Our data contribute to epidemiological surveillance from the wider UK population, and we capture common and generally mild paediatric presentations of COVID-19 that might be missed using clinician-based surveillance alone. Our data will also be useful for the vaccination debate.",pediatrics,fuzzy,94,100
 medRxiv,10.1101/2021.10.07.21264655,2021-10-07,https://medrxiv.org/cgi/content/short/2021.10.07.21264655,The consequences of a year of the COVID-19 pandemic for the mental health of young adult twins in England and Wales,Kaili Rimfeld; Margherita Malanchini; Ryan Arathimos; Agnieszka Gidziela; Oliver Pain; Andrew McMillan; Rachel Ogden; Louise Webster; Amy E Packer; Nicholas G Shakeshaft; Kerry L Schofield; Jean-Baptiste Pingault; Andrea G Allegrini; Argyris Stringaris; Sophie von Stumm; Cathryn M Lewis; Robert Plomin,"King's College London; Department of Psychology, Queen Mary University of London; King's College London; Department of Psychology, Queen Mary University of London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Clinical, Educational & Health Psychology, Division of Psychology & Language Sciences, Faculty of Brain Sciences, University College London; Clinical, Educational & Health Psychology, Division of Psychology & Language Sciences, Faculty of Brain Sciences, University College London; Mood, Brain & Development Unit, Emotion and Development Branch, National Institute of Mental Health; Psychology in Education Research Centre, Department of Education, University of York; King's College London; King's College London","The COVID-19 pandemic has impacted all our lives, not only through the infection itself, but also through the measures taken to control the viruss spread (e.g., lockdown). Here we investigated how the COVID-19 pandemic and unprecedented lockdown affected the mental health of young adults in England and Wales. We compared the mental health symptoms of up to 4,000 twins in their mid-twenties in 2018 prior to the COVID-19 pandemic (T1) to those in a four-wave longitudinal data collection during the pandemic in April, July, and October 2020, and in March 2021 (T2-T5). The average changes in mental health were small-to-medium and mainly occurred from 2018 (T1) to March 2020 (T2, one month following the start of lockdown; average Cohen d=0.14). Despite the expectation of catastrophic effects on the pandemic on mental health of our young adults, we did not observe trends in worsening mental health during the pandemic (T3-T5). Young people with pre-existing mental health problems were adversely affected at the beginning of the pandemic, but their increased problems largely subsided as the pandemic persisted. Twin analyses indicated that the aetiology of individual differences did not change during the lockdown. The average heritability of mental health symptoms was 33% across 5 waves of assessment, and the average genetic correlation between T1 and T2-T5 was .95, indicating that genetic effects before the pandemic (T1) are substantially correlated with genetic effects up to a year later (T2-T5). We conclude that on average the mental health of young adults in England and Wales has been remarkably resilient to the effects of the pandemic and associated lockdown.",psychiatry and clinical psychology,fuzzy,100,100
 medRxiv,10.1101/2021.10.05.21264543,2021-10-07,https://medrxiv.org/cgi/content/short/2021.10.05.21264543,Higher Hospitalization and Mortality Rates Among SARS-CoV-2 infected Persons in Rural America,Alfred Jerrod Anzalone; Ronald Horswell; Brian Hendricks; San Chu; William Hillegass; William Beasley; Jeremy Harper; Clifford Rosen; Lucio Miele; James McClay; Susan Santangelo; Sally Hodder; - N3C Consortium,University of Nebraska Medical Center; Pennington Biomedical Research Centre; West Virginia University; Pennington Biomedical Research Centre; University of Mississippi Medical Center; University of Oklahoma; Owl Health Works LLC; Maine Medical Center Research Institute; Louisiana State University Health Sciences Center; University of Nebraska Medical Center; Tufts University School of Medicine; West Virginia University; ,"IMPORTANCERural communities are among the most underserved and resource-scarce populations in the United States (US), yet there are limited data on COVID-19 mortality in rural America. Furthermore, rural data are rarely centralized, precluding comparability across urban and rural regions.
 
@@ -2202,23 +2160,6 @@ Research in contextO_ST_ABSEvidence before this studyC_ST_ABSA search was conduc
 Added value of this studyWe estimated the proportion of care home staff and residents with evidence of SARS-CoV-2 natural infection using data from over 3,000 staff and 1,500 residents in 201 geographically dispersed LTCFs in England. Population selection was independent of outbreak history and the sample is therefore more reflective of the population who reside and work in LTCFs. Our estimates of the proportion of residents with prior natural infection are substantially higher than estimates based on population-wide PCR testing, due to limited testing coverage at the start of the pandemic. 1361 individuals had at least one positive antibody test and participants were followed for up to 11 months, which allowed modelling of the time to loss of antibody in over 600 individuals in whom the date of primary infection could be reliably estimated. This is the longest reported serological follow up in a population of LTCF residents, a group who are known to be most at risk of severe outcomes following infection with SARS-CoV-2 and provides important evidence on the duration that nucleocapsid antibodies remained detectable over the first and second waves of the pandemic.
 
 Implications of all available researchA substantial proportion of the LTCF population will have some level of natural immunity to infection as a result of past infection. Immunological studies have highlighted greater antibody responses to vaccination in seropositive individuals, so vaccine efficacy in this population may be affected by this large pool of individuals who have survived past infection. In addition, although the presence of nucleocapsid-specific antibodies is generally considered as the standard marker for prior infection, we find that antibody waning is such that up to 50% of people will lose detectable antibody responses within eight months. Individual prior natural infection history is critical to assess the impact of factors such as vaccine response or protection against re-infection. These findings may have implications for duration of immunity following natural infection and indicate that alternative assays for prior infection should be developed.",epidemiology,fuzzy,100,100
-medRxiv,10.1101/2021.09.20.21263828,2021-09-23,https://medrxiv.org/cgi/content/short/2021.09.20.21263828,"Colchicine for COVID-19 in adults in the community (PRINCIPLE): a randomised, controlled, adaptive platform trial",- The PRINCIPLE Trial Collaborative Group; Jienchi Dorward; Ly-Mee Yu; Gail Hayward; Benjamin R Saville; Oghenekome Gbinigie; Oliver van Hecke; Emma Ogburn; Philip H Evans; Nicholas PB Thomas; Mahendra G Patel; Duncan Richards; Nicholas Berry; Michelle A Detry; Christina Saunders; Mark Fitzgerald; Victoria Harris; Milensu Shanyinde; Simon de Lusignan; Monique I Andersson; Christopher C Butler; FD Richard Hobbs,"; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom and Centre for the AIDS Programme of Research in South Africa ; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Berry Consultants, Texas, USA and Department of Biostatistics, Vanderbilt University School of Medicine, Tennessee, USA; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; College of Medicine and Health, University of Exeter and National Institute for Health Research, Clinical Research Network; Royal College of General Practitioners, London, UK, and National Institute for Health Research, Clinical Research Network; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom and School of Pharmacy and Medical Sciences, University of Bra; Oxford Clinical Trials Research Unit, Botnar Research Centre, University of Oxford, Oxford, UK; Berry Consultants, Texas, USA; Berry Consultants, Texas, USA; Berry Consultants, Texas, USA; Berry Consultants, Texas, USA; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom,; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom","ObjectivesColchicine has been proposed as a COVID-19 treatment, but its effect on time to recovery is unknown. We aimed to determine whether colchicine is effective at reducing time to recovery and COVID-19 related hospitalisations/deaths among people in the community.
-
-DesignProspective, multicentre, open-label, multi-arm, adaptive Platform Randomised Trial of Treatments in the Community for Epidemic and Pandemic Illnesses (PRINCIPLE).
-
-SettingNational trial run remotely from a central trial site and at multiple primary care centres across the United Kingdom.
-
-ParticipantsAdults aged [&ge;]65, or [&ge;]18 years with comorbidities or shortness of breath, and unwell [&le;]14 days with suspected COVID-19 in the community.
-
-InterventionsParticipants were randomised to usual care, usual care plus colchicine (500{micro}g daily for 14 days), or usual care plus other interventions.
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-Main outcome measuresThe co-primary endpoints were time to first self-reported recovery, and hospitalisation/death related to COVID-19, within 28 days, analysed using Bayesian models. The hypothesis for the time to recovery endpoint is evaluated first, and if superiority is declared on time to recovery, the hypothesis for the second co-primary endpoint of hospitalisation/death is then evaluated. To determine futility, we pre-specified a clinically meaningful benefit in time to first reported recovery as a hazard ratio of 1.2 or larger (equating to approximately 1.5 days benefit in the colchicine arm, assuming 9 days recovery in the usual care arm).
-
-ResultsThe trial opened on April 2, 2020, with randomisation to colchicine starting on March 04, 2021 and stopping on May 26, 2021, because the pre-specified time to recovery futility criterion was met. The primary analysis model included 2755 SARS-CoV-2 positive participants, randomised to colchicine (n=156), usual care (n=1145), and other treatments (n=1454). Time to first self-reported recovery was similar in the colchicine group compared with usual care with an estimated hazard ratio of 0.919 [95% credible interval 0.72 to 1.16] and an estimated increase of 1.14 days [-1.86 to 5.21] in median time to self-reported recovery for colchicine versus usual care. The probability of meaningful benefit in time to recovery was very low at 1.8%. Results were similar in comparisons with concurrent controls. COVID-19 related hospitalisations/deaths were similar in the colchicine group versus usual care, with an estimated odds ratio of 0.76 [0.28 to 1.89] and an estimated difference of -0.4% [-2.7% to 2.4]. One serious adverse event occurred in the colchicine group and one in usual care.
-
-ConclusionsColchicine did not improve time to recovery in people at higher risk of complications with COVID-19 in the community.
-
-Trial registrationISRCTN86534580.",infectious diseases,fuzzy,100,100
 medRxiv,10.1101/2021.09.16.21263684,2021-09-22,https://medrxiv.org/cgi/content/short/2021.09.16.21263684,The removal of airborne SARS-CoV-2 and other microbial bioaerosols by air filtration on COVID-19 surge units,Andrew Conway Morris; Katherine Sharrocks; Rachel Bousfield; Leanne Kermack; Mailis Maes; Ellen Higginson; Sally Forrest; Joannna Pereira-Dias; Claire Cormie; Timothy Old; Sophie Brooks; Islam Hamed; Alicia Koenig; Andrew Turner; Paul White; R. Andres Floto; Gordon Dougan; Effrossyni Gkrania-Klotsas; Theodore Gouliouris; Stephen Baker; Vilas Navapurkar,University of Cambridge; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; University of Cambridge; University of Cambridge; Cambridge University Hospitals NHS Foundation trust; Cambridge University Hospitals NHS Foundation Trust; University of Cambridge; Cambridge University Hospitals,"BackgroundThe COVID-19 pandemic has overwhelmed the respiratory isolation capacity in hospitals; many wards lacking high-frequency air changes have been repurposed for managing patients infected with SARS-CoV-2 requiring either standard or intensive care. Hospital-acquired COVID-19 is a recognised problem amongst both patients and staff, with growing evidence for the relevance of airborne transmission. This study examined the effect of air filtration and ultra-violet (UV) light sterilisation on detectable airborne SARS-CoV-2 and other microbial bioaerosols.
 
 MethodsWe conducted a crossover study of portable air filtration and sterilisation devices in a repurposed  surge COVID ward and  surge ICU. National Institute for Occupational Safety and Health (NIOSH) cyclonic aerosol samplers and PCR assays were used to detect the presence of airborne SARS-CoV-2 and other microbial bioaerosol with and without air/UV filtration.
@@ -2626,6 +2567,7 @@ MethodsWe fit a stochastic individual-based model of secondary schools to both c
 FindingsThe within-school reproduction number, Rschool, has remained below 1 from 31st August 2020 until 21st May 2021. Twice weekly mass testing using LFTs have helped to control within-school transmission in secondary schools in England. A strategy of serial contact testing alongside mass testing substantially reduces absences compared to strategies involving isolating close contacts, with only a marginal increase in within-school transmission.
 
 InterpretationSecondary school control strategies involving mass testing have the potential to control within-school transmission while substantially reducing absences compared to an isolation of close contacts policy.",infectious diseases,fuzzy,100,100
+medRxiv,10.1101/2021.07.12.21260360,2021-07-15,https://medrxiv.org/cgi/content/short/2021.07.12.21260360,The impact of hypoxia on B cells in COVID-19,Prasanti Kotagiri; Federica Mescia; Aimee Hanson; Lorinda Turner; Laura Bergamaschi; Ana Penalver; Nathan Richoz; Stephen Moore; Brian Ortmann; Benjamin Dunmore; Helene Ruffieux; Michael Morgan; Zewen Kelvin Tuong; Rachael Bashford Rogers; Myra Hosmillo; Stephen Baker; Anne Elmer; Ian Goodfellow; Ravindra Gupta; Nathalie Kingston; Paul Lehner; Nicholas Matheson; Sylvia Richardson; Caroline Saunders; Michael Weekes; Berthold Gottgens; Mark Toshner; Christoph Hess; Patrick Maxwell; Menna Clatworthy; James A Nathan; John Bradley; Paul Lyons; Natalie Burrows; Kenneth G C Smith,Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Oxford University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University,"Prominent early features of COVID-19 include severe, often clinically silent, hypoxia and a pronounced reduction in B cells, the latter important in defence against SARS-CoV-2. This brought to mind the phenotype of mice with VHL-deficient B cells, in which Hypoxia-Inducible Factors are constitutively active, suggesting hypoxia might drive B cell abnormalities in COVID-19. We demonstrated the breadth of early and persistent defects in B cell subsets in moderate/severe COVID-19, including reduced marginal zone-like, memory and transitional B cells, changes we also observed in B cell VHL-deficient mice. This was corroborated by hypoxia-related transcriptional changes in COVID-19 patients, and by similar B cell abnormalities in mice kept in hypoxic conditions, including reduced marginal zone and germinal center B cells. Thus hypoxia might contribute to B cell pathology in COVID-19, and in other hypoxic states. Through this mechanism it may impact on COVID-19 outcome, and be remediable through early oxygen therapy.",infectious diseases,fuzzy,100,100
 medRxiv,10.1101/2021.07.07.21253295,2021-07-08,https://medrxiv.org/cgi/content/short/2021.07.07.21253295,Mortality among Care Home Residents in England during the first and second waves of the COVID-19 pandemic: an analysis of 4.3 million adults over the age of 65,Anna Schultze; Emily Nightingale; David Evans; William J Hulme; Alicia Rosello; Chris Bates; Jonathan Cockburn; Brian MacKenna; Helen J Curtis; Caroline E Morton; Richard Croker; Seb Bacon; Helen I McDonald; Christopher T. Rentsch; Krishnan Bhaskaran; Rohini Mathur; Laurie A Tomlinson; Elizabeth J Williamson; Harriet Forbes; John Tazare; Daniel J Grint; Alex J Walker; Peter Inglesby; Nicholas J DeVito; Amir Mehrkar; George Hickman; Simon Davy; Tom Ward; Louis Fisher; Amelia CA Green; Kevin Wing; Angel YS Wong; Robert McManus; John Parry; Frank Hester; Sam Harper; Stephen JW Evans; Ian J Douglas; Liam Smeeth; Rosalind M Eggo; Ben Goldacre; David A Leon,"London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene & Tropical Medicine; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT","BackgroundResidents in care homes have been severely impacted by the COVID-19 pandemic. We describe trends in risk of mortality among care home residents compared to residents in private homes in England.
 
 MethodsOn behalf of NHS England, we used OpenSAFELY-TPP, an analytics platform running across the linked electronic health records of approximately a third of the English population, to calculate monthly age-standardised risks of death due to all causes and COVID-19 among adults aged >=65 years between 1/2/2019 and 31/03/2021. Care home residents were identified using linkage to the Care and Quality Commission.
@@ -2671,7 +2613,6 @@ Risk factors identified for persistent symptoms (12 weeks or more) suggestive of
 Clustering identified two distinct groups of individuals with different symptom profiles at 12 weeks, highlighting the heterogeneity of clinical presentation. The smaller cluster had higher prevalence of respiratory and related symptoms, while for those in the larger cluster tiredness was the dominant symptom, with lower prevalence of organ-specific symptoms.
 
 Implications of available evidenceThere is a high prevalence of persistent symptoms beyond 12 weeks after acute COVID-19, with little evidence of decline thereafter. This highlights the needs for greater support for patients, both through specialised services and, for those from low-income settings, financial support. The understanding that there are distinct clusters of persistent symptoms, the most common of which is dominated by fatigue, is important for the recognition and clinical management of the condition outside of specialised services.",infectious diseases,fuzzy,96,100
-medRxiv,10.1101/2021.06.28.21259529,2021-07-01,https://medrxiv.org/cgi/content/short/2021.06.28.21259529,Global patterns of genetic variation and association with clinical phenotypes at genes involved in SARS-CoV-2 infection,Chao Zhang; Anurag Verma; Yuanqing Feng; Marcelo C. R. Melo; Michael McQuillan; Matthew Hansen; Anastasia Lucas; Joseph Park; Alessia Ranciaro; Simon Thompson; Meghan A. Rubel; Michael C. Campbell; William Beggs; JIBRIL HIRBO; Sununguko Wata Mpoloka; Gaonyadiwe George Mokone; - Regeneron Genetic Center; Thomas Nyambo; Dawit Wolde Meskel; Gurja Belay; Charles Fokunang; Alfred K. Njamnshi; Sabah A. Omar; Scott Williams; Daniel Rader; Marylyn D Ritchie; Cesar de la Fuente Nunez; Giorgio Sirugo; Sarah Tishkoff,"University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; Perelman School of Medicine at the University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Howard; University of Pennsylvania; Vanderbilt University Medical Center; University of Botswana, Biological Sciences, Gaborone, Botswana; University of Botswana, Faculty of Medicine, Gaborone, Botswana; ; Department of Biochemistry, Kampala International University in Tanzania, Dar es Salaam, Tanzania; Addis Ababa University Department of Microbial Cellular and Molecular Biology, Addis Ababa, Ethiopia; Addis Ababa University Department of Microbial Cellular and Molecular Biology, Addis Ababa, Ethiopia; Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaounde I, Yaounde, Cameroon; Department of Neurology, Central Hospital Yaounde; Brain Research Africa Initiative (BRAIN), Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The ; Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya; Case Western Reserve University; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania","We investigated global patterns of genetic variation and signatures of natural selection at host genes relevant to SARS-CoV-2 infection (ACE2, TMPRSS2, DPP4, and LY6E). We analyzed novel data from 2,012 ethnically diverse Africans and 15,997 individuals of European and African ancestry with electronic health records, and integrated with global data from the 1000GP. At ACE2, we identified 41 non-synonymous variants that were rare in most populations, several of which impact protein function. However, three non-synonymous variants were common among Central African hunter-gatherers from Cameroon and are on haplotypes that exhibit signatures of positive selection. We identify strong signatures of selection impacting variation at regulatory regions influencing ACE2 expression in multiple African populations. At TMPRSS2, we identified 13 amino acid changes that are adaptive and specific to the human lineage. Genetic variants that are targets of natural selection are associated with clinical phenotypes common in patients with COVID-19.",genetic and genomic medicine,fuzzy,100,100
 medRxiv,10.1101/2021.06.23.21259400,2021-06-30,https://medrxiv.org/cgi/content/short/2021.06.23.21259400,Temporal trends in primary care-recorded self-harm during and beyond the first year of the COVID-19 pandemic: time series analysis of electronic healthcare records for 2.8 million patients in the Greater Manchester Care Record,Sarah Steeg; Lana Bojanić; George Tilston; Richard Williams; David A Jenkins; Matthew J Carr; Niels Peek; Darren M Ashcroft; Nav Kapur; Jennifer Voorhees; Roger T Webb,University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester,"BackgroundSurveillance of clinically treated self-harm episode frequency is an important component of suicide prevention in the dynamic context of COVID-19. Studies published to date have investigated the initial months following the onset of the pandemic, despite national and regional restrictions persisting to Summer 2021.
 
 MethodsWe conducted a descriptive time series analysis utilising data from the Greater Manchester Care Record, which contains de-identified, primary care health records of 2.8 million patients. Counts of incident and all episodes of self-harm recorded between 1st January 2019 and 31st May 2021 were made for all patients, with stratification by sex, age group, ethnicity, and index of multiple deprivation (IMD) quintile and examination of overall differences by national and regional restriction phases.
@@ -2722,13 +2663,6 @@ ResultsIn LS, symptoms impacted normal functioning for 12+ weeks in 1.2% (mean a
 ConclusionLong COVID is associated with sociodemographic and pre-existing health factors. Further investigations into causality should inform strategies to address long COVID in the population.",epidemiology,fuzzy,100,100
 medRxiv,10.1101/2021.06.22.21259336,2021-06-24,https://medrxiv.org/cgi/content/short/2021.06.22.21259336,Population disruption: estimating changes in population distribution in the UK during the COVID-19 pandemic,Hamish Gibbs; Naomi R Waterlow; James Cheshire; Leon Danon; Yang Liu; Chris Grundy; Adam J Kucharski; - LSHTM CMMID COVID-19 Working Group; Rosalind M Eggo,"London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University College London; Department of Engineering Mathematics, University of Bristol, UK.; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; -; London School of Hygiene & Tropical Medicine","Mobility data have demonstrated major changes in human movement patterns in response to COVID-19 and associated interventions in many countries. This can involve sub-national redistribution, short-term relocations as well as international migration. In this paper, we combine detailed location data from Facebook measuring the location of approximately 6 million daily active Facebook users in 5km2 tiles in the UK with census-derived population estimates to measure population mobility and redistribution. We provide time-varying population estimates and assess spatial population changes with respect to population density and four key reference dates in 2020 (First lockdown, End of term, Beginning of term, Christmas). We also show how population estimates derived from the distribution of Facebook users vary compared to mid-2020 small area population estimates by the UK national statistics agencies. We estimate that between March 2020 and March 2021, the total population of the UK declined and we identify important spatial variations in this population change, showing that low-density areas have experienced lower population decreases than urban areas. We estimate that, for the top 10% highest population tiles, the population has decreased by 6.6%. Further, we provide evidence that geographic redistributions of population within the UK coincide with dates of non-pharmaceutical interventions including lockdowns and movement restrictions, as well as seasonal patterns of migration around holiday dates. The methods used in this study reveal significant changes in population distribution at high spatial and temporal resolutions that have not previously been quantified by available demographic surveys in the UK. We found early indicators of potential longer-term changes in the population distribution of the UK although it is not clear if these changes may persist after the COVID-19 pandemic.",public and global health,fuzzy,100,100
 medRxiv,10.1101/2021.06.16.21258691,2021-06-21,https://medrxiv.org/cgi/content/short/2021.06.16.21258691,App-based COVID-19 surveillance and prediction: The COVID Symptom Study Sweden,Beatrice Kennedy; Hugo Fitipaldi; Ulf Hammar; Marlena Maziarz; Neli Tsereteli; Nikolay Oskolkov; Georgios Varotsis; Camilla A Franks; Diem T Nguyen; Lampros Spiliopoulos; Hans-Olov Adami; Jonas Björk; Stefan Engblom; Katja Fall; Anna Grimby-Ekman; Jan-Eric Litton; Mats Martinell; Anna Oudin; Torbjörn Sjöström; Toomas Timpka; Carole H Sudre; Mark S Graham; Julien Lavigne du Cadet; Andrew T. Chan; Richard Davies; Sajaysurya Ganesh; Anna May; Sébastien Ourselin; Joan Capdevila Pujol; Somesh Selvachandran; Jonathan Wolf; Tim D Spector; Claire J Steves; Maria F Gomez; Paul W Franks; Tove Fall,"Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Sweden; Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Sweden; Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Sweden; Diabetic Complications Unit, Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Sweden; Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Sweden; Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Sweden; Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Sweden; Diabetic Complications Unit, Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Sweden; Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Sweden; Diabetic Complications Unit, Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Sweden; Skåne University Hospital, Malmö, Sweden; Clinical Effectiveness Group, Institute of Health and Society, University of Oslo, Oslo, Norway; Dept of Medical Epidemiology and Biostatistics, Karolinska Inst; Division of Occupational and Environmental Medicine, Lund University, Sweden; Clinical Studies Sweden, Forum South, Skåne University Hospital, Lund, Sweden; Division of Scientific Computing, Department of Information Technology, Uppsala University, Sweden; Clinical Epidemiology and Biostatistics, School of Medical Sciences, Örebro University, Örebro, Sweden; Integrative Epidemiology, Institute of Environmental Med; Biostatistics, School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Sweden; Department of Public Health and Caring Sciences, Uppsala University, Sweden; Primary Care and Health, Region Uppsala, Sweden; Division for Occupational and environmental medicine, Lund University, Sweden; Department of Public Health and Clinical Medicine, Section of Sustainable Health,; Novus International Group AB, Sweden; Department of Medical and Health Sciences, Linkoping University, Sweden; MRC Unit for Lifelong Health and Ageing at UCL, University College London, London, UK; Centre for Medical Image Computing, University College London, London, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; ZOE Limited; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; ZOE Limited; ZOE Limited; ZOE Limited; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; ZOE Limited; ZOE Limited; ZOE Limited; Department of Twin Research and Genetic Epidemiology, King's College London, London, UK; Department of Twin Research and Genetic Epidemiology, King's College London, London, UK; Diabetic Complications Unit, Department of Clinical Sciences in Malmö, Lund University Diabetes Centre, Sweden; Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Sweden; Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Sweden","The app-based COVID Symptom Study was launched in Sweden in April 2020 to contribute to real-time COVID-19 surveillance. We enrolled 143,531 study participants ([&ge;]18 years) who contributed 10.6 million daily symptom reports between April 29, 2020 and February 10, 2021. Data from 19,161 self-reported PCR tests were used to create a symptom-based model to estimate the individual probability of symptomatic COVID-19, with an AUC of 0.78 (95% CI 0.74-0.83) in an external dataset. These individual probabilities were used to estimate daily regional COVID-19 prevalence, which were in turn used together with current hospital data to predict next week COVID-19 hospital admissions. We found that this hospital prediction model demonstrated a lower median absolute percentage error (MdAPE: 25.9%) across the five most populated regions in Sweden during the first pandemic wave than a model based on case notifications (MdAPE: 30.3%). During the second wave, the error rates were similar. When applying the same model to an English dataset, not including local COVID-19 test data, we observed MdAPEs of 22.3% and 19.0%, respectively, highlighting the transferability of the prediction model.",health informatics,fuzzy,100,100
-medRxiv,10.1101/2021.06.17.21259103,2021-06-21,https://medrxiv.org/cgi/content/short/2021.06.17.21259103,REACT-1 round 12 report: resurgence of SARS-CoV-2 infections in England associated with increased frequency of the Delta variant,Steven Riley; Caroline E. Walters; Haowei Wang; Oliver Eales; David Haw; Kylie E. C. Ainslie; Christina Atchinson; Claudio Fronterre; Peter J. Diggle; Andrew J. Page; Sophie J. Prosolek; Alexander J. Trotter; Le Viet Thanh; Nabil-Fareed Alikhan; Leigh M Jackson; Catherine Ludden; - The COVID-19 Genomics UK (COG-UK) Consortium; Deborah Ashby; Christl A Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Medical School, University of Exeter, UK; Department of Medicine, University of Cambridge, UK; -; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear","BackgroundEngland entered a third national lockdown from 6 January 2021 due to the COVID-19 pandemic. Despite a successful vaccine rollout during the first half of 2021, cases and hospitalisations have started to increase since the end of May as the SARS-CoV-2 Delta (B.1.617.2) variant increases in frequency. The final step of relaxation of COVID-19 restrictions in England has been delayed from 21 June to 19 July 2021.
-
-MethodsThe REal-time Assessment of Community Transmision-1 (REACT-1) study measures the prevalence of swab-positivity among random samples of the population of England. Round 12 of REACT-1 obtained self-administered swab collections from participants from 20 May 2021 to 7 June 2021; results are compared with those for round 11, in which swabs were collected from 15 April to 3 May 2021.
-
-ResultsBetween rounds 11 and 12, national prevalence increased from 0.10% (0.08%, 0.13%) to 0.15% (0.12%, 0.18%). During round 12, we detected exponential growth with a doubling time of 11 (7.1, 23) days and an R number of 1.44 (1.20, 1.73). The highest prevalence was found in the North West at 0.26% (0.16%, 0.41%) compared to 0.05% (0.02%, 0.12%) in the South West. In the North West, the locations of positive samples suggested a cluster in Greater Manchester and the east Lancashire area. Prevalence in those aged 5-49 was 2.5 times higher at 0.20% (0.16%, 0.26%) compared with those aged 50 years and above at 0.08% (0.06%, 0.11%). At the beginning of February 2021, the link between infection rates and hospitalisations and deaths started to weaken, although in late April 2021, infection rates and hospital admissions started to reconverge. When split by age, the weakened link between infection rates and hospitalisations at ages 65 years and above was maintained, while the trends converged below the age of 65 years. The majority of the infections in the younger group occurred in the unvaccinated population or those without a stated vaccine history. We observed the rapid replacement of the Alpha (B.1.1.7) variant of SARS-CoV-2 with the Delta variant during the period covered by rounds 11 and 12 of the study.
-
-DiscussionThe extent to which exponential growth continues, or slows down as a consequence of the continued rapid roll-out of the vaccination programme, including to young adults, requires close monitoring. Data on community prevalence are vital to track the course of the epidemic and inform ongoing decisions about the timing of further lifting of restrictions in England.",infectious diseases,fuzzy,100,100
 bioRxiv,10.1101/2021.06.21.449178,2021-06-21,https://biorxiv.org/cgi/content/short/2021.06.21.449178,Spatial transcriptomic characterization of COVID-19 pneumonitis identifies immune pathways related to tissue injury,Amy R Cross; Carlos de Andrea; Maria Villalba-Esparza; Manuel Landecho Acha; Lucia Cerundolo; Praveen Weeratunga; Rachel Etherington; Laura Denney; Graham Ogg; Ling-Pei Ho; Ian Roberts; Joanna Hester; Paul Klenerman; Ignacio Melero; Stephen Sansom; Fadi Issa,"University of Oxford; Universidad de Navarra; Department of Pathology, Clinica de la Universidad de Navarra, Pamplona, Spain; Clinica Universidad de Navarra; University of Oxford; Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, Universit; University of Oxford; University of Oxford; Medical Research Council Human Immunology Unit, Radcliffe Department of Medicine, Medical Research Council Weatherall Institute of Molecular Medicine, Universit; University of Oxford; Oxford University Hospitals NHS Foundation Trust; University of Oxford; University of Oxford; Universidad de Navarra; University of Oxford; University of Oxford","Severe lung damage in COVID-19 involves complex interactions between diverse populations of immune and stromal cells. In this study, we used a spatial transcriptomics approach to delineate the cells, pathways and genes present across the spectrum of histopathological damage in COVID-19 lung tissue. We applied correlation network-based approaches to deconvolve gene expression data from areas of interest within well preserved post-mortem lung samples from three patients. Despite substantial inter-patient heterogeneity we discovered evidence for a common immune cell signaling circuit in areas of severe tissue that involves crosstalk between cytotoxic lymphocytes and pro-inflammatory macrophages. Expression of IFNG by cytotoxic lymphocytes was associated with induction of chemokines including CXCL9, CXCL10 and CXCL11 which are known to promote the recruitment of CXCR3+ immune cells. The tumour necrosis factor (TNF) superfamily members BAFF (TNFSF13B) and TRAIL (TNFSF10) were found to be consistently upregulated in the areas with severe tissue damage. We used published spatial and single cell SARS-CoV-2 datasets to confirm our findings in the lung tissue from additional cohorts of COVID-19 patients. The resulting model of severe COVID-19 immune-mediated tissue pathology may inform future therapeutic strategies.
 
 One Sentence SummarySpatial analysis identifies IFN{gamma} response signatures as focal to severe alveolar damage in COVID-19 pneumonitis.",immunology,fuzzy,100,100
@@ -2963,6 +2897,28 @@ MethodsThe Virus Watch study is an online, prospective, community cohort study f
 ResultsOut of 24,887 illnesses reported, 915 tested positive for SARS-CoV-2 and 186 likely infector-infectee pairs in 186 households amongst 372 individuals were identified. The mean COVID-19 serial interval was 3.18 (95%CI: 2.55 - 3.81) days. There was no significant difference (p=0.267) between the mean serial interval for Variants of Concern (VOC) hotspots (mean = 3.64 days, (95%CI: 2.55 - 4.73)) days and non-VOC hotspots, (mean = 2.72 days, (95%CI: 1.48 - 3.96)).
 
 ConclusionsOur estimates of the average serial interval of COVID-19 are broadly similar to estimates from previous studies and we find no evidence that B.1.1.7 is associated with a change in serial intervals. Alternative explanations such as increased viral load, longer period of viral shedding or improved receptor binding may instead explain the increased transmissibility and rapid spread and should undergo further investigation.",epidemiology,fuzzy,100,100
+medRxiv,10.1101/2021.05.13.21257146,2021-05-17,https://medrxiv.org/cgi/content/short/2021.05.13.21257146,Sociodemographic inequality in COVID-19 vaccination coverage amongst elderly adults in England: a national linked data study,Vahe Nafilyan; Ted Dolby; Cameron Razieh; Charlotte Gaughan; Jasper Morgan; Daniel Ayoubkhani; Ann Sarah Walker; Kamlesh Khunti; Myer Glickman; Thomas Yates,"Office for National Statistics; Office for National Statistics; Diabetes Research Centre, University of Leicester; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Diabetes Research Centre, University of Leicester; Office for National Statistics; Diabetes Research Centre, University of Leicester","ObjectiveTo examine inequalities in COVID-19 vaccination rates amongst elderly adults in England
+
+DesignCohort study
+
+SettingPeople living in private households and communal establishments in England
+
+Participants6,829,643 adults aged [&ge;] 70 years (mean 78.7 years, 55.2% female) who were alive on 15 March 2021.
+
+Main outcome measuresHaving received the first dose of a vaccine against COVID-19 by 15 March 2021. We calculated vaccination rates and estimated unadjusted and adjusted odds ratios using logistic regression models.
+
+ResultsBy 15 March 2021, 93.2% of people living in England aged 70 years and over had received at least one dose of a COVID-19 vaccine. While vaccination rates differed across all factors considered apart from sex, the greatest disparities were seen between ethnic and religious groups. The lowest rates were in people of Black African and Black Caribbean ethnic backgrounds, where only 67.2% and 73.9% had received a vaccine, with adjusted odds of not being vaccinated at 5.01 (95% CI 4.86 - 5.16) and 4.85 (4.75 - 4.96) times greater than the White British group. The proportion of individuals self-identifying as Muslim and Buddhist who had received a vaccine was 79.1% and 84.1%, respectively. Older age, greater area deprivation, less advantaged socio-economic position (proxied by living in a rented home), being disabled and living either alone or in a multi-generational household were also associated with higher odds of not having received the vaccine.
+
+ConclusionPeople disproportionately affected seem most hesitant to COVID-19 vaccinations. Policy Interventions to improve these disparities are urgently needed.
+
+Summary BoxO_ST_ABSWhat is already known on this subject?C_ST_ABSThe UK began an ambitious vaccination programme to combat the COVID-19 pandemic on 8th December 2020. Existing evidence suggests that COVID-19 vaccination rates differ by level of area deprivation, ethnicity and certain underlying health conditions, such as learning disability and mental health problems.
+
+What does this study add?Our study shows that first dose vaccination rates in adults aged 70 or over differed markedly by ethnic group and self-reported religious affiliation, even after adjusting for geography, socio-demographic factors and underlying health conditions. Our study also highlights differences in vaccination rates by deprivation, household composition, and disability status, factors disproportionately associated with SARS-CoV-2 infection. Public health policy and community engagement aimed at promoting vaccination uptake is these groups are urgently needed.
+
+Strengths and limitations of this studyO_LIUsing nationwide linked population-level data from clinical records and the 2011 Census, we examined a wide range of socio-demographic characteristics not available n electronic health records
+C_LIO_LIMost demographic and socio-economic characteristics are derived from the 2011 Census and therefore are 10 years old. However, we focus primarily on characteristics that are unlikely to change over time, such as ethnicity or religion, or likely to be stable for our population
+C_LIO_LIBecause the data are based on the 2011 Census, it excluded people living in England in 2011 but not taking part in the 2011 Census; respondents who could not be linked to the 2011-2013 NHS patients register; recent migrants. Consequently, we excluded 5.4% of vaccinated people who could not be linked
+C_LI",public and global health,fuzzy,100,100
 medRxiv,10.1101/2021.05.12.21257102,2021-05-15,https://medrxiv.org/cgi/content/short/2021.05.12.21257102,"Spike-antibody responses following first and second doses of ChAdOx1 and BNT162b2 vaccines by age, gender, and clinical factors - a prospective community cohort study (Virus Watch)",Madhumita Shrotri; Ellen Fragaszy; Cyril Geismar; Vincent Nguyen; Sarah Beale; Isobel Braithwaite; Thomas Edward Byrne; Wing Lam Erica Fong; Jana Kovar; Annalan M D Navaratnam; Parth Patel; Anna Aryee; Jamie Lopez Bernal; Anne M Johnson; Alison Rodger; Andrew C Hayward; Robert W Aldridge,University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; Public Health England; University College London; University College London; University College London; University College London,"BackgroundVaccination constitutes the best long-term solution against Coronavirus Disease 2019 (COVID-19). Real-world immunogenicity data are sparse, particularly for ChAdOx1 and in populations with chronic conditions; and given the UKs extended dosing interval, it is also important to understand antibody responses in SARS-CoV-2-naive individuals following a single dose.
 
 MethodsAdults aged [&ge;]18 years from households enrolled in Virus Watch, a prospective community cohort study in England and Wales, provided capillary blood samples and self-reported vaccination status. Primary outcome variables were quantitative Spike total antibody levels (U/ml) and seropositivity to Spike ([&ge;]0.8 U/ml), as per Roches Elecsys Anti-SARS-CoV-2 S assay. Samples seropositive for Nucleocapsid, and samples taken prior to vaccination, were excluded. Outcomes were analysed by days since vaccination, vaccine type (BNT162b2 and ChAdOx1), and a range of self-reported demographic and clinical factors.
@@ -3003,13 +2959,6 @@ Key FindingsO_ST_ABSQuestionC_ST_ABSHow has the COVID-19 pandemic influenced emo
 FindingsUsing repeated longitudinal data from before and during the pandemic we provide evidence that emotional difficulty scores of primary school aged children are higher by an estimated 10.0 points (0.8 standard deviations) (95% CI: 5.0 to 15.0) by age 8.5 years than would be expected based on pre pandemic data.
 
 MeaningThe level of difference in emotional difficulties found in the current study has been linked to increased likelihood of mental health problems in adolescence and adulthood. Therefore, this increase in difficulties needs careful monitoring and support.",psychiatry and clinical psychology,fuzzy,100,100
-medRxiv,10.1101/2021.05.06.21256755,2021-05-13,https://medrxiv.org/cgi/content/short/2021.05.06.21256755,Clinical coding of long COVID in English primary care: a federated analysis of 58 million patient records in situ using OpenSAFELY,- The OpenSAFELY Collaborative; Alex J Walker; Brian MacKenna; Peter Inglesby; Christopher T Rentsch; Helen J Curtis; Caroline E Morton; Jessica Morley; Amir Mehrkar; Sebastian CJ Bacon; George Hickman; Christopher Bates; Richard Croker; David Evans; Tom Ward; Jonathan Cockburn; Simon Davy; Krishnan Bhaskaran; Anna Schultze; Elizabeth J Williamson; William J Hulme; Helen I McDonald; Laurie Tomlinson; Rohini Mathur; Rosalind M Eggo; Kevin Wing; Angel YS Wong; Harriet Forbes; John Tazare; John Parry; Frank Hester; Sam Harper; Shaun O'Hanlon; Alex Eavis; Richard Jarvis; Dima Avramov; Paul Griffiths; Aaron Fowles; Nasreen Parkes; Ian J Douglas; Stephen JW Evans; Liam Smeeth; Ben Goldacre,; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; TPP; TPP; EMIS; EMIS; EMIS; EMIS; EMIS; EMIS; EMIS; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundLong COVID is a term to describe new or persistent symptoms at least four weeks after onset of acute COVID-19. Clinical codes to describe this phenomenon were released in November 2020 in the UK, but it is not known how these codes have been used in practice.
-
-MethodsWorking on behalf of NHS England, we used OpenSAFELY data encompassing 96% of the English population. We measured the proportion of people with a recorded code for long COVID, overall and by demographic factors, electronic health record software system, and week. We also measured variation in recording amongst practices.
-
-ResultsLong COVID was recorded for 23,273 people. Coding was unevenly distributed amongst practices, with 26.7% of practices having not used the codes at all. Regional variation was high, ranging between 20.3 per 100,000 people for East of England (95% confidence interval 19.3-21.4) and 55.6 in London (95% CI 54.1-57.1). The rate was higher amongst women (52.1, 95% CI 51.3-52.9) compared to men (28.1, 95% CI 27.5-28.7), and higher amongst practices using EMIS software (53.7, 95% CI 52.9-54.4) compared to TPP software (20.9, 95% CI 20.3-21.4).
-
-ConclusionsLong COVID coding in primary care is low compared with early reports of long COVID prevalence. This may reflect under-coding, sub-optimal communication of clinical terms, under-diagnosis, a true low prevalence of long COVID diagnosed by clinicians, or a combination of factors. We recommend increased awareness of diagnostic codes, to facilitate research and planning of services; and surveys of clinicians experiences, to complement ongoing patient surveys.",epidemiology,fuzzy,100,100
 medRxiv,10.1101/2021.05.10.21256912,2021-05-11,https://medrxiv.org/cgi/content/short/2021.05.10.21256912,Household overcrowding and risk of SARS-CoV-2: analysis of the Virus Watch prospective community cohort study in England and Wales,Robert W Aldridge; Helen Pineo; Ellen Fragaszy; Max Eyre; Jana Kovar; Vincent Nguyen; Sarah Beale; Thomas Byrne; Anna Aryee; Colette Smith; Delanjathan Devakumar; Jonathon Taylor; Vittal Katikireddi; Wing Lam Erica Fong; Cyril Geismar; Parth Patel; Madhumita Shrotri; Isobel Braithwaite; Annalan M D Navaratnam; Anne M Johnson; Andrew Hayward,"Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK.; Institute for Environmental Design and Engineering, Bartlett School of Environment, Energy and Resources, University College London, London, UK.; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Institute of Epidemiology and Health Care, University Col; Centre of Health Informatics, Computing and Statistics, Lancaster Medical School, Lancaster University, Lancaster, LA1 4YW, UK; Institute of Epidemiology and Health Care, University College London, London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK.; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Institute of Epidemiology and Health Care, University Col; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK.; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK.; Institute for Global Health, University College London, London, UK.; Institute for Global Health, University College London, London, UK.; Department of Civil Engineering, Tampere University, Finland.; MRC/CSO Social and Public Health Sciences Unit, University of Glasgow Institute of Health and Wellbeing, Glasgow, UK.; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK.; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Institute of Epidemiology and Health Care, University Col; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK.; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK.; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK.; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Institute of Epidemiology and Health Care, University Col; Institute for Global Health, University College London, London, UK.; Institute of Epidemiology and Health Care, University College London, London, UK","BackgroundHousehold overcrowding is associated with increased risk of infectious diseases across contexts and countries. Limited data exist linking household overcrowding and risk of COVID-19. We used data collected from the Virus Watch cohort to examine the association between overcrowded households and SARS-CoV-2.
 
 MethodsThe Virus Watch study is a household community cohort of acute respiratory infections in England & Wales that began recruitment in June 2020. We calculated the persons per room for each household and classified accommodation as overcrowded when the number of rooms{square}was fewer than the number of people. We considered two primary outcomes - PCR-confirmed positive SARS-CoV-2 antigen tests and laboratory confirmed SARS-CoV-2 antibodies (Roche Elecsys anti-N total immunoglobulin assay). We used mixed effects logistic regression models that accounted for household structure to estimate the association between household overcrowding and SARS-CoV-2 infection.
@@ -3035,40 +2984,9 @@ Research in contextO_ST_ABSEvidence before this studyC_ST_ABSSARS-CoV-2 in child
 Added value of this studyWe provide systematic description of COVID-19 in UK school-aged children. Our data, collected in a digital surveillance platform through one of the largest UK citizen science initiatives, show that long illness duration after SARS-CoV-2 infection in school-aged children does occur, but is uncommon, with only a small proportion of children experiencing illness duration beyond four weeks; and the symptom burden in these children usually decreases over time. Almost all children have symptom resolution by eight weeks, providing reassurance about long-term outcomes. Additionally, symptom burden in children with long COVID was not greater than symptom burden in children with long illnesses due to causes other than SARS-CoV-2 infection.
 
 Implications of all the available evidenceOur data confirm that COVID-19 in UK school-aged children is usually of short duration and of low symptom burden. Some children do experience longer illness duration, validating their experience; however, most of these children usually recover with time. Our findings highlight that appropriate resources will be necessary for any child with prolonged illness, whether due to COVID-19 or other illness. Our study provides timely and critical data to inform discussions around the impact and implications of the pandemic on paediatric healthcare resource allocation.",epidemiology,fuzzy,94,100
-medRxiv,10.1101/2021.05.04.21256507,2021-05-06,https://medrxiv.org/cgi/content/short/2021.05.04.21256507,Describing the burden of the COVID-19 pandemic in people with psoriasis: findings from a global cross-sectional study,Satveer K Mahil; Mark Yates; Zenas Z Yiu; Sinead M Langan; Teresa Tsakok; Nick Dand; Kayleigh J Mason; Helen McAteer; Freya Meynall; Bolaji Coker; Alexandra Vincent; Dominic Urmston; Amber Vesty; Jade Kelly; Camille Lancelot; Lucy Moorhead; Herve Bachelez; Francesca Capon; Claudia R Contreras; Claudia De La Cruz; Paola Di Meglio; Paolo Gisondi; Denis Jullien; Jo Lambert; Luigi Naldi; Sam Norton; Luis Puig; Phyllis Spuls; Tiago Torres; Richard B Warren; Hoseah Waweru; John Weinman; Matt A Brown; James B Galloway; Christopher M Griffiths; Jonathan N Barker; Catherine H Smith,"St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; Centre for Rheumatic Diseases, King's College London; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; Faculty of Epidemiology, and Population Health, London School of Hygiene and Tropical Medicine, London, UK; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King's College London, London, UK; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; The Psoriasis Association, Northampton, UK; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; NIHR Biomedical Research Centre at Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; NIHR Biomedical Research Centre at Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; The Psoriasis Association, Northampton, UK; The Psoriasis Association, Northampton, UK; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; International Federation of Psoriasis Associations; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; Department of Dermatology, AP-HP Hopital Saint-Louis, Paris, France; King's College London; Catedra de Dermatologia, Hospital de Clinicas, Facultad de Ciencias Medicas, Universidad Nacional de Asuncion, Paraguay; Clinica Dermacross, Santiago, Chile; King's College London; Section of Dermatology and Venereology, University of Verona, Verona, Italy; Department of Dermatology, Edouard Herriot Hospital, Hospices Civils de Lyon, University of Lyon, Lyon, France; Department of Dermatology, Ghent University, Ghent, Belgium; Centro Studi GISED, Bergamo, Italy; Psychology Department, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, UK; Department of Dermatology, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Catalonia, Spain; Department of Dermatology, Amsterdam Public Health/Infection and Immunology, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands; Department of Dermatology, Centro Hospitalar do Porto, Portugal; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; International Federation of Psoriasis Associations; School of Cancer and Pharmaceutical Sciences, Kings College London, London, UK; Centre for Rheumatic Diseases, King's College London, London, UK; Centre for Rheumatic Diseases, King's College London, London, UK; 3Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Res; NIHR Biomedical Research Centre at Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK","BackgroundIndirect excess morbidity has emerged as a major concern in the COVID-19 pandemic. People with psoriasis may be particularly vulnerable to this because of prevalent anxiety and depression, multimorbidity and therapeutic use of immunosuppression.
-
-ObjectiveCharacterise the factors associated with worsening psoriasis in the COVID-19 pandemic, using mental health status (anxiety and depression) as the main exposure of interest.
-
-MethodsGlobal cross-sectional study using a primary outcome of self-reported worsening of psoriasis. Individuals with psoriasis completed an online self-report questionnaire (PsoProtectMe; Psoriasis Patient Registry for Outcomes, Therapy and Epidemiology of COVID-19 Infection Me) between May 2020 and January 2021. Each individual completed a validated screen for anxiety (Generalized Anxiety Disorder-2) and depression (Patient Health Questionnaire-2). Odds ratios (OR) and 95% confidence intervals (CI) were estimated using multivariable logistic regression.
-
-Results4,043 people with psoriasis (without COVID-19) from 86 countries self-reported to PsoProtectMe (mean age 47.2 years [SD 15.1]; mean BMI 27.6kg/m2 [SD 6.0], 2,684 [66.4%] female and 3,016 [74.6%] of white European ethnicity). 1,728 (42.7%) participants (1322 [77%] female) reported worsening of their psoriasis in the pandemic. A positive screen for anxiety or depression associated with worsening psoriasis in age and gender adjusted (OR 2.04, 95% CI 1.77-2.36), and fully adjusted (OR 2.01, 95% CI 1.72-2.34) logistic regression models. Female sex, obesity, shielding behaviour and systemic immunosuppressant non-adherence also associated with worsening psoriasis. The commonest reason for non-adherence was concern regarding complications related to COVID-19.
-
-ConclusionsThese data indicate an association between poor mental health and worsening psoriasis in the pandemic. Access to holistic care including psychological support may mitigate potentially long-lasting effects of the pandemic on health outcomes in psoriasis. The study also highlights an urgent need to address patient concerns about immunosuppressant-related risks, which may be contributing to non-adherence.",dermatology,fuzzy,100,100
 medRxiv,10.1101/2021.04.28.21256261,2021-05-02,https://medrxiv.org/cgi/content/short/2021.04.28.21256261,Aspirin and NSAID use and the risk of COVID-19,David Alden Drew; Chuan-Guo Guo; Karla Lee; Long Nguyen; Amit D Joshi; Chun-Han Lo; Wenjie Ma; Raaj S Mehta; Sohee Kwon; Christina M Astley; Mingyang Song; Richard Davies; Joan Capdevila; Mary M Ni Lochlainn; Carole Sudre; Mark S Graham; Thomas Varsavsky; Maria F. Gomez; Beatrice Kennedy; Hugo Fitipaldi; Jonathan Wolf; Timothy Spector; Sebastien Ourselin; Claire Steves; Andrew T. Chan,Massachusetts General Hospital; Massachusetts General Hospital; Department of Twin Research and Genetic Epidemiology; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Boston Children's Hospital; Massachusetts General Hospital; Zoe Global Ltd.; Zoe Global Ltd; King's College London; Kings College London; King's College London; Kings College London; Lund University; Uppsala University; Lund University; Zoe Global Ltd.; King's College London; King's College London; King's College London; Massachusetts General Hospital,"Early reports raised concern that use of non-steroidal anti-inflammatory drugs (NSAIDs) may increase risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease (COVID-19). Users of the COVID Symptom Study smartphone application reported use of aspirin and other NSAIDs between March 24 and May 8, 2020. Users were queried daily about symptoms, COVID-19 testing, and healthcare seeking behavior. Cox proportional hazards regression was used to determine the risk of COVID-19 among according to aspirin or non-aspirin NSAID users. Among 2,736,091 individuals in the U.S., U.K., and Sweden, we documented 8,966 incident reports of a positive COVID-19 test over 60,817,043 person-days of follow-up. Compared to non-users and after stratifying by age, sex, country, day of study entry, and race/ethnicity, non-aspirin NSAID use was associated with a modest risk for testing COVID-19 positive (HR 1.23 [1.09, 1.32]), but no significant association was observed among aspirin users (HR 1.13 [0.92, 1.38]). After adjustment for lifestyle factors, comorbidities and baseline symptoms, any NSAID use was not associated with risk (HR 1.02 [0.94, 1.10]). Results were similar for those seeking healthcare for COVID-19 and were not substantially different according to lifestyle and sociodemographic factors or after accounting for propensity to receive testing. Our results do not support an association of NSAID use, including aspirin, with COVID-19 infection. Previous reports of a potential association may be due to higher rates of comorbidities or use of NSAIDs to treat symptoms associated with COVID-19.
 
 One Sentence SummaryNSAID use is not associated with COVID-19 risk.",epidemiology,fuzzy,94,100
-medRxiv,10.1101/2021.04.30.21256119,2021-04-30,https://medrxiv.org/cgi/content/short/2021.04.30.21256119,Association between oral anticoagulants and COVID-19 related outcomes: two cohort studies,Angel YS Wong; Laurie Tomlinson; Jeremy P Brown; William Elson; Alex J Walker; Anna J Schultze; Caroline E Morton; David Evans; Peter Inglesby; Brian MacKenna; Krishnan Bhaskaran; Christopher T. Rentsch; Emma Powell; Elizabeth T. Williamson; Richard Croker; Seb Bacon; William Hulme; Chris Bates; Helen J Curtis; Amir Mehrkar; Jonathan Cockburn; Helen I McDonald; Rohini I Mathur; Kevin Wing; Harriet Forbes; Rosalind M Eggo; Stephen Evans; Liam Smeeth; Ben Goldacre; Ian J Douglas,"London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Trop. Med.; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; US Department of Veterans Affairs, London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; TPP; London School of Medicine and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Bristol; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine","ObjectivesWe investigated the role of routinely prescribed oral anticoagulants (OACs) in COVID-19 outcomes, comparing current OAC use versus non-use in Study 1; and warfarin versus direct oral anticoagulants (DOACs) in Study 2.
-
-DesignTwo cohort studies, on behalf of NHS England.
-
-SettingPrimary care data and pseudonymously-linked SARS-CoV-2 antigen testing data, hospital admissions, and death records from England.
-
-ParticipantsStudy 1: 70,464 people with atrial fibrillation (AF) and CHA{square}DS{square}-VASc score of 2. Study 2: 372,746 people with non-valvular AF.
-
-Main outcome measuresTime to test for SARS-CoV-2, testing positive for SARS-CoV-2, COVID-19 related hospital admission, COVID-19 deaths or non-COVID-19 deaths in Cox regression.
-
-ResultsIn Study 1, we included 52,416 current OAC users and 18,048 non-users. We observed no difference in risk of being tested for SARS-CoV-2 associated with current use (adjusted HR, 1.01, 95%CI, 0.96 to 1.05) versus non-use. We observed a lower risk of testing positive for SARS-CoV-2 (adjusted HR, 0.73, 95%CI, 0.60 to 0.90), and COVID-19 deaths (adjusted HR, 0.69, 95%CI, 0.49 to 0.97) associated with current use versus non-use. In Study 2, we included 92,339 warfarin users and 280,407 DOAC users. We observed a lower risk of COVID-19 deaths (adjusted HR, 0.79, 95%CI, 0.76 to 0.83) associated with warfarin versus DOACs. Similar associations were found for all other outcomes.
-
-ConclusionsAmong people with AF and a CHA{square}DS{square}-VASc score of 2, those receiving OACs had a lower risk of receiving a positive COVID-19 test and severe COVID-19 outcomes than non-users; this might be explained by a causal effect of OACs in preventing severe COVID-19 outcomes or more cautious behaviours leading to reduced infection risk. There was no evidence of a higher risk of severe COVID-19 outcomes associated with warfarin versus DOACs in people with non-valvular AF regardless of CHA{square}DS{square}-VASc score.
-
-Key pointsO_ST_ABSWhat is already known on this topicC_ST_ABSO_LICurrent studies suggest that prophylactic or therapeutic anticoagulant use, particularly low molecular weight heparin, lower the risk of pulmonary embolism and mortality during hospitalisation among patients with COVID-19.
-C_LIO_LIReduced vitamin K status has been reported to be correlated with severity of COVID-19. This could mean that warfarin, as a vitamin K antagonist, is associated with more severe COVID-19 disease than non-vitamin K anticoagulants.
-C_LI
-
-What this study addsO_LIIn 70,464 people with atrial fibrillation, at the threshold of being treated with an OAC based on risk of stroke, we observed a lower risk of testing positive for SARS-CoV-2 and COVID-19 related deaths associated with routinely prescribed OACs, relative to non-use.
-C_LIO_LIThis might be explained by OACs preventing severe COVID-19 outcomes, or more cautious behaviours and environmental factors reducing the risk of SARS-CoV-2 infection in those taking OACs.
-C_LIO_LIIn 372,746 people with non-valvular atrial fibrillation, there was no evidence of a higher risk of severe COVID-19 outcomes associated with warfarin compared with DOACs.
-C_LI",epidemiology,fuzzy,100,100
 medRxiv,10.1101/2021.04.26.21255732,2021-04-28,https://medrxiv.org/cgi/content/short/2021.04.26.21255732,Deprivation and Exposure to Public Activities during the COVID-19 Pandemic in England and Wales,Sarah Beale; Isobel Braithwaite; Annalan MD Navaratnam; Pia Hardelid; Alison Rodger; Anna Aryee; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Vincent Nguyen; Parth Patel; Madhumita Shrotri; Robert W Aldridge; Andrew C Hayward; - Virus Watch Collaborative,"University College London; University College London; University College London; University College London; University College London; Royal Free London NHS Foundation Trust,; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ","BackgroundDifferential exposure to public activities and non-household contacts may contribute to stark deprivation-related inequalities in SARS-CoV-2 infection and outcomes, but has not been directly investigated. We set out to investigate whether participants in Virus Watch - a large community cohort study based in England and Wales - reported different levels of exposure to public activities and non-household contacts during the Autumn-Winter phase of the COVID-19 pandemic according to postcode-level socioeconomic deprivation.
 
 MethodsParticipants (n=20120-25228 across surveys) reported their daily activities during three weekly periods in late November 2020, late December 2020, and mid-February 2021. Deprivation was quantified based on participants postcode of residence using English or Welsh Indices of Multiple Deprivation quintiles. We used Poisson mixed effect models with robust standard errors to estimate the relationship between deprivation and risk of exposure to public activities during each survey period.
@@ -3104,13 +3022,6 @@ Research in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched MEDLINE
 Added value of this studyThe ATOMIC2 trial was uniquely-designed to assess azithromycin as a standalone therapy in those with mild-moderately COVID-19 presenting to emergency care, but assessed as appropriate for initial ambulatory management without hospital admission. ATOMIC2 also uniquely assessed high-dose, long-duration treatment to investigate the efficacy of putative anti-inflammatory effects. We found that azithromycin 500 mg daily for 14 days did not reduce the proportion of participants who died or required hospital admission from any cause over the 28 days from randomisation.
 
 Implications of all the available evidenceOur findings, taken together with existing data, suggest there is no evidence that azithromycin reduces hospitalisation, respiratory failure or death compared with standard care, either in early disease in the community, or those hospitalised with severe disease, or in those with moderate disease managed on an ambulatory pathway.",infectious diseases,fuzzy,100,100
-medRxiv,10.1101/2021.04.22.21255949,2021-04-25,https://medrxiv.org/cgi/content/short/2021.04.22.21255949,Optimal health and economic impact of non-pharmaceutical intervention measures prior and post vaccination in England: a mathematical modelling study,Michael Tildesley; Anna Vassall; Steven Riley; Mark Jit; Frank Sandmann; Edward M Hill; Robin Thompson; Benjamin Atkins; John Edmunds; Louise M Dyson; Matt J Keeling,"University of Warwick; London School of Hygiene and Tropical Medicine; Dept Inf Dis Epi, Imperial College; London School of Hygiene & Tropical Medicine; Public Health England; University of Warwick; University of Warwick; University of Warwick; London School of Hygiene and Tropical Medicine; University of Warwick; University of Warwick","BackgroundEven with good progress on vaccination, SARS-CoV-2 infections in the UK may continue to impose a high burden of disease and therefore pose substantial challenges for health policy decision makers. Stringent government-mandated physical distancing measures (lockdown) have been demonstrated to be epidemiologically effective, but can have both positive and negative economic consequences. The duration and frequency of any intervention policy could, in theory, could be optimised to maximise economic benefits while achieving substantial reductions in disease.
-
-MethodsHere we use a pre-existing SARS-CoV-2 transmission model to assess the health and economic implications of different strengths of control through time in order to identify optimal approaches to non-pharmaceutical intervention stringency in the UK, considering the role of vaccination in reducing the need for future physical distancing measures. The model is calibrated to the COVID-19 epidemic in England and we carry out retrospective analysis of the optimal timing of precautionary breaks in 2020 and the optimal relaxation policy from the January 2021 lockdown, considering the willingness to pay for health improvement.
-
-ResultsWe find that the precise timing and intensity of interventions is highly dependent upon the objective of control. As intervention measures are relaxed, we predict a resurgence in cases, but the optimal intervention policy can be established dependent upon the willingness to pay (WTP) per QALY loss avoided. Our results show that establishing an optimal level of control can result in a reduction in net monetary loss of billions of pounds, dependent upon the precise WTP value.
-
-ConclusionsIt is vital, as the UK emerges from lockdown, but continues to face an on-going pandemic, to accurately establish the overall health and economic costs when making policy decisions. We demonstrate how some of these can be quantified, employing mechanistic infectious disease transmission models to establish optimal levels of control for the ongoing COVID-19 pandemic.",infectious diseases,fuzzy,100,100
 medRxiv,10.1101/2021.04.22.21255948,2021-04-25,https://medrxiv.org/cgi/content/short/2021.04.22.21255948,"Point of Care Testing using rapid automated Antigen Testing for SARS-COV-2 in Care Homes; an exploratory safety, usability and diagnostic agreement evaluation",Massimo Micocci; Peter Buckle; Gail Hayward; A. Joy Allen; Kerrie Davies; Patrick Kierkegaard; Karen Spilsbury; Carl Thompson; Anita Astle; Ros Heath; Claire Sharpe; Cyd Akrill; Dan Lasserson; Rafael Perera; Richard Body; Adam L Gordon,"NIHR London In Vitro Diagnostics Co-operative, Department of Surgery and Cancer, Imperial College London, London, UK; NIHR London In Vitro Diagnostics Co-operative, Department of Surgery and Cancer, Imperial College London, London, UK; NIHR Community Healthcare Medtech and IVD cooperative, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; NIHR Newcastle In Vitro Diagnostics Co-operative, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK; Healthcare Associated Infections Research Group, University of Leeds and Leeds Teaching Hospitals NHS Trust, Leeds, UK. NIHR Leeds In Vitro Diagnostics Co-opera; NIHR London In Vitro Diagnostics Co-operative, Department of Surgery and Cancer, Imperial College London, London, UK.; School of Healthcare, University of Leeds, Leeds, UK. NIHR Applied Research Collaboration Yorkshire and Humber, UK; School of Healthcare, University of Leeds, Leeds, UK. NIHR Applied Research Collaboration Yorkshire and Humber, UK; Wren Hall Nursing Home, Selston, UK; Landermeads Nursing Home, Nottingham, UK; Ashmere Nottinghamshire Ltd, Notts, UK; Springfield Healthcare, Leeds, UK; Warwick Medical School, University of Warwick, Coventry, UK; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; NIHR Applied Research Collaboration - Yorkshire and Humber (YHARC), UK; Division of Medical Sciences and Graduate Entry Medicine, School of Medicine, University of Nottingham, UK. NIHR Applied Research Collaboration-East Midlands (A","IntroductionSuccessful adoption of POCTs (Point-of-Care tests) for COVID-19 in care homes requires the identification of ideal use cases and a full understanding of contextual and usability factors that affect test results and minimise biosafety risks. This paper presents findings from a scoping-usability and test performance study of a microfluidic immunofluorescence assay for COVID-19 in care homes.
 
 MethodsA mixed-methods evaluation was conducted in four UK care homes to scope usability and to assess the agreement with qRT-PCR. A dry run with luminescent dye was carried out to explore biosafety issues.
@@ -3275,15 +3186,6 @@ ResultsSurvey response rate was 56% (20,792/36,998) in December 2020 and 52% (20
 
 ConclusionsOver four in five adults (86%) who were reluctant or intending to refuse a COVID-19 vaccine in December 2020 had changed their mind in February 2021 and planned on accepting, or had already accepted, a vaccine.",public and global health,fuzzy,100,100
 medRxiv,10.1101/2021.03.24.21254227,2021-03-26,https://medrxiv.org/cgi/content/short/2021.03.24.21254227,COVID-19 Vaccination Prioritization Based on Cardiovascular Risk Factors and Number-Needed-to-Vaccinate to Prevent Death,Darryl P Leong; Amitava Banerjee; Salim Yusuf,McMaster University; University College London; McMaster University,"The supply limitations of COVID-19 vaccines have led to the need to prioritize vaccine distribution. Obesity, diabetes and hypertension have been associated with an increased risk of severe COVID-19 infection. Approximately half as many individuals with a cardiovascular risk factor need to be vaccinated against COVID-19 to prevent related death as compared with individuals without a risk factor. Our analysis suggests that prioritizing adults with these cardiovascular risk factors for vaccination is likely to be an efficient way to reduce population COVID-19 mortality.",epidemiology,fuzzy,100,100
-medRxiv,10.1101/2021.03.26.21254390,2021-03-26,https://medrxiv.org/cgi/content/short/2021.03.26.21254390,Regional performance variation in external validation of four prediction models for severity of COVID-19 at hospital admission: An observational multi-centre cohort study,Kristin Wickstrom; Valeria Vitelli; Ewan Carr; Aleksander Rygh Holten; Rebecca Bendayan; Andrew Henry Reiner; Daniel Bean; Tom Searle; Anthony Shek; Zeljko Kraljevic; James T Teo; Richard Dobson; Kristian Tonby; Alvaro Kohn-Luque; Erik Koldberg Amundsen,Oslo University Hospital; University of Oslo; King's College London; Oslo University Hospital; King's College London; Oslo University Hospital; King's College London; King's College London; King's College London; King's College London; Kings College Hospital NHS Foundation Trust; Kings College London; Oslo University Hospital; University of Oslo; Oslo University Hospital,"BackgroundSeveral prediction models for coronavirus disease-19 (COVID-19) have been published. Prediction models should be externally validated to assess their performance before implementation. This observational cohort study aimed to validate published models of severity for hospitalized patients with COVID-19 using clinical and laboratory predictors.
-
-MethodsPrediction models fitting relevant inclusion criteria were chosen for validation. The outcome was either mortality or a composite outcome of mortality and ICU admission (severe disease). 1295 patients admitted with symptoms of COVID-19 at Kings Cross Hospital (KCH) in London, United Kingdom, and 307 patients at Oslo University Hospital (OUH) in Oslo, Norway were included. The performance of the models was assessed in terms of discrimination and calibration.
-
-ResultsWe identified two models for prediction of mortality (referred to as Xie and Zhang1) and two models for prediction of severe disease (Allenbach and Zhang2).
-
-The performance of the models was variable. For prediction of mortality Xie had good discrimination at OUH with an area under the receiver-operating characteristic (AUROC) 0.87 [95 % confidence interval (CI) 0.79-0.95] and acceptable discrimination at KCH, AUROC 0.79 [0.76-0.82]. In prediction of severe disease, Allenbach had acceptable discrimination (OUH AUROC 0.81 [0.74-0.88] and KCH AUROC 0.72 [0.68-0.75]). The Zhang models had moderate to poor discrimination. Initial calibration was poor for all models but improved with recalibration.
-
-ConclusionsThe performance of the four prediction models was variable. The Xie model had the best discrimination for mortality, while the Allenbach model had acceptable results for prediction of severe disease.",infectious diseases,fuzzy,100,100
 medRxiv,10.1101/2021.03.26.21254391,2021-03-26,https://medrxiv.org/cgi/content/short/2021.03.26.21254391,Vaccine effectiveness of the first dose of ChAdOx1 nCoV-19 and BNT162b2 against SARS-CoV-2 infection in residents of Long-Term Care Facilities (VIVALDI study),Madhumita Shrotri; Maria Krutikov; Tom Palmer; Rebecca Giddings; Borscha Azmi; Sathyavani Subbarao; Christopher Fuller; Aidan Irwin-Singer; Daniel Davies; Gokhan Tut; Jamie Lopez Bernal; Paul Moss; Andrew Hayward; Andrew Copas; Laura Shallcross,"University College London; University College London; University College London; University College London; University College London; Public Health England; University College London; Department of Health and Social Care, UK; Palantir Technologies UK Ltd; University of Birmingham; Public Health England; University of Birmingham; University College London; University College London; University College London","BackgroundThe effectiveness of SARS-CoV-2 vaccines in frail older adults living in Long-Term Care Facilities (LTCFs) is uncertain. We estimated protective effects of the first dose of ChAdOx1 and BNT162b2 vaccines against infection in this population.
 
 MethodsCohort study comparing vaccinated and unvaccinated LTCF residents in England, undergoing routine asymptomatic testing (8 December 2020 - 15 March 2021). We estimated the relative hazard of PCR-positive infection using Cox proportional hazards regression, adjusting for age, sex, prior infection, local SARS-CoV-2 incidence, LTCF bed capacity, and clustering by LTCF.
@@ -3544,6 +3446,25 @@ MethodsAll 178578 diagnosed cases of COVID-19 in Scotland from 1 March 2020 to 1
 ResultsWith those without risk conditions as reference category, the univariate rate ratio for severe COVID-19 was 3.21 (95% CI 3.01 to 3.41) in those with moderate risk conditions and 6.3 (95% CI 5.8 to 6.8) in those eligible for shielding. The highest rate was in solid organ transplant recipients: rate ratio 13.4 (95% CI 9.6 to 18.8). Risk of severe COVID-19 increased with the number of adults but decreased with the number of school-age children in the household. Severe COVID-19 was strongly associated with recent exposure to hospital (defined as 5 to 14 days before presentation date): rate ratio 12.3 (95% CI 11.5 to 13.2) overall. To test for causality, a case-crossover analysis was undertaken; with less recent exposure only (15 to 24 days before first testing positive) as reference category, the rate ratio associated with recent exposure only was 5.9 (95% CI 3.6 to 9.7). The population attributable risk fraction for recent exposure to hospital peaked at 50% in May 2020 and again at 65% in December 2020.
 
 ConclusionsThe effectiveness of shielding vulnerable individuals was limited by the inability to control transmission in hospital and from other adults in the household. For solid organ transplant recipients, in whom the efficacy of vaccines is uncertain, these results support a policy of offering vaccination to household contacts. Mitigating the impact of the epidemic requires control of nosocomial transmission.",epidemiology,fuzzy,100,100
+medRxiv,10.1101/2021.02.27.21252593,2021-03-01,https://medrxiv.org/cgi/content/short/2021.02.27.21252593,Surgical activity in England and Wales during the COVID-19 pandemic: a nationwide observational cohort study,Thomas D Dobbs; John A G Gibson; Alexander J Fowler; Tom E Abbott; Tasnin Shahid; Fatemeh Torabi; Rowena Griffiths; Ronan A Lyons; Rupert M Pearse; Iain S Whitaker,"Swansea University Medical School; Swansea University Medical School; Queen Mary, University of London; Queen Mary University of London; Queen Mary University of London; Swansea University; Swansea University; Swansea University; Queen Mary University of London; Swansea University Medical School","ObjectivesTo report the volume of surgical activity and the number of cancelled surgical procedures during the COVID-19 pandemic.
+
+Design and settingAnalysis of electronic health record data from the National Health Service (NHS) in England and Wales.
+
+MethodsWe used hospital episode statistics for all adult patients undergoing surgery between 1st January 2020 and 31st December 2020. We identified surgical procedures using a previously published list of procedure codes. Procedures were stratified by urgency of surgery as defined by NHS England. We calculated the deficit of surgical activity by comparing the expected number of procedures from the years 2016-2019 with the actual number of procedures in 2020. We estimated the cumulative number of cancelled procedures by 31st December 2021 according patterns of activity in 2020.
+
+ResultsThe total number of surgical procedures carried out in England and Wales in 2020 was 3,102,674 compared to the predicted number of 4,671,338. This represents a 33.6% reduction in the national volume of surgical activity. There were 763,730 emergency surgical procedures (13.4% reduction), compared to 2,338,944 elective surgical procedures (38.6% reduction). The cumulative number of cancelled or postponed procedures was 1,568,664. We estimate that this will increase to 2,358,420 by 31st December 2021.
+
+ConclusionsThe volume of surgical activity in England and Wales was reduced by 33.6% in 2020, resulting in over 1,568,664 cancelled operations. This deficit will continue to grow in 2021.
+
+Summary boxesO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIThe COVID-19 pandemic necessitated a rapid change in the provision of care, including the suspension of a large proportion of surgical activity
+C_LIO_LISurgical activity has yet to return to normal and has been further impacted by subsequent waves of the pandemic
+C_LIO_LIThis will lead to a large backlog of cases
+C_LI
+
+What this study addsO_LI3,102,674 surgical procedures were performed in England and Wales during 2020, a 33.6% reduction on the expected yearly surgical activity
+C_LIO_LIOver 1.5 million procedures were not performed, with this deficit likely to continue to grow to 2.3 million by the end of 2021
+C_LIO_LIThis deficit is the equivalent of more than 6 months of pre-pandemic surgical activity, requiring a monumental financial and logistic challenge to manage
+C_LI",surgery,fuzzy,100,100
 medRxiv,10.1101/2021.02.26.21252512,2021-03-01,https://medrxiv.org/cgi/content/short/2021.02.26.21252512,REACT-2 Round 5: increasing prevalence of SARS-CoV-2 antibodies demonstrate impact of the second wave and of vaccine roll-out in England,Helen Ward Professor; Graham Cooke Professor; Matthew Whitaker Mr; Rozlyn Redd Dr; Oliver Eales Mr; Jonathan Brown Mr; Katharine Collet Ms; Emily Cooper Ms; Daunt Anna Dr; Jones Kathryn Dr; Moshe Maya Ms; Michelle Willicombe Dr; Sophie Day Professor; Christina Atchison Dr; Ara Darzi Professor; Christl A Donnelly Professor; Steven Riley Professor; Deborah Ashby Professor; Wendy S Barclay Professor; Paul Elliott Professor,Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London,"BackgroundEngland has experienced high rates of SARS-CoV-2 infection during the COVID-19 pandemic, affecting in particular minority ethnic groups and more deprived communities. A vaccination programme began in England in December 2020, with priority given to administering the first dose to the largest number of older individuals, healthcare and care home workers.
 
 MethodsA cross-sectional community survey in England undertaken between 26 January and 8 February 2021 as the fifth round of the REal-time Assessment of Community Transmission-2 (REACT-2) programme. Participants completed questionnaires, including demographic details and clinical and COVID-19 vaccination histories, and self-administered a lateral flow immunoassay (LFIA) test to detect IgG against SARS-CoV-2 spike protein. There were sufficient numbers of participants to analyse antibody positivity after 21 days from vaccination with the PfizerBioNTech but not the AstraZeneca/Oxford vaccine which was introduced slightly later.
@@ -3682,7 +3603,6 @@ Our results show that absences as a result of COVID-19 infection rose steadily f
 In December, we observed a large rise in the number of absences per school in secondary school settings in the South East and Greater London, but such rises were not observed in other regions or in primary school settings. We conjecture that the increased transmissibility of the new variant in these regions may have contributed to this rise in cases in secondary schools. Finally, we observe a positive correlation between cases in the community and cases in schools in most regions, with weak evidence suggesting that cases in schools lag behind cases in the surrounding community. We conclude that there is not significant evidence to suggest that schools are playing a significant role in driving spread in the community and that careful monitoring may be required as schools re-open to determine the effect associated with open schools upon community incidence.",infectious diseases,fuzzy,100,100
 medRxiv,10.1101/2021.02.10.21251480,2021-02-12,https://medrxiv.org/cgi/content/short/2021.02.10.21251480,Symptom reporting in over 1 million people: community detection of COVID-19,Joshua Elliott; Matthew Whitaker; Barbara Bodinier; Steven Riley; Helen Ward; Graham Cooke; Ara Darzi; Marc Chadeau-Hyam; Paul Elliott,Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London,,infectious diseases,fuzzy,96,100
 medRxiv,10.1101/2021.02.11.21251587,2021-02-12,https://medrxiv.org/cgi/content/short/2021.02.11.21251587,Assessing the impact of secondary school reopening strategies on within-school COVID-19 transmission and absences: a modelling study,Trystan Leng; Edward M Hill; Robin N Thompson; Michael J Tildesley; Matt J Keeling; Louise J Dyson,University of Warwick; University of Warwick; University of  Warwick; University of Warwick; University of Warwick; University of Warwick,,infectious diseases,fuzzy,100,100
-medRxiv,10.1101/2021.02.11.21249258,2021-02-11,https://medrxiv.org/cgi/content/short/2021.02.11.21249258,"Tocilizumab in patients admitted to hospital with COVID-19 (RECOVERY): preliminary results of a randomised, controlled, open-label, platform trial",Peter W Horby; Mark Campbell; Natalie Staplin; Enti Spata; Jonathan R Emberson; Guilherme Pessoa-Amorim; Leon Peto; Christopher E Brightling; Rahuldeb Sarkar; Koshy Thomas; Vandana Jeebun; Abdul Ashish; Redmond Tully; David Chadwick; Muhammad Sharafat; Richard Stewart; Banu Rudran; J Kenneth Baillie; Maya H Buch; Lucy C Chappell; Jeremy N Day; Saul N Furst; Thomas Jaki; Katie Jeffery; Edmund Juszczak; Wei Shen Lim; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; Marion Mafham; Richard Haynes; Martin J Landray,"Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, United Kingdom; Medway Foundation NHS Trust, Gillingham, United Kingdom; King?s College London, London, United Kingdom; Basildon and Thurrock Hospitals NHS Foundation Trust, Basildon, United Kingdom; Department of Respiratory Medicine, North Tees & Hartlepool NHS Foundation Trust, Stockton-on-Tees, United Kingdom; Wrightington Wigan and Leigh NHS Foundation Trust, Wigan, United Kingdom; Royal Oldham Hospital, Northern Care Alliance, Oldham, United Kingdom; Centre for Clinical Infection, James Cook University Hospital, Middlesbrough, United Kingdom; North West Anglia NHS Foundation Trust, Peterborough, United Kingdom; Milton Keynes University Hospital, Milton Keynes, United Kingdom; Luton & Dunstable University Hospital, Luton, United Kingdom; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; School of Life Sciences, Kings College London, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, ; Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Respiratory Medicine Department, Nottingham University Hospitals NHS Foundation Trust, Nottingham, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom; Intensive Care National Audit and Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom","Findings: Between 23 April 2020 and 25 January 2021, 4116 adults were included in the assessment of tocilizumab, including 562 (14%) patients receiving invasive mechanical ventilation, 1686 (41%) receiving non-invasive respiratory support, and. 1868 (45%) receiving no respiratory support other than oxygen. Median CRP was 143 [IQR 107-205] mg/L and 3385 (82%) patients were receiving systemic corticosteroids at randomisation. Overall, 596 (29%) of the 2022 patients allocated tocilizumab and 694 (33%) of the 2094 patients allocated to usual care died within 28 days (rate ratio 0.86; 95% confidence interval [CI] 0.77-0.96; p=0.007). Consistent results were seen in all pre-specified subgroups of patients, including those receiving systemic corticosteroids. Patients allocated to tocilizumab were more likely to be discharged from hospital alive within 28 days (54% vs. 47%; rate ratio 1.23; 95% CI 1.12-1.34; p<0.0001). Among those not receiving invasive mechanical ventilation at baseline, patients allocated tocilizumab were less likely to reach the composite endpoint of invasive mechanical ventilation or death (33% vs. 38%; risk ratio 0.85; 95% CI 0.78-0.93; p=0.0005). Interpretation: In hospitalised COVID-19 patients with hypoxia and systemic inflammation, tocilizumab improved survival and other clinical outcomes regardless of the level of respiratory support received and in addition to the use of systemic corticosteroids.",infectious diseases,fuzzy,100,100
 medRxiv,10.1101/2021.02.08.21250525,2021-02-09,https://medrxiv.org/cgi/content/short/2021.02.08.21250525,"COVID-19 infection and outcomes in a population-based cohort of 17,173 adults with intellectual disabilities compared with the general population",Angela Henderson; Micheal Fleming; Sally-Ann Cooper; Jill Pell; Craig Melville; Daniel MacKay; Christopher Hatton; Deborah Kinnear,University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; Manchester Metropolitan University; University of Glasgow,"ObjectivesTo compare COVID-19 infection, severe infection, mortality, case-fatality, and excess deaths, among adults with intellectual disabilities and those without.
 
 DesignRecord-linkage of all adults recorded with intellectual disabilities in Scotlands Census, 2011, and a 5% sample of other adults, to COVID-19 test results (Electronic Communication of Surveillance in Scotland), hospitalisations (Scottish Morbidity Record 01), and deaths (National Records of Scotland).
@@ -3771,6 +3691,9 @@ Research in contextO_ST_ABSEvidence before this studyC_ST_ABSA recent systematic
 Added value of this studyUsing data from the Office for National Statistics (ONS) Public Health Data Asset on 29 million adults aged 30-100 years living in private households in England, we conducted an observational cohort study to examine the differences in the risk of death involving COVID-19 between ethnic groups in the first wave (from 24th January 2020 until 31st August 2020) and second wave (from 1st September to 28th December 2020). We find that in the first wave all ethnic minority groups were at elevated risk of COVID-19 related death compared to the White British population. In the second wave, the differences in the risk of COVID-19 related death attenuated for Black African and Black Caribbean groups, remained substantially higher in people from Bangladeshi background, and worsened in people from Pakistani background. We also find that some of the factors explaining these differences in mortality have changed in the two waves.
 
 Implications of all the available evidenceThe risk of COVID-19 mortality during the first wave of the pandemic was elevated in people from ethnic minority background. An appreciable reduction in the difference in COVID-19 mortality in the second wave of the pandemic between people from Black ethnic background and people from the White British group is reassuring, but the continued higher rate of mortality in people from Bangladeshi and Pakistani background is alarming and requires focused public health campaign and policy response. Focusing on treating underlying conditions, although important, may not be enough in reducing the inequalities in COVID-19 mortality. Focused public health policy as well as community mobilisation and participatory public health campaign involving community leaders may help reduce the existing and widening inequalities in COVID-19 mortality.",epidemiology,fuzzy,100,100
+medRxiv,10.1101/2021.02.03.21250974,2021-02-05,https://medrxiv.org/cgi/content/short/2021.02.03.21250974,Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the US,Estee Y Cramer; Evan L Ray; Velma K Lopez; Johannes Bracher; Andrea Brennen; Alvaro J Castro Rivadeneira; Aaron Gerding; Tilmann Gneiting; Katie H House; Yuxin Huang; Dasuni Jayawardena; Abdul H Kanji; Ayush Khandelwal; Khoa Le; Anja Muehlemann; Jarad Niemi; Apurv Shah; Ariane Stark; Yijin Wang; Nutcha Wattanachit; Martha W Zorn; Youyang Gu; Sansiddh Jain; Nayana Bannur; Ayush Deva; Mihir Kulkarni; Srujana Merugu; Alpan Raval; Siddhant Shingi; Avtansh Tiwari; Jerome White; Neil F Abernethy; Spencer Woody; Maytal Dahan; Spencer Fox; Kelly Gaither; Michael Lachmann; Lauren Ancel Meyers; James G Scott; Mauricio Tec; Ajitesh Srivastava; Glover E George; Jeffrey C Cegan; Ian D Dettwiller; William P England; Matthew W Farthing; Robert H Hunter; Brandon Lafferty; Igor Linkov; Michael L Mayo; Matthew D Parno; Michael A Rowland; Benjamin D Trump; Yanli Zhang-James; Samuel Chen; Stephen V Faraone; Jonathan Hess; Christopher P Morley; Asif Salekin; Dongliang Wang; Sabrina M Corsetti; Thomas M Baer; Marisa C Eisenberg; Karl Falb; Yitao Huang; Emily T Martin; Ella McCauley; Robert L Myers; Tom Schwarz; Daniel Sheldon; Graham Casey Gibson; Rose Yu; Liyao Gao; Yian Ma; Dongxia Wu; Xifeng Yan; Xiaoyong Jin; Yu-Xiang Wang; YangQuan Chen; Lihong Guo; Yanting Zhao; Quanquan Gu; Jinghui Chen; Lingxiao Wang; Pan Xu; Weitong Zhang; Difan Zou; Hannah Biegel; Joceline Lega; Steve McConnell; VP Nagraj; Stephanie L Guertin; Christopher Hulme-Lowe; Stephen D Turner; Yunfeng Shi; Xuegang Ban; Robert Walraven; Qi-Jun Hong; Stanley Kong; Axel van de Walle; James A Turtle; Michal Ben-Nun; Steven Riley; Pete Riley; Ugur Koyluoglu; David DesRoches; Pedro Forli; Bruce Hamory; Christina Kyriakides; Helen Leis; John Milliken; Michael Moloney; James Morgan; Ninad Nirgudkar; Gokce Ozcan; Noah Piwonka; Matt Ravi; Chris Schrader; Elizabeth Shakhnovich; Daniel Siegel; Ryan Spatz; Chris Stiefeling; Barrie Wilkinson; Alexander Wong; Sean Cavany; Guido Espana; Sean Moore; Rachel Oidtman; Alex Perkins; David Kraus; Andrea Kraus; Zhifeng Gao; Jiang Bian; Wei Cao; Juan Lavista Ferres; Chaozhuo Li; Tie-Yan Liu; Xing Xie; Shun Zhang; Shun Zheng; Alessandro Vespignani; Matteo Chinazzi; Jessica T Davis; Kunpeng Mu; Ana Pastore y Piontti; Xinyue Xiong; Andrew Zheng; Jackie Baek; Vivek Farias; Andreea Georgescu; Retsef Levi; Deeksha Sinha; Joshua Wilde; Georgia Perakis; Mohammed Amine Bennouna; David Nze-Ndong; Divya Singhvi; Ioannis Spantidakis; Leann Thayaparan; Asterios Tsiourvas; Arnab Sarker; Ali Jadbabaie; Devavrat Shah; Nicolas Della Penna; Leo A Celi; Saketh Sundar; Russ Wolfinger; Dave Osthus; Lauren Castro; Geoffrey Fairchild; Isaac Michaud; Dean Karlen; Matt Kinsey; Luke C. Mullany; Kaitlin Rainwater-Lovett; Lauren Shin; Katharine Tallaksen; Shelby Wilson; Elizabeth C Lee; Juan Dent; Kyra H Grantz; Alison L Hill; Joshua Kaminsky; Kathryn Kaminsky; Lindsay T Keegan; Stephen A Lauer; Joseph C Lemaitre; Justin Lessler; Hannah R Meredith; Javier Perez-Saez; Sam Shah; Claire P Smith; Shaun A Truelove; Josh Wills; Maximilian Marshall; Lauren Gardner; Kristen Nixon; John C. Burant; Lily Wang; Lei Gao; Zhiling Gu; Myungjin Kim; Xinyi Li; Guannan Wang; Yueying Wang; Shan Yu; Robert C Reiner; Ryan Barber; Emmanuela Gaikedu; Simon Hay; Steve Lim; Chris Murray; David Pigott; Heidi L Gurung; Prasith Baccam; Steven A Stage; Bradley T Suchoski; B. Aditya Prakash; Bijaya Adhikari; Jiaming Cui; Alexander Rodriguez; Anika Tabassum; Jiajia Xie; Pinar Keskinocak; John Asplund; Arden Baxter; Buse Eylul Oruc; Nicoleta Serban; Sercan O Arik; Mike Dusenberry; Arkady Epshteyn; Elli Kanal; Long T Le; Chun-Liang Li; Tomas Pfister; Dario Sava; Rajarishi Sinha; Thomas Tsai; Nate Yoder; Jinsung Yoon; Leyou Zhang; Sam Abbott; Nikos I Bosse; Sebastian Funk; Joel Hellewell; Sophie R Meakin; Katharine Sherratt; Mingyuan Zhou; Rahi Kalantari; Teresa K Yamana; Sen Pei; Jeffrey Shaman; Michael L Li; Dimitris Bertsimas; Omar Skali Lami; Saksham Soni; Hamza Tazi Bouardi; Turgay Ayer; Madeline Adee; Jagpreet Chhatwal; Ozden O Dalgic; Mary A Ladd; Benjamin P Linas; Peter Mueller; Jade Xiao; Yuanjia Wang; Qinxia Wang; Shanghong Xie; Donglin Zeng; Alden Green; Jacob Bien; Logan Brooks; Addison J Hu; Maria Jahja; Daniel McDonald; Balasubramanian Narasimhan; Collin Politsch; Samyak Rajanala; Aaron Rumack; Noah Simon; Ryan J Tibshirani; Rob Tibshirani; Valerie Ventura; Larry Wasserman; Eamon B O'Dea; John M Drake; Robert Pagano; Quoc T Tran; Lam Si Tung Ho; Huong Huynh; Jo W Walker; Rachel B Slayton; Michael A Johansson; Matthew Biggerstaff; Nicholas G Reich,"University of Massachusetts, Amherst; University of Massachusetts, Amherst; Centers for Disease Control and Prevention; Chair of Econometrics and Statistics, Karlsruhe Institute of Technology; Computational Statistics Group, Heidelberg Institute for Theoretical Studies; IQT; University of Massachusetts, Amherst; University of Massachusetts, Amherst; Institute of Stochastics, Karlsruhe Institute of Technology; University of Massachusetts, Amherst; University of Massachusetts, Amherst; University of Massachusetts, Amherst; University of Massachusetts, Amherst; University of Massachusetts, Amherst; University of Massachusetts, Amherst; Institute of Mathematical Statistics and Actuarial Science, University of Bern; Iowa State University; University of Massachusetts, Amherst; University of Massachusetts, Amherst; University of Massachusetts, Amherst; University of Massachusetts, Amherst; University of Massachusetts, Amherst; Unaffiliated; Wadhwani Institute of Artificial Intelligence; Wadhwani Institute of Artificial Intelligence; Wadhwani Institute of Artificial Intelligence; Wadhwani Institute of Artificial Intelligence; Wadhwani Institute of Artificial Intelligence; Wadhwani Institute of Artificial Intelligence; Wadhwani Institute of Artificial Intelligence; Wadhwani Institute of Artificial Intelligence; Wadhwani Institute of Artificial Intelligence; University of Washington; University of Texas at Austin; Texas Advanced Computing Center; University of Texas at Austin; Texas Advanced Computing Center; Santa Fe Institute; University of Texas at Austin; University of Texas at Austin; University of Texas at Austin; University of Southern California; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; State University of New York Upstate Medical University; State University of New York Upstate Medical University; State University of New York Upstate Medical University; State University of New York Upstate Medical University; State University of New York Upstate Medical University; Syracuse University; State University of New York Upstate Medical University; University of Michigan - Ann Arbor; Trinity University, San Antonio; University of Michigan - Ann Arbor; University of Michigan - Ann Arbor; University of Michigan - Ann Arbor; University of Michigan - Ann Arbor; University of Michigan - Ann Arbor; University of Michigan - Ann Arbor; University of Michigan - Ann Arbor; University of Massachusetts, Amherst; University of Massachusetts, Amherst; Northeastern University; University of California, San Diego; University of Washington; University of California, San Diego; University of California, San Diego; University of California at Santa Barbara; University of California at Santa Barbara; University of California at Santa Barbara; University of California, Merced; Jilin University; University of Science and Technology of China; University of California, Los Angeles; University of California, Los Angeles; University of California, Los Angeles; University of California, Los Angeles; University of California, Los Angeles; University of California, Los Angeles; University of Arizona; University of Arizona; Construx; Signature Science, LLC; Signature Science, LLC; Signature Science, LLC; Signature Science, LLC; Rensselaer Polytechnic Institute; University of Washington; Unaffiliated; Arizona State University; Brown University; Manhasset Secondary School; Brown University; Predictive Science, Inc; Predictive Science, Inc; Imperial College, London; Predictive Science, Inc; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; University of Notre Dame; University of Notre Dame; University of Notre Dame; University of Chicago; University of Notre Dame; University of Notre Dame; Masaryk University; Masaryk University; Microsoft; Microsoft; Microsoft; Microsoft; Microsoft; Microsoft; Microsoft; Microsoft; Microsoft; ISI Foundation; Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University; Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University; Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University; Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University; Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University; Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University; Operations Research Center, Massachusetts Institute of Technology; Operations Research Center, Massachusetts Institute of Technology; Sloan School of Management, Massachusetts Institute of Technology; Operations Research Center, Massachusetts Institute of Technology; Sloan School of Management, Massachusetts Institute of Technology; Operations Research Center, Massachusetts Institute of Technology; Operations Research Center, Massachusetts Institute of Technology; Massachusetts Institute of Technology; Massachusetts Institute of Technology; Massachusetts Institute of Technology; New York University; Massachusetts Institute of Technology; Massachusetts Institute of Technology; Massachusetts Institute of Technology; Institute for Data, Systems, and Society, Massachusetts Institute of Technology; Institute for Data, Systems, and Society, Massachusetts Institute of Technology; Institute for Data, Systems, and Society, Massachusetts Institute of Technology; Laboratory for Computational Physiology, Massachusetts Institute of Technology; Laboratory for Computational Physiology, Massachusetts Institute of Technology; River Hill High School; SAS Institute Inc; Los Alamos National Laboratory; Los Alamos National Laboratory; Los Alamos National Laboratory; Los Alamos National Laboratory; TRIUMF; University of Victoria; Johns Hopkins University Applied Physics Lab; Johns Hopkins University Applied Physics Lab; Johns Hopkins University Applied Physics Lab; Johns Hopkins University Applied Physics Lab; Johns Hopkins University Applied Physics Lab; Johns Hopkins University Applied Physics Lab; Johns Hopkins Bloomberg School of Public Health; Johns Hopkins Bloomberg School of Public Health; Johns Hopkins Bloomberg School of Public Health; Johns Hopkins University; Johns Hopkins Bloomberg School of Public Health; Unaffiliated; University of Utah; Johns Hopkins Bloomberg School of Public Health; Ecole Polytechnique Federale de Lausanne; Johns Hopkins Bloomberg School of Public Health; Johns Hopkins Bloomberg School of Public Health; Johns Hopkins Bloomberg School of Public Health; Unaffiliated; Johns Hopkins Bloomberg School of Public Health; Johns Hopkins Bloomberg School of Public Health; Unaffiliated; Johns Hopkins University; Johns Hopkins University; Johns Hopkins University; Unaffiliated; Iowa State University; Iowa State University; Iowa State University; Iowa State University; Clemson University; College of William & Mary; Iowa State University; University of Virginia; University of Washington; University of Washington; University of Washington; University of Washington; University of Washington; University of Washington; University of Washington; IEM, Inc.; IEM, Inc.; IEM, Inc.; IEM, Inc.; Georgia Institute of Technology; University of Iowa; Georgia Institute of Technology; Georgia Institute of Technology; Georgia Institute of Technology; Virginia Tech; Georgia Institute of Technology; Georgia Insitute of Technology; Metron, Inc.; Georgia Insitute of Technology; Georgia Insitute of Technology; Georgia Insitute of Technology; Google Cloud; Google Cloud; Google Cloud; Google Cloud; Google Cloud; Google Cloud; Google Cloud; Google Cloud; Google Cloud; Harvard University; Google Cloud; Google Cloud; Google Cloud; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; The University of Texas at Austin; The University of Texas at Austin; Columbia University; Columbia University; Columbia University; Operations Research Center, Massachusetts Institute of Technology; Sloan School of Management, Massachusetts Institute of Technology; Operations Research Center, Massachusetts Institute of Technology; Operations Research Center, Massachusetts Institute of Technology; Operations Research Center, Massachusetts Institute of Technology; Emory University Medical School; Georgia Insitute of Technology; MGH; MGH; Value Analytics Labs; MGH; Boston University School of Medicine; MGH; Georgia Insitute of Technology; Columbia University; Columbia University; Columbia University; UNC Chapel Hill; Carnegie Mellon University; University of Southern California; Carnegie Mellon University; Carnegie Mellon University; Carnegie Mellon University; University of British Columbia; Stanford University; Carnegie Mellon University; Stanford University; Carnegie Mellon University; University of Washington; Carnegie Mellon University; Stanford University; Carnegie Mellon University; Carnegie Mellon University; University of Georgia; University of Georgia; Unaffiliated; Walmart Inc.; Dalhousie University; Virtual Power System Inc.; Centers for Disease Control and Prevention; Centers for Disease Control and Prevention; Centers for Disease Control and Prevention; Centers for Disease Control and Prevention; University of Massachusetts, Amherst","Short-term probabilistic forecasts of the trajectory of the COVID-19 pandemic in the United States have served as a visible and important communication channel between the scientific modeling community and both the general public and decision-makers. Forecasting models provide specific, quantitative, and evaluable predictions that inform short-term decisions such as healthcare staffing needs, school closures, and allocation of medical supplies. Starting in April 2020, the US COVID-19 Forecast Hub (https://covid19forecasthub.org/) collected, disseminated, and synthesized tens of millions of specific predictions from more than 90 different academic, industry, and independent research groups. A multi-model ensemble forecast that combined predictions from dozens of different research groups every week provided the most consistently accurate probabilistic forecasts of incident deaths due to COVID-19 at the state and national level from April 2020 through October 2021. The performance of 27 individual models that submitted complete forecasts of COVID-19 deaths consistently throughout this year showed high variability in forecast skill across time, geospatial units, and forecast horizons. Two-thirds of the models evaluated showed better accuracy than a naive baseline model. Forecast accuracy degraded as models made predictions further into the future, with probabilistic error at a 20-week horizon 3-5 times larger than when predicting at a 1-week horizon. This project underscores the role that collaboration and active coordination between governmental public health agencies, academic modeling teams, and industry partners can play in developing modern modeling capabilities to support local, state, and federal response to outbreaks.
+
+Significance StatementThis paper compares the probabilistic accuracy of short-term forecasts of reported deaths due to COVID-19 during the first year and a half of the pandemic in the US. Results show high variation in accuracy between and within stand-alone models, and more consistent accuracy from an ensemble model that combined forecasts from all eligible models. This demonstrates that an ensemble model provided a reliable and comparatively accurate means of forecasting deaths during the COVID-19 pandemic that exceeded the performance of all of the models that contributed to it. This work strengthens the evidence base for synthesizing multiple models to support public health action.",epidemiology,fuzzy,100,100
 medRxiv,10.1101/2021.02.01.21250839,2021-02-03,https://medrxiv.org/cgi/content/short/2021.02.01.21250839,Extremely high SARS-CoV-2 seroprevalence in a strictly-Orthodox Jewish community in the UK,Katherine M Gaskell; Marina Johnson; Victoria Gould; Adam Hunt; Neil RH Stone; William Waites; Ben Kasstan; Tracey Chantler; Sham Lal; Chrissy h. Roberts; David Goldblatt; Rosalind M Eggo; Michael M Marks,"Department of Clinical Research, London School of Hygiene & Tropical Medicine, Keppel Street, London. WC1E 7HT UK; Great Ormond Street Institute of Child Health Biomedical Research Centre, University College London; Department of Clinical Research, London School of Hygiene & Tropical Medicine, Keppel Street, London. WC1E 7HT UK; Great Ormond Street Institute of Child Health Biomedical Research Centre, University College London; Department of Clinical Research, London School of Hygiene & Tropical Medicine, Keppel Street, London. WC1E 7HT UK & Hospital for Tropical Diseases, University C; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London. WC1E 7HT UK; Centre for Health, Law and Society, University of Bristol Law School, Bristol. BS1 1RJ; Department of Global Health and Development, London School of Hygiene & Tropical Medicine, Keppel Street, London. WC1E 7HT UK; Department of Clinical Research, London School of Hygiene & Tropical Medicine, Keppel Street, London. WC1E 7HT UK; Department of Clinical Research, London School of Hygiene & Tropical Medicine, Keppel Street, London. WC1E 7HT UK; Great Ormond Street Institute of Child Health Biomedical Research Centre, University College London; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London. WC1E 7HT UK; Department of Clinical Research, London School of Hygiene & Tropical Medicine, Keppel Street, London. WC1E 7HT UK & Hospital for Tropical Diseases, University C","BackgroundEthnic and religious minorities have been disproportionately affected by SARS-CoV-2 worldwide. The UK strictly-Orthodox Jewish community has been severely affected by the pandemic. This group shares characteristics with other ethnic minorities including larger family sizes, higher rates of household crowding and relative socioeconomic deprivation. We studied a UK strictly-Orthodox Jewish population to understand how COVID-19 had spread within this community.
 
 MethodsWe performed a household-focused cross-sectional SARS-CoV-2 serosurvey specific to three antigen targets. Randomly-selected households completed a standardised questionnaire and underwent serological testing with a multiplex assay for SARS-CoV-2 IgG antibodies. We report clinical illness and testing before the serosurvey, seroprevalence stratified by age and gender. We used random-effects models to identify factors associated with infection and antibody titres.
@@ -3961,7 +3884,6 @@ InterpretationSimilar associations of most individual-level factors with COVID-1
 
 FundingWellcome, Royal Society, National Institute for Health Research, National Institute for Health Research Oxford Biomedical Research Centre, UK Medical Research Council, Health Data Research UK.",infectious diseases,fuzzy,100,100
 medRxiv,10.1101/2021.01.19.21249840,2021-01-20,https://medrxiv.org/cgi/content/short/2021.01.19.21249840,Impact of SARS-CoV-2 B.1.1.7 Spike variant on neutralisation potency of sera from individuals vaccinated with Pfizer vaccine BNT162b2,Dami Collier; Anna De Marco; Isabella Ferreira; Bo Meng; Rawlings Datir; Alexandra C. Walls; Steven A. Kemp S; Jessica Bassi; Dora Pinto; Chiara Silacci Fregni; Siro Bianchi; M. Alejandra Tortorici; John Bowen; Katja Culap; Stefano Jaconi; Elisabetta Cameroni; Gyorgy Snell; Matteo S. Pizzuto; Alessandra Franzetti Pellanda; Christian Garzoni; Agostino Riva; - The CITIID-NIHR BioResource COVID-19 Collaboration; Anne Elmer; Nathalie Kingston; Barbara Graves; Laura McCoy; Ken Smith; John Bradley; Ceron Ceron-Gutierrez L; Gabriela Barcenas-Morales; Herbert W. Virgin; Antonio Lanzavecchia; Luca Piccoli; Rainer Doffinger; Mark Wills; David Veesler; Davide Corti; Ravindra Gupta,UCL; Vir Biotechnology; University of Cambridge; University of Cambridge; University of Cambridge; University of Washington; University of Cambridge; Vir Biotechnology; Vir Biotechnology; Vir Biotechnology; Vir Biotechnology; University of Washington; University of Washington; Vir Biotehcnology; Vir Biotechnology; Vir Biotechnology; Vir Biotechnology; Vir Biotechnology; Clinica Luganese Moncucco; Clinica Luganese Moncucco; Luigi Sacco Hospital; ; Addenbrookes Hospital; NIHR; Cambridge NIHR; UCL; University of Cambridge; University of Cambridge; Addenbrookes Hospital; Addenbrookes Hospital; Vir Biotechnology; Vir Biotechnology; Vir Biotechnology; Addenbrookes Hospital; University of Cambridge; University of Washington; Vir Biotechnology; University of Cambridge,"Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) transmission is uncontrolled in many parts of the world, compounded in some areas by higher transmission potential of the B1.1.7 variant now seen in 50 countries. It is unclear whether responses to SARS-CoV-2 vaccines based on the prototypic strain will be impacted by mutations found in B.1.1.7. Here we assessed immune responses following vaccination with mRNA-based vaccine BNT162b2. We measured neutralising antibody responses following a single immunization using pseudoviruses expressing the wild-type Spike protein or the 8 amino acid mutations found in the B.1.1.7 spike protein. The vaccine sera exhibited a broad range of neutralising titres against the wild-type pseudoviruses that were modestly reduced against B.1.1.7 variant. This reduction was also evident in sera from some convalescent patients. Decreased B.1.1.7 neutralisation was also observed with monoclonal antibodies targeting the N-terminal domain (9 out of 10), the Receptor Binding Motif (RBM) (5 out of 31), but not in neutralising mAbs binding outside the RBM. Introduction of the E484K mutation in a B.1.1.7 background to reflect newly emerging viruses in the UK led to a more substantial loss of neutralising activity by vaccine-elicited antibodies and mAbs (19 out of 31) over that conferred by the B.1.1.7 mutations alone. E484K emergence on a B.1.1.7 background represents a threat to the vaccine BNT162b.",infectious diseases,fuzzy,100,100
-medRxiv,10.1101/2021.01.14.21249801,2021-01-15,https://medrxiv.org/cgi/content/short/2021.01.14.21249801,Factor V is an immune inhibitor that is expressed at increased levels in leukocytes of patients with severe Covid-19,Jun Wang; Prasanti Kotagiri; Paul Lyons; Federica Mescia; Laura Bergamaschi; Lorinda Turner; Rafia Al-Lamki; Michael D Morgan; Fernando J Calero-Nieto; Karsten Bach; Nicole Mende; Nicola K Wilson; Emily R Watts; - Cambridge Institute of Therapeutic Immunology and Infectious Disease - NIHR Covid BioResource; Patrick Chinnery; Nathalie Kingston; Sofia Papadia; Kathleen Stirrups; Neil Walker; Ravindra K Gupta; Mark Toshner; Michael Weekes; James A Nathan; Sarah Walmsley; Willem Hendrik Ouwehand; Mary Kasanicki; Berthold Gottgens; John C Marioni; Smith GC Smith; Jordan S Pober; John R Bradley,University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Edinburgh; ; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; Cambridge University; University of Cambridge; University of Edinburgh; Prof; Cambridge University Hospitals; University of Cambridge; EMBL-EBI; University of Cambridge; Yale University; University of Cambridge,"Severe Covid-19 is associated with elevated plasma Factor V (FV) and increased risk of thromboembolism. We report that neutrophils, T regulatory cells (Tregs), and monocytes from patients with severe Covid-19 express FV, and expression correlates with T cell lymphopenia. In vitro full length FV, but not FV activated by thrombin cleavage, suppresses T cell proliferation. Increased and prolonged FV expression by cells of the innate and adaptive immune systems may contribute to lymphopenia in severe Covid-19. Activation by thrombin destroys the immunosuppressive properties of FV. Anticoagulation in Covid-19 patients may have the unintended consequence of suppressing the adaptive immune system.",infectious diseases,fuzzy,100,100
 medRxiv,10.1101/2021.01.15.21249885,2021-01-15,https://medrxiv.org/cgi/content/short/2021.01.15.21249885,Epidemiology of post-COVID syndrome following hospitalisation with coronavirus: a retrospective cohort study,Daniel Ayoubkhani; Kamlesh Khunti; Vahe Nafilyan; Thomas Maddox; Ben Humberstone; Ian Diamond; Amitava Banerjee,Office for National Statistics; University of Leicester; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University College London,"ObjectivesThe epidemiology of post-COVID syndrome (PCS) is currently undefined. We quantified rates of organ-specific impairment following recovery from COVID-19 hospitalisation compared with those in a matched control group, and how the rate ratio (RR) varies by age, sex, and ethnicity.
 
 DesignObservational, retrospective, matched cohort study.
@@ -4005,7 +3927,6 @@ MethodsNose and throat swabs from 28-September-2020 to 2-January-2021 in the UKs
 Results15,166(0.98%) of 1,553,687 swabs were PCR-positive, 8,545(56%) with three genes detected and 3,531(23%) SGTF. SGTF comprised an increasing, and triple-gene positives a decreasing, percentage of infections from late-November in most UK regions/countries, e.g. from 15% to 38% to 81% over 1.5 months in London. SGTF Ct values correspondingly declined substantially to similar levels to triple-gene positives. Population-level SGTF positivity remained low (<0.25%) in all regions/countries until late-November, when marked increases with and without self-reported symptoms occurred in southern England (to 1.5-3%), despite stable rates of non-SGTF cases. SGTF positivity rates increased on average 6% more rapidly than rates of non-SGTF positives (95% CI 4-9%) supporting addition rather than replacement with B.1.1.7/VOC202012/01. Excess growth rates for SGTF vs non-SGTF positives were similar in those up to high school age (5% (1-8%)) and older individuals (6% (4-9%)).
 
 ConclusionsDirect population-representative estimates show that the B.1.1.7/VOC202012/01 SARS-CoV-2 variant leads to higher infection rates, but does not seem particularly adapted to any age group.",infectious diseases,fuzzy,100,100
-medRxiv,10.1101/2021.01.11.20248765,2021-01-15,https://medrxiv.org/cgi/content/short/2021.01.11.20248765,Early immune pathology and persistent dysregulation characterise severe COVID-19,Laura Bergamaschi; Federica Mescia; Lorinda Turner; Aimee Hanson; Prasanti Kotagiri; Benjamin J. Dunmore; Helene Ruffieux; Aloka DeSa; Oisin Huhn; Michael D Morgan; Pehuen Pereyra Gerber; Mark R. Wills; Stephen Baker; Fernando J Calero Nieto; Rainer Doffinger; Gordon Dougan; Anne Elmer; Ian G Goodfellow; Ravindra K. Gupta; Myra Hosmillo; Kelvin Hunter; Nathalie Kingston; Paul J. Lehner; Nicholas J. Matheson; Jeremy K. Nicholson; Anna M. Petrunkina; Sylvia Richardson; Caroline Saunders; James E.D. Thaventhiran; Erik J.M. Toonen; Michael P. Weekes; - CambridgeInstituteofTherapeuticImmunologyandInfectiousDisease-NationalInstituteofHealthResearch(CITI; Berthold Gottgens; Mark Toshner; Christoph Hess; John R. Bradley; Paul A. Lyons; Kenneth G.C. Smith,"Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; MRC Biostatistics Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cancer Research UK, Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Clinical Research Centre, NIHR Clinical Research Facility, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge CB2 ; Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; The Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Murdoch, Western Australia WA 6150, Australia; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; MRC Biostatistics Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; Cambridge Clinical Research Centre, NIHR Clinical Research Facility, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge CB2 ; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; R&D Department, Hycult Biotech, 5405 PD Uden, The Netherlands; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; ; Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK","In a study of 207 SARS-CoV2-infected individuals with a range of severities followed over 12 weeks from symptom onset, we demonstrate that an early robust bystander CD8 T cell immune response, without systemic inflammation, is characteristic of asymptomatic or mild disease. Those presenting to hospital had delayed bystander responses and systemic inflammation already evident at around symptom onset. Such early evidence of inflammation suggests immunopathology may be inevitable in some individuals, or that preventative intervention might be needed before symptom onset. Viral load does not correlate with the development of this pathological response, but does with its subsequent severity. Immune recovery is complex, with profound persistent cellular abnormalities correlating with a change in the nature of the inflammatory response, where signatures characteristic of increased oxidative phosphorylation and reactive-oxygen species-associated inflammation replace those driven by TNF and IL-6. These late immunometabolic inflammatory changes and unresolved immune defects may have clinical implications.",infectious diseases,fuzzy,100,100
 medRxiv,10.1101/2021.01.15.21249871,2021-01-15,https://medrxiv.org/cgi/content/short/2021.01.15.21249871,Impact of COVID-19 on Care-Home Mortality and Life Expectancy in Scotland,Jennifer Kirsty Burton; Martin Reid; Ciara Gribben; David Caldwell; David N Clark; Peter Hanlon; Terence J Quinn; Colin Fischbacher; Peter Knight; Bruce Guthrie; David McAllister,University of Glasgow; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; University of Glasgow; University of Glasgow; Public Health Scotland; Public Health Scotland; University of Edinburgh; University of Glasgow,"IntroductionCOVID-19 deaths are commoner among care-home residents, but the mortality burden has not been quantified.
 
 MethodsCare-home residency was identified via a national primary care registration database linked to national mortality data. Life expectancy was estimated using Makeham-Gompertz models, to (i) describe yearly life expectancy from Nov 2015 to Oct 2020 (ii) compare life expectancy (during 2016-2018) between care-home residents and the wider Scottish population and (iii) apply care-home life expectancy estimates to COVID-19 death counts to estimate years of life lost (YLL).
@@ -4051,6 +3972,19 @@ MethodsWorking on behalf of NHS England we developed an open source software fra
 ResultsMuch activity recorded in general practice declined to some extent during the pandemic, but largely recovered by September 2020, with some exceptions. There was a large drop in coded activity for commonly used laboratory tests, with broad recovery to pre-pandemic levels by September. One exception was blood coagulation tests such as International Normalised Ratio (INR), with a smaller reduction (median tests per 1000 patients in 2020: February 8.0; April 6.2; September 7.0). The overall pattern of recording for respiratory symptoms was less affected, following an expected seasonal pattern and classified as ""no change"" from the previous year. Respiratory tract infections exhibited a sustained drop compared with pre-pandemic levels, not returning to pre-pandemic levels by September 2020. Various COVID-19 codes increased through the period. We observed a small decline associated with high level codes for long-term respiratory conditions such as chronic obstructive pulmonary disease (COPD) and asthma. Asthma annual reviews experienced a small drop but since recovered, while COPD annual reviews remain below baseline.
 
 ConclusionsWe successfully delivered an open source software framework to describe trends and variation in clinical activity across an unprecedented scale of primary care data. The COVD-19 pandemic led to a substantial change in healthcare activity. Most laboratory tests showed substantial reduction, largely recovering to near-normal levels by September 2020, with some important tests less affected. Records of respiratory infections decreased with the exception of codes related to COVID-19, whilst activity of other respiratory disease codes was mixed. We are expanding the NHS Service Restoration Observatory in collaboration with clinicians, commissioners and researchers and welcome feedback.",health systems and quality improvement,fuzzy,100,100
+medRxiv,10.1101/2020.12.27.20248896,2021-01-02,https://medrxiv.org/cgi/content/short/2020.12.27.20248896,Vaccination and Non-Pharmaceutical Interventions: when can the UK relax about COVID-19?,Sam Moore; Edward M Hill; Michael Tildesley; Louise M Dyson; Matt J Keeling,University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick,"BackgroundThe announcement of efficacious vaccine candidates against SARS-CoV-2 has been met with worldwide acclaim and relief. Many countries already have detailed plans for vaccine targeting based on minimising severe illness, death and healthcare burdens. Normally, relatively simple relationships between epidemiological parameters, vaccine efficacy and vaccine uptake predict the success of any immunisation programme. However, the dynamics of vaccination against SARS-CoV-2 is made more complex by age-dependent factors, changing levels of infection and the potential relaxation of non-pharmaceutical interventions (NPIs) as the perceived risk declines.
+
+MethodsIn this study we use an age-structured mathematical model, matched to a range of epidemiological data in the UK, that also captures the roll-out of a two-dose vaccination programme targeted at specific age groups.
+
+FindingsWe consider the interaction between the UK vaccination programme and future relaxation (or removal) of NPIs. Our predictions highlight the population-level risks of early relaxation leading to a pronounced wave of infection, hospital admissions and deaths. Only vaccines that offer high infection-blocking efficacy with high uptake in the general population allow relaxation of NPIs without a huge surge in deaths.
+
+InterpretationWhile the novel vaccines against SARS-CoV-2 offer a potential exit strategy for this outbreak, this is highly contingent on the infection-blocking (or transmission-blocking) action of the vaccine and the population uptake, both of which need to be carefully monitored as vaccine programmes are rolled out in the UK and other countries.
+
+Research in contextO_ST_ABSEvidence before this studyC_ST_ABSVaccination has been seen as a key tool in the fight against SARS-CoV-2. The vaccines already developed represent a major technological achievement and have been shown to generate significant immune responses, as well as offering considerable protection against disease. However, to date there is limited information on the degree of infection-blocking these vaccines are likely to induce. Mathematical models have already successfully been used to consider age- and risk-structured targeting of vaccination, highlighting the importance of prioritising older and high-risk individuals.
+
+Added value of this studyTranslating current knowledge and uncertainty of vaccine behaviour into meaningful public health messages requires models that fully capture the within-country epidemiology as well as the complex roll-out of a two-dose vaccination programme. We show that under reasonable assumptions for vaccine efficacy and uptake the UK is unlikely to reach herd immunity, which means that non-pharmaceutical interventions cannot be released without generating substantial waves of infection.
+
+Implications of all the available evidenceVaccination is likely to provide substantial individual protection to those receiving two doses, but the degree of protection to the wider population is still uncertain. While substantial immunisation of the most vulnerable groups will allow for some relaxation of controls, this must be done gradually to prevent large scale public health consequences.",infectious diseases,fuzzy,100,100
 medRxiv,10.1101/2020.12.30.20248603,2021-01-01,https://medrxiv.org/cgi/content/short/2020.12.30.20248603,SARS-CoV-2 positivity in asymptomatic-screened dental patients,David I Conway; Shauna Culshaw; Maura Edwards; Claire Clark; Chris Watling; Chris Robertson; Raymond Braid; Emma O'Keefe; Niall McGoldrick; Jacky Burns; Stacey Provan; Harper VanSteenhouse; Jodie Hay; Rory Gunson; - Dental COVID-19 Surveillance Survey Group,University of Glasgow and Public Health Scotland; University of Glasgow; NHS Ayrshire and Arran; Public Health Scotland; Public Health Scotland; Strathclyde University and Public Health Scotland; Public Health Scotland; NHS Fife; NHS Fife; NHS Fife; NHS Greater Glasgow & Clyde; BioClavis Ltd; University of Glasgow; NHS Greater Glasgow & Clyde; ,"Enhanced community surveillance is a key pillar of the public health response to COVID-19. Asymptomatic carriage of SARS-CoV-2 is a potentially significant source of transmission, yet remains relatively poorly understood. Disruption of dental services continues with significantly reduced capacity. Ongoing precautions include pre- and/or at appointment COVID-19 symptom screening and use of enhanced personal protective equipment (PPE). This study aimed to investigate SARS-CoV-2 infection in dental patients to inform community surveillance and improve understanding of risks in the dental setting. Thirty-one dental care centres across Scotland invited asymptomatic screened patients over 5-years-old to participate. Following verbal consent and completion of sociodemographic and symptom history questionnaire, trained dental teams took a combined oropharyngeal and nasal swab sample using standardised VTM-containing testkits. Samples were processed by the Lighthouse Lab and patients informed of their results by SMS/e-mail with appropriate self-isolation guidance in the event of a positive test. Over a 13-week period (from 3August to 31October2020) n=4,032 patients, largely representative of the population, were tested. Of these n=22 (0.5%; 95%CI 0.5%, 0.8%) tested positive for SARS-CoV-2. The positivity rate increased over the period, commensurate with uptick in community prevalence identified across all national testing monitoring data streams. All positive cases were successfully followed up by the national contact tracing program. To the best of our knowledge this is the first report of a COVID-19 testing survey in asymptomatic-screened patients presenting in a dental setting. The positivity rate in this patient group reflects the underlying prevalence in community at the time. These data are a salient reminder, particularly when community infection levels are rising, of the importance of appropriate ongoing Infection Prevention Control and PPE vigilance, which is relevant as healthcare team fatigue increases as the pandemic continues. Dental settings are a valuable location for public health surveillance.",dentistry and oral medicine,fuzzy,100,100
 medRxiv,10.1101/2020.12.24.20248822,2020-12-26,https://medrxiv.org/cgi/content/short/2020.12.24.20248822,Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England,Nicholas G Davies; Sam Abbott; Rosanna C. Barnard; Christopher I. Jarvis; Adam J. Kucharski; James D Munday; Carl A. B. Pearson; Timothy Russell; Damien Tully; Alex D. Washburne; Tom Wenseleers; Amy Gimma; William Waites; Kerry L. M. Wong; Kevin van Zandvoort; Justin D. Silverman; - CMMID COVID-19 Working Group; - The COVID-19 Genomics UK (COG-UK) Consortium; Karla Diaz-Ordaz; Ruth H Keogh; Rosalind M Eggo; Sebastian Funk; Mark Jit; Katherine E. Atkins; W. John Edmunds,"London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Selva Analytics LLC; KU Leuven; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; College of Information Science and Technology, Pennsylvania State University; ; ; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine","A novel SARS-CoV-2 variant, VOC 202012/01 (lineage B.1.1.7), emerged in southeast England in November 2020 and is rapidly spreading towards fixation. Using a variety of statistical and dynamic modelling approaches, we estimate that this variant has a 43-90% (range of 95% credible intervals 38-130%) higher reproduction number than preexisting variants. A fitted two-strain dynamic transmission model shows that VOC 202012/01 will lead to large resurgences of COVID-19 cases. Without stringent control measures, including limited closure of educational institutions and a greatly accelerated vaccine roll-out, COVID-19 hospitalisations and deaths across England in 2021 will exceed those in 2020. Concerningly, VOC 202012/01 has spread globally and exhibits a similar transmission increase (59-74%) in Denmark, Switzerland, and the United States.",epidemiology,fuzzy,100,100
 bioRxiv,10.1101/2020.12.23.424229,2020-12-25,https://biorxiv.org/cgi/content/short/2020.12.23.424229,Patterns of within-host genetic diversity in SARS-CoV-2,Gerry Tonkin-Hill; Inigo Martincorena; Roberto Amato; Andrew R J Lawson; Moritz Gerstung; Ian Johnston; David K Jackson; Naomi R Park; Stefanie V Lensing; Michael A Quail; Sónia Gonçalves; Cristina Ariani; Michael Spencer Chapman; William L Hamilton; Luke W Meredith; Grant Hall; Aminu S Jahun; Yasmin Chaudhry; Myra Hosmillo; Malte L Pinckert; Iliana Georgana; Anna Yakovleva; Laura G Caller; Sarah L Caddy; Theresa Feltwell; Fahad A Khokhar; Charlotte J Houldcroft; Martin D Curran; Surendra Parmar; - The COVID-19 Genomics UK (COG-UK) Consortium; Alex Alderton; Rachel Nelson; Ewan Harrison; John Sillitoe; Stephen D Bentley; Jeffrey C Barrett; M. Estee Torok; Ian G Goodfellow; Cordelia Langford; Dominic Kwiatkowski; - Wellcome Sanger Institute COVID-19 Surveillance Team,"Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; European Bioinformatics Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge and The Francis Crick Institute; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Department of Medicine, University of Cambridge and Cambridge Institute of Therapeutic Immunology and Infectious Disease; Department of Medicine, University of Cambridge; Public Health England; Public Health England; COG-UK; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute and European Bioinformatics Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Wellcome Sanger Institute; Wellcome Sanger Institute and Oxford University; ","Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1,181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within and between host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses.",genomics,fuzzy,100,100
@@ -4495,7 +4429,6 @@ Added value of this studyWe used daily mobility data aggregated from Facebook us
 Implications of all the available evidenceWe show that spatial mobility data available in near real-time can give information on connectivity that can be used to understand the impact of geographically-targeted interventions and in the future, to inform spatially-targeted intervention strategies.
 
 Data SharingData used in this study are available from the Facebook Data for Good Partner Program by application. Code and supplementary information for this paper are available online (https://github.com/hamishgibbs/facebook_mobility_uk), alongside publication.",epidemiology,fuzzy,100,100
-medRxiv,10.1101/2020.10.26.20219642,2020-10-27,https://medrxiv.org/cgi/content/short/2020.10.26.20219642,A2B-COVID: A method for evaluating potential SARS-CoV-2 transmission events,Christopher J R Illingworth; William L Hamilton; Christopher H Jackson; Ashley Popay; Luke Meredith; Charlotte J Houldcroft; Myra Hosmillo; Aminu Jahun; Matthew Routledge; Ben Warne; Laura Caller; Sarah Caddy; Anna Yakovleva; Grant Hall; Fahad A Khokhar; Theresa Feltwell; Malte Pinckert; Iliana Georgana; Yasmin Chaudhry; Martin Curran; Surendra Parmar; Dominic Sparkes; Lucy Rivett; Nick K Jones; Sushmita Sridhar; Sally Forest; Tom Dymond; Kayleigh Grainger; Chris Workman; Effrossyni Gkrania-Klotsas; Nicholas M Brown; Michael Weekes; Stephen Baker; Sharon J Peacock; Theodore Gouliouris; Ian G. Goodfellow; Daniela de Angelis; M. Estee Torok,"MRC Biostatistics Unit, University of Cambridge; Department of Medicine, University of Cambridge; MRC Biostatistics Unit, University of Cambridge; Public Health England Field Epidemiology Unit, Cambridge; Department of Pathology, University of Cambridge; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Cambridge University Hospitals NHS Foundation Trust, Cambridge; Department of Medicine, University of Cambridge; Francis Crick Institute; Cambridge Institute for Therapeutic Immunology and Infectious Disease; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge; Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Department of Medicine, University of Cambridge; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University; Cambridge University; Department of Medicine, University of Cambridge; Cambridge University Hospitals NHS Foundation Trust; University of Cambridge; MRC Biostatistics Unit, University of Cambridge; University of Cambridge","Identifying linked cases of infection is a key part of the public health response to viral infectious disease. Viral genome sequence data is of great value in this task, but requires careful analysis, and may need to be complemented by additional types of data. The Covid-19 pandemic has highlighted the urgent need for analytical methods which bring together sources of data to inform epidemiological investigations. We here describe A2B-COVID, an approach for the rapid identification of linked cases of coronavirus infection. Our method combines knowledge about infection dynamics, data describing the movements of individuals, and novel approaches to genome sequence data to assess whether or not cases of infection are consistent or inconsistent with linkage via transmission. We apply our method to analyse and compare data collected from two wards at Cambridge University Hospitals, showing qualitatively different patterns of linkage between cases on designated Covid-19 and non-Covid-19 wards. Our method is suitable for the rapid analysis of data from clinical or other potential outbreak settings.",epidemiology,fuzzy,100,100
 medRxiv,10.1101/2020.10.26.20219725,2020-10-27,https://medrxiv.org/cgi/content/short/2020.10.26.20219725,"Declining prevalence of antibody positivity to SARS-CoV-2: a community study of 365,000 adults",Helen Ward; Graham Cooke; Christina J Atchison; Matthew Whitaker; Joshua Elliott; Maya Moshe; Jonathan C Brown; Barney Flower; Anna Daunt; Kylie E. C. Ainslie; Deborah Ashby; Christl A. Donnelly; Steven Riley; Ara Darzi; Wendy Barclay; Paul Elliott,"Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London","BackgroundThe prevalence and persistence of antibodies following a peak SARS-CoV-2 infection provides insights into its spread in the community, the likelihood of reinfection and potential for some level of population immunity.
 
 MethodsPrevalence of antibody positivity in England, UK (REACT2) with three cross-sectional surveys between late June and September 2020. 365104 adults used a self-administered lateral flow immunoassay (LFIA) test for IgG. A laboratory comparison of LFIA results to neutralization activity in panel of sera was performed.
@@ -4533,6 +4466,17 @@ We constructed a network-based model to capture the interactions of a student po
 With all adhering to test, trace and isolation measures, we found that 22% (7% - 41%) of the student population could be infected during the autumn term, compared to 69% (56% - 76%) when assuming zero adherence to such measures. Irrespective of the adherence to isolation measures, on average a higher proportion of students resident on-campus became infected compared to students resident off-campus. Room isolation generated minimal benefits. Regular mass testing, together with high adherence to isolation and test and trace measures, could substantially reduce the proportion infected during the term compared to having no testing.
 
 Our findings suggest SARS-CoV-2 may readily transmit in a university setting if there is limited adherence to nonpharmaceutical interventions and/or there are delays in receiving test results. Following isolation guidance and effective contact tracing curbed transmission and reduced the expected time an adhering student would spend in isolation.",infectious diseases,fuzzy,100,100
+medRxiv,10.1101/2020.10.14.20212555,2020-10-16,https://medrxiv.org/cgi/content/short/2020.10.14.20212555,Multi-organ impairment in low-risk individuals with long COVID,Andrea Dennis; Malgorzata Wamil; Sandeep Kapur; Johann Alberts; Andrew Badley; Gustav Anton Decker; Stacey A Rizza; Rajarshi Banerjee; Amitava Banerjee,Perspectum; Great Western Hospitals NHS Foundation Trust; Mayo Clinic Healthcare; Alliance Medical; Mayo Clinic; Mayo Clinic International; Mayo Clinic; Perspectum; University College London,"BackgroundSevere acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection has disproportionately affected older individuals and those with underlying medical conditions. Research has focused on short-term outcomes in hospital, and single organ involvement. Consequently, impact of long COVID (persistent symptoms three months post-infection) across multiple organs in low-risk individuals is yet to be assessed.
+
+MethodsAn ongoing prospective, longitudinal, two-centre, observational study was performed in individuals symptomatic after recovery from acute SARS-CoV-2 infection. Symptoms and organ function (heart, lungs, kidneys, liver, pancreas, spleen) were assessed by standardised questionnaires (EQ-5D-5L, Dyspnoea-12), blood investigations and quantitative magnetic resonance imaging, defining single and multi-organ impairment by consensus definitions.
+
+FindingsBetween April and September 2020, 201 individuals (mean age 44 (SD 11.0) years, 70% female, 87% white, 31% healthcare workers) completed assessments following SARS-CoV-2 infection (median 140, IQR 105-160 days after initial symptoms). The prevalence of pre-existing conditions (obesity: 20%, hypertension: 6%; diabetes: 2%; heart disease: 4%) was low, and only 18% of individuals had been hospitalised with COVID-19. Fatigue (98%), muscle aches (88%), breathlessness (87%), and headaches (83%) were the most frequently reported symptoms. Ongoing cardiorespiratory (92%) and gastrointestinal (73%) symptoms were common, and 42% of individuals had ten or more symptoms.
+
+There was evidence of mild organ impairment in heart (32%), lungs (33%), kidneys (12%), liver (10%), pancreas (17%), and spleen (6%). Single (66%) and multi-organ (25%) impairment was observed, and was significantly associated with risk of prior COVID-19 hospitalisation (p<0.05).
+
+InterpretationIn a young, low-risk population with ongoing symptoms, almost 70% of individuals have impairment in one or more organs four months after initial symptoms of SARS-CoV-2 infection. There are implications not only for burden of long COVID but also public health approaches which have assumed low risk in young people with no comorbidities.
+
+FundingThis work was supported by the UKs National Consortium of Intelligent Medical Imaging through the Industry Strategy Challenge Fund, Innovate UK Grant 104688, and also through the European Unions Horizon 2020 research and innovation programme under grant agreement No 719445.",health policy,fuzzy,100,100
 medRxiv,10.1101/2020.10.12.20211342,2020-10-14,https://medrxiv.org/cgi/content/short/2020.10.12.20211342,Network Graph Representation of COVID-19 Scientific Publications to Aid Knowledge Discovery,George Cernile; Trevor Heritage; Neil Sebire; Ben Gordon; Taralyn Schwering; Shana Kazemlou; Yulia Borecki,Inspirata Ltd; Inspirata Ltd; HDRUK London UK; HDRUK London UK; Inspirata Ltd; Inspirata Ltd; Inspirata Ltd,"IntroductionNumerous scientific journal articles have been rapidly published related to COVID-19 making navigation and understanding of relationships difficult.
 
 MethodsA graph network was constructed from the publicly available CORD-19 database of COVID-19-related publications using an engine leveraging medical knowledgebases to identify discrete medical concepts and an open source tool (Gephi) used to visualise the network.
@@ -4560,21 +4504,6 @@ Controlling any rise in infection is a compromise between public health and soci
 medRxiv,10.1101/2020.10.11.20210625,2020-10-13,https://medrxiv.org/cgi/content/short/2020.10.11.20210625,Mental health service activity during COVID-19 lockdown among individuals with learning disabilities: South London and Maudsley data on services and mortality from January to July 2020,Evangelia Martin; Eleanor Nuzum; Matthew Broadbent; Robert Stewart,King's College London; King's College London; South London and Maudsley NHS Foundation Trust; King's College London,"The lockdown and social distancing policy imposed due to the COVID-19 pandemic is likely to have had a widespread impact on mental healthcare service provision and use. Previous reports from the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for 1.2m residents in South London) highlighted a shift to virtual contacts among those accessing community mental health and home treatment teams and an increase in deaths over the pandemics first wave. However, there is a need to quantify this for individuals with particular vulnerabilities, including those with learning disabilities and other neurodevelopmental disorders. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource with 24-hourly updates of electronic mental health records data, this paper describes daily caseloads and contact numbers (face-to-face and virtual) for individuals with potential neurodevelopmental disorders across community, specialist, crisis and inpatient services. The report focussed on the period 1st January to 31st July 2020. We also report on daily accepted and discharged trust referrals, total trust caseloads and daily inpatient admissions and discharges for individuals with potential neurodevelopmental disorders. In addition, daily deaths are described for all current and previous SLaM service users with potential neurodevelopmental disorders over this period. In summary, comparing periods before and after 16th March 2020 there was a shift from face-to-face contacts to virtual contacts across all teams. The largest declines in caseloads and total contacts were seen in Home Treatment Team, Liaison/A&E and Older Adult teams. Reduced accepted referrals and inpatient admissions were observed and there was an 103% increase in average daily deaths in the period after 16th March, compared to the period 1st January to 15th March (or a 282% increase if the 2-month period from 16th March to 15th May was considered alone).",psychiatry and clinical psychology,fuzzy,100,100
 medRxiv,10.1101/2020.10.08.20209411,2020-10-13,https://medrxiv.org/cgi/content/short/2020.10.08.20209411,"Elevated antiviral, myeloid and endothelial inflammatory markers in severe COVID-19",Ryan Thwaites; Ashley Sanchez Sevilla Uruchurtu; Matthew Siggins; Felicity Liew; Clark D Russell; Shona Moore; Edwin Carter; Simon Abrams; Charlotte-Eve Short; Thilipan Thaventhiran; Emma Bergstrom; Zoe Gardener; Stephanie Ascough; Christopher Chiu; Annemarie B Docherty; David Hunt; Yanick Crow; Tom Solomon; Graham Taylor; Lance Turtle; Ewen M Harrison; Malcolm Gracie Semple; J Kenneth Baillie; Peter JM Openshaw,"Imperial College London; Imperial College London; Imperial College London; Imperial College London; University of Edinburgh; University of Liverpool; University of Edinburgh; University of Liverpool; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Liverpool; Imperial College London; University ofLiverpool; University of Edinburgh; University of Liverpool; Roslin Institute, University of Edinburgh; Imperial College London","Introductory paragraphThe mechanisms that underpin COVID-19 disease severity, and determine the outcome of infection, are only beginning to be unraveled. The host inflammatory response contributes to lung injury, but circulating mediators levels fall below those in classical  cytokine storms. We analyzed serial plasma samples from 619 patients hospitalized with COVID-19 recruited through the prospective multicenter ISARIC clinical characterization protocol U.K. study and 39 milder community cases not requiring hospitalization. Elevated levels of numerous mediators including angiopoietin-2, CXCL10, and GM-CSF were seen at recruitment in patients who later died. Markers of endothelial injury (angiopoietin-2 and von-Willebrand factor A2) were detected early in some patients, while inflammatory cytokines and markers of lung injury persisted for several weeks in fatal COVID-19 despite decreasing antiviral cytokine levels. Overall, markers of myeloid or endothelial cell activation were associated with severe, progressive, and fatal disease indicating a central role for innate immune activation and vascular inflammation in COVID-19.",infectious diseases,fuzzy,91,100
 medRxiv,10.1101/2020.10.09.20209957,2020-10-13,https://medrxiv.org/cgi/content/short/2020.10.09.20209957,Development and validation of the 4C Deterioration model for adults hospitalised with COVID-19,Rishi K Gupta; Ewen M Harrison; Antonia Ho; Annemarie B Docherty; Stephen R Knight; Maarten van Smeden; Ibrahim Abubakar; Marc Lipman; Matteo Quartagno; Riinu B Pius; Iain Buchan; Gail Carson; Thomas M Drake; Jake Dunning; Cameron J Fairfield; Carrol Gamble; Christopher A Green; Sophie Halpin; Hayley Hardwick; Karl Holden; Peter Horby; Clare Jackson; Kenneth McLean; Laura Merson; Jonathan S Nguyen-Van-Tam; Lisa Norman; Piero L Olliaro; Mark G Pritchard; Clark D Russell; James Scott-Brown; Catherine A Shaw; Aziz Sheikh; Tom Solomon; Cathie LM Sudlow; Olivia V Swann; Lance Turtle; Peter JM Openshaw; J Kenneth Baillie; Malcolm Gracie Semple; Mahdad Noursadeghi,"University College London; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; Medical Research Council University of Glasgow Centre for Virus Research, Glasgow, UK; University of Edinburgh; Centre for Medical Informatics, The Usher Institute, University of Edinburgh; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands; Institute for Global Health, University College London, Gower Street, London, WC1E 6BT; UCL Respiratory, Division of Medicine, University College London, London, UK; MRC Clinical Trials Unit, Institute of Clinical Trials and Methodology, University College London, London, UK; University of Edinburgh; Institute of Population Health Sciences, University of Liverpool; University of Oxford; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; National Infection Service Public Health England; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; University of Liverpool; Institute of Microbiology & Infection, University of Birmingham; Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK; University of Liverpool; University of Liverpool; ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; University of Liverpool; Centre for Medical Informatics, The Usher Institute, University of Edinburgh; University of Oxford; Division of Epidemiology and Public Health, University of Nottingham School of Medicine, Nottingham, UK; University of Edinburgh; University of Oxford; University of Oxford; Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK; School of Informatics, University of Edinburgh, Edinburgh, UK; Department of Clinical Surgery, University of Edinburgh; Centre for Medical Informatics, The Usher Institute, University of Edinburgh; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life; University of Edinburgh; Department of Child Life and Health, University of Edinburgh, UK; Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK; Imperial College London; Roslin Institute, University of Edinburgh; University of Liverpool; Division of Infection and Immunity, University College London, Gower Street, London, WC1E 6BT","Prognostic models to predict the risk of clinical deterioration in acute COVID-19 are required to inform clinical management decisions. Among 75,016 consecutive adults across England, Scotland and Wales prospectively recruited to the ISARIC Coronavirus Clinical Characterisation Consortium (ISARIC4C) study, we developed and validated a multivariable logistic regression model for in-hospital clinical deterioration (defined as any requirement of ventilatory support or critical care, or death) using 11 routinely measured variables. We used internal-external cross-validation to show consistent measures of discrimination, calibration and clinical utility across eight geographical regions. We further validated the final model in held-out data from 8,252 individuals in London, with similarly consistent performance (C-statistic 0.77 (95% CI 0.75 to 0.78); calibration-in-the-large 0.01 (-0.04 to 0.06); calibration slope 0.96 (0.90 to 1.02)). Importantly, this model demonstrated higher net benefit than using other candidate scores to inform decision-making. Our 4C Deterioration model thus demonstrates unprecedented clinical utility and generalisability to predict clinical deterioration among adults hospitalised with COVID-19.",infectious diseases,fuzzy,100,100
-medRxiv,10.1101/2020.10.08.20209304,2020-10-12,https://medrxiv.org/cgi/content/short/2020.10.08.20209304,Prevalence of COVID-19-related risk factors and risk of severe influenza outcomes in cancer survivors: a matched cohort study using linked English electronic health records data,Helena Carreira; Helen Strongman; Maria Peppa; Helen I McDonald; Isabel dos-Santos-Silva; Susannah Stanway; Liam Smeeth; Krishnan Bhaskaran,"London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; NIHR Health Protection Research Unit in Immunisation; London School of Medicine and Tropical Medicine, NIHR Health Protection Research Unit in Immunisation; London School of Hygiene and Tropical Medicine; The Royal Marsden NHS Foundation Trust; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine","BackgroundPeople with active cancer are recognised as at risk of COVID-19 complications, but it is unclear whether the much larger population of cancer survivors is at elevated risk. We aimed to address this by comparing cancer survivors and cancer-free controls for (i) prevalence of comorbidities considered risk factors for COVID-19; and (ii) risk of severe influenza, as a marker of susceptibility to severe outcomes from epidemic respiratory viruses.
-
-MethodsWe included survivors ([&ge;]1 year) of the 20 most common cancers, and age, sex and general practice-matched cancer-free controls, derived from UK primary care data linked to cancer registrations, hospital admissions and death registrations. Comorbidity prevalences were calculated 1 and 5 years from cancer diagnosis. Risk of hospitalisation or death due to influenza was compared using Cox models adjusted for baseline demographics and comorbidities.
-
-Findings108,215 cancer survivors and 523,541 cancer-free controls were included. Cancer survivors had more asthma, other respiratory, cardiac, diabetes, neurological, renal, and liver disease, and less obesity, compared with controls, but there was variation by cancer site. There were 205 influenza hospitalisations/deaths, with cancer survivors at higher risk than controls (adjusted HR 2.78, 95% CI 2.04-3.80). Haematological cancer survivors had large elevated risks persisting for >10 years (HR overall 15.17, 7.84-29.35; HR >10 years from cancer diagnosis 10.06, 2.47-40.93). Survivors of other cancers had evidence of raised risk up to 5 years from cancer diagnosis only (HR 2.22, 1.31-3.74).
-
-InterpretationRisks of severe COVID-19 outcomes are likely to be elevated in cancer survivors. This should be taken into account in policies targeted at clinical risk groups, and vaccination for both influenza, and, when available, COVID-19, should be encouraged in cancer survivors.
-
-FundingWellcome Trust, Royal Society, NIHR.
-
-Research in contextO_ST_ABSEvidence before this studyC_ST_ABSFew data are available to date on how COVID-19 affects cancer survivors. We searched PubMed with the keywords ""influenza cancer survivors"" to identify studies that compared severe influenza outcomes in cancer survivors and in a control group. No study was identified.
-
-Added value of this studyIn this matched cohort study of routinely collected electronic health records, we demonstrated raised risks of influenza hospitalisation or mortality in survivors from haematological malignancies for >10 years after diagnosis, and in survivors from solid cancers up to 5 years after diagnosis.
-
-Implications of all the available evidenceCancer survivorship appears to be an important risk factor for severe influenza outcomes, suggesting that cancer survivors may also be at raised risk of poor COVID-19 outcomes. This should be taken into account in public health policies targeted at protecting clinical risk groups. Influenza vaccination should be encouraged in this group, and may need to be extended to a wider population of medium- to long-term cancer survivors than currently recommended.",oncology,fuzzy,100,100
 bioRxiv,10.1101/2020.10.10.331348,2020-10-11,https://biorxiv.org/cgi/content/short/2020.10.10.331348,Single-dose intranasal administration of AdCOVID elicits systemic and mucosal immunity against SARS-CoV-2 in mice,Rodney G. King; Aaron Silva-Sanchez; Jessica N. Peel; Davide Botta; Selene Meza-Perez; Rameeza Allie; Michael D. Schultz; Mingyong Liu; John E. Bradley; Shihong Qiu; Guang Yang; Fen Zhou; Esther Zumaquero; Thomas S. Simpler; Betty Mousseau; John T. Killian Jr.; Brittany Dean; Qiao Shang; Jennifer L. Tipper; Christopher Risley; Kevin S. Harrod; Ray Feng; Young Lee; Bethlehem Shiberu; Vyjayanthi Krishnan; Isabelle Peguillet; Jianfeng Zhang; Todd Green; Troy D. Randall; Bertrand Georges; Frances E Lund; Scot Roberts,"University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; University of Alabama at Birmingham; Altimmune Inc.; Altimmune Inc.; Altimmune Inc.; Altimmune Inc.; Altimmune Inc.; Altimmune Inc.; University of Alabama at Birmingham; University of Alabama at Birmingham; Altimmune, Inc.; University of Alabama at Birmingham; Altimmune Inc.","The coronavirus disease 2019 (COVID-19) pandemic has highlighted the urgent need for effective preventive vaccination to reduce burden and spread of severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) in humans. Intranasal vaccination is an attractive strategy to prevent COVID-19 as the nasal mucosa represents the first-line barrier to SARS-CoV-2 entry before viral spread to the lung. Although SARS-CoV-2 vaccine development is rapidly progressing, the current intramuscular vaccines are designed to elicit systemic immunity without conferring mucosal immunity. Here, we show that AdCOVID, an intranasal adenovirus type 5 (Ad5)-vectored vaccine encoding the receptor binding domain (RBD) of the SARS-CoV-2 spike protein, elicits a strong and focused immune response against RBD through the induction of mucosal IgA, serum neutralizing antibodies and CD4+ and CD8+ T cells with a Th1-like cytokine expression profile. Therefore, AdCOVID, which promotes concomitant systemic and local mucosal immunity, represents a promising COVID-19 vaccine candidate.",immunology,fuzzy,100,92
 medRxiv,10.1101/2020.10.07.20208918,2020-10-09,https://medrxiv.org/cgi/content/short/2020.10.07.20208918,Cardiovascular drugs and COVID-19 clinical outcomes: a living systematic review and meta-analysis,Innocent Gerald Asiimwe; Sudeep Pushpakom; Richard Turner; Ruwanthi Kolamunnage-Dona; Andrea Jorgensen; Munir Pirmohamed,University of Liverpool; University of Liverpool; University of Liverpool; University of Liverpool; University of Liverpool; University of Liverpool,"OBJECTIVETo continually evaluate the rapidly evolving evidence base on the role of cardiovascular drugs in COVID-19 clinical outcomes (susceptibility to infection, hospitalization, hospitalization length, disease severity, and all-cause mortality).
 
@@ -4701,6 +4630,7 @@ medRxiv,10.1101/2020.09.17.20196469,2020-09-18,https://medrxiv.org/cgi/content/s
 bioRxiv,10.1101/2020.09.16.297945,2020-09-16,https://biorxiv.org/cgi/content/short/2020.09.16.297945,Characterisation of protease activity during SARS-CoV-2 infection identifies novel viral cleavage sites and cellular targets for drug repurposing,Bjoern Meyer; Jeanne Chiaravalli; Stacy Gellenoncourt; Philip Brownridge; Dominic P. Bryne; Leonard A. Daly; Arturas Grauslys; Marius Walter; Fabrice Agou; Lisa A. Chakrabarti; Charles S. Craik; Claire E. Eyers; Patrick A. Eyers; Yann Gambin; Andrew R Jones; Emma Sierecki; Eric Verdin; Marco Vignuzzi; Edward Emmott,Institut Pasteur; Institut Pasteur; Institut Pasteur; University of Liverpool; University of Liverpool; University of Liverpool; University of Liverpool; Buck Institute for Aging; Institut Pasteur; Institut Pasteur; UCSF; University of Liverpool; University of Liverpool; UNSW; University of Liverpool; UNSW; Buck Institute for Aging; Institut Pasteur; University of Liverpool,"SARS-CoV-2 is the causative agent behind the COVID-19 pandemic, and responsible for over 170 million infections, and over 3.7 million deaths worldwide. Efforts to test, treat and vaccinate against this pathogen all benefit from an improved understanding of the basic biology of SARS-CoV-2. Both viral and cellular proteases play a crucial role in SARS-CoV-2 replication, and inhibitors targeting proteases have already shown success at inhibiting SARS-CoV-2 in cell culture models. Here, we study proteolytic cleavage of viral and cellular proteins in two cell line models of SARS-CoV-2 replication using mass spectrometry to identify protein neo-N-termini generated through protease activity. We identify previously unknown cleavage sites in multiple viral proteins, including major antigenic proteins S and N, which are the main targets for vaccine and antibody testing efforts. We discovered significant increases in cellular cleavage events consistent with cleavage by SARS-CoV-2 main protease, and identify 14 potential high-confidence substrates of the main and papain-like proteases, validating a subset with in vitro assays. We showed that siRNA depletion of these cellular proteins inhibits SARS-CoV-2 replication, and that drugs targeting two of these proteins: the tyrosine kinase SRC and Ser/Thr kinase MYLK, showed a dose-dependent reduction in SARS-CoV-2 titres. Overall, our study provides a powerful resource to understand proteolysis in the context of viral infection, and to inform the development of targeted strategies to inhibit SARS-CoV-2 and treat COVID-19.",microbiology,fuzzy,100,100
 medRxiv,10.1101/2020.09.12.20191973,2020-09-14,https://medrxiv.org/cgi/content/short/2020.09.12.20191973,Inequality in access to health and care services during lockdown - Findings from the COVID-19 survey in five UK national longitudinal studies,Constantin-Cristian Topriceanu; Andrew Wong; James C Moon; Alun Hughes; David Bann; Nishi Chaturvedi; Praveetha Patalay; Gabriella Conti; Gabriella Captur,University College London; UCL; UCL; UCL; University College London; UCL; University College London; UCL; University College London,"Background: Access to health services and adequate care is influenced by sex, ethnicity, socio-economic position (SEP) and burden of co-morbidities. However, it is unknown whether the COVID-19 pandemic further deepened these already existing health inequalities. Methods: Participants were from five longitudinal age-homogenous British cohorts (born in 2001, 1990, 1970, 1958 and 1946). A web and telephone-based survey provided data on cancelled surgical or medical appointments, and the number of care hours received during the UK COVID-19 national lockdown. Using binary or ordered logistic regression, we evaluated whether these outcomes differed by sex, ethnicity, SEP and having a chronic illness. Adjustment was made for study-design, non-response weights, psychological distress, presence of children or adolescents in the household, keyworker status, and whether participants had received a shielding letter. Meta-analyses were performed across the cohorts and meta-regression evaluated the effect of age as a moderator. Findings: 14891 participants were included. Females (OR 1.40, 95% confidence interval [1.27,1.55]) and those with a chronic illness (OR 1.84 [1.65-2.05]) experienced significantly more cancellations during lockdown (all p<0.0001). Ethnic minorities and those with a chronic illness required a higher number of care hours during the lockdown (both OR approx. 2.00, all p<0.002). Age was not independently associated with either outcome in meta-regression. SEP was not associated with cancellation or care hours. Interpretation: The UK government's lockdown approach during the COVID-19 pandemic appears to have deepened existing health inequalities, impacting predominantly females, ethnic-minorities and those with chronic illnesses. Public health authorities need to implement urgent policies to ensure equitable access to health and care for all in preparation for a second wave.",public and global health,fuzzy,100,100
 medRxiv,10.1101/2020.09.13.20193730,2020-09-14,https://medrxiv.org/cgi/content/short/2020.09.13.20193730,Mental health service activity during COVID-19 lockdown among individuals with Personality Disorders: South London and Maudsley data on services and mortality from January to May 2020,Eleanor Nuzum; Evangelia Martin; Matthew Broadbent; Robert Stewart,South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; King's College London,"The lockdown and social distancing policy imposed due to the COVID-19 pandemic is likely to have a widespread impact on mental healthcare for both services themselves and the people accessing those services. Previous reports from the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for 1.2m residents in South London) highlighted a shift to virtual contacts among those accessing community mental health and home treatment teams and an increase in deaths over the pandemics first wave. However, there is a need to understand this further for specific groups, including those diagnosed with a personality disorder who might have particular vulnerabilities. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource with 24-hourly updates of electronic mental health records data, this paper describes daily caseloads and contact numbers (face-to-face and virtual) for individuals with personality disorders across community, specialist, crisis and inpatient services. The report focussed on the period 1st January to 31st May 2020. We also report on daily accepted and discharged trust referrals, total trust caseloads and daily inpatient admissions and discharges for individuals with personality disorders. In addition, daily deaths are described for all current and previous SLaM service users with personality disorder over this period. In summary, comparing periods before and after 16th March 2020 there was a shift from face-to-face contacts to virtual contacts across all teams. Liaison and Older Adult teams showed the largest drop in caseloads, whereas Early Intervention in Psychosis service caseloads remained the same. Reduced accepted referrals and inpatient admissions were observed and there was a 28% increase in average daily deaths in the period after 16th March, compared to the period 1st January to 15th March.",psychiatry and clinical psychology,fuzzy,100,100
+medRxiv,10.1101/2020.09.10.20191841,2020-09-11,https://medrxiv.org/cgi/content/short/2020.09.10.20191841,The King's College London Coronavirus Health and Experiences of Colleagues at King's Study: SARS-CoV-2 antibody response in an occupational sample,Daniel Leightley; Valentina Vitiello; Gabriella Bergin-Cartwright; Alice Wickersham; Katrina A S Davis; Sharon Stevelink; Matthew Hotopf; Reza Razavi; - On behalf of the KCL CHECK research team,"Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; The School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and   Medicine, King's College London, London, UK.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London; The School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King's College London; ","We report test results for SARS-CoV-2 antibodies in an occupational group of postgraduate research students and current members of staff at Kings College London. Between June and July 2020, antibody testing kits were sent to n=2296 participants; n=2004 (86.3%) responded, of whom n=1882 (93.9%) returned valid test results. Of those that returned valid results, n=124 (6.6%) tested positive for SARS-CoV-2 antibodies, with initial comparisons showing variation by age group and clinical exposure.",epidemiology,fuzzy,100,100
 medRxiv,10.1101/2020.09.11.20192492,2020-09-11,https://medrxiv.org/cgi/content/short/2020.09.11.20192492,Resurgence of SARS-CoV-2 in England: detection by community antigen surveillance,Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E Walters; Haowei Wang; Christina J Atchison; Claudio Fronterre; Peter J Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Lancaster University; Imperial College London; Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London","Background Based on cases and deaths, transmission of SARS-CoV-2 in England peaked in late March and early April 2020 and then declined until the end of June. Since the start of July, cases have increased, while deaths have continued to decrease. Methods We report results from 594,000 swabs tested for SARS-CoV-2 virus obtained from a representative sample of people in England over four rounds collected regardless of symptoms, starting in May 2020 and finishing at the beginning of September 2020. Swabs for the most recent two rounds were taken between 24th July and 11th August and for round 4 between 22nd August and 7th September. We estimate weighted overall prevalence, doubling times between and within rounds and associated reproduction numbers. We obtained unweighted prevalence estimates by sub-groups: age, sex, region, ethnicity, key worker status, household size, for which we also estimated odds of infection. We identified clusters of swab-positive participants who were closer, on average, to other swab-positive participants than would be expected. Findings Over all four rounds of the study, we found that 72% (67%, 76%) of swab-positive individuals were asymptomatic at the time of swab and in the week prior. The epidemic declined between rounds 1 and 2, and rounds 2 and 3. However, the epidemic was increasing between rounds 3 and 4, with a doubling time of 17 (13, 23) days corresponding to an R value of 1.3 (1.2, 1.4). When analysing round 3 alone, we found that the epidemic had started to grow again with 93% probability. Using only the most recent round 4 data, we estimated a doubling time of 7.7 (5.5, 12.7) days, corresponding to an R value of 1.7 (1.4, 2.0). Cycle threshold values were lower (viral loads were higher) for rounds 1 and 4 than they were for rounds 2 and 3. In round 4, we observed the highest prevalence in participants aged 18 to 24 years at 0.25% (0.16%, 0.41%), increasing from 0.08% (0.04%, 0.18%) in round 3. We observed the lowest prevalence in those aged 65 and older at 0.04% (0.02%, 0.06%) which was stable compared with round 3. Participants of Asian ethnicity had elevated odds of infection. We identified clusters in and around London, transient clusters in the Midlands, and an expanding area of clustering in the North West and more recently in Yorkshire and the Humber. Interpretation Although low levels of transmission persisted in England through to mid-summer 2020, the prevalence of SARS-CoV-2 is now increasing. We found evidence of accelerating transmission at the end of August and beginning of September. Representative community antigen sampling can increase situational awareness and help improve public health decision making even at low prevalence.",infectious diseases,fuzzy,100,100
 medRxiv,10.1101/2020.09.04.20187781,2020-09-09,https://medrxiv.org/cgi/content/short/2020.09.04.20187781,Hydroxychloroquine for prevention of COVID-19 mortality: a population-based cohort study,Christopher T Rentsch; Nicholas J DeVito; Brian MacKenna; Caroline E Morton; Krishnan Bhaskaran; Jeremy P Brown; Anna Schultze; William J Hulme; Richard Croker; Alex J Walker; Elizabeth J Williamson; Chris Bates; Seb Bacon; Amir Mehrkar; Helen J Curtis; David Evans; Kevin Wing; Peter Inglesby; Rohini Mathur; Henry Drysdale; Angel YS Wong; Helen I McDonald; Jonathan Cockburn; Harriet Forbes; John Parry; Frank Hester; Sam Harper; Liam Smeeth; Ian J Douglas; William G Dixon; Stephen JW Evans; Laurie Tomlinson; Ben Goldacre,London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; The Phoenix Partnership; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Medicine and Tropical Medicine; The Phoenix Partnership; London School of Hygiene and Tropical Medicine; The Phoenix Partnership; The Phoenix Partnership; The Phoenix Partnership; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; The University of Manchester; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundHydroxychloroquine has been shown to inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in vitro, but early clinical studies found no benefit treating patients with coronavirus disease 2019 (COVID-19). We set out to evaluate the effectiveness of hydroxychloroquine for prevention, as opposed to treatment, of COVID-19 mortality.
 
@@ -4764,7 +4694,6 @@ ConclusionExisting triage tools have good but not excellent prediction for adver
 
 RegistrationISRCTN registry, ISRCTN28342533, http://www.isrctn.com/ISRCTN28342533",emergency medicine,fuzzy,100,100
 medRxiv,10.1101/2020.09.02.20186502,2020-09-03,https://medrxiv.org/cgi/content/short/2020.09.02.20186502,Real-time monitoring of COVID-19 dynamics using automated trend fitting and anomaly detection,Thibaut Jombart; Stephane Ghozzi; Dirk Schumacher; Quentin Leclerc; Mark Jit; Stefan Flasche; Felix Greaves; Tom Ward; Rosalind M Eggo; Emily Nightingale; Sophie Meakin; Oliver J Brady; - Centre for Mathematical Modelling of Infectious Diseases COVID-19 Working Group; Graham Medley; Michael Hohle; John Edmunds,"London School of Hygiene and Tropical Medicine (LSHTM); Department of Epidemiology, Helmholtz Centre for Infection Research, Brunswick, Lower Saxony, Germany; R Epidemics Consortium; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; LSHTM; Joint Biosecurity Centre; Joint Biosecurity Centre; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; LSHTM; London School of Hygiene and Tropical Medicine; ; LSHTM; Department of Mathematics, Stockholm University, Sweden; LSHTM","As several countries gradually release social distancing measures, rapid detection of new localised COVID-19 hotspots and subsequent intervention will be key to avoiding large-scale resurgence of transmission. We introduce ASMODEE (Automatic Selection of Models and Outlier Detection for Epidemics), a new tool for detecting sudden changes in COVID-19 incidence. Our approach relies on automatically selecting the best (fitting or predicting) model from a range of user-defined time series models, excluding the most recent data points, to characterise the main trend in an incidence. We then derive prediction intervals and classify data points outside this interval as outliers, which provides an objective criterion for identifying departures from previous trends. We also provide a method for selecting the optimal breakpoints, used to define how many recent data points are to be excluded from the trend fitting procedure. The analysis of simulated COVID-19 outbreaks suggest ASMODEE compares favourably with a state-of-art outbreak-detection algorithm while being simpler and more flexible. We illustrate our method using publicly available data of NHS Pathways reporting potential COVID-19 cases in England at a fine spatial scale, for which we provide a template automated analysis pipeline. ASMODEE is implemented in the free R package trendbreaker.",health informatics,fuzzy,100,100
-medRxiv,10.1101/2020.09.02.20186817,2020-09-03,https://medrxiv.org/cgi/content/short/2020.09.02.20186817,Revealing the extent of the COVID-19 pandemic in Kenya based on serological and PCR-test data,John Ojal; Samuel PC Brand; Vincent Were; Emelda A Okiro; Ivy Kadzo Kombe; Caroline Mburu; Rabia Aziza; Morris Ogero; Ambrose Agweyu; George M Warimwe; Sophie Uyoga; Ifedayo M. O Adetifa; John Anthony Scott; Edward Otieno; Lynette I Ochola-Oyier; Charles Nyaigoti Agoti; Kadondi Kasera; Patrick Amoth; Mercy Mwangangi; Rashid Aman; Wangari Ng'ang'a; Benjamin Tsofa; Philip Bejon; Edwine Barasa; Matt J Keeling; D James Nokes,"Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya and London School of Hygiene and Tropical Medicine; The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, UK.; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; KEMRI-Wellcome Trust Research Programme; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, UK.; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; KEMRI-Wellcome Trust Research Programme; KEMRI Wellcome Trust Research Programme; KEMRI-Wellcome Trust Research Programme; London School of Hygiene & Tropical Medicine; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Ministry of Health, Government of Kenya, Kenya; Ministry of Health, Government of Kenya, Kenya; Ministry of Health, Government of Kenya, Kenya; Ministry of Health, Government of Kenya, Kenya; Presidential Policy & Strategy Unit, The Presidency, Government of Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; KEMRI-Wellcome Trust Research Programme; The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, UK; KEMRI-Wellcome Trust Research Programme, Kenya and School of Life Sciences, University of Warwick, UK","Policy makers in Africa need robust estimates of the current and future spread of SARS-CoV-2. Data suitable for this purpose are scant. We used national surveillance PCR test, serological survey and mobility data to develop and fit a county-specific transmission model for Kenya. We estimate that the SARS-CoV-2 pandemic peaked before the end of July 2020 in the major urban counties, with 34 - 41% of residents infected, and will peak elsewhere in the country within 2-3 months. Despite this penetration, reported severe cases and deaths are low. Our analysis suggests the COVID-19 disease burden in Kenya may be far less than initially feared. A similar scenario across sub-Saharan Africa would have implications for balancing the consequences of restrictions with those of COVID-19.",epidemiology,fuzzy,100,100
 medRxiv,10.1101/2020.09.01.20183822,2020-09-02,https://medrxiv.org/cgi/content/short/2020.09.01.20183822,Trust and Transparency in times of Crisis: Results from an Online Survey During the First Wave (April 2020) of the COVID-19 Epidemic in the UK,Luisa Enria; Naomi Waterlow; Nina Trivedy Rogers; Hannah Brindle; Sham Lal; Rosalind M Eggo; Shelley Lees; Chrissy h Roberts,London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; UCL; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine (LSHTM),"BackgroundThe success of a governments COVID-19 control strategy relies on public trust and broad acceptance of response measures. We investigated public perceptions of the UK governments COVID-19 response, focusing on the relationship between trust and transparency, during the first wave (April 2020) of the COVID-19 pandemic in the United Kingdom.
 
 MethodsAnonymous survey data were collected (2020-04-06 to 2020-04-22) from 9,322 respondents, aged 20+ using an online questionnaire. We took a mixed methods approach to data analysis, combining statistical analyses, structural topic modelling (STM) and qualitative thematic coding of a sub-set of responses. Missing data were imputed via multiple imputation.
@@ -4916,6 +4845,26 @@ FindingsWe find a 0{middle dot}5% (95% credible interval: -0{middle dot}2%-1{mid
 InterpretationOur study provides some evidence of an effect of long-term NO2 exposure on COVID-19 mortality, while the effect of PM2{middle dot}5 remains more uncertain.
 
 FundingMedical Research Council, Wellcome Trust, Environmental Protection Agency and National Institutes of Health.",public and global health,fuzzy,100,100
+medRxiv,10.1101/2020.08.10.20171033,2020-08-11,https://medrxiv.org/cgi/content/short/2020.08.10.20171033,Post-exertion oxygen saturation as a prognostic factor for adverse outcome in patients attending the emergency department with suspected COVID-19: Observational cohort study,Steve Goodacre; Ben Thomas; Ellen Lee; Laura Sutton; Katie Biggs; Carl Marincowitz; Amanda Loban; Simon Waterhouse; Richard Simmonds; Jose Schutter; Sarah Connelly; Elena Sheldon; Jamie Hall; Emma Young; Andrew Bentley; Kirsty Challen; Chris Fitzsimmons; Tim Harris; Fiona Lecky; Andrew Lee; Ian Maconochie; Darren Walter,"University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; Manchester University NHS Foundation Trust, Wythenshawe Hospital; Lancashire Teaching Hospitals NHS Foundation Trust; Sheffield Children's NHS Foundation Trust; Barts Health NHS Trust; University of Sheffield; University of Sheffield; Imperial College Healthcare NHS Trust; Manchester University NHS Foundation Trust","BackgroundMeasurement of post-exertion oxygen saturation has been proposed to assess illness severity in suspected COVID-19 infection. We aimed to determine the accuracy of post-exertional oxygen saturation for predicting adverse outcome in suspected COVID-19.
+
+MethodsWe undertook an observational cohort study across 70 emergency departments during first wave of the COVID-19 pandemic in the United Kingdom. We collected data prospectively, using a standardised assessment form, and retrospectively, using hospital records, from patients with suspected COVID-19, and reviewed hospital records at 30 days for adverse outcome (death or receiving organ support). Patients with post-exertion oxygen saturation recorded were selected for this analysis.
+
+ResultsWe analysed data from 817 patients with post-exertion oxygen saturation recorded after excluding 54 in whom measurement appeared unfeasible. The c-statistic for post-exertion change in oxygen saturation was 0.589 (95% confidence interval 0.465 to 0.713), and the positive and negative likelihood ratios of a 3% or more desaturation were respectively 1.78 (1.25 to 2.53) and 0.67 (0.46 to 0.98). Multivariable analysis showed that post-exertion oxygen saturation was not a significant predictor of adverse outcome when baseline clinical assessment was taken into account (p=0.368). Secondary analysis excluding patients in whom post-exertion measurement appeared inappropriate resulted in a c-statistic of 0.699 (0.581 to 0.817), likelihood ratios of 1.98 (1.26 to 3.10) and 0.61 (0.35 to 1.07), and some evidence of additional prognostic value on multivariable analysis (p=0.019).
+
+ConclusionsPost-exertion oxygen saturation provides modest prognostic information in the assessment of patients attending the emergency department with suspected COVID-19.
+
+RegistrationISRCTN registry, ISRCTN56149622, http://www.isrctn.com/ISRCTN28342533
+
+Key messagesWhat is already known on this subject?
+
+O_LIPost exertional decrease in oxygen saturation can be used to predict prognosis in chronic lung diseases
+C_LIO_LIPost exertional desaturation has been proposed as a way of predicting adverse outcome in people with suspected COVID-19
+C_LI
+
+What this study adds:
+
+O_LIPost-exertion oxygen saturation provides modest prognostic information in the assessment of patients attending the emergency department with suspected COVID-19
+C_LI",emergency medicine,fuzzy,100,100
 medRxiv,10.1101/2020.08.07.20169490,2020-08-07,https://medrxiv.org/cgi/content/short/2020.08.07.20169490,HIV infection and COVID-19 death: population-based cohort analysis of UK primary care data and linked national death registrations within the OpenSAFELY platform,Krishnan Bhaskaran; Christopher T Rentsch; Brian MacKenna; Anna Schultz; Amir Mehrkar; Chris Bates; Rosalind M Eggo; Caroline E Morton; Seb Bacon; Peter Inglesby; Ian J Douglas; Alex J Walker; Helen I McDonald; Jonathan Cockburn; Elizabeth J Williamson; David Evans; Harriet J Forbes; Helen J Curtis; William Hulme; John Parry; Frank Hester; Sam Harper; Stephen JW Evans; Liam Smeeth; Ben Goldacre,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; TPP; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; TPP; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; TPP; TPP; TPP; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundIt is unclear whether HIV infection is associated with risk of COVID-19 death. We aimed to investigate this in a large-scale population-based study in England.
 
 MethodsWorking on behalf of NHS England, we used the OpenSAFELY platform to analyse routinely collected electronic primary care data linked to national death registrations. People with a primary care record for HIV infection were compared to people without HIV. COVID-19 death was defined by ICD-10 codes U07.1 or U07.2 anywhere on the death certificate. Cox regression models were used to estimate the association between HIV infection and COVID-19 death, initially adjusted for age and sex, then adding adjustment for index of multiple deprivation and ethnicity, and finally for a broad range of comorbidities. Interaction terms were added to assess effect modification by age, sex, ethnicity, comorbidities and calendar time.
@@ -4925,15 +4874,6 @@ Results17.3 million adults were included, of whom 27,480 (0.16%) had HIV recorde
 InterpretationHIV infection was associated with a markedly raised risk of COVID-19 death in a country with high levels of antiretroviral therapy coverage and viral suppression; the association was larger in people of black ethnicity.",infectious diseases,fuzzy,100,100
 medRxiv,10.1101/2020.08.05.20169078,2020-08-06,https://medrxiv.org/cgi/content/short/2020.08.05.20169078,Transient dynamics of SARS-CoV-2 as England exited national lockdown,Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E Walters; Haowei Wang; Christina J Atchison; Peter Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Imperial College London; Imperial College London; Imperial College Healthcare NHS Trust; Imperial College London; Imperial College London; Imperial College Healthcare NHS Trust; Imperial College London School of Public Health","Control of the COVID-19 pandemic requires a detailed understanding of prevalence of SARS-CoV-2 virus in the population. Case-based surveillance is necessarily biased towards symptomatic individuals and sensitive to varying patterns of reporting in space and time. The real-time assessment of community transmission antigen study (REACT-1) is designed to overcome these limitations by obtaining prevalence data based on a nose and throat swab RT-PCR test among a representative community-based sample in England, including asymptomatic individuals. Here, we describe results comparing rounds 1 and 2 carried out during May and mid June / early July 2020 respectively across 315 lower tier local authority areas. In round 1 we found 159 positive samples from 120,620 tested swabs while round 2 there were 123 positive samples from 159,199 tested swabs, indicating a downwards trend in prevalence from 0.13% (95% CI, 0.11%, 0.15%) to 0.077% (0.065%, 0.092%), a halving time of 38 (28, 58) days, and an R of 0.89 (0.86, 0.93). The proportion of swab-positive participants who were asymptomatic at the time of sampling increased from 69% (61%, 76%) in round 1 to 81% (73%, 87%) in round 2. Although health care and care home workers were infected far more frequently than other workers in round 1, the odds were markedly reduced in round 2. Age patterns of infection changed between rounds, with a reduction by a factor of five in prevalence in 18 to 24 year olds. Our data were suggestive of increased risk of infection in Black and Asian (mainly South Asian) ethnicities. Using regional and detailed case location data, we detected increased infection intensity in and near London. Under multiple sensitivity analyses, our results were robust to the possibility of false positives. At the end of the initial lockdown in England, we found continued decline in prevalence and a shift in the pattern of infection by age and occupation. Community-based sampling, including asymptomatic individuals, is necessary to fully understand the nature of ongoing transmission.",infectious diseases,fuzzy,100,100
 medRxiv,10.1101/2020.08.01.20166405,2020-08-04,https://medrxiv.org/cgi/content/short/2020.08.01.20166405,"Physical activity, BMI and COVID-19: an observational and Mendelian randomisation study",Xiaomeng Zhang; Xue Li; Ziwen Sun; Yazhou He; Wei Xu; Harry Campbell; Malcolm G Dunlop; Maria Timofeeva; Evropi Theodoratou,University of Edinburgh; Zhejiang University; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh,"Physical activity (PA) is known to be a protective lifestyle factor against several non-communicable diseases while its impact on infectious diseases, including Coronavirus Disease 2019 (COVID-19) is not as clear. We performed univariate and multivariate logistic regression to identify associations between body mass index (BMI) and both objectively and subjectively measured PA collected prospectively and COVID-19 related outcomes (Overall COVID-19, inpatient COVID-19, outpatient COVID-19, and COVID-19 death) in the UK Biobank (UKBB) cohort. Subsequently, we tested causality by using two-sample Mendelian randomisation (MR) analysis. In the multivariable model, the increased acceleration vector magnitude PA (AMPA) was associated with a decreased probability of overall and outpatient COVID-19. No association was found between self-reported moderate-to-vigorous PA (MVPA) or BMI and COVID-19 related outcomes. Although no causal association was found by MR analyses, this may be due to limited power and we conclude policies to encourage and facilitate exercise at a population level during the pandemic should be considered.",infectious diseases,fuzzy,100,100
-medRxiv,10.1101/2020.08.03.20164897,2020-08-04,https://medrxiv.org/cgi/content/short/2020.08.03.20164897,Risk of hospitalisation with coronavirus disease 2019 in healthcare workers and their households:a nationwide linkage cohort study,Anoop SV Shah; Rachael Wood; Ciara Gribben; David Caldwell; Jennifer Bishop; Amanda Weir; Sharon Kennedy; Martin Reid; Alison Smith-Palmer; David Goldberg; Jim McMenamin; Colin Fischbacher; Chris Robertson; Sharon Hutchinson; Paul M McKeigue; Helen M Colhoun; David McAllister,London School of Hygiene and Tropical Medicine; Public Health Scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; Health protection scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; University of Edinburgh; University of Edinburgh; University of Glasgow,"ObjectiveMany healthcare staff work in high-risk settings for contracting and transmitting Severe Acute Respiratory Syndrome Coronavirus 2. Their risk of hospitalisation for coronavirus disease 2019 (COVID-19), and that of their households, is poorly understood.
-
-Design and settings and participantsDuring the peak period for COVID-19 infection in Scotland (1st March 2020 to 6th June 2020) we conducted a national record linkage study to compare the risk of COVID-19 hospitalisation among healthcare workers (age: 18-65 years), their households and other members of the general population.
-
-Main outcomeHospitalisation with COVID-19
-
-ResultsThe cohort comprised 158,445 healthcare workers, the majority being patient facing (90,733 / 158,445; 57.3%), and 229,905 household members. Of all COVID-19 hospitalisations in the working age population (18-65-year-old), 17.2% (360 / 2,097) were in healthcare workers or their households. Adjusting for age, sex, ethnicity, socio-economic deprivation and comorbidity, the risk of COVID-19 hospitalisation in non-patient facing healthcare workers and their households was similar to the risk in the general population (hazards ratio [HR] 0.81; 95%CI 0.52-1.26 and 0.86; 95%CI 0.49-1.51 respectively). In models adjusting for the same covariates however, patient facing healthcare workers, compared to non-patient facing healthcare workers, were at higher risk (HR 3.30; 95%CI 2.13-5.13); so too were household members of patient facing healthcare workers (HR 1.79; 95%CI 1.10-2.91). On sub-dividing patient-facing healthcare workers into those who worked in front-door, intensive care and non-intensive care aerosol generating settings and other, those in  front door roles were at higher risk (HR 2.09; 95%CI 1.49-2.94). For most patient facing healthcare workers and their households, the estimated absolute risk of COVID-19 hospitalisation was less than 0.5% but was 1% and above in older men with comorbidity.
-
-ConclusionsHealthcare workers and their households contribute a sixth of hospitalised COVID-19 cases. Whilst the absolute risk of hospitalisation was low overall, patient facing healthcare workers and their households had 3- and 2-fold increased risks of COVID-19 hospitalisation.",epidemiology,fuzzy,100,100
 medRxiv,10.1101/2020.08.03.20167122,2020-08-04,https://medrxiv.org/cgi/content/short/2020.08.03.20167122,Ethnic minority groups in England and Wales - factors affecting the size and timing of elevated COVID-19 mortality: a retrospective cohort study linking Census and death records,Daniel Ayoubkhani; Vahe Nafilyan; Chris White; Peter Goldblatt; Charlotte Gaughan; Louisa Blackwell; Nicky Rogers; Amitava Banerjee; Kamlesh Khunti; Myer Glickman; Ben Humberstone; Ian Diamond,"Office for National Statistics; Office for National Statistics; Office for National Statistics; UCL Institute for Health Equity; Office for National Statistics; Office for National Statistics; Office for National Statistics; Institute of Health Informatics, University College London; Diabetes Research Centre, University of Leicester; Office for National Statistics; Office for National Statistics; Office for National Statistics","ObjectivesTo estimate population-level associations between ethnicity and coronavirus disease 2019 (COVID-19) mortality, and to investigate how ethnicity-specific mortality risk evolved over the course of the pandemic.
 
 DesignRetrospective cohort study using linked administrative data.
@@ -5197,6 +5137,23 @@ What is already known on this topic- Unprecedented control measures, such as nat
 What this study adds- The percentage of individuals from the general community in England testing positive for SARS-CoV-2 clearly declined between 26 April and 28 June 2020 from around one in three 300 to around one in a thousand.
 - Risk factors for testing positive included having a job with direct patient contact, having had (indirect) contact with a hospital in the past 2 weeks, and working outside your home.
 - Positive tests commonly occurred without symptoms being reported and the percentage of individuals with a positive test that reported no symptoms was stable over time.",infectious diseases,fuzzy,100,100
+medRxiv,10.1101/2020.07.03.20145912,2020-07-06,https://medrxiv.org/cgi/content/short/2020.07.03.20145912,Ultraviolet A Radiation and COVID-19 Deaths: A Multi Country Study,Mark Cherrie; Tom Clemens; Claudio Colandrea; Zhiqiang Feng; David Webb; Chris Dibben; Richard B Weller,University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh,"ObjectivesTo determine whether UVA exposure might be associated with COVID-19 deaths
+
+DesignEcological regression, with replication in two other countries and pooled estimation
+
+Setting2,474 counties of the contiguous USA, 6,755 municipalities in Italy, 6,274 small areas in England. Only small areas in their  Vitamin D winter (monthly mean UVvitd of under 165 KJ/m2) from Jan to April 2020.
+
+Participants
+
+The  at-risk population is the total small area population, with measures to incorporate spatial infection into the model. The model is adjusted for potential confounders including long-term winter temperature and humidity.
+
+Main outcome measuresWe derive UVA measures for each area from remote sensed data and estimate their relationship with COVID-19 mortality with a random effect for States, in a multilevel zero-inflated negative binomial model. In the USA and England death certificates had to record COVID-19. In Italy excess deaths in 2020 over expected from 2015-19.
+
+Data sourcesSatellite derived mean daily UVA dataset from Japan Aerospace Exploration Agency. Data on deaths compiled by Center for Disease Control (USA), Office for National Statistics (England) and Italian Institute of Statistics.
+
+ResultsDaily mean UVA (January-April 2020) varied between 450 to 1,000 KJ/m2 across the three countries. Our fully adjusted model showed an inverse correlation between UVA and COVID-19 mortality with a Mortality Risk Ratio (MRR) of 0.71 (0.60 to 0.85) per 100KJ/m2 increase UVA in the USA, 0.81 (0.71 to 0.93) in Italy and 0.49 (0.38 to 0.64) in England. Pooled MRR was 0.68 (0.52 to 0.88).
+
+ConclusionsOur analysis, replicated in 3 independent national datasets, suggests ambient UVA exposure is associated with lower COVID-19 specific mortality. This effect is independent of vitamin D, as it occurred at irradiances below that likely to induce significant cutaneous vitamin D3 synthesis. Causal interpretations must be made cautiously in observational studies. Nonetheless this study suggests strategies for reduction of COVID-19 mortality.",epidemiology,fuzzy,100,100
 medRxiv,10.1101/2020.07.03.20145839,2020-07-04,https://medrxiv.org/cgi/content/short/2020.07.03.20145839,"The Impact of COVID-19 on Adjusted Mortality Risk in Care Homes for Older Adults in Wales, United Kingdom: A retrospective population-based cohort study for mortality in 2016-2020",Joe Hollinghurst; Jane Lyons; Richard Fry; Ashley Akbari; Mike Gravenor; Alan Watkins; Fiona Verity; Ronan A Lyons,Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University,"BackgroundMortality in care homes has had a prominent focus during the COVID-19 outbreak. Multiple and interconnected challenges face the care home sector in the prevention and management of outbreaks of COVID-19, including adequate supply of personal protective equipment, staff shortages, and insufficient or lack of timely COVID-19 testing. Care homes are particularly vulnerable to infectious diseases.
 
 AimTo analyse the mortality of older care home residents in Wales during COVID-19 lockdown and compare this across the population of Wales and the previous 4-years.
@@ -5294,6 +5251,13 @@ FindingsWe identified 148,588 people with COPD and 817,973 people with asthma re
 InterpretationThese results do not support a major role of ICS in protecting against COVID-19 related deaths. Observed increased risks of COVID-19 related death among people with COPD and asthma receiving ICS can be plausibly explained by unmeasured confounding due to disease severity.
 
 FundingThis work was supported by the Medical Research Council MR/V015737/1.",respiratory medicine,fuzzy,100,100
+medRxiv,10.1101/2020.06.18.20134742,2020-06-20,https://medrxiv.org/cgi/content/short/2020.06.18.20134742,Racial and ethnic determinants of Covid-19 risk,Chun-Han Lo; Long H. Nguyen; David A. Drew; Mark S. Graham; Erica T. Warner; Amit D. Joshi; Christina M. Astley; Chuan-Guo Guo; Wenjie Ma; Raaj S. Mehta; Sohee Kwon; Mingyang Song; Richard Davies; Joan Capdevila; Karla A. Lee; Mary Ni Lochlainn; Thomas Varsavsky; Carole H. Sudre; Jonathan Wolf; Yvette C. Cozier; Lynn Rosenberg; Lynne R. Wilkens; Christopher A. Haiman; Loic Le Marchand; Julie R. Palmer; Tim D. Spector; Sebastien Ourselin; Claire J. Steves; Andrew T. Chan; - COPE Consortium,"Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A.; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A.; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A.; School of Biomedical Engineering & Imaging Sciences, King's College London, London, U.K.; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A.; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A.; Computational Epidemiology Lab and Division of Endocrinology, Boston Children's Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A.; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A.; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A.; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A.; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A.; Zoe Global Limited, London, U.K.; Zoe Global Limited, London, U.K.; Department of Twin Research and Genetic Epidemiology, King's College London, London, U.K.; Department of Twin Research and Genetic Epidemiology, King's College London, London, U.K.; School of Biomedical Engineering & Imaging Sciences, King's College London, London, U.K.; School of Biomedical Engineering & Imaging Sciences, King's College London, London, U.K.; Zoe Global Limited, London, U.K.; Slone Epidemiology Center, Boston University, Boston, Massachusetts, U.S.A.; Slone Epidemiology Center, Boston University, Boston, Massachusetts, U.S.A.; Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, U.S.A.; Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, California, U.; Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, U.S.A.; Slone Epidemiology Center, Boston University, Boston, Massachusetts, U.S.A.; Department of Twin Research and Genetic Epidemiology, King's College London, London, U.K.; School of Biomedical Engineering & Imaging Sciences, King's College London, London, U.K.; Department of Twin Research and Genetic Epidemiology, King's College London, London, U.K.; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A.; ","BackgroundRacial and ethnic minorities have disproportionately high hospitalization rates and mortality related to the novel coronavirus disease 2019 (Covid-19). There are comparatively scant data on race and ethnicity as determinants of infection risk.
+
+MethodsWe used a smartphone application (beginning March 24, 2020 in the United Kingdom [U.K.] and March 29, 2020 in the United States [U.S.]) to recruit 2,414,601 participants who reported their race/ethnicity through May 25, 2020 and employed logistic regression to determine the adjusted odds ratios (aORs) and 95% confidence intervals (CIs) for a positive Covid-19 test among racial and ethnic groups.
+
+ResultsWe documented 8,858 self-reported cases of Covid-19 among 2,259,841 non-Hispanic white; 79 among 9,615 Hispanic; 186 among 18,176 Black; 598 among 63,316 Asian; and 347 among 63,653 other racial minority participants. Compared with non-Hispanic white participants, the risk for a positive Covid-19 test was increased across racial minorities (aORs ranging from 1.24 to 3.51). After adjustment for socioeconomic indices and Covid-19 exposure risk factors, the associations (aOR [95% CI]) were attenuated but remained significant for Hispanic (1.58 [1.24-2.02]) and Black participants (2.56 [1.93-3.39]) in the U.S. and South Asian (1.52 [1.38-1.67]) and Middle Eastern participants (1.56 [1.25-1.95]) in the U.K. A higher risk of Covid-19 and seeking or receiving treatment was also observed for several racial/ethnic minority subgroups.
+
+ConclusionsOur results demonstrate an increase in Covid-19 risk among racial and ethnic minorities not completely explained by other risk factors for Covid-19, comorbidities, and sociodemographic characteristics. Further research investigating these disparities are needed to inform public health measures.",public and global health,fuzzy,100,100
 medRxiv,10.1101/2020.06.17.20133959,2020-06-20,https://medrxiv.org/cgi/content/short/2020.06.17.20133959,A downscaling approach to compare COVID-19 count data from databases aggregated at different spatial scales,Andre Python; Andreas Bender; Marta Blangiardo; Janine B Illian; Ying Lin; Baoli Liu; Tim C D Lucas; Siwei Tan; Yingying Wen; Davit Svanidze; Jianwei Yin,University of Oxford; LMU Munich; Imperial College London; Glasgow University; Fuzhou University; Oxford University; University of Oxford; Zhejiang University; Zhejiang University; Goettingen University; Zhejiang University,"As the COVID-19 pandemic continues to threaten various regions around the world, obtaining accurate and reliable COVID-19 data is crucial for governments and local communities aiming at rigorously assessing the extent and magnitude of the virus spread and deploying efficient interventions. Using data reported between January and February 2020 in China, we compared counts of COVID-19 from near-real time spatially disaggregated data (city-level) with fine-spatial scale predictions from a Bayesian downscaling regression model applied to a reference province-level dataset. The results highlight discrepancies in the counts of coronavirus-infected cases at district level and identify districts that may require further investigation.",epidemiology,fuzzy,100,100
 medRxiv,10.1101/2020.06.16.20133116,2020-06-18,https://medrxiv.org/cgi/content/short/2020.06.16.20133116,Mental health during the COVID-19 pandemic in two longitudinal UK population cohorts,Alex Siu Fung Kwong; Rebecca M Pearson; Mark J Adams; Kate Northstone; Kate Tilling; Daniel Smith; Chloe Fawns-Ritchie; Helen Bould; Naomi Warne; Stan Zammit; David J Gunnell; Paul Moran; Nadia Micali; Abraham Reichenberg; Matthew Hickman; Dheeraj Rai; Simon Haworth; Archie Campbell; Drew Altschul; Robin Flaig; Andrew M McIntosh; Deborah A Lawlor; David Porteous; Nicholas J Timpson,University of Bristol; University of Bristol; University of Edinburgh; University of Bristol; University of Bristol; University of Bristol; University of Edinburgh; University of Bristol; University of Bristol; Cardiff University; University of Bristol; University of Bristol; UCL; Mount Sinai; University of Bristol; University of Bristol; University of Bristol; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Bristol; University of Edinburgh; University of Bristol,"BackgroundThe impact of COVID-19 on mental health is unclear. Evidence from longitudinal studies with pre pandemic data are needed to address (1) how mental health has changed from pre-pandemic levels to during the COVID-19 pandemic and (2), whether there are groups at greater risk of poorer mental health during the pandemic?
 
@@ -5326,6 +5290,7 @@ MethodsMultivariate logistic regression analysis performed on age-matched sample
 ResultsHospital cohort: significantly higher prevalence of delirium in the frail sample, with no difference in fever or cough. Community-based cohort :significantly higher prevalence of probable delirium in frailer, older adults, and fatigue and shortness of breath.
 
 ConclusionsThis is the first study demonstrating higher prevalence of delirium as a COVID-19 symptom in older adults with frailty compared to other older adults. This emphasises need for systematic frailty assessment and screening for delirium in acutely ill older patients in hospital and community settings. Clinicians should suspect COVID-19 in frail adults with delirium.",geriatric medicine,fuzzy,94,100
+medRxiv,10.1101/2020.06.13.20130419,2020-06-16,https://medrxiv.org/cgi/content/short/2020.06.13.20130419,Mental health service activity during COVID-19 lockdown: South London and Maudsley data on working age community and home treatment team services and mortality from February to mid-May 2020,Robert Stewart; Evangelia Martin; Matthew Broadbent,King's College London; King's College London; South London and Maudsley NHS Foundation Trust,"The lockdown and social distancing policy response to the COVID-19 pandemic in the UK has a potentially important impact on provision of mental healthcare; however, there has been relatively little quantification of this. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource with 24-hourly updates of electronic mental health records data, this paper describes daily caseloads and contact numbers (face-to-face and virtual) for home treatment teams (HTTs) and working age adult community mental health teams (CMHTs) from 1st February to 15th May 2020 at the South London and Maudsley NHS Trust (SLaM), a large mental health service provider for 1.2m residents in south London. In addition daily deaths are described for all current and previous SLaM service users over this period and the same dates in 2019. In summary, comparing periods before and after 16th March 2020 the CMHT sector showed relatively stable caseloads and total contact numbers, but a substantial shift from face-to-face to virtual contacts, while HTTs showed the same changeover but reductions in caseloads and total contacts (although potentially an activity rise again during May). Number of deaths for the two months between 16th March and 15th May were 2.4-fold higher in 2020 than 2019, with 958 excess deaths.",psychiatry and clinical psychology,fuzzy,100,100
 medRxiv,10.1101/2020.06.12.20129056,2020-06-16,https://medrxiv.org/cgi/content/short/2020.06.12.20129056,Symptom clusters in Covid19: A potential clinical prediction tool from the COVID Symptom study app,Carole H Sudre; Karla Lee; Mary Ni Lochlainn; Thomas Varsavsky; Benjamin Murray; Mark S. Graham; Cristina Menni; Marc Modat; Ruth C.E. Bowyer; Long H Nguyen; David Alden Drew; Amit D Joshi; Wenjie Ma; Chuan Guo Guo; Chun Han Lo; Sajaysurya Ganesh; Abubakar Buwe; Joan Capdevila Pujol; Julien Lavigne du Cadet; Alessia Visconti; Maxim Freydin; Julia S. El Sayed Moustafa; Mario Falchi; Richard Davies; Maria F. Gomez; Tove Fall; M. Jorge Cardoso; Jonathan Wolf; Paul W Franks; Andrew T Chan; Timothy D Spector; Claire J Steves; Sebastien Ourselin,King's College London; Department of Twin Research and Genetic Epidemiology; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Zoe Global Limited; Zoe Global Limited; Zoe Global Limited; Zoe Global Limited; King's College London; King's College London; King's College London; King's College London; Zoe Global Limited; Lund University; Lund University; King's College London; Zoe Global Limited; Lund University; Massachusetts General Hospital; King's College London; King's College London; King's College London,"As no one symptom can predict disease severity or the need for dedicated medical support in COVID-19, we asked if documenting symptom time series over the first few days informs outcome. Unsupervised time series clustering over symptom presentation was performed on data collected from a training dataset of completed cases enlisted early from the COVID Symptom Study Smartphone application, yielding six distinct symptom presentations. Clustering was validated on an independent replication dataset between May 1-May 28th, 2020. Using the first 5 days of symptom logging, the ROC-AUC of need for respiratory support was 78.8%, substantially outperforming personal characteristics alone (ROC-AUC 69.5%). Such an approach could be used to monitor at-risk patients and predict medical resource requirements days before they are required.
 
 One sentence summaryLongitudinal clustering of symptoms can predict the need for respiratory support in severe COVID-19.",health informatics,fuzzy,94,100
@@ -5400,6 +5365,19 @@ ResultsThere were 56,961 excess deaths and 8,986 were non-COVID excess deaths. E
 
 ConclusionsContinuous monitoring of excess mortality trends and further integration of age- and gender-stratified and underlying cause of death data beyond COVID-19 will allow dynamic assessment of the impacts of indirect and direct mortality of the COVID-19 pandemic.",epidemiology,fuzzy,100,100
 medRxiv,10.1101/2020.06.05.20122226,2020-06-07,https://medrxiv.org/cgi/content/short/2020.06.05.20122226,"Different adiposity measures across sex, age, ethnicity, and COVID-19",Naveed Sattar; Frederick K Ho; Jason MR Gill; Nazim Ghouri; Stuart R Gray; Carlos A Celis-Morales; Srinivasa Vittal Katikireddi; Colin Berry; Jill P Pell; John JV McMurray; Paul Welsh,University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University Of Glasgow,"We examined the link between BMI and risk of a positive test for SARS-CoV-2 and risk of COVID-19-related death among UK Biobank participants. Among 4855 participants tested for SARS-CoV-2 in hospital, 839 were positive and of these 189 died from COVID-19. Poisson models with penalised thin plate splines were run relating exposures of interest to test positivity and case-fatality, adjusting for confounding factors. BMI was associated strongly with positive test, and risk of death related to COVID-19. The gradient of risk in relation to BMI was steeper in those under 70, compared with those aged 70 years or older for COVID-19 related death (Pinteraction=0.03). BMI was more strongly related to test positivity (Pinteraction=0.010) and death (Pinteraction=0.002) in non-whites, compared with whites. These data add support for adiposity being more strongly linked to COVID-19-related deaths in younger people and non-white ethnicities. If future studies confirm causality, lifestyle interventions to improve adiposity status may be important to reduce the risk of COVID-19 in all, but perhaps particularly, non-white communities.",epidemiology,fuzzy,100,100
+medRxiv,10.1101/2020.06.02.20120642,2020-06-05,https://medrxiv.org/cgi/content/short/2020.06.02.20120642,Estimating excess visual loss in people with neovascular age-related macular degeneration during the COVID-19 pandemic,Darren S Thomas; Alasdair Warwick; Abraham Olvera-Barrios; Catherine Egan; Roy Schwartz; Sudeshna Patra; Haralabos Eleftheriadis; Anthony P Khawaja; Andrew Lotery; Philipp L Mueller; Robin Hamilton; Ella Preston; Paul Taylor; Adnan Tufail; - UK EMR Users Group,"Institute of Health Informatics, University College London, London, UK; Institute of Cardiovascular Science, University College London, London, UK & Moorfields Eye Hospital NHS Foundation Trust, London, UK.; Moorfields Eye Hospital NHS Turst & Institute of Ophthalmology UCL; Moorfields Eye Hospital NHS Foundation Trust, London, UK & Institute of Ophthalmology, UCL; Moorfields Eye Hospital NHS Foundation Trust, London, UK & Institute of Health Informatics, University College London, London, UK; Bart's Health NHS Trust, London, UK; King's College Hospital NHS Trust, London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK & Institute of Ophthalmology, UCL; Faculty of Medicine, University of Southampton, Southampton, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK & Institute of Ophthalmology, UCL; Moorfields Eye Hospital NHS Foundation Trust, London, UK; Institute of Health Informatics, University College London, London, UK; Moorfields Eye Hospital NHS Trust & Institute of Ophthalmology UCL; ","ObjectivesTo report the reduction in new neovascular age-related macular degeneration (nAMD) referrals during the COVID-19 pandemic and estimate the impact of delayed treatment on visual outcomes at one year.
+
+DesignRetrospective clinical audit and simulation model.
+
+SettingMultiple UK NHS ophthalmology centres.
+
+ParticipantsData on the reduction in new nAMD referrals was obtained from four NHS Trusts in England comparing April 2020 to April 2019. To estimate the potential impact on one-year visual outcomes, a stratified bootstrap simulation model was developed drawing on an electronic medical records dataset of 20,825 nAMD eyes from 27 NHS Trusts.
+
+Main outcome measuresSimulated mean visual acuity and proportions of eyes with vision [&le;]6/60, [&le;]6/24 and [&ge;]6/12 at one year under four hypothetical scenarios: no treatment delay, 3, 6 and 9-month treatment delays. Estimated additional number of eyes with vision [&le;]6/60 at one year nationally.
+
+ResultsThe number of nAMD referrals at four major eye treatment hospital groups based in England dropped on average by 72% (range 65 to 87%) in April 2020 compared to April 2019. Simulated one-year visual outcomes for 1000 nAMD eyes with a 3-month treatment delay suggested an increase in the proportion of eyes with vision [&le;]6/60 from 15.5% (13.2 to 17.9) to 23.3% (20.7 to25.9), and a decrease in the proportion of eyes with vision [&ge;]6/12 (driving vision) from 35.1% (32.1 to 38.1) to 26.4% (23.8 to29.2). Outcomes worsened incrementally with longer modelled delays. Assuming nAMD referrals are reduced to this level at the national level for only one month, these simulated results suggest an additional 186-365 eyes with vision [&le;]6/60 at one-year with even a short treatment delay.
+
+ConclusionsWe report a large decrease in nAMD referrals during the first month of COVID-19 lockdown and provide an important public health message regarding the risk of delayed treatment. As a conservative estimate, a treatment delay of 3 months could lead to a >50% relative increase in the number of eyes with vision [&le;]6/60 and 25% relative decrease in the number of eyes with driving vision at one year.",ophthalmology,fuzzy,100,100
 medRxiv,10.1101/2020.06.02.20118489,2020-06-05,https://medrxiv.org/cgi/content/short/2020.06.02.20118489,Development and implementation of a customised rapid syndromic diagnostic test for severe pneumonia,Vilas Navapurkar; Josefin Bartholdson-Scott; Mailis Maes; Thomas P Hellyer; Ellen Higginson; Sally Forrest; Joana Pereira Dias; Surendra Parmar; Emma Heasman-Hunt; Petra Polgarova; Joanne Brown; Lissamma Titti; William PW Smith; Jonathan Scott; Anthony Rostron; Matthew Routledge; David Sapsford; M. Estee Torok; Ronan McMullan; David Enoch; Vanessa Wong; - VAPrapid investigators; Martin D Curran; Nicholas Brown; A John Simpson; Jurgen Herre; Gordon Dougan; Andrew Conway Morris,"Cambridge University Hospitals NHS Foundation Trust; University of Cambridge; University of Cambridge; Translational and Clinical Research Institute, Newcastle University, United Kingdom; University of Cambridge; University of Cambridge; University of Cambridge; Public Health England Microbiology Laboratory, Addenbrooke's Hospital, Cambridge; Public Health England Microbiology Laboratory, Addenbrooke's Hospital, Cambridge; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; University of Cambridge; Translational and Clinical Research Institute, Newcastle University, United Kingdom; Translational and Clinical Research Institute, Newcastle University, United Kingdom; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS FoundationTrust; Wellcome-Wolfson Institute for Experimental Medicine, Queens University Belfast, United Kingdom; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; ; Public Health England Microbiology Laboratory, Addenbrookes Hospital, Cambridge; Public Health England Microbiology Laboratory, Addenbrooke's Hospital, Cambridge; Translational and Clinical Research Institute, Newcastle University, United Kingdom; Cambridge University Hospitals NHS Foundation Trust; University of Cambridge; University of Cambridge","BackgroundMicrobial cultures for the diagnosis of pneumonia take several days to return a result, and are frequently negative, compromising antimicrobial stewardship. The objective of this study was to establish the performance of a syndromic molecular diagnostic approach, using a custom TaqMan array card (TAC) covering 52 respiratory pathogens, and assess its impact on antimicrobial prescribing.
 
 MethodsThe TAC was validated against a retrospective multi-centre cohort of broncho-alveolar lavage samples. The TAC was assessed prospectively in patients undergoing investigation for suspected pneumonia, with a comparator cohort formed of patients investigated when the TAC laboratory team were unavailable.
@@ -5411,13 +5389,6 @@ Results128 stored samples were tested, with sensitivity of 97% (95% CI 88-100%).
 ConclusionsImplementation of a syndromic molecular diagnostic approach to pneumonia led to faster results, with high sensitivity and impact on antibiotic prescribing.
 
 Trial registrationThe prospective study was registered with clinicaltrials.gov NCT03996330",intensive care and critical care medicine,fuzzy,100,100
-medRxiv,10.1101/2020.06.04.20121434,2020-06-05,https://medrxiv.org/cgi/content/short/2020.06.04.20121434,The impact of school reopening on the spread of COVID-19 in England,Matt J Keeling; Michael J Tildesley; Benjamin D Atkins; Bridget Penman; Emma Southall; Glen Guyver-Fletcher; Alex Holmes; Hector McKimm; Erin E Gorsich; Edward M Hill; Louise Dyson,University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick,"By mid-May, cases of COVID-19 in the UK had been declining for over a month; a multi-phase emergence from lockdown was planned, including a scheduled partial reopening of schools on 1st June. Although evidence suggests that children generally display mild symptoms, the size of the school-age population means the total impact of reopening schools is unclear. Here, we present work from mid-May that focused on the imminent opening of schools and consider what these results imply for future policy.
-
-We compared eight strategies for reopening primary and secondary schools in England. Modifying a transmission model fitted to UK SARS-CoV-2 data, we assessed how reopening schools affects contact patterns, anticipated secondary infections and the relative change in the reproduction number, R. We determined the associated public health impact and its sensitivity to changes in social-distancing within the wider community.
-
-We predicted reopening schools with half-sized classes or focused on younger children was unlikely to push R above one. Older children generally have more social contacts, so reopening secondary schools results in more cases than reopening primary schools, while reopening both could have pushed R above one in some regions. Reductions in community social-distancing were found to outweigh and exacerbate any impacts of reopening. In particular, opening schools when the reproduction number R is already above one generates the largest increase in cases.
-
-Our work indicates that while any school reopening will result in increased mixing and infection amongst children and the wider population, reopening schools alone in June was unlikely to push R above one. Ultimately, reopening decisions are a difficult trade-off between epidemiological consequences and the emotional, educational and developmental needs of children. Into the future, there are difficult questions about what controls can be instigated such that schools can remain open if cases increase.",infectious diseases,fuzzy,100,100
 medRxiv,10.1101/2020.06.04.20122069,2020-06-05,https://medrxiv.org/cgi/content/short/2020.06.04.20122069,Mechanical ventilation utilization in COVID-19: A systematic review and meta-analysis,Mohammed A Almeshari; Nowaf Y Alobaidi; Mansour Al Asmri; Eyas Alhuthail; Ziyad Alshehri; Farhan Alenezi; Elizabeth Sapey; Dhruv Parekh,University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Taibah University; King Saud bin Abdulaziz University for Health Sciences; University of Birmingham; University of Birmingham,"BackgroundIn December 2019, SARS-CoV-2 caused a global pandemic with a viral infection called COVID-19. The disease usually causes respiratory symptoms but in a small proportion of patients can lead to a pneumonitis, Adult Respiratory Distress Syndrome and death. Invasive Mechanical Ventilation (IMV) is considered a life-saving treatment for COVID-19 patients and a huge demand for IMV devices was reported globally. This review aims to provide insight on the initial IMV practises for COVID-19 patients in the initial phase of the pandemic.
 
 MethodsElectronic databases (Embase and MEDLINE) were searched for applicable articles using relevant keywords. The references of included articles were hand searched. Articles that reported the use of IMV in adult COVID-19 patients were included in the review. The NIH quality assessment tool for cohort and cross-sectional studies was used to appraise studies.
@@ -5566,6 +5537,17 @@ FindingsWe screened 270 studies and included 6. The pooled estimate for the asym
 InterpretationThe asymptomatic proportion of SARS-CoV-2 infections is relatively low when estimated from methodologically-appropriate studies. Further investigation into the degree and duration of infectiousness for asymptomatic infections is warranted.
 
 FundingMedical Research Council",infectious diseases,fuzzy,100,100
+medRxiv,10.1101/2020.05.18.20086157,2020-05-22,https://medrxiv.org/cgi/content/short/2020.05.18.20086157,COVID-19 in Great Britain: epidemiological and clinical characteristics of the first few hundred (FF100) cases: a descriptive case series and case control analysis,Nicola L Boddington; Andre Charlett; Suzanne Elgohari; Jemma L Walker; Helen Mcdonald; Chloe Byers; Laura Coughlan; Tatiana Garcia Vilaplana; Rosie Whillock; Mary Sinnathamby; Nikolaos Panagiotopoulos; Louise Letley; Pauline MacDonald; Roberto Vivancos; Obaghe Edeghere; Joseph Shingleton; Emma Bennett; Daniel J Grint; Helen Strongman; Kathryn E Mansfield; Christopher Rentsch; Caroline Minassian; Ian J Douglas; Rohini Mathur; Maria Peppa; Simon Cottrell; Jim McMenamin; Maria Zambon; Mary Ramsay; Gavin Dabrera; Vanessa Saliba; Jamie Lopez Bernal,Public Health England; Public Health England; Public Health England; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Public Health Wales; Public Health Scotland; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England,"ObjectivesFollowing detection of the first virologically-confirmed cases of COVID-19 in Great Britain, an enhanced surveillance study was initiated by Public Health England to describe the clinical presentation, course of disease and underlying health conditions associated with infection of the first few hundred cases.
+
+MethodsInformation was collected on the first COVID-19 cases according to the First Few X WHO protocol. Case-control analyses of the sensitivity, specificity and predictive value of symptoms and underlying health conditions associated with infection were conducted. Point prevalences of underlying health conditions among the UK general population were presented.
+
+FindingsThe majority of FF100 cases were imported (51.4%), of which the majority had recent travel to Italy (71.4%). 24.7% were secondary cases acquired mainly through household contact (40.4%). Children had lower odds of COVID-19 infection compared with the general population.
+
+The clinical presentation of cases was dominated by cough, fever and fatigue. Non-linear relationships with age were observed for fever, and sensitivity and specificity of symptoms varied by age.
+
+Conditions associated with higher odds of COVID-19 infection (after adjusting for age and sex) were chronic heart disease, immunosuppression and multimorbidity.
+
+ConclusionThis study presents the first epidemiological and clinical summary of COVID-19 cases in Great Britain. The FFX study design enabled systematic data collection. The study characterized underlying health conditions associated with infection and set relative risks in context with population prevalence estimates. It also provides important evidence for generating case definitions to support public health risk assessment, clinical triage and diagnostic algorithms.",epidemiology,fuzzy,100,100
 medRxiv,10.1101/2020.05.18.20105288,2020-05-21,https://medrxiv.org/cgi/content/short/2020.05.18.20105288,Current tobacco smoking and risk from COVID-19: results from a population symptom app in over 2.4 million people,Nicholas S Hopkinson; Niccolo Rossi; Julia El-Sayed Moustafa; Anthony A Laverty; Jennifer K Quint; Maxim B Freydin; Alessia Visconti; Benjamin Murray; Marc Modat; Sebastien Ourselin; Kerrin Small; Richard Davies; Jonathan Wolf; Timothy Spector; Claire J Steves; Mario Falchi,"Imperial College London; King's College London; King's College London; Imperial College London; Imperial College, London; King's College London; King's College, London; King's College, London; King's College, London; King's College, London; King's College, London; Zoe Global Ltd; Zoe Global Ltd; King's College London; King's College London; King's College, London","BackgroundThe association between current tobacco smoking, the risk of developing COVID-19 and the severity of illness is an important information gap.
 
 MethodsUK users of the COVID Symptom Study app provided baseline data including demographics, anthropometrics, smoking status and medical conditions, were asked to log symptoms daily from 24th March 2020 to 23rd April 2020. Participants reporting that they did not feel physically normal were taken through a series of questions, including 14 potential COVID-19 symptoms and any hospital attendance. The main study outcome was the association between current smoking and the development of ""classic"" symptoms of COVID-19 during the pandemic defined as fever, new persistent cough and breathlessness. The number of concurrent COVID-19 symptoms was used as a proxy for severity. In addition, association of subcutaneous adipose tissue expression of ACE2, both the receptor for SARS-CoV-2 and a potential mediator of disease severity, with smoking status was assessed in a subset of 541 twins from the TwinsUK cohort.
@@ -5822,11 +5804,6 @@ Research in contextO_ST_ABSEvidence before this studyC_ST_ABSSeveral prognostic
 Added value of this studyThis study used data from Wuhan, China to derive and internally validate multivariable models to predict poor outcome and death in COVID-19 patients after hospital admission, with external validation using data from Kings College Hospital, London, UK. Mortality and poor outcome occurred in 4.3% and 9.7% of patients in Wuhan, compared to 34.1% and 42.9% of patients in London. Models based on age, sex and simple routinely available laboratory tests (lymphocyte count, neutrophil count, platelet count, CRP and creatinine) had good discrimination and calibration in internal validation, but performed only moderately well in external validation. Models based on age, sex, symptoms and comorbidity were adequate in internal validation for poor outcome (ICU admission or death) but had poor performance for death alone.
 
 Implications of all the available evidenceThis study and others find that relatively simple risk prediction models using demographic, clinical and laboratory data perform well in internal validation but at best moderately in external validation, either because derivation and external validation populations are small (Xie et al3) and/or because they vary greatly in casemix and severity (our study). There are three decision points where risk prediction may be most useful: (1) deciding who to test; (2) deciding which patients in the community are at high-risk of poor outcomes; and (3) identifying patients at high-risk at the point of hospital admission. Larger studies focusing on particular decision points, with rapid external validation in multiple datasets are needed. A key gap is risk prediction tools for use in community triage (decisions to admit, or to keep at home with varying intensities of follow-up including telemonitoring) or in low income settings where laboratory tests may not be routinely available at the point of decision-making. This requires systematic data collection in community and low-income settings to derive and evaluate appropriate models.",public and global health,fuzzy,100,100
-medRxiv,10.1101/2020.04.27.20081810,2020-05-03,https://medrxiv.org/cgi/content/short/2020.04.27.20081810,Clinical classifiers of COVID-19 infection from novel ultra-high-throughput proteomics,Christoph B. Messner; Vadim Demichev; Daniel Wendisch; Laura Michalick; Matthew White; Anja Freiwald; Kathrin Textoris-Taube; Spyros I. Vernardis; Anna-Sophia Egger; Marco Kreidl; Daniela Ludwig; Christiane Kilian; Federica Agostini; Aleksej Zelezniak; Charlotte Thibeault; Moritz Pfeiffer; Stefan Hippenstiel; Andreas Hocke; Christof von Kalle; Archie Campbell; Caroline Hayward; David J. Porteous; Riccardo E. Marioni; Claudia Langenberg; Kathryn S. Lilley; Wolfgang M. Kuebler; Michael Muelleder; Christian Drosten; Martin Witzenrath; Florian Kurth; Leif Erik Sander; Markus Ralser,"The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, United Kingdom; The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, United Kingdom; Charite Universitaetsmedizin, Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; Charite Universitaetsmedizin, Institute of Physiology, 10117 Berlin, Germany; The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, United Kingdom; Charite Universitaetsmedizin, Core Facility - High Throughput Mass Spectrometry, 10117 Berlin, German; Charite Universitaetsmedizin, Core Facility - High Throughput Mass Spectrometry, 10117 Berlin, Germany; The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, United Kingdom; The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, United Kingdom; The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, United Kingdom; Charite Universitaetsmedizin, Department of Biochemistry, 10117 Berlin, Germany; Charite Universitaetsmedizin, Department of Biochemistry, 10117 Berlin, Germany; Charite Universitaetsmedizin, Department of Biochemistry, 10117 Berlin, Germany; Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden; Charite Universitaetsmedizin, Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; Charite Universitaetsmedizin, Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; Charite Universitaetsmedizin, Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; Charite Universitaetsmedizin, Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; Berlin Institute of Health (BIH), and  Charite Universitaetsmedizin, Clinical Study Center (CSC), 10117 Berlin, Germany; Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh United Kingdom and Usher Institute, Universi; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom; Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh EH4 2XU, United Kingdom; Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh EH4 2XU, United Kingdom; MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, United Kingdom; Department of Biochemistry, The University of Cambridge, Cambridge, CB21GA, United Kingdom; Charite Universitaetsmedizin, Berlin, Institute of Physiology, 10117 Berlin, Germany; Charite Universitaetsmedizin, Core Facility - High Throughput Mass Spectrometry, 10117 Berlin, Germany; Charite Universitaetsmedizin, Berlin, Department of Virology, 10117 Berlin, Germany; Charite Universitaetsmedizin, Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; Charite Universitaetsmedizin, Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany and Department of Tropical Medicine, Bernhard; Charite Universitaetsmedizin, Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; Charite Universitaetsmedizin, Berlin, Department of Biochemistry, 10117 Berlin, and The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, Lon","The COVID-19 pandemic is an unprecedented global challenge. Highly variable in its presentation, spread and clinical outcome, novel point-of-care diagnostic classifiers are urgently required. Here, we describe a set of COVID-19 clinical classifiers discovered using a newly designed low-cost high-throughput mass spectrometry-based platform. Introducing a new sample preparation pipeline coupled with short-gradient high-flow liquid chromatography and mass spectrometry, our methodology facilitates clinical implementation and increases sample throughput and quantification precision. Providing a rapid assessment of serum or plasma samples at scale, we report 27 biomarkers that distinguish mild and severe forms of COVID-19, of which some may have potential as therapeutic targets. These proteins highlight the role of complement factors, the coagulation system, inflammation modulators as well as pro-inflammatory signalling upstream and downstream of Interleukin 6. Application of novel methodologies hence transforms proteomics from a research tool into a rapid-response, clinically actionable technology adaptable to infectious outbreaks.
-
-Highlights- A completely redesigned clinical proteomics platform increases throughput and precision while reducing costs.
-- 27 biomarkers are differentially expressed between WHO severity grades for COVID-19.
-- The study highlights potential therapeutic targets that include complement factors, the coagulation system, inflammation modulators as well as pro-inflammatory signalling both upstream and downstream of interleukin 6.",infectious diseases,fuzzy,100,100
 medRxiv,10.1101/2020.04.27.20081711,2020-05-03,https://medrxiv.org/cgi/content/short/2020.04.27.20081711,Response strategies for COVID-19 epidemics in African settings: a mathematical modelling study,Kevin van Zandvoort; Christopher I Jarvis; Carl Pearson; Nicholas G Davies; CMMID COVID-19 working group; Timothy W Russell; Adam J Kucharski; Mark J Jit; Stefan Flasche; Rosalind M Eggo; Francesco Checchi,London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; ; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; LSHTM; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine,"BackgroundThe health impact of COVID-19 may differ in African settings as compared to countries in Europe or China due to demographic, epidemiological, environmental and socio-economic factors. We evaluated strategies to reduce SARS-CoV-2 burden in African countries, so as to support decisions that balance minimising mortality, protecting health services and safeguarding livelihoods.
 
 MethodsWe used a Susceptible-Exposed-Infectious-Recovered mathematical model, stratified by age, to predict the evolution of COVID-19 epidemics in three countries representing a range of age distributions in Africa (from oldest to youngest average age: Mauritius, Nigeria and Niger), under various effectiveness assumptions for combinations of different non-pharmaceutical interventions: self-isolation of symptomatic people, physical distancing, and  shielding (physical isolation) of the high-risk population. We adapted model parameters to better represent uncertainty about what might be expected in African populations, in particular by shifting the distribution of severity risk towards younger ages and increasing the case-fatality ratio.
@@ -5914,6 +5891,13 @@ Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSIn late 2019, sever
 Added value of this studyHere we use publicly-available mobility data and a stochastic branching process model to evaluate the efficacy of the cordon sanitaire to limiting the spread of COVID-19 from Wuhan to other cities in mainland China, while accounting for underreporting and uncertainty. We find that although travel restrictions led to a significant decrease in the number of individuals leaving Wuhan during the busy post-Lunar New Year holiday travel period, local transmission was likely already established in major cities. Thus, the travel restrictions likely did not affect the epidemic trajectory substantially in these cities.
 
 Implications of all the available evidenceA cordon sanitaire around the epicentre alone may not be able to reduce COVID-19 incidence when implemented after local transmission has occurred in highly connected neighbors. Local non-pharmaceutical interventions to reduce transmissibility (e.g., school and workplace closures) may have contributed more to the observed decrease in incidence in mainland China.",epidemiology,fuzzy,100,100
+medRxiv,10.1101/2020.04.15.20066407,2020-04-20,https://medrxiv.org/cgi/content/short/2020.04.15.20066407,Evaluation of antibody testing for SARS-Cov-2 using ELISA and lateral flow immunoassays,Emily R Adams; Mark Ainsworth; Rekha Anand; Monique I Andersson; Kathryn Auckland; J Kenneth Baillie; Eleanor Barnes; Sally Beer; John Bell; Tamsin Berry; Sagida Bibi; Miles Carroll; Senthil Chinnakannan; Elizabeth Clutterbuck; Richard J Cornall; Derrick W Crook; Thushan De Silva; Wanwisa Dejnirattisai; Kate E Dingle; Christina Dold; Alexis Espinosa; David W Eyre; Helen Farmer; Maria Fernandez Mendoza; Dominique Georgiou; Sarah J Hoosdally; Alistair Hunter; Katie Jeffrey; Paul Klenerman; Julian Knight; Clarice Knowles; Andrew J Kwok; Ullrich Leuschner; Robert Levin; Chang Liu; Cesar Lopez-Camacho; Jose Carlos Martinez Garrido; Philippa C Matthews; Hannah McGivern; Alexander J Mentzer; Jonathan Milton; Juthathip Mongkolsapaya; Shona C Moore; Marta S Oliveira; Fiona Pereira; Elena Perez Lopez; Timothy Peto; Rutger J Ploeg; Andrew Pollard; Tessa Prince; David J Roberts; Justine K Rudkin; Veronica Sanchez; Gavin R Screaton; Malcolm G Semple; Donal T Skelly; Jose Slon-Campos; Elliot Nathan Smith; Alberto Jose Sobrino Diaz; Julie Staves; David Stuart; Piyada Supasa; Tomas Surik; Hannah Thraves; Pat Tsang; Lance Turtle; A Sarah Walker; Beibei Wang; Charlotte Washington; Nicholas Watkins; James Whitehouse,"Liverpool School of Tropical Medicine; Oxford University Hospitals NHS Foundation Trust; NHSBT Birmingham,; Department of Microbiology, Oxford University Hospital NHS Foundation Trust; The Wellcome Centre for Human Genetics, University of Oxford; Roslin Institute, University of Edinburgh; Nuffield Department of Medicine, University of Oxford; Oxford University Hospitals NHS Foundation Trust; Department of Medicine, University of Oxford; Department of Health and Social Care, University of Oxford; Oxford Vaccine group, Department of Pediatrics, University of Oxford; Nuffield Department of Medicine, Centre of Tropical Medicine and Global Health and Public Health England; Nuffield Department of Medicine, University of Oxford; Oxford Vaccine Group, Department of Paediatrics, University of Oxford; Nuffield Department of Medicine, University of Oxford; NIHR Oxford Biomedical Research Centre; Department of Infection, Immunity and Cardiovascular, Disease, The Medical School, University of Sheffield; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford; NIHR Oxford Biomedical Research Centre, University of Oxford; Oxford Vaccine Group, Department of Paediatrics, University of Oxford; Oxford University Hospitals NHS Foundation Trust; Big Data Institute, University of Oxford; Department of Health and Social Care, University of Oxford; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Nuffield Department of Medicine, University of Oxford; NHSBT Basildon; Department of Clinical Medicine, Oxford University Hospitals NHS Foundation Trusts; Nuffield Department so Medicine, University of Oxford; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford; Department of Health and Social Care, University of Oxford; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford; NHSBT Oxford; Worthing Hospital, Worthing, West Sussex; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford; Wellcome Centre of Genetics, Nuffield Department of Medicine, University of Oxford; Oxford University Hospitals NHS Foundation Trust; Nuffield Department of Medicine, University of Medicine; Nuffield Department of Surgical Sciences, University of Oxford and UK QUOD Consortium; Wellcome Centre for Human Genetics, University of Oxford; Nuffield Department of Surgical Sciences, University of Oxford and UK QUOD Consortium; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford; NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, University of Liverpool; Nuffield Department of Surgical Sciences,  University of Oxford and UK QUOD Consortium; Imperial College London; Oxford University Hospitals NHS Foundation Trust; NIHR Oxford Biomedical Research centre, University of Oxford; Nuffield Department of Surgical Sciences, University of Oxford and UK QUOD Consortium; Department of Paediatrics, University of Oxford; NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, University of Liverpool; NHSBT Oxford; Nuffield Department of Population Health & Big Data Institute, University of Oxford; Oxford University Hospitals NHS Foundation Trust; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford; Health Protection Unit In Emerging and Zoonotic Infection, University of Liverpool; Nuffield Department of Clinical Neurosciences, University of Oxford; University of Oxford; Department of Health and Social Care, University of Oxford; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals,; Wellcome Centre for Human Genetics, Nuffield Department of Medicine; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford; Nuffield Department of Surgical Sciences, University of Oxford and UK QUOD Consortium; Oxford University Hospitals NHS Foundation Trust; NHSBT Oxford; NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, University of Liverpool; Nuffield Department of Medicine, University of Oxford; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford; NHSBT, Birmingham; NHSBT, Cambridge; Department of Health and Social Care, University of Oxford","BackgroundThe COVID-19 pandemic caused >1 million infections during January-March 2020. There is an urgent need for reliable antibody detection approaches to support diagnosis, vaccine development, safe release of individuals from quarantine, and population lock-down exit strategies. We set out to evaluate the performance of ELISA and lateral flow immunoassay (LFIA) devices.
+
+MethodsWe tested plasma for COVID (SARS-CoV-2) IgM and IgG antibodies by ELISA and using nine different LFIA devices. We used a panel of plasma samples from individuals who have had confirmed COVID infection based on a PCR result (n=40), and pre-pandemic negative control samples banked in the UK prior to December-2019 (n=142).
+
+ResultsELISA detected IgM or IgG in 34/40 individuals with a confirmed history of COVID infection (sensitivity 85%, 95%CI 70-94%), vs. 0/50 pre-pandemic controls (specificity 100% [95%CI 93-100%]). IgG levels were detected in 31/31 COVID-positive individuals tested [&ge;]10 days after symptom onset (sensitivity 100%, 95%CI 89-100%). IgG titres rose during the 3 weeks post symptom onset and began to fall by 8 weeks, but remained above the detection threshold. Point estimates for the sensitivity of LFIA devices ranged from 55-70% versus RT-PCR and 65-85% versus ELISA, with specificity 95-100% and 93-100% respectively. Within the limits of the study size, the performance of most LFIA devices was similar.
+
+ConclusionsCurrently available commercial LFIA devices do not perform sufficiently well for individual patient applications. However, ELISA can be calibrated to be specific for detecting and quantifying SARS-CoV-2 IgM and IgG and is highly sensitive for IgG from 10 days following first symptoms.",infectious diseases,fuzzy,100,100
 medRxiv,10.1101/2020.04.14.20065417,2020-04-17,https://medrxiv.org/cgi/content/short/2020.04.14.20065417,Clinical academic research in the time of Corona: a simulation study in England and a call for action,Amitava Banerjee; Michail Katsoulis; Alvina G Lai; Laura Pasea; Thomas A Treibel; Charlotte Manisty; Spiros Denaxas; Giovanni Quarta; Harry Hemingway; Joao Cavalcante; Mahdad Nousardeghi; James C Moon,"University College London; University College London; University College London; University College London; University College London; University College London; University College London; Ospedale Papa Giovanni XXIII, Bergamo, Italy; University College London; Minneapolis Heart Institute, Minneapolis, Minnesota. USA; University College London; University College London","BackgroundCoronavirus (COVID-19) poses health system challenges in every country. As with any public health emergency, a major component of the global response is timely, effective science. However, particular factors specific to COVID-19 must be overcome to ensure that research efforts are optimised. We aimed to model the impact of COVID-19 on the clinical academic response in the UK, and to provide recommendations for COVID-related research.
 
 MethodsWe constructed a simple stochastic model to determine clinical academic capacity in the UK in four policy approaches to COVID-19 with differing population infection rates: ""Italy model"" (6%), ""mitigation"" (10%), ""relaxed mitigation"" (40%) and ""do-nothing"" (80%) scenarios. The ability to conduct research in the COVID-19 climate is affected by the following key factors: (i) infection growth rate and population infection rate (from UK COVID-19 statistics and WHO); (ii) strain on the healthcare system (from published model); and (iii) availability of clinical academic staff with appropriate skillsets affected by frontline clinical activity and sickness (from UK statistics).
@@ -6020,13 +6004,6 @@ RESULTSWe included 15 randomised trials investigating the effect of masks (14 tr
 
 CONCLUSIONSMost included trials had poor design, reporting and sparse events. There was insufficient evidence to provide a recommendation on the use of facial barriers without other measures. We found insufficient evidence for a difference between surgical masks and N95 respirators and limited evidence to support effectiveness of quarantine. Based on observational evidence from the previous SARS epidemic included in the previous version of our Cochrane review we recommend the use of masks combined with other measures.",public and global health,fuzzy,100,100
 medRxiv,10.1101/2020.03.24.20043018,2020-03-27,https://medrxiv.org/cgi/content/short/2020.03.24.20043018,Age-dependent effects in the transmission and control of COVID-19 epidemics,Nicholas G Davies; Petra Klepac; Yang Liu; Kiesha Prem; Mark Jit; CMMID COVID-19 working group; Rosalind M Eggo,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; ; London School of Hygiene and Tropical Medicine,"The COVID-19 pandemic has shown a markedly low proportion of cases among children. Age disparities in observed cases could be explained by children having lower susceptibility to infection, lower propensity to show clinical symptoms, or both. We evaluate these possibilities by fitting an age-structured mathematical model to epidemic data from six countries. We estimate that clinical symptoms occur in 25% (95% CrI: 19-32%) of infections in 10-19-year-olds, rising to 76% (68-82%) in over-70s, and that susceptibility to infection in under-20s is approximately half that of older adults. Accordingly, we find that interventions aimed at children may have a relatively small impact on total cases, particularly if the transmissibility of subclinical infections is low. The age-specific clinical fraction and susceptibility we have estimated has implications for the expected global burden of COVID-19 because of demographic differences across settings: in younger populations, the expected clinical attack rate would be lower, although it is likely that comorbidities in low-income countries will affect disease severity. Without effective control measures, regions with older populations may see disproportionally more clinical cases, particularly in the later stages of the pandemic.",epidemiology,fuzzy,100,100
-medRxiv,10.1101/2020.03.22.20040287,2020-03-24,https://medrxiv.org/cgi/content/short/2020.03.22.20040287,Estimating excess 1- year mortality from COVID-19 according to underlying conditions and age in England: a rapid analysis using NHS health records in 3.8 million adults,Amitava Banerjee; Laura Pasea; Steve Harris; Arturo Gonzalez-Izquierdo; Ana Torralbo; Laura Shallcross; Mahdad Noursadeghi; Deenan Pillay; Christina Pagel; Wai Keong Wong; Claudia Langenberg; Bryan Williams; Spiros Denaxas; Harry Hemingway,University College London; University College London; University College London Hospitals NHS Trust; University College London; University College London; UCL; University College London; University College London; University College London; University College London Hospitals NHS Trust; University of Cambridge; University College London; University College London; University College London,"BackgroundThe medical, health service, societal and economic impact of the COVID-19 emergency has unknown effects on overall population mortality. Previous models of population mortality are based on death over days among infected people, nearly all of whom (to date at least) have underlying conditions. Models have not incorporated information on high risk conditions or their longer term background (pre-COVID-19) mortality. We estimated the excess number of deaths over 1 year under different COVID-19 incidence rates and differing mortality impacts.
-
-MethodsUsing population based linked primary and secondary care electronic health records in England (HDR UK - CALIBER), we report the prevalence of underlying conditions defined by UK Public Health England COVID-19 guidelines (16 March 2020) in 3,862,012 individuals aged [&ge;]30 years from 1997-2017. We used previously validated phenotypes, openly available (https://caliberresearch.org/portal), for each condition using ICD-10 diagnosis, Read, procedure and medication codes. We estimated the 1-year mortality in each condition, and developed simple models of excess COVID-19-related deaths assuming relative risk (RR) of the impact of the emergency (compared to background mortality) of 1.2, 1.5 and 2.0.
-
-Findings20.0% of the population are at risk according to current PHE guidelines, of which; 13.7% were age>70 years and 6.3% aged [&le;]70 years with [&ge;]1 underlying condition (cardiovascular disease (2.3%), diabetes (2.2%), steroid therapy (1.9%), severe obesity (0.9%), chronic kidney disease (0.6%) and chronic obstructive pulmonary disease, COPD (0.5%). Multimorbidity (co-occurrence of [&ge;]2 conditions in an individual) was common (10.1%). The 1-year mortality in the at-risk population was 4.46%, and age and underlying conditions combine to influence background risk, varying markedly across conditions (5.9% in age>70 years, 8.6% for COPD and 13.1% in those with [&ge;]3 or more conditions). In a suppression scenario (at SARS CoV2 rates of 0.001% of the UK population), there would be minimal excess deaths (3 and 7 excess deaths at relative risk, RR, 1.5 and 2.0 respectively). At SARS CoV2 rates of 10% of the UK population (mitigation) the model estimates the numbers of excess deaths as: 13791, 34479 and 68957 (at RR 1.2, 1.5 and 2.0 respectively). At SARS CoV2 rates of 80% in the UK population (""do-nothing""), the model estimates the number of excess deaths as 110332, 275,830 and 551,659 (at RR 1.2, 1.5 and 2.0) respectively.
-
-InterpretationWe provide the public, researchers and policy makers a simple model to estimate the excess mortality over 1 year from COVID-19, based on underlying conditions at different ages. If the relative mortality impact of COVID-19 were to be about 20% (similar magnitude as the established winter vs summer mortality excess), then the excess deaths would be 0 when 1 in 100 000 (suppression), 13791 when 1 in 10 (mitigation) and 110332 when 8 in 10 are infected (""do nothing"") scenario. However, the relative impact of COVID-19 is unknown. If the emergency were to double the mortality risk, then we estimate 7, 68957 and 551,659 excess deaths in the same scenarios. These results may inform the need for more stringent suppression measures as well as efforts to target those at highest risk for a range of preventive interventions.",public and global health,fuzzy,100,100
 medRxiv,10.1101/2020.03.20.20039537,2020-03-23,https://medrxiv.org/cgi/content/short/2020.03.20.20039537,The Population Attributable Fraction (PAF) of cases due to gatherings and groups with relevance to COVID-19 mitigation strategies,Ellen Brooks-Pollock; Jonathan M Read; Thomas House; Graham Medley; Matt J Keeling; Leon Danon,University of Bristol; Lancaster University; University of Manchester; London School of Hygiene and Tropical Medicine; University of Warwick; University of Exeter,"BackgroundMany countries have banned groups and gatherings as part of their response to the pandemic caused by the coronavirus, SARS-CoV-2. Although there are outbreak reports involving mass gatherings, the contribution to overall transmission is unknown.
 
 MethodsWe used data from a survey of social contact behaviour that specifically asked about contact with groups to estimate the Population Attributable Fraction (PAF) due to groups as the relative change in the Basic Reproduction Number when groups are prevented.
@@ -6048,7 +6025,6 @@ medRxiv,10.1101/2020.03.05.20031773,2020-03-08,https://medrxiv.org/cgi/content/s
 
 AimTo estimate the infection and case fatality ratio of COVID-19, using data from passengers of the Diamond Princess cruise ship while correcting for delays between confirmation-and-death, and age-structure of the population.",epidemiology,fuzzy,100,100
 medRxiv,10.1101/2020.02.26.20028167,2020-02-27,https://medrxiv.org/cgi/content/short/2020.02.26.20028167,Estimation of country-level basic reproductive ratios for novel Coronavirus (COVID-19) using synthetic contact matrices,Joe Hilton; Matt J Keeling,University of Warwick; University of Warwick,"The outbreak of novel coronavirus (COVID-19) has the potential for global spread, infecting large numbers in all countries. In this case, estimating the country-specific basic reproductive ratio is a vital first step in public-health planning. The basic reproductive ratio (R0) is determined by both the nature of pathogen and the network of contacts through which the disease can spread - with this network determined by socio-demographics including age-structure and household composition. Here we focus on the age-structured transmission within the population, using data from China to inform age-dependent susceptibility and synthetic age-mixing matrices to inform the contact network. This allows us to determine the country-specific basic reproductive ratio as a multiplicative scaling of the value from China. We predict that R0 will be highest across Eastern Europe and Japan, and lowest across Africa, Central America and South-Western Asia. This pattern is largely driven by the ratio of children to older adults in each country and the observed propensity of clinical cases in the elderly.",epidemiology,fuzzy,100,100
-medRxiv,10.1101/2020.02.14.20023036,2020-02-17,https://medrxiv.org/cgi/content/short/2020.02.14.20023036,The Efficacy of Contact Tracing for the Containment of the 2019 Novel Coronavirus (COVID-19).,Matt J Keeling; T. Deirdre Hollingsworth; Jonathan M Read,University of Warwick; Oxford University; Lancaster University,"Contact tracing is a central public health response to infectious disease outbreaks, especially in the early stages of an outbreak when specific treatments are limited. Importation of novel Coronavirus (COVID-19) from China and elsewhere into the United Kingdom highlights the need to understand the impact of contact tracing as a control measure. Using detailed survey information on social encounters coupled to predictive models, we investigate the likely efficacy of the current UK definition of a close contact (within 2 meters for 15 minutes or more) and the distribution of secondary cases that may go untraced. Taking recent estimates for COVID-19 transmission, we show that less than 1 in 5 cases will generate any subsequent untraced cases, although this comes at a high logistical burden with an average of 36.1 individuals (95th percentiles 0-182) traced per case. Changes to the definition of a close contact can reduce this burden, but with increased risk of untraced cases; we estimate that any definition where close contact requires more than 4 hours of contact is likely to lead to uncontrolled spread.",public and global health,fuzzy,100,100
 medRxiv,10.1101/2020.02.12.20022566,2020-02-14,https://medrxiv.org/cgi/content/short/2020.02.12.20022566,A spatial model of CoVID-19 transmission in England and Wales: early spread and peak timing,Leon Danon; Ellen Brooks-Pollock; Mick Bailey; Matt J Keeling,University of Exeter; University of Bristol; University of Bristol; University of Warwick,"BackgroundAn outbreak of a novel coronavirus, named CoVID-19, was first reported in China on 31 December 2019. As of 9 February 2020, cases have been reported in 25 countries, including probable cases of human-to-human transmission in England.
 
 MethodsWe adapted an existing national-scale metapopulation model to capture the spread of CoVID-19 in England and Wales. We used 2011 census data to capture population sizes and population movement, together with parameter estimates from the current outbreak in China.
diff --git a/data/covid/preprints.exact.csv b/data/covid/preprints.exact.csv
index 8b897c93..b787e9ef 100644
--- a/data/covid/preprints.exact.csv
+++ b/data/covid/preprints.exact.csv
@@ -501,37 +501,9 @@ MethodsParticipants (n=1,154) who had received the first dose of a COVID-19 vacc
 Results457/1,154 (39.60%) participants reported non-household contacts post-vaccination compared with 371/1,154 (32.15%) participants pre-vaccination. 100/1,154 (8.67%) participants reported use of non-essential shops or services post-vaccination compared with 74/1,154 (6.41%) participants pre-vaccination. Post-vaccination status was associated with increased odds of reporting non-household contacts (OR 1.65, 95% CI 1.31-2.06, p<0.001) and use of non-essential shops or services (OR 1.50, 95% CI 1.03-2.17, p=0.032). This effect varied between men and women and different age groups.
 
 ConclusionParticipants had higher odds of reporting non-household contacts and use of non-essential shops or services within 14 days of their first COVID-19 vaccine compared to pre-vaccination. Public health emphasis on maintaining protective behaviours during this post-vaccination time period when individuals have yet to develop full protection from vaccination could reduce risk of SARS-CoV-2 infection.",public and global health,exact,100,100
-medRxiv,10.1101/2022.08.13.22278733,2022-08-16,https://medrxiv.org/cgi/content/short/2022.08.13.22278733,QCovid 4 - Predicting risk of death or hospitalisation from COVID-19 in adults testing positive for SARS-CoV-2 infection during the Omicron wave in England,Julia Hippisley-Cox; Kamlesh Khunti; Aziz Sheikh; Jonathan Nguyen-Van-Tam; Carol Coupland,University of Oxford; University of Leicester; University of Edinburgh; University of Nottingham; University of Oxford,"ObjectivesTo (a) derive and validate risk prediction algorithms (QCovid4) to estimate risk of COVID-19 mortality and hospitalisation in UK adults with a SARS-CoV-2 positive test during the  Omicron pandemic wave in England and (b) evaluate performance with earlier versions of algorithms developed in previous pandemic waves and the high-risk cohort identified by NHS Digital in England.
+medRxiv,10.1101/2022.08.17.22278893,2022-08-18,https://medrxiv.org/cgi/content/short/2022.08.17.22278893,Uptake of Sotrovimab for prevention of severe COVID-19 and its safety in the community in England,Martina Patone; Holly Tibble; Andrew JHL Snelling; Carol Coupland; Aziz Sheikh; Julia Hippisley-Cox,University of Oxford; University of Edinburgh; University of Oxford; University of Oxford; University of Edinburgh; University of Oxford,"Sotrovimab is a neutralising monoclonal antibody (nMAB), currently administrated in England to treat extremely clinically vulnerable COVID-19 patients. Trials have shown it to have mild or moderate side effects, however safety in real-world settings has not been yet evaluated. We used national databases to investigate its uptake and safety in community patients across England. We used a cohort study to describe uptake and a self-controlled case series design to evaluate the risks of 49 pre-specified suspected adverse events in the 2-28 days post-treatment. Between December 11, 2021 and May 24, 2022, there were 172,860 COVID-19 patients eligible for treatment. Of the 22,815 people who received Sotrovimab, 21,487 (94.2%) had a positive SARS-CoV-2 test and 5,999 (26.3%) were not on the eligible list. Between treated and untreated eligible individuals, the mean age (54.6, SD: 16.1 vs 54.1, SD: 18.3) and sex distribution (women: 60.9% vs 58.1%; men: 38.9% vs 41.1%) were similar. There were marked variations in uptake between ethnic groups, which was higher amongst Indian (15.0%; 95%CI 13.8, 16.3), Other Asian (13.7%; 95%CI 11.9, 15.8), White (13.4%; 95%CI 13.3, 13.6), and Bangladeshi (11.4%; 95%CI 8.8, 14.6); and lower amongst Black Caribbean individuals (6.4%; 95%CI 5.4, 7.5) and Black Africans (4.7%; 95%CI 4.1, 5.4). We found no increased risk of any of the suspected adverse events in the overall period of 2-28 days post-treatment, but an increased risk of rheumatoid arthritis (IRR 3.08, 95% CI 1.44, 6.58) and of systematic lupus erythematosus (IRR 5.15, 95% CI 1.60, 16.60) in the 2-3 days post-treatment, when we narrowed the risk period.
 
-DesignPopulation-based cohort study using the QResearch database linked to national data on COVID-19 vaccination, high risk patients prioritised for COVID-19 therapeutics, SARS-CoV-2 results, hospitalisation, cancer registry, systemic anticancer treatment, radiotherapy and the national death registry.
-
-Settings and study period1.3 million adults in the derivation cohort and 0.15 million adults in the validation cohort aged 18-100 years with a SARS-CoV-2 positive test between 11th December 2021 and 31st March 2022 with follow up to 30th June 2022.
-
-Main outcome measuresOur primary outcome was COVID-19 death. The secondary outcome of interest was COVID-19 hospital admission. Models fitted in the derivation cohort to derive risk equations using a range of predictor variables. Performance evaluated in a separate validation cohort.
-
-ResultsOf 1,297,984 people with a SARS-CoV-2 positive test in the derivation cohort, 18,756 (1.45%) had a COVID-19 related hospital admission and 3,878 (0.3%) had a COVID-19 death during follow-up. Of the 145,404 people in the validation cohort, there were 2,124 (1.46%) COVID-19 admissions and 461 (0.3%) COVID-19 deaths.
-
-The COVID-19 mortality rate in men increased with age and deprivation. In the QCovid4 model in men hazard ratios were highest for those with the following conditions (for 95% CI see Figure 1): kidney transplant (6.1-fold increase); Downs syndrome (4.9-fold); radiotherapy (3.1-fold); type 1 diabetes (3.4-fold); chemotherapy grade A (3.8-fold), grade B (5.8-fold); grade C (10.9-fold); solid organ transplant ever (2.4-fold); dementia (1.62-fold); Parkinsons disease (2.2-fold); liver cirrhosis (2.5-fold). Other conditions associated with increased COVID-19 mortality included learning disability, chronic kidney disease (stages 4 and 5), blood cancer, respiratory cancer, immunosuppressants, oral steroids, COPD, coronary heart disease, stroke, atrial fibrillation, heart failure, thromboembolism, rheumatoid/SLE, schizophrenia/bipolar disease sickle cell/HIV/SCID; type 2 diabetes. Results were similar in the model in women.
-
-O_FIG O_LINKSMALLFIG WIDTH=100 HEIGHT=200 SRC=""FIGDIR/small/22278733v1_fig1.gif"" ALT=""Figure 1"">
-View larger version (35K):
-org.highwire.dtl.DTLVardef@4e93b7org.highwire.dtl.DTLVardef@c3e600org.highwire.dtl.DTLVardef@1311bd4org.highwire.dtl.DTLVardef@11a3246_HPS_FORMAT_FIGEXP  M_FIG O_FLOATNOFigure 1C_FLOATNO QCOVID4 (mortality): Adjusted hazard ratios for COVID-19 death in men mutually adjusted and also adjusted for fractional polynomial terms for age and BMI
-
-C_FIG COVID-19 mortality risk was lower among those who had received COVID-19 vaccination compared with unvaccinated individuals with evidence of a dose response relationship. The reduced mortality rates associated with prior SARS-CoV-2 infection were similar in men (adjusted hazard ratio (HR) 0.51 (95% CI 0.40, 0.64)) and women (adjusted HR 0.55 (95%CI 0.45, 0.67)).
-
-The QCOVID4 algorithm explained 76.6% (95%CI 74.4 to 78.8) of the variation in time to COVID-19 death (R2) in women. The D statistic was 3.70 (95%CI 3.48 to 3.93) and the Harrells C statistic was 0.965 (95%CI 0.951 to 0.978). The corresponding results for COVID-19 death in men were similar with R2 76.0% (95% 73.9 to 78.2); D statistic 3.65 (95%CI 3.43 to 3.86) and C statistic of 0.970 (95%CI 0.962 to 0.979). QCOVID4 discrimination for mortality was slightly higher than that for QCOVID1 and QCOVID2, but calibration was much improved.
-
-ConclusionThe QCovid4 risk algorithm modelled from data during the UKs Omicron wave now includes vaccination dose and prior SARS-CoV-2 infection and predicts COVID-19 mortality among people with a positive test. It has excellent performance and could be used for targeting COVID-19 vaccination and therapeutics. Although large disparities in risks of severe COVID-19 outcomes among ethnic minority groups were observed during the early waves of the pandemic, these are much reduced now with no increased risk of mortality by ethnic group.
-
-What is knownO_LIThe QCOVID risk assessment algorithm for predicting risk of COVID-19 death or hospital admission based on individual characteristics has been used in England to identify people at high risk of severe COVID-19 outcomes, adding an additional 1.5 million people to the national shielded patient list in England and in the UK for prioritising people for COVID-19 vaccination.
-C_LIO_LIThere are ethnic disparities in severe COVID-19 outcomes which were most marked in the first pandemic wave in 2020.
-C_LIO_LICOVID-19 vaccinations and therapeutics (monoclonal antibodies and antivirals) are available but need to be targeted to those at highest risk of severe outcomes.
-C_LI
-
-What this study addsO_LIThe QCOVID4 risk algorithm using data from the Omicron wave now includes number of vaccination doses and prior SARS-CoV-2 infection. It has excellent performance both for ranking individuals (discrimination) and predicting levels of absolute risk (calibration) and can be used for targeting COVID-19 vaccination and therapeutics as well as individualised risk assessment.
-C_LIO_LIQCOVID4 more accurately identifies individuals at highest levels of absolute risk for targeted interventions than the  conditions-based approach adopted by NHS Digital based on relative risk of a list of medical conditions.
-C_LIO_LIAlthough large disparities in risks of severe COVID-19 outcomes among ethnic minority groups were observed during the early waves of the pandemic, these are much reduced now with no increased risk of mortality by ethnic group.
-C_LI",epidemiology,exact,100,100
+FundingNational Institute of Health Research (Grant reference 135561)",epidemiology,exact,100,100
 medRxiv,10.1101/2022.08.08.22278532,2022-08-09,https://medrxiv.org/cgi/content/short/2022.08.08.22278532,Clinical effectiveness of SARS-CoV-2 booster vaccine against Omicron infection in residents and staff of Long-Term Care Facilities: a prospective cohort study (VIVALDI),Oliver Stirrup; Madhumita Shrotri; Natalie L Adams; Maria Krutikov; Hadjer Nacer-Laidi; Borscha Azmi; Tom Palmer; Christopher Fuller; Aidan Irwin-Singer; Verity Baynton; Gokhan Tut; Paul Moss; Andrew Hayward; Andrew Copas; Laura Shallcross,University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; Department of Health and Social Care; Department of Health and Social Care; University of Birmingham; University of Birmingham; University College London; University College London; University College London,"BackgroundSuccessive SARS-CoV-2 variants have caused severe disease in long-term care facility (LTCF) residents. Primary vaccination provides strong short-term protection, but data are limited on duration of protection following booster vaccines, particularly against the Omicron variant. We investigated effectiveness of booster vaccination against infections, hospitalisations and deaths among LTCF residents and staff in England.
 
 MethodsWe included residents and staff of LTCFs within the VIVALDI study (ISRCTN 14447421) who underwent routine, asymptomatic testing (December 12 2021-March 31 2022). Cox regression was used to estimate relative hazards of SARS-CoV-2 infection, and associated hospitalisation and death at 0-13, 14-48, 49-83 and 84 days after dose 3 of SARS-CoV-2 vaccination compared to 2 doses (after 84+ days), stratified by previous SARS-CoV-2 infection and adjusting for age, sex, LTCF capacity and local SARS-CoV-2 incidence.
@@ -541,6 +513,13 @@ Results14175 residents and 19973 staff were included. In residents without prior
 ConclusionsBooster vaccination provides sustained protection against severe outcomes following infection with the Omicron variant, but no protection against infection from 3 months onwards. Ongoing surveillance for SARS-CoV-2 in LTCFs is crucial.
 
 SummaryThe COVID-19 pandemic has severely impacted residents in long-term care facilities (LTCFs). Booster vaccination provides sustained moderate protection against severe outcomes, but no protection against infection was apparent from around 3 months onwards. Ongoing surveillance in LTCFs is crucial.",infectious diseases,exact,100,100
+medRxiv,10.1101/2022.08.07.22278510,2022-08-09,https://medrxiv.org/cgi/content/short/2022.08.07.22278510,Metabolomic and gut microbiome profiles across the spectrum of community-based COVID and non-COVID disease: A COVID-19 Biobank study.,Marc F Österdahl; Ronan Whiston; Carole H Sudre; Francesco Asnicar; Nathan J Cheetham; Aitor Blanco Miguez; Vicky Bowyer; Michela Antonelli; Olivia Snell; Liane dos Santos Canas; Christina Hu; Jonathan Wolf; Cristina Menni; Michael Malim; Deborah Hart; Tim Spector; Sarah Berry; Nicola Segata; Katie Doores; Sebastien Ourselin; Emma L Duncan; Claire J Steves,King's College London; King's College London; King's College London; University of Trento; King's College London; University of Trento; King's College London; King's College London; King's College London; King's College London; ZOE Global Ltd.; ZOE Global Ltd.; King's College London; King's College London; King's College London; King's College London; King's College London; University of Trento; King's College London; King's College London; King's College London; King's College London,"Whilst many with SARS-CoV-2 infection have mild disease, managed in the community, individuals with cardiovascular risk factors experienced often more severe acute disease, requiring hospitalisation. Increasing concern has also developed over long symptom duration in many individuals, including the majority who managed acutely in the community. Risk factors for long symptom duration, including biological variables, are still poorly defined.
+
+We examine post-illness metabolomic and gut-microbiome profiles, in community-dwelling participants with SARS-CoV-2, ranging from asymptomatic illness to Post-COVID Syndrome, and participants with prolonged non-COVID-19 illnesses. We also assess a pre-established metabolomic biomarker score for its association with illness duration.
+
+We found an atherogenic-dyslipidaemic metabolic profile, and greater biomarker scores, associated with longer illness, both in individuals with and without SARS-CoV-2 infection. We found no association between illness duration and gut microbiome in convalescence.
+
+Findings highlight the potential role of cardiometabolic dysfunction to the experience of long illness duration, including after COVID-19.",epidemiology,exact,100,100
 medRxiv,10.1101/2022.07.28.22278152,2022-07-31,https://medrxiv.org/cgi/content/short/2022.07.28.22278152,"Confirmed SARS-CoV-2 infection in Scottish neonates 2020-2022: a national, population-based cohort study",Anna Goulding; Fiona McQuaid; Laura Lindsay; Utkarsh Agrawal; Bonnie Auyeung; Clara Calvert; Jade Carruthers; Cheryl Denny; Jack Donaghy; Sam Hillman; Lisa Hopcroft; Leanne Hopkins; Colin McCowan; Terry Mclaughlin; Emily Moore; Lewis Ritchie; Colin R Simpson; Bob Taylor; Lynda Fenton; Louisa Pollock; Christopher Gale; Jenny J Kurinczuk; Chris Robertson; Aziz Sheikh; Sarah Stock; Rachael Wood,Public Health Scotland; University of Edinburgh; Public Health Scotland; University of St Andrews; University of Edinburgh; University of Edinburgh; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; University of Oxford; University of Edinburgh; University of St Andrews; Public Health Scotland; Public Health Scotland; University of Aberdeen; Victoria University of Wellington; Public Health Scotland; Public Health Scotland; University of Glasgow; Imperial College London; University of Oxford; University of Strathclyde; University of Edinburgh; University of Edinburgh; Public Health Scotland,"ObjectiveTo examine infants in Scotland aged 0-27 days with confirmed SARS-CoV-2 infection; the risk of neonatal infection by factors including maternal infection status and gestation at birth; and the need for hospital admission among infected neonates.
 
 DesignPopulation-based cohort study.
@@ -710,6 +689,13 @@ Methods and analysisThis mixed-method, multi-site study is informed by the princ
 Ethics and disseminationLOCOMOTION is sponsored by the University of Leeds and approved by Yorkshire & The Humber - Bradford Leeds Research Ethics Committee (ref: 21/YH/0276). Dissemination plans include academic and lay publications, and partnerships with national and regional policymakers to influence service specifications and targeted funding streams.
 
 Study registrationClinicalTrials.gov: NCT05057260; ISRCTN15022307.",health systems and quality improvement,exact,100,100
+medRxiv,10.1101/2022.04.03.22272610,2022-04-04,https://medrxiv.org/cgi/content/short/2022.04.03.22272610,Cardiac impairment in Long Covid 1-year post-SARS-CoV-2 infection,Adriana Roca-Fernandez; Malgorzata Wamil; Alison Telford; Valentina Carapella; Alessandra Borlotti; David Monteiro; Helena Thomaides-Brears; Matthew D Kelly; Andrea Dennis; Rajarshi Banerjee; Matthew Robson; Michael Brady; Gregory Lip; Sacha Bull; Melissa J Heightman; Ntobeko Ntusi; Amitava Banerjee,"Perspectum Diagnostics; Great Western Hospital Foundation NHS Trust, Swindon, UK; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; University of Liverpool; Royal Berkshire Hospital, Reading; UCLH; University of Cape Town, Cape Town, South Africa; University College London","BackgroundLong Covid is associated with multiple symptoms and impairment in multiple organs. Cardiac impairment has been reported to varying degrees by varying methodologies in cross-sectional studies. Using cardiac magnetic resonance (CMR), we investigated the 12-month trajectory of cardiac impairment in individuals with Long Covid.
+
+Methods534 individuals with Long Covid underwent baseline CMR (T1 and T2 mapping, cardiac mass, volumes, function, and strain) and multi-organ MRI at 6 months (IQR 4.3,7.3) since first post-COVID-19 symptoms and 330 were rescanned at 12.6 (IQR 11.4, 14.2) months if abnormal findings were reported at baseline. Symptoms, standardised questionnaires, and blood samples were collected at both timepoints. Cardiac impairment was defined as one or more of: low left or right ventricular ejection fraction (LVEF and RVEF), high left or right ventricular end diastolic volume (LVEDV and RVEDV), low 3D left ventricular global longitudinal strain (GLS), or elevated native T1 in [&ge;]3 cardiac segments. A significant change over time was reported by comparison with 92 healthy controls.
+
+ResultsThe technical success of this multiorgan assessment in non-acute settings was 99.1% at baseline, and 98.3% at follow up, with 99.6% and 98.8% for CMR respectively. Of individuals with Long Covid, 102/534 [19%] had cardiac impairment at baseline; 71/102 had complete paired data at 12 months. Of those, 58% presented with ongoing cardiac impairment at 12 months. High sensitivity cardiac troponin I and B-type natriuretic peptide were not predictive of CMR findings, symptoms, or clinical outcomes. At baseline, low LVEF, high RVEDV and low GLS were associated with cardiac impairment. Low LVEF at baseline was associated with persistent cardiac impairment at 12 months.
+
+ConclusionCardiac impairment, other than myocarditis, is present in 1 in 5 individuals with Long Covid at 6 months, persisting in over half of those at 12 months. Cardiac-related blood biomarkers are unable to identify cardiac impairment in Long COVID. Subtypes of disease (based on symptoms, examination, and investigations) and predictive biomarkers are yet to be established. Interventional trials with pre-specified subgroup analyses are required to inform therapeutic options.",cardiovascular medicine,exact,100,100
 medRxiv,10.1101/2022.03.29.22273042,2022-04-04,https://medrxiv.org/cgi/content/short/2022.03.29.22273042,The new normal? Dynamics and scale of the SARS-CoV-2 variant Omicron epidemic in England,Oliver Eales; Leonardo de Oliveira Martins; Andrew Page; Haowei Wang; Barbara Bodinier; David Tang; David Haw; Jakob Jonnerby; Christina Atchison; Deborah Ashby; Wendy Barclay; Graham Taylor; Graham Cooke; Helen Ward; Ara Darzi; Steven Riley; Paul Elliott; Christl A Donnelly; Marc Chadeau-Hyam,"Imperial College London; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Environment and Health, School of Public Health, Imperial College London, UK","The SARS-CoV-2 pandemic has been characterised by the regular emergence of genomic variants which have led to substantial changes in the epidemiology of the virus. With natural and vaccine-induced population immunity at high levels, evolutionary pressure favours variants better able to evade SARS-CoV-2 neutralising antibodies. The Omicron variant was first detected in late November 2021 and exhibited a high degree of immune evasion, leading to increased infection rates in many countries. However, estimates of the magnitude of the Omicron wave have relied mainly on routine testing data, which are prone to several biases. Here we infer the dynamics of the Omicron wave in England using PCR testing and genomic sequencing obtained by the REal-time Assessment of Community Transmission-1 (REACT-1) study, a series of cross-sectional surveys testing random samples of the population of England. We estimate an initial peak in national Omicron prevalence of 6.89% (5.34%, 10.61%) during January 2022, followed by a resurgence in SARS-CoV-2 infections in England during February-March 2022 as the more transmissible Omicron sub-lineage, BA.2 replaced BA.1 and BA.1.1. Assuming the emergence of further distinct genomic variants, intermittent epidemics of similar magnitude as the Omicron wave may become the  new normal.",infectious diseases,exact,100,100
 medRxiv,10.1101/2022.03.22.22271707,2022-03-23,https://medrxiv.org/cgi/content/short/2022.03.22.22271707,Vitamin D Supplements for Prevention of Covid-19 or other Acute Respiratory Infections: a Phase 3 Randomized Controlled Trial (CORONAVIT),David Jolliffe; Hayley Holt; Matthew Greenig; Mohammad Talaei; Natalia Perdek; Paul Pfeffer; Giulia Vivaldi; Sheena Maltby; Jane Symons; Nicola Barlow; Alexa Normandale; Rajvinder Garcha; Alex Richter; Sian Faustini; Christopher Orton; David Ford; Ronan Lyons; Gwyneth Davies; Frank Kee; Christopher Griffiths; John Norrie; Aziz Sheikh; Seif Shaheen; Clare Relton; Adrian Martineau,Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Jane Symons Media; City Hospital Birmingham; City Hospital Birmingham; City Hospital Birmingham; University of Birmingham; University of Birmingham; Swansea University; Swansea University; Swansea University; Swansea University; Queen's University Belfast; Queen Mary University of London; University of Edinburgh; University of Edinburgh; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London,"OBJECTIVESTo determine whether population-level implementation of a test-and- treat approach to correction of sub-optimal vitamin D status (25-hydroxyvitamin D [25(OH)D] <75 nmol/L) influences risk of all-cause acute respiratory infection (ARI) or coronavirus disease 2019 (COVID-19).
 
@@ -806,7 +792,6 @@ This is the first study to examine and describe waning of immunity over a one-ye
 
 Implications of all the available evidenceTaken together, our findings indicate high short-term immunity against SARS-CoV2 infection and very high immunity against severe clinical outcomes of COVID-19 for LTCF residents and staff following vaccination. However substantial waning in vaccine-derived immunity is seen beyond 3 months, irrespective of vaccine type, suggesting the need for regular boosting to maintain protection in this vulnerable cohort. Although this analysis took place in the pre-Omicron period, these trends of waning immunity over time are likely to be generalisable across variants, carrying important implications for long-term vaccination policy in LTCFs. Ongoing surveillance in this vulnerable cohort remains crucial, in order to describe further changes in vaccine-induced immunity, particularly in the context of new variants.",infectious diseases,exact,100,100
 bioRxiv,10.1101/2022.03.08.481609,2022-03-08,https://biorxiv.org/cgi/content/short/2022.03.08.481609,The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK,Verity Hill; Louis du Plessis; Thomas P Alexander Peacock; Dinesh Aggarwal; Alessandro Carabelli; Rachel Colquhoun; Nicholas Ellaby; Eileen Gallagher; Natalie Groves; Ben Jackson; JT McCrone; Anna Price; Theo Sanderson; Emily Scher; Joel Alexander Southgate; Erik Volz; - The COVID-19 genomics UK (COG-UK) consortium; Wendy S Barclay; Jeffrey Barrett; Meera Chand; Thomas R Connor; Ian G. Goodfellow; Ravindra K Gupta; Ewan Harrison; Nicholas Loman; Richard Myers; David L Robertson; Oliver Pybus; Andrew Rambaut,The University of Edinburgh; University of Oxford; University College London (UCL); University of Cambridge; University of Cambridge; University of Edinburgh; UK Health Security Agency; Uk Health Security Agency; UK Health Security Agency; University of Edinburgh; University of Edinburgh; Cardiff University; Sanger Institute; University of Edinburgh; Cardiff University; Imperial College London; -; Imperial College London; Sanger Institute; UK Health Security Agency; Cardiff University; University of Cambridge; University of Cambridge; Sanger Institute; University of Birmingham; UK Health Security Agency; University of Glasgow; University of Oxford; University of Edinburgh,"The first SARS-CoV-2 variant of concern (VOC) to be designated was lineage B.1.1.7, later labelled by the World Health Organisation (WHO) as Alpha. Originating in early Autumn but discovered in December 2020, it spread rapidly and caused large waves of infections worldwide. The Alpha variant is notable for being defined by a long ancestral phylogenetic branch with an increased evolutionary rate, along which only two sequences have been sampled. Alpha genomes comprise a well-supported monophyletic clade within which the evolutionary rate is more typical of SARS-CoV-2. The Alpha epidemic continued to grow despite the continued restrictions on social mixing across the UK, and the imposition of new restrictions, in particular the English national lockdown in November 2020. While these interventions succeeded in reducing the absolute number of cases, the impact of these non-pharmaceutical interventions was predominantly to drive the decline of the SARS-CoV-2 lineages which preceded Alpha. We investigate the only two sampled sequences that fall on the branch ancestral to Alpha. We find that one is likely to be a true intermediate sequence, providing information about the order of mutational events that led to Alpha. We explore alternate hypotheses that can explain how Alpha acquired a large number of mutations yet remained largely unobserved in a region of high genomic surveillance: an under-sampled geographical location, a non-human animal population, or a chronically-infected individual. We conclude that the last hypothesis provides the best explanation of the observed behaviour and dynamics of the variant, although we find that the individual need not be immunocompromised, as persistently-infected immunocompetent hosts also display a higher within-host rate of evolution. Finally, we compare the ancestral branches and mutation profiles of other VOCs to each other, and identify that Delta appears to be an outlier both in terms of the genomic locations of its defining mutations, and its lack of rapid evolutionary rate on the ancestral branch. As new variants, such as Omicron, continue to evolve (potentially through similar mechanisms) it remains important to investigate the origins of other variants to identify ways to potentially disrupt their evolution and emergence.",evolutionary biology,exact,100,100
-medRxiv,10.1101/2022.03.06.21267462,2022-03-08,https://medrxiv.org/cgi/content/short/2022.03.06.21267462,Risk of myocarditis and pericarditis following COVID-19 vaccination in England and Wales,Samanatha Ip; Fatemeh Torabi; Spiros Denaxas; Ashley Akbari; Hoda Abbasizanjani; Rochelle Knight; Jennifer Anne Cooper; Rachel Denholm; Spencer Keene; Thomas Bolton; Sam Hollings; Efosa Omigi; Teri-Louise North; Arun Karthikeyan Suseeladevi; Emanuele Di Angelantonio; Kamlesh Khunti; Jonathan A C Sterne; Cathie Sudlow; William Whiteley; Angela Wood; Venexia Walker; - British Heart Foundation Data Science Centre (HDR UK) CVD-COVID-UK/COVID-IMPACT Consortium; - UK Covid-19 Longitudinal Health and Wellbeing National Core Study; - UK Covid-19 Data and Connectivity National Core Study,University of Cambridge; Swansea University; University College London; Swansea University; Swansea University; University of Bristol; University of Bristol; University of Bristol; University of Cambridge; Health Data Research UK; NHS Digital; NHS Digital; University of Bristol; University of Bristol; University of Cambridge; University of Leicester; University of Bristol; Health Data Research UK; University of Edinburgh; University of Cambridge; University of Bristol; ; ; ,"We describe our analyses of data from over 49.7 million people in England, representing near-complete coverage of the relevant population, to assess the risk of myocarditis and pericarditis following BNT162b2 and ChAdOx1 COVID-19 vaccination. A self-controlled case series (SCCS) design has previously reported increased risk of myocarditis after first ChAdOx1, BNT162b2, and mRNA-1273 dose and after second doses of mRNA COVID-19 vaccines in England. Here, we use a cohort design to estimate hazard ratios for hospitalised or fatal myocarditis/pericarditis after first and second doses of BNT162b2 and ChAdOx1 vaccinations. SCCS and cohort designs are subject to different assumptions and biases and therefore provide the opportunity for triangulation of evidence. In contrast to the findings from the SCCS approach previously reported for England, we found evidence for lower incidence of hospitalised or fatal myocarditis/pericarditis after first ChAdOx1 and BNT162b2 vaccination, as well as little evidence to suggest higher incidence of these events after second dose of either vaccination.",epidemiology,exact,100,100
 medRxiv,10.1101/2022.02.24.22271466,2022-02-25,https://medrxiv.org/cgi/content/short/2022.02.24.22271466,Risk of COVID-19 related deaths for SARS-CoV-2 Omicron (B.1.1.529) compared with Delta (B.1.617.2),Isobel L. Ward; Charlotte Bermingham; Daniel Ayoubkhani; Owen J. Gethings; Koen Pouwels; Thomas Yates; Kamlesh Khunti; Julia Hippisley-Cox; Amitava Banerjee; Ann Sarah Walker; Vahe Nafilyan,"Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford; Diabetes Research Centre, University of Leicester; Diabetes Research Centre, University of Leicester; University of Oxford; University College London; University of Oxford; Office for National Statistics","ObjectiveTo assess the risk of death involving COVID-19 following infection from Omicron (B.1.1.539/BA.1) relative to Delta (B.1.617.2).
 
 DesignRetrospective cohort study.
@@ -947,6 +932,9 @@ RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed,
 Added value of this studyWe used national databases of COVID-19 case surveillance, laboratory testing, and vaccination from Brazil to investigate effectiveness of CoronaVac, ChAdOx1, Ad26.COV2.S and BNT162b2 among individuals with a prior, laboratory-confirmed SARS-CoV-2 infection. We matched >22,000 RT-PCR-confirmed re-infections with >145,000 RT-PCR-negative controls using a test-negative design. All four vaccines were effective against symptomatic SARS-CoV-2 infections, with effectiveness from 14 days after series completion ranging from 39-65%. For vaccines with two-dose regimens, the second dose provided significantly increased effectiveness compared with one dose. Effectiveness against COVID-19-associated hospitalization or death from 14 days after series completion was >80% for CoronaVac, ChAdOx1and BNT162b2.
 
 Implications of all the available evidenceWe find evidence that four vaccines, using three different platforms, all provide protection to previously infected individuals against symptomatic SARS-CoV-2 infection and severe outcomes, with a second dose conferring significant additional benefits. These results support the provision of a full vaccine series among individuals with prior SARS-CoV-2 infection.",infectious diseases,exact,100,100
+medRxiv,10.1101/2021.12.23.21268276,2021-12-25,https://medrxiv.org/cgi/content/short/2021.12.23.21268276,Risk of myocarditis following sequential COVID-19 vaccinations by age and sex,Martina Patone; Winnie Xue Mei; Lahiru Handunnetthi; Sharon Dixon; Francesco Zaccardi; Manu Shankar-Hari; Peter Watkinson; Kamlesh Khunti; Anthony Harnden; Carol AC Coupland; Keith M. Channon; Nicholas L Mills; Aziz Sheikh; Julia Hippisley-Cox,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Leicester; University of Edinburgh; University of Oxford; University of Leicester; University of Oxford; University of Oxford; University of Oxford; University of Edinburgh; University of Edinburgh; University of Oxford,"In an updated self-controlled case series analysis of 42,200,614 people aged 13 years or more, we evaluate the association between COVID-19 vaccination and myocarditis, stratified by age and sex, including 10,978,507 people receiving a third vaccine dose. Myocarditis risk was increased during 1-28 days following a third dose of BNT162b2 (IRR 2.02, 95%CI 1.40, 2.91). Associations were strongest in males younger than 40 years for all vaccine types with an additional 3 (95%CI 1, 5) and 12 (95% CI 1,17) events per million estimated in the 1-28 days following a first dose of BNT162b2 and mRNA-1273, respectively; 14 (95%CI 8, 17), 12 (95%CI 1, 7) and 101 (95%CI 95, 104) additional events following a second dose of ChAdOx1, BNT162b2 and mRNA-1273, respectively; and 13 (95%CI 7, 15) additional events following a third dose of BNT162b2, compared with 7 (95%CI 2, 11) additional events following COVID-19 infection. An association between COVID-19 infection and myocarditis was observed in all ages for both sexes but was substantially higher in those older than 40 years. These findings have important implications for public health and vaccination policy.
+
+FundingHealth Data Research UK.",epidemiology,exact,100,100
 medRxiv,10.1101/2021.12.22.21268252,2021-12-24,https://medrxiv.org/cgi/content/short/2021.12.22.21268252,Rapid increase in Omicron infections in England during December 2021: REACT-1 study,Paul Elliott; Barbara Bodinier; Oliver Eales; Haowei Wang; David Haw; Joshua Elliott; Matthew Whitaker; Jakob Jonnerby; David Tang; Caroline E. Walters; Christina Atchinson; Peter J. Diggle; Andrew J. Page; Alex Trotter; Deborah Ashby; Wendy Barclay; Graham Taylor; Helen Ward; Ara Darzi; Graham Cooke; Marc Chadeau-Hyam; Christl A Donnelly,"School of Public Health, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; Imperial College London; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; Imperial College London; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; Quadram Institute, Norwich, UK; Quadram Institute Bioscience; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research; Imperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research Centre, UKInstitute of Global Health Innovation at ; Department of Infectious Disease, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency","BackgroundThe highest-ever recorded numbers of daily severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in England has been observed during December 2021 and have coincided with a rapid rise in the highly transmissible Omicron variant despite high levels of vaccination in the population. Although additional COVID-19 measures have been introduced in England and internationally to contain the epidemic, there remains uncertainty about the spread and severity of Omicron infections among the general population.
 
 MethodsThe REal-time Assessment of Community Transmission-1 (REACT-1) study has been monitoring the prevalence of SARS-CoV-2 infection in England since May 2020. REACT-1 obtains self-administered throat and nose swabs from a random sample of the population of England at ages 5 years and over. Swabs are tested for SARS-CoV-2 infection by reverse transcription polymerase chain reaction (RT-PCR) and samples testing positive are sent for viral genome sequencing. To date 16 rounds have been completed, each including [~]100,000 or more participants with data collected over a period of 2 to 3 weeks per month. Socio-demographic, lifestyle and clinical information (including previous history of COVID-19 and symptoms prior to swabbing) is collected by online or telephone questionnaire. Here we report results from round 14 (9-27 September 2021), round 15 (19 October - 05 November 2021) and round 16 (23 November - 14 December 2021) for a total of 297,728 participants with a valid RT-PCR test result, of whom 259,225 (87.1%) consented for linkage to their NHS records including detailed information on vaccination (vaccination status, date). We used these data to estimate community prevalence and trends by age and region, to evaluate vaccine effectiveness against infection in children ages 12 to 17 years, and effect of a third (booster) dose in adults, and to monitor the emergence of the Omicron variant in England.
@@ -956,13 +944,6 @@ ResultsWe observed a high overall prevalence of 1.41% (1.33%, 1.51%) in the comm
 ConclusionA large fall in swab positivity from round 15 to round 16 among 12 to 17 year olds, most of whom have been vaccinated, contrasts with the continuing high prevalence among 5 to 11 year olds who have largely not been vaccinated. Likewise there were large falls in swab positivity among people aged 65 years and over, the vast majority of whom have had a third (booster) vaccine dose; these results reinforce the importance of the vaccine and booster campaign. However, the rapidly increasing prevalence of SARS-CoV-2 infections in England during December 2021, coincident with the rapid rise of Omicron infections, may lead to renewed pressure on health services. Additional measures beyond vaccination may be needed to control the current wave of infections and prevent health services (in England and other countries) from being overwhelmed.
 
 SummaryThe unprecedented rise in SARS-CoV-2 infections is concurrent with rapid spread of the Omicron variant in England and globally. We analysed prevalence of SARS-CoV-2 and its dynamics in England from end of November to mid-December 2021 among almost 100,000 participants from the REACT-1 study. Prevalence was high during December 2021 with rapid growth nationally and in London, and of the proportion of infections due to Omicron. We observed a large fall in swab positivity among mostly vaccinated older children (12-17 years) compared with unvaccinated younger children (5-11 years), and in adults who received a third vs. two doses of vaccine. Our results reiterate the importance of vaccination and booster campaigns; however, additional measures may be needed to control the rapid growth of the Omicron variant.",epidemiology,exact,100,100
-medRxiv,10.1101/2021.12.21.21268214,2021-12-23,https://medrxiv.org/cgi/content/short/2021.12.21.21268214,Comparative effectiveness of ChAdOx1 versus BNT162b2 vaccines against SARS-CoV-2 infections in England and Wales: A cohort analysis using trial emulation in the Virus Watch community data,Vincent Grigori Nguyen; Alexei Yavlinsky; Sarah Beale; Susan J Hoskins; Vasileios Lampos; Isobel Braithwaite; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Annalan M D Navaratnam; Parth Patel; Madhumita Shrotri; Sophie Weber; Andrew Hayward; Robert W Aldridge,University College London; University College London; University College London; Univerity College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London,"IntroductionInfections of SARS-CoV-2 in vaccinated individuals have been increasing globally. Understanding the associations between vaccine type and a post-vaccination infection could help prevent further COVID-19 waves. In this paper, we use trial emulation to understand the impact of a phased introduction of the vaccine in the UK driven by vulnerability and exposure status. We estimate the comparative effectiveness of COVID-19 vaccines (ChAdOx1 versus BNT162b2) against post-vaccination infections of SARS-CoV-2 in a community setting in England and Wales.
-
-MethodTrial emulation was conducted by pooling results from six cohorts whose recruitment was staggered between 1st January 2021 and 31st March 2021 and followed until 12th November 2021. Eligibility for each trial was based upon age (18+ at the time of vaccination), without prior signs of infection or an infection within the first 14 days of the first dose. Time from vaccination of ChAdOx1 or BNT162b2 until SARS-CoV-2 infection (positive polymerase chain reaction or lateral flow test after 14 of the vaccination) was modelled using Cox proportional hazards model for each cohort and adjusted for age at vaccination, gender, minority ethnic status, clinically vulnerable status and index of multiple deprivation quintile. For those without SARS-CoV-2 infection during the study period, follow-up was until loss-of-follow-up or end of study (12th November 2021). Pooled hazard ratios were generated using random-effects meta-analysis.
-
-ResultsAcross six cohorts, there were a total of 21,283 participants who were eligible and vaccinated with either ChAdOx1 (n = 13,813) or BNT162b2 (n = 7,470) with a median follow-up time of 266 days (IQR: 235 - 282). By November 12th 2021, 750 (5.4%) adults who had ChAdOx1 as their vaccine experienced a SARS-CoV-2 infection, compared to 296 (4.0%) who had BNT162b2. We found that people who received ChAdOx1 vaccinations had 10.54 per 1000 people higher cumulative incidence for SARS-CoV-2 infection compared to BNT162b2 for infections during a maximum of 315 days of follow-up. When adjusted for age at vaccination, sex, minority ethnic status, index of multiple deprivation, and clinical vulnerability status, we found a pooled adjusted hazard ratio of 1.35 [HR: 1.35, 95%CI: 1.15 - 1.58], demonstrating a 35% increase in SARS-CoV-2 infections in people who received ChAdOx1 compared to BNT162b2.
-
-DiscussionWe found evidence of greater effectiveness of receiving BNT162b2 compared to ChAdOx1 vaccines against SARS-CoV-2 infection in England and Wales during a time period when Delta became the most prevalent variant of concern. Our findings demonstrate the importance of booster (third) doses to maintain protection and suggest that these should be prioritised to those who received ChAdOx1 as their primary course.",epidemiology,exact,100,100
 bioRxiv,10.1101/2021.12.17.473248,2021-12-21,https://biorxiv.org/cgi/content/short/2021.12.17.473248,"SARS-CoV-2 Omicron spike mediated immune escape, infectivity and cell-cell fusion",Bo Meng; Isabella Ferreira; Adam Abdullahi; Niluka Goonawardane; Akatsuki Saito; Izumi Kimura; Daichi Yamasoba; Steven A Kemp; Guido Papa; Saman Fatihi; Surabhi Rathore; Pehuen Perera Gerba; Terumasa Ikeda; Mako Toyoda; Toong Seng Tan; Jin Kuramochi; Shigeki Mitsunaga; Takamasa Ueno; Oscar Charles; Dami Collier; - CITIID-NIHR BioResource COVID-19 Collaboration; - The Genotype to Phenotype Japan (G2P-Japan) Consortium; - Ecuador-COVID19 Consortium; John Bradley; Jinwook Choi; Kenneth Smith; Elo Madissoon; Kerstin Meyer; Petra Mlcochova; Rainer Doffinger; Sarah A Teichmann; Leo James; Joo Hyeon Lee; Teresa Brevini; Matteo Pizzuto; Myra Hosmillo; Donna Mallery; Samantha Zepeda; Alexandra Walls; Anshu Joshi; John Bowen; John Briggs; Alex Sigal; Laurelle Jackson; Sandile Cele; Anna De Marco; Fotios Sampaziotis; Davide Corti; David Veesler; Nicholas Matheson; Ian Goodfellow; Lipi Thukral; Kei Sato; Ravindra K Gupta,"University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Miyazaki; The University of Tokyo; Kumamoto University; University of Cambridge; LMB Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; CSIR Institute of Genomics and Integrative Biology, Delhi, India; University of Cambridge; Kumamoto Univ; Kumamoto University, Kumamoto; Kuramochi Clinic Interpark; Kuramochi Clinic Interpark; National Institute of Genetics, Mishima, Shizuoka; Kumamoto University, Kumamoto; University College London; University of Cambridge; -; -; -; University of Cambridge; University of Cambridge; University of Cambridge; Wellcome Sanger Institute; Wellcome Sanger Institute; University of Cambridge; Cambridge University Hospitals NHS Trust; Cambridge University; MRC LMB; University of Cambridge; University of Cambridge; Humabs Biomed SA; University of Cambridge; MRC LMB Cambridge; University of Washington; University of Washington; University of Washington; University of Washington; University of Heidelberg; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Humabs Biomed SA; University of Cambridge; Humabs Biomed SA; University of Washington; University of Cambridge; University of Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; The University of Tokyo; University of Cambridge","The SARS-CoV-2 Omicron BA.1 variant emerged in late 2021 and is characterised by multiple spike mutations across all spike domains. Here we show that Omicron BA.1 has higher affinity for ACE2 compared to Delta, and confers very significant evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralising antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralisation. Importantly, antiviral drugs remdesevir and molnupiravir retain efficacy against Omicron BA.1. We found that in human nasal epithelial 3D cultures replication was similar for both Omicron and Delta. However, in lower airway organoids, Calu-3 lung cells and gut adenocarcinoma cell lines live Omicron virus demonstrated significantly lower replication in comparison to Delta. We noted that despite presence of mutations predicted to favour spike S1/S2 cleavage, the spike protein is less efficiently cleaved in live Omicron virions compared to Delta virions. We mapped the replication differences between the variants to entry efficiency using spike pseudotyped virus (PV) entry assays. The defect for Omicron PV in specific cell types correlated with higher cellular RNA expression of TMPRSS2, and accordingly knock down of TMPRSS2 impacted Delta entry to a greater extent as compared to Omicron. Furthermore, drug inhibitors targeting specific entry pathways demonstrated that the Omicron spike inefficiently utilises the cellular protease TMPRSS2 that mediates cell entry via plasma membrane fusion. Instead, we demonstrate that Omicron spike has greater dependency on cell entry via the endocytic pathway requiring the activity of endosomal cathepsins to cleave spike. Consistent with suboptimal S1/S2 cleavage and inability to utilise TMPRSS2, syncytium formation by the Omicron spike was dramatically impaired compared to the Delta spike. Overall, Omicron appears to have gained significant evasion from neutralising antibodies whilst maintaining sensitivity to antiviral drugs targeting the polymerase. Omicron has shifted cellular tropism away from TMPRSS2 expressing cells that are enriched in cells found in the lower respiratory and GI tracts, with implications for altered pathogenesis.",microbiology,exact,100,100
 medRxiv,10.1101/2021.12.20.21268098,2021-12-21,https://medrxiv.org/cgi/content/short/2021.12.20.21268098,"Therapies for Long COVID in non-hospitalised individuals - from symptoms, patient-reported outcomes, and immunology to targeted therapies (The TLC Study): Study protocol",Shamil Haroon; Krishnarajah Nirantharakumar; Sarah Hughes; Anuradhaa Subramanian; Olalekan Lee Aiyegbusi; Elin Haf Davies; Puja Myles; Tim Williams; Grace Turner; Joht Singh Chandan; Christel McMullan; Janet Lord; David Wraith; Kirsty McGee; Alastair Denniston; Tom Taverner; Louise Jackson; Elizabeth Sapey; Georgios Gkoutos; Krishna Gokhale; Edward Leggett; Clare Iles; Christopher Frost; Gary McNamara; Amy Bamford; Tom Marshall; Dawit Zemedikun; Gary Price; Steven Marwaha; Nikita Simms-Williams; Kirsty Brown; Anita Walker; Karen Jones; Karen Matthews; Jennifer Camaradou; Michael Saint-Cricq; Sumita Kumar; Yvonne Alder; David Stanton; Lisa Agyen; Megan Baber; Hannah Blaize; Melanie Calvert,University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Aparito; Medicines and Healthcare Products Regulatory Agency; Medicines and Healthcare Products Regulatory Agency; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; University of Birmingham; University ofBirmingham; University of Birmingham; Medicines and Healthcare Products Regulatory Agency; Medicines and Healthcare Products Regulatory Agency; Aparito; Aparito; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; N/A; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; University ofBirmingham,"IntroductionIndividuals with COVID-19 frequently experience symptoms and impaired quality of life beyond 4-12 weeks, commonly referred to as Long COVID. Whether Long COVID is one or several distinct syndromes is unknown. Establishing the evidence base for appropriate therapies is needed. We aim to evaluate the symptom burden and underlying pathophysiology of Long COVID syndromes in non-hospitalised individuals and evaluate potential therapies.
 
@@ -1031,6 +1012,13 @@ Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe systematically s
 Added value of this studyIn a diverse population of adults post-hospital admission with COVID-19, our large UK prospective multi-centre study reports several novel findings: the minority felt fully recovered at one year with minimal recovery from five months across any health domain; female sex and obesity are associated with being less likely to feel fully recovered at one year; several inflammatory mediators were increased in individuals with the most severe physical, mental health, and cognitive impairments compared to individuals with milder ongoing impairments.
 
 Implications of all the available evidenceBoth pharmacological and non-pharmacological interventions are urgently needed to improve the ongoing burden following hospitalisation for COVID-19 both for individuals and healthcare systems; our findings support the use of a precision medicine approach with potential treatable traits of systemic inflammation and obesity.",infectious diseases,exact,100,100
+medRxiv,10.1101/2021.12.14.21267460,2021-12-15,https://medrxiv.org/cgi/content/short/2021.12.14.21267460,Differential Risk of SARS-CoV-2 Infection by Occupation: Evidence from the Virus Watch prospective cohort study in England and Wales,Sarah Beale; Susan J Hoskins; Thomas Edward Byrne; Erica Wing Lam Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Annalan MD Navaratnam; Vincent Nguyen; Parth Patel; Alexei Yavlinsky; Anne Johnson; Martie Van Tongeren; Robert W Aldridge; Andrew Hayward,University College London; Univerity College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University of Manchester; University College London; University College London,"BackgroundWorkers differ in their risk of SARS-CoV-2 infection according to their occupation, but the direct contribution of occupation to this relationship is unclear. This study aimed to investigate how infection risk differed across occupational groups in England and Wales up to April 2022, after adjustment for potential confounding and stratification by pandemic phase.
+
+MethodsData from 15,190 employed/self-employed participants in the Virus Watch prospective cohort study were used to generate risk ratios for virologically- or serologically-confirmed SARS-CoV-2 infection using robust Poisson regression, adjusting for socio-demographic and health-related factors and non-work public activities. We calculated attributable fractions (AF) amongst the exposed for belonging to each occupational group based on adjusted risk ratios (aRR).
+
+FindingsIncreased risk was seen in nurses (aRR=1.44, 1.25-1.65; AF=30%, 20-39%), doctors (aRR=1.33, 1.08-1.65; AF=25%, 7-39%), carers (1.45, 1.19-1.76; AF=31%, 16-43%), primary school teachers (aRR=1.67, 1.42-1.96; AF=40%, 30-49%), secondary school teachers (aRR=1.48, 1.26-1.72; AF=32%, 21-42%), and teaching support occupations (aRR=1.42, 1.23-1.64; AF=29%, 18-39%) compared to office-based professional occupations. Differential risk was apparent in the earlier phases (Feb 2020 - May 2021) and attenuated later (June - October 2021) for most groups, although teachers and teaching support workers demonstrated persistently elevated risk across waves.
+
+InterpretationOccupational differentials in SARS-CoV-2 infection risk vary over time and are robust to adjustment for socio-demographic, health-related, and non-workplace activity-related potential confounders. Direct investigation into workplace factors underlying elevated risk and how these change over time is needed to inform occupational health interventions.",epidemiology,exact,100,100
 medRxiv,10.1101/2021.12.08.21267353,2021-12-08,https://medrxiv.org/cgi/content/short/2021.12.08.21267353,The challenge of limited vaccine supplies: impact of prior infection on anti-spike IgG antibody trajectories after a single COVID-19 vaccination,Jia Wei; Philippa Matthews; Nicole Stoesser; Ian Diamond; Ruth Studley; Emma Rourke; Duncan Cook; John Bell; John Newton; Jeremy Farrar; Alison Howarth; Brian Marsden; Sarah Hoosdally; Yvonne Jones; David Stuart; Derrick W Crook; tim E peto; Ann Sarah Walker; David W Eyre; Koen B Pouwels; - COVID-19 Infection Survey team,University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; NIHR Oxford Biomedical Research Centre; oxford university; University of Oxford; University of Oxford; University of Oxford; ,"Given high SARS-CoV-2 incidence, coupled with slow and inequitable vaccine roll-out, there is an urgent need for evidence to underpin optimum vaccine deployment, aiming to maximise global population immunity at speed. We evaluate whether a single vaccination in previously infected individuals generates similar initial and subsequent antibody responses to two vaccinations in those without prior infection. We compared anti-spike IgG antibody responses after a single dose of ChAdOx1, BNT162b2, or mRNA-1273 SARS-CoV-2 vaccines in the COVID-19 Infection Survey in the UK general population. In 100,849 adults who received at least one vaccination, 13,404 (13.3%) had serological and/or PCR evidence of prior infection. Prior infection significantly boosted antibody responses for all three vaccines, producing a higher peak level and longer half-life, and a response comparable to those without prior infection receiving two vaccinations. In those with prior infection, median time above the positivity threshold was estimated to last for >1 year after the first dose. Single-dose vaccination targeted to those previously infected may provide protection in populations with high rates of previous infection faced with limited vaccine supply, as an interim measure while vaccine campaigns are scaled up.",infectious diseases,exact,100,100
 medRxiv,10.1101/2021.11.24.21266818,2021-12-01,https://medrxiv.org/cgi/content/short/2021.11.24.21266818,Trends and associated factors for Covid-19 hospitalisation and fatality risk in 2.3 million adults in England,Thomas Beaney; Ana Luisa Neves; Ahmed Alboksmaty; Kelsey Flott; Aidan Fowler; Jonathan R Benger; Paul Aylin; Sarah Elkin; Ara Darzi; Jonathan Clarke,Imperial College London; Imperial College London; Imperial College London; Imperial College London; NHS England and Improvement; NHS Digital; Imperial College London; Imperial College London; Imperial College London; Imperial College London,"BackgroundThe Covid-19 case fatality ratio varies between countries and over time but it is unclear whether variation is explained by the underlying risk in those infected. This study aims to describe the trends and risk factors for admission and mortality rates over time in England.
 
@@ -1150,13 +1138,6 @@ Results1696 (15.2%) of 11,130 participants were seropositive. Factors independen
 ConclusionsHigher alcohol consumption and reduced light physical exercise represent new modifiable risk factors for SARS-CoV-2 infection. Recognised associations between Asian/Asian British ethnic origin and obesity and increased risk of SARS-CoV-2 seropositivity were independent of other sociodemographic, behavioural, nutritional, clinical and pharmacological factors investigated. Among seropositive participants, higher titres of anti-Spike antibodies in people of Asian ancestry and in obese people were not explained by greater COVID-19 disease severity in these groups.
 
 FundingBarts Charity, Health Data Research UK.",epidemiology,exact,100,100
-medRxiv,10.1101/2021.11.03.21265877,2021-11-03,https://medrxiv.org/cgi/content/short/2021.11.03.21265877,REACT-1 round 15 interim report: High and rising prevalence of SARS-CoV-2 infection in England from end of September 2021 followed by a fall in late October 2021,Marc Chadeau-Hyam; Oliver Eales; Barbara Bodinier; Haowei Wang; David J Haw; Matthew Whitaker; Caroline E Walters; Christina J Atchison; Peter J Diggle; Andrew J Page; Deborah Ashby; Wendy Barclay; Graham P Taylor; Graham Cooke; Helen Ward; Ara Darzi; Christl A. Donnelly; Paul Elliott,Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Quadram Institute; Imperial College London; Imperial College London; Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London School of Public Health,"BackgroundThe third wave of COVID-19 in England coincided with the rapid spread of the Delta variant of SARS-CoV-2 from the end of May 2021. Case incidence data from the national testing programme (Pillar 2) in England may be affected by changes in testing behaviour and other biases. Community surveys may provide important contextual information to inform policy and the public health response.
-
-MethodsWe estimated patterns of community prevalence of SARS-CoV-2 infection in England using RT-PCR swab-positivity, demographic and other risk factor data from round 15 (interim) of the REal-time Assessment of Community Transmission-1 (REACT-1) study (round 15a, carried out from 19 to 29 October 2021). We compared these findings with those from round 14 (9 to 27 September 2021).
-
-ResultsDuring mid- to late-October 2021 (round 15a) weighted prevalence was 1.72% (1.61%, 1.84%) compared to 0.83% (0.76%, 0.89%) in September 2021 (round 14). The overall reproduction number (R) from round 14 to round 15a was 1.12 (1.11, 1.14) with increases in prevalence over this period (September to October) across age groups and regions except Yorkshire and The Humber. However, within round 15a (mid- to late-October) there was evidence of a fall in prevalence with R of 0.76 (0.65, 0.88). The highest weighted prevalence was observed among children aged 5 to 12 years at 5.85% (5.10%, 6.70%) and 13 to 17 years at 5.75% (5.02%, 6.57%). At regional level, there was an almost four-fold increase in weighted prevalence in South West from round 14 at 0.59% (0.43%,0.80%) to round 15a at 2.18% (1.84%, 2.58%), with highest smoothed prevalence at subregional level also found in South West in round 15a. Age, sex, key worker status, and presence of children in the home jointly contributed to the risk of swab-positivity. Among the 126 sequenced positive swabs obtained up until 23 October, all were Delta variant; 13 (10.3%) were identified as the AY.4.2 sub-lineage.
-
-DiscussionWe observed the highest overall prevalence of swab-positivity seen in the REACT-1 study in England to date in round 15a (October 2021), with a two-fold rise in swab-positivity from round 14 (September 2021). Despite evidence of a fall in prevalence from mid- to late-October 2021, prevalence remains high, particularly in school-aged children, with evidence also of higher prevalence in households with one or more children. Thus, vaccination of children aged 12 and over remains a high priority (with possible extension to children aged 5-12) to help reduce within-household transmission and disruptions to education, as well as among adults, to lessen the risk of serious disease among those infected.",epidemiology,exact,100,100
 medRxiv,10.1101/2021.10.22.21265368,2021-10-25,https://medrxiv.org/cgi/content/short/2021.10.22.21265368,Psychological Distress Before and During the COVID-19 Pandemic: Sociodemographic Inequalities in 11 UK Longitudinal Studies,Kishan Patel; Elaine Robertson; Alex Siu Fung Kwong; Gareth J Griffith; Kathryn Willan; Michael J Green; Giorgio Di Gessa; Charlotte Huggins; Eoin McElroy; Ellen J Thompson; Jane Maddock; Claire L Niedzwiedz; Morag Henderson; Marcus Richards; Andrew Steptoe; George B Ploubidis; Bettina Moltrecht; Charlotte Booth; Emla Fitzsimons; Richard Silverwood; Praveetha Patalay; David Porteous; Srinivasa Vittal Katikireddi,University College London; University of Glasgow; University of Bristol; University of Bristol; Bradford Institute for Health Research; University of Glasgow; University College London; University of Edinburgh; University of Leicester; University College London; University College London; University of Glasgow; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University of Edinburgh; University of Glasgow,"ImportanceHow population mental health has evolved across the COVID-19 pandemic under varied lockdown measures is poorly understood, with impacts on health inequalities unclear.
 
 ObjectiveWe investigated changes in mental health and sociodemographic inequalities from before and across the first year of the COVID-19 pandemic in 11 longitudinal studies.
@@ -1221,23 +1202,6 @@ Research in contextO_ST_ABSEvidence before this studyC_ST_ABSA search was conduc
 Added value of this studyWe estimated the proportion of care home staff and residents with evidence of SARS-CoV-2 natural infection using data from over 3,000 staff and 1,500 residents in 201 geographically dispersed LTCFs in England. Population selection was independent of outbreak history and the sample is therefore more reflective of the population who reside and work in LTCFs. Our estimates of the proportion of residents with prior natural infection are substantially higher than estimates based on population-wide PCR testing, due to limited testing coverage at the start of the pandemic. 1361 individuals had at least one positive antibody test and participants were followed for up to 11 months, which allowed modelling of the time to loss of antibody in over 600 individuals in whom the date of primary infection could be reliably estimated. This is the longest reported serological follow up in a population of LTCF residents, a group who are known to be most at risk of severe outcomes following infection with SARS-CoV-2 and provides important evidence on the duration that nucleocapsid antibodies remained detectable over the first and second waves of the pandemic.
 
 Implications of all available researchA substantial proportion of the LTCF population will have some level of natural immunity to infection as a result of past infection. Immunological studies have highlighted greater antibody responses to vaccination in seropositive individuals, so vaccine efficacy in this population may be affected by this large pool of individuals who have survived past infection. In addition, although the presence of nucleocapsid-specific antibodies is generally considered as the standard marker for prior infection, we find that antibody waning is such that up to 50% of people will lose detectable antibody responses within eight months. Individual prior natural infection history is critical to assess the impact of factors such as vaccine response or protection against re-infection. These findings may have implications for duration of immunity following natural infection and indicate that alternative assays for prior infection should be developed.",epidemiology,exact,100,100
-medRxiv,10.1101/2021.09.20.21263828,2021-09-23,https://medrxiv.org/cgi/content/short/2021.09.20.21263828,"Colchicine for COVID-19 in adults in the community (PRINCIPLE): a randomised, controlled, adaptive platform trial",- The PRINCIPLE Trial Collaborative Group; Jienchi Dorward; Ly-Mee Yu; Gail Hayward; Benjamin R Saville; Oghenekome Gbinigie; Oliver van Hecke; Emma Ogburn; Philip H Evans; Nicholas PB Thomas; Mahendra G Patel; Duncan Richards; Nicholas Berry; Michelle A Detry; Christina Saunders; Mark Fitzgerald; Victoria Harris; Milensu Shanyinde; Simon de Lusignan; Monique I Andersson; Christopher C Butler; FD Richard Hobbs,"; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom and Centre for the AIDS Programme of Research in South Africa ; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Berry Consultants, Texas, USA and Department of Biostatistics, Vanderbilt University School of Medicine, Tennessee, USA; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; College of Medicine and Health, University of Exeter and National Institute for Health Research, Clinical Research Network; Royal College of General Practitioners, London, UK, and National Institute for Health Research, Clinical Research Network; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom and School of Pharmacy and Medical Sciences, University of Bra; Oxford Clinical Trials Research Unit, Botnar Research Centre, University of Oxford, Oxford, UK; Berry Consultants, Texas, USA; Berry Consultants, Texas, USA; Berry Consultants, Texas, USA; Berry Consultants, Texas, USA; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom,; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom","ObjectivesColchicine has been proposed as a COVID-19 treatment, but its effect on time to recovery is unknown. We aimed to determine whether colchicine is effective at reducing time to recovery and COVID-19 related hospitalisations/deaths among people in the community.
-
-DesignProspective, multicentre, open-label, multi-arm, adaptive Platform Randomised Trial of Treatments in the Community for Epidemic and Pandemic Illnesses (PRINCIPLE).
-
-SettingNational trial run remotely from a central trial site and at multiple primary care centres across the United Kingdom.
-
-ParticipantsAdults aged [&ge;]65, or [&ge;]18 years with comorbidities or shortness of breath, and unwell [&le;]14 days with suspected COVID-19 in the community.
-
-InterventionsParticipants were randomised to usual care, usual care plus colchicine (500{micro}g daily for 14 days), or usual care plus other interventions.
-
-Main outcome measuresThe co-primary endpoints were time to first self-reported recovery, and hospitalisation/death related to COVID-19, within 28 days, analysed using Bayesian models. The hypothesis for the time to recovery endpoint is evaluated first, and if superiority is declared on time to recovery, the hypothesis for the second co-primary endpoint of hospitalisation/death is then evaluated. To determine futility, we pre-specified a clinically meaningful benefit in time to first reported recovery as a hazard ratio of 1.2 or larger (equating to approximately 1.5 days benefit in the colchicine arm, assuming 9 days recovery in the usual care arm).
-
-ResultsThe trial opened on April 2, 2020, with randomisation to colchicine starting on March 04, 2021 and stopping on May 26, 2021, because the pre-specified time to recovery futility criterion was met. The primary analysis model included 2755 SARS-CoV-2 positive participants, randomised to colchicine (n=156), usual care (n=1145), and other treatments (n=1454). Time to first self-reported recovery was similar in the colchicine group compared with usual care with an estimated hazard ratio of 0.919 [95% credible interval 0.72 to 1.16] and an estimated increase of 1.14 days [-1.86 to 5.21] in median time to self-reported recovery for colchicine versus usual care. The probability of meaningful benefit in time to recovery was very low at 1.8%. Results were similar in comparisons with concurrent controls. COVID-19 related hospitalisations/deaths were similar in the colchicine group versus usual care, with an estimated odds ratio of 0.76 [0.28 to 1.89] and an estimated difference of -0.4% [-2.7% to 2.4]. One serious adverse event occurred in the colchicine group and one in usual care.
-
-ConclusionsColchicine did not improve time to recovery in people at higher risk of complications with COVID-19 in the community.
-
-Trial registrationISRCTN86534580.",infectious diseases,exact,100,100
 medRxiv,10.1101/2021.09.13.21263487,2021-09-16,https://medrxiv.org/cgi/content/short/2021.09.13.21263487,SARS-CoV-2 anti-spike IgG antibody responses after second dose of ChAdOx1 or BNT162b2 in the UK general population,Jia Wei; Koen B. Pouwels; Nicole Stoesser; Philippa C. Matthews; Ian Diamond; Ruth Studley; Emma Rourke; Duncan Cook; John I Bell; John N Newton; Jeremy Farrar; Alison Howarth; Brian D. Marsden; Sarah Hoosdally; E Yvonne Jones; David I Stuart; Derrick W. Crook; Tim E.A. Peto; A.Sarah Walker; David W. Eyre,University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"We investigated anti-spike IgG antibody responses and correlates of protection following second doses of ChAdOx1 or BNT162b2 SARS-CoV-2 vaccines in the UK general population. In 222,493 individuals, we found significant boosting of anti-spike IgG by second doses of both vaccines in all ages and using different dosing intervals, including the 3-week interval for BNT162b2. After second vaccination, BNT162b2 generated higher peak levels than ChAdOX1. Older individuals and males had lower peak levels with BNT162b2 but not ChAdOx1, while declines were similar across ages and sexes with ChAdOX1 or BNT162b2. Prior infection significantly increased antibody peak level and half-life with both vaccines. Anti-spike IgG levels were associated with protection from infection after vaccination and, to an even greater degree, after prior infection. At least 67% protection against infection was estimated to last for 2-3 months after two ChAdOx1 doses and 5-8 months after two BNT162b2 doses in those without prior infection, and 1-2 years for those unvaccinated after natural infection. A third booster dose may be needed, prioritised to ChAdOx1 recipients and those more clinically vulnerable.",infectious diseases,exact,100,100
 medRxiv,10.1101/2021.09.09.21263026,2021-09-13,https://medrxiv.org/cgi/content/short/2021.09.09.21263026,The clinically extremely vulnerable to COVID: Identification and changes in health care while self-isolating (shielding) during the coronavirus pandemic,Jessica Erin Butler; Mintu Nath; Dimitra Blana; William P Ball; Nicola Beech; Corri Black; Graham Osler; Sebastien Peytrignet; Katie Wilde; Artur Wozniak; Simon Sawhney,University of Aberdeen; University of Aberdeen; University of Aberdeen; University of Aberdeen; NHS Grampian; NHS Grampian and University of Aberdeen; NHS Grampian; Health Foundation; University of Aberdeen; University of Aberdeen; NHS Grampian and University of Aberdeen,"BackgroundIn March 2020, the government of Scotland identified people deemed clinically extremely vulnerable to COVID due to their pre-existing health conditions. These people were advised to strictly self-isolate (shield) at the start of the pandemic, except for necessary healthcare. We examined who was identified as clinically extremely vulnerable, how their healthcare changed during isolation, and whether this process exacerbated healthcare inequalities.
 
@@ -1420,7 +1384,6 @@ ResultsIn round 13 interim, we found 237 positives from 47,729 swabs giving a we
 
 DiscussionWe are entering a critical period with a number of important competing processes: continued vaccination rollout to the whole adult population in England, increased natural immunity through infection, reduced social mixing of children during school holidays, increased proportion of mixing occurring outdoors during summer, the intended full opening of hospitality and entertainment and cessation of mandated social distancing and mask wearing. Surveillance programmes are essential during this next phase of the epidemic to provide clear evidence to the government and the public on the levels and trends in prevalence of infections and their relationship to vaccine coverage, hospitalisations, deaths and Long COVID.",infectious diseases,exact,100,100
 medRxiv,10.1101/2021.07.02.21259897,2021-07-05,https://medrxiv.org/cgi/content/short/2021.07.02.21259897,Anti-spike antibody response to natural SARS-CoV-2 infection in the general population,Jia Wei; Philippa C Matthews; Nicole Stoesser; Thomas Maddox; Luke Lorenzi; Ruth Studley; John I Bell; John N Newton; Jeremy Farrar; Ian Diamond; Emma Rourke; Alison Howarth; Brian D Marsden; Sarah Hoosdally; E Yvonne Jones; David I Stuart; Derrick W Crook; Tim E.A. Peto; Koen B. Pouwels; A. Sarah Walker; David W Eyre,University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; Office for National Statistics; Office for National Statistics; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; NIHR Oxford Biomedical Research Centre; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"We estimated the duration and determinants of antibody response after SARS-CoV-2 infection in the general population using representative data from 7,256 United Kingdom COVID-19 infection survey participants who had positive swab SARS-CoV-2 PCR tests from 26-April-2020 to 14-June-2021. A latent class model classified 24% of participants as  non-responders not developing anti-spike antibodies. These seronegative non-responders were older, had higher SARS-CoV-2 cycle threshold values during infection (i.e. lower viral burden), and less frequently reported any symptoms. Among those who seroconverted, using Bayesian linear mixed models, the estimated anti-spike IgG peak level was 7.3-fold higher than the level previously associated with 50% protection against reinfection, with higher peak levels in older participants and those of non-white ethnicity. The estimated anti-spike IgG half-life was 184 days, being longer in females and those of white ethnicity. We estimated antibody levels associated with protection against reinfection likely last 1.5-2 years on average, with levels associated with protection from severe infection present for several years. These estimates could inform planning for vaccination booster strategies.",infectious diseases,exact,100,100
-medRxiv,10.1101/2021.06.28.21259529,2021-07-01,https://medrxiv.org/cgi/content/short/2021.06.28.21259529,Global patterns of genetic variation and association with clinical phenotypes at genes involved in SARS-CoV-2 infection,Chao Zhang; Anurag Verma; Yuanqing Feng; Marcelo C. R. Melo; Michael McQuillan; Matthew Hansen; Anastasia Lucas; Joseph Park; Alessia Ranciaro; Simon Thompson; Meghan A. Rubel; Michael C. Campbell; William Beggs; JIBRIL HIRBO; Sununguko Wata Mpoloka; Gaonyadiwe George Mokone; - Regeneron Genetic Center; Thomas Nyambo; Dawit Wolde Meskel; Gurja Belay; Charles Fokunang; Alfred K. Njamnshi; Sabah A. Omar; Scott Williams; Daniel Rader; Marylyn D Ritchie; Cesar de la Fuente Nunez; Giorgio Sirugo; Sarah Tishkoff,"University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; Perelman School of Medicine at the University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Howard; University of Pennsylvania; Vanderbilt University Medical Center; University of Botswana, Biological Sciences, Gaborone, Botswana; University of Botswana, Faculty of Medicine, Gaborone, Botswana; ; Department of Biochemistry, Kampala International University in Tanzania, Dar es Salaam, Tanzania; Addis Ababa University Department of Microbial Cellular and Molecular Biology, Addis Ababa, Ethiopia; Addis Ababa University Department of Microbial Cellular and Molecular Biology, Addis Ababa, Ethiopia; Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaounde I, Yaounde, Cameroon; Department of Neurology, Central Hospital Yaounde; Brain Research Africa Initiative (BRAIN), Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The ; Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya; Case Western Reserve University; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania","We investigated global patterns of genetic variation and signatures of natural selection at host genes relevant to SARS-CoV-2 infection (ACE2, TMPRSS2, DPP4, and LY6E). We analyzed novel data from 2,012 ethnically diverse Africans and 15,997 individuals of European and African ancestry with electronic health records, and integrated with global data from the 1000GP. At ACE2, we identified 41 non-synonymous variants that were rare in most populations, several of which impact protein function. However, three non-synonymous variants were common among Central African hunter-gatherers from Cameroon and are on haplotypes that exhibit signatures of positive selection. We identify strong signatures of selection impacting variation at regulatory regions influencing ACE2 expression in multiple African populations. At TMPRSS2, we identified 13 amino acid changes that are adaptive and specific to the human lineage. Genetic variants that are targets of natural selection are associated with clinical phenotypes common in patients with COVID-19.",genetic and genomic medicine,exact,100,100
 medRxiv,10.1101/2021.06.21.21259237,2021-06-28,https://medrxiv.org/cgi/content/short/2021.06.21.21259237,Changes in mobility pre and post first SARS-CoV-2 vaccination: findings from a prospective community cohort study including GPS movement tracking in England and Wales (Virus Watch),Vincent Nguyen; Yunzhe Liu; Richard Mumford; Ben Flanagan; Parth Patel; Isobel Braithwaite; Madhumita Shrotri; Thomas Edward Byrne; Sarah Beale; Anna Aryee; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Annalan M D Navaratnam; Pia Hardelid; Jana Kovar; Addy Pope; Tao Cheng; Andrew Hayward; Robert W Aldridge; - The Virus watch Collaborative,"Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; SpaceTimeLab, Department of Civil, Environmental and Geomatic Engineering, University College London, London, UK; Esri UK; Esri UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; Institute of Epidemiology and Health Care, University College London, London, UK; Esri UK; SpaceTimeLab, Department of Civil, Environmental and Geomatic Engineering, University College London, London, UK; Institute of Epidemiology and Health Care, University College London, London, UK; Centre for Public Health Data Science, Institute of Health Informatics, University College London, UK; ","BackgroundSome evidence suggests that individuals may change adherence to public health policies aimed at reducing contact, transmission and spread of the SARS-CoV-2 virus after they receive their first SARS-CoV-2 vaccination. In this study, we aim to estimate the rate of change in average daily travel distance from a participants registered address before and after SARS-CoV-2 vaccination.
 
 MethodParticipants were recruited into Virus Watch starting in June 2020. Weekly surveys were sent out to participants and vaccination status was collected from January 2021 onwards. Between September 2020 and February 2021, we invited 13,120 adult Virus Watch participants to contribute towards our tracker sub-cohort which uses the Global Positioning System (GPS) to collect data on movement. We used segmented linear regression to estimate the median daily travel distance before and after the first self-reported SARS-CoV-2 vaccine dose.
@@ -1541,47 +1504,9 @@ In total, 390 outbreaks were identified from SOI data and 264 of them allowed fo
 
 ConclusionsOur linked dataset analysis approach allows early identification of geographical regions and industrial sectors with higher rates of COVID-19 workplace outbreaks as well as estimation of attack rates by enterprise size and sector. This can be used to inform interventions to limit transmission of the virus. Our approach to analysing the workplace outbreak data can also be applied to calculation of outbreak rates and attack rates in other types of settings such as care homes, hospitals and educational settings.",epidemiology,exact,100,100
 medRxiv,10.1101/2021.05.08.21256867,2021-05-14,https://medrxiv.org/cgi/content/short/2021.05.08.21256867,SARS-CoV-2 lineage dynamics in England from January to March 2021 inferred from representative community samples,Oliver Eales; Andrew Page; Sonja N. Tang; Caroline E. Walters; Haowei Wang; David Haw; Alexander J. Trotter; Thanh Le Viet; Ebenezer Foster-Nyarko; Sophie Prosolek; Christina Atchinson; Deborah Ashby; Graham Cooke; Wendy Barclay; Christl A Donnelly; Justin O'Grady; Erik Volz; - The COVID-19 Genomics UK (COG-UK) Consortium; Ara Darzi; Helen Ward; Paul Elliott; Steven Riley,"School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; ; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc","Genomic surveillance for SARS-CoV-2 lineages informs our understanding of possible future changes in transmissibility and vaccine efficacy. However, small changes in the frequency of one lineage over another are often difficult to interpret because surveillance samples are obtained from a variety of sources. Here, we describe lineage dynamics and phylogenetic relationships using sequences obtained from a random community sample who provided a throat and nose swab for rt-PCR during the first three months of 2021 as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. Overall, diversity decreased during the first quarter of 2021, with the B.1.1.7 lineage (first identified in Kent) predominant, driven by a 0.3 unit higher reproduction number over the prior wild type. During January, positive samples were more likely B.1.1.7 in younger and middle-aged adults (aged 18 to 54) than in other age groups. Although individuals infected with the B.1.1.7 lineage were no more likely to report one or more classic COVID-19 symptoms compared to those infected with wild type, they were more likely to be antibody positive 6 weeks after infection. Viral load was higher in B.1.1.7 infection as measured by cycle threshold (Ct) values, but did not account for the increased rate of testing positive for antibodies. The presence of infections with non-imported B.1.351 lineage (first identified in South Africa) during January, but not during February or March, suggests initial establishment in the community followed by fade-out. However, this occurred during a period of stringent social distancing and targeted public health interventions and does not immediately imply similar lineages could not become established in the future. Sequence data from representative community surveys such as REACT-1 can augment routine genomic surveillance.",infectious diseases,exact,100,100
-medRxiv,10.1101/2021.05.06.21256755,2021-05-13,https://medrxiv.org/cgi/content/short/2021.05.06.21256755,Clinical coding of long COVID in English primary care: a federated analysis of 58 million patient records in situ using OpenSAFELY,- The OpenSAFELY Collaborative; Alex J Walker; Brian MacKenna; Peter Inglesby; Christopher T Rentsch; Helen J Curtis; Caroline E Morton; Jessica Morley; Amir Mehrkar; Sebastian CJ Bacon; George Hickman; Christopher Bates; Richard Croker; David Evans; Tom Ward; Jonathan Cockburn; Simon Davy; Krishnan Bhaskaran; Anna Schultze; Elizabeth J Williamson; William J Hulme; Helen I McDonald; Laurie Tomlinson; Rohini Mathur; Rosalind M Eggo; Kevin Wing; Angel YS Wong; Harriet Forbes; John Tazare; John Parry; Frank Hester; Sam Harper; Shaun O'Hanlon; Alex Eavis; Richard Jarvis; Dima Avramov; Paul Griffiths; Aaron Fowles; Nasreen Parkes; Ian J Douglas; Stephen JW Evans; Liam Smeeth; Ben Goldacre,; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; TPP; TPP; EMIS; EMIS; EMIS; EMIS; EMIS; EMIS; EMIS; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundLong COVID is a term to describe new or persistent symptoms at least four weeks after onset of acute COVID-19. Clinical codes to describe this phenomenon were released in November 2020 in the UK, but it is not known how these codes have been used in practice.
-
-MethodsWorking on behalf of NHS England, we used OpenSAFELY data encompassing 96% of the English population. We measured the proportion of people with a recorded code for long COVID, overall and by demographic factors, electronic health record software system, and week. We also measured variation in recording amongst practices.
-
-ResultsLong COVID was recorded for 23,273 people. Coding was unevenly distributed amongst practices, with 26.7% of practices having not used the codes at all. Regional variation was high, ranging between 20.3 per 100,000 people for East of England (95% confidence interval 19.3-21.4) and 55.6 in London (95% CI 54.1-57.1). The rate was higher amongst women (52.1, 95% CI 51.3-52.9) compared to men (28.1, 95% CI 27.5-28.7), and higher amongst practices using EMIS software (53.7, 95% CI 52.9-54.4) compared to TPP software (20.9, 95% CI 20.3-21.4).
-
-ConclusionsLong COVID coding in primary care is low compared with early reports of long COVID prevalence. This may reflect under-coding, sub-optimal communication of clinical terms, under-diagnosis, a true low prevalence of long COVID diagnosed by clinicians, or a combination of factors. We recommend increased awareness of diagnostic codes, to facilitate research and planning of services; and surveys of clinicians experiences, to complement ongoing patient surveys.",epidemiology,exact,100,100
 medRxiv,10.1101/2021.05.05.21256668,2021-05-09,https://medrxiv.org/cgi/content/short/2021.05.05.21256668,COVID-19: Affect recognition through voice analysis during the winter lockdown in Scotland,Sofia de la Fuente Garcia; Fasih Haider; Saturnino Luz,The University of Edinburgh; The University of Edinburgh; The University of Edinburgh,"The COVID-19 pandemic has led to unprecedented restrictions in peoples lifestyle which have affected their psychological wellbeing. In this context, this paper investigates the use of social signal processing techniques for remote assessment of emotions. It presents a machine learning method for affect recognition applied to recordings taken during the COVID-19 winter lockdown in Scotland (UK). This method is exclusively based on acoustic features extracted from voice recordings collected through home and mobile devices (i.e. phones, tablets), thus providing insight into the feasibility of monitoring peoples psychological wellbeing remotely, automatically and at scale. The proposed model is able to predict affect with a concordance correlation coefficient of 0.4230 (using Random Forest) and 0.3354 (using Decision Trees) for arousal and valence respectively.
 
 Clinical relevanceIn 2018/2019, 12% and 14% of Scottish adults reported depression and anxiety symptoms. Remote emotion recognition through home devices would support the detection of these difficulties, which are often underdiagnosed and, if untreated, may lead to temporal or chronic disability.",health informatics,exact,100,100
-medRxiv,10.1101/2021.05.04.21256507,2021-05-06,https://medrxiv.org/cgi/content/short/2021.05.04.21256507,Describing the burden of the COVID-19 pandemic in people with psoriasis: findings from a global cross-sectional study,Satveer K Mahil; Mark Yates; Zenas Z Yiu; Sinead M Langan; Teresa Tsakok; Nick Dand; Kayleigh J Mason; Helen McAteer; Freya Meynall; Bolaji Coker; Alexandra Vincent; Dominic Urmston; Amber Vesty; Jade Kelly; Camille Lancelot; Lucy Moorhead; Herve Bachelez; Francesca Capon; Claudia R Contreras; Claudia De La Cruz; Paola Di Meglio; Paolo Gisondi; Denis Jullien; Jo Lambert; Luigi Naldi; Sam Norton; Luis Puig; Phyllis Spuls; Tiago Torres; Richard B Warren; Hoseah Waweru; John Weinman; Matt A Brown; James B Galloway; Christopher M Griffiths; Jonathan N Barker; Catherine H Smith,"St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; Centre for Rheumatic Diseases, King's College London; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; Faculty of Epidemiology, and Population Health, London School of Hygiene and Tropical Medicine, London, UK; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King's College London, London, UK; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; The Psoriasis Association, Northampton, UK; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; NIHR Biomedical Research Centre at Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; NIHR Biomedical Research Centre at Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; The Psoriasis Association, Northampton, UK; The Psoriasis Association, Northampton, UK; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; International Federation of Psoriasis Associations; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; Department of Dermatology, AP-HP Hopital Saint-Louis, Paris, France; King's College London; Catedra de Dermatologia, Hospital de Clinicas, Facultad de Ciencias Medicas, Universidad Nacional de Asuncion, Paraguay; Clinica Dermacross, Santiago, Chile; King's College London; Section of Dermatology and Venereology, University of Verona, Verona, Italy; Department of Dermatology, Edouard Herriot Hospital, Hospices Civils de Lyon, University of Lyon, Lyon, France; Department of Dermatology, Ghent University, Ghent, Belgium; Centro Studi GISED, Bergamo, Italy; Psychology Department, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, UK; Department of Dermatology, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Catalonia, Spain; Department of Dermatology, Amsterdam Public Health/Infection and Immunology, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands; Department of Dermatology, Centro Hospitalar do Porto, Portugal; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; International Federation of Psoriasis Associations; School of Cancer and Pharmaceutical Sciences, Kings College London, London, UK; Centre for Rheumatic Diseases, King's College London, London, UK; Centre for Rheumatic Diseases, King's College London, London, UK; 3Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Res; NIHR Biomedical Research Centre at Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK","BackgroundIndirect excess morbidity has emerged as a major concern in the COVID-19 pandemic. People with psoriasis may be particularly vulnerable to this because of prevalent anxiety and depression, multimorbidity and therapeutic use of immunosuppression.
-
-ObjectiveCharacterise the factors associated with worsening psoriasis in the COVID-19 pandemic, using mental health status (anxiety and depression) as the main exposure of interest.
-
-MethodsGlobal cross-sectional study using a primary outcome of self-reported worsening of psoriasis. Individuals with psoriasis completed an online self-report questionnaire (PsoProtectMe; Psoriasis Patient Registry for Outcomes, Therapy and Epidemiology of COVID-19 Infection Me) between May 2020 and January 2021. Each individual completed a validated screen for anxiety (Generalized Anxiety Disorder-2) and depression (Patient Health Questionnaire-2). Odds ratios (OR) and 95% confidence intervals (CI) were estimated using multivariable logistic regression.
-
-Results4,043 people with psoriasis (without COVID-19) from 86 countries self-reported to PsoProtectMe (mean age 47.2 years [SD 15.1]; mean BMI 27.6kg/m2 [SD 6.0], 2,684 [66.4%] female and 3,016 [74.6%] of white European ethnicity). 1,728 (42.7%) participants (1322 [77%] female) reported worsening of their psoriasis in the pandemic. A positive screen for anxiety or depression associated with worsening psoriasis in age and gender adjusted (OR 2.04, 95% CI 1.77-2.36), and fully adjusted (OR 2.01, 95% CI 1.72-2.34) logistic regression models. Female sex, obesity, shielding behaviour and systemic immunosuppressant non-adherence also associated with worsening psoriasis. The commonest reason for non-adherence was concern regarding complications related to COVID-19.
-
-ConclusionsThese data indicate an association between poor mental health and worsening psoriasis in the pandemic. Access to holistic care including psychological support may mitigate potentially long-lasting effects of the pandemic on health outcomes in psoriasis. The study also highlights an urgent need to address patient concerns about immunosuppressant-related risks, which may be contributing to non-adherence.",dermatology,exact,100,100
-medRxiv,10.1101/2021.04.30.21256119,2021-04-30,https://medrxiv.org/cgi/content/short/2021.04.30.21256119,Association between oral anticoagulants and COVID-19 related outcomes: two cohort studies,Angel YS Wong; Laurie Tomlinson; Jeremy P Brown; William Elson; Alex J Walker; Anna J Schultze; Caroline E Morton; David Evans; Peter Inglesby; Brian MacKenna; Krishnan Bhaskaran; Christopher T. Rentsch; Emma Powell; Elizabeth T. Williamson; Richard Croker; Seb Bacon; William Hulme; Chris Bates; Helen J Curtis; Amir Mehrkar; Jonathan Cockburn; Helen I McDonald; Rohini I Mathur; Kevin Wing; Harriet Forbes; Rosalind M Eggo; Stephen Evans; Liam Smeeth; Ben Goldacre; Ian J Douglas,"London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Trop. Med.; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; US Department of Veterans Affairs, London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; TPP; London School of Medicine and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Bristol; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine","ObjectivesWe investigated the role of routinely prescribed oral anticoagulants (OACs) in COVID-19 outcomes, comparing current OAC use versus non-use in Study 1; and warfarin versus direct oral anticoagulants (DOACs) in Study 2.
-
-DesignTwo cohort studies, on behalf of NHS England.
-
-SettingPrimary care data and pseudonymously-linked SARS-CoV-2 antigen testing data, hospital admissions, and death records from England.
-
-ParticipantsStudy 1: 70,464 people with atrial fibrillation (AF) and CHA{square}DS{square}-VASc score of 2. Study 2: 372,746 people with non-valvular AF.
-
-Main outcome measuresTime to test for SARS-CoV-2, testing positive for SARS-CoV-2, COVID-19 related hospital admission, COVID-19 deaths or non-COVID-19 deaths in Cox regression.
-
-ResultsIn Study 1, we included 52,416 current OAC users and 18,048 non-users. We observed no difference in risk of being tested for SARS-CoV-2 associated with current use (adjusted HR, 1.01, 95%CI, 0.96 to 1.05) versus non-use. We observed a lower risk of testing positive for SARS-CoV-2 (adjusted HR, 0.73, 95%CI, 0.60 to 0.90), and COVID-19 deaths (adjusted HR, 0.69, 95%CI, 0.49 to 0.97) associated with current use versus non-use. In Study 2, we included 92,339 warfarin users and 280,407 DOAC users. We observed a lower risk of COVID-19 deaths (adjusted HR, 0.79, 95%CI, 0.76 to 0.83) associated with warfarin versus DOACs. Similar associations were found for all other outcomes.
-
-ConclusionsAmong people with AF and a CHA{square}DS{square}-VASc score of 2, those receiving OACs had a lower risk of receiving a positive COVID-19 test and severe COVID-19 outcomes than non-users; this might be explained by a causal effect of OACs in preventing severe COVID-19 outcomes or more cautious behaviours leading to reduced infection risk. There was no evidence of a higher risk of severe COVID-19 outcomes associated with warfarin versus DOACs in people with non-valvular AF regardless of CHA{square}DS{square}-VASc score.
-
-Key pointsO_ST_ABSWhat is already known on this topicC_ST_ABSO_LICurrent studies suggest that prophylactic or therapeutic anticoagulant use, particularly low molecular weight heparin, lower the risk of pulmonary embolism and mortality during hospitalisation among patients with COVID-19.
-C_LIO_LIReduced vitamin K status has been reported to be correlated with severity of COVID-19. This could mean that warfarin, as a vitamin K antagonist, is associated with more severe COVID-19 disease than non-vitamin K anticoagulants.
-C_LI
-
-What this study addsO_LIIn 70,464 people with atrial fibrillation, at the threshold of being treated with an OAC based on risk of stroke, we observed a lower risk of testing positive for SARS-CoV-2 and COVID-19 related deaths associated with routinely prescribed OACs, relative to non-use.
-C_LIO_LIThis might be explained by OACs preventing severe COVID-19 outcomes, or more cautious behaviours and environmental factors reducing the risk of SARS-CoV-2 infection in those taking OACs.
-C_LIO_LIIn 372,746 people with non-valvular atrial fibrillation, there was no evidence of a higher risk of severe COVID-19 outcomes associated with warfarin compared with DOACs.
-C_LI",epidemiology,exact,100,100
 medRxiv,10.1101/2021.04.26.21255732,2021-04-28,https://medrxiv.org/cgi/content/short/2021.04.26.21255732,Deprivation and Exposure to Public Activities during the COVID-19 Pandemic in England and Wales,Sarah Beale; Isobel Braithwaite; Annalan MD Navaratnam; Pia Hardelid; Alison Rodger; Anna Aryee; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Vincent Nguyen; Parth Patel; Madhumita Shrotri; Robert W Aldridge; Andrew C Hayward; - Virus Watch Collaborative,"University College London; University College London; University College London; University College London; University College London; Royal Free London NHS Foundation Trust,; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ","BackgroundDifferential exposure to public activities and non-household contacts may contribute to stark deprivation-related inequalities in SARS-CoV-2 infection and outcomes, but has not been directly investigated. We set out to investigate whether participants in Virus Watch - a large community cohort study based in England and Wales - reported different levels of exposure to public activities and non-household contacts during the Autumn-Winter phase of the COVID-19 pandemic according to postcode-level socioeconomic deprivation.
 
 MethodsParticipants (n=20120-25228 across surveys) reported their daily activities during three weekly periods in late November 2020, late December 2020, and mid-February 2021. Deprivation was quantified based on participants postcode of residence using English or Welsh Indices of Multiple Deprivation quintiles. We used Poisson mixed effect models with robust standard errors to estimate the relationship between deprivation and risk of exposure to public activities during each survey period.
@@ -1681,15 +1606,6 @@ ResultsSurvey response rate was 56% (20,792/36,998) in December 2020 and 52% (20
 
 ConclusionsOver four in five adults (86%) who were reluctant or intending to refuse a COVID-19 vaccine in December 2020 had changed their mind in February 2021 and planned on accepting, or had already accepted, a vaccine.",public and global health,exact,100,100
 medRxiv,10.1101/2021.03.24.21254227,2021-03-26,https://medrxiv.org/cgi/content/short/2021.03.24.21254227,COVID-19 Vaccination Prioritization Based on Cardiovascular Risk Factors and Number-Needed-to-Vaccinate to Prevent Death,Darryl P Leong; Amitava Banerjee; Salim Yusuf,McMaster University; University College London; McMaster University,"The supply limitations of COVID-19 vaccines have led to the need to prioritize vaccine distribution. Obesity, diabetes and hypertension have been associated with an increased risk of severe COVID-19 infection. Approximately half as many individuals with a cardiovascular risk factor need to be vaccinated against COVID-19 to prevent related death as compared with individuals without a risk factor. Our analysis suggests that prioritizing adults with these cardiovascular risk factors for vaccination is likely to be an efficient way to reduce population COVID-19 mortality.",epidemiology,exact,100,100
-medRxiv,10.1101/2021.03.26.21254390,2021-03-26,https://medrxiv.org/cgi/content/short/2021.03.26.21254390,Regional performance variation in external validation of four prediction models for severity of COVID-19 at hospital admission: An observational multi-centre cohort study,Kristin Wickstrom; Valeria Vitelli; Ewan Carr; Aleksander Rygh Holten; Rebecca Bendayan; Andrew Henry Reiner; Daniel Bean; Tom Searle; Anthony Shek; Zeljko Kraljevic; James T Teo; Richard Dobson; Kristian Tonby; Alvaro Kohn-Luque; Erik Koldberg Amundsen,Oslo University Hospital; University of Oslo; King's College London; Oslo University Hospital; King's College London; Oslo University Hospital; King's College London; King's College London; King's College London; King's College London; Kings College Hospital NHS Foundation Trust; Kings College London; Oslo University Hospital; University of Oslo; Oslo University Hospital,"BackgroundSeveral prediction models for coronavirus disease-19 (COVID-19) have been published. Prediction models should be externally validated to assess their performance before implementation. This observational cohort study aimed to validate published models of severity for hospitalized patients with COVID-19 using clinical and laboratory predictors.
-
-MethodsPrediction models fitting relevant inclusion criteria were chosen for validation. The outcome was either mortality or a composite outcome of mortality and ICU admission (severe disease). 1295 patients admitted with symptoms of COVID-19 at Kings Cross Hospital (KCH) in London, United Kingdom, and 307 patients at Oslo University Hospital (OUH) in Oslo, Norway were included. The performance of the models was assessed in terms of discrimination and calibration.
-
-ResultsWe identified two models for prediction of mortality (referred to as Xie and Zhang1) and two models for prediction of severe disease (Allenbach and Zhang2).
-
-The performance of the models was variable. For prediction of mortality Xie had good discrimination at OUH with an area under the receiver-operating characteristic (AUROC) 0.87 [95 % confidence interval (CI) 0.79-0.95] and acceptable discrimination at KCH, AUROC 0.79 [0.76-0.82]. In prediction of severe disease, Allenbach had acceptable discrimination (OUH AUROC 0.81 [0.74-0.88] and KCH AUROC 0.72 [0.68-0.75]). The Zhang models had moderate to poor discrimination. Initial calibration was poor for all models but improved with recalibration.
-
-ConclusionsThe performance of the four prediction models was variable. The Xie model had the best discrimination for mortality, while the Allenbach model had acceptable results for prediction of severe disease.",infectious diseases,exact,100,100
 medRxiv,10.1101/2021.03.26.21254391,2021-03-26,https://medrxiv.org/cgi/content/short/2021.03.26.21254391,Vaccine effectiveness of the first dose of ChAdOx1 nCoV-19 and BNT162b2 against SARS-CoV-2 infection in residents of Long-Term Care Facilities (VIVALDI study),Madhumita Shrotri; Maria Krutikov; Tom Palmer; Rebecca Giddings; Borscha Azmi; Sathyavani Subbarao; Christopher Fuller; Aidan Irwin-Singer; Daniel Davies; Gokhan Tut; Jamie Lopez Bernal; Paul Moss; Andrew Hayward; Andrew Copas; Laura Shallcross,"University College London; University College London; University College London; University College London; University College London; Public Health England; University College London; Department of Health and Social Care, UK; Palantir Technologies UK Ltd; University of Birmingham; Public Health England; University of Birmingham; University College London; University College London; University College London","BackgroundThe effectiveness of SARS-CoV-2 vaccines in frail older adults living in Long-Term Care Facilities (LTCFs) is uncertain. We estimated protective effects of the first dose of ChAdOx1 and BNT162b2 vaccines against infection in this population.
 
 MethodsCohort study comparing vaccinated and unvaccinated LTCF residents in England, undergoing routine asymptomatic testing (8 December 2020 - 15 March 2021). We estimated the relative hazard of PCR-positive infection using Cox proportional hazards regression, adjusting for age, sex, prior infection, local SARS-CoV-2 incidence, LTCF bed capacity, and clustering by LTCF.
@@ -1744,6 +1660,25 @@ medRxiv,10.1101/2021.03.04.21252931,2021-03-08,https://medrxiv.org/cgi/content/s
 
 TMPRSS2 rs12329760 is a common variant associated with a significantly decreased risk of severe COVID19. Further studies are needed to assess the expression of the TMPRSS2 across different age groups. Moreover, our results identify TMPRSS2 as a promising drug target, with a potential role for camostat mesilate, a drug approved for the treatment of chronic pancreatitis and postoperative reflux esophagitis, in the treatment of COVID19. Clinical trials are needed to confirm this.",genetic and genomic medicine,exact,100,100
 medRxiv,10.1101/2021.03.02.21252444,2021-03-03,https://medrxiv.org/cgi/content/short/2021.03.02.21252444,An overview of the National COVID-19 Chest Imaging Database: data quality and cohort analysis,Dominic Cushnan; Oscar Bennett; Rosalind Berka; Ottavia Bertolli; Ashwin Chopra; Samie Dorgham; Alberto Favaro; Tara Ganepola; Mark Halling-Brown; Gergely Imreh; Joseph Jacob; Emily Jefferson; François Lemarchand; Daniel Schofield; Jeremy C Wyatt; - NCCID Collaborative,"AI Lab, NHSX, London, UK; Faculty, London, UK; Faculty, London, UK; Faculty, London, UK; Faculty, London, UK; Faculty, London, UK; Faculty, London, UK; Faculty, London, UK; Scientific Computing, Royal Surrey NHS Foundation Trust, Guildford, UK; Faculty, London, UK; Centre for Medical Image Computing, University College London, London, UK; Health Informatics Centre (HIC), School of Medicine, University of Dundee, UK; AI Lab, NHSX, London, UK; AI Lab, NHSX, London, UK; University of Southampton, Southampton, UK; ","The National COVID-19 Chest Imaging Database (NCCID) is a centralised database containing chest X-rays, chest Computed Tomography (CT) scans and cardiac Magnetic Resonance Images (MRI) from patients across the UK, jointly established by NHSX, the British Society of Thoracic Imaging (BSTI), Royal Surrey NHS Foundation Trust (RSNFT) and Faculty. The objective of the initiative is to support a better understanding of the coronavirus SARS-CoV-2 disease (COVID-19) and development of machine learning (ML) technologies that will improve care for patients hospitalised with a severe COVID-19 infection. The NCCID is now accumulating data from 20 NHS Trusts and Health Boards across England and Wales, with a total contribution of approximately 25,000 imaging studies in the training set (at time of writing) and is actively being used as a research tool by several organisations. This paper introduces the training dataset, including a snapshot analysis performed by NHSX covering: the completeness of clinical data, the availability of image data for the various use-cases (diagnosis, prognosis and longitudinal risk) and potential model confounders within the imaging data. The aim is to inform both existing and potential data users of the NCCIDs suitability for developing diagnostic/prognostic models. In addition, a cohort analysis was performed to measure the representativeness of the NCCID to the wider COVID-19 affected population. Three major aspects were included: geographic, demographic and temporal coverage, revealing good alignment in some categories, e.g., sex and identifying areas for improvements to data collection methods, particularly with respect to geographic coverage. All analyses and discussions are focused on the implications for building ML tools that will generalise well to the clinical use cases.",radiology and imaging,exact,100,100
+medRxiv,10.1101/2021.02.27.21252593,2021-03-01,https://medrxiv.org/cgi/content/short/2021.02.27.21252593,Surgical activity in England and Wales during the COVID-19 pandemic: a nationwide observational cohort study,Thomas D Dobbs; John A G Gibson; Alexander J Fowler; Tom E Abbott; Tasnin Shahid; Fatemeh Torabi; Rowena Griffiths; Ronan A Lyons; Rupert M Pearse; Iain S Whitaker,"Swansea University Medical School; Swansea University Medical School; Queen Mary, University of London; Queen Mary University of London; Queen Mary University of London; Swansea University; Swansea University; Swansea University; Queen Mary University of London; Swansea University Medical School","ObjectivesTo report the volume of surgical activity and the number of cancelled surgical procedures during the COVID-19 pandemic.
+
+Design and settingAnalysis of electronic health record data from the National Health Service (NHS) in England and Wales.
+
+MethodsWe used hospital episode statistics for all adult patients undergoing surgery between 1st January 2020 and 31st December 2020. We identified surgical procedures using a previously published list of procedure codes. Procedures were stratified by urgency of surgery as defined by NHS England. We calculated the deficit of surgical activity by comparing the expected number of procedures from the years 2016-2019 with the actual number of procedures in 2020. We estimated the cumulative number of cancelled procedures by 31st December 2021 according patterns of activity in 2020.
+
+ResultsThe total number of surgical procedures carried out in England and Wales in 2020 was 3,102,674 compared to the predicted number of 4,671,338. This represents a 33.6% reduction in the national volume of surgical activity. There were 763,730 emergency surgical procedures (13.4% reduction), compared to 2,338,944 elective surgical procedures (38.6% reduction). The cumulative number of cancelled or postponed procedures was 1,568,664. We estimate that this will increase to 2,358,420 by 31st December 2021.
+
+ConclusionsThe volume of surgical activity in England and Wales was reduced by 33.6% in 2020, resulting in over 1,568,664 cancelled operations. This deficit will continue to grow in 2021.
+
+Summary boxesO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIThe COVID-19 pandemic necessitated a rapid change in the provision of care, including the suspension of a large proportion of surgical activity
+C_LIO_LISurgical activity has yet to return to normal and has been further impacted by subsequent waves of the pandemic
+C_LIO_LIThis will lead to a large backlog of cases
+C_LI
+
+What this study addsO_LI3,102,674 surgical procedures were performed in England and Wales during 2020, a 33.6% reduction on the expected yearly surgical activity
+C_LIO_LIOver 1.5 million procedures were not performed, with this deficit likely to continue to grow to 2.3 million by the end of 2021
+C_LIO_LIThis deficit is the equivalent of more than 6 months of pre-pandemic surgical activity, requiring a monumental financial and logistic challenge to manage
+C_LI",surgery,exact,100,100
 medRxiv,10.1101/2021.02.23.21251975,2021-02-25,https://medrxiv.org/cgi/content/short/2021.02.23.21251975,The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers (UK-REACH): Protocol for a prospective longitudinal cohort study of healthcare and ancillary workers in UK healthcare settings,Katherine Woolf; Carl Melbourne; Luke Bryant; Anna Louise Guyatt; Ian Christopher McManus; Amit Gupta; Robert C Free; Laura Nellums; Sue Carr; Catherine John; Christopher A Martin; Louise V Wain; Laura J Gray; Claire Garwood; Vishant Modhwadia; Keith Abrams; Martin D Tobin; Kamlesh Khunti; Manish Pareek; - UK-REACH Study Collaborative Group,"University College London; University of Leicester; University of Leicester; University of Leicester; University College London; University Hospitals Oxford NHS Foundation Trust; University of Leicester; University of Nottingham; General Medical Council, University Hospitals Leicester NHS Trust; University of Leicester; University of Leicester; University of Leicester; University of Leicester; University of Leicester; University of Leicester; University of York; University of Leicester; University of Leicester; University of Leicester; ","IntroductionThe COVID-19 pandemic has resulted in significant morbidity and mortality, and has devastated economies in many countries. Amongst the groups identified as being at increased risk from COVID-19 are healthcare workers (HCWs) and ethnic minority groups. Emerging evidence suggests HCWs from ethnic minority groups are at increased risk of adverse COVID-19-related physical and mental health outcomes. To date there has been no large-scale analysis of these risks in UK healthcare workers or ancillary workers in healthcare settings, stratified by ethnicity or occupation type, and adjusted for potential confounders. This paper reports the protocol for a prospective longitudinal questionnaire study of UK HCWs, as part of the UK-REACH programme (The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers).
 
 Methods and analysisA baseline questionnaire with follow-up questionnaires at 4 and 8 months will be administered to a national cohort of UK healthcare workers and ancillary workers in healthcare settings, and those registered with UK healthcare regulators. With consent, data will be linked to health records, and participants followed up for 25 years.
@@ -1931,7 +1866,6 @@ InterpretationSimilar associations of most individual-level factors with COVID-1
 
 FundingWellcome, Royal Society, National Institute for Health Research, National Institute for Health Research Oxford Biomedical Research Centre, UK Medical Research Council, Health Data Research UK.",infectious diseases,exact,100,100
 medRxiv,10.1101/2021.01.19.21249840,2021-01-20,https://medrxiv.org/cgi/content/short/2021.01.19.21249840,Impact of SARS-CoV-2 B.1.1.7 Spike variant on neutralisation potency of sera from individuals vaccinated with Pfizer vaccine BNT162b2,Dami Collier; Anna De Marco; Isabella Ferreira; Bo Meng; Rawlings Datir; Alexandra C. Walls; Steven A. Kemp S; Jessica Bassi; Dora Pinto; Chiara Silacci Fregni; Siro Bianchi; M. Alejandra Tortorici; John Bowen; Katja Culap; Stefano Jaconi; Elisabetta Cameroni; Gyorgy Snell; Matteo S. Pizzuto; Alessandra Franzetti Pellanda; Christian Garzoni; Agostino Riva; - The CITIID-NIHR BioResource COVID-19 Collaboration; Anne Elmer; Nathalie Kingston; Barbara Graves; Laura McCoy; Ken Smith; John Bradley; Ceron Ceron-Gutierrez L; Gabriela Barcenas-Morales; Herbert W. Virgin; Antonio Lanzavecchia; Luca Piccoli; Rainer Doffinger; Mark Wills; David Veesler; Davide Corti; Ravindra Gupta,UCL; Vir Biotechnology; University of Cambridge; University of Cambridge; University of Cambridge; University of Washington; University of Cambridge; Vir Biotechnology; Vir Biotechnology; Vir Biotechnology; Vir Biotechnology; University of Washington; University of Washington; Vir Biotehcnology; Vir Biotechnology; Vir Biotechnology; Vir Biotechnology; Vir Biotechnology; Clinica Luganese Moncucco; Clinica Luganese Moncucco; Luigi Sacco Hospital; ; Addenbrookes Hospital; NIHR; Cambridge NIHR; UCL; University of Cambridge; University of Cambridge; Addenbrookes Hospital; Addenbrookes Hospital; Vir Biotechnology; Vir Biotechnology; Vir Biotechnology; Addenbrookes Hospital; University of Cambridge; University of Washington; Vir Biotechnology; University of Cambridge,"Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) transmission is uncontrolled in many parts of the world, compounded in some areas by higher transmission potential of the B1.1.7 variant now seen in 50 countries. It is unclear whether responses to SARS-CoV-2 vaccines based on the prototypic strain will be impacted by mutations found in B.1.1.7. Here we assessed immune responses following vaccination with mRNA-based vaccine BNT162b2. We measured neutralising antibody responses following a single immunization using pseudoviruses expressing the wild-type Spike protein or the 8 amino acid mutations found in the B.1.1.7 spike protein. The vaccine sera exhibited a broad range of neutralising titres against the wild-type pseudoviruses that were modestly reduced against B.1.1.7 variant. This reduction was also evident in sera from some convalescent patients. Decreased B.1.1.7 neutralisation was also observed with monoclonal antibodies targeting the N-terminal domain (9 out of 10), the Receptor Binding Motif (RBM) (5 out of 31), but not in neutralising mAbs binding outside the RBM. Introduction of the E484K mutation in a B.1.1.7 background to reflect newly emerging viruses in the UK led to a more substantial loss of neutralising activity by vaccine-elicited antibodies and mAbs (19 out of 31) over that conferred by the B.1.1.7 mutations alone. E484K emergence on a B.1.1.7 background represents a threat to the vaccine BNT162b.",infectious diseases,exact,100,100
-medRxiv,10.1101/2021.01.14.21249801,2021-01-15,https://medrxiv.org/cgi/content/short/2021.01.14.21249801,Factor V is an immune inhibitor that is expressed at increased levels in leukocytes of patients with severe Covid-19,Jun Wang; Prasanti Kotagiri; Paul Lyons; Federica Mescia; Laura Bergamaschi; Lorinda Turner; Rafia Al-Lamki; Michael D Morgan; Fernando J Calero-Nieto; Karsten Bach; Nicole Mende; Nicola K Wilson; Emily R Watts; - Cambridge Institute of Therapeutic Immunology and Infectious Disease - NIHR Covid BioResource; Patrick Chinnery; Nathalie Kingston; Sofia Papadia; Kathleen Stirrups; Neil Walker; Ravindra K Gupta; Mark Toshner; Michael Weekes; James A Nathan; Sarah Walmsley; Willem Hendrik Ouwehand; Mary Kasanicki; Berthold Gottgens; John C Marioni; Smith GC Smith; Jordan S Pober; John R Bradley,University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Edinburgh; ; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; Cambridge University; University of Cambridge; University of Edinburgh; Prof; Cambridge University Hospitals; University of Cambridge; EMBL-EBI; University of Cambridge; Yale University; University of Cambridge,"Severe Covid-19 is associated with elevated plasma Factor V (FV) and increased risk of thromboembolism. We report that neutrophils, T regulatory cells (Tregs), and monocytes from patients with severe Covid-19 express FV, and expression correlates with T cell lymphopenia. In vitro full length FV, but not FV activated by thrombin cleavage, suppresses T cell proliferation. Increased and prolonged FV expression by cells of the innate and adaptive immune systems may contribute to lymphopenia in severe Covid-19. Activation by thrombin destroys the immunosuppressive properties of FV. Anticoagulation in Covid-19 patients may have the unintended consequence of suppressing the adaptive immune system.",infectious diseases,exact,100,100
 medRxiv,10.1101/2021.01.15.21249885,2021-01-15,https://medrxiv.org/cgi/content/short/2021.01.15.21249885,Epidemiology of post-COVID syndrome following hospitalisation with coronavirus: a retrospective cohort study,Daniel Ayoubkhani; Kamlesh Khunti; Vahe Nafilyan; Thomas Maddox; Ben Humberstone; Ian Diamond; Amitava Banerjee,Office for National Statistics; University of Leicester; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University College London,"ObjectivesThe epidemiology of post-COVID syndrome (PCS) is currently undefined. We quantified rates of organ-specific impairment following recovery from COVID-19 hospitalisation compared with those in a matched control group, and how the rate ratio (RR) varies by age, sex, and ethnicity.
 
 DesignObservational, retrospective, matched cohort study.
@@ -1975,7 +1909,6 @@ MethodsNose and throat swabs from 28-September-2020 to 2-January-2021 in the UKs
 Results15,166(0.98%) of 1,553,687 swabs were PCR-positive, 8,545(56%) with three genes detected and 3,531(23%) SGTF. SGTF comprised an increasing, and triple-gene positives a decreasing, percentage of infections from late-November in most UK regions/countries, e.g. from 15% to 38% to 81% over 1.5 months in London. SGTF Ct values correspondingly declined substantially to similar levels to triple-gene positives. Population-level SGTF positivity remained low (<0.25%) in all regions/countries until late-November, when marked increases with and without self-reported symptoms occurred in southern England (to 1.5-3%), despite stable rates of non-SGTF cases. SGTF positivity rates increased on average 6% more rapidly than rates of non-SGTF positives (95% CI 4-9%) supporting addition rather than replacement with B.1.1.7/VOC202012/01. Excess growth rates for SGTF vs non-SGTF positives were similar in those up to high school age (5% (1-8%)) and older individuals (6% (4-9%)).
 
 ConclusionsDirect population-representative estimates show that the B.1.1.7/VOC202012/01 SARS-CoV-2 variant leads to higher infection rates, but does not seem particularly adapted to any age group.",infectious diseases,exact,100,100
-medRxiv,10.1101/2021.01.11.20248765,2021-01-15,https://medrxiv.org/cgi/content/short/2021.01.11.20248765,Early immune pathology and persistent dysregulation characterise severe COVID-19,Laura Bergamaschi; Federica Mescia; Lorinda Turner; Aimee Hanson; Prasanti Kotagiri; Benjamin J. Dunmore; Helene Ruffieux; Aloka DeSa; Oisin Huhn; Michael D Morgan; Pehuen Pereyra Gerber; Mark R. Wills; Stephen Baker; Fernando J Calero Nieto; Rainer Doffinger; Gordon Dougan; Anne Elmer; Ian G Goodfellow; Ravindra K. Gupta; Myra Hosmillo; Kelvin Hunter; Nathalie Kingston; Paul J. Lehner; Nicholas J. Matheson; Jeremy K. Nicholson; Anna M. Petrunkina; Sylvia Richardson; Caroline Saunders; James E.D. Thaventhiran; Erik J.M. Toonen; Michael P. Weekes; - CambridgeInstituteofTherapeuticImmunologyandInfectiousDisease-NationalInstituteofHealthResearch(CITI; Berthold Gottgens; Mark Toshner; Christoph Hess; John R. Bradley; Paul A. Lyons; Kenneth G.C. Smith,"Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; MRC Biostatistics Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cancer Research UK, Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Clinical Research Centre, NIHR Clinical Research Facility, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge CB2 ; Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; The Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Murdoch, Western Australia WA 6150, Australia; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; MRC Biostatistics Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; Cambridge Clinical Research Centre, NIHR Clinical Research Facility, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge CB2 ; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; R&D Department, Hycult Biotech, 5405 PD Uden, The Netherlands; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; ; Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK","In a study of 207 SARS-CoV2-infected individuals with a range of severities followed over 12 weeks from symptom onset, we demonstrate that an early robust bystander CD8 T cell immune response, without systemic inflammation, is characteristic of asymptomatic or mild disease. Those presenting to hospital had delayed bystander responses and systemic inflammation already evident at around symptom onset. Such early evidence of inflammation suggests immunopathology may be inevitable in some individuals, or that preventative intervention might be needed before symptom onset. Viral load does not correlate with the development of this pathological response, but does with its subsequent severity. Immune recovery is complex, with profound persistent cellular abnormalities correlating with a change in the nature of the inflammatory response, where signatures characteristic of increased oxidative phosphorylation and reactive-oxygen species-associated inflammation replace those driven by TNF and IL-6. These late immunometabolic inflammatory changes and unresolved immune defects may have clinical implications.",infectious diseases,exact,100,100
 medRxiv,10.1101/2021.01.11.21249461,2021-01-13,https://medrxiv.org/cgi/content/short/2021.01.11.21249461,A national retrospective cohort study of mechanical ventilator availability and its association with mortality risk in intensive care patients with COVID-19,Harrison Wilde; Thomas A Mellan; Iwona Hawryluk; John Dennis; Spiros Denaxas; Christina Pagel; Andrew Duncan; Samir Bhatt; Seth Flaxman; Bilal A Mateen; Sebastian Vollmer,University of Warwick; Imperial College; Imperial College London; University of Exeter; University College London; University College London; Imperial College London; Imperial College London; Imperial College London; The Alan Turing Institute; University of Warwick,"ObjectivesTo determine if there is an association between survival rates in intensive care units (ICU) and occupancy of the unit on the day of admission.
 
 DesignNational retrospective observational cohort study during the COVID-19 pandemic.
@@ -2170,6 +2103,17 @@ ResultsThere were 17,576 positive tests over the three rounds. Antibody prevalen
 The decline from rounds 1 to 3 was largest in those who did not report a history of COVID-19, (-64.0% [-75.6, -52.3]), compared to -22.3% ([-27.0, -17.7]) in those with SARS-CoV-2 infection confirmed on PCR.
 
 DiscussionThese findings provide evidence of variable waning in antibody positivity over time such that, at the start of the second wave of infection in England, only 4.4% of adults had detectable IgG antibodies using an LFIA. Antibody positivity was greater in those who reported a positive PCR and lower in older people and those with asymptomatic infection. These data suggest the possibility of decreasing population immunity and increasing risk of reinfection as detectable antibodies decline in the population.",infectious diseases,exact,100,100
+medRxiv,10.1101/2020.10.14.20212555,2020-10-16,https://medrxiv.org/cgi/content/short/2020.10.14.20212555,Multi-organ impairment in low-risk individuals with long COVID,Andrea Dennis; Malgorzata Wamil; Sandeep Kapur; Johann Alberts; Andrew Badley; Gustav Anton Decker; Stacey A Rizza; Rajarshi Banerjee; Amitava Banerjee,Perspectum; Great Western Hospitals NHS Foundation Trust; Mayo Clinic Healthcare; Alliance Medical; Mayo Clinic; Mayo Clinic International; Mayo Clinic; Perspectum; University College London,"BackgroundSevere acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection has disproportionately affected older individuals and those with underlying medical conditions. Research has focused on short-term outcomes in hospital, and single organ involvement. Consequently, impact of long COVID (persistent symptoms three months post-infection) across multiple organs in low-risk individuals is yet to be assessed.
+
+MethodsAn ongoing prospective, longitudinal, two-centre, observational study was performed in individuals symptomatic after recovery from acute SARS-CoV-2 infection. Symptoms and organ function (heart, lungs, kidneys, liver, pancreas, spleen) were assessed by standardised questionnaires (EQ-5D-5L, Dyspnoea-12), blood investigations and quantitative magnetic resonance imaging, defining single and multi-organ impairment by consensus definitions.
+
+FindingsBetween April and September 2020, 201 individuals (mean age 44 (SD 11.0) years, 70% female, 87% white, 31% healthcare workers) completed assessments following SARS-CoV-2 infection (median 140, IQR 105-160 days after initial symptoms). The prevalence of pre-existing conditions (obesity: 20%, hypertension: 6%; diabetes: 2%; heart disease: 4%) was low, and only 18% of individuals had been hospitalised with COVID-19. Fatigue (98%), muscle aches (88%), breathlessness (87%), and headaches (83%) were the most frequently reported symptoms. Ongoing cardiorespiratory (92%) and gastrointestinal (73%) symptoms were common, and 42% of individuals had ten or more symptoms.
+
+There was evidence of mild organ impairment in heart (32%), lungs (33%), kidneys (12%), liver (10%), pancreas (17%), and spleen (6%). Single (66%) and multi-organ (25%) impairment was observed, and was significantly associated with risk of prior COVID-19 hospitalisation (p<0.05).
+
+InterpretationIn a young, low-risk population with ongoing symptoms, almost 70% of individuals have impairment in one or more organs four months after initial symptoms of SARS-CoV-2 infection. There are implications not only for burden of long COVID but also public health approaches which have assumed low risk in young people with no comorbidities.
+
+FundingThis work was supported by the UKs National Consortium of Intelligent Medical Imaging through the Industry Strategy Challenge Fund, Innovate UK Grant 104688, and also through the European Unions Horizon 2020 research and innovation programme under grant agreement No 719445.",health policy,exact,100,100
 medRxiv,10.1101/2020.10.12.20211227,2020-10-14,https://medrxiv.org/cgi/content/short/2020.10.12.20211227,High and increasing prevalence of SARS-CoV-2 swab positivity in England during end September beginning October 2020: REACT-1 round 5 updated report,Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E Walters; Haowei Wang; Christina J Atchison; Claudio Fronterre; Peter J Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Lancaster University; Imperial College London; Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London School of Public Health","BackgroundREACT-1 is quantifying prevalence of SARS-CoV-2 infection among random samples of the population in England based on PCR testing of self-administered nose and throat swabs. Here we report results from the fifth round of observations for swabs collected from the 18th September to 5th October 2020. This report updates and should be read alongside our round 5 interim report.
 
 MethodsRepresentative samples of the population aged 5 years and over in England with sample size ranging from 120,000 to 175,000 people at each round. Prevalence of PCR-confirmed SARS-CoV-2 infection, estimation of reproduction number (R) and time trends between and within rounds using exponential growth or decay models.
@@ -2179,21 +2123,6 @@ Results175,000 volunteers tested across England between 18th September and 5th O
 ConclusionRapid growth has led to high prevalence of SARS-CoV-2 virus in England, with highest rates in the North of England. Prevalence has increased in all age groups, including those at highest risk. Improved compliance with existing policy and, as necessary, additional interventions are required to control the spread of SARS-CoV-2 in the community and limit the numbers of hospital admissions and deaths from COVID-19.",infectious diseases,exact,100,100
 medRxiv,10.1101/2020.10.11.20210625,2020-10-13,https://medrxiv.org/cgi/content/short/2020.10.11.20210625,Mental health service activity during COVID-19 lockdown among individuals with learning disabilities: South London and Maudsley data on services and mortality from January to July 2020,Evangelia Martin; Eleanor Nuzum; Matthew Broadbent; Robert Stewart,King's College London; King's College London; South London and Maudsley NHS Foundation Trust; King's College London,"The lockdown and social distancing policy imposed due to the COVID-19 pandemic is likely to have had a widespread impact on mental healthcare service provision and use. Previous reports from the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for 1.2m residents in South London) highlighted a shift to virtual contacts among those accessing community mental health and home treatment teams and an increase in deaths over the pandemics first wave. However, there is a need to quantify this for individuals with particular vulnerabilities, including those with learning disabilities and other neurodevelopmental disorders. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource with 24-hourly updates of electronic mental health records data, this paper describes daily caseloads and contact numbers (face-to-face and virtual) for individuals with potential neurodevelopmental disorders across community, specialist, crisis and inpatient services. The report focussed on the period 1st January to 31st July 2020. We also report on daily accepted and discharged trust referrals, total trust caseloads and daily inpatient admissions and discharges for individuals with potential neurodevelopmental disorders. In addition, daily deaths are described for all current and previous SLaM service users with potential neurodevelopmental disorders over this period. In summary, comparing periods before and after 16th March 2020 there was a shift from face-to-face contacts to virtual contacts across all teams. The largest declines in caseloads and total contacts were seen in Home Treatment Team, Liaison/A&E and Older Adult teams. Reduced accepted referrals and inpatient admissions were observed and there was an 103% increase in average daily deaths in the period after 16th March, compared to the period 1st January to 15th March (or a 282% increase if the 2-month period from 16th March to 15th May was considered alone).",psychiatry and clinical psychology,exact,100,100
 medRxiv,10.1101/2020.10.09.20209957,2020-10-13,https://medrxiv.org/cgi/content/short/2020.10.09.20209957,Development and validation of the 4C Deterioration model for adults hospitalised with COVID-19,Rishi K Gupta; Ewen M Harrison; Antonia Ho; Annemarie B Docherty; Stephen R Knight; Maarten van Smeden; Ibrahim Abubakar; Marc Lipman; Matteo Quartagno; Riinu B Pius; Iain Buchan; Gail Carson; Thomas M Drake; Jake Dunning; Cameron J Fairfield; Carrol Gamble; Christopher A Green; Sophie Halpin; Hayley Hardwick; Karl Holden; Peter Horby; Clare Jackson; Kenneth McLean; Laura Merson; Jonathan S Nguyen-Van-Tam; Lisa Norman; Piero L Olliaro; Mark G Pritchard; Clark D Russell; James Scott-Brown; Catherine A Shaw; Aziz Sheikh; Tom Solomon; Cathie LM Sudlow; Olivia V Swann; Lance Turtle; Peter JM Openshaw; J Kenneth Baillie; Malcolm Gracie Semple; Mahdad Noursadeghi,"University College London; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; Medical Research Council University of Glasgow Centre for Virus Research, Glasgow, UK; University of Edinburgh; Centre for Medical Informatics, The Usher Institute, University of Edinburgh; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands; Institute for Global Health, University College London, Gower Street, London, WC1E 6BT; UCL Respiratory, Division of Medicine, University College London, London, UK; MRC Clinical Trials Unit, Institute of Clinical Trials and Methodology, University College London, London, UK; University of Edinburgh; Institute of Population Health Sciences, University of Liverpool; University of Oxford; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; National Infection Service Public Health England; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; University of Liverpool; Institute of Microbiology & Infection, University of Birmingham; Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK; University of Liverpool; University of Liverpool; ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; University of Liverpool; Centre for Medical Informatics, The Usher Institute, University of Edinburgh; University of Oxford; Division of Epidemiology and Public Health, University of Nottingham School of Medicine, Nottingham, UK; University of Edinburgh; University of Oxford; University of Oxford; Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK; School of Informatics, University of Edinburgh, Edinburgh, UK; Department of Clinical Surgery, University of Edinburgh; Centre for Medical Informatics, The Usher Institute, University of Edinburgh; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life; University of Edinburgh; Department of Child Life and Health, University of Edinburgh, UK; Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK; Imperial College London; Roslin Institute, University of Edinburgh; University of Liverpool; Division of Infection and Immunity, University College London, Gower Street, London, WC1E 6BT","Prognostic models to predict the risk of clinical deterioration in acute COVID-19 are required to inform clinical management decisions. Among 75,016 consecutive adults across England, Scotland and Wales prospectively recruited to the ISARIC Coronavirus Clinical Characterisation Consortium (ISARIC4C) study, we developed and validated a multivariable logistic regression model for in-hospital clinical deterioration (defined as any requirement of ventilatory support or critical care, or death) using 11 routinely measured variables. We used internal-external cross-validation to show consistent measures of discrimination, calibration and clinical utility across eight geographical regions. We further validated the final model in held-out data from 8,252 individuals in London, with similarly consistent performance (C-statistic 0.77 (95% CI 0.75 to 0.78); calibration-in-the-large 0.01 (-0.04 to 0.06); calibration slope 0.96 (0.90 to 1.02)). Importantly, this model demonstrated higher net benefit than using other candidate scores to inform decision-making. Our 4C Deterioration model thus demonstrates unprecedented clinical utility and generalisability to predict clinical deterioration among adults hospitalised with COVID-19.",infectious diseases,exact,100,100
-medRxiv,10.1101/2020.10.08.20209304,2020-10-12,https://medrxiv.org/cgi/content/short/2020.10.08.20209304,Prevalence of COVID-19-related risk factors and risk of severe influenza outcomes in cancer survivors: a matched cohort study using linked English electronic health records data,Helena Carreira; Helen Strongman; Maria Peppa; Helen I McDonald; Isabel dos-Santos-Silva; Susannah Stanway; Liam Smeeth; Krishnan Bhaskaran,"London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; NIHR Health Protection Research Unit in Immunisation; London School of Medicine and Tropical Medicine, NIHR Health Protection Research Unit in Immunisation; London School of Hygiene and Tropical Medicine; The Royal Marsden NHS Foundation Trust; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine","BackgroundPeople with active cancer are recognised as at risk of COVID-19 complications, but it is unclear whether the much larger population of cancer survivors is at elevated risk. We aimed to address this by comparing cancer survivors and cancer-free controls for (i) prevalence of comorbidities considered risk factors for COVID-19; and (ii) risk of severe influenza, as a marker of susceptibility to severe outcomes from epidemic respiratory viruses.
-
-MethodsWe included survivors ([&ge;]1 year) of the 20 most common cancers, and age, sex and general practice-matched cancer-free controls, derived from UK primary care data linked to cancer registrations, hospital admissions and death registrations. Comorbidity prevalences were calculated 1 and 5 years from cancer diagnosis. Risk of hospitalisation or death due to influenza was compared using Cox models adjusted for baseline demographics and comorbidities.
-
-Findings108,215 cancer survivors and 523,541 cancer-free controls were included. Cancer survivors had more asthma, other respiratory, cardiac, diabetes, neurological, renal, and liver disease, and less obesity, compared with controls, but there was variation by cancer site. There were 205 influenza hospitalisations/deaths, with cancer survivors at higher risk than controls (adjusted HR 2.78, 95% CI 2.04-3.80). Haematological cancer survivors had large elevated risks persisting for >10 years (HR overall 15.17, 7.84-29.35; HR >10 years from cancer diagnosis 10.06, 2.47-40.93). Survivors of other cancers had evidence of raised risk up to 5 years from cancer diagnosis only (HR 2.22, 1.31-3.74).
-
-InterpretationRisks of severe COVID-19 outcomes are likely to be elevated in cancer survivors. This should be taken into account in policies targeted at clinical risk groups, and vaccination for both influenza, and, when available, COVID-19, should be encouraged in cancer survivors.
-
-FundingWellcome Trust, Royal Society, NIHR.
-
-Research in contextO_ST_ABSEvidence before this studyC_ST_ABSFew data are available to date on how COVID-19 affects cancer survivors. We searched PubMed with the keywords ""influenza cancer survivors"" to identify studies that compared severe influenza outcomes in cancer survivors and in a control group. No study was identified.
-
-Added value of this studyIn this matched cohort study of routinely collected electronic health records, we demonstrated raised risks of influenza hospitalisation or mortality in survivors from haematological malignancies for >10 years after diagnosis, and in survivors from solid cancers up to 5 years after diagnosis.
-
-Implications of all the available evidenceCancer survivorship appears to be an important risk factor for severe influenza outcomes, suggesting that cancer survivors may also be at raised risk of poor COVID-19 outcomes. This should be taken into account in public health policies targeted at protecting clinical risk groups. Influenza vaccination should be encouraged in this group, and may need to be extended to a wider population of medium- to long-term cancer survivors than currently recommended.",oncology,exact,100,100
 medRxiv,10.1101/2020.10.03.20206375,2020-10-06,https://medrxiv.org/cgi/content/short/2020.10.03.20206375,"Renin Angiotensin System Inhibition and Susceptibility and Outcomes from COVID-19: A Systematic Review and Meta-analysis of 69,200 COVID-19 Patients",Yi Zhang; Shikai Yu; Yawei Xu; Bryan Williams,"Shanghai Tenth Peoples Hospital; Shanghai Tenth People's Hospital, Tongji University School of Medicine; Shanghai Tenth People Hospital; University College London","BackgroundEarly observational studies suggested that the use of the renin angiotensin system (RAS) inhibitors, specifically angiotensin converting enzyme inhibitors or angiotensin receptor blockers, may increase the risk of infection with SARS-CoV-2 and adversely affect the prognosis or survival of infected patients. To explore the impact of RAS inhibitor use on the risk of SARS-CoV-2 infection and the prognosis of SARS-CoV-2 infected patients, from all published studies.
 
 Methods and FindingsA systematic review and meta-analysis of the use of RAS inhibitors in relation to infection with SARS-CoV-2 and/or the severity and mortality associated with COVID-19 was conducted. English language bibliographic databases PubMed, Web of Science, OVID Embase, Scopus, MedRxiv, BioRxiv, searched from Jan 1st, 2020 to July 20th, 2020. 58 observational studies (69,200 COVID-19 patients and 3,103,335 controls) were included. There was no difference in the susceptibility to SARS-CoV-2 infection between RAS inhibitor users and non-users (unadjusted OR 1.05, 95% CI 0.90 to 1.21), (adjusted OR 0.93, 95% CI 0.85 to 1.02), (adjusted HR 1.07, 95% CI 0.87 to 1.31). There was no significant difference in the severe Covid-19 case rate between RAS inhibitor users and non-users (unadjusted OR 1.05, 95% CI 0.81 to 1.36), (adjusted OR 0.76, 95% CI 0.52 to 1.12), or in mortality due to COVID-19 between RAS inhibitor users and non-users (unadjusted OR 1.12, 95% CI 0.88 to 1.44), (adjusted OR 0.97, 95% CI 0.77 to 1.23), (adjusted HR 0.62, 95% CI 0.34 to 1.14).
@@ -2262,6 +2191,7 @@ There were no significant differences in non-COVID-related intensive care admiss
 ConclusionIn this large, single-centre study, there was a change in hospitalised case-mix when comparing April 2019 with April 2020: an increase in conditions which potentially reflect social isolation (falls, drug and alcohol misuse and psychiatric illness) and a decrease in conditions which rarely require in-patient hospital treatment (musculoskeletal pain and non-cardiac chest pain) especially among younger adults. These results highlight two areas for further research; the impact of social isolation on health and whether younger adults could be offered alternative health services to avoid potentially unnecessary hospital assessment.",emergency medicine,exact,100,100
 medRxiv,10.1101/2020.09.12.20191973,2020-09-14,https://medrxiv.org/cgi/content/short/2020.09.12.20191973,Inequality in access to health and care services during lockdown - Findings from the COVID-19 survey in five UK national longitudinal studies,Constantin-Cristian Topriceanu; Andrew Wong; James C Moon; Alun Hughes; David Bann; Nishi Chaturvedi; Praveetha Patalay; Gabriella Conti; Gabriella Captur,University College London; UCL; UCL; UCL; University College London; UCL; University College London; UCL; University College London,"Background: Access to health services and adequate care is influenced by sex, ethnicity, socio-economic position (SEP) and burden of co-morbidities. However, it is unknown whether the COVID-19 pandemic further deepened these already existing health inequalities. Methods: Participants were from five longitudinal age-homogenous British cohorts (born in 2001, 1990, 1970, 1958 and 1946). A web and telephone-based survey provided data on cancelled surgical or medical appointments, and the number of care hours received during the UK COVID-19 national lockdown. Using binary or ordered logistic regression, we evaluated whether these outcomes differed by sex, ethnicity, SEP and having a chronic illness. Adjustment was made for study-design, non-response weights, psychological distress, presence of children or adolescents in the household, keyworker status, and whether participants had received a shielding letter. Meta-analyses were performed across the cohorts and meta-regression evaluated the effect of age as a moderator. Findings: 14891 participants were included. Females (OR 1.40, 95% confidence interval [1.27,1.55]) and those with a chronic illness (OR 1.84 [1.65-2.05]) experienced significantly more cancellations during lockdown (all p<0.0001). Ethnic minorities and those with a chronic illness required a higher number of care hours during the lockdown (both OR approx. 2.00, all p<0.002). Age was not independently associated with either outcome in meta-regression. SEP was not associated with cancellation or care hours. Interpretation: The UK government's lockdown approach during the COVID-19 pandemic appears to have deepened existing health inequalities, impacting predominantly females, ethnic-minorities and those with chronic illnesses. Public health authorities need to implement urgent policies to ensure equitable access to health and care for all in preparation for a second wave.",public and global health,exact,100,100
 medRxiv,10.1101/2020.09.13.20193730,2020-09-14,https://medrxiv.org/cgi/content/short/2020.09.13.20193730,Mental health service activity during COVID-19 lockdown among individuals with Personality Disorders: South London and Maudsley data on services and mortality from January to May 2020,Eleanor Nuzum; Evangelia Martin; Matthew Broadbent; Robert Stewart,South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; King's College London,"The lockdown and social distancing policy imposed due to the COVID-19 pandemic is likely to have a widespread impact on mental healthcare for both services themselves and the people accessing those services. Previous reports from the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for 1.2m residents in South London) highlighted a shift to virtual contacts among those accessing community mental health and home treatment teams and an increase in deaths over the pandemics first wave. However, there is a need to understand this further for specific groups, including those diagnosed with a personality disorder who might have particular vulnerabilities. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource with 24-hourly updates of electronic mental health records data, this paper describes daily caseloads and contact numbers (face-to-face and virtual) for individuals with personality disorders across community, specialist, crisis and inpatient services. The report focussed on the period 1st January to 31st May 2020. We also report on daily accepted and discharged trust referrals, total trust caseloads and daily inpatient admissions and discharges for individuals with personality disorders. In addition, daily deaths are described for all current and previous SLaM service users with personality disorder over this period. In summary, comparing periods before and after 16th March 2020 there was a shift from face-to-face contacts to virtual contacts across all teams. Liaison and Older Adult teams showed the largest drop in caseloads, whereas Early Intervention in Psychosis service caseloads remained the same. Reduced accepted referrals and inpatient admissions were observed and there was a 28% increase in average daily deaths in the period after 16th March, compared to the period 1st January to 15th March.",psychiatry and clinical psychology,exact,100,100
+medRxiv,10.1101/2020.09.10.20191841,2020-09-11,https://medrxiv.org/cgi/content/short/2020.09.10.20191841,The King's College London Coronavirus Health and Experiences of Colleagues at King's Study: SARS-CoV-2 antibody response in an occupational sample,Daniel Leightley; Valentina Vitiello; Gabriella Bergin-Cartwright; Alice Wickersham; Katrina A S Davis; Sharon Stevelink; Matthew Hotopf; Reza Razavi; - On behalf of the KCL CHECK research team,"Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; The School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and   Medicine, King's College London, London, UK.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London; The School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King's College London; ","We report test results for SARS-CoV-2 antibodies in an occupational group of postgraduate research students and current members of staff at Kings College London. Between June and July 2020, antibody testing kits were sent to n=2296 participants; n=2004 (86.3%) responded, of whom n=1882 (93.9%) returned valid test results. Of those that returned valid results, n=124 (6.6%) tested positive for SARS-CoV-2 antibodies, with initial comparisons showing variation by age group and clinical exposure.",epidemiology,exact,100,100
 medRxiv,10.1101/2020.09.11.20192492,2020-09-11,https://medrxiv.org/cgi/content/short/2020.09.11.20192492,Resurgence of SARS-CoV-2 in England: detection by community antigen surveillance,Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E Walters; Haowei Wang; Christina J Atchison; Claudio Fronterre; Peter J Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Lancaster University; Imperial College London; Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London","Background Based on cases and deaths, transmission of SARS-CoV-2 in England peaked in late March and early April 2020 and then declined until the end of June. Since the start of July, cases have increased, while deaths have continued to decrease. Methods We report results from 594,000 swabs tested for SARS-CoV-2 virus obtained from a representative sample of people in England over four rounds collected regardless of symptoms, starting in May 2020 and finishing at the beginning of September 2020. Swabs for the most recent two rounds were taken between 24th July and 11th August and for round 4 between 22nd August and 7th September. We estimate weighted overall prevalence, doubling times between and within rounds and associated reproduction numbers. We obtained unweighted prevalence estimates by sub-groups: age, sex, region, ethnicity, key worker status, household size, for which we also estimated odds of infection. We identified clusters of swab-positive participants who were closer, on average, to other swab-positive participants than would be expected. Findings Over all four rounds of the study, we found that 72% (67%, 76%) of swab-positive individuals were asymptomatic at the time of swab and in the week prior. The epidemic declined between rounds 1 and 2, and rounds 2 and 3. However, the epidemic was increasing between rounds 3 and 4, with a doubling time of 17 (13, 23) days corresponding to an R value of 1.3 (1.2, 1.4). When analysing round 3 alone, we found that the epidemic had started to grow again with 93% probability. Using only the most recent round 4 data, we estimated a doubling time of 7.7 (5.5, 12.7) days, corresponding to an R value of 1.7 (1.4, 2.0). Cycle threshold values were lower (viral loads were higher) for rounds 1 and 4 than they were for rounds 2 and 3. In round 4, we observed the highest prevalence in participants aged 18 to 24 years at 0.25% (0.16%, 0.41%), increasing from 0.08% (0.04%, 0.18%) in round 3. We observed the lowest prevalence in those aged 65 and older at 0.04% (0.02%, 0.06%) which was stable compared with round 3. Participants of Asian ethnicity had elevated odds of infection. We identified clusters in and around London, transient clusters in the Midlands, and an expanding area of clustering in the North West and more recently in Yorkshire and the Humber. Interpretation Although low levels of transmission persisted in England through to mid-summer 2020, the prevalence of SARS-CoV-2 is now increasing. We found evidence of accelerating transmission at the end of August and beginning of September. Representative community antigen sampling can increase situational awareness and help improve public health decision making even at low prevalence.",infectious diseases,exact,100,100
 medRxiv,10.1101/2020.09.04.20187781,2020-09-09,https://medrxiv.org/cgi/content/short/2020.09.04.20187781,Hydroxychloroquine for prevention of COVID-19 mortality: a population-based cohort study,Christopher T Rentsch; Nicholas J DeVito; Brian MacKenna; Caroline E Morton; Krishnan Bhaskaran; Jeremy P Brown; Anna Schultze; William J Hulme; Richard Croker; Alex J Walker; Elizabeth J Williamson; Chris Bates; Seb Bacon; Amir Mehrkar; Helen J Curtis; David Evans; Kevin Wing; Peter Inglesby; Rohini Mathur; Henry Drysdale; Angel YS Wong; Helen I McDonald; Jonathan Cockburn; Harriet Forbes; John Parry; Frank Hester; Sam Harper; Liam Smeeth; Ian J Douglas; William G Dixon; Stephen JW Evans; Laurie Tomlinson; Ben Goldacre,London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; The Phoenix Partnership; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Medicine and Tropical Medicine; The Phoenix Partnership; London School of Hygiene and Tropical Medicine; The Phoenix Partnership; The Phoenix Partnership; The Phoenix Partnership; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; The University of Manchester; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundHydroxychloroquine has been shown to inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in vitro, but early clinical studies found no benefit treating patients with coronavirus disease 2019 (COVID-19). We set out to evaluate the effectiveness of hydroxychloroquine for prevention, as opposed to treatment, of COVID-19 mortality.
 
@@ -2383,6 +2313,26 @@ FindingsWe find a 0{middle dot}5% (95% credible interval: -0{middle dot}2%-1{mid
 InterpretationOur study provides some evidence of an effect of long-term NO2 exposure on COVID-19 mortality, while the effect of PM2{middle dot}5 remains more uncertain.
 
 FundingMedical Research Council, Wellcome Trust, Environmental Protection Agency and National Institutes of Health.",public and global health,exact,100,100
+medRxiv,10.1101/2020.08.10.20171033,2020-08-11,https://medrxiv.org/cgi/content/short/2020.08.10.20171033,Post-exertion oxygen saturation as a prognostic factor for adverse outcome in patients attending the emergency department with suspected COVID-19: Observational cohort study,Steve Goodacre; Ben Thomas; Ellen Lee; Laura Sutton; Katie Biggs; Carl Marincowitz; Amanda Loban; Simon Waterhouse; Richard Simmonds; Jose Schutter; Sarah Connelly; Elena Sheldon; Jamie Hall; Emma Young; Andrew Bentley; Kirsty Challen; Chris Fitzsimmons; Tim Harris; Fiona Lecky; Andrew Lee; Ian Maconochie; Darren Walter,"University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; Manchester University NHS Foundation Trust, Wythenshawe Hospital; Lancashire Teaching Hospitals NHS Foundation Trust; Sheffield Children's NHS Foundation Trust; Barts Health NHS Trust; University of Sheffield; University of Sheffield; Imperial College Healthcare NHS Trust; Manchester University NHS Foundation Trust","BackgroundMeasurement of post-exertion oxygen saturation has been proposed to assess illness severity in suspected COVID-19 infection. We aimed to determine the accuracy of post-exertional oxygen saturation for predicting adverse outcome in suspected COVID-19.
+
+MethodsWe undertook an observational cohort study across 70 emergency departments during first wave of the COVID-19 pandemic in the United Kingdom. We collected data prospectively, using a standardised assessment form, and retrospectively, using hospital records, from patients with suspected COVID-19, and reviewed hospital records at 30 days for adverse outcome (death or receiving organ support). Patients with post-exertion oxygen saturation recorded were selected for this analysis.
+
+ResultsWe analysed data from 817 patients with post-exertion oxygen saturation recorded after excluding 54 in whom measurement appeared unfeasible. The c-statistic for post-exertion change in oxygen saturation was 0.589 (95% confidence interval 0.465 to 0.713), and the positive and negative likelihood ratios of a 3% or more desaturation were respectively 1.78 (1.25 to 2.53) and 0.67 (0.46 to 0.98). Multivariable analysis showed that post-exertion oxygen saturation was not a significant predictor of adverse outcome when baseline clinical assessment was taken into account (p=0.368). Secondary analysis excluding patients in whom post-exertion measurement appeared inappropriate resulted in a c-statistic of 0.699 (0.581 to 0.817), likelihood ratios of 1.98 (1.26 to 3.10) and 0.61 (0.35 to 1.07), and some evidence of additional prognostic value on multivariable analysis (p=0.019).
+
+ConclusionsPost-exertion oxygen saturation provides modest prognostic information in the assessment of patients attending the emergency department with suspected COVID-19.
+
+RegistrationISRCTN registry, ISRCTN56149622, http://www.isrctn.com/ISRCTN28342533
+
+Key messagesWhat is already known on this subject?
+
+O_LIPost exertional decrease in oxygen saturation can be used to predict prognosis in chronic lung diseases
+C_LIO_LIPost exertional desaturation has been proposed as a way of predicting adverse outcome in people with suspected COVID-19
+C_LI
+
+What this study adds:
+
+O_LIPost-exertion oxygen saturation provides modest prognostic information in the assessment of patients attending the emergency department with suspected COVID-19
+C_LI",emergency medicine,exact,100,100
 medRxiv,10.1101/2020.08.07.20169490,2020-08-07,https://medrxiv.org/cgi/content/short/2020.08.07.20169490,HIV infection and COVID-19 death: population-based cohort analysis of UK primary care data and linked national death registrations within the OpenSAFELY platform,Krishnan Bhaskaran; Christopher T Rentsch; Brian MacKenna; Anna Schultz; Amir Mehrkar; Chris Bates; Rosalind M Eggo; Caroline E Morton; Seb Bacon; Peter Inglesby; Ian J Douglas; Alex J Walker; Helen I McDonald; Jonathan Cockburn; Elizabeth J Williamson; David Evans; Harriet J Forbes; Helen J Curtis; William Hulme; John Parry; Frank Hester; Sam Harper; Stephen JW Evans; Liam Smeeth; Ben Goldacre,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; TPP; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; TPP; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; TPP; TPP; TPP; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundIt is unclear whether HIV infection is associated with risk of COVID-19 death. We aimed to investigate this in a large-scale population-based study in England.
 
 MethodsWorking on behalf of NHS England, we used the OpenSAFELY platform to analyse routinely collected electronic primary care data linked to national death registrations. People with a primary care record for HIV infection were compared to people without HIV. COVID-19 death was defined by ICD-10 codes U07.1 or U07.2 anywhere on the death certificate. Cox regression models were used to estimate the association between HIV infection and COVID-19 death, initially adjusted for age and sex, then adding adjustment for index of multiple deprivation and ethnicity, and finally for a broad range of comorbidities. Interaction terms were added to assess effect modification by age, sex, ethnicity, comorbidities and calendar time.
@@ -2391,15 +2341,6 @@ Results17.3 million adults were included, of whom 27,480 (0.16%) had HIV recorde
 
 InterpretationHIV infection was associated with a markedly raised risk of COVID-19 death in a country with high levels of antiretroviral therapy coverage and viral suppression; the association was larger in people of black ethnicity.",infectious diseases,exact,100,100
 medRxiv,10.1101/2020.08.05.20169078,2020-08-06,https://medrxiv.org/cgi/content/short/2020.08.05.20169078,Transient dynamics of SARS-CoV-2 as England exited national lockdown,Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E Walters; Haowei Wang; Christina J Atchison; Peter Diggle; Deborah Ashby; Christl A. Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Imperial College London; Imperial College London; Imperial College Healthcare NHS Trust; Imperial College London; Imperial College London; Imperial College Healthcare NHS Trust; Imperial College London School of Public Health","Control of the COVID-19 pandemic requires a detailed understanding of prevalence of SARS-CoV-2 virus in the population. Case-based surveillance is necessarily biased towards symptomatic individuals and sensitive to varying patterns of reporting in space and time. The real-time assessment of community transmission antigen study (REACT-1) is designed to overcome these limitations by obtaining prevalence data based on a nose and throat swab RT-PCR test among a representative community-based sample in England, including asymptomatic individuals. Here, we describe results comparing rounds 1 and 2 carried out during May and mid June / early July 2020 respectively across 315 lower tier local authority areas. In round 1 we found 159 positive samples from 120,620 tested swabs while round 2 there were 123 positive samples from 159,199 tested swabs, indicating a downwards trend in prevalence from 0.13% (95% CI, 0.11%, 0.15%) to 0.077% (0.065%, 0.092%), a halving time of 38 (28, 58) days, and an R of 0.89 (0.86, 0.93). The proportion of swab-positive participants who were asymptomatic at the time of sampling increased from 69% (61%, 76%) in round 1 to 81% (73%, 87%) in round 2. Although health care and care home workers were infected far more frequently than other workers in round 1, the odds were markedly reduced in round 2. Age patterns of infection changed between rounds, with a reduction by a factor of five in prevalence in 18 to 24 year olds. Our data were suggestive of increased risk of infection in Black and Asian (mainly South Asian) ethnicities. Using regional and detailed case location data, we detected increased infection intensity in and near London. Under multiple sensitivity analyses, our results were robust to the possibility of false positives. At the end of the initial lockdown in England, we found continued decline in prevalence and a shift in the pattern of infection by age and occupation. Community-based sampling, including asymptomatic individuals, is necessary to fully understand the nature of ongoing transmission.",infectious diseases,exact,100,100
-medRxiv,10.1101/2020.08.03.20164897,2020-08-04,https://medrxiv.org/cgi/content/short/2020.08.03.20164897,Risk of hospitalisation with coronavirus disease 2019 in healthcare workers and their households:a nationwide linkage cohort study,Anoop SV Shah; Rachael Wood; Ciara Gribben; David Caldwell; Jennifer Bishop; Amanda Weir; Sharon Kennedy; Martin Reid; Alison Smith-Palmer; David Goldberg; Jim McMenamin; Colin Fischbacher; Chris Robertson; Sharon Hutchinson; Paul M McKeigue; Helen M Colhoun; David McAllister,London School of Hygiene and Tropical Medicine; Public Health Scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; Health protection scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; University of Edinburgh; University of Edinburgh; University of Glasgow,"ObjectiveMany healthcare staff work in high-risk settings for contracting and transmitting Severe Acute Respiratory Syndrome Coronavirus 2. Their risk of hospitalisation for coronavirus disease 2019 (COVID-19), and that of their households, is poorly understood.
-
-Design and settings and participantsDuring the peak period for COVID-19 infection in Scotland (1st March 2020 to 6th June 2020) we conducted a national record linkage study to compare the risk of COVID-19 hospitalisation among healthcare workers (age: 18-65 years), their households and other members of the general population.
-
-Main outcomeHospitalisation with COVID-19
-
-ResultsThe cohort comprised 158,445 healthcare workers, the majority being patient facing (90,733 / 158,445; 57.3%), and 229,905 household members. Of all COVID-19 hospitalisations in the working age population (18-65-year-old), 17.2% (360 / 2,097) were in healthcare workers or their households. Adjusting for age, sex, ethnicity, socio-economic deprivation and comorbidity, the risk of COVID-19 hospitalisation in non-patient facing healthcare workers and their households was similar to the risk in the general population (hazards ratio [HR] 0.81; 95%CI 0.52-1.26 and 0.86; 95%CI 0.49-1.51 respectively). In models adjusting for the same covariates however, patient facing healthcare workers, compared to non-patient facing healthcare workers, were at higher risk (HR 3.30; 95%CI 2.13-5.13); so too were household members of patient facing healthcare workers (HR 1.79; 95%CI 1.10-2.91). On sub-dividing patient-facing healthcare workers into those who worked in front-door, intensive care and non-intensive care aerosol generating settings and other, those in  front door roles were at higher risk (HR 2.09; 95%CI 1.49-2.94). For most patient facing healthcare workers and their households, the estimated absolute risk of COVID-19 hospitalisation was less than 0.5% but was 1% and above in older men with comorbidity.
-
-ConclusionsHealthcare workers and their households contribute a sixth of hospitalised COVID-19 cases. Whilst the absolute risk of hospitalisation was low overall, patient facing healthcare workers and their households had 3- and 2-fold increased risks of COVID-19 hospitalisation.",epidemiology,exact,100,100
 medRxiv,10.1101/2020.08.03.20167122,2020-08-04,https://medrxiv.org/cgi/content/short/2020.08.03.20167122,Ethnic minority groups in England and Wales - factors affecting the size and timing of elevated COVID-19 mortality: a retrospective cohort study linking Census and death records,Daniel Ayoubkhani; Vahe Nafilyan; Chris White; Peter Goldblatt; Charlotte Gaughan; Louisa Blackwell; Nicky Rogers; Amitava Banerjee; Kamlesh Khunti; Myer Glickman; Ben Humberstone; Ian Diamond,"Office for National Statistics; Office for National Statistics; Office for National Statistics; UCL Institute for Health Equity; Office for National Statistics; Office for National Statistics; Office for National Statistics; Institute of Health Informatics, University College London; Diabetes Research Centre, University of Leicester; Office for National Statistics; Office for National Statistics; Office for National Statistics","ObjectivesTo estimate population-level associations between ethnicity and coronavirus disease 2019 (COVID-19) mortality, and to investigate how ethnicity-specific mortality risk evolved over the course of the pandemic.
 
 DesignRetrospective cohort study using linked administrative data.
@@ -2617,6 +2558,7 @@ InterpretationThese results do not support a major role of ICS in protecting aga
 
 FundingThis work was supported by the Medical Research Council MR/V015737/1.",respiratory medicine,exact,100,100
 medRxiv,10.1101/2020.06.17.20133959,2020-06-20,https://medrxiv.org/cgi/content/short/2020.06.17.20133959,A downscaling approach to compare COVID-19 count data from databases aggregated at different spatial scales,Andre Python; Andreas Bender; Marta Blangiardo; Janine B Illian; Ying Lin; Baoli Liu; Tim C D Lucas; Siwei Tan; Yingying Wen; Davit Svanidze; Jianwei Yin,University of Oxford; LMU Munich; Imperial College London; Glasgow University; Fuzhou University; Oxford University; University of Oxford; Zhejiang University; Zhejiang University; Goettingen University; Zhejiang University,"As the COVID-19 pandemic continues to threaten various regions around the world, obtaining accurate and reliable COVID-19 data is crucial for governments and local communities aiming at rigorously assessing the extent and magnitude of the virus spread and deploying efficient interventions. Using data reported between January and February 2020 in China, we compared counts of COVID-19 from near-real time spatially disaggregated data (city-level) with fine-spatial scale predictions from a Bayesian downscaling regression model applied to a reference province-level dataset. The results highlight discrepancies in the counts of coronavirus-infected cases at district level and identify districts that may require further investigation.",epidemiology,exact,100,100
+medRxiv,10.1101/2020.06.13.20130419,2020-06-16,https://medrxiv.org/cgi/content/short/2020.06.13.20130419,Mental health service activity during COVID-19 lockdown: South London and Maudsley data on working age community and home treatment team services and mortality from February to mid-May 2020,Robert Stewart; Evangelia Martin; Matthew Broadbent,King's College London; King's College London; South London and Maudsley NHS Foundation Trust,"The lockdown and social distancing policy response to the COVID-19 pandemic in the UK has a potentially important impact on provision of mental healthcare; however, there has been relatively little quantification of this. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource with 24-hourly updates of electronic mental health records data, this paper describes daily caseloads and contact numbers (face-to-face and virtual) for home treatment teams (HTTs) and working age adult community mental health teams (CMHTs) from 1st February to 15th May 2020 at the South London and Maudsley NHS Trust (SLaM), a large mental health service provider for 1.2m residents in south London. In addition daily deaths are described for all current and previous SLaM service users over this period and the same dates in 2019. In summary, comparing periods before and after 16th March 2020 the CMHT sector showed relatively stable caseloads and total contact numbers, but a substantial shift from face-to-face to virtual contacts, while HTTs showed the same changeover but reductions in caseloads and total contacts (although potentially an activity rise again during May). Number of deaths for the two months between 16th March and 15th May were 2.4-fold higher in 2020 than 2019, with 958 excess deaths.",psychiatry and clinical psychology,exact,100,100
 medRxiv,10.1101/2020.06.12.20129494,2020-06-14,https://medrxiv.org/cgi/content/short/2020.06.12.20129494,Impact on mental health care and on mental health service users of the COVID-19 pandemic: a mixed methods survey of UK mental health care staff,Sonia Johnson; Christian Dalton-Locke; Norha Vera San Juan; Una Foye; Sian Oram; Alexandra Papamichail; Sabine Landau; Rachel Rowan Olive; Tamar Jeynes; Prisha Shah; Luke Sheridan Rains; Brynmor Lloyd-Evans; Sarah Carr; Helen Killaspy; Steve Gillard; Alan Simpson; - The COVID-19 Mental Health Policy Research Unit Group,"NIHR Mental Health Policy Research Unit, Division of Psychiatry, University College London, London, UK; NIHR Mental Health Policy Research Unit, Division of Psychiatry, University College London, London, UK; NIHR Mental Health Policy Research Unit, Institute of Psychiatry, Psychology & Neuroscience, King s College London, London, UK; NIHR Mental Health Policy Research Unit, Institute of Psychiatry, Psychology & Neuroscience, King s College London, London, UK; NIHR Mental Health Policy Research Unit, Institute of Psychiatry, Psychology & Neuroscience, King s College London, London, UK; NIHR Mental Health Policy Research Unit, Institute of Psychiatry, Psychology & Neuroscience, King s College London, London, UK; NIHR Mental Health Policy Research Unit, Institute of Psychiatry, Psychology & Neuroscience, King s College London, London, UK; Division of Psychiatry (NIHR Mental Health Policy Research Unit COVID-19 Co-Production Group), University College London, London, UK; Division of Psychiatry (NIHR Mental Health Policy Research Unit COVID-19 Co-Production Group), University College London, London, UK; Division of Psychiatry (NIHR Mental Health Policy Research Unit COVID-19 Co-Production Group), University College London, London, UK; NIHR Mental Health Policy Research Unit, Division of Psychiatry, University College London, London, UK; NIHR Mental Health Policy Research Unit, Division of Psychiatry, University College London, London, UK; School of Social Policy/ Institute for Mental Health, University of Birmingham, Birmingham, UK; 1.	NIHR Mental Health Policy Research Unit, Division of Psychiatry, University College London, London, UK; Population Health Research Institute, St George s, University of London, London, UK; NIHR Mental Health Policy Research Unit, Institute of Psychiatry, Psychology & Neuroscience, King s College London, London, UK; ","PurposeThe COVID-19 pandemic has potential to disrupt and burden the mental health care system, and to magnify inequalities experienced by mental health service users.
 
 MethodsWe investigated staff reports regarding the impact of the COVID-19 pandemic in its early weeks on mental health care and mental health service users in the UK using a mixed methods online survey. Recruitment channels included professional associations and networks, charities and social media. Quantitative findings were reported with descriptive statistics, and content analysis conducted for qualitative data.
@@ -2653,6 +2595,19 @@ Main outcome measuresAll-cause mortality weekly rates for each municipality, bas
 ResultsThere was strong evidence of excess mortality for Northern Italy; Lombardia showed higher mortality rates than expected from the end of February, with 23,946 (23,013 to 24,786) total excess deaths. North-West and North-East regions showed higher mortality from the beginning of March, with 6,942 (6,142 to 7,667) and 8,033 (7,061 to 9,044) total excess deaths respectively. After discounting for the number of COVID-19-confirmed deaths, Lombardia still registered 10,197 (9,264 to 11,037) excess deaths, while regions in the North-West and North-East had 2,572 (1,772 to 3,297) and 2,047 (1,075 to 3,058) extra deaths, respectively. We observed marked geographical differences at municipality level. The city of Bergamo (Lombardia) showed the largest percent excess 88.9% (81.9% to 95.2%) at the peak of the pandemic. An excess of 84.2% (73.8% to 93.4%) was also estimated at the same time for the city of Pesaro (Central Italy), in stark contrast with the rest of the region, which does not show evidence of excess deaths.
 
 ConclusionsOur study gives a comprehensive picture of the evolution of all-cause mortality in Italy from 2016 to 2020 and describes the spatio-temporal differences in excess mortality during the COVID-19 pandemic. Our model shows heterogeneous impact of COVID-19, and it can be used to help policy- makers target measures to limit the burden on the health-care system as well as reducing social and economic consequences. Our probabilistic methodology is useful for real-time mortality surveillance, continuously monitoring local temporal trends and flagging where and when mortality rates deviate from the expected range, which might suggest a second wave of the pandemic.",public and global health,exact,100,100
+medRxiv,10.1101/2020.06.02.20120642,2020-06-05,https://medrxiv.org/cgi/content/short/2020.06.02.20120642,Estimating excess visual loss in people with neovascular age-related macular degeneration during the COVID-19 pandemic,Darren S Thomas; Alasdair Warwick; Abraham Olvera-Barrios; Catherine Egan; Roy Schwartz; Sudeshna Patra; Haralabos Eleftheriadis; Anthony P Khawaja; Andrew Lotery; Philipp L Mueller; Robin Hamilton; Ella Preston; Paul Taylor; Adnan Tufail; - UK EMR Users Group,"Institute of Health Informatics, University College London, London, UK; Institute of Cardiovascular Science, University College London, London, UK & Moorfields Eye Hospital NHS Foundation Trust, London, UK.; Moorfields Eye Hospital NHS Turst & Institute of Ophthalmology UCL; Moorfields Eye Hospital NHS Foundation Trust, London, UK & Institute of Ophthalmology, UCL; Moorfields Eye Hospital NHS Foundation Trust, London, UK & Institute of Health Informatics, University College London, London, UK; Bart's Health NHS Trust, London, UK; King's College Hospital NHS Trust, London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK & Institute of Ophthalmology, UCL; Faculty of Medicine, University of Southampton, Southampton, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK & Institute of Ophthalmology, UCL; Moorfields Eye Hospital NHS Foundation Trust, London, UK; Institute of Health Informatics, University College London, London, UK; Moorfields Eye Hospital NHS Trust & Institute of Ophthalmology UCL; ","ObjectivesTo report the reduction in new neovascular age-related macular degeneration (nAMD) referrals during the COVID-19 pandemic and estimate the impact of delayed treatment on visual outcomes at one year.
+
+DesignRetrospective clinical audit and simulation model.
+
+SettingMultiple UK NHS ophthalmology centres.
+
+ParticipantsData on the reduction in new nAMD referrals was obtained from four NHS Trusts in England comparing April 2020 to April 2019. To estimate the potential impact on one-year visual outcomes, a stratified bootstrap simulation model was developed drawing on an electronic medical records dataset of 20,825 nAMD eyes from 27 NHS Trusts.
+
+Main outcome measuresSimulated mean visual acuity and proportions of eyes with vision [&le;]6/60, [&le;]6/24 and [&ge;]6/12 at one year under four hypothetical scenarios: no treatment delay, 3, 6 and 9-month treatment delays. Estimated additional number of eyes with vision [&le;]6/60 at one year nationally.
+
+ResultsThe number of nAMD referrals at four major eye treatment hospital groups based in England dropped on average by 72% (range 65 to 87%) in April 2020 compared to April 2019. Simulated one-year visual outcomes for 1000 nAMD eyes with a 3-month treatment delay suggested an increase in the proportion of eyes with vision [&le;]6/60 from 15.5% (13.2 to 17.9) to 23.3% (20.7 to25.9), and a decrease in the proportion of eyes with vision [&ge;]6/12 (driving vision) from 35.1% (32.1 to 38.1) to 26.4% (23.8 to29.2). Outcomes worsened incrementally with longer modelled delays. Assuming nAMD referrals are reduced to this level at the national level for only one month, these simulated results suggest an additional 186-365 eyes with vision [&le;]6/60 at one-year with even a short treatment delay.
+
+ConclusionsWe report a large decrease in nAMD referrals during the first month of COVID-19 lockdown and provide an important public health message regarding the risk of delayed treatment. As a conservative estimate, a treatment delay of 3 months could lead to a >50% relative increase in the number of eyes with vision [&le;]6/60 and 25% relative decrease in the number of eyes with driving vision at one year.",ophthalmology,exact,100,100
 medRxiv,10.1101/2020.06.01.20116608,2020-06-03,https://medrxiv.org/cgi/content/short/2020.06.01.20116608,Is death from Covid-19 a multistep process?,Neil Pearce; Giovenale Moirano; Milena Maule; Manolis Kogevinas; Xavier Rodo; Deborah Lawlor; Jan Vandenbroucke; Christina Vandenbroucke-Grauls; Fernando P Polack; Adnan Custovic,"London School of Hygiene and Tropical Medicine; University of Turin, Italy; University of Turin, Italy; ISGlobal; ISGlobal; University of Bristol; Leiden University Medical Center; Amsterdam UMC; Vanderbilt Unversity; Imperial College London","Covid-19 death has a different relationship with age than is the case for other severe respiratory pathogens. The Covid-19 death rate increases exponentially with age, and the main risk factors are age itself, as well as having underlying conditions such as hypertension, diabetes, cardiovascular disease, severe chronic respiratory disease and cancer. Furthermore, the almost complete lack of deaths in children suggests that infection alone is not sufficient to cause death; rather, one must have gone through a number of changes, either as a result of undefined aspects of aging, or as a result of chronic disease. These characteristics of Covid-19 death are consistent with the multistep model of disease, a model which has primarily been used for cancer, and more recently for amyotrophic lateral sclerosis (ALS). We applied the multi-step model to data on Covid-19 case fatality rates (CFRs) from China, South Korea, Italy, Spain and Japan. In all countries we found that a plot of ln (CFR) against ln (age) was approximately linear with a slope of about 5. As a comparison, we also conducted similar analyses for selected other respiratory diseases. SARS showed a similar log-log age-pattern to that of Covid-19, albeit with a lower slope, whereas seasonal and pandemic influenza showed quite different age-patterns. Thus, death from Covid-19 and SARS appears to follow a distinct age-pattern, consistent with a multistep model of disease that in the case of Covid-19 is probably defined by comorbidities and age producing immune-related susceptibility. Identification of these steps would be potentially important for prevention and therapy for SARS-COV-2 infection.",infectious diseases,exact,100,100
 medRxiv,10.1101/2020.05.27.20083287,2020-06-01,https://medrxiv.org/cgi/content/short/2020.05.27.20083287,Estimating excess mortality in people with cancer and multimorbidity in the COVID-19 emergency,Alvina G Lai; Laura Pasea; Amitava Banerjee; Spiros Denaxas; Michail Katsoulis; Wai Hoong Chang; Bryan Williams; Deenan Pillay; Mahdad Noursadeghi; David Linch; Derralynn Hughes; Martin D Forster; Clare Turnbull; Natalie K Fitzpatrick; Kathryn Boyd; Graham R Foster; Matt Cooper; Monica Jones; Kathy Pritchard-Jones; Richard Sullivan; Geoff Hall; Charlie Davie; Mark Lawler; Harry Hemingway,"University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; Royal Free NHS Foundation Trust; University College London; Institute of Cancer Research; University College London; Northern Ireland Cancer Network; Queen Mary University of London; DATA-CAN, Health Data Research UK hub for cancer hosted by UCLPartners; DATA-CAN, Health Data Research UK hub for cancer hosted by UCLPartners; DATA-CAN, Health Data Research UK hub for cancer hosted by UCLPartners; Kings College London; DATA-CAN, Health Data Research UK hub for cancer hosted by UCLPartners; DATA-CAN, Health Data Research UK hub for cancer hosted by UCLPartners; DATA-CAN, Health Data Research UK hub for cancer hosted by UCLPartners; University College London","BackgroundCancer and multiple non-cancer conditions are considered by the Centers for Disease Control and Prevention (CDC) as high risk conditions in the COVID-19 emergency. Professional societies have recommended changes in cancer service provision to minimize COVID-19 risks to cancer patients and health care workers. However, we do not know the extent to which cancer patients, in whom multi-morbidity is common, may be at higher overall risk of mortality as a net result of multiple factors including COVID-19 infection, changes in health services, and socioeconomic factors.
 
@@ -2698,6 +2653,17 @@ FindingsWe screened 270 studies and included 6. The pooled estimate for the asym
 InterpretationThe asymptomatic proportion of SARS-CoV-2 infections is relatively low when estimated from methodologically-appropriate studies. Further investigation into the degree and duration of infectiousness for asymptomatic infections is warranted.
 
 FundingMedical Research Council",infectious diseases,exact,100,100
+medRxiv,10.1101/2020.05.18.20086157,2020-05-22,https://medrxiv.org/cgi/content/short/2020.05.18.20086157,COVID-19 in Great Britain: epidemiological and clinical characteristics of the first few hundred (FF100) cases: a descriptive case series and case control analysis,Nicola L Boddington; Andre Charlett; Suzanne Elgohari; Jemma L Walker; Helen Mcdonald; Chloe Byers; Laura Coughlan; Tatiana Garcia Vilaplana; Rosie Whillock; Mary Sinnathamby; Nikolaos Panagiotopoulos; Louise Letley; Pauline MacDonald; Roberto Vivancos; Obaghe Edeghere; Joseph Shingleton; Emma Bennett; Daniel J Grint; Helen Strongman; Kathryn E Mansfield; Christopher Rentsch; Caroline Minassian; Ian J Douglas; Rohini Mathur; Maria Peppa; Simon Cottrell; Jim McMenamin; Maria Zambon; Mary Ramsay; Gavin Dabrera; Vanessa Saliba; Jamie Lopez Bernal,Public Health England; Public Health England; Public Health England; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Public Health Wales; Public Health Scotland; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England,"ObjectivesFollowing detection of the first virologically-confirmed cases of COVID-19 in Great Britain, an enhanced surveillance study was initiated by Public Health England to describe the clinical presentation, course of disease and underlying health conditions associated with infection of the first few hundred cases.
+
+MethodsInformation was collected on the first COVID-19 cases according to the First Few X WHO protocol. Case-control analyses of the sensitivity, specificity and predictive value of symptoms and underlying health conditions associated with infection were conducted. Point prevalences of underlying health conditions among the UK general population were presented.
+
+FindingsThe majority of FF100 cases were imported (51.4%), of which the majority had recent travel to Italy (71.4%). 24.7% were secondary cases acquired mainly through household contact (40.4%). Children had lower odds of COVID-19 infection compared with the general population.
+
+The clinical presentation of cases was dominated by cough, fever and fatigue. Non-linear relationships with age were observed for fever, and sensitivity and specificity of symptoms varied by age.
+
+Conditions associated with higher odds of COVID-19 infection (after adjusting for age and sex) were chronic heart disease, immunosuppression and multimorbidity.
+
+ConclusionThis study presents the first epidemiological and clinical summary of COVID-19 cases in Great Britain. The FFX study design enabled systematic data collection. The study characterized underlying health conditions associated with infection and set relative risks in context with population prevalence estimates. It also provides important evidence for generating case definitions to support public health risk assessment, clinical triage and diagnostic algorithms.",epidemiology,exact,100,100
 medRxiv,10.1101/2020.05.11.20098269,2020-05-18,https://medrxiv.org/cgi/content/short/2020.05.11.20098269,Accessibility and allocation of public parks and gardens during COVID-19 social distancing in England and Wales,Niloofar Shoari; Majid Ezzati; Jill Baumgartner; Diego Malacarne; Daniela Fecht,Imperial College London; Imperial College London; McGill University; Imperial College London; Imperial College London,"Visiting parks and gardens may attenuate the adverse physical and mental health impacts of social distancing implemented to reduce the spread of COVID-19. We quantified access to public parks and gardens in urban areas of England and Wales, and the potential for park crowdedness during periods of high use. We combined data from the Office for National Statistics and Ordnance Survey to quantify (i) the number of parks within 500 and 1,000 metres of urban postcodes (i.e., availability), (ii) the distance of postcodes to the nearest park (i.e., accessibility), and (iii) per-capita space in each park for people living within 1,000m. We examined how these measures vary by city and share of homes that are flats. Around 25.4 million people can access public parks or gardens within a ten-minute walk, while 3.8 million residents live farther away; of these 21% are children and 13% are elderly. Areas with a higher share of flats on average are closer to a park but people living in these areas are potentially less able to meet social distancing requirements while in parks during periods of high use. Cities in England and Wales can provide residents with access to green space that enables outdoor exercise and play during social distancing. Cities aiming to facilitate social distancing while keeping public green spaces open might require implementing measures such as dedicated park times for different age groups or entry allocation systems that, combined with smartphone apps or drones, can monitor and manage the total number of people using the park.",public and global health,exact,100,100
 medRxiv,10.1101/2020.05.08.20095687,2020-05-14,https://medrxiv.org/cgi/content/short/2020.05.08.20095687,Rapid implementation of real-time SARS-CoV-2 sequencing to investigate healthcare-associated COVID-19 infections,Luke W Meredith; William L Hamilton; Ben Warne; Charlotte J Houldcroft; Myra Hosmillo; Aminu Jahun; Martin D Curran; Surendra Parmar; Laura Caller; Sarah L Caddy; Fahad A Khokhar; Anna Yakovleva; Grant R Hall; Theresa Feltwell; Sally N Forret; Sushmita Sridhar; Michael p Weekes; Stephen Baker; Nicholas Brown; Elinor Moore; Theodore Gouliouris; Ashley Popay; Iain Roddick; Mark Reacher; Sharon Peacock; Gordon Dougan; M. Estee Torok; Ian Goodfellow,University of Cambridge; University of Cambridge; Cambridge University Hospitals NHS Foundation Trust; University of Cambridge; University of Cambridge; University of Cambridge; Public Health England; Public Health England; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; Cambridge University; Cambridge University; Public Health England; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Public Health England; Public Health England; Public Health England; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge,"BackgroundThe burden and impact of healthcare-associated COVID-19 infections is unknown. We aimed to examine the utility of rapid sequencing of SARS-CoV-2 combined with detailed epidemiological analysis to investigate healthcare-associated COVID-19 infections and to inform infection control measures.
 
@@ -2894,10 +2860,3 @@ DATA EXTRACTION AND ANALYSISSix authors independently assessed risk of bias usin
 RESULTSWe included 15 randomised trials investigating the effect of masks (14 trials) in healthcare workers and the general population and of quarantine (1 trial). We found no trials testing eye protection. Compared to no masks there was no reduction of influenza-like illness (ILI) cases (Risk Ratio 0.93, 95%CI 0.83 to 1.05) or influenza (Risk Ratio 0.84, 95%CI 0.61-1.17) for masks in the general population, nor in healthcare workers (Risk Ratio 0.37, 95%CI 0.05 to 2.50). There was no difference between surgical masks and N95 respirators: for ILI (Risk Ratio 0.83, 95%CI 0.63 to 1.08), for influenza (Risk Ratio 1.02, 95%CI 0.73 to 1.43). Harms were poorly reported and limited to discomfort with lower compliance. The only trial testing quarantining workers with household ILI contacts found a reduction in ILI cases, but increased risk of quarantined workers contracting influenza. All trials were conducted during seasonal ILI activity.
 
 CONCLUSIONSMost included trials had poor design, reporting and sparse events. There was insufficient evidence to provide a recommendation on the use of facial barriers without other measures. We found insufficient evidence for a difference between surgical masks and N95 respirators and limited evidence to support effectiveness of quarantine. Based on observational evidence from the previous SARS epidemic included in the previous version of our Cochrane review we recommend the use of masks combined with other measures.",public and global health,exact,100,100
-medRxiv,10.1101/2020.03.22.20040287,2020-03-24,https://medrxiv.org/cgi/content/short/2020.03.22.20040287,Estimating excess 1- year mortality from COVID-19 according to underlying conditions and age in England: a rapid analysis using NHS health records in 3.8 million adults,Amitava Banerjee; Laura Pasea; Steve Harris; Arturo Gonzalez-Izquierdo; Ana Torralbo; Laura Shallcross; Mahdad Noursadeghi; Deenan Pillay; Christina Pagel; Wai Keong Wong; Claudia Langenberg; Bryan Williams; Spiros Denaxas; Harry Hemingway,University College London; University College London; University College London Hospitals NHS Trust; University College London; University College London; UCL; University College London; University College London; University College London; University College London Hospitals NHS Trust; University of Cambridge; University College London; University College London; University College London,"BackgroundThe medical, health service, societal and economic impact of the COVID-19 emergency has unknown effects on overall population mortality. Previous models of population mortality are based on death over days among infected people, nearly all of whom (to date at least) have underlying conditions. Models have not incorporated information on high risk conditions or their longer term background (pre-COVID-19) mortality. We estimated the excess number of deaths over 1 year under different COVID-19 incidence rates and differing mortality impacts.
-
-MethodsUsing population based linked primary and secondary care electronic health records in England (HDR UK - CALIBER), we report the prevalence of underlying conditions defined by UK Public Health England COVID-19 guidelines (16 March 2020) in 3,862,012 individuals aged [&ge;]30 years from 1997-2017. We used previously validated phenotypes, openly available (https://caliberresearch.org/portal), for each condition using ICD-10 diagnosis, Read, procedure and medication codes. We estimated the 1-year mortality in each condition, and developed simple models of excess COVID-19-related deaths assuming relative risk (RR) of the impact of the emergency (compared to background mortality) of 1.2, 1.5 and 2.0.
-
-Findings20.0% of the population are at risk according to current PHE guidelines, of which; 13.7% were age>70 years and 6.3% aged [&le;]70 years with [&ge;]1 underlying condition (cardiovascular disease (2.3%), diabetes (2.2%), steroid therapy (1.9%), severe obesity (0.9%), chronic kidney disease (0.6%) and chronic obstructive pulmonary disease, COPD (0.5%). Multimorbidity (co-occurrence of [&ge;]2 conditions in an individual) was common (10.1%). The 1-year mortality in the at-risk population was 4.46%, and age and underlying conditions combine to influence background risk, varying markedly across conditions (5.9% in age>70 years, 8.6% for COPD and 13.1% in those with [&ge;]3 or more conditions). In a suppression scenario (at SARS CoV2 rates of 0.001% of the UK population), there would be minimal excess deaths (3 and 7 excess deaths at relative risk, RR, 1.5 and 2.0 respectively). At SARS CoV2 rates of 10% of the UK population (mitigation) the model estimates the numbers of excess deaths as: 13791, 34479 and 68957 (at RR 1.2, 1.5 and 2.0 respectively). At SARS CoV2 rates of 80% in the UK population (""do-nothing""), the model estimates the number of excess deaths as 110332, 275,830 and 551,659 (at RR 1.2, 1.5 and 2.0) respectively.
-
-InterpretationWe provide the public, researchers and policy makers a simple model to estimate the excess mortality over 1 year from COVID-19, based on underlying conditions at different ages. If the relative mortality impact of COVID-19 were to be about 20% (similar magnitude as the established winter vs summer mortality excess), then the excess deaths would be 0 when 1 in 100 000 (suppression), 13791 when 1 in 10 (mitigation) and 110332 when 8 in 10 are infected (""do nothing"") scenario. However, the relative impact of COVID-19 is unknown. If the emergency were to double the mortality risk, then we estimate 7, 68957 and 551,659 excess deaths in the same scenarios. These results may inform the need for more stringent suppression measures as well as efforts to target those at highest risk for a range of preventive interventions.",public and global health,exact,100,100
diff --git a/data/covid/preprints.exact.json b/data/covid/preprints.exact.json
index 4eacab1a..7dd3fc54 100644
--- a/data/covid/preprints.exact.json
+++ b/data/covid/preprints.exact.json
@@ -757,13 +757,13 @@
   },
   {
     "site": "medRxiv",
-    "doi": "10.1101/2022.08.13.22278733",
-    "date": "2022-08-16",
-    "link": "https://medrxiv.org/cgi/content/short/2022.08.13.22278733",
-    "title": "QCovid 4 - Predicting risk of death or hospitalisation from COVID-19 in adults testing positive for SARS-CoV-2 infection during the Omicron wave in England",
-    "authors": "Julia Hippisley-Cox; Kamlesh Khunti; Aziz Sheikh; Jonathan Nguyen-Van-Tam; Carol Coupland",
-    "affiliations": "University of Oxford; University of Leicester; University of Edinburgh; University of Nottingham; University of Oxford",
-    "abstract": "ObjectivesTo (a) derive and validate risk prediction algorithms (QCovid4) to estimate risk of COVID-19 mortality and hospitalisation in UK adults with a SARS-CoV-2 positive test during the  Omicron pandemic wave in England and (b) evaluate performance with earlier versions of algorithms developed in previous pandemic waves and the high-risk cohort identified by NHS Digital in England.\n\nDesignPopulation-based cohort study using the QResearch database linked to national data on COVID-19 vaccination, high risk patients prioritised for COVID-19 therapeutics, SARS-CoV-2 results, hospitalisation, cancer registry, systemic anticancer treatment, radiotherapy and the national death registry.\n\nSettings and study period1.3 million adults in the derivation cohort and 0.15 million adults in the validation cohort aged 18-100 years with a SARS-CoV-2 positive test between 11th December 2021 and 31st March 2022 with follow up to 30th June 2022.\n\nMain outcome measuresOur primary outcome was COVID-19 death. The secondary outcome of interest was COVID-19 hospital admission. Models fitted in the derivation cohort to derive risk equations using a range of predictor variables. Performance evaluated in a separate validation cohort.\n\nResultsOf 1,297,984 people with a SARS-CoV-2 positive test in the derivation cohort, 18,756 (1.45%) had a COVID-19 related hospital admission and 3,878 (0.3%) had a COVID-19 death during follow-up. Of the 145,404 people in the validation cohort, there were 2,124 (1.46%) COVID-19 admissions and 461 (0.3%) COVID-19 deaths.\n\nThe COVID-19 mortality rate in men increased with age and deprivation. In the QCovid4 model in men hazard ratios were highest for those with the following conditions (for 95% CI see Figure 1): kidney transplant (6.1-fold increase); Downs syndrome (4.9-fold); radiotherapy (3.1-fold); type 1 diabetes (3.4-fold); chemotherapy grade A (3.8-fold), grade B (5.8-fold); grade C (10.9-fold); solid organ transplant ever (2.4-fold); dementia (1.62-fold); Parkinsons disease (2.2-fold); liver cirrhosis (2.5-fold). Other conditions associated with increased COVID-19 mortality included learning disability, chronic kidney disease (stages 4 and 5), blood cancer, respiratory cancer, immunosuppressants, oral steroids, COPD, coronary heart disease, stroke, atrial fibrillation, heart failure, thromboembolism, rheumatoid/SLE, schizophrenia/bipolar disease sickle cell/HIV/SCID; type 2 diabetes. Results were similar in the model in women.\n\nO_FIG O_LINKSMALLFIG WIDTH=100 HEIGHT=200 SRC=\"FIGDIR/small/22278733v1_fig1.gif\" ALT=\"Figure 1\">\nView larger version (35K):\norg.highwire.dtl.DTLVardef@4e93b7org.highwire.dtl.DTLVardef@c3e600org.highwire.dtl.DTLVardef@1311bd4org.highwire.dtl.DTLVardef@11a3246_HPS_FORMAT_FIGEXP  M_FIG O_FLOATNOFigure 1C_FLOATNO QCOVID4 (mortality): Adjusted hazard ratios for COVID-19 death in men mutually adjusted and also adjusted for fractional polynomial terms for age and BMI\n\nC_FIG COVID-19 mortality risk was lower among those who had received COVID-19 vaccination compared with unvaccinated individuals with evidence of a dose response relationship. The reduced mortality rates associated with prior SARS-CoV-2 infection were similar in men (adjusted hazard ratio (HR) 0.51 (95% CI 0.40, 0.64)) and women (adjusted HR 0.55 (95%CI 0.45, 0.67)).\n\nThe QCOVID4 algorithm explained 76.6% (95%CI 74.4 to 78.8) of the variation in time to COVID-19 death (R2) in women. The D statistic was 3.70 (95%CI 3.48 to 3.93) and the Harrells C statistic was 0.965 (95%CI 0.951 to 0.978). The corresponding results for COVID-19 death in men were similar with R2 76.0% (95% 73.9 to 78.2); D statistic 3.65 (95%CI 3.43 to 3.86) and C statistic of 0.970 (95%CI 0.962 to 0.979). QCOVID4 discrimination for mortality was slightly higher than that for QCOVID1 and QCOVID2, but calibration was much improved.\n\nConclusionThe QCovid4 risk algorithm modelled from data during the UKs Omicron wave now includes vaccination dose and prior SARS-CoV-2 infection and predicts COVID-19 mortality among people with a positive test. It has excellent performance and could be used for targeting COVID-19 vaccination and therapeutics. Although large disparities in risks of severe COVID-19 outcomes among ethnic minority groups were observed during the early waves of the pandemic, these are much reduced now with no increased risk of mortality by ethnic group.\n\nWhat is knownO_LIThe QCOVID risk assessment algorithm for predicting risk of COVID-19 death or hospital admission based on individual characteristics has been used in England to identify people at high risk of severe COVID-19 outcomes, adding an additional 1.5 million people to the national shielded patient list in England and in the UK for prioritising people for COVID-19 vaccination.\nC_LIO_LIThere are ethnic disparities in severe COVID-19 outcomes which were most marked in the first pandemic wave in 2020.\nC_LIO_LICOVID-19 vaccinations and therapeutics (monoclonal antibodies and antivirals) are available but need to be targeted to those at highest risk of severe outcomes.\nC_LI\n\nWhat this study addsO_LIThe QCOVID4 risk algorithm using data from the Omicron wave now includes number of vaccination doses and prior SARS-CoV-2 infection. It has excellent performance both for ranking individuals (discrimination) and predicting levels of absolute risk (calibration) and can be used for targeting COVID-19 vaccination and therapeutics as well as individualised risk assessment.\nC_LIO_LIQCOVID4 more accurately identifies individuals at highest levels of absolute risk for targeted interventions than the  conditions-based approach adopted by NHS Digital based on relative risk of a list of medical conditions.\nC_LIO_LIAlthough large disparities in risks of severe COVID-19 outcomes among ethnic minority groups were observed during the early waves of the pandemic, these are much reduced now with no increased risk of mortality by ethnic group.\nC_LI",
+    "doi": "10.1101/2022.08.17.22278893",
+    "date": "2022-08-18",
+    "link": "https://medrxiv.org/cgi/content/short/2022.08.17.22278893",
+    "title": "Uptake of Sotrovimab for prevention of severe COVID-19 and its safety in the community in England",
+    "authors": "Martina Patone; Holly Tibble; Andrew JHL Snelling; Carol Coupland; Aziz Sheikh; Julia Hippisley-Cox",
+    "affiliations": "University of Oxford; University of Edinburgh; University of Oxford; University of Oxford; University of Edinburgh; University of Oxford",
+    "abstract": "Sotrovimab is a neutralising monoclonal antibody (nMAB), currently administrated in England to treat extremely clinically vulnerable COVID-19 patients. Trials have shown it to have mild or moderate side effects, however safety in real-world settings has not been yet evaluated. We used national databases to investigate its uptake and safety in community patients across England. We used a cohort study to describe uptake and a self-controlled case series design to evaluate the risks of 49 pre-specified suspected adverse events in the 2-28 days post-treatment. Between December 11, 2021 and May 24, 2022, there were 172,860 COVID-19 patients eligible for treatment. Of the 22,815 people who received Sotrovimab, 21,487 (94.2%) had a positive SARS-CoV-2 test and 5,999 (26.3%) were not on the eligible list. Between treated and untreated eligible individuals, the mean age (54.6, SD: 16.1 vs 54.1, SD: 18.3) and sex distribution (women: 60.9% vs 58.1%; men: 38.9% vs 41.1%) were similar. There were marked variations in uptake between ethnic groups, which was higher amongst Indian (15.0%; 95%CI 13.8, 16.3), Other Asian (13.7%; 95%CI 11.9, 15.8), White (13.4%; 95%CI 13.3, 13.6), and Bangladeshi (11.4%; 95%CI 8.8, 14.6); and lower amongst Black Caribbean individuals (6.4%; 95%CI 5.4, 7.5) and Black Africans (4.7%; 95%CI 4.1, 5.4). We found no increased risk of any of the suspected adverse events in the overall period of 2-28 days post-treatment, but an increased risk of rheumatoid arthritis (IRR 3.08, 95% CI 1.44, 6.58) and of systematic lupus erythematosus (IRR 5.15, 95% CI 1.60, 16.60) in the 2-3 days post-treatment, when we narrowed the risk period.\n\nFundingNational Institute of Health Research (Grant reference 135561)",
     "category": "epidemiology",
     "match_type": "exact",
     "author_similarity": 100,
@@ -783,6 +783,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2022.08.07.22278510",
+    "date": "2022-08-09",
+    "link": "https://medrxiv.org/cgi/content/short/2022.08.07.22278510",
+    "title": "Metabolomic and gut microbiome profiles across the spectrum of community-based COVID and non-COVID disease: A COVID-19 Biobank study.",
+    "authors": "Marc F \u00d6sterdahl; Ronan Whiston; Carole H Sudre; Francesco Asnicar; Nathan J Cheetham; Aitor Blanco Miguez; Vicky Bowyer; Michela Antonelli; Olivia Snell; Liane dos Santos Canas; Christina Hu; Jonathan Wolf; Cristina Menni; Michael Malim; Deborah Hart; Tim Spector; Sarah Berry; Nicola Segata; Katie Doores; Sebastien Ourselin; Emma L Duncan; Claire J Steves",
+    "affiliations": "King's College London; King's College London; King's College London; University of Trento; King's College London; University of Trento; King's College London; King's College London; King's College London; King's College London; ZOE Global Ltd.; ZOE Global Ltd.; King's College London; King's College London; King's College London; King's College London; King's College London; University of Trento; King's College London; King's College London; King's College London; King's College London",
+    "abstract": "Whilst many with SARS-CoV-2 infection have mild disease, managed in the community, individuals with cardiovascular risk factors experienced often more severe acute disease, requiring hospitalisation. Increasing concern has also developed over long symptom duration in many individuals, including the majority who managed acutely in the community. Risk factors for long symptom duration, including biological variables, are still poorly defined.\n\nWe examine post-illness metabolomic and gut-microbiome profiles, in community-dwelling participants with SARS-CoV-2, ranging from asymptomatic illness to Post-COVID Syndrome, and participants with prolonged non-COVID-19 illnesses. We also assess a pre-established metabolomic biomarker score for its association with illness duration.\n\nWe found an atherogenic-dyslipidaemic metabolic profile, and greater biomarker scores, associated with longer illness, both in individuals with and without SARS-CoV-2 infection. We found no association between illness duration and gut microbiome in convalescence.\n\nFindings highlight the potential role of cardiometabolic dysfunction to the experience of long illness duration, including after COVID-19.",
+    "category": "epidemiology",
+    "match_type": "exact",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2022.07.28.22278152",
@@ -1091,6 +1105,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2022.04.03.22272610",
+    "date": "2022-04-04",
+    "link": "https://medrxiv.org/cgi/content/short/2022.04.03.22272610",
+    "title": "Cardiac impairment in Long Covid 1-year post-SARS-CoV-2 infection",
+    "authors": "Adriana Roca-Fernandez; Malgorzata Wamil; Alison Telford; Valentina Carapella; Alessandra Borlotti; David Monteiro; Helena Thomaides-Brears; Matthew D Kelly; Andrea Dennis; Rajarshi Banerjee; Matthew Robson; Michael Brady; Gregory Lip; Sacha Bull; Melissa J Heightman; Ntobeko Ntusi; Amitava Banerjee",
+    "affiliations": "Perspectum Diagnostics; Great Western Hospital Foundation NHS Trust, Swindon, UK; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; University of Liverpool; Royal Berkshire Hospital, Reading; UCLH; University of Cape Town, Cape Town, South Africa; University College London",
+    "abstract": "BackgroundLong Covid is associated with multiple symptoms and impairment in multiple organs. Cardiac impairment has been reported to varying degrees by varying methodologies in cross-sectional studies. Using cardiac magnetic resonance (CMR), we investigated the 12-month trajectory of cardiac impairment in individuals with Long Covid.\n\nMethods534 individuals with Long Covid underwent baseline CMR (T1 and T2 mapping, cardiac mass, volumes, function, and strain) and multi-organ MRI at 6 months (IQR 4.3,7.3) since first post-COVID-19 symptoms and 330 were rescanned at 12.6 (IQR 11.4, 14.2) months if abnormal findings were reported at baseline. Symptoms, standardised questionnaires, and blood samples were collected at both timepoints. Cardiac impairment was defined as one or more of: low left or right ventricular ejection fraction (LVEF and RVEF), high left or right ventricular end diastolic volume (LVEDV and RVEDV), low 3D left ventricular global longitudinal strain (GLS), or elevated native T1 in [&ge;]3 cardiac segments. A significant change over time was reported by comparison with 92 healthy controls.\n\nResultsThe technical success of this multiorgan assessment in non-acute settings was 99.1% at baseline, and 98.3% at follow up, with 99.6% and 98.8% for CMR respectively. Of individuals with Long Covid, 102/534 [19%] had cardiac impairment at baseline; 71/102 had complete paired data at 12 months. Of those, 58% presented with ongoing cardiac impairment at 12 months. High sensitivity cardiac troponin I and B-type natriuretic peptide were not predictive of CMR findings, symptoms, or clinical outcomes. At baseline, low LVEF, high RVEDV and low GLS were associated with cardiac impairment. Low LVEF at baseline was associated with persistent cardiac impairment at 12 months.\n\nConclusionCardiac impairment, other than myocarditis, is present in 1 in 5 individuals with Long Covid at 6 months, persisting in over half of those at 12 months. Cardiac-related blood biomarkers are unable to identify cardiac impairment in Long COVID. Subtypes of disease (based on symptoms, examination, and investigations) and predictive biomarkers are yet to be established. Interventional trials with pre-specified subgroup analyses are required to inform therapeutic options.",
+    "category": "cardiovascular medicine",
+    "match_type": "exact",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2022.03.29.22273042",
@@ -1189,20 +1217,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2022.03.06.21267462",
-    "date": "2022-03-08",
-    "link": "https://medrxiv.org/cgi/content/short/2022.03.06.21267462",
-    "title": "Risk of myocarditis and pericarditis following COVID-19 vaccination in England and Wales",
-    "authors": "Samanatha Ip; Fatemeh Torabi; Spiros Denaxas; Ashley Akbari; Hoda Abbasizanjani; Rochelle Knight; Jennifer Anne Cooper; Rachel Denholm; Spencer Keene; Thomas Bolton; Sam Hollings; Efosa Omigi; Teri-Louise North; Arun Karthikeyan Suseeladevi; Emanuele Di Angelantonio; Kamlesh Khunti; Jonathan A C Sterne; Cathie Sudlow; William Whiteley; Angela Wood; Venexia Walker; - British Heart Foundation Data Science Centre (HDR UK) CVD-COVID-UK/COVID-IMPACT Consortium; - UK Covid-19 Longitudinal Health and Wellbeing National Core Study; - UK Covid-19 Data and Connectivity National Core Study",
-    "affiliations": "University of Cambridge; Swansea University; University College London; Swansea University; Swansea University; University of Bristol; University of Bristol; University of Bristol; University of Cambridge; Health Data Research UK; NHS Digital; NHS Digital; University of Bristol; University of Bristol; University of Cambridge; University of Leicester; University of Bristol; Health Data Research UK; University of Edinburgh; University of Cambridge; University of Bristol; ; ; ",
-    "abstract": "We describe our analyses of data from over 49.7 million people in England, representing near-complete coverage of the relevant population, to assess the risk of myocarditis and pericarditis following BNT162b2 and ChAdOx1 COVID-19 vaccination. A self-controlled case series (SCCS) design has previously reported increased risk of myocarditis after first ChAdOx1, BNT162b2, and mRNA-1273 dose and after second doses of mRNA COVID-19 vaccines in England. Here, we use a cohort design to estimate hazard ratios for hospitalised or fatal myocarditis/pericarditis after first and second doses of BNT162b2 and ChAdOx1 vaccinations. SCCS and cohort designs are subject to different assumptions and biases and therefore provide the opportunity for triangulation of evidence. In contrast to the findings from the SCCS approach previously reported for England, we found evidence for lower incidence of hospitalised or fatal myocarditis/pericarditis after first ChAdOx1 and BNT162b2 vaccination, as well as little evidence to suggest higher incidence of these events after second dose of either vaccination.",
-    "category": "epidemiology",
-    "match_type": "exact",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2022.02.24.22271466",
@@ -1387,13 +1401,13 @@
   },
   {
     "site": "medRxiv",
-    "doi": "10.1101/2021.12.22.21268252",
-    "date": "2021-12-24",
-    "link": "https://medrxiv.org/cgi/content/short/2021.12.22.21268252",
-    "title": "Rapid increase in Omicron infections in England during December 2021: REACT-1 study",
-    "authors": "Paul Elliott; Barbara Bodinier; Oliver Eales; Haowei Wang; David Haw; Joshua Elliott; Matthew Whitaker; Jakob Jonnerby; David Tang; Caroline E. Walters; Christina Atchinson; Peter J. Diggle; Andrew J. Page; Alex Trotter; Deborah Ashby; Wendy Barclay; Graham Taylor; Helen Ward; Ara Darzi; Graham Cooke; Marc Chadeau-Hyam; Christl A Donnelly",
-    "affiliations": "School of Public Health, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; Imperial College London; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; Imperial College London; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; Quadram Institute, Norwich, UK; Quadram Institute Bioscience; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research; Imperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research Centre, UKInstitute of Global Health Innovation at ; Department of Infectious Disease, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency",
-    "abstract": "BackgroundThe highest-ever recorded numbers of daily severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in England has been observed during December 2021 and have coincided with a rapid rise in the highly transmissible Omicron variant despite high levels of vaccination in the population. Although additional COVID-19 measures have been introduced in England and internationally to contain the epidemic, there remains uncertainty about the spread and severity of Omicron infections among the general population.\n\nMethodsThe REal-time Assessment of Community Transmission-1 (REACT-1) study has been monitoring the prevalence of SARS-CoV-2 infection in England since May 2020. REACT-1 obtains self-administered throat and nose swabs from a random sample of the population of England at ages 5 years and over. Swabs are tested for SARS-CoV-2 infection by reverse transcription polymerase chain reaction (RT-PCR) and samples testing positive are sent for viral genome sequencing. To date 16 rounds have been completed, each including [~]100,000 or more participants with data collected over a period of 2 to 3 weeks per month. Socio-demographic, lifestyle and clinical information (including previous history of COVID-19 and symptoms prior to swabbing) is collected by online or telephone questionnaire. Here we report results from round 14 (9-27 September 2021), round 15 (19 October - 05 November 2021) and round 16 (23 November - 14 December 2021) for a total of 297,728 participants with a valid RT-PCR test result, of whom 259,225 (87.1%) consented for linkage to their NHS records including detailed information on vaccination (vaccination status, date). We used these data to estimate community prevalence and trends by age and region, to evaluate vaccine effectiveness against infection in children ages 12 to 17 years, and effect of a third (booster) dose in adults, and to monitor the emergence of the Omicron variant in England.\n\nResultsWe observed a high overall prevalence of 1.41% (1.33%, 1.51%) in the community during round 16. We found strong evidence of an increase in prevalence during round 16 with an estimated reproduction number R of 1.13 (1.06, 1.09) for the whole of round 16 and 1.27 (1.14, 1.40) when restricting to observations from 1 December onwards. The reproduction number in those aged 18-54 years was estimated at 1.23 (1.14, 1.33) for the whole of round 16 and 1.41 (1.23, 1.61) from 1 December. Our data also provide strong evidence of a steep increase in prevalence in London with an estimated R of 1.62 (1.34, 1.93) from 1 December onwards and a daily prevalence reaching 6.07% (4.06%, 9.00%) on 14 December 2021. As of 1 to 11 December 2021, of the 275 lineages determined, 11 (4.0%) corresponded to the Omicron variant. The first Omicron infection was detected in London on 3 December, and subsequent infections mostly appeared in the South of England. The 11 Omicron cases were all aged 18 to 54 years, double-vaccinated (reflecting the large numbers of people who have received two doses of vaccine in this age group) but not boosted, 9 were men, 5 lived in London and 7 were symptomatic (5 with classic COVID-19 symptoms: loss or change of sense of smell or taste, fever, persistent cough), 2 were asymptomatic, and symptoms were unknown for 2 cases. The proportion of Omicron (vs Delta or Delta sub-lineages) was found to increase rapidly with a daily increase of 66.0% (32.7%, 127.3%) in the odds of Omicron (vs. Delta) infection, conditional on swab positivity. Highest prevalence of swab positivity by age was observed in (unvaccinated) children aged 5 to 11 years (4.74% [4.15%, 5.40%]) similar to the prevalence observed at these ages in round 15. In contrast, prevalence in children aged 12 to 17 years more than halved from 5.35% (4.78%, 5.99%) in round 15 to 2.31% (1.91%, 2.80%) in round 16. As of 14 December 2021, 76.6% children at ages 12 to 17 years had received at least one vaccine dose; we estimated that vaccine effectiveness against infection was 57.9% (44.1%, 68.3%) in this age group. In addition, the prevalence of swab positivity in adults aged 65 years and over fell by over 40% from 0.84% (0.72%, 0.99%) in round 15 to 0.48% (0.39%,0.59%) in round 16 and for those aged 75 years and over it fell by two-thirds from 0.63% (0.48%,0.82%) to 0.21% (0.13%,0.32%). At these ages a high proportion of participants (>90%) had received a third vaccine dose; we estimated that adults having received a third vaccine dose had a three- to four-fold lower risk of testing positive compared to those who had received two doses.\n\nConclusionA large fall in swab positivity from round 15 to round 16 among 12 to 17 year olds, most of whom have been vaccinated, contrasts with the continuing high prevalence among 5 to 11 year olds who have largely not been vaccinated. Likewise there were large falls in swab positivity among people aged 65 years and over, the vast majority of whom have had a third (booster) vaccine dose; these results reinforce the importance of the vaccine and booster campaign. However, the rapidly increasing prevalence of SARS-CoV-2 infections in England during December 2021, coincident with the rapid rise of Omicron infections, may lead to renewed pressure on health services. Additional measures beyond vaccination may be needed to control the current wave of infections and prevent health services (in England and other countries) from being overwhelmed.\n\nSummaryThe unprecedented rise in SARS-CoV-2 infections is concurrent with rapid spread of the Omicron variant in England and globally. We analysed prevalence of SARS-CoV-2 and its dynamics in England from end of November to mid-December 2021 among almost 100,000 participants from the REACT-1 study. Prevalence was high during December 2021 with rapid growth nationally and in London, and of the proportion of infections due to Omicron. We observed a large fall in swab positivity among mostly vaccinated older children (12-17 years) compared with unvaccinated younger children (5-11 years), and in adults who received a third vs. two doses of vaccine. Our results reiterate the importance of vaccination and booster campaigns; however, additional measures may be needed to control the rapid growth of the Omicron variant.",
+    "doi": "10.1101/2021.12.23.21268276",
+    "date": "2021-12-25",
+    "link": "https://medrxiv.org/cgi/content/short/2021.12.23.21268276",
+    "title": "Risk of myocarditis following sequential COVID-19 vaccinations by age and sex",
+    "authors": "Martina Patone; Winnie Xue Mei; Lahiru Handunnetthi; Sharon Dixon; Francesco Zaccardi; Manu Shankar-Hari; Peter Watkinson; Kamlesh Khunti; Anthony Harnden; Carol AC Coupland; Keith M. Channon; Nicholas L Mills; Aziz Sheikh; Julia Hippisley-Cox",
+    "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Leicester; University of Edinburgh; University of Oxford; University of Leicester; University of Oxford; University of Oxford; University of Oxford; University of Edinburgh; University of Edinburgh; University of Oxford",
+    "abstract": "In an updated self-controlled case series analysis of 42,200,614 people aged 13 years or more, we evaluate the association between COVID-19 vaccination and myocarditis, stratified by age and sex, including 10,978,507 people receiving a third vaccine dose. Myocarditis risk was increased during 1-28 days following a third dose of BNT162b2 (IRR 2.02, 95%CI 1.40, 2.91). Associations were strongest in males younger than 40 years for all vaccine types with an additional 3 (95%CI 1, 5) and 12 (95% CI 1,17) events per million estimated in the 1-28 days following a first dose of BNT162b2 and mRNA-1273, respectively; 14 (95%CI 8, 17), 12 (95%CI 1, 7) and 101 (95%CI 95, 104) additional events following a second dose of ChAdOx1, BNT162b2 and mRNA-1273, respectively; and 13 (95%CI 7, 15) additional events following a third dose of BNT162b2, compared with 7 (95%CI 2, 11) additional events following COVID-19 infection. An association between COVID-19 infection and myocarditis was observed in all ages for both sexes but was substantially higher in those older than 40 years. These findings have important implications for public health and vaccination policy.\n\nFundingHealth Data Research UK.",
     "category": "epidemiology",
     "match_type": "exact",
     "author_similarity": 100,
@@ -1401,13 +1415,13 @@
   },
   {
     "site": "medRxiv",
-    "doi": "10.1101/2021.12.21.21268214",
-    "date": "2021-12-23",
-    "link": "https://medrxiv.org/cgi/content/short/2021.12.21.21268214",
-    "title": "Comparative effectiveness of ChAdOx1 versus BNT162b2 vaccines against SARS-CoV-2 infections in England and Wales: A cohort analysis using trial emulation in the Virus Watch community data",
-    "authors": "Vincent Grigori Nguyen; Alexei Yavlinsky; Sarah Beale; Susan J Hoskins; Vasileios Lampos; Isobel Braithwaite; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Annalan M D Navaratnam; Parth Patel; Madhumita Shrotri; Sophie Weber; Andrew Hayward; Robert W Aldridge",
-    "affiliations": "University College London; University College London; University College London; Univerity College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London",
-    "abstract": "IntroductionInfections of SARS-CoV-2 in vaccinated individuals have been increasing globally. Understanding the associations between vaccine type and a post-vaccination infection could help prevent further COVID-19 waves. In this paper, we use trial emulation to understand the impact of a phased introduction of the vaccine in the UK driven by vulnerability and exposure status. We estimate the comparative effectiveness of COVID-19 vaccines (ChAdOx1 versus BNT162b2) against post-vaccination infections of SARS-CoV-2 in a community setting in England and Wales.\n\nMethodTrial emulation was conducted by pooling results from six cohorts whose recruitment was staggered between 1st January 2021 and 31st March 2021 and followed until 12th November 2021. Eligibility for each trial was based upon age (18+ at the time of vaccination), without prior signs of infection or an infection within the first 14 days of the first dose. Time from vaccination of ChAdOx1 or BNT162b2 until SARS-CoV-2 infection (positive polymerase chain reaction or lateral flow test after 14 of the vaccination) was modelled using Cox proportional hazards model for each cohort and adjusted for age at vaccination, gender, minority ethnic status, clinically vulnerable status and index of multiple deprivation quintile. For those without SARS-CoV-2 infection during the study period, follow-up was until loss-of-follow-up or end of study (12th November 2021). Pooled hazard ratios were generated using random-effects meta-analysis.\n\nResultsAcross six cohorts, there were a total of 21,283 participants who were eligible and vaccinated with either ChAdOx1 (n = 13,813) or BNT162b2 (n = 7,470) with a median follow-up time of 266 days (IQR: 235 - 282). By November 12th 2021, 750 (5.4%) adults who had ChAdOx1 as their vaccine experienced a SARS-CoV-2 infection, compared to 296 (4.0%) who had BNT162b2. We found that people who received ChAdOx1 vaccinations had 10.54 per 1000 people higher cumulative incidence for SARS-CoV-2 infection compared to BNT162b2 for infections during a maximum of 315 days of follow-up. When adjusted for age at vaccination, sex, minority ethnic status, index of multiple deprivation, and clinical vulnerability status, we found a pooled adjusted hazard ratio of 1.35 [HR: 1.35, 95%CI: 1.15 - 1.58], demonstrating a 35% increase in SARS-CoV-2 infections in people who received ChAdOx1 compared to BNT162b2.\n\nDiscussionWe found evidence of greater effectiveness of receiving BNT162b2 compared to ChAdOx1 vaccines against SARS-CoV-2 infection in England and Wales during a time period when Delta became the most prevalent variant of concern. Our findings demonstrate the importance of booster (third) doses to maintain protection and suggest that these should be prioritised to those who received ChAdOx1 as their primary course.",
+    "doi": "10.1101/2021.12.22.21268252",
+    "date": "2021-12-24",
+    "link": "https://medrxiv.org/cgi/content/short/2021.12.22.21268252",
+    "title": "Rapid increase in Omicron infections in England during December 2021: REACT-1 study",
+    "authors": "Paul Elliott; Barbara Bodinier; Oliver Eales; Haowei Wang; David Haw; Joshua Elliott; Matthew Whitaker; Jakob Jonnerby; David Tang; Caroline E. Walters; Christina Atchinson; Peter J. Diggle; Andrew J. Page; Alex Trotter; Deborah Ashby; Wendy Barclay; Graham Taylor; Helen Ward; Ara Darzi; Graham Cooke; Marc Chadeau-Hyam; Christl A Donnelly",
+    "affiliations": "School of Public Health, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; Imperial College London; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; Imperial College London; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; Quadram Institute, Norwich, UK; Quadram Institute Bioscience; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research; Imperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research Centre, UKInstitute of Global Health Innovation at ; Department of Infectious Disease, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency",
+    "abstract": "BackgroundThe highest-ever recorded numbers of daily severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in England has been observed during December 2021 and have coincided with a rapid rise in the highly transmissible Omicron variant despite high levels of vaccination in the population. Although additional COVID-19 measures have been introduced in England and internationally to contain the epidemic, there remains uncertainty about the spread and severity of Omicron infections among the general population.\n\nMethodsThe REal-time Assessment of Community Transmission-1 (REACT-1) study has been monitoring the prevalence of SARS-CoV-2 infection in England since May 2020. REACT-1 obtains self-administered throat and nose swabs from a random sample of the population of England at ages 5 years and over. Swabs are tested for SARS-CoV-2 infection by reverse transcription polymerase chain reaction (RT-PCR) and samples testing positive are sent for viral genome sequencing. To date 16 rounds have been completed, each including [~]100,000 or more participants with data collected over a period of 2 to 3 weeks per month. Socio-demographic, lifestyle and clinical information (including previous history of COVID-19 and symptoms prior to swabbing) is collected by online or telephone questionnaire. Here we report results from round 14 (9-27 September 2021), round 15 (19 October - 05 November 2021) and round 16 (23 November - 14 December 2021) for a total of 297,728 participants with a valid RT-PCR test result, of whom 259,225 (87.1%) consented for linkage to their NHS records including detailed information on vaccination (vaccination status, date). We used these data to estimate community prevalence and trends by age and region, to evaluate vaccine effectiveness against infection in children ages 12 to 17 years, and effect of a third (booster) dose in adults, and to monitor the emergence of the Omicron variant in England.\n\nResultsWe observed a high overall prevalence of 1.41% (1.33%, 1.51%) in the community during round 16. We found strong evidence of an increase in prevalence during round 16 with an estimated reproduction number R of 1.13 (1.06, 1.09) for the whole of round 16 and 1.27 (1.14, 1.40) when restricting to observations from 1 December onwards. The reproduction number in those aged 18-54 years was estimated at 1.23 (1.14, 1.33) for the whole of round 16 and 1.41 (1.23, 1.61) from 1 December. Our data also provide strong evidence of a steep increase in prevalence in London with an estimated R of 1.62 (1.34, 1.93) from 1 December onwards and a daily prevalence reaching 6.07% (4.06%, 9.00%) on 14 December 2021. As of 1 to 11 December 2021, of the 275 lineages determined, 11 (4.0%) corresponded to the Omicron variant. The first Omicron infection was detected in London on 3 December, and subsequent infections mostly appeared in the South of England. The 11 Omicron cases were all aged 18 to 54 years, double-vaccinated (reflecting the large numbers of people who have received two doses of vaccine in this age group) but not boosted, 9 were men, 5 lived in London and 7 were symptomatic (5 with classic COVID-19 symptoms: loss or change of sense of smell or taste, fever, persistent cough), 2 were asymptomatic, and symptoms were unknown for 2 cases. The proportion of Omicron (vs Delta or Delta sub-lineages) was found to increase rapidly with a daily increase of 66.0% (32.7%, 127.3%) in the odds of Omicron (vs. Delta) infection, conditional on swab positivity. Highest prevalence of swab positivity by age was observed in (unvaccinated) children aged 5 to 11 years (4.74% [4.15%, 5.40%]) similar to the prevalence observed at these ages in round 15. In contrast, prevalence in children aged 12 to 17 years more than halved from 5.35% (4.78%, 5.99%) in round 15 to 2.31% (1.91%, 2.80%) in round 16. As of 14 December 2021, 76.6% children at ages 12 to 17 years had received at least one vaccine dose; we estimated that vaccine effectiveness against infection was 57.9% (44.1%, 68.3%) in this age group. In addition, the prevalence of swab positivity in adults aged 65 years and over fell by over 40% from 0.84% (0.72%, 0.99%) in round 15 to 0.48% (0.39%,0.59%) in round 16 and for those aged 75 years and over it fell by two-thirds from 0.63% (0.48%,0.82%) to 0.21% (0.13%,0.32%). At these ages a high proportion of participants (>90%) had received a third vaccine dose; we estimated that adults having received a third vaccine dose had a three- to four-fold lower risk of testing positive compared to those who had received two doses.\n\nConclusionA large fall in swab positivity from round 15 to round 16 among 12 to 17 year olds, most of whom have been vaccinated, contrasts with the continuing high prevalence among 5 to 11 year olds who have largely not been vaccinated. Likewise there were large falls in swab positivity among people aged 65 years and over, the vast majority of whom have had a third (booster) vaccine dose; these results reinforce the importance of the vaccine and booster campaign. However, the rapidly increasing prevalence of SARS-CoV-2 infections in England during December 2021, coincident with the rapid rise of Omicron infections, may lead to renewed pressure on health services. Additional measures beyond vaccination may be needed to control the current wave of infections and prevent health services (in England and other countries) from being overwhelmed.\n\nSummaryThe unprecedented rise in SARS-CoV-2 infections is concurrent with rapid spread of the Omicron variant in England and globally. We analysed prevalence of SARS-CoV-2 and its dynamics in England from end of November to mid-December 2021 among almost 100,000 participants from the REACT-1 study. Prevalence was high during December 2021 with rapid growth nationally and in London, and of the proportion of infections due to Omicron. We observed a large fall in swab positivity among mostly vaccinated older children (12-17 years) compared with unvaccinated younger children (5-11 years), and in adults who received a third vs. two doses of vaccine. Our results reiterate the importance of vaccination and booster campaigns; however, additional measures may be needed to control the rapid growth of the Omicron variant.",
     "category": "epidemiology",
     "match_type": "exact",
     "author_similarity": 100,
@@ -1511,6 +1525,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2021.12.14.21267460",
+    "date": "2021-12-15",
+    "link": "https://medrxiv.org/cgi/content/short/2021.12.14.21267460",
+    "title": "Differential Risk of SARS-CoV-2 Infection by Occupation: Evidence from the Virus Watch prospective cohort study in England and Wales",
+    "authors": "Sarah Beale; Susan J Hoskins; Thomas Edward Byrne; Erica Wing Lam Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Annalan MD Navaratnam; Vincent Nguyen; Parth Patel; Alexei Yavlinsky; Anne Johnson; Martie Van Tongeren; Robert W Aldridge; Andrew Hayward",
+    "affiliations": "University College London; Univerity College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University of Manchester; University College London; University College London",
+    "abstract": "BackgroundWorkers differ in their risk of SARS-CoV-2 infection according to their occupation, but the direct contribution of occupation to this relationship is unclear. This study aimed to investigate how infection risk differed across occupational groups in England and Wales up to April 2022, after adjustment for potential confounding and stratification by pandemic phase.\n\nMethodsData from 15,190 employed/self-employed participants in the Virus Watch prospective cohort study were used to generate risk ratios for virologically- or serologically-confirmed SARS-CoV-2 infection using robust Poisson regression, adjusting for socio-demographic and health-related factors and non-work public activities. We calculated attributable fractions (AF) amongst the exposed for belonging to each occupational group based on adjusted risk ratios (aRR).\n\nFindingsIncreased risk was seen in nurses (aRR=1.44, 1.25-1.65; AF=30%, 20-39%), doctors (aRR=1.33, 1.08-1.65; AF=25%, 7-39%), carers (1.45, 1.19-1.76; AF=31%, 16-43%), primary school teachers (aRR=1.67, 1.42-1.96; AF=40%, 30-49%), secondary school teachers (aRR=1.48, 1.26-1.72; AF=32%, 21-42%), and teaching support occupations (aRR=1.42, 1.23-1.64; AF=29%, 18-39%) compared to office-based professional occupations. Differential risk was apparent in the earlier phases (Feb 2020 - May 2021) and attenuated later (June - October 2021) for most groups, although teachers and teaching support workers demonstrated persistently elevated risk across waves.\n\nInterpretationOccupational differentials in SARS-CoV-2 infection risk vary over time and are robust to adjustment for socio-demographic, health-related, and non-workplace activity-related potential confounders. Direct investigation into workplace factors underlying elevated risk and how these change over time is needed to inform occupational health interventions.",
+    "category": "epidemiology",
+    "match_type": "exact",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.12.08.21267353",
@@ -1721,20 +1749,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2021.11.03.21265877",
-    "date": "2021-11-03",
-    "link": "https://medrxiv.org/cgi/content/short/2021.11.03.21265877",
-    "title": "REACT-1 round 15 interim report: High and rising prevalence of SARS-CoV-2 infection in England from end of September 2021 followed by a fall in late October 2021",
-    "authors": "Marc Chadeau-Hyam; Oliver Eales; Barbara Bodinier; Haowei Wang; David J Haw; Matthew Whitaker; Caroline E Walters; Christina J Atchison; Peter J Diggle; Andrew J Page; Deborah Ashby; Wendy Barclay; Graham P Taylor; Graham Cooke; Helen Ward; Ara Darzi; Christl A. Donnelly; Paul Elliott",
-    "affiliations": "Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Quadram Institute; Imperial College London; Imperial College London; Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London School of Public Health",
-    "abstract": "BackgroundThe third wave of COVID-19 in England coincided with the rapid spread of the Delta variant of SARS-CoV-2 from the end of May 2021. Case incidence data from the national testing programme (Pillar 2) in England may be affected by changes in testing behaviour and other biases. Community surveys may provide important contextual information to inform policy and the public health response.\n\nMethodsWe estimated patterns of community prevalence of SARS-CoV-2 infection in England using RT-PCR swab-positivity, demographic and other risk factor data from round 15 (interim) of the REal-time Assessment of Community Transmission-1 (REACT-1) study (round 15a, carried out from 19 to 29 October 2021). We compared these findings with those from round 14 (9 to 27 September 2021).\n\nResultsDuring mid- to late-October 2021 (round 15a) weighted prevalence was 1.72% (1.61%, 1.84%) compared to 0.83% (0.76%, 0.89%) in September 2021 (round 14). The overall reproduction number (R) from round 14 to round 15a was 1.12 (1.11, 1.14) with increases in prevalence over this period (September to October) across age groups and regions except Yorkshire and The Humber. However, within round 15a (mid- to late-October) there was evidence of a fall in prevalence with R of 0.76 (0.65, 0.88). The highest weighted prevalence was observed among children aged 5 to 12 years at 5.85% (5.10%, 6.70%) and 13 to 17 years at 5.75% (5.02%, 6.57%). At regional level, there was an almost four-fold increase in weighted prevalence in South West from round 14 at 0.59% (0.43%,0.80%) to round 15a at 2.18% (1.84%, 2.58%), with highest smoothed prevalence at subregional level also found in South West in round 15a. Age, sex, key worker status, and presence of children in the home jointly contributed to the risk of swab-positivity. Among the 126 sequenced positive swabs obtained up until 23 October, all were Delta variant; 13 (10.3%) were identified as the AY.4.2 sub-lineage.\n\nDiscussionWe observed the highest overall prevalence of swab-positivity seen in the REACT-1 study in England to date in round 15a (October 2021), with a two-fold rise in swab-positivity from round 14 (September 2021). Despite evidence of a fall in prevalence from mid- to late-October 2021, prevalence remains high, particularly in school-aged children, with evidence also of higher prevalence in households with one or more children. Thus, vaccination of children aged 12 and over remains a high priority (with possible extension to children aged 5-12) to help reduce within-household transmission and disruptions to education, as well as among adults, to lessen the risk of serious disease among those infected.",
-    "category": "epidemiology",
-    "match_type": "exact",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.10.22.21265368",
@@ -1819,20 +1833,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2021.09.20.21263828",
-    "date": "2021-09-23",
-    "link": "https://medrxiv.org/cgi/content/short/2021.09.20.21263828",
-    "title": "Colchicine for COVID-19 in adults in the community (PRINCIPLE): a randomised, controlled, adaptive platform trial",
-    "authors": "- The PRINCIPLE Trial Collaborative Group; Jienchi Dorward; Ly-Mee Yu; Gail Hayward; Benjamin R Saville; Oghenekome Gbinigie; Oliver van Hecke; Emma Ogburn; Philip H Evans; Nicholas PB Thomas; Mahendra G Patel; Duncan Richards; Nicholas Berry; Michelle A Detry; Christina Saunders; Mark Fitzgerald; Victoria Harris; Milensu Shanyinde; Simon de Lusignan; Monique I Andersson; Christopher C Butler; FD Richard Hobbs",
-    "affiliations": "; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom and Centre for the AIDS Programme of Research in South Africa ; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Berry Consultants, Texas, USA and Department of Biostatistics, Vanderbilt University School of Medicine, Tennessee, USA; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; College of Medicine and Health, University of Exeter and National Institute for Health Research, Clinical Research Network; Royal College of General Practitioners, London, UK, and National Institute for Health Research, Clinical Research Network; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom and School of Pharmacy and Medical Sciences, University of Bra; Oxford Clinical Trials Research Unit, Botnar Research Centre, University of Oxford, Oxford, UK; Berry Consultants, Texas, USA; Berry Consultants, Texas, USA; Berry Consultants, Texas, USA; Berry Consultants, Texas, USA; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom,; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom",
-    "abstract": "ObjectivesColchicine has been proposed as a COVID-19 treatment, but its effect on time to recovery is unknown. We aimed to determine whether colchicine is effective at reducing time to recovery and COVID-19 related hospitalisations/deaths among people in the community.\n\nDesignProspective, multicentre, open-label, multi-arm, adaptive Platform Randomised Trial of Treatments in the Community for Epidemic and Pandemic Illnesses (PRINCIPLE).\n\nSettingNational trial run remotely from a central trial site and at multiple primary care centres across the United Kingdom.\n\nParticipantsAdults aged [&ge;]65, or [&ge;]18 years with comorbidities or shortness of breath, and unwell [&le;]14 days with suspected COVID-19 in the community.\n\nInterventionsParticipants were randomised to usual care, usual care plus colchicine (500{micro}g daily for 14 days), or usual care plus other interventions.\n\nMain outcome measuresThe co-primary endpoints were time to first self-reported recovery, and hospitalisation/death related to COVID-19, within 28 days, analysed using Bayesian models. The hypothesis for the time to recovery endpoint is evaluated first, and if superiority is declared on time to recovery, the hypothesis for the second co-primary endpoint of hospitalisation/death is then evaluated. To determine futility, we pre-specified a clinically meaningful benefit in time to first reported recovery as a hazard ratio of 1.2 or larger (equating to approximately 1.5 days benefit in the colchicine arm, assuming 9 days recovery in the usual care arm).\n\nResultsThe trial opened on April 2, 2020, with randomisation to colchicine starting on March 04, 2021 and stopping on May 26, 2021, because the pre-specified time to recovery futility criterion was met. The primary analysis model included 2755 SARS-CoV-2 positive participants, randomised to colchicine (n=156), usual care (n=1145), and other treatments (n=1454). Time to first self-reported recovery was similar in the colchicine group compared with usual care with an estimated hazard ratio of 0.919 [95% credible interval 0.72 to 1.16] and an estimated increase of 1.14 days [-1.86 to 5.21] in median time to self-reported recovery for colchicine versus usual care. The probability of meaningful benefit in time to recovery was very low at 1.8%. Results were similar in comparisons with concurrent controls. COVID-19 related hospitalisations/deaths were similar in the colchicine group versus usual care, with an estimated odds ratio of 0.76 [0.28 to 1.89] and an estimated difference of -0.4% [-2.7% to 2.4]. One serious adverse event occurred in the colchicine group and one in usual care.\n\nConclusionsColchicine did not improve time to recovery in people at higher risk of complications with COVID-19 in the community.\n\nTrial registrationISRCTN86534580.",
-    "category": "infectious diseases",
-    "match_type": "exact",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.09.13.21263487",
@@ -2169,20 +2169,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2021.06.28.21259529",
-    "date": "2021-07-01",
-    "link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259529",
-    "title": "Global patterns of genetic variation and association with clinical phenotypes at genes involved in SARS-CoV-2 infection",
-    "authors": "Chao Zhang; Anurag Verma; Yuanqing Feng; Marcelo C. R. Melo; Michael McQuillan; Matthew Hansen; Anastasia Lucas; Joseph Park; Alessia Ranciaro; Simon Thompson; Meghan A. Rubel; Michael C. Campbell; William Beggs; JIBRIL HIRBO; Sununguko Wata Mpoloka; Gaonyadiwe George Mokone; - Regeneron Genetic Center; Thomas Nyambo; Dawit Wolde Meskel; Gurja Belay; Charles Fokunang; Alfred K. Njamnshi; Sabah A. Omar; Scott Williams; Daniel Rader; Marylyn D Ritchie; Cesar de la Fuente Nunez; Giorgio Sirugo; Sarah Tishkoff",
-    "affiliations": "University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; Perelman School of Medicine at the University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Howard; University of Pennsylvania; Vanderbilt University Medical Center; University of Botswana, Biological Sciences, Gaborone, Botswana; University of Botswana, Faculty of Medicine, Gaborone, Botswana; ; Department of Biochemistry, Kampala International University in Tanzania, Dar es Salaam, Tanzania; Addis Ababa University Department of Microbial Cellular and Molecular Biology, Addis Ababa, Ethiopia; Addis Ababa University Department of Microbial Cellular and Molecular Biology, Addis Ababa, Ethiopia; Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaounde I, Yaounde, Cameroon; Department of Neurology, Central Hospital Yaounde; Brain Research Africa Initiative (BRAIN), Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The ; Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya; Case Western Reserve University; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania",
-    "abstract": "We investigated global patterns of genetic variation and signatures of natural selection at host genes relevant to SARS-CoV-2 infection (ACE2, TMPRSS2, DPP4, and LY6E). We analyzed novel data from 2,012 ethnically diverse Africans and 15,997 individuals of European and African ancestry with electronic health records, and integrated with global data from the 1000GP. At ACE2, we identified 41 non-synonymous variants that were rare in most populations, several of which impact protein function. However, three non-synonymous variants were common among Central African hunter-gatherers from Cameroon and are on haplotypes that exhibit signatures of positive selection. We identify strong signatures of selection impacting variation at regulatory regions influencing ACE2 expression in multiple African populations. At TMPRSS2, we identified 13 amino acid changes that are adaptive and specific to the human lineage. Genetic variants that are targets of natural selection are associated with clinical phenotypes common in patients with COVID-19.",
-    "category": "genetic and genomic medicine",
-    "match_type": "exact",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.06.21.21259237",
@@ -2407,20 +2393,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2021.05.06.21256755",
-    "date": "2021-05-13",
-    "link": "https://medrxiv.org/cgi/content/short/2021.05.06.21256755",
-    "title": "Clinical coding of long COVID in English primary care: a federated analysis of 58 million patient records in situ using OpenSAFELY",
-    "authors": "- The OpenSAFELY Collaborative; Alex J Walker; Brian MacKenna; Peter Inglesby; Christopher T Rentsch; Helen J Curtis; Caroline E Morton; Jessica Morley; Amir Mehrkar; Sebastian CJ Bacon; George Hickman; Christopher Bates; Richard Croker; David Evans; Tom Ward; Jonathan Cockburn; Simon Davy; Krishnan Bhaskaran; Anna Schultze; Elizabeth J Williamson; William J Hulme; Helen I McDonald; Laurie Tomlinson; Rohini Mathur; Rosalind M Eggo; Kevin Wing; Angel YS Wong; Harriet Forbes; John Tazare; John Parry; Frank Hester; Sam Harper; Shaun O'Hanlon; Alex Eavis; Richard Jarvis; Dima Avramov; Paul Griffiths; Aaron Fowles; Nasreen Parkes; Ian J Douglas; Stephen JW Evans; Liam Smeeth; Ben Goldacre",
-    "affiliations": "; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; TPP; TPP; EMIS; EMIS; EMIS; EMIS; EMIS; EMIS; EMIS; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford",
-    "abstract": "BackgroundLong COVID is a term to describe new or persistent symptoms at least four weeks after onset of acute COVID-19. Clinical codes to describe this phenomenon were released in November 2020 in the UK, but it is not known how these codes have been used in practice.\n\nMethodsWorking on behalf of NHS England, we used OpenSAFELY data encompassing 96% of the English population. We measured the proportion of people with a recorded code for long COVID, overall and by demographic factors, electronic health record software system, and week. We also measured variation in recording amongst practices.\n\nResultsLong COVID was recorded for 23,273 people. Coding was unevenly distributed amongst practices, with 26.7% of practices having not used the codes at all. Regional variation was high, ranging between 20.3 per 100,000 people for East of England (95% confidence interval 19.3-21.4) and 55.6 in London (95% CI 54.1-57.1). The rate was higher amongst women (52.1, 95% CI 51.3-52.9) compared to men (28.1, 95% CI 27.5-28.7), and higher amongst practices using EMIS software (53.7, 95% CI 52.9-54.4) compared to TPP software (20.9, 95% CI 20.3-21.4).\n\nConclusionsLong COVID coding in primary care is low compared with early reports of long COVID prevalence. This may reflect under-coding, sub-optimal communication of clinical terms, under-diagnosis, a true low prevalence of long COVID diagnosed by clinicians, or a combination of factors. We recommend increased awareness of diagnostic codes, to facilitate research and planning of services; and surveys of clinicians experiences, to complement ongoing patient surveys.",
-    "category": "epidemiology",
-    "match_type": "exact",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.05.05.21256668",
@@ -2435,34 +2407,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2021.05.04.21256507",
-    "date": "2021-05-06",
-    "link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256507",
-    "title": "Describing the burden of the COVID-19 pandemic in people with psoriasis: findings from a global cross-sectional study",
-    "authors": "Satveer K Mahil; Mark Yates; Zenas Z Yiu; Sinead M Langan; Teresa Tsakok; Nick Dand; Kayleigh J Mason; Helen McAteer; Freya Meynall; Bolaji Coker; Alexandra Vincent; Dominic Urmston; Amber Vesty; Jade Kelly; Camille Lancelot; Lucy Moorhead; Herve Bachelez; Francesca Capon; Claudia R Contreras; Claudia De La Cruz; Paola Di Meglio; Paolo Gisondi; Denis Jullien; Jo Lambert; Luigi Naldi; Sam Norton; Luis Puig; Phyllis Spuls; Tiago Torres; Richard B Warren; Hoseah Waweru; John Weinman; Matt A Brown; James B Galloway; Christopher M Griffiths; Jonathan N Barker; Catherine H Smith",
-    "affiliations": "St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; Centre for Rheumatic Diseases, King's College London; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; Faculty of Epidemiology, and Population Health, London School of Hygiene and Tropical Medicine, London, UK; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King's College London, London, UK; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; The Psoriasis Association, Northampton, UK; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; NIHR Biomedical Research Centre at Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; NIHR Biomedical Research Centre at Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; The Psoriasis Association, Northampton, UK; The Psoriasis Association, Northampton, UK; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; International Federation of Psoriasis Associations; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; Department of Dermatology, AP-HP Hopital Saint-Louis, Paris, France; King's College London; Catedra de Dermatologia, Hospital de Clinicas, Facultad de Ciencias Medicas, Universidad Nacional de Asuncion, Paraguay; Clinica Dermacross, Santiago, Chile; King's College London; Section of Dermatology and Venereology, University of Verona, Verona, Italy; Department of Dermatology, Edouard Herriot Hospital, Hospices Civils de Lyon, University of Lyon, Lyon, France; Department of Dermatology, Ghent University, Ghent, Belgium; Centro Studi GISED, Bergamo, Italy; Psychology Department, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, UK; Department of Dermatology, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Catalonia, Spain; Department of Dermatology, Amsterdam Public Health/Infection and Immunology, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands; Department of Dermatology, Centro Hospitalar do Porto, Portugal; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; International Federation of Psoriasis Associations; School of Cancer and Pharmaceutical Sciences, Kings College London, London, UK; Centre for Rheumatic Diseases, King's College London, London, UK; Centre for Rheumatic Diseases, King's College London, London, UK; 3Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Res; NIHR Biomedical Research Centre at Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK",
-    "abstract": "BackgroundIndirect excess morbidity has emerged as a major concern in the COVID-19 pandemic. People with psoriasis may be particularly vulnerable to this because of prevalent anxiety and depression, multimorbidity and therapeutic use of immunosuppression.\n\nObjectiveCharacterise the factors associated with worsening psoriasis in the COVID-19 pandemic, using mental health status (anxiety and depression) as the main exposure of interest.\n\nMethodsGlobal cross-sectional study using a primary outcome of self-reported worsening of psoriasis. Individuals with psoriasis completed an online self-report questionnaire (PsoProtectMe; Psoriasis Patient Registry for Outcomes, Therapy and Epidemiology of COVID-19 Infection Me) between May 2020 and January 2021. Each individual completed a validated screen for anxiety (Generalized Anxiety Disorder-2) and depression (Patient Health Questionnaire-2). Odds ratios (OR) and 95% confidence intervals (CI) were estimated using multivariable logistic regression.\n\nResults4,043 people with psoriasis (without COVID-19) from 86 countries self-reported to PsoProtectMe (mean age 47.2 years [SD 15.1]; mean BMI 27.6kg/m2 [SD 6.0], 2,684 [66.4%] female and 3,016 [74.6%] of white European ethnicity). 1,728 (42.7%) participants (1322 [77%] female) reported worsening of their psoriasis in the pandemic. A positive screen for anxiety or depression associated with worsening psoriasis in age and gender adjusted (OR 2.04, 95% CI 1.77-2.36), and fully adjusted (OR 2.01, 95% CI 1.72-2.34) logistic regression models. Female sex, obesity, shielding behaviour and systemic immunosuppressant non-adherence also associated with worsening psoriasis. The commonest reason for non-adherence was concern regarding complications related to COVID-19.\n\nConclusionsThese data indicate an association between poor mental health and worsening psoriasis in the pandemic. Access to holistic care including psychological support may mitigate potentially long-lasting effects of the pandemic on health outcomes in psoriasis. The study also highlights an urgent need to address patient concerns about immunosuppressant-related risks, which may be contributing to non-adherence.",
-    "category": "dermatology",
-    "match_type": "exact",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2021.04.30.21256119",
-    "date": "2021-04-30",
-    "link": "https://medrxiv.org/cgi/content/short/2021.04.30.21256119",
-    "title": "Association between oral anticoagulants and COVID-19 related outcomes: two cohort studies",
-    "authors": "Angel YS Wong; Laurie Tomlinson; Jeremy P Brown; William Elson; Alex J Walker; Anna J Schultze; Caroline E Morton; David Evans; Peter Inglesby; Brian MacKenna; Krishnan Bhaskaran; Christopher T. Rentsch; Emma Powell; Elizabeth T. Williamson; Richard Croker; Seb Bacon; William Hulme; Chris Bates; Helen J Curtis; Amir Mehrkar; Jonathan Cockburn; Helen I McDonald; Rohini I Mathur; Kevin Wing; Harriet Forbes; Rosalind M Eggo; Stephen Evans; Liam Smeeth; Ben Goldacre; Ian J Douglas",
-    "affiliations": "London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Trop. Med.; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; US Department of Veterans Affairs, London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; TPP; London School of Medicine and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Bristol; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine",
-    "abstract": "ObjectivesWe investigated the role of routinely prescribed oral anticoagulants (OACs) in COVID-19 outcomes, comparing current OAC use versus non-use in Study 1; and warfarin versus direct oral anticoagulants (DOACs) in Study 2.\n\nDesignTwo cohort studies, on behalf of NHS England.\n\nSettingPrimary care data and pseudonymously-linked SARS-CoV-2 antigen testing data, hospital admissions, and death records from England.\n\nParticipantsStudy 1: 70,464 people with atrial fibrillation (AF) and CHA{square}DS{square}-VASc score of 2. Study 2: 372,746 people with non-valvular AF.\n\nMain outcome measuresTime to test for SARS-CoV-2, testing positive for SARS-CoV-2, COVID-19 related hospital admission, COVID-19 deaths or non-COVID-19 deaths in Cox regression.\n\nResultsIn Study 1, we included 52,416 current OAC users and 18,048 non-users. We observed no difference in risk of being tested for SARS-CoV-2 associated with current use (adjusted HR, 1.01, 95%CI, 0.96 to 1.05) versus non-use. We observed a lower risk of testing positive for SARS-CoV-2 (adjusted HR, 0.73, 95%CI, 0.60 to 0.90), and COVID-19 deaths (adjusted HR, 0.69, 95%CI, 0.49 to 0.97) associated with current use versus non-use. In Study 2, we included 92,339 warfarin users and 280,407 DOAC users. We observed a lower risk of COVID-19 deaths (adjusted HR, 0.79, 95%CI, 0.76 to 0.83) associated with warfarin versus DOACs. Similar associations were found for all other outcomes.\n\nConclusionsAmong people with AF and a CHA{square}DS{square}-VASc score of 2, those receiving OACs had a lower risk of receiving a positive COVID-19 test and severe COVID-19 outcomes than non-users; this might be explained by a causal effect of OACs in preventing severe COVID-19 outcomes or more cautious behaviours leading to reduced infection risk. There was no evidence of a higher risk of severe COVID-19 outcomes associated with warfarin versus DOACs in people with non-valvular AF regardless of CHA{square}DS{square}-VASc score.\n\nKey pointsO_ST_ABSWhat is already known on this topicC_ST_ABSO_LICurrent studies suggest that prophylactic or therapeutic anticoagulant use, particularly low molecular weight heparin, lower the risk of pulmonary embolism and mortality during hospitalisation among patients with COVID-19.\nC_LIO_LIReduced vitamin K status has been reported to be correlated with severity of COVID-19. This could mean that warfarin, as a vitamin K antagonist, is associated with more severe COVID-19 disease than non-vitamin K anticoagulants.\nC_LI\n\nWhat this study addsO_LIIn 70,464 people with atrial fibrillation, at the threshold of being treated with an OAC based on risk of stroke, we observed a lower risk of testing positive for SARS-CoV-2 and COVID-19 related deaths associated with routinely prescribed OACs, relative to non-use.\nC_LIO_LIThis might be explained by OACs preventing severe COVID-19 outcomes, or more cautious behaviours and environmental factors reducing the risk of SARS-CoV-2 infection in those taking OACs.\nC_LIO_LIIn 372,746 people with non-valvular atrial fibrillation, there was no evidence of a higher risk of severe COVID-19 outcomes associated with warfarin compared with DOACs.\nC_LI",
-    "category": "epidemiology",
-    "match_type": "exact",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.04.26.21255732",
@@ -2617,20 +2561,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2021.03.26.21254390",
-    "date": "2021-03-26",
-    "link": "https://medrxiv.org/cgi/content/short/2021.03.26.21254390",
-    "title": "Regional performance variation in external validation of four prediction models for severity of COVID-19 at hospital admission: An observational multi-centre cohort study",
-    "authors": "Kristin Wickstrom; Valeria Vitelli; Ewan Carr; Aleksander Rygh Holten; Rebecca Bendayan; Andrew Henry Reiner; Daniel Bean; Tom Searle; Anthony Shek; Zeljko Kraljevic; James T Teo; Richard Dobson; Kristian Tonby; Alvaro Kohn-Luque; Erik Koldberg Amundsen",
-    "affiliations": "Oslo University Hospital; University of Oslo; King's College London; Oslo University Hospital; King's College London; Oslo University Hospital; King's College London; King's College London; King's College London; King's College London; Kings College Hospital NHS Foundation Trust; Kings College London; Oslo University Hospital; University of Oslo; Oslo University Hospital",
-    "abstract": "BackgroundSeveral prediction models for coronavirus disease-19 (COVID-19) have been published. Prediction models should be externally validated to assess their performance before implementation. This observational cohort study aimed to validate published models of severity for hospitalized patients with COVID-19 using clinical and laboratory predictors.\n\nMethodsPrediction models fitting relevant inclusion criteria were chosen for validation. The outcome was either mortality or a composite outcome of mortality and ICU admission (severe disease). 1295 patients admitted with symptoms of COVID-19 at Kings Cross Hospital (KCH) in London, United Kingdom, and 307 patients at Oslo University Hospital (OUH) in Oslo, Norway were included. The performance of the models was assessed in terms of discrimination and calibration.\n\nResultsWe identified two models for prediction of mortality (referred to as Xie and Zhang1) and two models for prediction of severe disease (Allenbach and Zhang2).\n\nThe performance of the models was variable. For prediction of mortality Xie had good discrimination at OUH with an area under the receiver-operating characteristic (AUROC) 0.87 [95 % confidence interval (CI) 0.79-0.95] and acceptable discrimination at KCH, AUROC 0.79 [0.76-0.82]. In prediction of severe disease, Allenbach had acceptable discrimination (OUH AUROC 0.81 [0.74-0.88] and KCH AUROC 0.72 [0.68-0.75]). The Zhang models had moderate to poor discrimination. Initial calibration was poor for all models but improved with recalibration.\n\nConclusionsThe performance of the four prediction models was variable. The Xie model had the best discrimination for mortality, while the Allenbach model had acceptable results for prediction of severe disease.",
-    "category": "infectious diseases",
-    "match_type": "exact",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.03.26.21254391",
@@ -2743,6 +2673,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2021.02.27.21252593",
+    "date": "2021-03-01",
+    "link": "https://medrxiv.org/cgi/content/short/2021.02.27.21252593",
+    "title": "Surgical activity in England and Wales during the COVID-19 pandemic: a nationwide observational cohort study",
+    "authors": "Thomas D Dobbs; John A G Gibson; Alexander J Fowler; Tom E Abbott; Tasnin Shahid; Fatemeh Torabi; Rowena Griffiths; Ronan A Lyons; Rupert M Pearse; Iain S Whitaker",
+    "affiliations": "Swansea University Medical School; Swansea University Medical School; Queen Mary, University of London; Queen Mary University of London; Queen Mary University of London; Swansea University; Swansea University; Swansea University; Queen Mary University of London; Swansea University Medical School",
+    "abstract": "ObjectivesTo report the volume of surgical activity and the number of cancelled surgical procedures during the COVID-19 pandemic.\n\nDesign and settingAnalysis of electronic health record data from the National Health Service (NHS) in England and Wales.\n\nMethodsWe used hospital episode statistics for all adult patients undergoing surgery between 1st January 2020 and 31st December 2020. We identified surgical procedures using a previously published list of procedure codes. Procedures were stratified by urgency of surgery as defined by NHS England. We calculated the deficit of surgical activity by comparing the expected number of procedures from the years 2016-2019 with the actual number of procedures in 2020. We estimated the cumulative number of cancelled procedures by 31st December 2021 according patterns of activity in 2020.\n\nResultsThe total number of surgical procedures carried out in England and Wales in 2020 was 3,102,674 compared to the predicted number of 4,671,338. This represents a 33.6% reduction in the national volume of surgical activity. There were 763,730 emergency surgical procedures (13.4% reduction), compared to 2,338,944 elective surgical procedures (38.6% reduction). The cumulative number of cancelled or postponed procedures was 1,568,664. We estimate that this will increase to 2,358,420 by 31st December 2021.\n\nConclusionsThe volume of surgical activity in England and Wales was reduced by 33.6% in 2020, resulting in over 1,568,664 cancelled operations. This deficit will continue to grow in 2021.\n\nSummary boxesO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIThe COVID-19 pandemic necessitated a rapid change in the provision of care, including the suspension of a large proportion of surgical activity\nC_LIO_LISurgical activity has yet to return to normal and has been further impacted by subsequent waves of the pandemic\nC_LIO_LIThis will lead to a large backlog of cases\nC_LI\n\nWhat this study addsO_LI3,102,674 surgical procedures were performed in England and Wales during 2020, a 33.6% reduction on the expected yearly surgical activity\nC_LIO_LIOver 1.5 million procedures were not performed, with this deficit likely to continue to grow to 2.3 million by the end of 2021\nC_LIO_LIThis deficit is the equivalent of more than 6 months of pre-pandemic surgical activity, requiring a monumental financial and logistic challenge to manage\nC_LI",
+    "category": "surgery",
+    "match_type": "exact",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.02.23.21251975",
@@ -2953,20 +2897,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2021.01.14.21249801",
-    "date": "2021-01-15",
-    "link": "https://medrxiv.org/cgi/content/short/2021.01.14.21249801",
-    "title": "Factor V is an immune inhibitor that is expressed at increased levels in leukocytes of patients with severe Covid-19",
-    "authors": "Jun Wang; Prasanti Kotagiri; Paul Lyons; Federica Mescia; Laura Bergamaschi; Lorinda Turner; Rafia Al-Lamki; Michael D Morgan; Fernando J Calero-Nieto; Karsten Bach; Nicole Mende; Nicola K Wilson; Emily R Watts; - Cambridge Institute of Therapeutic Immunology and Infectious Disease - NIHR Covid BioResource; Patrick Chinnery; Nathalie Kingston; Sofia Papadia; Kathleen Stirrups; Neil Walker; Ravindra K Gupta; Mark Toshner; Michael Weekes; James A Nathan; Sarah Walmsley; Willem Hendrik Ouwehand; Mary Kasanicki; Berthold Gottgens; John C Marioni; Smith GC Smith; Jordan S Pober; John R Bradley",
-    "affiliations": "University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Edinburgh; ; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; Cambridge University; University of Cambridge; University of Edinburgh; Prof; Cambridge University Hospitals; University of Cambridge; EMBL-EBI; University of Cambridge; Yale University; University of Cambridge",
-    "abstract": "Severe Covid-19 is associated with elevated plasma Factor V (FV) and increased risk of thromboembolism. We report that neutrophils, T regulatory cells (Tregs), and monocytes from patients with severe Covid-19 express FV, and expression correlates with T cell lymphopenia. In vitro full length FV, but not FV activated by thrombin cleavage, suppresses T cell proliferation. Increased and prolonged FV expression by cells of the innate and adaptive immune systems may contribute to lymphopenia in severe Covid-19. Activation by thrombin destroys the immunosuppressive properties of FV. Anticoagulation in Covid-19 patients may have the unintended consequence of suppressing the adaptive immune system.",
-    "category": "infectious diseases",
-    "match_type": "exact",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.01.15.21249885",
@@ -3009,20 +2939,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2021.01.11.20248765",
-    "date": "2021-01-15",
-    "link": "https://medrxiv.org/cgi/content/short/2021.01.11.20248765",
-    "title": "Early immune pathology and persistent dysregulation characterise severe COVID-19",
-    "authors": "Laura Bergamaschi; Federica Mescia; Lorinda Turner; Aimee Hanson; Prasanti Kotagiri; Benjamin J. Dunmore; Helene Ruffieux; Aloka DeSa; Oisin Huhn; Michael D Morgan; Pehuen Pereyra Gerber; Mark R. Wills; Stephen Baker; Fernando J Calero Nieto; Rainer Doffinger; Gordon Dougan; Anne Elmer; Ian G Goodfellow; Ravindra K. Gupta; Myra Hosmillo; Kelvin Hunter; Nathalie Kingston; Paul J. Lehner; Nicholas J. Matheson; Jeremy K. Nicholson; Anna M. Petrunkina; Sylvia Richardson; Caroline Saunders; James E.D. Thaventhiran; Erik J.M. Toonen; Michael P. Weekes; - CambridgeInstituteofTherapeuticImmunologyandInfectiousDisease-NationalInstituteofHealthResearch(CITI; Berthold Gottgens; Mark Toshner; Christoph Hess; John R. Bradley; Paul A. Lyons; Kenneth G.C. Smith",
-    "affiliations": "Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; MRC Biostatistics Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cancer Research UK, Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Clinical Research Centre, NIHR Clinical Research Facility, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge CB2 ; Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; The Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Murdoch, Western Australia WA 6150, Australia; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; MRC Biostatistics Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; Cambridge Clinical Research Centre, NIHR Clinical Research Facility, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge CB2 ; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; R&D Department, Hycult Biotech, 5405 PD Uden, The Netherlands; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; ; Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK",
-    "abstract": "In a study of 207 SARS-CoV2-infected individuals with a range of severities followed over 12 weeks from symptom onset, we demonstrate that an early robust bystander CD8 T cell immune response, without systemic inflammation, is characteristic of asymptomatic or mild disease. Those presenting to hospital had delayed bystander responses and systemic inflammation already evident at around symptom onset. Such early evidence of inflammation suggests immunopathology may be inevitable in some individuals, or that preventative intervention might be needed before symptom onset. Viral load does not correlate with the development of this pathological response, but does with its subsequent severity. Immune recovery is complex, with profound persistent cellular abnormalities correlating with a change in the nature of the inflammatory response, where signatures characteristic of increased oxidative phosphorylation and reactive-oxygen species-associated inflammation replace those driven by TNF and IL-6. These late immunometabolic inflammatory changes and unresolved immune defects may have clinical implications.",
-    "category": "infectious diseases",
-    "match_type": "exact",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.01.11.21249461",
@@ -3359,6 +3275,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2020.10.14.20212555",
+    "date": "2020-10-16",
+    "link": "https://medrxiv.org/cgi/content/short/2020.10.14.20212555",
+    "title": "Multi-organ impairment in low-risk individuals with long COVID",
+    "authors": "Andrea Dennis; Malgorzata Wamil; Sandeep Kapur; Johann Alberts; Andrew Badley; Gustav Anton Decker; Stacey A Rizza; Rajarshi Banerjee; Amitava Banerjee",
+    "affiliations": "Perspectum; Great Western Hospitals NHS Foundation Trust; Mayo Clinic Healthcare; Alliance Medical; Mayo Clinic; Mayo Clinic International; Mayo Clinic; Perspectum; University College London",
+    "abstract": "BackgroundSevere acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection has disproportionately affected older individuals and those with underlying medical conditions. Research has focused on short-term outcomes in hospital, and single organ involvement. Consequently, impact of long COVID (persistent symptoms three months post-infection) across multiple organs in low-risk individuals is yet to be assessed.\n\nMethodsAn ongoing prospective, longitudinal, two-centre, observational study was performed in individuals symptomatic after recovery from acute SARS-CoV-2 infection. Symptoms and organ function (heart, lungs, kidneys, liver, pancreas, spleen) were assessed by standardised questionnaires (EQ-5D-5L, Dyspnoea-12), blood investigations and quantitative magnetic resonance imaging, defining single and multi-organ impairment by consensus definitions.\n\nFindingsBetween April and September 2020, 201 individuals (mean age 44 (SD 11.0) years, 70% female, 87% white, 31% healthcare workers) completed assessments following SARS-CoV-2 infection (median 140, IQR 105-160 days after initial symptoms). The prevalence of pre-existing conditions (obesity: 20%, hypertension: 6%; diabetes: 2%; heart disease: 4%) was low, and only 18% of individuals had been hospitalised with COVID-19. Fatigue (98%), muscle aches (88%), breathlessness (87%), and headaches (83%) were the most frequently reported symptoms. Ongoing cardiorespiratory (92%) and gastrointestinal (73%) symptoms were common, and 42% of individuals had ten or more symptoms.\n\nThere was evidence of mild organ impairment in heart (32%), lungs (33%), kidneys (12%), liver (10%), pancreas (17%), and spleen (6%). Single (66%) and multi-organ (25%) impairment was observed, and was significantly associated with risk of prior COVID-19 hospitalisation (p<0.05).\n\nInterpretationIn a young, low-risk population with ongoing symptoms, almost 70% of individuals have impairment in one or more organs four months after initial symptoms of SARS-CoV-2 infection. There are implications not only for burden of long COVID but also public health approaches which have assumed low risk in young people with no comorbidities.\n\nFundingThis work was supported by the UKs National Consortium of Intelligent Medical Imaging through the Industry Strategy Challenge Fund, Innovate UK Grant 104688, and also through the European Unions Horizon 2020 research and innovation programme under grant agreement No 719445.",
+    "category": "health policy",
+    "match_type": "exact",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2020.10.12.20211227",
@@ -3401,20 +3331,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2020.10.08.20209304",
-    "date": "2020-10-12",
-    "link": "https://medrxiv.org/cgi/content/short/2020.10.08.20209304",
-    "title": "Prevalence of COVID-19-related risk factors and risk of severe influenza outcomes in cancer survivors: a matched cohort study using linked English electronic health records data",
-    "authors": "Helena Carreira; Helen Strongman; Maria Peppa; Helen I McDonald; Isabel dos-Santos-Silva; Susannah Stanway; Liam Smeeth; Krishnan Bhaskaran",
-    "affiliations": "London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; NIHR Health Protection Research Unit in Immunisation; London School of Medicine and Tropical Medicine, NIHR Health Protection Research Unit in Immunisation; London School of Hygiene and Tropical Medicine; The Royal Marsden NHS Foundation Trust; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine",
-    "abstract": "BackgroundPeople with active cancer are recognised as at risk of COVID-19 complications, but it is unclear whether the much larger population of cancer survivors is at elevated risk. We aimed to address this by comparing cancer survivors and cancer-free controls for (i) prevalence of comorbidities considered risk factors for COVID-19; and (ii) risk of severe influenza, as a marker of susceptibility to severe outcomes from epidemic respiratory viruses.\n\nMethodsWe included survivors ([&ge;]1 year) of the 20 most common cancers, and age, sex and general practice-matched cancer-free controls, derived from UK primary care data linked to cancer registrations, hospital admissions and death registrations. Comorbidity prevalences were calculated 1 and 5 years from cancer diagnosis. Risk of hospitalisation or death due to influenza was compared using Cox models adjusted for baseline demographics and comorbidities.\n\nFindings108,215 cancer survivors and 523,541 cancer-free controls were included. Cancer survivors had more asthma, other respiratory, cardiac, diabetes, neurological, renal, and liver disease, and less obesity, compared with controls, but there was variation by cancer site. There were 205 influenza hospitalisations/deaths, with cancer survivors at higher risk than controls (adjusted HR 2.78, 95% CI 2.04-3.80). Haematological cancer survivors had large elevated risks persisting for >10 years (HR overall 15.17, 7.84-29.35; HR >10 years from cancer diagnosis 10.06, 2.47-40.93). Survivors of other cancers had evidence of raised risk up to 5 years from cancer diagnosis only (HR 2.22, 1.31-3.74).\n\nInterpretationRisks of severe COVID-19 outcomes are likely to be elevated in cancer survivors. This should be taken into account in policies targeted at clinical risk groups, and vaccination for both influenza, and, when available, COVID-19, should be encouraged in cancer survivors.\n\nFundingWellcome Trust, Royal Society, NIHR.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSFew data are available to date on how COVID-19 affects cancer survivors. We searched PubMed with the keywords \"influenza cancer survivors\" to identify studies that compared severe influenza outcomes in cancer survivors and in a control group. No study was identified.\n\nAdded value of this studyIn this matched cohort study of routinely collected electronic health records, we demonstrated raised risks of influenza hospitalisation or mortality in survivors from haematological malignancies for >10 years after diagnosis, and in survivors from solid cancers up to 5 years after diagnosis.\n\nImplications of all the available evidenceCancer survivorship appears to be an important risk factor for severe influenza outcomes, suggesting that cancer survivors may also be at raised risk of poor COVID-19 outcomes. This should be taken into account in public health policies targeted at protecting clinical risk groups. Influenza vaccination should be encouraged in this group, and may need to be extended to a wider population of medium- to long-term cancer survivors than currently recommended.",
-    "category": "oncology",
-    "match_type": "exact",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2020.10.03.20206375",
@@ -3583,6 +3499,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2020.09.10.20191841",
+    "date": "2020-09-11",
+    "link": "https://medrxiv.org/cgi/content/short/2020.09.10.20191841",
+    "title": "The King's College London Coronavirus Health and Experiences of Colleagues at King's Study: SARS-CoV-2 antibody response in an occupational sample",
+    "authors": "Daniel Leightley; Valentina Vitiello; Gabriella Bergin-Cartwright; Alice Wickersham; Katrina A S Davis; Sharon Stevelink; Matthew Hotopf; Reza Razavi; - On behalf of the KCL CHECK research team",
+    "affiliations": "Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; The School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and   Medicine, King's College London, London, UK.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London; The School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King's College London; ",
+    "abstract": "We report test results for SARS-CoV-2 antibodies in an occupational group of postgraduate research students and current members of staff at Kings College London. Between June and July 2020, antibody testing kits were sent to n=2296 participants; n=2004 (86.3%) responded, of whom n=1882 (93.9%) returned valid test results. Of those that returned valid results, n=124 (6.6%) tested positive for SARS-CoV-2 antibodies, with initial comparisons showing variation by age group and clinical exposure.",
+    "category": "epidemiology",
+    "match_type": "exact",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2020.09.11.20192492",
@@ -3779,6 +3709,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2020.08.10.20171033",
+    "date": "2020-08-11",
+    "link": "https://medrxiv.org/cgi/content/short/2020.08.10.20171033",
+    "title": "Post-exertion oxygen saturation as a prognostic factor for adverse outcome in patients attending the emergency department with suspected COVID-19: Observational cohort study",
+    "authors": "Steve Goodacre; Ben Thomas; Ellen Lee; Laura Sutton; Katie Biggs; Carl Marincowitz; Amanda Loban; Simon Waterhouse; Richard Simmonds; Jose Schutter; Sarah Connelly; Elena Sheldon; Jamie Hall; Emma Young; Andrew Bentley; Kirsty Challen; Chris Fitzsimmons; Tim Harris; Fiona Lecky; Andrew Lee; Ian Maconochie; Darren Walter",
+    "affiliations": "University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; Manchester University NHS Foundation Trust, Wythenshawe Hospital; Lancashire Teaching Hospitals NHS Foundation Trust; Sheffield Children's NHS Foundation Trust; Barts Health NHS Trust; University of Sheffield; University of Sheffield; Imperial College Healthcare NHS Trust; Manchester University NHS Foundation Trust",
+    "abstract": "BackgroundMeasurement of post-exertion oxygen saturation has been proposed to assess illness severity in suspected COVID-19 infection. We aimed to determine the accuracy of post-exertional oxygen saturation for predicting adverse outcome in suspected COVID-19.\n\nMethodsWe undertook an observational cohort study across 70 emergency departments during first wave of the COVID-19 pandemic in the United Kingdom. We collected data prospectively, using a standardised assessment form, and retrospectively, using hospital records, from patients with suspected COVID-19, and reviewed hospital records at 30 days for adverse outcome (death or receiving organ support). Patients with post-exertion oxygen saturation recorded were selected for this analysis.\n\nResultsWe analysed data from 817 patients with post-exertion oxygen saturation recorded after excluding 54 in whom measurement appeared unfeasible. The c-statistic for post-exertion change in oxygen saturation was 0.589 (95% confidence interval 0.465 to 0.713), and the positive and negative likelihood ratios of a 3% or more desaturation were respectively 1.78 (1.25 to 2.53) and 0.67 (0.46 to 0.98). Multivariable analysis showed that post-exertion oxygen saturation was not a significant predictor of adverse outcome when baseline clinical assessment was taken into account (p=0.368). Secondary analysis excluding patients in whom post-exertion measurement appeared inappropriate resulted in a c-statistic of 0.699 (0.581 to 0.817), likelihood ratios of 1.98 (1.26 to 3.10) and 0.61 (0.35 to 1.07), and some evidence of additional prognostic value on multivariable analysis (p=0.019).\n\nConclusionsPost-exertion oxygen saturation provides modest prognostic information in the assessment of patients attending the emergency department with suspected COVID-19.\n\nRegistrationISRCTN registry, ISRCTN56149622, http://www.isrctn.com/ISRCTN28342533\n\nKey messagesWhat is already known on this subject?\n\nO_LIPost exertional decrease in oxygen saturation can be used to predict prognosis in chronic lung diseases\nC_LIO_LIPost exertional desaturation has been proposed as a way of predicting adverse outcome in people with suspected COVID-19\nC_LI\n\nWhat this study adds:\n\nO_LIPost-exertion oxygen saturation provides modest prognostic information in the assessment of patients attending the emergency department with suspected COVID-19\nC_LI",
+    "category": "emergency medicine",
+    "match_type": "exact",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2020.08.07.20169490",
@@ -3807,20 +3751,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2020.08.03.20164897",
-    "date": "2020-08-04",
-    "link": "https://medrxiv.org/cgi/content/short/2020.08.03.20164897",
-    "title": "Risk of hospitalisation with coronavirus disease 2019 in healthcare workers and their households:a nationwide linkage cohort study",
-    "authors": "Anoop SV Shah; Rachael Wood; Ciara Gribben; David Caldwell; Jennifer Bishop; Amanda Weir; Sharon Kennedy; Martin Reid; Alison Smith-Palmer; David Goldberg; Jim McMenamin; Colin Fischbacher; Chris Robertson; Sharon Hutchinson; Paul M McKeigue; Helen M Colhoun; David McAllister",
-    "affiliations": "London School of Hygiene and Tropical Medicine; Public Health Scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; Health protection scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; University of Edinburgh; University of Edinburgh; University of Glasgow",
-    "abstract": "ObjectiveMany healthcare staff work in high-risk settings for contracting and transmitting Severe Acute Respiratory Syndrome Coronavirus 2. Their risk of hospitalisation for coronavirus disease 2019 (COVID-19), and that of their households, is poorly understood.\n\nDesign and settings and participantsDuring the peak period for COVID-19 infection in Scotland (1st March 2020 to 6th June 2020) we conducted a national record linkage study to compare the risk of COVID-19 hospitalisation among healthcare workers (age: 18-65 years), their households and other members of the general population.\n\nMain outcomeHospitalisation with COVID-19\n\nResultsThe cohort comprised 158,445 healthcare workers, the majority being patient facing (90,733 / 158,445; 57.3%), and 229,905 household members. Of all COVID-19 hospitalisations in the working age population (18-65-year-old), 17.2% (360 / 2,097) were in healthcare workers or their households. Adjusting for age, sex, ethnicity, socio-economic deprivation and comorbidity, the risk of COVID-19 hospitalisation in non-patient facing healthcare workers and their households was similar to the risk in the general population (hazards ratio [HR] 0.81; 95%CI 0.52-1.26 and 0.86; 95%CI 0.49-1.51 respectively). In models adjusting for the same covariates however, patient facing healthcare workers, compared to non-patient facing healthcare workers, were at higher risk (HR 3.30; 95%CI 2.13-5.13); so too were household members of patient facing healthcare workers (HR 1.79; 95%CI 1.10-2.91). On sub-dividing patient-facing healthcare workers into those who worked in front-door, intensive care and non-intensive care aerosol generating settings and other, those in  front door roles were at higher risk (HR 2.09; 95%CI 1.49-2.94). For most patient facing healthcare workers and their households, the estimated absolute risk of COVID-19 hospitalisation was less than 0.5% but was 1% and above in older men with comorbidity.\n\nConclusionsHealthcare workers and their households contribute a sixth of hospitalised COVID-19 cases. Whilst the absolute risk of hospitalisation was low overall, patient facing healthcare workers and their households had 3- and 2-fold increased risks of COVID-19 hospitalisation.",
-    "category": "epidemiology",
-    "match_type": "exact",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2020.08.03.20167122",
@@ -4171,6 +4101,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2020.06.13.20130419",
+    "date": "2020-06-16",
+    "link": "https://medrxiv.org/cgi/content/short/2020.06.13.20130419",
+    "title": "Mental health service activity during COVID-19 lockdown: South London and Maudsley data on working age community and home treatment team services and mortality from February to mid-May 2020",
+    "authors": "Robert Stewart; Evangelia Martin; Matthew Broadbent",
+    "affiliations": "King's College London; King's College London; South London and Maudsley NHS Foundation Trust",
+    "abstract": "The lockdown and social distancing policy response to the COVID-19 pandemic in the UK has a potentially important impact on provision of mental healthcare; however, there has been relatively little quantification of this. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource with 24-hourly updates of electronic mental health records data, this paper describes daily caseloads and contact numbers (face-to-face and virtual) for home treatment teams (HTTs) and working age adult community mental health teams (CMHTs) from 1st February to 15th May 2020 at the South London and Maudsley NHS Trust (SLaM), a large mental health service provider for 1.2m residents in south London. In addition daily deaths are described for all current and previous SLaM service users over this period and the same dates in 2019. In summary, comparing periods before and after 16th March 2020 the CMHT sector showed relatively stable caseloads and total contact numbers, but a substantial shift from face-to-face to virtual contacts, while HTTs showed the same changeover but reductions in caseloads and total contacts (although potentially an activity rise again during May). Number of deaths for the two months between 16th March and 15th May were 2.4-fold higher in 2020 than 2019, with 958 excess deaths.",
+    "category": "psychiatry and clinical psychology",
+    "match_type": "exact",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2020.06.12.20129494",
@@ -4227,6 +4171,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2020.06.02.20120642",
+    "date": "2020-06-05",
+    "link": "https://medrxiv.org/cgi/content/short/2020.06.02.20120642",
+    "title": "Estimating excess visual loss in people with neovascular age-related macular degeneration during the COVID-19 pandemic",
+    "authors": "Darren S Thomas; Alasdair Warwick; Abraham Olvera-Barrios; Catherine Egan; Roy Schwartz; Sudeshna Patra; Haralabos Eleftheriadis; Anthony P Khawaja; Andrew Lotery; Philipp L Mueller; Robin Hamilton; Ella Preston; Paul Taylor; Adnan Tufail; - UK EMR Users Group",
+    "affiliations": "Institute of Health Informatics, University College London, London, UK; Institute of Cardiovascular Science, University College London, London, UK & Moorfields Eye Hospital NHS Foundation Trust, London, UK.; Moorfields Eye Hospital NHS Turst & Institute of Ophthalmology UCL; Moorfields Eye Hospital NHS Foundation Trust, London, UK & Institute of Ophthalmology, UCL; Moorfields Eye Hospital NHS Foundation Trust, London, UK & Institute of Health Informatics, University College London, London, UK; Bart's Health NHS Trust, London, UK; King's College Hospital NHS Trust, London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK & Institute of Ophthalmology, UCL; Faculty of Medicine, University of Southampton, Southampton, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK & Institute of Ophthalmology, UCL; Moorfields Eye Hospital NHS Foundation Trust, London, UK; Institute of Health Informatics, University College London, London, UK; Moorfields Eye Hospital NHS Trust & Institute of Ophthalmology UCL; ",
+    "abstract": "ObjectivesTo report the reduction in new neovascular age-related macular degeneration (nAMD) referrals during the COVID-19 pandemic and estimate the impact of delayed treatment on visual outcomes at one year.\n\nDesignRetrospective clinical audit and simulation model.\n\nSettingMultiple UK NHS ophthalmology centres.\n\nParticipantsData on the reduction in new nAMD referrals was obtained from four NHS Trusts in England comparing April 2020 to April 2019. To estimate the potential impact on one-year visual outcomes, a stratified bootstrap simulation model was developed drawing on an electronic medical records dataset of 20,825 nAMD eyes from 27 NHS Trusts.\n\nMain outcome measuresSimulated mean visual acuity and proportions of eyes with vision [&le;]6/60, [&le;]6/24 and [&ge;]6/12 at one year under four hypothetical scenarios: no treatment delay, 3, 6 and 9-month treatment delays. Estimated additional number of eyes with vision [&le;]6/60 at one year nationally.\n\nResultsThe number of nAMD referrals at four major eye treatment hospital groups based in England dropped on average by 72% (range 65 to 87%) in April 2020 compared to April 2019. Simulated one-year visual outcomes for 1000 nAMD eyes with a 3-month treatment delay suggested an increase in the proportion of eyes with vision [&le;]6/60 from 15.5% (13.2 to 17.9) to 23.3% (20.7 to25.9), and a decrease in the proportion of eyes with vision [&ge;]6/12 (driving vision) from 35.1% (32.1 to 38.1) to 26.4% (23.8 to29.2). Outcomes worsened incrementally with longer modelled delays. Assuming nAMD referrals are reduced to this level at the national level for only one month, these simulated results suggest an additional 186-365 eyes with vision [&le;]6/60 at one-year with even a short treatment delay.\n\nConclusionsWe report a large decrease in nAMD referrals during the first month of COVID-19 lockdown and provide an important public health message regarding the risk of delayed treatment. As a conservative estimate, a treatment delay of 3 months could lead to a >50% relative increase in the number of eyes with vision [&le;]6/60 and 25% relative decrease in the number of eyes with driving vision at one year.",
+    "category": "ophthalmology",
+    "match_type": "exact",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2020.06.01.20116608",
@@ -4297,6 +4255,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2020.05.18.20086157",
+    "date": "2020-05-22",
+    "link": "https://medrxiv.org/cgi/content/short/2020.05.18.20086157",
+    "title": "COVID-19 in Great Britain: epidemiological and clinical characteristics of the first few hundred (FF100) cases: a descriptive case series and case control analysis",
+    "authors": "Nicola L Boddington; Andre Charlett; Suzanne Elgohari; Jemma L Walker; Helen Mcdonald; Chloe Byers; Laura Coughlan; Tatiana Garcia Vilaplana; Rosie Whillock; Mary Sinnathamby; Nikolaos Panagiotopoulos; Louise Letley; Pauline MacDonald; Roberto Vivancos; Obaghe Edeghere; Joseph Shingleton; Emma Bennett; Daniel J Grint; Helen Strongman; Kathryn E Mansfield; Christopher Rentsch; Caroline Minassian; Ian J Douglas; Rohini Mathur; Maria Peppa; Simon Cottrell; Jim McMenamin; Maria Zambon; Mary Ramsay; Gavin Dabrera; Vanessa Saliba; Jamie Lopez Bernal",
+    "affiliations": "Public Health England; Public Health England; Public Health England; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Public Health Wales; Public Health Scotland; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England",
+    "abstract": "ObjectivesFollowing detection of the first virologically-confirmed cases of COVID-19 in Great Britain, an enhanced surveillance study was initiated by Public Health England to describe the clinical presentation, course of disease and underlying health conditions associated with infection of the first few hundred cases.\n\nMethodsInformation was collected on the first COVID-19 cases according to the First Few X WHO protocol. Case-control analyses of the sensitivity, specificity and predictive value of symptoms and underlying health conditions associated with infection were conducted. Point prevalences of underlying health conditions among the UK general population were presented.\n\nFindingsThe majority of FF100 cases were imported (51.4%), of which the majority had recent travel to Italy (71.4%). 24.7% were secondary cases acquired mainly through household contact (40.4%). Children had lower odds of COVID-19 infection compared with the general population.\n\nThe clinical presentation of cases was dominated by cough, fever and fatigue. Non-linear relationships with age were observed for fever, and sensitivity and specificity of symptoms varied by age.\n\nConditions associated with higher odds of COVID-19 infection (after adjusting for age and sex) were chronic heart disease, immunosuppression and multimorbidity.\n\nConclusionThis study presents the first epidemiological and clinical summary of COVID-19 cases in Great Britain. The FFX study design enabled systematic data collection. The study characterized underlying health conditions associated with infection and set relative risks in context with population prevalence estimates. It also provides important evidence for generating case definitions to support public health risk assessment, clinical triage and diagnostic algorithms.",
+    "category": "epidemiology",
+    "match_type": "exact",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2020.05.11.20098269",
@@ -4576,19 +4548,5 @@
     "match_type": "exact",
     "author_similarity": 100,
     "affiliation_similarity": 100
-  },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2020.03.22.20040287",
-    "date": "2020-03-24",
-    "link": "https://medrxiv.org/cgi/content/short/2020.03.22.20040287",
-    "title": "Estimating excess 1- year mortality from COVID-19 according to underlying conditions and age in England: a rapid analysis using NHS health records in 3.8 million adults",
-    "authors": "Amitava Banerjee; Laura Pasea; Steve Harris; Arturo Gonzalez-Izquierdo; Ana Torralbo; Laura Shallcross; Mahdad Noursadeghi; Deenan Pillay; Christina Pagel; Wai Keong Wong; Claudia Langenberg; Bryan Williams; Spiros Denaxas; Harry Hemingway",
-    "affiliations": "University College London; University College London; University College London Hospitals NHS Trust; University College London; University College London; UCL; University College London; University College London; University College London; University College London Hospitals NHS Trust; University of Cambridge; University College London; University College London; University College London",
-    "abstract": "BackgroundThe medical, health service, societal and economic impact of the COVID-19 emergency has unknown effects on overall population mortality. Previous models of population mortality are based on death over days among infected people, nearly all of whom (to date at least) have underlying conditions. Models have not incorporated information on high risk conditions or their longer term background (pre-COVID-19) mortality. We estimated the excess number of deaths over 1 year under different COVID-19 incidence rates and differing mortality impacts.\n\nMethodsUsing population based linked primary and secondary care electronic health records in England (HDR UK - CALIBER), we report the prevalence of underlying conditions defined by UK Public Health England COVID-19 guidelines (16 March 2020) in 3,862,012 individuals aged [&ge;]30 years from 1997-2017. We used previously validated phenotypes, openly available (https://caliberresearch.org/portal), for each condition using ICD-10 diagnosis, Read, procedure and medication codes. We estimated the 1-year mortality in each condition, and developed simple models of excess COVID-19-related deaths assuming relative risk (RR) of the impact of the emergency (compared to background mortality) of 1.2, 1.5 and 2.0.\n\nFindings20.0% of the population are at risk according to current PHE guidelines, of which; 13.7% were age>70 years and 6.3% aged [&le;]70 years with [&ge;]1 underlying condition (cardiovascular disease (2.3%), diabetes (2.2%), steroid therapy (1.9%), severe obesity (0.9%), chronic kidney disease (0.6%) and chronic obstructive pulmonary disease, COPD (0.5%). Multimorbidity (co-occurrence of [&ge;]2 conditions in an individual) was common (10.1%). The 1-year mortality in the at-risk population was 4.46%, and age and underlying conditions combine to influence background risk, varying markedly across conditions (5.9% in age>70 years, 8.6% for COPD and 13.1% in those with [&ge;]3 or more conditions). In a suppression scenario (at SARS CoV2 rates of 0.001% of the UK population), there would be minimal excess deaths (3 and 7 excess deaths at relative risk, RR, 1.5 and 2.0 respectively). At SARS CoV2 rates of 10% of the UK population (mitigation) the model estimates the numbers of excess deaths as: 13791, 34479 and 68957 (at RR 1.2, 1.5 and 2.0 respectively). At SARS CoV2 rates of 80% in the UK population (\"do-nothing\"), the model estimates the number of excess deaths as 110332, 275,830 and 551,659 (at RR 1.2, 1.5 and 2.0) respectively.\n\nInterpretationWe provide the public, researchers and policy makers a simple model to estimate the excess mortality over 1 year from COVID-19, based on underlying conditions at different ages. If the relative mortality impact of COVID-19 were to be about 20% (similar magnitude as the established winter vs summer mortality excess), then the excess deaths would be 0 when 1 in 100 000 (suppression), 13791 when 1 in 10 (mitigation) and 110332 when 8 in 10 are infected (\"do nothing\") scenario. However, the relative impact of COVID-19 is unknown. If the emergency were to double the mortality risk, then we estimate 7, 68957 and 551,659 excess deaths in the same scenarios. These results may inform the need for more stringent suppression measures as well as efforts to target those at highest risk for a range of preventive interventions.",
-    "category": "public and global health",
-    "match_type": "exact",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
   }
 ]
\ No newline at end of file
diff --git a/data/covid/preprints.json b/data/covid/preprints.json
index 13e84c0c..dbafcc74 100644
--- a/data/covid/preprints.json
+++ b/data/covid/preprints.json
@@ -657,20 +657,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2023.02.28.23286559",
-    "date": "2023-03-01",
-    "link": "https://medrxiv.org/cgi/content/short/2023.02.28.23286559",
-    "title": "Elevated symptoms of depression and anxiety among family members and friends of critically ill COVID-19 patients - An observational study of five cohorts across four countries",
-    "authors": "Anik\u00f3 Lovik; Juan Gonz\u00e1lez-Hij\u00f3n; Asle Hoffart; Chloe Fawns-Ritchie; Ingibj\u00f6rg Magn\u00fasd\u00f3ttir; Li Lu; Anna B\u00e1ra Unnarsd\u00f3ttir; Anna K. K\u00e4hler; Archie Campbell; Arna Hauksd\u00f3ttir; Charilaos Chourpiliadis; Daniel L McCartney; Edda Bj\u00f6rk Thordard\u00f3ttir; Emily E. Joyce; Emma M. Frans; J\u00f3hanna Jakobsd\u00f3ttir; Lill Trogstad; Ole A. Andreassen; Per Magnus; Sverre Urnes Johnson; Patrick F. Sullivan; Thor Aspelund; David J. Porteous; Helga Ask; Omid V. Ebrahimi; Unnur Anna Valdimarsd\u00f3ttir; Fang Fang",
-    "affiliations": "Karolinska Institutet and Leiden University; Karolinska Institutet; University of Oslo; University of Edinburgh; University of Iceland; University of Oslo; University of Iceland; Karolinska Institutet; University of Edinburgh; University of Iceland; Karolinska Institutet; University of Edinburgh; University of Iceland; Karolinska Institutet; Karolinska Institutet; University of Iceland; Norwegian Institute of Public Health; University of Oslo; Norwegian Institute of Public Health; University of Oslo; Karolinska Institutet; University of Iceland; University of Edinburgh; University of Oslo; University of Oslo; Karolinska Institutet; Karolinska Institutet",
-    "abstract": "BackgroundLittle is known regarding the mental health impact of having a significant person (family member and/or close friend) with COVID-19 of different severity.\n\nMethodsThe study included five prospective cohorts from four countries (Iceland, Norway, Sweden, and the UK) with self-reported data on COVID-19 and symptoms of depression and anxiety during March 2020-March 2022. We calculated the prevalence ratio (PR) of depression and anxiety in relation to having a significant person with COVID-19 and performed a longitudinal analysis in the Swedish cohort to describe the temporal patterns of the results.\n\nResults162,237 and 168,783 individuals were included in the analysis of depression and anxiety, respectively, of whom 24,718 and 27,003 reported a significant person with COVID-19. Overall, the PR was 1.07 (95% CI: 1.05-1.10) for depression and 1.08 (95% CI: 1.03-1.13) for anxiety among significant others of COVID-19 patients. The respective PRs for depression and anxiety were 1.04 (95% CI: 1.01-1.07) and 1.03 (95% CI: 0.98-1.07) if the significant person was never hospitalized, 1.15 (95% CI: 1.08-1.23) and 1.24 (95% CI: 1.14-1.34) if the patient was hospitalized, 1.42 (95% CI: 1.27-1.57) and 1.45 (95% CI: 1.31-1.60) if admitted to the ICU, and 1.34 (95% CI: 1.22-1.46) and 1.36 (95% CI: 1.22-1.51) if the significant person died. Individuals of hospitalized, ICU admitted, or deceased patients showed higher prevalence of depression and anxiety during the entire 12 months after the COVID-19 diagnosis of the significant person.\n\nConclusionsClose friends and family members of critically ill COVID-19 patients show elevated prevalence of depression and anxiety throughout the first year after the diagnosis.",
-    "category": "public and global health",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2023.02.17.23286079",
@@ -965,20 +951,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2022.12.09.22283280",
-    "date": "2022-12-13",
-    "link": "https://medrxiv.org/cgi/content/short/2022.12.09.22283280",
-    "title": "Identification of a protein expression signature distinguishing early from organising diffuse alveolar damage in COVID-19 patients.",
-    "authors": "Helen Ashwin; Luke Milross; Julie Wilson; Joaquim Majo; Jimmy T. H. Lee; Grant Calder; Bethany Hunter; Sally James; Dimitris Lagos; Nathalie Signoret; Andrew Filby; Omer Ali Bayraktar; Andrew J Fisher; Paul M Kaye",
-    "affiliations": "University of York; Newcastle University; University of York; Newcastle upon Tyne Hospitals NHS Foundation Trust; Sanger Institute; University of York; Newcastle University; University of York; University of York; University of York; Newcastle University; Sanger Institute; Newcastle University; University of York",
-    "abstract": "Diffuse alveolar damage (DAD) is a histopathological finding associated with severe viral infections, including SARS-CoV-2. However, the mechanisms mediating progression of DAD are poorly understood. Applying protein digital spatial profiling to lung tissue obtained from a cohort of 27 COVID-19 autopsy cases from the UK, we identified a protein signature (ARG1, CD127, GZMB, IDO1, Ki67, phospho-PRAS40 (T246), and VISTA that distinguishes early / exudative DAD from late / organising DAD with good predictive accuracy. These proteins warrant further investigation as potential immunotherapeutic targets to modulate DAD progression and improve patient outcome.",
-    "category": "pathology",
-    "match_type": "fuzzy",
-    "author_similarity": 92,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2022.11.29.22282883",
@@ -1273,20 +1245,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2022.09.09.22279754",
-    "date": "2022-09-09",
-    "link": "https://medrxiv.org/cgi/content/short/2022.09.09.22279754",
-    "title": "Contact patterns of UK home delivery drivers and their use of protective measures during the COVID-19 pandemic: a cross-sectional study",
-    "authors": "Jessica R E Bridgen; Hua Wei; Carl A Whitfield; Yang Han; Ian Hall; Chris Jewell; Martie JA van Tongeren; Jonathan M Read",
-    "affiliations": "Lancaster University; The University of Manchester; University of Manchester; University of Manchester; University of Manchester; Lancaster University; University of Manchester; Lancaster University",
-    "abstract": "ObjectivesTo quantify contact patterns of UK home delivery drivers and identify protective measures adopted during the pandemic.\n\nMethodsWe conducted a cross-sectional online survey to measure the interactions of 170 UK delivery drivers during a working shift between 7 December 2020 and 31 March 2021.\n\nResultsDelivery drivers had a mean number of 71.6 (95% Confidence Interval (CI) 61.0 to 84.1) customer contacts per shift and 15.0 (95%CI 11.19 to 19.20) depot contacts per shift. Maintaining physical distancing with customers was more common than at delivery depots. Prolonged contact (more than 5 minutes) with customers was reported by 5.4% of drivers on their last shift. We found 3.0% of drivers had tested positive for SARS-CoV-2 since the start of the pandemic and 16.8% of drivers had self-isolated due to a suspected or confirmed case of COVID-19. Additionally, 5.3% (95%CI 2.3% to 10.2%) of participants reported having worked whilst ill with COVID-19 symptoms, or with a member of their household having a suspected or confirmed case of COVID-19.\n\nConclusionDelivery drivers had a large number of face-to-face customer and depot contacts per shift compared to other working adults during this time. However, transmission risk may be curtailed as contact with customers was of short duration. Most drivers were unable to maintain physical distance with customers and at depots at all times. Usage of protective items such as face masks and hand sanitizer was widespread.",
-    "category": "occupational and environmental health",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2022.09.01.22279473",
@@ -1359,13 +1317,13 @@
   },
   {
     "site": "medRxiv",
-    "doi": "10.1101/2022.08.13.22278733",
-    "date": "2022-08-16",
-    "link": "https://medrxiv.org/cgi/content/short/2022.08.13.22278733",
-    "title": "QCovid 4 - Predicting risk of death or hospitalisation from COVID-19 in adults testing positive for SARS-CoV-2 infection during the Omicron wave in England",
-    "authors": "Julia Hippisley-Cox; Kamlesh Khunti; Aziz Sheikh; Jonathan Nguyen-Van-Tam; Carol Coupland",
-    "affiliations": "University of Oxford; University of Leicester; University of Edinburgh; University of Nottingham; University of Oxford",
-    "abstract": "ObjectivesTo (a) derive and validate risk prediction algorithms (QCovid4) to estimate risk of COVID-19 mortality and hospitalisation in UK adults with a SARS-CoV-2 positive test during the  Omicron pandemic wave in England and (b) evaluate performance with earlier versions of algorithms developed in previous pandemic waves and the high-risk cohort identified by NHS Digital in England.\n\nDesignPopulation-based cohort study using the QResearch database linked to national data on COVID-19 vaccination, high risk patients prioritised for COVID-19 therapeutics, SARS-CoV-2 results, hospitalisation, cancer registry, systemic anticancer treatment, radiotherapy and the national death registry.\n\nSettings and study period1.3 million adults in the derivation cohort and 0.15 million adults in the validation cohort aged 18-100 years with a SARS-CoV-2 positive test between 11th December 2021 and 31st March 2022 with follow up to 30th June 2022.\n\nMain outcome measuresOur primary outcome was COVID-19 death. The secondary outcome of interest was COVID-19 hospital admission. Models fitted in the derivation cohort to derive risk equations using a range of predictor variables. Performance evaluated in a separate validation cohort.\n\nResultsOf 1,297,984 people with a SARS-CoV-2 positive test in the derivation cohort, 18,756 (1.45%) had a COVID-19 related hospital admission and 3,878 (0.3%) had a COVID-19 death during follow-up. Of the 145,404 people in the validation cohort, there were 2,124 (1.46%) COVID-19 admissions and 461 (0.3%) COVID-19 deaths.\n\nThe COVID-19 mortality rate in men increased with age and deprivation. In the QCovid4 model in men hazard ratios were highest for those with the following conditions (for 95% CI see Figure 1): kidney transplant (6.1-fold increase); Downs syndrome (4.9-fold); radiotherapy (3.1-fold); type 1 diabetes (3.4-fold); chemotherapy grade A (3.8-fold), grade B (5.8-fold); grade C (10.9-fold); solid organ transplant ever (2.4-fold); dementia (1.62-fold); Parkinsons disease (2.2-fold); liver cirrhosis (2.5-fold). Other conditions associated with increased COVID-19 mortality included learning disability, chronic kidney disease (stages 4 and 5), blood cancer, respiratory cancer, immunosuppressants, oral steroids, COPD, coronary heart disease, stroke, atrial fibrillation, heart failure, thromboembolism, rheumatoid/SLE, schizophrenia/bipolar disease sickle cell/HIV/SCID; type 2 diabetes. Results were similar in the model in women.\n\nO_FIG O_LINKSMALLFIG WIDTH=100 HEIGHT=200 SRC=\"FIGDIR/small/22278733v1_fig1.gif\" ALT=\"Figure 1\">\nView larger version (35K):\norg.highwire.dtl.DTLVardef@4e93b7org.highwire.dtl.DTLVardef@c3e600org.highwire.dtl.DTLVardef@1311bd4org.highwire.dtl.DTLVardef@11a3246_HPS_FORMAT_FIGEXP  M_FIG O_FLOATNOFigure 1C_FLOATNO QCOVID4 (mortality): Adjusted hazard ratios for COVID-19 death in men mutually adjusted and also adjusted for fractional polynomial terms for age and BMI\n\nC_FIG COVID-19 mortality risk was lower among those who had received COVID-19 vaccination compared with unvaccinated individuals with evidence of a dose response relationship. The reduced mortality rates associated with prior SARS-CoV-2 infection were similar in men (adjusted hazard ratio (HR) 0.51 (95% CI 0.40, 0.64)) and women (adjusted HR 0.55 (95%CI 0.45, 0.67)).\n\nThe QCOVID4 algorithm explained 76.6% (95%CI 74.4 to 78.8) of the variation in time to COVID-19 death (R2) in women. The D statistic was 3.70 (95%CI 3.48 to 3.93) and the Harrells C statistic was 0.965 (95%CI 0.951 to 0.978). The corresponding results for COVID-19 death in men were similar with R2 76.0% (95% 73.9 to 78.2); D statistic 3.65 (95%CI 3.43 to 3.86) and C statistic of 0.970 (95%CI 0.962 to 0.979). QCOVID4 discrimination for mortality was slightly higher than that for QCOVID1 and QCOVID2, but calibration was much improved.\n\nConclusionThe QCovid4 risk algorithm modelled from data during the UKs Omicron wave now includes vaccination dose and prior SARS-CoV-2 infection and predicts COVID-19 mortality among people with a positive test. It has excellent performance and could be used for targeting COVID-19 vaccination and therapeutics. Although large disparities in risks of severe COVID-19 outcomes among ethnic minority groups were observed during the early waves of the pandemic, these are much reduced now with no increased risk of mortality by ethnic group.\n\nWhat is knownO_LIThe QCOVID risk assessment algorithm for predicting risk of COVID-19 death or hospital admission based on individual characteristics has been used in England to identify people at high risk of severe COVID-19 outcomes, adding an additional 1.5 million people to the national shielded patient list in England and in the UK for prioritising people for COVID-19 vaccination.\nC_LIO_LIThere are ethnic disparities in severe COVID-19 outcomes which were most marked in the first pandemic wave in 2020.\nC_LIO_LICOVID-19 vaccinations and therapeutics (monoclonal antibodies and antivirals) are available but need to be targeted to those at highest risk of severe outcomes.\nC_LI\n\nWhat this study addsO_LIThe QCOVID4 risk algorithm using data from the Omicron wave now includes number of vaccination doses and prior SARS-CoV-2 infection. It has excellent performance both for ranking individuals (discrimination) and predicting levels of absolute risk (calibration) and can be used for targeting COVID-19 vaccination and therapeutics as well as individualised risk assessment.\nC_LIO_LIQCOVID4 more accurately identifies individuals at highest levels of absolute risk for targeted interventions than the  conditions-based approach adopted by NHS Digital based on relative risk of a list of medical conditions.\nC_LIO_LIAlthough large disparities in risks of severe COVID-19 outcomes among ethnic minority groups were observed during the early waves of the pandemic, these are much reduced now with no increased risk of mortality by ethnic group.\nC_LI",
+    "doi": "10.1101/2022.08.17.22278893",
+    "date": "2022-08-18",
+    "link": "https://medrxiv.org/cgi/content/short/2022.08.17.22278893",
+    "title": "Uptake of Sotrovimab for prevention of severe COVID-19 and its safety in the community in England",
+    "authors": "Martina Patone; Holly Tibble; Andrew JHL Snelling; Carol Coupland; Aziz Sheikh; Julia Hippisley-Cox",
+    "affiliations": "University of Oxford; University of Edinburgh; University of Oxford; University of Oxford; University of Edinburgh; University of Oxford",
+    "abstract": "Sotrovimab is a neutralising monoclonal antibody (nMAB), currently administrated in England to treat extremely clinically vulnerable COVID-19 patients. Trials have shown it to have mild or moderate side effects, however safety in real-world settings has not been yet evaluated. We used national databases to investigate its uptake and safety in community patients across England. We used a cohort study to describe uptake and a self-controlled case series design to evaluate the risks of 49 pre-specified suspected adverse events in the 2-28 days post-treatment. Between December 11, 2021 and May 24, 2022, there were 172,860 COVID-19 patients eligible for treatment. Of the 22,815 people who received Sotrovimab, 21,487 (94.2%) had a positive SARS-CoV-2 test and 5,999 (26.3%) were not on the eligible list. Between treated and untreated eligible individuals, the mean age (54.6, SD: 16.1 vs 54.1, SD: 18.3) and sex distribution (women: 60.9% vs 58.1%; men: 38.9% vs 41.1%) were similar. There were marked variations in uptake between ethnic groups, which was higher amongst Indian (15.0%; 95%CI 13.8, 16.3), Other Asian (13.7%; 95%CI 11.9, 15.8), White (13.4%; 95%CI 13.3, 13.6), and Bangladeshi (11.4%; 95%CI 8.8, 14.6); and lower amongst Black Caribbean individuals (6.4%; 95%CI 5.4, 7.5) and Black Africans (4.7%; 95%CI 4.1, 5.4). We found no increased risk of any of the suspected adverse events in the overall period of 2-28 days post-treatment, but an increased risk of rheumatoid arthritis (IRR 3.08, 95% CI 1.44, 6.58) and of systematic lupus erythematosus (IRR 5.15, 95% CI 1.60, 16.60) in the 2-3 days post-treatment, when we narrowed the risk period.\n\nFundingNational Institute of Health Research (Grant reference 135561)",
     "category": "epidemiology",
     "match_type": "fuzzy",
     "author_similarity": 100,
@@ -1385,6 +1343,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2022.08.07.22278510",
+    "date": "2022-08-09",
+    "link": "https://medrxiv.org/cgi/content/short/2022.08.07.22278510",
+    "title": "Metabolomic and gut microbiome profiles across the spectrum of community-based COVID and non-COVID disease: A COVID-19 Biobank study.",
+    "authors": "Marc F \u00d6sterdahl; Ronan Whiston; Carole H Sudre; Francesco Asnicar; Nathan J Cheetham; Aitor Blanco Miguez; Vicky Bowyer; Michela Antonelli; Olivia Snell; Liane dos Santos Canas; Christina Hu; Jonathan Wolf; Cristina Menni; Michael Malim; Deborah Hart; Tim Spector; Sarah Berry; Nicola Segata; Katie Doores; Sebastien Ourselin; Emma L Duncan; Claire J Steves",
+    "affiliations": "King's College London; King's College London; King's College London; University of Trento; King's College London; University of Trento; King's College London; King's College London; King's College London; King's College London; ZOE Global Ltd.; ZOE Global Ltd.; King's College London; King's College London; King's College London; King's College London; King's College London; University of Trento; King's College London; King's College London; King's College London; King's College London",
+    "abstract": "Whilst many with SARS-CoV-2 infection have mild disease, managed in the community, individuals with cardiovascular risk factors experienced often more severe acute disease, requiring hospitalisation. Increasing concern has also developed over long symptom duration in many individuals, including the majority who managed acutely in the community. Risk factors for long symptom duration, including biological variables, are still poorly defined.\n\nWe examine post-illness metabolomic and gut-microbiome profiles, in community-dwelling participants with SARS-CoV-2, ranging from asymptomatic illness to Post-COVID Syndrome, and participants with prolonged non-COVID-19 illnesses. We also assess a pre-established metabolomic biomarker score for its association with illness duration.\n\nWe found an atherogenic-dyslipidaemic metabolic profile, and greater biomarker scores, associated with longer illness, both in individuals with and without SARS-CoV-2 infection. We found no association between illness duration and gut microbiome in convalescence.\n\nFindings highlight the potential role of cardiometabolic dysfunction to the experience of long illness duration, including after COVID-19.",
+    "category": "epidemiology",
+    "match_type": "fuzzy",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2022.08.08.22278493",
@@ -1469,6 +1441,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2022.07.20.22277838",
+    "date": "2022-07-21",
+    "link": "https://medrxiv.org/cgi/content/short/2022.07.20.22277838",
+    "title": "National and regional prevalence of SARS-CoV-2 antibodies in primary and secondary school children in England: the School Infection Survey, a national open cohort study, November 2021",
+    "authors": "Annabel A Powell; Georgina Ireland; Rebecca Leeson; Andrea Lacey; Ben Ford; John Poh; Samreen Ijaz; Justin Shute; Peter Cherepanov; Richard Tedder; Christian Bottomley; Fiona Dawe; Punam Mangtani; Peter Jones; Patrick Nguipdop-Djomo; Shamez Ladhani",
+    "affiliations": "UK Health Security Agency; UK Health Security Agency; Office for National Statistics; Office for National Statistics; Office for National Statistics; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; Imperial College London; Francis Crick Institute; London School of Hygiene & Tropical Medicine; Office for National Statistics; London School of Hygiene & Tropical Medicine; Office for National Statistics; London School of Hygiene & Tropical Medicine; UK Health Security Agency",
+    "abstract": "BackgroundRisk factors for infection and, therefore, antibody positivity rates will be different in children compared to adults. We aim to estimate national and regional prevalence of SARS-CoV-2 antibodies in primary (4-11-year-olds) and secondary (11-15-year-olds) school children between 10 November and 10 December 2021.\n\nMethodsCross-sectional surveillance in England using two stage sampling, firstly stratifying into regions and selecting local authorities, then selecting schools according to a stratified sample within selected local authorities. Participants were sampled using a novel oral fluid validated assay for SARS-CoV-2 spike and nucleocapsid IgG antibodies.\n\nResults4,980 students from 117 state-funded schools (2,706 from 83 primary schools, 2,274 from 34 secondary schools) provided a valid sample. After weighting for age, sex and ethnicity, and adjusting for assay accuracy, the national prevalence of SARS-CoV-2 antibodies in primary school students, who were all unvaccinated, was 40.1% (95%CI; 37.3-43.0). Antibody prevalence increased with age (p<0.001) and were higher in urban than rural schools (p=0.01). In secondary school students, the adjusted, weighted national prevalence of SARS-CoV-2 antibodies was 82.4% (95%CI; 79.5-85.1); including 57.5% (95%CI; 53.9-61.1) in unvaccinated and 97.5% (95%CI; 96.1-98.5) in vaccinated students. Antibody prevalence increased with age (p<0.001), and was not significantly different in urban versus rural students (p=0.1).\n\nConclusionsUsing a validated oral fluid assay, we estimated national and regional seroprevalence of SARS-CoV-2 antibodies in primary and secondary school students. In November 2021, 40% of primary school students and nearly all secondary school students in England had SARS-CoV2 antibodies through a combination of natural infection and vaccination.",
+    "category": "epidemiology",
+    "match_type": "fuzzy",
+    "author_similarity": 92,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2022.07.21.22277893",
@@ -1653,14 +1639,14 @@
   },
   {
     "site": "medRxiv",
-    "doi": "10.1101/2022.06.09.22276196",
+    "doi": "10.1101/2022.06.08.22276134",
     "date": "2022-06-14",
-    "link": "https://medrxiv.org/cgi/content/short/2022.06.09.22276196",
-    "title": "Accelerated waning of the humoral response to SARS-CoV-2 vaccines in obesity",
-    "authors": "Agatha A. van der Klaauw MD, PhD; Emily C. Horner BSc; Pehuen Pereyra-Gerber PhD; Utkarsh Agrawal PhD; William S. Foster BSc, MRes,; Sarah Spencer MD, BSc; Bensi Vergese BSc Hons.; Miriam E. Smith BSc PhD; Elana Henning B.Soc.Sc; Isobel D. Ramsay MA BM BCh; Jack A. Smith BSc MBiol; Stephane M. Guillaume BSc; Hayley J. Sharpe BSc, PhD; Iain M. Hay BSc, PhD; Sam Thompson BSc; Silvia Innocentin BSc., Ph.D; Lucy H Booth BSc; Chris Robertson Ph.D.; Colin McCowan Ph.D.; Thomas E Mulroney PhD; Martin J O'Reilly; Thevinya P Guragama; Lihinya P Guragama; Maria A Rust BSc; Alex Ferreira; Soraya Ebrahimi MSc; Lourdes Ceron-Gutierrez MSc.; Jacopo Scotucci MD; Barbara Kronsteiner Ph.D.; Susanna J. Dunachie MD., Ph.D.; Paul Klenerman MD., Ph.D.; - PITCH Consortium; Adrian J. Park MD PhD; Francesco Rubino MD.,; Hannah Stark BSc; Nathalie Kingson PhD; Rainer Doffinger PhD; Michelle A. Linterman BBmedSc (H; Nicholas J. Matheson MA BM BCh; Aziz Sheikh MD; I. Sadaf Farooqi MD, PhD; James E. Thaventhiran MD, PhD",
-    "affiliations": "University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Meta; Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR; Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, UK; Department of Medi; School of Medicine, University of St. Andrews; Immunology, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT; Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR; University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Meta; University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Meta; University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Meta; 1. Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, UK 2. Department of; 1. Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, UK 2. Department of; Immunology, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT; Signalling, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT; Signalling, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT; Cambridge Institute for Medical Research, Cambridge UK.; Flow cytometry core, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT; Babraham Institute, Babraham Research Campus, Cambridge; Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR; Department of Mathematics and Statistics, University of Strathclyde; School of Medicine, University of St. Andrews; Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR; Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR; Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR; Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR; Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR; Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR; NIHR Cambridge Clinical Research Facility, Departments of Immunology and Clinical Biochemistry; NIHR Cambridge Clinical Research Facility, Departments of Immunology and Clinical Biochemistry; University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Meta; Nuffield Department of Clinical Medicine, University of Oxford; Nuffield Department of Clinical Medicine, University of Oxford; Nuffield Department of Clinical Medicine, University of Oxford; ; Cambridge University Hospitals NHS Foundation Trust, Department of Clinical Biochemistry, Cambridge, United Kingdom; Kings College London, Department of Diabetes, School of Life Course Science, London; NIHR BioResource; NIHR BioResource; NIHR Cambridge Clinical Research Facility, Departments of Immunology, Clinical Biochemistry; Immunology, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT; 1. Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, UK 2. Department of; Usher Institute, University of Edinburgh; University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Meta; Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR",
-    "abstract": "Obesity is associated with an increased risk of severe Covid-19. However, the effectiveness of SARS-CoV-2 vaccines in people with obesity is unknown. Here we studied the relationship between body mass index (BMI), hospitalization and mortality due to Covid-19 amongst 3.5 million people in Scotland. Vaccinated people with severe obesity (BMI>40 kg/m2) were significantly more likely to experience hospitalization or death from Covid-19. Excess risk increased with time since vaccination. To investigate the underlying mechanisms, we conducted a prospective longitudinal study of the immune response in a clinical cohort of vaccinated people with severe obesity. Compared with normal weight people, six months after their second vaccine dose, significantly more people with severe obesity had unquantifiable titres of neutralizing antibody against authentic SARS-CoV-2 virus, reduced frequencies of antigen-experienced SARS-CoV-2 Spike-binding B cells, and a dissociation between anti-Spike antibody levels and neutralizing capacity. Neutralizing capacity was restored by a third dose of vaccine, but again declined more rapidly in people with severe obesity. We demonstrate that waning of SARS-CoV-2 vaccine-induced humoral immunity is accelerated in people with severe obesity and associated with increased hospitalization and mortality from breakthrough infections. Given the prevalence of obesity, our findings have significant implications for global public health.",
-    "category": "infectious diseases",
+    "link": "https://medrxiv.org/cgi/content/short/2022.06.08.22276134",
+    "title": "Implementation of a digital early warning score (NEWS2) in a cardiac specialist and general hospital settings in the COVID-19 pandemic: A qualitative study.",
+    "authors": "Baneen Alhmoud; Timothy Bonicci; Riyaz Patel; Daniel Melley; Louise Hicks; Amitava Banerjee",
+    "affiliations": "University College London, University College London Hospital, Barts Health Trust.; University College London, University College London Hospital; University College London, University College London Hospital.; Barts Health Trust; Barts Health Trust; University College London, University College London Hospital, Barts Health Trust.",
+    "abstract": "ObjectivesTo evaluate implementation of EHR-integrated NEWS2 in a cardiac care setting and a general hospital setting in the COVID-19 pandemic.\n\nDesignThematic analysis of qualitative semi-structured interviews with purposefully sampled nurses and managers, as well as online surveys.\n\nSettingsSpecialist cardiac hospital (St Bartholomews Hospital) and General teaching hospital (University College London Hospital).\n\nParticipantsEleven nurses and managers from cardiology, cardiac surgery, oncology, and intensive care wards (St Bartholomews) and medical, haematology and intensive care wards (UCLH) were interviewed and sixty-seven were surveyed online.\n\nResultsThree main themes emerged: (i) Implementing NEWS2 challenges and supports; (ii) Value of NEWS2 to alarm, escalate, particularly during the pandemic; and (iii) Digitalisation: EHR integration and automation. The value of NEWS2 was partly positive in escalation, yet there were concerns by nurses who undervalued NEWS2 particularly in cardiac care. Challenges, like clinicians behaviours, lack of resources and training and the perception of NEWS2 value, limit the success of this implementation. Changes in guidelines in the pandemic have led to overlooking NEWS2. EHR integration and automated monitoring are improvement solutions that are not fully employed yet.\n\nConclusionWhether in specialist or general medical settings, the health professionals implementing EWS in healthcare face cultural and systems related challenges to adopting NEWS2 and digital solutions. The validity of NEWS2 in specialised settings and complex conditions is not yet apparent and requires comprehensive validation. EHRs integration and automation are powerful tools to facilitate NEWS2 if its principles are reviewed and rectified, and resources and training are accessible. Further examination of implementation from the cultural and automation domains are needed.",
+    "category": "health informatics",
     "match_type": "fuzzy",
     "author_similarity": 100,
     "affiliation_similarity": 100
@@ -1861,20 +1847,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2022.05.09.22274846",
-    "date": "2022-05-10",
-    "link": "https://medrxiv.org/cgi/content/short/2022.05.09.22274846",
-    "title": "Assessing the impacts of timing on the health benefits, cost-effectiveness and relative affordability of COVID-19 vaccination programmes in 27 African Countries",
-    "authors": "Yang Liu; Carl AB Pearson; Andres Madriz Montero; Sergio Torres-Rueda; Elias Asfaw; Benjamin Uzochukwu; Tom Drake; Eleanor Bergren; Rosalind M Eggo; Francis Ruiz; Nicaise Ndembi; Justice Nonvignon; Mark Jit; Anna Vassall",
-    "affiliations": "London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Africa Centres for Disease Control and Prevention; University of Nigeria Nsukka; Centre for Global Development; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Institute of Human Virology Nigeria; Africa Centres for Disease Control and Prevention; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine",
-    "abstract": "BackgroundThe COVID-19 vaccine supply shortage in 2021 constrained rollout efforts in Africa while populations experienced waves of epidemics. As supply picks up, a key question becomes if vaccination remains an impactful and cost-effective strategy given changes in the timing of implementation.\n\nMethodsWe assessed the impact of timing using an epidemiological and economic model. We fitted our mathematical epidemiological model to reported COVID-19 deaths in 27 African countries to estimate the existing immunity (resulting from infection) before substantial vaccine rollout. We then projected health outcomes for different programme start dates (2021-01-01 to 2021-12-01, n = 12) and roll-out rates (slow, medium, fast; 275, 826, and 2066 doses/ million population-day, respectively) for viral vector and mRNA vaccines. Rollout rates used were derived from observed uptake trajectories. We collected data on vaccine delivery costs by country income group. Lastly, we calculated incremental cost-effectiveness ratios and relative affordability.\n\nFindingsVaccination programmes with early start dates incur the most health benefits and are most cost-effective. While incurring the most health benefits, fast vaccine roll-outs are not always the most cost-effective. At a willingness-to-pay threshold of 0.5xGDP per capita, vaccine programmes starting in August 2021 using mRNA and viral vector vaccines were cost-effective in 6-10 and 17-18 of 27 countries, respectively.\n\nInterpretationAfrican countries with large proportions of their populations unvaccinated by late 2021 may find vaccination programmes less cost-effective than they could have been earlier in 2021. Lower vaccine purchasing costs and/or the emergence of new variants may improve cost-effectiveness.\n\nFundingBill and Melinda Gates Foundation, World Health Organization, National Institute of Health Research (UK), Health Data Research (UK)",
-    "category": "health economics",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2022.05.06.22274658",
@@ -2043,20 +2015,6 @@
     "author_similarity": 90,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2022.04.11.22273690",
-    "date": "2022-04-17",
-    "link": "https://medrxiv.org/cgi/content/short/2022.04.11.22273690",
-    "title": "Evaluation of isotype specific salivary antibody assays for detecting previous SARS-CoV-2 infection in children and adults",
-    "authors": "Amy C Thomas; Elizabeth Oliver; Holly Baum; Kapil Gupter; Kathryn Shelley; Anna Long; Hayley Jones; Joyce Smith; Benjamin Hitchings; Natalie di Bartolo; Kate Vasileiou; Fruzsina Rabi; Hanin Alamir; Malak Eghleilib; Ore Francis; Jennifer Oliver; Begonia Morales-Aza; Ulrike Obst; Debbie Shattock; Rachael Barr; Lucy Collingwood; Kaltun Duale; Niall Grace; Guillaume Gonnage Livera; Lindsay Bishop; Harriet Downing; Fernanda Rodrigues; Nicholas J Timpson; Caroline J Relton; Ashley Mark Toye; Derek N Woolfson; Imre Berger; Anu Goenka; Andrew  D. Mark Davidson; Kathleen M Gillespie; Alistair JK Williams; Mick Bailey; Ellen Brooks-Pollock; Adam Finn; Alice Halliday; - CoMMinS Study Team",
-    "affiliations": "University of Bristol; University of Bristol; University of Bristol; University of Bristol and Imophoron Ltd.; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; Universidade de Coimbra; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; -",
-    "abstract": "Saliva is easily obtainable non-invasively and potentially suitable for detecting both current and previous SARS-CoV-2 infection. We established 6 standardised enzyme linked immunosorbent assays (ELISA) capable of detecting IgA and IgG antibodies to whole SARS-CoV-2 spike protein, to its receptor binding domain region and to nucleocapsid protein in saliva. In test accuracy (n=320), we found that spike IgG performed best (ROC AUC: 95.0%, 92.8-97.3%), followed by spike IgA (ROC AUC: 89.9%, 86.5-93.2%) for discriminating between pre-pandemic and post COVID-19 saliva samples. Using machine learning, diagnostic performance was improved when a combination of tests was used. As expected, salivary IgA was poorly correlated with serum, indicating an oral mucosal response whereas salivary IgG responses were predictive of those in serum. When deployed to 20 household outbreaks undergoing Delta and Omicron infection, antibody responses were heterogeneous but remained a reliable indicator of recent infection. Intriguingly, unvaccinated children showed evidence of exposure almost exclusively through specific IgA responses in the absence of evidence of viral infection. We have provided robust standardisation, evaluation, and field-testing of salivary antibody assays as tools for monitoring SARS-CoV-2 immune responses. Future work should focus on investigating salivary antibody responses following infection and vaccination to understand patterns of SARS-CoV-2 transmission and inform ongoing vaccination strategies.",
-    "category": "infectious diseases",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2022.04.14.22272888",
@@ -2115,17 +2073,17 @@
   },
   {
     "site": "medRxiv",
-    "doi": "10.1101/2022.04.04.22273427",
-    "date": "2022-04-05",
-    "link": "https://medrxiv.org/cgi/content/short/2022.04.04.22273427",
-    "title": "Sustained patient use and improved outcomes with digital transformation of a COPD service: RECEIVER trial and DYNAMIC-SCOT COVID-19 scale-up response.",
-    "authors": "Anna Taylor; Andrew Cushing; Morgan Dow; Jacqueline Anderson; Grace McDowell; Maureen Manthe; Sandosh Padmanabhan; Shane Burns; Paul McGineess; David J Lowe; Christopher M Carlin",
-    "affiliations": "Queen Elizabeth University Hospital, Glasgow; LenusHealth, Edinburgh; LenusHealth, Edinburgh; Queen Elizabeth University Hospital, Glasgow; Queen Elizabeth University Hospital, Glasgow; Queen Elizabeth University Hospital, Glasgow; Institute of Cardiovascular and Medical Sciences, University of Glasgow; LenusHealth, Edinburgh; LenusHealth, Edinburgh; Queen Elizabeth University Hospital, Glasgow; Queen Elizabeth University Hospital, Glasgow",
-    "abstract": "IntroductionLenusCOPD has been co-designed to enable digital transformation of COPD services for proactive preventative care. Patient-facing progressive web application, clinician dashboard and support website integrate patient-reported outcomes (PROs), self-management resources, structured clinical summary, wearable and home NIV data with asynchronous patient-clinician messaging. We commenced the implementation-effectiveness observational cohort RECEIVER trial in September 2019, with the primary endpoint of sustained patient usage and secondary endpoints including admissions, mortality, exacerbations, service workload and quality of life. We paused recruitment in March 2021 and provided LenusCOPD as routine care in the \"DYNAMIC-SCOT\" COVID-19 response service scale-up.\n\nMethods83 RECEIVER trial participants and 142 DYNAMIC-SCOT participants had completed minimum 1 year follow-up when we censored data on 31st August 2021. We established a control cohort with 5 patients matched per RECEIVER participant from de-identified contemporary routine clinical data.\n\nResultsSustained patient app utilisation was noted in both cohorts. Median time to admission or death was 43 days in control, 338 days in RECEIVER and 400 days in DYNAMIC-SCOT participants who had had a respiratory-related admission in the preceding year. The 12-month risk of admission or death was 74% in control patients, 53% in RECEIVER and 47% in the DYNAMIC-SCOT sub-cohort participants. There was a median of 2.5 COPD exacerbations per patient per year with stable quality of life across follow up and a manageable workload for clinical users.\n\nConclusionsA high proportion of people continued to use the co-designed LenusCOPD application during extended follow-up. Outcome data supports scale-up of this digital service transformation.\n\nKey messages\n\nWhat is the key question?Can sustained patient interaction and improved patient outcomes be achieved with digital transformation of a COPD service?\n\nWhat is the bottom line?Participants continue to use the LenusCOPD patient app, with an average of 3-3.5 interactions per person per week sustained >1-year post-onboarding. COPD- related hospital admissions and occupied bed days were reduced following LenusCOPD onboarding in participants with a history of a severe exacerbation in the previous year, with a median time to readmission of 380 days compared with 50 days in a contemporary matched control patient cohort.\n\nWhy read on?Feasibility and utility results support scale-up adoption of these digital tools, to support optimised co-management of COPD and other long-term conditions within a continuous implementation-evaluation framework. This will establish a test-bed infrastructure for additional innovations including artificial intelligence-insights for MDT decision support.",
-    "category": "respiratory medicine",
+    "doi": "10.1101/2022.04.03.22272610",
+    "date": "2022-04-04",
+    "link": "https://medrxiv.org/cgi/content/short/2022.04.03.22272610",
+    "title": "Cardiac impairment in Long Covid 1-year post-SARS-CoV-2 infection",
+    "authors": "Adriana Roca-Fernandez; Malgorzata Wamil; Alison Telford; Valentina Carapella; Alessandra Borlotti; David Monteiro; Helena Thomaides-Brears; Matthew D Kelly; Andrea Dennis; Rajarshi Banerjee; Matthew Robson; Michael Brady; Gregory Lip; Sacha Bull; Melissa J Heightman; Ntobeko Ntusi; Amitava Banerjee",
+    "affiliations": "Perspectum Diagnostics; Great Western Hospital Foundation NHS Trust, Swindon, UK; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; University of Liverpool; Royal Berkshire Hospital, Reading; UCLH; University of Cape Town, Cape Town, South Africa; University College London",
+    "abstract": "BackgroundLong Covid is associated with multiple symptoms and impairment in multiple organs. Cardiac impairment has been reported to varying degrees by varying methodologies in cross-sectional studies. Using cardiac magnetic resonance (CMR), we investigated the 12-month trajectory of cardiac impairment in individuals with Long Covid.\n\nMethods534 individuals with Long Covid underwent baseline CMR (T1 and T2 mapping, cardiac mass, volumes, function, and strain) and multi-organ MRI at 6 months (IQR 4.3,7.3) since first post-COVID-19 symptoms and 330 were rescanned at 12.6 (IQR 11.4, 14.2) months if abnormal findings were reported at baseline. Symptoms, standardised questionnaires, and blood samples were collected at both timepoints. Cardiac impairment was defined as one or more of: low left or right ventricular ejection fraction (LVEF and RVEF), high left or right ventricular end diastolic volume (LVEDV and RVEDV), low 3D left ventricular global longitudinal strain (GLS), or elevated native T1 in [&ge;]3 cardiac segments. A significant change over time was reported by comparison with 92 healthy controls.\n\nResultsThe technical success of this multiorgan assessment in non-acute settings was 99.1% at baseline, and 98.3% at follow up, with 99.6% and 98.8% for CMR respectively. Of individuals with Long Covid, 102/534 [19%] had cardiac impairment at baseline; 71/102 had complete paired data at 12 months. Of those, 58% presented with ongoing cardiac impairment at 12 months. High sensitivity cardiac troponin I and B-type natriuretic peptide were not predictive of CMR findings, symptoms, or clinical outcomes. At baseline, low LVEF, high RVEDV and low GLS were associated with cardiac impairment. Low LVEF at baseline was associated with persistent cardiac impairment at 12 months.\n\nConclusionCardiac impairment, other than myocarditis, is present in 1 in 5 individuals with Long Covid at 6 months, persisting in over half of those at 12 months. Cardiac-related blood biomarkers are unable to identify cardiac impairment in Long COVID. Subtypes of disease (based on symptoms, examination, and investigations) and predictive biomarkers are yet to be established. Interventional trials with pre-specified subgroup analyses are required to inform therapeutic options.",
+    "category": "cardiovascular medicine",
     "match_type": "fuzzy",
     "author_similarity": 100,
-    "affiliation_similarity": 91
+    "affiliation_similarity": 100
   },
   {
     "site": "medRxiv",
@@ -2323,6 +2281,20 @@
     "author_similarity": 94,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2022.03.10.22272081",
+    "date": "2022-03-12",
+    "link": "https://medrxiv.org/cgi/content/short/2022.03.10.22272081",
+    "title": "Interstitial lung damage following COVID-19 hospitalisation: an interim analysis of the UKILD Post-COVID study.",
+    "authors": "I Stewart; J Jacob; PM George; PL Molyneaux; JC Porter; RJ Allen; JK Baillie; SL Barratt; P Beirne; SM Bianchi; JF Blaikley; J Chalmers; RC Chambers; N Chadhuri; C Coleman; G Collier; EK Denneny; A Docherty; O Elneima; RA Evans; L Fabbri; MA Gibbons; FV Gleeson; B Gooptu; NJ Greening; B Guillen Guio; IP Hall; NA Hanley; V Harris; E Harrison; M Heightman; TE Hillman; A Horsley; L Houchen-Wolloff; I Jarrold; SR Johnson; MG Jones; F Khan; R Lawson; OC Leavy; N Lone; M Marks; H McAuley; P Mehta; E Omer; D Parekh; K Piper Hanley; M Plate; J Pearl; K Poinasamy; JK Quint; B Raman; M Richardson; P Rivera-Ortega; L Saunders; R Saunders; MG Semple; M Sereno; A Shikotra; AJ Simpson; A Singapuri; DJF Smith; M Spears; LG Spencer; S Stanel; D Thickett; AAR Thompson; M Thorpe; R Thwaites; SLF Walsh; S Walker; ND Weatherley; M Weeks; JM Wild; DG Wootton; CE Brightling; LP Ho; LV Wain; RG Jenkins",
+    "affiliations": "National Heart & Lung Institute, Imperial College London; Respiratory Medicine, University College London; Royal Brompton and Harefield NHS Foundation Trust; National Heart & Lung Institute, Imperial College London; University College London; University of Leicester; University of Edinburgh; North Bristol NHS Trust; Leeds Teaching Hospitals & University of Leeds; Sheffield Teaching Hospitals NHS Foundation Trust; University of Manchester; University of Dundee; Respiratory Medicine, University College London; University of Manchester; University of Nottingham; University of Sheffield; University College London; University of Edinburgh; University Hospitals of Leicester NHS Trust; University Hospitals of Leicester NHS Trust; National Heart & Lung Institute, Imperial College London; Royal Devon and Exeter NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; University of Leicester; University of Leicester; University of Leicester; University of Nottingham; University of Manchester; University Hospitals of Leicester NHS Trust; University of Edinburgh; University College London Hospital; University College London Hospital; University of Manchester; University Hospitals of Leicester NHS Trust; Asthma UK British Lung Foundation; University of Nottingham; Faculty of Medicine, University of Southampton; University of Nottingham; Sheffield Teaching Hospitals NHS Foundation Trust; University of Leicester; Usher Institute, University of Edinburgh; University College London Hospital; University of Leicester; University College London Hospital; University of Leicester; University of Birmingham; University of Manchester; University College London Hospital; University of Leicester; British Lung Foundation; National Heart & Lung Institute, Imperial College London; University of Oxford; University of Leicester; University of Manchester; University of Sheffield; University of Leicester; Liverpool University; University of Leicester; University Hospitals of Leicester NHS Trust; Newcastle University; University of Leicester; Royal Brompton and Harefield NHS Foundation Trust; Perth Royal Infirmary, NHS Tayside; Liverpool University Hospitals NHS Foundation Trust; University of Manchester; University of Birmingham; University of Sheffield; University of Edinburgh; National Heart & Lung Institute, Imperial College London; National Heart & Lung Institute, Imperial College London; Sheffield Teaching NHS Foundation Trust; Sheffield Teaching NHS Foundation Trust; National Heart & Lung Institute, Imperial College London; Sheffield Teaching NHS Foundation Trust; University of Liverpool; University Hospitals of Leicester NHS Trust; University of Oxford; University of Leicester; National Heart & Lung Institute, Imperial College London",
+    "abstract": "IntroductionShared characteristics between COVID-19 and pulmonary fibrosis, including symptoms, genetic architecture, and circulating biomarkers, suggests interstitial lung disease (ILD) development may be associated with SARS-CoV-2 infection.\n\nMethodsThe UKILD Post-COVID study planned interim analysis was designed to stratify risk groups and estimate the prevalence of Post-COVID Interstitial Lung Damage (ILDam) using the Post-HOSPitalisation COVID-19 (PHOSP-COVID) Study. Demographics, radiological patterns and missing data were assessed descriptively. Bayes binomial regression was used to estimate the risk ratio of persistent lung damage >10% involvement in linked, clinically indicated CT scans. Indexing thresholds of percent predicted DLco, chest X-ray findings and severity of admission were used to generate risk strata. Number of cases within strata were used to estimate the amount of suspected Post-COVID ILDam.\n\nResultsA total 3702 people were included in the UKILD interim cohort, 2406 completed an early follow-up research visit within 240 days of discharge and 1296 had follow-up through routine clinical review. We linked the cohort to 87 clinically indicated CTs with visually scored radiological patterns (median 119 days from discharge; interquartile range 83 to 155, max 240), of which 74 people had ILDam. ILDam was associated with abnormal chest X-ray (RR 1.21 95%CrI 1.05; 1.40), percent predicted DLco<80% (RR 1.25 95%CrI 1.00; 1.56) and severe admission (RR 1.27 95%CrI 1.07; 1.55). A risk index based on these features suggested 6.9% of the interim cohort had moderate to very-high risk of Post-COVID ILDam. Comparable radiological patterns were observed in repeat scans >90 days in a subset of participants.\n\nConclusionThese interim data highlight that ILDam was not uncommon in clinically indicated thoracic CT up to 8 months following SARS-CoV-2 hospitalisation. Whether the ILDam will progress to ILD is currently unknown, however health services should radiologically and physiologically monitor individuals who have Post-COVID ILDam risk factors.",
+    "category": "respiratory medicine",
+    "match_type": "fuzzy",
+    "author_similarity": 91,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2022.03.09.22272098",
@@ -2351,20 +2323,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2022.03.06.21267462",
-    "date": "2022-03-08",
-    "link": "https://medrxiv.org/cgi/content/short/2022.03.06.21267462",
-    "title": "Risk of myocarditis and pericarditis following COVID-19 vaccination in England and Wales",
-    "authors": "Samanatha Ip; Fatemeh Torabi; Spiros Denaxas; Ashley Akbari; Hoda Abbasizanjani; Rochelle Knight; Jennifer Anne Cooper; Rachel Denholm; Spencer Keene; Thomas Bolton; Sam Hollings; Efosa Omigi; Teri-Louise North; Arun Karthikeyan Suseeladevi; Emanuele Di Angelantonio; Kamlesh Khunti; Jonathan A C Sterne; Cathie Sudlow; William Whiteley; Angela Wood; Venexia Walker; - British Heart Foundation Data Science Centre (HDR UK) CVD-COVID-UK/COVID-IMPACT Consortium; - UK Covid-19 Longitudinal Health and Wellbeing National Core Study; - UK Covid-19 Data and Connectivity National Core Study",
-    "affiliations": "University of Cambridge; Swansea University; University College London; Swansea University; Swansea University; University of Bristol; University of Bristol; University of Bristol; University of Cambridge; Health Data Research UK; NHS Digital; NHS Digital; University of Bristol; University of Bristol; University of Cambridge; University of Leicester; University of Bristol; Health Data Research UK; University of Edinburgh; University of Cambridge; University of Bristol; ; ; ",
-    "abstract": "We describe our analyses of data from over 49.7 million people in England, representing near-complete coverage of the relevant population, to assess the risk of myocarditis and pericarditis following BNT162b2 and ChAdOx1 COVID-19 vaccination. A self-controlled case series (SCCS) design has previously reported increased risk of myocarditis after first ChAdOx1, BNT162b2, and mRNA-1273 dose and after second doses of mRNA COVID-19 vaccines in England. Here, we use a cohort design to estimate hazard ratios for hospitalised or fatal myocarditis/pericarditis after first and second doses of BNT162b2 and ChAdOx1 vaccinations. SCCS and cohort designs are subject to different assumptions and biases and therefore provide the opportunity for triangulation of evidence. In contrast to the findings from the SCCS approach previously reported for England, we found evidence for lower incidence of hospitalised or fatal myocarditis/pericarditis after first ChAdOx1 and BNT162b2 vaccination, as well as little evidence to suggest higher incidence of these events after second dose of either vaccination.",
-    "category": "epidemiology",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2022.03.02.22271762",
@@ -2785,6 +2743,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2021.12.23.21268276",
+    "date": "2021-12-25",
+    "link": "https://medrxiv.org/cgi/content/short/2021.12.23.21268276",
+    "title": "Risk of myocarditis following sequential COVID-19 vaccinations by age and sex",
+    "authors": "Martina Patone; Winnie Xue Mei; Lahiru Handunnetthi; Sharon Dixon; Francesco Zaccardi; Manu Shankar-Hari; Peter Watkinson; Kamlesh Khunti; Anthony Harnden; Carol AC Coupland; Keith M. Channon; Nicholas L Mills; Aziz Sheikh; Julia Hippisley-Cox",
+    "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Leicester; University of Edinburgh; University of Oxford; University of Leicester; University of Oxford; University of Oxford; University of Oxford; University of Edinburgh; University of Edinburgh; University of Oxford",
+    "abstract": "In an updated self-controlled case series analysis of 42,200,614 people aged 13 years or more, we evaluate the association between COVID-19 vaccination and myocarditis, stratified by age and sex, including 10,978,507 people receiving a third vaccine dose. Myocarditis risk was increased during 1-28 days following a third dose of BNT162b2 (IRR 2.02, 95%CI 1.40, 2.91). Associations were strongest in males younger than 40 years for all vaccine types with an additional 3 (95%CI 1, 5) and 12 (95% CI 1,17) events per million estimated in the 1-28 days following a first dose of BNT162b2 and mRNA-1273, respectively; 14 (95%CI 8, 17), 12 (95%CI 1, 7) and 101 (95%CI 95, 104) additional events following a second dose of ChAdOx1, BNT162b2 and mRNA-1273, respectively; and 13 (95%CI 7, 15) additional events following a third dose of BNT162b2, compared with 7 (95%CI 2, 11) additional events following COVID-19 infection. An association between COVID-19 infection and myocarditis was observed in all ages for both sexes but was substantially higher in those older than 40 years. These findings have important implications for public health and vaccination policy.\n\nFundingHealth Data Research UK.",
+    "category": "epidemiology",
+    "match_type": "fuzzy",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.12.23.21268279",
@@ -2813,20 +2785,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2021.12.21.21268214",
-    "date": "2021-12-23",
-    "link": "https://medrxiv.org/cgi/content/short/2021.12.21.21268214",
-    "title": "Comparative effectiveness of ChAdOx1 versus BNT162b2 vaccines against SARS-CoV-2 infections in England and Wales: A cohort analysis using trial emulation in the Virus Watch community data",
-    "authors": "Vincent Grigori Nguyen; Alexei Yavlinsky; Sarah Beale; Susan J Hoskins; Vasileios Lampos; Isobel Braithwaite; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Annalan M D Navaratnam; Parth Patel; Madhumita Shrotri; Sophie Weber; Andrew Hayward; Robert W Aldridge",
-    "affiliations": "University College London; University College London; University College London; Univerity College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London",
-    "abstract": "IntroductionInfections of SARS-CoV-2 in vaccinated individuals have been increasing globally. Understanding the associations between vaccine type and a post-vaccination infection could help prevent further COVID-19 waves. In this paper, we use trial emulation to understand the impact of a phased introduction of the vaccine in the UK driven by vulnerability and exposure status. We estimate the comparative effectiveness of COVID-19 vaccines (ChAdOx1 versus BNT162b2) against post-vaccination infections of SARS-CoV-2 in a community setting in England and Wales.\n\nMethodTrial emulation was conducted by pooling results from six cohorts whose recruitment was staggered between 1st January 2021 and 31st March 2021 and followed until 12th November 2021. Eligibility for each trial was based upon age (18+ at the time of vaccination), without prior signs of infection or an infection within the first 14 days of the first dose. Time from vaccination of ChAdOx1 or BNT162b2 until SARS-CoV-2 infection (positive polymerase chain reaction or lateral flow test after 14 of the vaccination) was modelled using Cox proportional hazards model for each cohort and adjusted for age at vaccination, gender, minority ethnic status, clinically vulnerable status and index of multiple deprivation quintile. For those without SARS-CoV-2 infection during the study period, follow-up was until loss-of-follow-up or end of study (12th November 2021). Pooled hazard ratios were generated using random-effects meta-analysis.\n\nResultsAcross six cohorts, there were a total of 21,283 participants who were eligible and vaccinated with either ChAdOx1 (n = 13,813) or BNT162b2 (n = 7,470) with a median follow-up time of 266 days (IQR: 235 - 282). By November 12th 2021, 750 (5.4%) adults who had ChAdOx1 as their vaccine experienced a SARS-CoV-2 infection, compared to 296 (4.0%) who had BNT162b2. We found that people who received ChAdOx1 vaccinations had 10.54 per 1000 people higher cumulative incidence for SARS-CoV-2 infection compared to BNT162b2 for infections during a maximum of 315 days of follow-up. When adjusted for age at vaccination, sex, minority ethnic status, index of multiple deprivation, and clinical vulnerability status, we found a pooled adjusted hazard ratio of 1.35 [HR: 1.35, 95%CI: 1.15 - 1.58], demonstrating a 35% increase in SARS-CoV-2 infections in people who received ChAdOx1 compared to BNT162b2.\n\nDiscussionWe found evidence of greater effectiveness of receiving BNT162b2 compared to ChAdOx1 vaccines against SARS-CoV-2 infection in England and Wales during a time period when Delta became the most prevalent variant of concern. Our findings demonstrate the importance of booster (third) doses to maintain protection and suggest that these should be prioritised to those who received ChAdOx1 as their primary course.",
-    "category": "epidemiology",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "bioRxiv",
     "doi": "10.1101/2021.12.17.473248",
@@ -2981,6 +2939,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 92
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2021.12.14.21267460",
+    "date": "2021-12-15",
+    "link": "https://medrxiv.org/cgi/content/short/2021.12.14.21267460",
+    "title": "Differential Risk of SARS-CoV-2 Infection by Occupation: Evidence from the Virus Watch prospective cohort study in England and Wales",
+    "authors": "Sarah Beale; Susan J Hoskins; Thomas Edward Byrne; Erica Wing Lam Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Annalan MD Navaratnam; Vincent Nguyen; Parth Patel; Alexei Yavlinsky; Anne Johnson; Martie Van Tongeren; Robert W Aldridge; Andrew Hayward",
+    "affiliations": "University College London; Univerity College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University of Manchester; University College London; University College London",
+    "abstract": "BackgroundWorkers differ in their risk of SARS-CoV-2 infection according to their occupation, but the direct contribution of occupation to this relationship is unclear. This study aimed to investigate how infection risk differed across occupational groups in England and Wales up to April 2022, after adjustment for potential confounding and stratification by pandemic phase.\n\nMethodsData from 15,190 employed/self-employed participants in the Virus Watch prospective cohort study were used to generate risk ratios for virologically- or serologically-confirmed SARS-CoV-2 infection using robust Poisson regression, adjusting for socio-demographic and health-related factors and non-work public activities. We calculated attributable fractions (AF) amongst the exposed for belonging to each occupational group based on adjusted risk ratios (aRR).\n\nFindingsIncreased risk was seen in nurses (aRR=1.44, 1.25-1.65; AF=30%, 20-39%), doctors (aRR=1.33, 1.08-1.65; AF=25%, 7-39%), carers (1.45, 1.19-1.76; AF=31%, 16-43%), primary school teachers (aRR=1.67, 1.42-1.96; AF=40%, 30-49%), secondary school teachers (aRR=1.48, 1.26-1.72; AF=32%, 21-42%), and teaching support occupations (aRR=1.42, 1.23-1.64; AF=29%, 18-39%) compared to office-based professional occupations. Differential risk was apparent in the earlier phases (Feb 2020 - May 2021) and attenuated later (June - October 2021) for most groups, although teachers and teaching support workers demonstrated persistently elevated risk across waves.\n\nInterpretationOccupational differentials in SARS-CoV-2 infection risk vary over time and are robust to adjustment for socio-demographic, health-related, and non-workplace activity-related potential confounders. Direct investigation into workplace factors underlying elevated risk and how these change over time is needed to inform occupational health interventions.",
+    "category": "epidemiology",
+    "match_type": "fuzzy",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.12.13.21267723",
@@ -2995,6 +2967,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2021.12.09.21267516",
+    "date": "2021-12-09",
+    "link": "https://medrxiv.org/cgi/content/short/2021.12.09.21267516",
+    "title": "Changes in the trajectory of Long Covid symptoms following COVID-19 vaccination: community-based cohort study",
+    "authors": "Daniel Ayoubkhani; Charlotte Bermingham; Koen B Pouwels; Myer Glickman; Vahe Nafilyan; Francesco Zaccardi; Kamlesh Khunti; Nisreen A Alwan; Ann Sarah Walker",
+    "affiliations": "Office for National Statistics; Office for National Statistics; University of Oxford; Office for National Statistics; Office for National Statistics; University of Leicester; University of Leicester; University of Southampton; University of Oxford",
+    "abstract": "ObjectiveTo estimate associations between COVID-19 vaccination and Long Covid symptoms in adults who were infected with SARS-CoV-2 prior to vaccination.\n\nDesignObservational cohort study using individual-level interrupted time series analysis.\n\nSettingRandom sample from the community population of the UK.\n\nParticipants28,356 COVID-19 Infection Survey participants (mean age 46 years, 56% female, 89% white) aged 18 to 69 years who received at least their first vaccination after test-confirmed infection.\n\nMain outcome measuresPresence of long Covid symptoms at least 12 weeks after infection over the follow-up period 3 February to 5 September 2021.\n\nResultsMedian follow-up was 141 days from first vaccination (among all participants) and 67 days from second vaccination (84% of participants). First vaccination was associated with an initial 12.8% decrease (95% confidence interval: -18.6% to -6.6%) in the odds of Long Covid, but increasing by 0.3% (-0.6% to +1.2%) per week after the first dose. Second vaccination was associated with an 8.8% decrease (-14.1% to -3.1%) in the odds of Long Covid, with the odds subsequently decreasing by 0.8% (-1.2% to -0.4%) per week. There was no statistical evidence of heterogeneity in associations between vaccination and Long Covid by socio-demographic characteristics, health status, whether hospitalised with acute COVID-19, vaccine type (adenovirus vector or mRNA), or duration from infection to vaccination.\n\nConclusionsThe likelihood of Long Covid symptoms reduced after COVID-19 vaccination, and the improvement was sustained over the follow-up period after the second dose. Vaccination may contribute to a reduction in the population health burden of Long Covid, though longer follow-up time is needed.\n\nSummary boxWhat is already known on this topic\n\nO_LICOVID-19 vaccines are effective at reducing rates of SARS-CoV-2 infection, transmission, hospitalisation, and death\nC_LIO_LIThe incidence of Long Covid may be reduced if infected after vaccination, but the relationship between vaccination and pre-existing long COVID symptoms is unclear, as published studies are generally small and with self-selected participants\nC_LI\n\nWhat this study adds\n\nO_LIThe likelihood of Long Covid symptoms reduced after COVID-19 vaccination, and the improvement was sustained over the follow-up period after the second dose\nC_LIO_LIThere was no evidence of differences in this relationship by socio-demographic characteristics, health-related factors, vaccine type, or duration from infection to vaccination\nC_LIO_LIAlthough causality cannot be inferred from this observational evidence, vaccination may contribute to a reduction in the population health burden of Long Covid; further research is needed to understand the biological mechanisms that may ultimately contribute to the development of therapeutics for Long Covid\nC_LI",
+    "category": "epidemiology",
+    "match_type": "fuzzy",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.12.08.21267458",
@@ -3149,20 +3135,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2021.11.23.21266574",
-    "date": "2021-11-24",
-    "link": "https://medrxiv.org/cgi/content/short/2021.11.23.21266574",
-    "title": "Reinfection with SARS-CoV-2: outcome, risk factors and vaccine efficacy in a Scottish cohort",
-    "authors": "Paul M McKeigue; David McAllister; Chris Robertson; Diane Stockton; Helen Colhoun",
-    "affiliations": "University of Edinburgh; University of Glasgow; University of Strathclyde; Public Health Scotland; University of Edinburgh",
-    "abstract": "BackgroundThe objective of this study was to investigate how protection against COVID-19 conferred by previous infection is modified by vaccination.\n\nMethodsIn a cohort of all 152655 individuals in Scotland alive at 90 days after a positive test for SARS-CoV-2 (confirmed by cycle threshold < 30, or two tests) followed till 22 September 2021, rate ratios for reinfection were estimated with calendar time or tests as timescale.\n\nFindingsRates of detected and hospitalised reinfection with COVID-19 while unvaccinated were respectively 6.8 (95% CI 6.4 to 7.2) and 0.18 (95% CI 0.12 to 0.25) per 1000 person-months. These rates were respectively 68% and 74% lower than in a matched cohort of individuals who had not previously tested positive. Efficacy of two doses of vaccine in those with previous infection was estimated as as 84% (95 percent CI 81% to 86%) against detected reinfection and 71% (95 percent CI 29% to 88%) against hospitalised or fatal reinfection. The rate of detected reinfection after two doses of vaccine was 1.35 (95% CI 1.02 to 1.78) times higher in those vaccinated before first infection than in those unvaccinated at first infection.\n\nInterpretationThe combination of natural infection and vaccination provides maximal protection against new infection with SARS-CoV-2: prior vaccination does not impair this protection.\n\nFundingNo specific funding was received for this work.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSIn a recent systematic review of cohort studies reported up to July 2021, the average reduction in COVID-19 infection rates in those with previous infection compared with those without evidence of previous infection was 90%. There is little information about the protective effect of previous infection against severe COVID-19, or about how the protective effects of previous infection against reinfection and severe disease are modified by vaccination.\n\nWhat this paper addsIn unvaccinated individuals the protection against hospitalised COVID-19 conferred by previous infection is similar to that induced by vaccination. In those with previous infection, vaccination reduces the rates of reinfection and hospitalised COVID-19 by about 70%.\n\nImplications of all the available evidenceThe combination of natural infection and vaccination provides maximal protection against COVID-19: prior vaccination does not seriously impair this protection.",
-    "category": "epidemiology",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.11.19.21266529",
@@ -3317,20 +3289,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "bioRxiv",
-    "doi": "10.1101/2021.11.05.467529",
-    "date": "2021-11-08",
-    "link": "https://biorxiv.org/cgi/content/short/2021.11.05.467529",
-    "title": "Structural basis of main proteases of coronavirus bound to drug candidate PF-07321332",
-    "authors": "Jian Li; Cheng Lin; Xuelan Zhou; Fanglin Zhong; Pei Zeng; Haihai Jiang; Yang Yang; Peter McCormick; Yang Fu; Jin Zhang",
-    "affiliations": "College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China.; School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China.; Shenzhen Crystalo Biopharmaceutical Co., Ltd, Shenzhen 518118, China.; Jiangxi Jmerry Biopharmaceutical Co., Ltd, Ganzhou 341000, China.; Jiangxi Jmerry Biopharmaceutical Co., Ltd, Ganzhou 341000, China.; School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China.; Shenzhen Crystalo Biopharmaceutical Co., Ltd, Shenzhen 518118, China.; William Harvey Research Institute, Queen Mary University of London; School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China 518055; School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China.",
-    "abstract": "The high mutation rate of COVID-19 and the prevalence of multiple variants strongly support the need for pharmacological options to complement vaccine strategies. One region that appears highly conserved among different genus of coronaviruses is the substrate binding site of the main protease (Mpro or 3CLpro), making it an attractive target for the development of broad-spectrum drugs for multiple coronaviruses. PF-07321332 developed by Pfizer is the first orally administered inhibitor targeting the main protease of SARS-CoV-2, which also has shown potency against other coronaviruses. Here we report three crystal structures of main protease of SARS-CoV-2, SARS-CoV and MERS-CoV bound to the inhibitor PF-07321332. The structures reveal a ligand-binding site that is conserved among SARS-CoV-2, SARS-CoV and MERS-CoV, providing insights into the mechanism of inhibition of viral replication. The long and narrow cavity in the cleft between domains I and II of main protease harbors multiple inhibitor binding sites, where PF-07321332 occupies subsites S1, S2 and S4 and appears more restricted compared with other inhibitors. A detailed analysis of these structures illuminated key structural determinants essential for inhibition and elucidated the binding mode of action of main proteases from different coronaviruses. Given the importance of main protease for the treatment of SARS-CoV-2 infection, insights derived from this study should accelerate the design of safer and more effective antivirals.",
-    "category": "biophysics",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.11.04.21265918",
@@ -3359,20 +3317,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2021.11.03.21265877",
-    "date": "2021-11-03",
-    "link": "https://medrxiv.org/cgi/content/short/2021.11.03.21265877",
-    "title": "REACT-1 round 15 interim report: High and rising prevalence of SARS-CoV-2 infection in England from end of September 2021 followed by a fall in late October 2021",
-    "authors": "Marc Chadeau-Hyam; Oliver Eales; Barbara Bodinier; Haowei Wang; David J Haw; Matthew Whitaker; Caroline E Walters; Christina J Atchison; Peter J Diggle; Andrew J Page; Deborah Ashby; Wendy Barclay; Graham P Taylor; Graham Cooke; Helen Ward; Ara Darzi; Christl A. Donnelly; Paul Elliott",
-    "affiliations": "Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Lancaster University; Quadram Institute; Imperial College London; Imperial College London; Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London School of Public Health",
-    "abstract": "BackgroundThe third wave of COVID-19 in England coincided with the rapid spread of the Delta variant of SARS-CoV-2 from the end of May 2021. Case incidence data from the national testing programme (Pillar 2) in England may be affected by changes in testing behaviour and other biases. Community surveys may provide important contextual information to inform policy and the public health response.\n\nMethodsWe estimated patterns of community prevalence of SARS-CoV-2 infection in England using RT-PCR swab-positivity, demographic and other risk factor data from round 15 (interim) of the REal-time Assessment of Community Transmission-1 (REACT-1) study (round 15a, carried out from 19 to 29 October 2021). We compared these findings with those from round 14 (9 to 27 September 2021).\n\nResultsDuring mid- to late-October 2021 (round 15a) weighted prevalence was 1.72% (1.61%, 1.84%) compared to 0.83% (0.76%, 0.89%) in September 2021 (round 14). The overall reproduction number (R) from round 14 to round 15a was 1.12 (1.11, 1.14) with increases in prevalence over this period (September to October) across age groups and regions except Yorkshire and The Humber. However, within round 15a (mid- to late-October) there was evidence of a fall in prevalence with R of 0.76 (0.65, 0.88). The highest weighted prevalence was observed among children aged 5 to 12 years at 5.85% (5.10%, 6.70%) and 13 to 17 years at 5.75% (5.02%, 6.57%). At regional level, there was an almost four-fold increase in weighted prevalence in South West from round 14 at 0.59% (0.43%,0.80%) to round 15a at 2.18% (1.84%, 2.58%), with highest smoothed prevalence at subregional level also found in South West in round 15a. Age, sex, key worker status, and presence of children in the home jointly contributed to the risk of swab-positivity. Among the 126 sequenced positive swabs obtained up until 23 October, all were Delta variant; 13 (10.3%) were identified as the AY.4.2 sub-lineage.\n\nDiscussionWe observed the highest overall prevalence of swab-positivity seen in the REACT-1 study in England to date in round 15a (October 2021), with a two-fold rise in swab-positivity from round 14 (September 2021). Despite evidence of a fall in prevalence from mid- to late-October 2021, prevalence remains high, particularly in school-aged children, with evidence also of higher prevalence in households with one or more children. Thus, vaccination of children aged 12 and over remains a high priority (with possible extension to children aged 5-12) to help reduce within-household transmission and disruptions to education, as well as among adults, to lessen the risk of serious disease among those infected.",
-    "category": "epidemiology",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.10.28.21265593",
@@ -3499,20 +3443,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2021.10.06.21264467",
-    "date": "2021-10-07",
-    "link": "https://medrxiv.org/cgi/content/short/2021.10.06.21264467",
-    "title": "Illness characteristics of COVID-19 in children infected with the SARS-CoV-2 Delta variant",
-    "authors": "Erika Molteni; Carole Helene Sudre; Liane S Canas; Sunil S Bhopal; Robert C Hughes; Liyuan Chen; Jie Deng; Benjamin Murray; Eric Kerfoot; Michela S Antonelli; Mark S Graham; Kerstin Klaser; Anna May; Christina Hu; Joan Capdevila Pujol; Jonathan Wolf; Alexander Hammers; Timothy D Spector; Sebastien Ourselin; Marc Modat; Claire Steves; Michael Absoud; Emma L Duncan",
-    "affiliations": "King's College London; School of Biomedical Engineering & Imaging Sciences, Kings College London, London, UK.; King's College London; Newcastle University; Department of Population Health, Faculty of Epidemiology & Population Health, London School of Hygiene & Tropical Medicine, Keppel Street, London, UK.; School of Biomedical Engineering & Imaging Sciences, Kings College London, London, UK.; School of Biomedical Engineering & Imaging Sciences, Kings College London, London, UK.; School of Biomedical Engineering & Imaging Sciences, Kings College London, London, UK.; School of Biomedical Engineering & Imaging Sciences, Kings College London, London, UK.; King's College London; King's College London; King's College London; ZOE Limited London, UK; ZOE Limited London, UK.; ZOE Limited London, UK.; ZOE Limited London, UK.; School of Biomedical Engineering & Imaging Sciences, Kings College London, London, UK.; King's College London; School of Biomedical Engineering & Imaging Sciences, Kings College London, London, UK.; School of Biomedical Engineering & Imaging Sciences, Kings College London, London, UK.; King's College London; Childrens Neurosciences, Evelina London Childrens Hospital, St Thomas Hospital, Kings Health Partners, Academic Health Science Centre, London, UK.; Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK.",
-    "abstract": "BackgroundThe Delta (B.1.617.2) SARS-CoV-2 variant became the predominant UK circulating strain in May 2021. Whether COVID-19 from Delta infection differs to infection with other variants in children is unknown.\n\nMethodsThrough the prospective COVID Symptom Study, 109,626 UK school-aged children were proxy-reported between December 28, 2020 and July 8, 2021. We selected all symptomatic children who tested positive for SARS-CoV-2 and were proxy-reported at least weekly, within two timeframes: December 28, 2020 to May 6, 2021 (Alpha (B.1.1.7) the main UK circulating variant); and May 26 to July 8, 2021 (Delta the main UK circulating variant). We assessed illness profiles (symptom prevalence, duration, and burden), hospital presentation, and presence of long ([&ge;]28 day) illness; and calculated odds ratios for symptoms presenting within the first 28 days of illness.\n\nFindings694 (276 younger [5-11 years], 418 older [12-17 years]) symptomatic children tested positive for SARS-CoV-2 with Alpha infection and 706 (227 younger and 479 older) children with Delta infection. Median illness duration was short with either variant (overall cohort: 5 days (IQR 2-9.75) with Alpha, 5 days (IQR 2-9) with Delta). The seven most prevalent symptoms were common to both variants. Symptom burden over the first 28 days was slightly greater with Delta compared with Alpha infection (in younger children, 3 (IQR 2-5) with Alpha, 4 (IQR 2-7) with Delta; in older children 5 (IQR 3-8) with Alpha and 6 (IQR 3-9) with Delta infection in older children). The odds of several symptoms were higher with Delta than Alpha infection, including headache and fever. Few children presented to hospital, and long illness duration was uncommon, with either variant.\n\nInterpretationCOVID-19 in UK school-aged children due to SARS-CoV-2 Delta strain B.1.617.2 resembles illness due to the Alpha variant B.1.1.7., with short duration and similar symptom burden.\n\nFundingZOE Limited, UK Government Department of Health and Social Care, Wellcome Trust, UK Engineering and Physical Sciences Research Council, UK Research and Innovation London Medical Imaging & Artificial Intelligence Centre for Value Based Healthcare, UK National Institute for Health Research, UK Medical Research Council, British Heart Foundation and Alzheimers Society.\n\nEthicsEthics approval was granted by KCL Ethics Committee (reference LRS-19/20-18210).\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSTo identify existing evidence for differences in COVID-19 due to infection with Alpha (B.1.1.7) or Delta (B.1.617.2) SARS-CoV-2 variants, we searched PubMed for peer-reviewed articles and medRxiv for preprint publications between March 1, and September 17, 2021 using keywords (\"SARS-CoV-2\" OR \"COVID-19\") AND (children OR p?ediatric*) AND (\"delta variant\" OR \"B.1.617.2\"). We did not restrict our search by language. Of twenty published articles identified in PubMed, we found one case study describing disease presentation associated with Delta variant infection in a child. Another study examining the increase in hospitalization rates of paediatric cases in USA from August 1, 2020 to August 27, 2021 stated that \"It is not known whether the B.1.617.2 (Delta) variant [...] causes different clinical outcomes in children and adolescents compared with variants that circulated earlier.\" Four studies reported cases of transmission of the Delta variant in school and community contexts; and two discussed screening testing in school-aged children (thus not directly relevant to the research question here). Remaining papers did not target paediatric age specifically. We found no studies investigating differences in COVID-19 presentation (e.g., duration, burden, individual symptoms) in school-aged children either in the UK or world-wide.\n\nAdded value of this studyWe describe and compare illness profiles in symptomatic UK school-aged children (aged 5-17 years) with COVID-19 when either Alpha or Delta strains were the predominant circulating SARS-CoV-2 variant. Our data, collected through one of the largest UK citizen science epidemiological initiatives, show that symptom profile and illness duration of COVID-19 are broadly similar between the strains. Although there were slightly more symptoms with Delta than with Alpha, particularly in older children, this was offset by similar symptom duration (whether considered for symptoms individually or for illness overall). Our study adds quantitative information to the debate on whether there are meaningful clinical differences in COVID-19 due to Alpha vs. Delta variants; and contributes to the discussion regarding rationale for vaccinating children (particularly younger children) against SARS-CoV-2.\n\nImplications of all the available evidenceOur data confirm that COVID-19 in UK school-aged children is usually of short duration and similar symptom burden, whether due to Delta or Alpha. Our data contribute to epidemiological surveillance from the wider UK population, and we capture common and generally mild paediatric presentations of COVID-19 that might be missed using clinician-based surveillance alone. Our data will also be useful for the vaccination debate.",
-    "category": "pediatrics",
-    "match_type": "fuzzy",
-    "author_similarity": 94,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.10.07.21264655",
@@ -3597,20 +3527,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2021.09.20.21263828",
-    "date": "2021-09-23",
-    "link": "https://medrxiv.org/cgi/content/short/2021.09.20.21263828",
-    "title": "Colchicine for COVID-19 in adults in the community (PRINCIPLE): a randomised, controlled, adaptive platform trial",
-    "authors": "- The PRINCIPLE Trial Collaborative Group; Jienchi Dorward; Ly-Mee Yu; Gail Hayward; Benjamin R Saville; Oghenekome Gbinigie; Oliver van Hecke; Emma Ogburn; Philip H Evans; Nicholas PB Thomas; Mahendra G Patel; Duncan Richards; Nicholas Berry; Michelle A Detry; Christina Saunders; Mark Fitzgerald; Victoria Harris; Milensu Shanyinde; Simon de Lusignan; Monique I Andersson; Christopher C Butler; FD Richard Hobbs",
-    "affiliations": "; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom and Centre for the AIDS Programme of Research in South Africa ; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Berry Consultants, Texas, USA and Department of Biostatistics, Vanderbilt University School of Medicine, Tennessee, USA; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; College of Medicine and Health, University of Exeter and National Institute for Health Research, Clinical Research Network; Royal College of General Practitioners, London, UK, and National Institute for Health Research, Clinical Research Network; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom and School of Pharmacy and Medical Sciences, University of Bra; Oxford Clinical Trials Research Unit, Botnar Research Centre, University of Oxford, Oxford, UK; Berry Consultants, Texas, USA; Berry Consultants, Texas, USA; Berry Consultants, Texas, USA; Berry Consultants, Texas, USA; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom,; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom",
-    "abstract": "ObjectivesColchicine has been proposed as a COVID-19 treatment, but its effect on time to recovery is unknown. We aimed to determine whether colchicine is effective at reducing time to recovery and COVID-19 related hospitalisations/deaths among people in the community.\n\nDesignProspective, multicentre, open-label, multi-arm, adaptive Platform Randomised Trial of Treatments in the Community for Epidemic and Pandemic Illnesses (PRINCIPLE).\n\nSettingNational trial run remotely from a central trial site and at multiple primary care centres across the United Kingdom.\n\nParticipantsAdults aged [&ge;]65, or [&ge;]18 years with comorbidities or shortness of breath, and unwell [&le;]14 days with suspected COVID-19 in the community.\n\nInterventionsParticipants were randomised to usual care, usual care plus colchicine (500{micro}g daily for 14 days), or usual care plus other interventions.\n\nMain outcome measuresThe co-primary endpoints were time to first self-reported recovery, and hospitalisation/death related to COVID-19, within 28 days, analysed using Bayesian models. The hypothesis for the time to recovery endpoint is evaluated first, and if superiority is declared on time to recovery, the hypothesis for the second co-primary endpoint of hospitalisation/death is then evaluated. To determine futility, we pre-specified a clinically meaningful benefit in time to first reported recovery as a hazard ratio of 1.2 or larger (equating to approximately 1.5 days benefit in the colchicine arm, assuming 9 days recovery in the usual care arm).\n\nResultsThe trial opened on April 2, 2020, with randomisation to colchicine starting on March 04, 2021 and stopping on May 26, 2021, because the pre-specified time to recovery futility criterion was met. The primary analysis model included 2755 SARS-CoV-2 positive participants, randomised to colchicine (n=156), usual care (n=1145), and other treatments (n=1454). Time to first self-reported recovery was similar in the colchicine group compared with usual care with an estimated hazard ratio of 0.919 [95% credible interval 0.72 to 1.16] and an estimated increase of 1.14 days [-1.86 to 5.21] in median time to self-reported recovery for colchicine versus usual care. The probability of meaningful benefit in time to recovery was very low at 1.8%. Results were similar in comparisons with concurrent controls. COVID-19 related hospitalisations/deaths were similar in the colchicine group versus usual care, with an estimated odds ratio of 0.76 [0.28 to 1.89] and an estimated difference of -0.4% [-2.7% to 2.4]. One serious adverse event occurred in the colchicine group and one in usual care.\n\nConclusionsColchicine did not improve time to recovery in people at higher risk of complications with COVID-19 in the community.\n\nTrial registrationISRCTN86534580.",
-    "category": "infectious diseases",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.09.16.21263684",
@@ -4241,6 +4157,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2021.07.12.21260360",
+    "date": "2021-07-15",
+    "link": "https://medrxiv.org/cgi/content/short/2021.07.12.21260360",
+    "title": "The impact of hypoxia on B cells in COVID-19",
+    "authors": "Prasanti Kotagiri; Federica Mescia; Aimee Hanson; Lorinda Turner; Laura Bergamaschi; Ana Penalver; Nathan Richoz; Stephen Moore; Brian Ortmann; Benjamin Dunmore; Helene Ruffieux; Michael Morgan; Zewen Kelvin Tuong; Rachael Bashford Rogers; Myra Hosmillo; Stephen Baker; Anne Elmer; Ian Goodfellow; Ravindra Gupta; Nathalie Kingston; Paul Lehner; Nicholas Matheson; Sylvia Richardson; Caroline Saunders; Michael Weekes; Berthold Gottgens; Mark Toshner; Christoph Hess; Patrick Maxwell; Menna Clatworthy; James A Nathan; John Bradley; Paul Lyons; Natalie Burrows; Kenneth G C Smith",
+    "affiliations": "Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Oxford University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University",
+    "abstract": "Prominent early features of COVID-19 include severe, often clinically silent, hypoxia and a pronounced reduction in B cells, the latter important in defence against SARS-CoV-2. This brought to mind the phenotype of mice with VHL-deficient B cells, in which Hypoxia-Inducible Factors are constitutively active, suggesting hypoxia might drive B cell abnormalities in COVID-19. We demonstrated the breadth of early and persistent defects in B cell subsets in moderate/severe COVID-19, including reduced marginal zone-like, memory and transitional B cells, changes we also observed in B cell VHL-deficient mice. This was corroborated by hypoxia-related transcriptional changes in COVID-19 patients, and by similar B cell abnormalities in mice kept in hypoxic conditions, including reduced marginal zone and germinal center B cells. Thus hypoxia might contribute to B cell pathology in COVID-19, and in other hypoxic states. Through this mechanism it may impact on COVID-19 outcome, and be remediable through early oxygen therapy.",
+    "category": "infectious diseases",
+    "match_type": "fuzzy",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.07.07.21253295",
@@ -4311,20 +4241,6 @@
     "author_similarity": 96,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2021.06.28.21259529",
-    "date": "2021-07-01",
-    "link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259529",
-    "title": "Global patterns of genetic variation and association with clinical phenotypes at genes involved in SARS-CoV-2 infection",
-    "authors": "Chao Zhang; Anurag Verma; Yuanqing Feng; Marcelo C. R. Melo; Michael McQuillan; Matthew Hansen; Anastasia Lucas; Joseph Park; Alessia Ranciaro; Simon Thompson; Meghan A. Rubel; Michael C. Campbell; William Beggs; JIBRIL HIRBO; Sununguko Wata Mpoloka; Gaonyadiwe George Mokone; - Regeneron Genetic Center; Thomas Nyambo; Dawit Wolde Meskel; Gurja Belay; Charles Fokunang; Alfred K. Njamnshi; Sabah A. Omar; Scott Williams; Daniel Rader; Marylyn D Ritchie; Cesar de la Fuente Nunez; Giorgio Sirugo; Sarah Tishkoff",
-    "affiliations": "University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; Perelman School of Medicine at the University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Howard; University of Pennsylvania; Vanderbilt University Medical Center; University of Botswana, Biological Sciences, Gaborone, Botswana; University of Botswana, Faculty of Medicine, Gaborone, Botswana; ; Department of Biochemistry, Kampala International University in Tanzania, Dar es Salaam, Tanzania; Addis Ababa University Department of Microbial Cellular and Molecular Biology, Addis Ababa, Ethiopia; Addis Ababa University Department of Microbial Cellular and Molecular Biology, Addis Ababa, Ethiopia; Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaounde I, Yaounde, Cameroon; Department of Neurology, Central Hospital Yaounde; Brain Research Africa Initiative (BRAIN), Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The ; Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya; Case Western Reserve University; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania",
-    "abstract": "We investigated global patterns of genetic variation and signatures of natural selection at host genes relevant to SARS-CoV-2 infection (ACE2, TMPRSS2, DPP4, and LY6E). We analyzed novel data from 2,012 ethnically diverse Africans and 15,997 individuals of European and African ancestry with electronic health records, and integrated with global data from the 1000GP. At ACE2, we identified 41 non-synonymous variants that were rare in most populations, several of which impact protein function. However, three non-synonymous variants were common among Central African hunter-gatherers from Cameroon and are on haplotypes that exhibit signatures of positive selection. We identify strong signatures of selection impacting variation at regulatory regions influencing ACE2 expression in multiple African populations. At TMPRSS2, we identified 13 amino acid changes that are adaptive and specific to the human lineage. Genetic variants that are targets of natural selection are associated with clinical phenotypes common in patients with COVID-19.",
-    "category": "genetic and genomic medicine",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.06.23.21259400",
@@ -4465,20 +4381,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2021.06.17.21259103",
-    "date": "2021-06-21",
-    "link": "https://medrxiv.org/cgi/content/short/2021.06.17.21259103",
-    "title": "REACT-1 round 12 report: resurgence of SARS-CoV-2 infections in England associated with increased frequency of the Delta variant",
-    "authors": "Steven Riley; Caroline E. Walters; Haowei Wang; Oliver Eales; David Haw; Kylie E. C. Ainslie; Christina Atchinson; Claudio Fronterre; Peter J. Diggle; Andrew J. Page; Sophie J. Prosolek; Alexander J. Trotter; Le Viet Thanh; Nabil-Fareed Alikhan; Leigh M Jackson; Catherine Ludden; - The COVID-19 Genomics UK (COG-UK) Consortium; Deborah Ashby; Christl A Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott",
-    "affiliations": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Medical School, University of Exeter, UK; Department of Medicine, University of Cambridge, UK; -; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear",
-    "abstract": "BackgroundEngland entered a third national lockdown from 6 January 2021 due to the COVID-19 pandemic. Despite a successful vaccine rollout during the first half of 2021, cases and hospitalisations have started to increase since the end of May as the SARS-CoV-2 Delta (B.1.617.2) variant increases in frequency. The final step of relaxation of COVID-19 restrictions in England has been delayed from 21 June to 19 July 2021.\n\nMethodsThe REal-time Assessment of Community Transmision-1 (REACT-1) study measures the prevalence of swab-positivity among random samples of the population of England. Round 12 of REACT-1 obtained self-administered swab collections from participants from 20 May 2021 to 7 June 2021; results are compared with those for round 11, in which swabs were collected from 15 April to 3 May 2021.\n\nResultsBetween rounds 11 and 12, national prevalence increased from 0.10% (0.08%, 0.13%) to 0.15% (0.12%, 0.18%). During round 12, we detected exponential growth with a doubling time of 11 (7.1, 23) days and an R number of 1.44 (1.20, 1.73). The highest prevalence was found in the North West at 0.26% (0.16%, 0.41%) compared to 0.05% (0.02%, 0.12%) in the South West. In the North West, the locations of positive samples suggested a cluster in Greater Manchester and the east Lancashire area. Prevalence in those aged 5-49 was 2.5 times higher at 0.20% (0.16%, 0.26%) compared with those aged 50 years and above at 0.08% (0.06%, 0.11%). At the beginning of February 2021, the link between infection rates and hospitalisations and deaths started to weaken, although in late April 2021, infection rates and hospital admissions started to reconverge. When split by age, the weakened link between infection rates and hospitalisations at ages 65 years and above was maintained, while the trends converged below the age of 65 years. The majority of the infections in the younger group occurred in the unvaccinated population or those without a stated vaccine history. We observed the rapid replacement of the Alpha (B.1.1.7) variant of SARS-CoV-2 with the Delta variant during the period covered by rounds 11 and 12 of the study.\n\nDiscussionThe extent to which exponential growth continues, or slows down as a consequence of the continued rapid roll-out of the vaccination programme, including to young adults, requires close monitoring. Data on community prevalence are vital to track the course of the epidemic and inform ongoing decisions about the timing of further lifting of restrictions in England.",
-    "category": "infectious diseases",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "bioRxiv",
     "doi": "10.1101/2021.06.21.449178",
@@ -4899,6 +4801,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2021.05.13.21257146",
+    "date": "2021-05-17",
+    "link": "https://medrxiv.org/cgi/content/short/2021.05.13.21257146",
+    "title": "Sociodemographic inequality in COVID-19 vaccination coverage amongst elderly adults in England: a national linked data study",
+    "authors": "Vahe Nafilyan; Ted Dolby; Cameron Razieh; Charlotte Gaughan; Jasper Morgan; Daniel Ayoubkhani; Ann Sarah Walker; Kamlesh Khunti; Myer Glickman; Thomas Yates",
+    "affiliations": "Office for National Statistics; Office for National Statistics; Diabetes Research Centre, University of Leicester; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Diabetes Research Centre, University of Leicester; Office for National Statistics; Diabetes Research Centre, University of Leicester",
+    "abstract": "ObjectiveTo examine inequalities in COVID-19 vaccination rates amongst elderly adults in England\n\nDesignCohort study\n\nSettingPeople living in private households and communal establishments in England\n\nParticipants6,829,643 adults aged [&ge;] 70 years (mean 78.7 years, 55.2% female) who were alive on 15 March 2021.\n\nMain outcome measuresHaving received the first dose of a vaccine against COVID-19 by 15 March 2021. We calculated vaccination rates and estimated unadjusted and adjusted odds ratios using logistic regression models.\n\nResultsBy 15 March 2021, 93.2% of people living in England aged 70 years and over had received at least one dose of a COVID-19 vaccine. While vaccination rates differed across all factors considered apart from sex, the greatest disparities were seen between ethnic and religious groups. The lowest rates were in people of Black African and Black Caribbean ethnic backgrounds, where only 67.2% and 73.9% had received a vaccine, with adjusted odds of not being vaccinated at 5.01 (95% CI 4.86 - 5.16) and 4.85 (4.75 - 4.96) times greater than the White British group. The proportion of individuals self-identifying as Muslim and Buddhist who had received a vaccine was 79.1% and 84.1%, respectively. Older age, greater area deprivation, less advantaged socio-economic position (proxied by living in a rented home), being disabled and living either alone or in a multi-generational household were also associated with higher odds of not having received the vaccine.\n\nConclusionPeople disproportionately affected seem most hesitant to COVID-19 vaccinations. Policy Interventions to improve these disparities are urgently needed.\n\nSummary BoxO_ST_ABSWhat is already known on this subject?C_ST_ABSThe UK began an ambitious vaccination programme to combat the COVID-19 pandemic on 8th December 2020. Existing evidence suggests that COVID-19 vaccination rates differ by level of area deprivation, ethnicity and certain underlying health conditions, such as learning disability and mental health problems.\n\nWhat does this study add?Our study shows that first dose vaccination rates in adults aged 70 or over differed markedly by ethnic group and self-reported religious affiliation, even after adjusting for geography, socio-demographic factors and underlying health conditions. Our study also highlights differences in vaccination rates by deprivation, household composition, and disability status, factors disproportionately associated with SARS-CoV-2 infection. Public health policy and community engagement aimed at promoting vaccination uptake is these groups are urgently needed.\n\nStrengths and limitations of this studyO_LIUsing nationwide linked population-level data from clinical records and the 2011 Census, we examined a wide range of socio-demographic characteristics not available n electronic health records\nC_LIO_LIMost demographic and socio-economic characteristics are derived from the 2011 Census and therefore are 10 years old. However, we focus primarily on characteristics that are unlikely to change over time, such as ethnicity or religion, or likely to be stable for our population\nC_LIO_LIBecause the data are based on the 2011 Census, it excluded people living in England in 2011 but not taking part in the 2011 Census; respondents who could not be linked to the 2011-2013 NHS patients register; recent migrants. Consequently, we excluded 5.4% of vaccinated people who could not be linked\nC_LI",
+    "category": "public and global health",
+    "match_type": "fuzzy",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.05.12.21257102",
@@ -4955,20 +4871,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2021.05.06.21256755",
-    "date": "2021-05-13",
-    "link": "https://medrxiv.org/cgi/content/short/2021.05.06.21256755",
-    "title": "Clinical coding of long COVID in English primary care: a federated analysis of 58 million patient records in situ using OpenSAFELY",
-    "authors": "- The OpenSAFELY Collaborative; Alex J Walker; Brian MacKenna; Peter Inglesby; Christopher T Rentsch; Helen J Curtis; Caroline E Morton; Jessica Morley; Amir Mehrkar; Sebastian CJ Bacon; George Hickman; Christopher Bates; Richard Croker; David Evans; Tom Ward; Jonathan Cockburn; Simon Davy; Krishnan Bhaskaran; Anna Schultze; Elizabeth J Williamson; William J Hulme; Helen I McDonald; Laurie Tomlinson; Rohini Mathur; Rosalind M Eggo; Kevin Wing; Angel YS Wong; Harriet Forbes; John Tazare; John Parry; Frank Hester; Sam Harper; Shaun O'Hanlon; Alex Eavis; Richard Jarvis; Dima Avramov; Paul Griffiths; Aaron Fowles; Nasreen Parkes; Ian J Douglas; Stephen JW Evans; Liam Smeeth; Ben Goldacre",
-    "affiliations": "; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; TPP; TPP; EMIS; EMIS; EMIS; EMIS; EMIS; EMIS; EMIS; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford",
-    "abstract": "BackgroundLong COVID is a term to describe new or persistent symptoms at least four weeks after onset of acute COVID-19. Clinical codes to describe this phenomenon were released in November 2020 in the UK, but it is not known how these codes have been used in practice.\n\nMethodsWorking on behalf of NHS England, we used OpenSAFELY data encompassing 96% of the English population. We measured the proportion of people with a recorded code for long COVID, overall and by demographic factors, electronic health record software system, and week. We also measured variation in recording amongst practices.\n\nResultsLong COVID was recorded for 23,273 people. Coding was unevenly distributed amongst practices, with 26.7% of practices having not used the codes at all. Regional variation was high, ranging between 20.3 per 100,000 people for East of England (95% confidence interval 19.3-21.4) and 55.6 in London (95% CI 54.1-57.1). The rate was higher amongst women (52.1, 95% CI 51.3-52.9) compared to men (28.1, 95% CI 27.5-28.7), and higher amongst practices using EMIS software (53.7, 95% CI 52.9-54.4) compared to TPP software (20.9, 95% CI 20.3-21.4).\n\nConclusionsLong COVID coding in primary care is low compared with early reports of long COVID prevalence. This may reflect under-coding, sub-optimal communication of clinical terms, under-diagnosis, a true low prevalence of long COVID diagnosed by clinicians, or a combination of factors. We recommend increased awareness of diagnostic codes, to facilitate research and planning of services; and surveys of clinicians experiences, to complement ongoing patient surveys.",
-    "category": "epidemiology",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.05.10.21256912",
@@ -5011,20 +4913,6 @@
     "author_similarity": 94,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2021.05.04.21256507",
-    "date": "2021-05-06",
-    "link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256507",
-    "title": "Describing the burden of the COVID-19 pandemic in people with psoriasis: findings from a global cross-sectional study",
-    "authors": "Satveer K Mahil; Mark Yates; Zenas Z Yiu; Sinead M Langan; Teresa Tsakok; Nick Dand; Kayleigh J Mason; Helen McAteer; Freya Meynall; Bolaji Coker; Alexandra Vincent; Dominic Urmston; Amber Vesty; Jade Kelly; Camille Lancelot; Lucy Moorhead; Herve Bachelez; Francesca Capon; Claudia R Contreras; Claudia De La Cruz; Paola Di Meglio; Paolo Gisondi; Denis Jullien; Jo Lambert; Luigi Naldi; Sam Norton; Luis Puig; Phyllis Spuls; Tiago Torres; Richard B Warren; Hoseah Waweru; John Weinman; Matt A Brown; James B Galloway; Christopher M Griffiths; Jonathan N Barker; Catherine H Smith",
-    "affiliations": "St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; Centre for Rheumatic Diseases, King's College London; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; Faculty of Epidemiology, and Population Health, London School of Hygiene and Tropical Medicine, London, UK; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King's College London, London, UK; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; The Psoriasis Association, Northampton, UK; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; NIHR Biomedical Research Centre at Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; NIHR Biomedical Research Centre at Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; The Psoriasis Association, Northampton, UK; The Psoriasis Association, Northampton, UK; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; International Federation of Psoriasis Associations; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; Department of Dermatology, AP-HP Hopital Saint-Louis, Paris, France; King's College London; Catedra de Dermatologia, Hospital de Clinicas, Facultad de Ciencias Medicas, Universidad Nacional de Asuncion, Paraguay; Clinica Dermacross, Santiago, Chile; King's College London; Section of Dermatology and Venereology, University of Verona, Verona, Italy; Department of Dermatology, Edouard Herriot Hospital, Hospices Civils de Lyon, University of Lyon, Lyon, France; Department of Dermatology, Ghent University, Ghent, Belgium; Centro Studi GISED, Bergamo, Italy; Psychology Department, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, UK; Department of Dermatology, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Catalonia, Spain; Department of Dermatology, Amsterdam Public Health/Infection and Immunology, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands; Department of Dermatology, Centro Hospitalar do Porto, Portugal; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; International Federation of Psoriasis Associations; School of Cancer and Pharmaceutical Sciences, Kings College London, London, UK; Centre for Rheumatic Diseases, King's College London, London, UK; Centre for Rheumatic Diseases, King's College London, London, UK; 3Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Res; NIHR Biomedical Research Centre at Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK",
-    "abstract": "BackgroundIndirect excess morbidity has emerged as a major concern in the COVID-19 pandemic. People with psoriasis may be particularly vulnerable to this because of prevalent anxiety and depression, multimorbidity and therapeutic use of immunosuppression.\n\nObjectiveCharacterise the factors associated with worsening psoriasis in the COVID-19 pandemic, using mental health status (anxiety and depression) as the main exposure of interest.\n\nMethodsGlobal cross-sectional study using a primary outcome of self-reported worsening of psoriasis. Individuals with psoriasis completed an online self-report questionnaire (PsoProtectMe; Psoriasis Patient Registry for Outcomes, Therapy and Epidemiology of COVID-19 Infection Me) between May 2020 and January 2021. Each individual completed a validated screen for anxiety (Generalized Anxiety Disorder-2) and depression (Patient Health Questionnaire-2). Odds ratios (OR) and 95% confidence intervals (CI) were estimated using multivariable logistic regression.\n\nResults4,043 people with psoriasis (without COVID-19) from 86 countries self-reported to PsoProtectMe (mean age 47.2 years [SD 15.1]; mean BMI 27.6kg/m2 [SD 6.0], 2,684 [66.4%] female and 3,016 [74.6%] of white European ethnicity). 1,728 (42.7%) participants (1322 [77%] female) reported worsening of their psoriasis in the pandemic. A positive screen for anxiety or depression associated with worsening psoriasis in age and gender adjusted (OR 2.04, 95% CI 1.77-2.36), and fully adjusted (OR 2.01, 95% CI 1.72-2.34) logistic regression models. Female sex, obesity, shielding behaviour and systemic immunosuppressant non-adherence also associated with worsening psoriasis. The commonest reason for non-adherence was concern regarding complications related to COVID-19.\n\nConclusionsThese data indicate an association between poor mental health and worsening psoriasis in the pandemic. Access to holistic care including psychological support may mitigate potentially long-lasting effects of the pandemic on health outcomes in psoriasis. The study also highlights an urgent need to address patient concerns about immunosuppressant-related risks, which may be contributing to non-adherence.",
-    "category": "dermatology",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.04.28.21256261",
@@ -5039,20 +4927,6 @@
     "author_similarity": 94,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2021.04.30.21256119",
-    "date": "2021-04-30",
-    "link": "https://medrxiv.org/cgi/content/short/2021.04.30.21256119",
-    "title": "Association between oral anticoagulants and COVID-19 related outcomes: two cohort studies",
-    "authors": "Angel YS Wong; Laurie Tomlinson; Jeremy P Brown; William Elson; Alex J Walker; Anna J Schultze; Caroline E Morton; David Evans; Peter Inglesby; Brian MacKenna; Krishnan Bhaskaran; Christopher T. Rentsch; Emma Powell; Elizabeth T. Williamson; Richard Croker; Seb Bacon; William Hulme; Chris Bates; Helen J Curtis; Amir Mehrkar; Jonathan Cockburn; Helen I McDonald; Rohini I Mathur; Kevin Wing; Harriet Forbes; Rosalind M Eggo; Stephen Evans; Liam Smeeth; Ben Goldacre; Ian J Douglas",
-    "affiliations": "London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Trop. Med.; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; US Department of Veterans Affairs, London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; TPP; London School of Medicine and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Bristol; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine",
-    "abstract": "ObjectivesWe investigated the role of routinely prescribed oral anticoagulants (OACs) in COVID-19 outcomes, comparing current OAC use versus non-use in Study 1; and warfarin versus direct oral anticoagulants (DOACs) in Study 2.\n\nDesignTwo cohort studies, on behalf of NHS England.\n\nSettingPrimary care data and pseudonymously-linked SARS-CoV-2 antigen testing data, hospital admissions, and death records from England.\n\nParticipantsStudy 1: 70,464 people with atrial fibrillation (AF) and CHA{square}DS{square}-VASc score of 2. Study 2: 372,746 people with non-valvular AF.\n\nMain outcome measuresTime to test for SARS-CoV-2, testing positive for SARS-CoV-2, COVID-19 related hospital admission, COVID-19 deaths or non-COVID-19 deaths in Cox regression.\n\nResultsIn Study 1, we included 52,416 current OAC users and 18,048 non-users. We observed no difference in risk of being tested for SARS-CoV-2 associated with current use (adjusted HR, 1.01, 95%CI, 0.96 to 1.05) versus non-use. We observed a lower risk of testing positive for SARS-CoV-2 (adjusted HR, 0.73, 95%CI, 0.60 to 0.90), and COVID-19 deaths (adjusted HR, 0.69, 95%CI, 0.49 to 0.97) associated with current use versus non-use. In Study 2, we included 92,339 warfarin users and 280,407 DOAC users. We observed a lower risk of COVID-19 deaths (adjusted HR, 0.79, 95%CI, 0.76 to 0.83) associated with warfarin versus DOACs. Similar associations were found for all other outcomes.\n\nConclusionsAmong people with AF and a CHA{square}DS{square}-VASc score of 2, those receiving OACs had a lower risk of receiving a positive COVID-19 test and severe COVID-19 outcomes than non-users; this might be explained by a causal effect of OACs in preventing severe COVID-19 outcomes or more cautious behaviours leading to reduced infection risk. There was no evidence of a higher risk of severe COVID-19 outcomes associated with warfarin versus DOACs in people with non-valvular AF regardless of CHA{square}DS{square}-VASc score.\n\nKey pointsO_ST_ABSWhat is already known on this topicC_ST_ABSO_LICurrent studies suggest that prophylactic or therapeutic anticoagulant use, particularly low molecular weight heparin, lower the risk of pulmonary embolism and mortality during hospitalisation among patients with COVID-19.\nC_LIO_LIReduced vitamin K status has been reported to be correlated with severity of COVID-19. This could mean that warfarin, as a vitamin K antagonist, is associated with more severe COVID-19 disease than non-vitamin K anticoagulants.\nC_LI\n\nWhat this study addsO_LIIn 70,464 people with atrial fibrillation, at the threshold of being treated with an OAC based on risk of stroke, we observed a lower risk of testing positive for SARS-CoV-2 and COVID-19 related deaths associated with routinely prescribed OACs, relative to non-use.\nC_LIO_LIThis might be explained by OACs preventing severe COVID-19 outcomes, or more cautious behaviours and environmental factors reducing the risk of SARS-CoV-2 infection in those taking OACs.\nC_LIO_LIIn 372,746 people with non-valvular atrial fibrillation, there was no evidence of a higher risk of severe COVID-19 outcomes associated with warfarin compared with DOACs.\nC_LI",
-    "category": "epidemiology",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.04.26.21255732",
@@ -5095,20 +4969,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2021.04.22.21255949",
-    "date": "2021-04-25",
-    "link": "https://medrxiv.org/cgi/content/short/2021.04.22.21255949",
-    "title": "Optimal health and economic impact of non-pharmaceutical intervention measures prior and post vaccination in England: a mathematical modelling study",
-    "authors": "Michael Tildesley; Anna Vassall; Steven Riley; Mark Jit; Frank Sandmann; Edward M Hill; Robin Thompson; Benjamin Atkins; John Edmunds; Louise M Dyson; Matt J Keeling",
-    "affiliations": "University of Warwick; London School of Hygiene and Tropical Medicine; Dept Inf Dis Epi, Imperial College; London School of Hygiene & Tropical Medicine; Public Health England; University of Warwick; University of Warwick; University of Warwick; London School of Hygiene and Tropical Medicine; University of Warwick; University of Warwick",
-    "abstract": "BackgroundEven with good progress on vaccination, SARS-CoV-2 infections in the UK may continue to impose a high burden of disease and therefore pose substantial challenges for health policy decision makers. Stringent government-mandated physical distancing measures (lockdown) have been demonstrated to be epidemiologically effective, but can have both positive and negative economic consequences. The duration and frequency of any intervention policy could, in theory, could be optimised to maximise economic benefits while achieving substantial reductions in disease.\n\nMethodsHere we use a pre-existing SARS-CoV-2 transmission model to assess the health and economic implications of different strengths of control through time in order to identify optimal approaches to non-pharmaceutical intervention stringency in the UK, considering the role of vaccination in reducing the need for future physical distancing measures. The model is calibrated to the COVID-19 epidemic in England and we carry out retrospective analysis of the optimal timing of precautionary breaks in 2020 and the optimal relaxation policy from the January 2021 lockdown, considering the willingness to pay for health improvement.\n\nResultsWe find that the precise timing and intensity of interventions is highly dependent upon the objective of control. As intervention measures are relaxed, we predict a resurgence in cases, but the optimal intervention policy can be established dependent upon the willingness to pay (WTP) per QALY loss avoided. Our results show that establishing an optimal level of control can result in a reduction in net monetary loss of billions of pounds, dependent upon the precise WTP value.\n\nConclusionsIt is vital, as the UK emerges from lockdown, but continues to face an on-going pandemic, to accurately establish the overall health and economic costs when making policy decisions. We demonstrate how some of these can be quantified, employing mechanistic infectious disease transmission models to establish optimal levels of control for the ongoing COVID-19 pandemic.",
-    "category": "infectious diseases",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.04.22.21255948",
@@ -5389,20 +5249,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2021.03.26.21254390",
-    "date": "2021-03-26",
-    "link": "https://medrxiv.org/cgi/content/short/2021.03.26.21254390",
-    "title": "Regional performance variation in external validation of four prediction models for severity of COVID-19 at hospital admission: An observational multi-centre cohort study",
-    "authors": "Kristin Wickstrom; Valeria Vitelli; Ewan Carr; Aleksander Rygh Holten; Rebecca Bendayan; Andrew Henry Reiner; Daniel Bean; Tom Searle; Anthony Shek; Zeljko Kraljevic; James T Teo; Richard Dobson; Kristian Tonby; Alvaro Kohn-Luque; Erik Koldberg Amundsen",
-    "affiliations": "Oslo University Hospital; University of Oslo; King's College London; Oslo University Hospital; King's College London; Oslo University Hospital; King's College London; King's College London; King's College London; King's College London; Kings College Hospital NHS Foundation Trust; Kings College London; Oslo University Hospital; University of Oslo; Oslo University Hospital",
-    "abstract": "BackgroundSeveral prediction models for coronavirus disease-19 (COVID-19) have been published. Prediction models should be externally validated to assess their performance before implementation. This observational cohort study aimed to validate published models of severity for hospitalized patients with COVID-19 using clinical and laboratory predictors.\n\nMethodsPrediction models fitting relevant inclusion criteria were chosen for validation. The outcome was either mortality or a composite outcome of mortality and ICU admission (severe disease). 1295 patients admitted with symptoms of COVID-19 at Kings Cross Hospital (KCH) in London, United Kingdom, and 307 patients at Oslo University Hospital (OUH) in Oslo, Norway were included. The performance of the models was assessed in terms of discrimination and calibration.\n\nResultsWe identified two models for prediction of mortality (referred to as Xie and Zhang1) and two models for prediction of severe disease (Allenbach and Zhang2).\n\nThe performance of the models was variable. For prediction of mortality Xie had good discrimination at OUH with an area under the receiver-operating characteristic (AUROC) 0.87 [95 % confidence interval (CI) 0.79-0.95] and acceptable discrimination at KCH, AUROC 0.79 [0.76-0.82]. In prediction of severe disease, Allenbach had acceptable discrimination (OUH AUROC 0.81 [0.74-0.88] and KCH AUROC 0.72 [0.68-0.75]). The Zhang models had moderate to poor discrimination. Initial calibration was poor for all models but improved with recalibration.\n\nConclusionsThe performance of the four prediction models was variable. The Xie model had the best discrimination for mortality, while the Allenbach model had acceptable results for prediction of severe disease.",
-    "category": "infectious diseases",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.03.26.21254391",
@@ -5823,6 +5669,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2021.02.27.21252593",
+    "date": "2021-03-01",
+    "link": "https://medrxiv.org/cgi/content/short/2021.02.27.21252593",
+    "title": "Surgical activity in England and Wales during the COVID-19 pandemic: a nationwide observational cohort study",
+    "authors": "Thomas D Dobbs; John A G Gibson; Alexander J Fowler; Tom E Abbott; Tasnin Shahid; Fatemeh Torabi; Rowena Griffiths; Ronan A Lyons; Rupert M Pearse; Iain S Whitaker",
+    "affiliations": "Swansea University Medical School; Swansea University Medical School; Queen Mary, University of London; Queen Mary University of London; Queen Mary University of London; Swansea University; Swansea University; Swansea University; Queen Mary University of London; Swansea University Medical School",
+    "abstract": "ObjectivesTo report the volume of surgical activity and the number of cancelled surgical procedures during the COVID-19 pandemic.\n\nDesign and settingAnalysis of electronic health record data from the National Health Service (NHS) in England and Wales.\n\nMethodsWe used hospital episode statistics for all adult patients undergoing surgery between 1st January 2020 and 31st December 2020. We identified surgical procedures using a previously published list of procedure codes. Procedures were stratified by urgency of surgery as defined by NHS England. We calculated the deficit of surgical activity by comparing the expected number of procedures from the years 2016-2019 with the actual number of procedures in 2020. We estimated the cumulative number of cancelled procedures by 31st December 2021 according patterns of activity in 2020.\n\nResultsThe total number of surgical procedures carried out in England and Wales in 2020 was 3,102,674 compared to the predicted number of 4,671,338. This represents a 33.6% reduction in the national volume of surgical activity. There were 763,730 emergency surgical procedures (13.4% reduction), compared to 2,338,944 elective surgical procedures (38.6% reduction). The cumulative number of cancelled or postponed procedures was 1,568,664. We estimate that this will increase to 2,358,420 by 31st December 2021.\n\nConclusionsThe volume of surgical activity in England and Wales was reduced by 33.6% in 2020, resulting in over 1,568,664 cancelled operations. This deficit will continue to grow in 2021.\n\nSummary boxesO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIThe COVID-19 pandemic necessitated a rapid change in the provision of care, including the suspension of a large proportion of surgical activity\nC_LIO_LISurgical activity has yet to return to normal and has been further impacted by subsequent waves of the pandemic\nC_LIO_LIThis will lead to a large backlog of cases\nC_LI\n\nWhat this study addsO_LI3,102,674 surgical procedures were performed in England and Wales during 2020, a 33.6% reduction on the expected yearly surgical activity\nC_LIO_LIOver 1.5 million procedures were not performed, with this deficit likely to continue to grow to 2.3 million by the end of 2021\nC_LIO_LIThis deficit is the equivalent of more than 6 months of pre-pandemic surgical activity, requiring a monumental financial and logistic challenge to manage\nC_LI",
+    "category": "surgery",
+    "match_type": "fuzzy",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.02.26.21252512",
@@ -6019,20 +5879,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2021.02.11.21249258",
-    "date": "2021-02-11",
-    "link": "https://medrxiv.org/cgi/content/short/2021.02.11.21249258",
-    "title": "Tocilizumab in patients admitted to hospital with COVID-19 (RECOVERY): preliminary results of a randomised, controlled, open-label, platform trial",
-    "authors": "Peter W Horby; Mark Campbell; Natalie Staplin; Enti Spata; Jonathan R Emberson; Guilherme Pessoa-Amorim; Leon Peto; Christopher E Brightling; Rahuldeb Sarkar; Koshy Thomas; Vandana Jeebun; Abdul Ashish; Redmond Tully; David Chadwick; Muhammad Sharafat; Richard Stewart; Banu Rudran; J Kenneth Baillie; Maya H Buch; Lucy C Chappell; Jeremy N Day; Saul N Furst; Thomas Jaki; Katie Jeffery; Edmund Juszczak; Wei Shen Lim; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; Marion Mafham; Richard Haynes; Martin J Landray",
-    "affiliations": "Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, United Kingdom; Medway Foundation NHS Trust, Gillingham, United Kingdom; King?s College London, London, United Kingdom; Basildon and Thurrock Hospitals NHS Foundation Trust, Basildon, United Kingdom; Department of Respiratory Medicine, North Tees & Hartlepool NHS Foundation Trust, Stockton-on-Tees, United Kingdom; Wrightington Wigan and Leigh NHS Foundation Trust, Wigan, United Kingdom; Royal Oldham Hospital, Northern Care Alliance, Oldham, United Kingdom; Centre for Clinical Infection, James Cook University Hospital, Middlesbrough, United Kingdom; North West Anglia NHS Foundation Trust, Peterborough, United Kingdom; Milton Keynes University Hospital, Milton Keynes, United Kingdom; Luton & Dunstable University Hospital, Luton, United Kingdom; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; School of Life Sciences, Kings College London, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, ; Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Respiratory Medicine Department, Nottingham University Hospitals NHS Foundation Trust, Nottingham, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom; Intensive Care National Audit and Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom",
-    "abstract": "Findings: Between 23 April 2020 and 25 January 2021, 4116 adults were included in the assessment of tocilizumab, including 562 (14%) patients receiving invasive mechanical ventilation, 1686 (41%) receiving non-invasive respiratory support, and. 1868 (45%) receiving no respiratory support other than oxygen. Median CRP was 143 [IQR 107-205] mg/L and 3385 (82%) patients were receiving systemic corticosteroids at randomisation. Overall, 596 (29%) of the 2022 patients allocated tocilizumab and 694 (33%) of the 2094 patients allocated to usual care died within 28 days (rate ratio 0.86; 95% confidence interval [CI] 0.77-0.96; p=0.007). Consistent results were seen in all pre-specified subgroups of patients, including those receiving systemic corticosteroids. Patients allocated to tocilizumab were more likely to be discharged from hospital alive within 28 days (54% vs. 47%; rate ratio 1.23; 95% CI 1.12-1.34; p<0.0001). Among those not receiving invasive mechanical ventilation at baseline, patients allocated tocilizumab were less likely to reach the composite endpoint of invasive mechanical ventilation or death (33% vs. 38%; risk ratio 0.85; 95% CI 0.78-0.93; p=0.0005). Interpretation: In hospitalised COVID-19 patients with hypoxia and systemic inflammation, tocilizumab improved survival and other clinical outcomes regardless of the level of respiratory support received and in addition to the use of systemic corticosteroids.",
-    "category": "infectious diseases",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.02.08.21250525",
@@ -6131,6 +5977,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2021.02.03.21250974",
+    "date": "2021-02-05",
+    "link": "https://medrxiv.org/cgi/content/short/2021.02.03.21250974",
+    "title": "Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the US",
+    "authors": "Estee Y Cramer; Evan L Ray; Velma K Lopez; Johannes Bracher; Andrea Brennen; Alvaro J Castro Rivadeneira; Aaron Gerding; Tilmann Gneiting; Katie H House; Yuxin Huang; Dasuni Jayawardena; Abdul H Kanji; Ayush Khandelwal; Khoa Le; Anja Muehlemann; Jarad Niemi; Apurv Shah; Ariane Stark; Yijin Wang; Nutcha Wattanachit; Martha W Zorn; Youyang Gu; Sansiddh Jain; Nayana Bannur; Ayush Deva; Mihir Kulkarni; Srujana Merugu; Alpan Raval; Siddhant Shingi; Avtansh Tiwari; Jerome White; Neil F Abernethy; Spencer Woody; Maytal Dahan; Spencer Fox; Kelly Gaither; Michael Lachmann; Lauren Ancel Meyers; James G Scott; Mauricio Tec; Ajitesh Srivastava; Glover E George; Jeffrey C Cegan; Ian D Dettwiller; William P England; Matthew W Farthing; Robert H Hunter; Brandon Lafferty; Igor Linkov; Michael L Mayo; Matthew D Parno; Michael A Rowland; Benjamin D Trump; Yanli Zhang-James; Samuel Chen; Stephen V Faraone; Jonathan Hess; Christopher P Morley; Asif Salekin; Dongliang Wang; Sabrina M Corsetti; Thomas M Baer; Marisa C Eisenberg; Karl Falb; Yitao Huang; Emily T Martin; Ella McCauley; Robert L Myers; Tom Schwarz; Daniel Sheldon; Graham Casey Gibson; Rose Yu; Liyao Gao; Yian Ma; Dongxia Wu; Xifeng Yan; Xiaoyong Jin; Yu-Xiang Wang; YangQuan Chen; Lihong Guo; Yanting Zhao; Quanquan Gu; Jinghui Chen; Lingxiao Wang; Pan Xu; Weitong Zhang; Difan Zou; Hannah Biegel; Joceline Lega; Steve McConnell; VP Nagraj; Stephanie L Guertin; Christopher Hulme-Lowe; Stephen D Turner; Yunfeng Shi; Xuegang Ban; Robert Walraven; Qi-Jun Hong; Stanley Kong; Axel van de Walle; James A Turtle; Michal Ben-Nun; Steven Riley; Pete Riley; Ugur Koyluoglu; David DesRoches; Pedro Forli; Bruce Hamory; Christina Kyriakides; Helen Leis; John Milliken; Michael Moloney; James Morgan; Ninad Nirgudkar; Gokce Ozcan; Noah Piwonka; Matt Ravi; Chris Schrader; Elizabeth Shakhnovich; Daniel Siegel; Ryan Spatz; Chris Stiefeling; Barrie Wilkinson; Alexander Wong; Sean Cavany; Guido Espana; Sean Moore; Rachel Oidtman; Alex Perkins; David Kraus; Andrea Kraus; Zhifeng Gao; Jiang Bian; Wei Cao; Juan Lavista Ferres; Chaozhuo Li; Tie-Yan Liu; Xing Xie; Shun Zhang; Shun Zheng; Alessandro Vespignani; Matteo Chinazzi; Jessica T Davis; Kunpeng Mu; Ana Pastore y Piontti; Xinyue Xiong; Andrew Zheng; Jackie Baek; Vivek Farias; Andreea Georgescu; Retsef Levi; Deeksha Sinha; Joshua Wilde; Georgia Perakis; Mohammed Amine Bennouna; David Nze-Ndong; Divya Singhvi; Ioannis Spantidakis; Leann Thayaparan; Asterios Tsiourvas; Arnab Sarker; Ali Jadbabaie; Devavrat Shah; Nicolas Della Penna; Leo A Celi; Saketh Sundar; Russ Wolfinger; Dave Osthus; Lauren Castro; Geoffrey Fairchild; Isaac Michaud; Dean Karlen; Matt Kinsey; Luke C. Mullany; Kaitlin Rainwater-Lovett; Lauren Shin; Katharine Tallaksen; Shelby Wilson; Elizabeth C Lee; Juan Dent; Kyra H Grantz; Alison L Hill; Joshua Kaminsky; Kathryn Kaminsky; Lindsay T Keegan; Stephen A Lauer; Joseph C Lemaitre; Justin Lessler; Hannah R Meredith; Javier Perez-Saez; Sam Shah; Claire P Smith; Shaun A Truelove; Josh Wills; Maximilian Marshall; Lauren Gardner; Kristen Nixon; John C. Burant; Lily Wang; Lei Gao; Zhiling Gu; Myungjin Kim; Xinyi Li; Guannan Wang; Yueying Wang; Shan Yu; Robert C Reiner; Ryan Barber; Emmanuela Gaikedu; Simon Hay; Steve Lim; Chris Murray; David Pigott; Heidi L Gurung; Prasith Baccam; Steven A Stage; Bradley T Suchoski; B. Aditya Prakash; Bijaya Adhikari; Jiaming Cui; Alexander Rodriguez; Anika Tabassum; Jiajia Xie; Pinar Keskinocak; John Asplund; Arden Baxter; Buse Eylul Oruc; Nicoleta Serban; Sercan O Arik; Mike Dusenberry; Arkady Epshteyn; Elli Kanal; Long T Le; Chun-Liang Li; Tomas Pfister; Dario Sava; Rajarishi Sinha; Thomas Tsai; Nate Yoder; Jinsung Yoon; Leyou Zhang; Sam Abbott; Nikos I Bosse; Sebastian Funk; Joel Hellewell; Sophie R Meakin; Katharine Sherratt; Mingyuan Zhou; Rahi Kalantari; Teresa K Yamana; Sen Pei; Jeffrey Shaman; Michael L Li; Dimitris Bertsimas; Omar Skali Lami; Saksham Soni; Hamza Tazi Bouardi; Turgay Ayer; Madeline Adee; Jagpreet Chhatwal; Ozden O Dalgic; Mary A Ladd; Benjamin P Linas; Peter Mueller; Jade Xiao; Yuanjia Wang; Qinxia Wang; Shanghong Xie; Donglin Zeng; Alden Green; Jacob Bien; Logan Brooks; Addison J Hu; Maria Jahja; Daniel McDonald; Balasubramanian Narasimhan; Collin Politsch; Samyak Rajanala; Aaron Rumack; Noah Simon; Ryan J Tibshirani; Rob Tibshirani; Valerie Ventura; Larry Wasserman; Eamon B O'Dea; John M Drake; Robert Pagano; Quoc T Tran; Lam Si Tung Ho; Huong Huynh; Jo W Walker; Rachel B Slayton; Michael A Johansson; Matthew Biggerstaff; Nicholas G Reich",
+    "affiliations": "University of Massachusetts, Amherst; University of Massachusetts, Amherst; Centers for Disease Control and Prevention; Chair of Econometrics and Statistics, Karlsruhe Institute of Technology; Computational Statistics Group, Heidelberg Institute for Theoretical Studies; IQT; University of Massachusetts, Amherst; University of Massachusetts, Amherst; Institute of Stochastics, Karlsruhe Institute of Technology; University of Massachusetts, Amherst; University of Massachusetts, Amherst; University of Massachusetts, Amherst; University of Massachusetts, Amherst; University of Massachusetts, Amherst; University of Massachusetts, Amherst; Institute of Mathematical Statistics and Actuarial Science, University of Bern; Iowa State University; University of Massachusetts, Amherst; University of Massachusetts, Amherst; University of Massachusetts, Amherst; University of Massachusetts, Amherst; University of Massachusetts, Amherst; Unaffiliated; Wadhwani Institute of Artificial Intelligence; Wadhwani Institute of Artificial Intelligence; Wadhwani Institute of Artificial Intelligence; Wadhwani Institute of Artificial Intelligence; Wadhwani Institute of Artificial Intelligence; Wadhwani Institute of Artificial Intelligence; Wadhwani Institute of Artificial Intelligence; Wadhwani Institute of Artificial Intelligence; Wadhwani Institute of Artificial Intelligence; University of Washington; University of Texas at Austin; Texas Advanced Computing Center; University of Texas at Austin; Texas Advanced Computing Center; Santa Fe Institute; University of Texas at Austin; University of Texas at Austin; University of Texas at Austin; University of Southern California; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; State University of New York Upstate Medical University; State University of New York Upstate Medical University; State University of New York Upstate Medical University; State University of New York Upstate Medical University; State University of New York Upstate Medical University; Syracuse University; State University of New York Upstate Medical University; University of Michigan - Ann Arbor; Trinity University, San Antonio; University of Michigan - Ann Arbor; University of Michigan - Ann Arbor; University of Michigan - Ann Arbor; University of Michigan - Ann Arbor; University of Michigan - Ann Arbor; University of Michigan - Ann Arbor; University of Michigan - Ann Arbor; University of Massachusetts, Amherst; University of Massachusetts, Amherst; Northeastern University; University of California, San Diego; University of Washington; University of California, San Diego; University of California, San Diego; University of California at Santa Barbara; University of California at Santa Barbara; University of California at Santa Barbara; University of California, Merced; Jilin University; University of Science and Technology of China; University of California, Los Angeles; University of California, Los Angeles; University of California, Los Angeles; University of California, Los Angeles; University of California, Los Angeles; University of California, Los Angeles; University of Arizona; University of Arizona; Construx; Signature Science, LLC; Signature Science, LLC; Signature Science, LLC; Signature Science, LLC; Rensselaer Polytechnic Institute; University of Washington; Unaffiliated; Arizona State University; Brown University; Manhasset Secondary School; Brown University; Predictive Science, Inc; Predictive Science, Inc; Imperial College, London; Predictive Science, Inc; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; University of Notre Dame; University of Notre Dame; University of Notre Dame; University of Chicago; University of Notre Dame; University of Notre Dame; Masaryk University; Masaryk University; Microsoft; Microsoft; Microsoft; Microsoft; Microsoft; Microsoft; Microsoft; Microsoft; Microsoft; ISI Foundation; Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University; Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University; Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University; Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University; Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University; Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University; Operations Research Center, Massachusetts Institute of Technology; Operations Research Center, Massachusetts Institute of Technology; Sloan School of Management, Massachusetts Institute of Technology; Operations Research Center, Massachusetts Institute of Technology; Sloan School of Management, Massachusetts Institute of Technology; Operations Research Center, Massachusetts Institute of Technology; Operations Research Center, Massachusetts Institute of Technology; Massachusetts Institute of Technology; Massachusetts Institute of Technology; Massachusetts Institute of Technology; New York University; Massachusetts Institute of Technology; Massachusetts Institute of Technology; Massachusetts Institute of Technology; Institute for Data, Systems, and Society, Massachusetts Institute of Technology; Institute for Data, Systems, and Society, Massachusetts Institute of Technology; Institute for Data, Systems, and Society, Massachusetts Institute of Technology; Laboratory for Computational Physiology, Massachusetts Institute of Technology; Laboratory for Computational Physiology, Massachusetts Institute of Technology; River Hill High School; SAS Institute Inc; Los Alamos National Laboratory; Los Alamos National Laboratory; Los Alamos National Laboratory; Los Alamos National Laboratory; TRIUMF; University of Victoria; Johns Hopkins University Applied Physics Lab; Johns Hopkins University Applied Physics Lab; Johns Hopkins University Applied Physics Lab; Johns Hopkins University Applied Physics Lab; Johns Hopkins University Applied Physics Lab; Johns Hopkins University Applied Physics Lab; Johns Hopkins Bloomberg School of Public Health; Johns Hopkins Bloomberg School of Public Health; Johns Hopkins Bloomberg School of Public Health; Johns Hopkins University; Johns Hopkins Bloomberg School of Public Health; Unaffiliated; University of Utah; Johns Hopkins Bloomberg School of Public Health; Ecole Polytechnique Federale de Lausanne; Johns Hopkins Bloomberg School of Public Health; Johns Hopkins Bloomberg School of Public Health; Johns Hopkins Bloomberg School of Public Health; Unaffiliated; Johns Hopkins Bloomberg School of Public Health; Johns Hopkins Bloomberg School of Public Health; Unaffiliated; Johns Hopkins University; Johns Hopkins University; Johns Hopkins University; Unaffiliated; Iowa State University; Iowa State University; Iowa State University; Iowa State University; Clemson University; College of William & Mary; Iowa State University; University of Virginia; University of Washington; University of Washington; University of Washington; University of Washington; University of Washington; University of Washington; University of Washington; IEM, Inc.; IEM, Inc.; IEM, Inc.; IEM, Inc.; Georgia Institute of Technology; University of Iowa; Georgia Institute of Technology; Georgia Institute of Technology; Georgia Institute of Technology; Virginia Tech; Georgia Institute of Technology; Georgia Insitute of Technology; Metron, Inc.; Georgia Insitute of Technology; Georgia Insitute of Technology; Georgia Insitute of Technology; Google Cloud; Google Cloud; Google Cloud; Google Cloud; Google Cloud; Google Cloud; Google Cloud; Google Cloud; Google Cloud; Harvard University; Google Cloud; Google Cloud; Google Cloud; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; The University of Texas at Austin; The University of Texas at Austin; Columbia University; Columbia University; Columbia University; Operations Research Center, Massachusetts Institute of Technology; Sloan School of Management, Massachusetts Institute of Technology; Operations Research Center, Massachusetts Institute of Technology; Operations Research Center, Massachusetts Institute of Technology; Operations Research Center, Massachusetts Institute of Technology; Emory University Medical School; Georgia Insitute of Technology; MGH; MGH; Value Analytics Labs; MGH; Boston University School of Medicine; MGH; Georgia Insitute of Technology; Columbia University; Columbia University; Columbia University; UNC Chapel Hill; Carnegie Mellon University; University of Southern California; Carnegie Mellon University; Carnegie Mellon University; Carnegie Mellon University; University of British Columbia; Stanford University; Carnegie Mellon University; Stanford University; Carnegie Mellon University; University of Washington; Carnegie Mellon University; Stanford University; Carnegie Mellon University; Carnegie Mellon University; University of Georgia; University of Georgia; Unaffiliated; Walmart Inc.; Dalhousie University; Virtual Power System Inc.; Centers for Disease Control and Prevention; Centers for Disease Control and Prevention; Centers for Disease Control and Prevention; Centers for Disease Control and Prevention; University of Massachusetts, Amherst",
+    "abstract": "Short-term probabilistic forecasts of the trajectory of the COVID-19 pandemic in the United States have served as a visible and important communication channel between the scientific modeling community and both the general public and decision-makers. Forecasting models provide specific, quantitative, and evaluable predictions that inform short-term decisions such as healthcare staffing needs, school closures, and allocation of medical supplies. Starting in April 2020, the US COVID-19 Forecast Hub (https://covid19forecasthub.org/) collected, disseminated, and synthesized tens of millions of specific predictions from more than 90 different academic, industry, and independent research groups. A multi-model ensemble forecast that combined predictions from dozens of different research groups every week provided the most consistently accurate probabilistic forecasts of incident deaths due to COVID-19 at the state and national level from April 2020 through October 2021. The performance of 27 individual models that submitted complete forecasts of COVID-19 deaths consistently throughout this year showed high variability in forecast skill across time, geospatial units, and forecast horizons. Two-thirds of the models evaluated showed better accuracy than a naive baseline model. Forecast accuracy degraded as models made predictions further into the future, with probabilistic error at a 20-week horizon 3-5 times larger than when predicting at a 1-week horizon. This project underscores the role that collaboration and active coordination between governmental public health agencies, academic modeling teams, and industry partners can play in developing modern modeling capabilities to support local, state, and federal response to outbreaks.\n\nSignificance StatementThis paper compares the probabilistic accuracy of short-term forecasts of reported deaths due to COVID-19 during the first year and a half of the pandemic in the US. Results show high variation in accuracy between and within stand-alone models, and more consistent accuracy from an ensemble model that combined forecasts from all eligible models. This demonstrates that an ensemble model provided a reliable and comparatively accurate means of forecasting deaths during the COVID-19 pandemic that exceeded the performance of all of the models that contributed to it. This work strengthens the evidence base for synthesizing multiple models to support public health action.",
+    "category": "epidemiology",
+    "match_type": "fuzzy",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.02.01.21250839",
@@ -6355,20 +6215,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2021.01.14.21249801",
-    "date": "2021-01-15",
-    "link": "https://medrxiv.org/cgi/content/short/2021.01.14.21249801",
-    "title": "Factor V is an immune inhibitor that is expressed at increased levels in leukocytes of patients with severe Covid-19",
-    "authors": "Jun Wang; Prasanti Kotagiri; Paul Lyons; Federica Mescia; Laura Bergamaschi; Lorinda Turner; Rafia Al-Lamki; Michael D Morgan; Fernando J Calero-Nieto; Karsten Bach; Nicole Mende; Nicola K Wilson; Emily R Watts; - Cambridge Institute of Therapeutic Immunology and Infectious Disease - NIHR Covid BioResource; Patrick Chinnery; Nathalie Kingston; Sofia Papadia; Kathleen Stirrups; Neil Walker; Ravindra K Gupta; Mark Toshner; Michael Weekes; James A Nathan; Sarah Walmsley; Willem Hendrik Ouwehand; Mary Kasanicki; Berthold Gottgens; John C Marioni; Smith GC Smith; Jordan S Pober; John R Bradley",
-    "affiliations": "University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Edinburgh; ; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; Cambridge University; University of Cambridge; University of Edinburgh; Prof; Cambridge University Hospitals; University of Cambridge; EMBL-EBI; University of Cambridge; Yale University; University of Cambridge",
-    "abstract": "Severe Covid-19 is associated with elevated plasma Factor V (FV) and increased risk of thromboembolism. We report that neutrophils, T regulatory cells (Tregs), and monocytes from patients with severe Covid-19 express FV, and expression correlates with T cell lymphopenia. In vitro full length FV, but not FV activated by thrombin cleavage, suppresses T cell proliferation. Increased and prolonged FV expression by cells of the innate and adaptive immune systems may contribute to lymphopenia in severe Covid-19. Activation by thrombin destroys the immunosuppressive properties of FV. Anticoagulation in Covid-19 patients may have the unintended consequence of suppressing the adaptive immune system.",
-    "category": "infectious diseases",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.01.15.21249885",
@@ -6411,20 +6257,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2021.01.11.20248765",
-    "date": "2021-01-15",
-    "link": "https://medrxiv.org/cgi/content/short/2021.01.11.20248765",
-    "title": "Early immune pathology and persistent dysregulation characterise severe COVID-19",
-    "authors": "Laura Bergamaschi; Federica Mescia; Lorinda Turner; Aimee Hanson; Prasanti Kotagiri; Benjamin J. Dunmore; Helene Ruffieux; Aloka DeSa; Oisin Huhn; Michael D Morgan; Pehuen Pereyra Gerber; Mark R. Wills; Stephen Baker; Fernando J Calero Nieto; Rainer Doffinger; Gordon Dougan; Anne Elmer; Ian G Goodfellow; Ravindra K. Gupta; Myra Hosmillo; Kelvin Hunter; Nathalie Kingston; Paul J. Lehner; Nicholas J. Matheson; Jeremy K. Nicholson; Anna M. Petrunkina; Sylvia Richardson; Caroline Saunders; James E.D. Thaventhiran; Erik J.M. Toonen; Michael P. Weekes; - CambridgeInstituteofTherapeuticImmunologyandInfectiousDisease-NationalInstituteofHealthResearch(CITI; Berthold Gottgens; Mark Toshner; Christoph Hess; John R. Bradley; Paul A. Lyons; Kenneth G.C. Smith",
-    "affiliations": "Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; MRC Biostatistics Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cancer Research UK, Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Clinical Research Centre, NIHR Clinical Research Facility, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge CB2 ; Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; The Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Murdoch, Western Australia WA 6150, Australia; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; MRC Biostatistics Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; Cambridge Clinical Research Centre, NIHR Clinical Research Facility, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge CB2 ; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; R&D Department, Hycult Biotech, 5405 PD Uden, The Netherlands; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; ; Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK",
-    "abstract": "In a study of 207 SARS-CoV2-infected individuals with a range of severities followed over 12 weeks from symptom onset, we demonstrate that an early robust bystander CD8 T cell immune response, without systemic inflammation, is characteristic of asymptomatic or mild disease. Those presenting to hospital had delayed bystander responses and systemic inflammation already evident at around symptom onset. Such early evidence of inflammation suggests immunopathology may be inevitable in some individuals, or that preventative intervention might be needed before symptom onset. Viral load does not correlate with the development of this pathological response, but does with its subsequent severity. Immune recovery is complex, with profound persistent cellular abnormalities correlating with a change in the nature of the inflammatory response, where signatures characteristic of increased oxidative phosphorylation and reactive-oxygen species-associated inflammation replace those driven by TNF and IL-6. These late immunometabolic inflammatory changes and unresolved immune defects may have clinical implications.",
-    "category": "infectious diseases",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2021.01.15.21249871",
@@ -6467,6 +6299,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2020.12.27.20248896",
+    "date": "2021-01-02",
+    "link": "https://medrxiv.org/cgi/content/short/2020.12.27.20248896",
+    "title": "Vaccination and Non-Pharmaceutical Interventions: when can the UK relax about COVID-19?",
+    "authors": "Sam Moore; Edward M Hill; Michael Tildesley; Louise M Dyson; Matt J Keeling",
+    "affiliations": "University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick",
+    "abstract": "BackgroundThe announcement of efficacious vaccine candidates against SARS-CoV-2 has been met with worldwide acclaim and relief. Many countries already have detailed plans for vaccine targeting based on minimising severe illness, death and healthcare burdens. Normally, relatively simple relationships between epidemiological parameters, vaccine efficacy and vaccine uptake predict the success of any immunisation programme. However, the dynamics of vaccination against SARS-CoV-2 is made more complex by age-dependent factors, changing levels of infection and the potential relaxation of non-pharmaceutical interventions (NPIs) as the perceived risk declines.\n\nMethodsIn this study we use an age-structured mathematical model, matched to a range of epidemiological data in the UK, that also captures the roll-out of a two-dose vaccination programme targeted at specific age groups.\n\nFindingsWe consider the interaction between the UK vaccination programme and future relaxation (or removal) of NPIs. Our predictions highlight the population-level risks of early relaxation leading to a pronounced wave of infection, hospital admissions and deaths. Only vaccines that offer high infection-blocking efficacy with high uptake in the general population allow relaxation of NPIs without a huge surge in deaths.\n\nInterpretationWhile the novel vaccines against SARS-CoV-2 offer a potential exit strategy for this outbreak, this is highly contingent on the infection-blocking (or transmission-blocking) action of the vaccine and the population uptake, both of which need to be carefully monitored as vaccine programmes are rolled out in the UK and other countries.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSVaccination has been seen as a key tool in the fight against SARS-CoV-2. The vaccines already developed represent a major technological achievement and have been shown to generate significant immune responses, as well as offering considerable protection against disease. However, to date there is limited information on the degree of infection-blocking these vaccines are likely to induce. Mathematical models have already successfully been used to consider age- and risk-structured targeting of vaccination, highlighting the importance of prioritising older and high-risk individuals.\n\nAdded value of this studyTranslating current knowledge and uncertainty of vaccine behaviour into meaningful public health messages requires models that fully capture the within-country epidemiology as well as the complex roll-out of a two-dose vaccination programme. We show that under reasonable assumptions for vaccine efficacy and uptake the UK is unlikely to reach herd immunity, which means that non-pharmaceutical interventions cannot be released without generating substantial waves of infection.\n\nImplications of all the available evidenceVaccination is likely to provide substantial individual protection to those receiving two doses, but the degree of protection to the wider population is still uncertain. While substantial immunisation of the most vulnerable groups will allow for some relaxation of controls, this must be done gradually to prevent large scale public health consequences.",
+    "category": "infectious diseases",
+    "match_type": "fuzzy",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2020.12.30.20248603",
@@ -7307,20 +7153,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2020.10.26.20219642",
-    "date": "2020-10-27",
-    "link": "https://medrxiv.org/cgi/content/short/2020.10.26.20219642",
-    "title": "A2B-COVID: A method for evaluating potential SARS-CoV-2 transmission events",
-    "authors": "Christopher J R Illingworth; William L Hamilton; Christopher H Jackson; Ashley Popay; Luke Meredith; Charlotte J Houldcroft; Myra Hosmillo; Aminu Jahun; Matthew Routledge; Ben Warne; Laura Caller; Sarah Caddy; Anna Yakovleva; Grant Hall; Fahad A Khokhar; Theresa Feltwell; Malte Pinckert; Iliana Georgana; Yasmin Chaudhry; Martin Curran; Surendra Parmar; Dominic Sparkes; Lucy Rivett; Nick K Jones; Sushmita Sridhar; Sally Forest; Tom Dymond; Kayleigh Grainger; Chris Workman; Effrossyni Gkrania-Klotsas; Nicholas M Brown; Michael Weekes; Stephen Baker; Sharon J Peacock; Theodore Gouliouris; Ian G. Goodfellow; Daniela de Angelis; M. Estee Torok",
-    "affiliations": "MRC Biostatistics Unit, University of Cambridge; Department of Medicine, University of Cambridge; MRC Biostatistics Unit, University of Cambridge; Public Health England Field Epidemiology Unit, Cambridge; Department of Pathology, University of Cambridge; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Cambridge University Hospitals NHS Foundation Trust, Cambridge; Department of Medicine, University of Cambridge; Francis Crick Institute; Cambridge Institute for Therapeutic Immunology and Infectious Disease; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge; Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Department of Medicine, University of Cambridge; Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University; Cambridge University; Department of Medicine, University of Cambridge; Cambridge University Hospitals NHS Foundation Trust; University of Cambridge; MRC Biostatistics Unit, University of Cambridge; University of Cambridge",
-    "abstract": "Identifying linked cases of infection is a key part of the public health response to viral infectious disease. Viral genome sequence data is of great value in this task, but requires careful analysis, and may need to be complemented by additional types of data. The Covid-19 pandemic has highlighted the urgent need for analytical methods which bring together sources of data to inform epidemiological investigations. We here describe A2B-COVID, an approach for the rapid identification of linked cases of coronavirus infection. Our method combines knowledge about infection dynamics, data describing the movements of individuals, and novel approaches to genome sequence data to assess whether or not cases of infection are consistent or inconsistent with linkage via transmission. We apply our method to analyse and compare data collected from two wards at Cambridge University Hospitals, showing qualitatively different patterns of linkage between cases on designated Covid-19 and non-Covid-19 wards. Our method is suitable for the rapid analysis of data from clinical or other potential outbreak settings.",
-    "category": "epidemiology",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2020.10.26.20219725",
@@ -7391,6 +7223,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2020.10.14.20212555",
+    "date": "2020-10-16",
+    "link": "https://medrxiv.org/cgi/content/short/2020.10.14.20212555",
+    "title": "Multi-organ impairment in low-risk individuals with long COVID",
+    "authors": "Andrea Dennis; Malgorzata Wamil; Sandeep Kapur; Johann Alberts; Andrew Badley; Gustav Anton Decker; Stacey A Rizza; Rajarshi Banerjee; Amitava Banerjee",
+    "affiliations": "Perspectum; Great Western Hospitals NHS Foundation Trust; Mayo Clinic Healthcare; Alliance Medical; Mayo Clinic; Mayo Clinic International; Mayo Clinic; Perspectum; University College London",
+    "abstract": "BackgroundSevere acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection has disproportionately affected older individuals and those with underlying medical conditions. Research has focused on short-term outcomes in hospital, and single organ involvement. Consequently, impact of long COVID (persistent symptoms three months post-infection) across multiple organs in low-risk individuals is yet to be assessed.\n\nMethodsAn ongoing prospective, longitudinal, two-centre, observational study was performed in individuals symptomatic after recovery from acute SARS-CoV-2 infection. Symptoms and organ function (heart, lungs, kidneys, liver, pancreas, spleen) were assessed by standardised questionnaires (EQ-5D-5L, Dyspnoea-12), blood investigations and quantitative magnetic resonance imaging, defining single and multi-organ impairment by consensus definitions.\n\nFindingsBetween April and September 2020, 201 individuals (mean age 44 (SD 11.0) years, 70% female, 87% white, 31% healthcare workers) completed assessments following SARS-CoV-2 infection (median 140, IQR 105-160 days after initial symptoms). The prevalence of pre-existing conditions (obesity: 20%, hypertension: 6%; diabetes: 2%; heart disease: 4%) was low, and only 18% of individuals had been hospitalised with COVID-19. Fatigue (98%), muscle aches (88%), breathlessness (87%), and headaches (83%) were the most frequently reported symptoms. Ongoing cardiorespiratory (92%) and gastrointestinal (73%) symptoms were common, and 42% of individuals had ten or more symptoms.\n\nThere was evidence of mild organ impairment in heart (32%), lungs (33%), kidneys (12%), liver (10%), pancreas (17%), and spleen (6%). Single (66%) and multi-organ (25%) impairment was observed, and was significantly associated with risk of prior COVID-19 hospitalisation (p<0.05).\n\nInterpretationIn a young, low-risk population with ongoing symptoms, almost 70% of individuals have impairment in one or more organs four months after initial symptoms of SARS-CoV-2 infection. There are implications not only for burden of long COVID but also public health approaches which have assumed low risk in young people with no comorbidities.\n\nFundingThis work was supported by the UKs National Consortium of Intelligent Medical Imaging through the Industry Strategy Challenge Fund, Innovate UK Grant 104688, and also through the European Unions Horizon 2020 research and innovation programme under grant agreement No 719445.",
+    "category": "health policy",
+    "match_type": "fuzzy",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2020.10.12.20211342",
@@ -7489,20 +7335,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2020.10.08.20209304",
-    "date": "2020-10-12",
-    "link": "https://medrxiv.org/cgi/content/short/2020.10.08.20209304",
-    "title": "Prevalence of COVID-19-related risk factors and risk of severe influenza outcomes in cancer survivors: a matched cohort study using linked English electronic health records data",
-    "authors": "Helena Carreira; Helen Strongman; Maria Peppa; Helen I McDonald; Isabel dos-Santos-Silva; Susannah Stanway; Liam Smeeth; Krishnan Bhaskaran",
-    "affiliations": "London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; NIHR Health Protection Research Unit in Immunisation; London School of Medicine and Tropical Medicine, NIHR Health Protection Research Unit in Immunisation; London School of Hygiene and Tropical Medicine; The Royal Marsden NHS Foundation Trust; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine",
-    "abstract": "BackgroundPeople with active cancer are recognised as at risk of COVID-19 complications, but it is unclear whether the much larger population of cancer survivors is at elevated risk. We aimed to address this by comparing cancer survivors and cancer-free controls for (i) prevalence of comorbidities considered risk factors for COVID-19; and (ii) risk of severe influenza, as a marker of susceptibility to severe outcomes from epidemic respiratory viruses.\n\nMethodsWe included survivors ([&ge;]1 year) of the 20 most common cancers, and age, sex and general practice-matched cancer-free controls, derived from UK primary care data linked to cancer registrations, hospital admissions and death registrations. Comorbidity prevalences were calculated 1 and 5 years from cancer diagnosis. Risk of hospitalisation or death due to influenza was compared using Cox models adjusted for baseline demographics and comorbidities.\n\nFindings108,215 cancer survivors and 523,541 cancer-free controls were included. Cancer survivors had more asthma, other respiratory, cardiac, diabetes, neurological, renal, and liver disease, and less obesity, compared with controls, but there was variation by cancer site. There were 205 influenza hospitalisations/deaths, with cancer survivors at higher risk than controls (adjusted HR 2.78, 95% CI 2.04-3.80). Haematological cancer survivors had large elevated risks persisting for >10 years (HR overall 15.17, 7.84-29.35; HR >10 years from cancer diagnosis 10.06, 2.47-40.93). Survivors of other cancers had evidence of raised risk up to 5 years from cancer diagnosis only (HR 2.22, 1.31-3.74).\n\nInterpretationRisks of severe COVID-19 outcomes are likely to be elevated in cancer survivors. This should be taken into account in policies targeted at clinical risk groups, and vaccination for both influenza, and, when available, COVID-19, should be encouraged in cancer survivors.\n\nFundingWellcome Trust, Royal Society, NIHR.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSFew data are available to date on how COVID-19 affects cancer survivors. We searched PubMed with the keywords \"influenza cancer survivors\" to identify studies that compared severe influenza outcomes in cancer survivors and in a control group. No study was identified.\n\nAdded value of this studyIn this matched cohort study of routinely collected electronic health records, we demonstrated raised risks of influenza hospitalisation or mortality in survivors from haematological malignancies for >10 years after diagnosis, and in survivors from solid cancers up to 5 years after diagnosis.\n\nImplications of all the available evidenceCancer survivorship appears to be an important risk factor for severe influenza outcomes, suggesting that cancer survivors may also be at raised risk of poor COVID-19 outcomes. This should be taken into account in public health policies targeted at protecting clinical risk groups. Influenza vaccination should be encouraged in this group, and may need to be extended to a wider population of medium- to long-term cancer survivors than currently recommended.",
-    "category": "oncology",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "bioRxiv",
     "doi": "10.1101/2020.10.10.331348",
@@ -7811,6 +7643,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2020.09.10.20191841",
+    "date": "2020-09-11",
+    "link": "https://medrxiv.org/cgi/content/short/2020.09.10.20191841",
+    "title": "The King's College London Coronavirus Health and Experiences of Colleagues at King's Study: SARS-CoV-2 antibody response in an occupational sample",
+    "authors": "Daniel Leightley; Valentina Vitiello; Gabriella Bergin-Cartwright; Alice Wickersham; Katrina A S Davis; Sharon Stevelink; Matthew Hotopf; Reza Razavi; - On behalf of the KCL CHECK research team",
+    "affiliations": "Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; The School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and   Medicine, King's College London, London, UK.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London; The School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King's College London; ",
+    "abstract": "We report test results for SARS-CoV-2 antibodies in an occupational group of postgraduate research students and current members of staff at Kings College London. Between June and July 2020, antibody testing kits were sent to n=2296 participants; n=2004 (86.3%) responded, of whom n=1882 (93.9%) returned valid test results. Of those that returned valid results, n=124 (6.6%) tested positive for SARS-CoV-2 antibodies, with initial comparisons showing variation by age group and clinical exposure.",
+    "category": "epidemiology",
+    "match_type": "fuzzy",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2020.09.11.20192492",
@@ -7909,20 +7755,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2020.09.02.20186817",
-    "date": "2020-09-03",
-    "link": "https://medrxiv.org/cgi/content/short/2020.09.02.20186817",
-    "title": "Revealing the extent of the COVID-19 pandemic in Kenya based on serological and PCR-test data",
-    "authors": "John Ojal; Samuel PC Brand; Vincent Were; Emelda A Okiro; Ivy Kadzo Kombe; Caroline Mburu; Rabia Aziza; Morris Ogero; Ambrose Agweyu; George M Warimwe; Sophie Uyoga; Ifedayo M. O Adetifa; John Anthony Scott; Edward Otieno; Lynette I Ochola-Oyier; Charles Nyaigoti Agoti; Kadondi Kasera; Patrick Amoth; Mercy Mwangangi; Rashid Aman; Wangari Ng'ang'a; Benjamin Tsofa; Philip Bejon; Edwine Barasa; Matt J Keeling; D James Nokes",
-    "affiliations": "Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya and London School of Hygiene and Tropical Medicine; The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, UK.; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; KEMRI-Wellcome Trust Research Programme; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, UK.; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; KEMRI-Wellcome Trust Research Programme; KEMRI Wellcome Trust Research Programme; KEMRI-Wellcome Trust Research Programme; London School of Hygiene & Tropical Medicine; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Ministry of Health, Government of Kenya, Kenya; Ministry of Health, Government of Kenya, Kenya; Ministry of Health, Government of Kenya, Kenya; Ministry of Health, Government of Kenya, Kenya; Presidential Policy & Strategy Unit, The Presidency, Government of Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; KEMRI-Wellcome Trust Research Programme; The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, UK; KEMRI-Wellcome Trust Research Programme, Kenya and School of Life Sciences, University of Warwick, UK",
-    "abstract": "Policy makers in Africa need robust estimates of the current and future spread of SARS-CoV-2. Data suitable for this purpose are scant. We used national surveillance PCR test, serological survey and mobility data to develop and fit a county-specific transmission model for Kenya. We estimate that the SARS-CoV-2 pandemic peaked before the end of July 2020 in the major urban counties, with 34 - 41% of residents infected, and will peak elsewhere in the country within 2-3 months. Despite this penetration, reported severe cases and deaths are low. Our analysis suggests the COVID-19 disease burden in Kenya may be far less than initially feared. A similar scenario across sub-Saharan Africa would have implications for balancing the consequences of restrictions with those of COVID-19.",
-    "category": "epidemiology",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2020.09.01.20183822",
@@ -8203,6 +8035,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2020.08.10.20171033",
+    "date": "2020-08-11",
+    "link": "https://medrxiv.org/cgi/content/short/2020.08.10.20171033",
+    "title": "Post-exertion oxygen saturation as a prognostic factor for adverse outcome in patients attending the emergency department with suspected COVID-19: Observational cohort study",
+    "authors": "Steve Goodacre; Ben Thomas; Ellen Lee; Laura Sutton; Katie Biggs; Carl Marincowitz; Amanda Loban; Simon Waterhouse; Richard Simmonds; Jose Schutter; Sarah Connelly; Elena Sheldon; Jamie Hall; Emma Young; Andrew Bentley; Kirsty Challen; Chris Fitzsimmons; Tim Harris; Fiona Lecky; Andrew Lee; Ian Maconochie; Darren Walter",
+    "affiliations": "University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; Manchester University NHS Foundation Trust, Wythenshawe Hospital; Lancashire Teaching Hospitals NHS Foundation Trust; Sheffield Children's NHS Foundation Trust; Barts Health NHS Trust; University of Sheffield; University of Sheffield; Imperial College Healthcare NHS Trust; Manchester University NHS Foundation Trust",
+    "abstract": "BackgroundMeasurement of post-exertion oxygen saturation has been proposed to assess illness severity in suspected COVID-19 infection. We aimed to determine the accuracy of post-exertional oxygen saturation for predicting adverse outcome in suspected COVID-19.\n\nMethodsWe undertook an observational cohort study across 70 emergency departments during first wave of the COVID-19 pandemic in the United Kingdom. We collected data prospectively, using a standardised assessment form, and retrospectively, using hospital records, from patients with suspected COVID-19, and reviewed hospital records at 30 days for adverse outcome (death or receiving organ support). Patients with post-exertion oxygen saturation recorded were selected for this analysis.\n\nResultsWe analysed data from 817 patients with post-exertion oxygen saturation recorded after excluding 54 in whom measurement appeared unfeasible. The c-statistic for post-exertion change in oxygen saturation was 0.589 (95% confidence interval 0.465 to 0.713), and the positive and negative likelihood ratios of a 3% or more desaturation were respectively 1.78 (1.25 to 2.53) and 0.67 (0.46 to 0.98). Multivariable analysis showed that post-exertion oxygen saturation was not a significant predictor of adverse outcome when baseline clinical assessment was taken into account (p=0.368). Secondary analysis excluding patients in whom post-exertion measurement appeared inappropriate resulted in a c-statistic of 0.699 (0.581 to 0.817), likelihood ratios of 1.98 (1.26 to 3.10) and 0.61 (0.35 to 1.07), and some evidence of additional prognostic value on multivariable analysis (p=0.019).\n\nConclusionsPost-exertion oxygen saturation provides modest prognostic information in the assessment of patients attending the emergency department with suspected COVID-19.\n\nRegistrationISRCTN registry, ISRCTN56149622, http://www.isrctn.com/ISRCTN28342533\n\nKey messagesWhat is already known on this subject?\n\nO_LIPost exertional decrease in oxygen saturation can be used to predict prognosis in chronic lung diseases\nC_LIO_LIPost exertional desaturation has been proposed as a way of predicting adverse outcome in people with suspected COVID-19\nC_LI\n\nWhat this study adds:\n\nO_LIPost-exertion oxygen saturation provides modest prognostic information in the assessment of patients attending the emergency department with suspected COVID-19\nC_LI",
+    "category": "emergency medicine",
+    "match_type": "fuzzy",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2020.08.07.20169490",
@@ -8245,20 +8091,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2020.08.03.20164897",
-    "date": "2020-08-04",
-    "link": "https://medrxiv.org/cgi/content/short/2020.08.03.20164897",
-    "title": "Risk of hospitalisation with coronavirus disease 2019 in healthcare workers and their households:a nationwide linkage cohort study",
-    "authors": "Anoop SV Shah; Rachael Wood; Ciara Gribben; David Caldwell; Jennifer Bishop; Amanda Weir; Sharon Kennedy; Martin Reid; Alison Smith-Palmer; David Goldberg; Jim McMenamin; Colin Fischbacher; Chris Robertson; Sharon Hutchinson; Paul M McKeigue; Helen M Colhoun; David McAllister",
-    "affiliations": "London School of Hygiene and Tropical Medicine; Public Health Scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; Health protection scotland; Public health scotland; Public health scotland; Public health scotland; Public health scotland; University of Edinburgh; University of Edinburgh; University of Glasgow",
-    "abstract": "ObjectiveMany healthcare staff work in high-risk settings for contracting and transmitting Severe Acute Respiratory Syndrome Coronavirus 2. Their risk of hospitalisation for coronavirus disease 2019 (COVID-19), and that of their households, is poorly understood.\n\nDesign and settings and participantsDuring the peak period for COVID-19 infection in Scotland (1st March 2020 to 6th June 2020) we conducted a national record linkage study to compare the risk of COVID-19 hospitalisation among healthcare workers (age: 18-65 years), their households and other members of the general population.\n\nMain outcomeHospitalisation with COVID-19\n\nResultsThe cohort comprised 158,445 healthcare workers, the majority being patient facing (90,733 / 158,445; 57.3%), and 229,905 household members. Of all COVID-19 hospitalisations in the working age population (18-65-year-old), 17.2% (360 / 2,097) were in healthcare workers or their households. Adjusting for age, sex, ethnicity, socio-economic deprivation and comorbidity, the risk of COVID-19 hospitalisation in non-patient facing healthcare workers and their households was similar to the risk in the general population (hazards ratio [HR] 0.81; 95%CI 0.52-1.26 and 0.86; 95%CI 0.49-1.51 respectively). In models adjusting for the same covariates however, patient facing healthcare workers, compared to non-patient facing healthcare workers, were at higher risk (HR 3.30; 95%CI 2.13-5.13); so too were household members of patient facing healthcare workers (HR 1.79; 95%CI 1.10-2.91). On sub-dividing patient-facing healthcare workers into those who worked in front-door, intensive care and non-intensive care aerosol generating settings and other, those in  front door roles were at higher risk (HR 2.09; 95%CI 1.49-2.94). For most patient facing healthcare workers and their households, the estimated absolute risk of COVID-19 hospitalisation was less than 0.5% but was 1% and above in older men with comorbidity.\n\nConclusionsHealthcare workers and their households contribute a sixth of hospitalised COVID-19 cases. Whilst the absolute risk of hospitalisation was low overall, patient facing healthcare workers and their households had 3- and 2-fold increased risks of COVID-19 hospitalisation.",
-    "category": "epidemiology",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2020.08.03.20167122",
@@ -8679,6 +8511,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2020.07.03.20145912",
+    "date": "2020-07-06",
+    "link": "https://medrxiv.org/cgi/content/short/2020.07.03.20145912",
+    "title": "Ultraviolet A Radiation and COVID-19 Deaths: A Multi Country Study",
+    "authors": "Mark Cherrie; Tom Clemens; Claudio Colandrea; Zhiqiang Feng; David Webb; Chris Dibben; Richard B Weller",
+    "affiliations": "University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh; University of Edinburgh",
+    "abstract": "ObjectivesTo determine whether UVA exposure might be associated with COVID-19 deaths\n\nDesignEcological regression, with replication in two other countries and pooled estimation\n\nSetting2,474 counties of the contiguous USA, 6,755 municipalities in Italy, 6,274 small areas in England. Only small areas in their  Vitamin D winter (monthly mean UVvitd of under 165 KJ/m2) from Jan to April 2020.\n\nParticipants\n\nThe  at-risk population is the total small area population, with measures to incorporate spatial infection into the model. The model is adjusted for potential confounders including long-term winter temperature and humidity.\n\nMain outcome measuresWe derive UVA measures for each area from remote sensed data and estimate their relationship with COVID-19 mortality with a random effect for States, in a multilevel zero-inflated negative binomial model. In the USA and England death certificates had to record COVID-19. In Italy excess deaths in 2020 over expected from 2015-19.\n\nData sourcesSatellite derived mean daily UVA dataset from Japan Aerospace Exploration Agency. Data on deaths compiled by Center for Disease Control (USA), Office for National Statistics (England) and Italian Institute of Statistics.\n\nResultsDaily mean UVA (January-April 2020) varied between 450 to 1,000 KJ/m2 across the three countries. Our fully adjusted model showed an inverse correlation between UVA and COVID-19 mortality with a Mortality Risk Ratio (MRR) of 0.71 (0.60 to 0.85) per 100KJ/m2 increase UVA in the USA, 0.81 (0.71 to 0.93) in Italy and 0.49 (0.38 to 0.64) in England. Pooled MRR was 0.68 (0.52 to 0.88).\n\nConclusionsOur analysis, replicated in 3 independent national datasets, suggests ambient UVA exposure is associated with lower COVID-19 specific mortality. This effect is independent of vitamin D, as it occurred at irradiances below that likely to induce significant cutaneous vitamin D3 synthesis. Causal interpretations must be made cautiously in observational studies. Nonetheless this study suggests strategies for reduction of COVID-19 mortality.",
+    "category": "epidemiology",
+    "match_type": "fuzzy",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2020.07.03.20145839",
@@ -8847,6 +8693,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2020.06.18.20134742",
+    "date": "2020-06-20",
+    "link": "https://medrxiv.org/cgi/content/short/2020.06.18.20134742",
+    "title": "Racial and ethnic determinants of Covid-19 risk",
+    "authors": "Chun-Han Lo; Long H. Nguyen; David A. Drew; Mark S. Graham; Erica T. Warner; Amit D. Joshi; Christina M. Astley; Chuan-Guo Guo; Wenjie Ma; Raaj S. Mehta; Sohee Kwon; Mingyang Song; Richard Davies; Joan Capdevila; Karla A. Lee; Mary Ni Lochlainn; Thomas Varsavsky; Carole H. Sudre; Jonathan Wolf; Yvette C. Cozier; Lynn Rosenberg; Lynne R. Wilkens; Christopher A. Haiman; Loic Le Marchand; Julie R. Palmer; Tim D. Spector; Sebastien Ourselin; Claire J. Steves; Andrew T. Chan; - COPE Consortium",
+    "affiliations": "Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A.; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A.; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A.; School of Biomedical Engineering & Imaging Sciences, King's College London, London, U.K.; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A.; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A.; Computational Epidemiology Lab and Division of Endocrinology, Boston Children's Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A.; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A.; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A.; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A.; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A.; Zoe Global Limited, London, U.K.; Zoe Global Limited, London, U.K.; Department of Twin Research and Genetic Epidemiology, King's College London, London, U.K.; Department of Twin Research and Genetic Epidemiology, King's College London, London, U.K.; School of Biomedical Engineering & Imaging Sciences, King's College London, London, U.K.; School of Biomedical Engineering & Imaging Sciences, King's College London, London, U.K.; Zoe Global Limited, London, U.K.; Slone Epidemiology Center, Boston University, Boston, Massachusetts, U.S.A.; Slone Epidemiology Center, Boston University, Boston, Massachusetts, U.S.A.; Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, U.S.A.; Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, California, U.; Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, U.S.A.; Slone Epidemiology Center, Boston University, Boston, Massachusetts, U.S.A.; Department of Twin Research and Genetic Epidemiology, King's College London, London, U.K.; School of Biomedical Engineering & Imaging Sciences, King's College London, London, U.K.; Department of Twin Research and Genetic Epidemiology, King's College London, London, U.K.; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A.; ",
+    "abstract": "BackgroundRacial and ethnic minorities have disproportionately high hospitalization rates and mortality related to the novel coronavirus disease 2019 (Covid-19). There are comparatively scant data on race and ethnicity as determinants of infection risk.\n\nMethodsWe used a smartphone application (beginning March 24, 2020 in the United Kingdom [U.K.] and March 29, 2020 in the United States [U.S.]) to recruit 2,414,601 participants who reported their race/ethnicity through May 25, 2020 and employed logistic regression to determine the adjusted odds ratios (aORs) and 95% confidence intervals (CIs) for a positive Covid-19 test among racial and ethnic groups.\n\nResultsWe documented 8,858 self-reported cases of Covid-19 among 2,259,841 non-Hispanic white; 79 among 9,615 Hispanic; 186 among 18,176 Black; 598 among 63,316 Asian; and 347 among 63,653 other racial minority participants. Compared with non-Hispanic white participants, the risk for a positive Covid-19 test was increased across racial minorities (aORs ranging from 1.24 to 3.51). After adjustment for socioeconomic indices and Covid-19 exposure risk factors, the associations (aOR [95% CI]) were attenuated but remained significant for Hispanic (1.58 [1.24-2.02]) and Black participants (2.56 [1.93-3.39]) in the U.S. and South Asian (1.52 [1.38-1.67]) and Middle Eastern participants (1.56 [1.25-1.95]) in the U.K. A higher risk of Covid-19 and seeking or receiving treatment was also observed for several racial/ethnic minority subgroups.\n\nConclusionsOur results demonstrate an increase in Covid-19 risk among racial and ethnic minorities not completely explained by other risk factors for Covid-19, comorbidities, and sociodemographic characteristics. Further research investigating these disparities are needed to inform public health measures.",
+    "category": "public and global health",
+    "match_type": "fuzzy",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2020.06.17.20133959",
@@ -8903,6 +8763,20 @@
     "author_similarity": 94,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2020.06.13.20130419",
+    "date": "2020-06-16",
+    "link": "https://medrxiv.org/cgi/content/short/2020.06.13.20130419",
+    "title": "Mental health service activity during COVID-19 lockdown: South London and Maudsley data on working age community and home treatment team services and mortality from February to mid-May 2020",
+    "authors": "Robert Stewart; Evangelia Martin; Matthew Broadbent",
+    "affiliations": "King's College London; King's College London; South London and Maudsley NHS Foundation Trust",
+    "abstract": "The lockdown and social distancing policy response to the COVID-19 pandemic in the UK has a potentially important impact on provision of mental healthcare; however, there has been relatively little quantification of this. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource with 24-hourly updates of electronic mental health records data, this paper describes daily caseloads and contact numbers (face-to-face and virtual) for home treatment teams (HTTs) and working age adult community mental health teams (CMHTs) from 1st February to 15th May 2020 at the South London and Maudsley NHS Trust (SLaM), a large mental health service provider for 1.2m residents in south London. In addition daily deaths are described for all current and previous SLaM service users over this period and the same dates in 2019. In summary, comparing periods before and after 16th March 2020 the CMHT sector showed relatively stable caseloads and total contact numbers, but a substantial shift from face-to-face to virtual contacts, while HTTs showed the same changeover but reductions in caseloads and total contacts (although potentially an activity rise again during May). Number of deaths for the two months between 16th March and 15th May were 2.4-fold higher in 2020 than 2019, with 958 excess deaths.",
+    "category": "psychiatry and clinical psychology",
+    "match_type": "fuzzy",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2020.06.12.20129056",
@@ -9059,28 +8933,28 @@
   },
   {
     "site": "medRxiv",
-    "doi": "10.1101/2020.06.02.20118489",
+    "doi": "10.1101/2020.06.02.20120642",
     "date": "2020-06-05",
-    "link": "https://medrxiv.org/cgi/content/short/2020.06.02.20118489",
-    "title": "Development and implementation of a customised rapid syndromic diagnostic test for severe pneumonia",
-    "authors": "Vilas Navapurkar; Josefin Bartholdson-Scott; Mailis Maes; Thomas P Hellyer; Ellen Higginson; Sally Forrest; Joana Pereira Dias; Surendra Parmar; Emma Heasman-Hunt; Petra Polgarova; Joanne Brown; Lissamma Titti; William PW Smith; Jonathan Scott; Anthony Rostron; Matthew Routledge; David Sapsford; M. Estee Torok; Ronan McMullan; David Enoch; Vanessa Wong; - VAPrapid investigators; Martin D Curran; Nicholas Brown; A John Simpson; Jurgen Herre; Gordon Dougan; Andrew Conway Morris",
-    "affiliations": "Cambridge University Hospitals NHS Foundation Trust; University of Cambridge; University of Cambridge; Translational and Clinical Research Institute, Newcastle University, United Kingdom; University of Cambridge; University of Cambridge; University of Cambridge; Public Health England Microbiology Laboratory, Addenbrooke's Hospital, Cambridge; Public Health England Microbiology Laboratory, Addenbrooke's Hospital, Cambridge; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; University of Cambridge; Translational and Clinical Research Institute, Newcastle University, United Kingdom; Translational and Clinical Research Institute, Newcastle University, United Kingdom; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS FoundationTrust; Wellcome-Wolfson Institute for Experimental Medicine, Queens University Belfast, United Kingdom; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; ; Public Health England Microbiology Laboratory, Addenbrookes Hospital, Cambridge; Public Health England Microbiology Laboratory, Addenbrooke's Hospital, Cambridge; Translational and Clinical Research Institute, Newcastle University, United Kingdom; Cambridge University Hospitals NHS Foundation Trust; University of Cambridge; University of Cambridge",
-    "abstract": "BackgroundMicrobial cultures for the diagnosis of pneumonia take several days to return a result, and are frequently negative, compromising antimicrobial stewardship. The objective of this study was to establish the performance of a syndromic molecular diagnostic approach, using a custom TaqMan array card (TAC) covering 52 respiratory pathogens, and assess its impact on antimicrobial prescribing.\n\nMethodsThe TAC was validated against a retrospective multi-centre cohort of broncho-alveolar lavage samples. The TAC was assessed prospectively in patients undergoing investigation for suspected pneumonia, with a comparator cohort formed of patients investigated when the TAC laboratory team were unavailable.\n\nCo-primary outcomes were sensitivity compared to conventional microbiology and, for the prospective study, time to result. Metagenomic sequencing was performed to validate findings in prospective samples. Antibiotic free days (AFD) were compared between the study cohort and comparator group.\n\nResults128 stored samples were tested, with sensitivity of 97% (95% CI 88-100%). Prospectively 95 patients were tested by TAC, with 71 forming the comparator group. TAC returned results 51 hours (IQR 41-69 hours) faster than culture and with sensitivity of 92% (95% CI 83-98%) compared to conventional microbiology. 94% of organisms identified by sequencing were detected by TAC. There was a significant difference in the distribution of AFDs with more AFDs in the TAC group (p=0.02). TAC group were more likely to experience antimicrobial de-escalation (OR 2.9 (95%1.5-5.5).\n\nConclusionsImplementation of a syndromic molecular diagnostic approach to pneumonia led to faster results, with high sensitivity and impact on antibiotic prescribing.\n\nTrial registrationThe prospective study was registered with clinicaltrials.gov NCT03996330",
-    "category": "intensive care and critical care medicine",
+    "link": "https://medrxiv.org/cgi/content/short/2020.06.02.20120642",
+    "title": "Estimating excess visual loss in people with neovascular age-related macular degeneration during the COVID-19 pandemic",
+    "authors": "Darren S Thomas; Alasdair Warwick; Abraham Olvera-Barrios; Catherine Egan; Roy Schwartz; Sudeshna Patra; Haralabos Eleftheriadis; Anthony P Khawaja; Andrew Lotery; Philipp L Mueller; Robin Hamilton; Ella Preston; Paul Taylor; Adnan Tufail; - UK EMR Users Group",
+    "affiliations": "Institute of Health Informatics, University College London, London, UK; Institute of Cardiovascular Science, University College London, London, UK & Moorfields Eye Hospital NHS Foundation Trust, London, UK.; Moorfields Eye Hospital NHS Turst & Institute of Ophthalmology UCL; Moorfields Eye Hospital NHS Foundation Trust, London, UK & Institute of Ophthalmology, UCL; Moorfields Eye Hospital NHS Foundation Trust, London, UK & Institute of Health Informatics, University College London, London, UK; Bart's Health NHS Trust, London, UK; King's College Hospital NHS Trust, London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK & Institute of Ophthalmology, UCL; Faculty of Medicine, University of Southampton, Southampton, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK & Institute of Ophthalmology, UCL; Moorfields Eye Hospital NHS Foundation Trust, London, UK; Institute of Health Informatics, University College London, London, UK; Moorfields Eye Hospital NHS Trust & Institute of Ophthalmology UCL; ",
+    "abstract": "ObjectivesTo report the reduction in new neovascular age-related macular degeneration (nAMD) referrals during the COVID-19 pandemic and estimate the impact of delayed treatment on visual outcomes at one year.\n\nDesignRetrospective clinical audit and simulation model.\n\nSettingMultiple UK NHS ophthalmology centres.\n\nParticipantsData on the reduction in new nAMD referrals was obtained from four NHS Trusts in England comparing April 2020 to April 2019. To estimate the potential impact on one-year visual outcomes, a stratified bootstrap simulation model was developed drawing on an electronic medical records dataset of 20,825 nAMD eyes from 27 NHS Trusts.\n\nMain outcome measuresSimulated mean visual acuity and proportions of eyes with vision [&le;]6/60, [&le;]6/24 and [&ge;]6/12 at one year under four hypothetical scenarios: no treatment delay, 3, 6 and 9-month treatment delays. Estimated additional number of eyes with vision [&le;]6/60 at one year nationally.\n\nResultsThe number of nAMD referrals at four major eye treatment hospital groups based in England dropped on average by 72% (range 65 to 87%) in April 2020 compared to April 2019. Simulated one-year visual outcomes for 1000 nAMD eyes with a 3-month treatment delay suggested an increase in the proportion of eyes with vision [&le;]6/60 from 15.5% (13.2 to 17.9) to 23.3% (20.7 to25.9), and a decrease in the proportion of eyes with vision [&ge;]6/12 (driving vision) from 35.1% (32.1 to 38.1) to 26.4% (23.8 to29.2). Outcomes worsened incrementally with longer modelled delays. Assuming nAMD referrals are reduced to this level at the national level for only one month, these simulated results suggest an additional 186-365 eyes with vision [&le;]6/60 at one-year with even a short treatment delay.\n\nConclusionsWe report a large decrease in nAMD referrals during the first month of COVID-19 lockdown and provide an important public health message regarding the risk of delayed treatment. As a conservative estimate, a treatment delay of 3 months could lead to a >50% relative increase in the number of eyes with vision [&le;]6/60 and 25% relative decrease in the number of eyes with driving vision at one year.",
+    "category": "ophthalmology",
     "match_type": "fuzzy",
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
   {
     "site": "medRxiv",
-    "doi": "10.1101/2020.06.04.20121434",
+    "doi": "10.1101/2020.06.02.20118489",
     "date": "2020-06-05",
-    "link": "https://medrxiv.org/cgi/content/short/2020.06.04.20121434",
-    "title": "The impact of school reopening on the spread of COVID-19 in England",
-    "authors": "Matt J Keeling; Michael J Tildesley; Benjamin D Atkins; Bridget Penman; Emma Southall; Glen Guyver-Fletcher; Alex Holmes; Hector McKimm; Erin E Gorsich; Edward M Hill; Louise Dyson",
-    "affiliations": "University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick",
-    "abstract": "By mid-May, cases of COVID-19 in the UK had been declining for over a month; a multi-phase emergence from lockdown was planned, including a scheduled partial reopening of schools on 1st June. Although evidence suggests that children generally display mild symptoms, the size of the school-age population means the total impact of reopening schools is unclear. Here, we present work from mid-May that focused on the imminent opening of schools and consider what these results imply for future policy.\n\nWe compared eight strategies for reopening primary and secondary schools in England. Modifying a transmission model fitted to UK SARS-CoV-2 data, we assessed how reopening schools affects contact patterns, anticipated secondary infections and the relative change in the reproduction number, R. We determined the associated public health impact and its sensitivity to changes in social-distancing within the wider community.\n\nWe predicted reopening schools with half-sized classes or focused on younger children was unlikely to push R above one. Older children generally have more social contacts, so reopening secondary schools results in more cases than reopening primary schools, while reopening both could have pushed R above one in some regions. Reductions in community social-distancing were found to outweigh and exacerbate any impacts of reopening. In particular, opening schools when the reproduction number R is already above one generates the largest increase in cases.\n\nOur work indicates that while any school reopening will result in increased mixing and infection amongst children and the wider population, reopening schools alone in June was unlikely to push R above one. Ultimately, reopening decisions are a difficult trade-off between epidemiological consequences and the emotional, educational and developmental needs of children. Into the future, there are difficult questions about what controls can be instigated such that schools can remain open if cases increase.",
-    "category": "infectious diseases",
+    "link": "https://medrxiv.org/cgi/content/short/2020.06.02.20118489",
+    "title": "Development and implementation of a customised rapid syndromic diagnostic test for severe pneumonia",
+    "authors": "Vilas Navapurkar; Josefin Bartholdson-Scott; Mailis Maes; Thomas P Hellyer; Ellen Higginson; Sally Forrest; Joana Pereira Dias; Surendra Parmar; Emma Heasman-Hunt; Petra Polgarova; Joanne Brown; Lissamma Titti; William PW Smith; Jonathan Scott; Anthony Rostron; Matthew Routledge; David Sapsford; M. Estee Torok; Ronan McMullan; David Enoch; Vanessa Wong; - VAPrapid investigators; Martin D Curran; Nicholas Brown; A John Simpson; Jurgen Herre; Gordon Dougan; Andrew Conway Morris",
+    "affiliations": "Cambridge University Hospitals NHS Foundation Trust; University of Cambridge; University of Cambridge; Translational and Clinical Research Institute, Newcastle University, United Kingdom; University of Cambridge; University of Cambridge; University of Cambridge; Public Health England Microbiology Laboratory, Addenbrooke's Hospital, Cambridge; Public Health England Microbiology Laboratory, Addenbrooke's Hospital, Cambridge; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; University of Cambridge; Translational and Clinical Research Institute, Newcastle University, United Kingdom; Translational and Clinical Research Institute, Newcastle University, United Kingdom; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS FoundationTrust; Wellcome-Wolfson Institute for Experimental Medicine, Queens University Belfast, United Kingdom; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; ; Public Health England Microbiology Laboratory, Addenbrookes Hospital, Cambridge; Public Health England Microbiology Laboratory, Addenbrooke's Hospital, Cambridge; Translational and Clinical Research Institute, Newcastle University, United Kingdom; Cambridge University Hospitals NHS Foundation Trust; University of Cambridge; University of Cambridge",
+    "abstract": "BackgroundMicrobial cultures for the diagnosis of pneumonia take several days to return a result, and are frequently negative, compromising antimicrobial stewardship. The objective of this study was to establish the performance of a syndromic molecular diagnostic approach, using a custom TaqMan array card (TAC) covering 52 respiratory pathogens, and assess its impact on antimicrobial prescribing.\n\nMethodsThe TAC was validated against a retrospective multi-centre cohort of broncho-alveolar lavage samples. The TAC was assessed prospectively in patients undergoing investigation for suspected pneumonia, with a comparator cohort formed of patients investigated when the TAC laboratory team were unavailable.\n\nCo-primary outcomes were sensitivity compared to conventional microbiology and, for the prospective study, time to result. Metagenomic sequencing was performed to validate findings in prospective samples. Antibiotic free days (AFD) were compared between the study cohort and comparator group.\n\nResults128 stored samples were tested, with sensitivity of 97% (95% CI 88-100%). Prospectively 95 patients were tested by TAC, with 71 forming the comparator group. TAC returned results 51 hours (IQR 41-69 hours) faster than culture and with sensitivity of 92% (95% CI 83-98%) compared to conventional microbiology. 94% of organisms identified by sequencing were detected by TAC. There was a significant difference in the distribution of AFDs with more AFDs in the TAC group (p=0.02). TAC group were more likely to experience antimicrobial de-escalation (OR 2.9 (95%1.5-5.5).\n\nConclusionsImplementation of a syndromic molecular diagnostic approach to pneumonia led to faster results, with high sensitivity and impact on antibiotic prescribing.\n\nTrial registrationThe prospective study was registered with clinicaltrials.gov NCT03996330",
+    "category": "intensive care and critical care medicine",
     "match_type": "fuzzy",
     "author_similarity": 100,
     "affiliation_similarity": 100
@@ -9309,6 +9183,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2020.05.18.20086157",
+    "date": "2020-05-22",
+    "link": "https://medrxiv.org/cgi/content/short/2020.05.18.20086157",
+    "title": "COVID-19 in Great Britain: epidemiological and clinical characteristics of the first few hundred (FF100) cases: a descriptive case series and case control analysis",
+    "authors": "Nicola L Boddington; Andre Charlett; Suzanne Elgohari; Jemma L Walker; Helen Mcdonald; Chloe Byers; Laura Coughlan; Tatiana Garcia Vilaplana; Rosie Whillock; Mary Sinnathamby; Nikolaos Panagiotopoulos; Louise Letley; Pauline MacDonald; Roberto Vivancos; Obaghe Edeghere; Joseph Shingleton; Emma Bennett; Daniel J Grint; Helen Strongman; Kathryn E Mansfield; Christopher Rentsch; Caroline Minassian; Ian J Douglas; Rohini Mathur; Maria Peppa; Simon Cottrell; Jim McMenamin; Maria Zambon; Mary Ramsay; Gavin Dabrera; Vanessa Saliba; Jamie Lopez Bernal",
+    "affiliations": "Public Health England; Public Health England; Public Health England; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Public Health Wales; Public Health Scotland; Public Health England; Public Health England; Public Health England; Public Health England; Public Health England",
+    "abstract": "ObjectivesFollowing detection of the first virologically-confirmed cases of COVID-19 in Great Britain, an enhanced surveillance study was initiated by Public Health England to describe the clinical presentation, course of disease and underlying health conditions associated with infection of the first few hundred cases.\n\nMethodsInformation was collected on the first COVID-19 cases according to the First Few X WHO protocol. Case-control analyses of the sensitivity, specificity and predictive value of symptoms and underlying health conditions associated with infection were conducted. Point prevalences of underlying health conditions among the UK general population were presented.\n\nFindingsThe majority of FF100 cases were imported (51.4%), of which the majority had recent travel to Italy (71.4%). 24.7% were secondary cases acquired mainly through household contact (40.4%). Children had lower odds of COVID-19 infection compared with the general population.\n\nThe clinical presentation of cases was dominated by cough, fever and fatigue. Non-linear relationships with age were observed for fever, and sensitivity and specificity of symptoms varied by age.\n\nConditions associated with higher odds of COVID-19 infection (after adjusting for age and sex) were chronic heart disease, immunosuppression and multimorbidity.\n\nConclusionThis study presents the first epidemiological and clinical summary of COVID-19 cases in Great Britain. The FFX study design enabled systematic data collection. The study characterized underlying health conditions associated with infection and set relative risks in context with population prevalence estimates. It also provides important evidence for generating case definitions to support public health risk assessment, clinical triage and diagnostic algorithms.",
+    "category": "epidemiology",
+    "match_type": "fuzzy",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2020.05.18.20105288",
@@ -9645,20 +9533,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2020.04.27.20081810",
-    "date": "2020-05-03",
-    "link": "https://medrxiv.org/cgi/content/short/2020.04.27.20081810",
-    "title": "Clinical classifiers of COVID-19 infection from novel ultra-high-throughput proteomics",
-    "authors": "Christoph B. Messner; Vadim Demichev; Daniel Wendisch; Laura Michalick; Matthew White; Anja Freiwald; Kathrin Textoris-Taube; Spyros I. Vernardis; Anna-Sophia Egger; Marco Kreidl; Daniela Ludwig; Christiane Kilian; Federica Agostini; Aleksej Zelezniak; Charlotte Thibeault; Moritz Pfeiffer; Stefan Hippenstiel; Andreas Hocke; Christof von Kalle; Archie Campbell; Caroline Hayward; David J. Porteous; Riccardo E. Marioni; Claudia Langenberg; Kathryn S. Lilley; Wolfgang M. Kuebler; Michael Muelleder; Christian Drosten; Martin Witzenrath; Florian Kurth; Leif Erik Sander; Markus Ralser",
-    "affiliations": "The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, United Kingdom; The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, United Kingdom; Charite Universitaetsmedizin, Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; Charite Universitaetsmedizin, Institute of Physiology, 10117 Berlin, Germany; The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, United Kingdom; Charite Universitaetsmedizin, Core Facility - High Throughput Mass Spectrometry, 10117 Berlin, German; Charite Universitaetsmedizin, Core Facility - High Throughput Mass Spectrometry, 10117 Berlin, Germany; The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, United Kingdom; The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, United Kingdom; The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, United Kingdom; Charite Universitaetsmedizin, Department of Biochemistry, 10117 Berlin, Germany; Charite Universitaetsmedizin, Department of Biochemistry, 10117 Berlin, Germany; Charite Universitaetsmedizin, Department of Biochemistry, 10117 Berlin, Germany; Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden; Charite Universitaetsmedizin, Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; Charite Universitaetsmedizin, Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; Charite Universitaetsmedizin, Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; Charite Universitaetsmedizin, Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; Berlin Institute of Health (BIH), and  Charite Universitaetsmedizin, Clinical Study Center (CSC), 10117 Berlin, Germany; Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh United Kingdom and Usher Institute, Universi; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom; Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh EH4 2XU, United Kingdom; Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh EH4 2XU, United Kingdom; MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, United Kingdom; Department of Biochemistry, The University of Cambridge, Cambridge, CB21GA, United Kingdom; Charite Universitaetsmedizin, Berlin, Institute of Physiology, 10117 Berlin, Germany; Charite Universitaetsmedizin, Core Facility - High Throughput Mass Spectrometry, 10117 Berlin, Germany; Charite Universitaetsmedizin, Berlin, Department of Virology, 10117 Berlin, Germany; Charite Universitaetsmedizin, Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; Charite Universitaetsmedizin, Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany and Department of Tropical Medicine, Bernhard; Charite Universitaetsmedizin, Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany; Charite Universitaetsmedizin, Berlin, Department of Biochemistry, 10117 Berlin, and The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, Lon",
-    "abstract": "The COVID-19 pandemic is an unprecedented global challenge. Highly variable in its presentation, spread and clinical outcome, novel point-of-care diagnostic classifiers are urgently required. Here, we describe a set of COVID-19 clinical classifiers discovered using a newly designed low-cost high-throughput mass spectrometry-based platform. Introducing a new sample preparation pipeline coupled with short-gradient high-flow liquid chromatography and mass spectrometry, our methodology facilitates clinical implementation and increases sample throughput and quantification precision. Providing a rapid assessment of serum or plasma samples at scale, we report 27 biomarkers that distinguish mild and severe forms of COVID-19, of which some may have potential as therapeutic targets. These proteins highlight the role of complement factors, the coagulation system, inflammation modulators as well as pro-inflammatory signalling upstream and downstream of Interleukin 6. Application of novel methodologies hence transforms proteomics from a research tool into a rapid-response, clinically actionable technology adaptable to infectious outbreaks.\n\nHighlights- A completely redesigned clinical proteomics platform increases throughput and precision while reducing costs.\n- 27 biomarkers are differentially expressed between WHO severity grades for COVID-19.\n- The study highlights potential therapeutic targets that include complement factors, the coagulation system, inflammation modulators as well as pro-inflammatory signalling both upstream and downstream of interleukin 6.",
-    "category": "infectious diseases",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2020.04.27.20081711",
@@ -9813,6 +9687,20 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
+  {
+    "site": "medRxiv",
+    "doi": "10.1101/2020.04.15.20066407",
+    "date": "2020-04-20",
+    "link": "https://medrxiv.org/cgi/content/short/2020.04.15.20066407",
+    "title": "Evaluation of antibody testing for SARS-Cov-2 using ELISA and lateral flow immunoassays",
+    "authors": "Emily R Adams; Mark Ainsworth; Rekha Anand; Monique I Andersson; Kathryn Auckland; J Kenneth Baillie; Eleanor Barnes; Sally Beer; John Bell; Tamsin Berry; Sagida Bibi; Miles Carroll; Senthil Chinnakannan; Elizabeth Clutterbuck; Richard J Cornall; Derrick W Crook; Thushan De Silva; Wanwisa Dejnirattisai; Kate E Dingle; Christina Dold; Alexis Espinosa; David W Eyre; Helen Farmer; Maria Fernandez Mendoza; Dominique Georgiou; Sarah J Hoosdally; Alistair Hunter; Katie Jeffrey; Paul Klenerman; Julian Knight; Clarice Knowles; Andrew J Kwok; Ullrich Leuschner; Robert Levin; Chang Liu; Cesar Lopez-Camacho; Jose Carlos Martinez Garrido; Philippa C Matthews; Hannah McGivern; Alexander J Mentzer; Jonathan Milton; Juthathip Mongkolsapaya; Shona C Moore; Marta S Oliveira; Fiona Pereira; Elena Perez Lopez; Timothy Peto; Rutger J Ploeg; Andrew Pollard; Tessa Prince; David J Roberts; Justine K Rudkin; Veronica Sanchez; Gavin R Screaton; Malcolm G Semple; Donal T Skelly; Jose Slon-Campos; Elliot Nathan Smith; Alberto Jose Sobrino Diaz; Julie Staves; David Stuart; Piyada Supasa; Tomas Surik; Hannah Thraves; Pat Tsang; Lance Turtle; A Sarah Walker; Beibei Wang; Charlotte Washington; Nicholas Watkins; James Whitehouse",
+    "affiliations": "Liverpool School of Tropical Medicine; Oxford University Hospitals NHS Foundation Trust; NHSBT Birmingham,; Department of Microbiology, Oxford University Hospital NHS Foundation Trust; The Wellcome Centre for Human Genetics, University of Oxford; Roslin Institute, University of Edinburgh; Nuffield Department of Medicine, University of Oxford; Oxford University Hospitals NHS Foundation Trust; Department of Medicine, University of Oxford; Department of Health and Social Care, University of Oxford; Oxford Vaccine group, Department of Pediatrics, University of Oxford; Nuffield Department of Medicine, Centre of Tropical Medicine and Global Health and Public Health England; Nuffield Department of Medicine, University of Oxford; Oxford Vaccine Group, Department of Paediatrics, University of Oxford; Nuffield Department of Medicine, University of Oxford; NIHR Oxford Biomedical Research Centre; Department of Infection, Immunity and Cardiovascular, Disease, The Medical School, University of Sheffield; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford; NIHR Oxford Biomedical Research Centre, University of Oxford; Oxford Vaccine Group, Department of Paediatrics, University of Oxford; Oxford University Hospitals NHS Foundation Trust; Big Data Institute, University of Oxford; Department of Health and Social Care, University of Oxford; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Nuffield Department of Medicine, University of Oxford; NHSBT Basildon; Department of Clinical Medicine, Oxford University Hospitals NHS Foundation Trusts; Nuffield Department so Medicine, University of Oxford; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford; Department of Health and Social Care, University of Oxford; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford; NHSBT Oxford; Worthing Hospital, Worthing, West Sussex; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford; Wellcome Centre of Genetics, Nuffield Department of Medicine, University of Oxford; Oxford University Hospitals NHS Foundation Trust; Nuffield Department of Medicine, University of Medicine; Nuffield Department of Surgical Sciences, University of Oxford and UK QUOD Consortium; Wellcome Centre for Human Genetics, University of Oxford; Nuffield Department of Surgical Sciences, University of Oxford and UK QUOD Consortium; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford; NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, University of Liverpool; Nuffield Department of Surgical Sciences,  University of Oxford and UK QUOD Consortium; Imperial College London; Oxford University Hospitals NHS Foundation Trust; NIHR Oxford Biomedical Research centre, University of Oxford; Nuffield Department of Surgical Sciences, University of Oxford and UK QUOD Consortium; Department of Paediatrics, University of Oxford; NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, University of Liverpool; NHSBT Oxford; Nuffield Department of Population Health & Big Data Institute, University of Oxford; Oxford University Hospitals NHS Foundation Trust; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford; Health Protection Unit In Emerging and Zoonotic Infection, University of Liverpool; Nuffield Department of Clinical Neurosciences, University of Oxford; University of Oxford; Department of Health and Social Care, University of Oxford; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals,; Wellcome Centre for Human Genetics, Nuffield Department of Medicine; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford; Nuffield Department of Surgical Sciences, University of Oxford and UK QUOD Consortium; Oxford University Hospitals NHS Foundation Trust; NHSBT Oxford; NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, University of Liverpool; Nuffield Department of Medicine, University of Oxford; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford; NHSBT, Birmingham; NHSBT, Cambridge; Department of Health and Social Care, University of Oxford",
+    "abstract": "BackgroundThe COVID-19 pandemic caused >1 million infections during January-March 2020. There is an urgent need for reliable antibody detection approaches to support diagnosis, vaccine development, safe release of individuals from quarantine, and population lock-down exit strategies. We set out to evaluate the performance of ELISA and lateral flow immunoassay (LFIA) devices.\n\nMethodsWe tested plasma for COVID (SARS-CoV-2) IgM and IgG antibodies by ELISA and using nine different LFIA devices. We used a panel of plasma samples from individuals who have had confirmed COVID infection based on a PCR result (n=40), and pre-pandemic negative control samples banked in the UK prior to December-2019 (n=142).\n\nResultsELISA detected IgM or IgG in 34/40 individuals with a confirmed history of COVID infection (sensitivity 85%, 95%CI 70-94%), vs. 0/50 pre-pandemic controls (specificity 100% [95%CI 93-100%]). IgG levels were detected in 31/31 COVID-positive individuals tested [&ge;]10 days after symptom onset (sensitivity 100%, 95%CI 89-100%). IgG titres rose during the 3 weeks post symptom onset and began to fall by 8 weeks, but remained above the detection threshold. Point estimates for the sensitivity of LFIA devices ranged from 55-70% versus RT-PCR and 65-85% versus ELISA, with specificity 95-100% and 93-100% respectively. Within the limits of the study size, the performance of most LFIA devices was similar.\n\nConclusionsCurrently available commercial LFIA devices do not perform sufficiently well for individual patient applications. However, ELISA can be calibrated to be specific for detecting and quantifying SARS-CoV-2 IgM and IgG and is highly sensitive for IgG from 10 days following first symptoms.",
+    "category": "infectious diseases",
+    "match_type": "fuzzy",
+    "author_similarity": 100,
+    "affiliation_similarity": 100
+  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2020.04.14.20065417",
@@ -9981,20 +9869,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2020.03.22.20040287",
-    "date": "2020-03-24",
-    "link": "https://medrxiv.org/cgi/content/short/2020.03.22.20040287",
-    "title": "Estimating excess 1- year mortality from COVID-19 according to underlying conditions and age in England: a rapid analysis using NHS health records in 3.8 million adults",
-    "authors": "Amitava Banerjee; Laura Pasea; Steve Harris; Arturo Gonzalez-Izquierdo; Ana Torralbo; Laura Shallcross; Mahdad Noursadeghi; Deenan Pillay; Christina Pagel; Wai Keong Wong; Claudia Langenberg; Bryan Williams; Spiros Denaxas; Harry Hemingway",
-    "affiliations": "University College London; University College London; University College London Hospitals NHS Trust; University College London; University College London; UCL; University College London; University College London; University College London; University College London Hospitals NHS Trust; University of Cambridge; University College London; University College London; University College London",
-    "abstract": "BackgroundThe medical, health service, societal and economic impact of the COVID-19 emergency has unknown effects on overall population mortality. Previous models of population mortality are based on death over days among infected people, nearly all of whom (to date at least) have underlying conditions. Models have not incorporated information on high risk conditions or their longer term background (pre-COVID-19) mortality. We estimated the excess number of deaths over 1 year under different COVID-19 incidence rates and differing mortality impacts.\n\nMethodsUsing population based linked primary and secondary care electronic health records in England (HDR UK - CALIBER), we report the prevalence of underlying conditions defined by UK Public Health England COVID-19 guidelines (16 March 2020) in 3,862,012 individuals aged [&ge;]30 years from 1997-2017. We used previously validated phenotypes, openly available (https://caliberresearch.org/portal), for each condition using ICD-10 diagnosis, Read, procedure and medication codes. We estimated the 1-year mortality in each condition, and developed simple models of excess COVID-19-related deaths assuming relative risk (RR) of the impact of the emergency (compared to background mortality) of 1.2, 1.5 and 2.0.\n\nFindings20.0% of the population are at risk according to current PHE guidelines, of which; 13.7% were age>70 years and 6.3% aged [&le;]70 years with [&ge;]1 underlying condition (cardiovascular disease (2.3%), diabetes (2.2%), steroid therapy (1.9%), severe obesity (0.9%), chronic kidney disease (0.6%) and chronic obstructive pulmonary disease, COPD (0.5%). Multimorbidity (co-occurrence of [&ge;]2 conditions in an individual) was common (10.1%). The 1-year mortality in the at-risk population was 4.46%, and age and underlying conditions combine to influence background risk, varying markedly across conditions (5.9% in age>70 years, 8.6% for COPD and 13.1% in those with [&ge;]3 or more conditions). In a suppression scenario (at SARS CoV2 rates of 0.001% of the UK population), there would be minimal excess deaths (3 and 7 excess deaths at relative risk, RR, 1.5 and 2.0 respectively). At SARS CoV2 rates of 10% of the UK population (mitigation) the model estimates the numbers of excess deaths as: 13791, 34479 and 68957 (at RR 1.2, 1.5 and 2.0 respectively). At SARS CoV2 rates of 80% in the UK population (\"do-nothing\"), the model estimates the number of excess deaths as 110332, 275,830 and 551,659 (at RR 1.2, 1.5 and 2.0) respectively.\n\nInterpretationWe provide the public, researchers and policy makers a simple model to estimate the excess mortality over 1 year from COVID-19, based on underlying conditions at different ages. If the relative mortality impact of COVID-19 were to be about 20% (similar magnitude as the established winter vs summer mortality excess), then the excess deaths would be 0 when 1 in 100 000 (suppression), 13791 when 1 in 10 (mitigation) and 110332 when 8 in 10 are infected (\"do nothing\") scenario. However, the relative impact of COVID-19 is unknown. If the emergency were to double the mortality risk, then we estimate 7, 68957 and 551,659 excess deaths in the same scenarios. These results may inform the need for more stringent suppression measures as well as efforts to target those at highest risk for a range of preventive interventions.",
-    "category": "public and global health",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2020.03.20.20039537",
@@ -10065,20 +9939,6 @@
     "author_similarity": 100,
     "affiliation_similarity": 100
   },
-  {
-    "site": "medRxiv",
-    "doi": "10.1101/2020.02.14.20023036",
-    "date": "2020-02-17",
-    "link": "https://medrxiv.org/cgi/content/short/2020.02.14.20023036",
-    "title": "The Efficacy of Contact Tracing for the Containment of the 2019 Novel Coronavirus (COVID-19).",
-    "authors": "Matt J Keeling; T. Deirdre Hollingsworth; Jonathan M Read",
-    "affiliations": "University of Warwick; Oxford University; Lancaster University",
-    "abstract": "Contact tracing is a central public health response to infectious disease outbreaks, especially in the early stages of an outbreak when specific treatments are limited. Importation of novel Coronavirus (COVID-19) from China and elsewhere into the United Kingdom highlights the need to understand the impact of contact tracing as a control measure. Using detailed survey information on social encounters coupled to predictive models, we investigate the likely efficacy of the current UK definition of a close contact (within 2 meters for 15 minutes or more) and the distribution of secondary cases that may go untraced. Taking recent estimates for COVID-19 transmission, we show that less than 1 in 5 cases will generate any subsequent untraced cases, although this comes at a high logistical burden with an average of 36.1 individuals (95th percentiles 0-182) traced per case. Changes to the definition of a close contact can reduce this burden, but with increased risk of untraced cases; we estimate that any definition where close contact requires more than 4 hours of contact is likely to lead to uncontrolled spread.",
-    "category": "public and global health",
-    "match_type": "fuzzy",
-    "author_similarity": 100,
-    "affiliation_similarity": 100
-  },
   {
     "site": "medRxiv",
     "doi": "10.1101/2020.02.12.20022566",
diff --git a/data/covid/raw-preprints.json b/data/covid/raw-preprints.json
index 6647d60d..486a5368 100644
--- a/data/covid/raw-preprints.json
+++ b/data/covid/raw-preprints.json
@@ -1,4 +1,290 @@
 [
+  {
+    "rel_doi": "10.1101/2023.11.28.568639",
+    "rel_title": "Mechanism-based classification of SARS-CoV-2 Variants by Molecular Dynamics Resembles Phylogenetic Tree",
+    "rel_date": "2023-11-29",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.28.568639",
+    "rel_abs": "The COVID-19 pandemics has demonstrated the vulnerability of our societies to viral infectious disease. The mitigation of COVID-19 was complicated by the emergence of Variants of Concern (VOCs) with varying properties including increased transmissibility and immune evasion. Traditional population sequencing proved to be slow and not conducive for timely action. To tackle this challenge, we introduce the Persistence Score (PS) that assesses the pandemic potential of VOCs based on molecular dynamics of the interactions between the SARS-CoV-2 Receptor Binding Domain (RBD) and the ACE2 residues. Our mechanism-based classification approach successfully grouped VOCs into clinically relevant subgroups with higher sensitivity than classical affinity estimations and allows for risk assessment of hypothetical new VOCs. The PS-based interaction analysis across VOCs resembled the phylogenetic tree of SARS-Cov-2 demonstrating its predictive relevance for pandemic preparedness. Thus, PS allows for early detection of a variant's pandemic potential, and an early risk evaluation for data-driven policymaking.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Thais Arns",
+        "author_inst": "Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, avenue du Swing, L-4367, Belvaux, Luxembourg"
+      },
+      {
+        "author_name": "Aymeric Fouquier dHerouel",
+        "author_inst": "Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, avenue du Swing, L-4367, Belvaux, Luxembourg."
+      },
+      {
+        "author_name": "Patrick May",
+        "author_inst": "Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, avenue du Swing, L-4367, Belvaux, Luxembourg"
+      },
+      {
+        "author_name": "Alexandre Tkatchenko",
+        "author_inst": "Department of Physics and Material Science, University of Luxembourg, 6, avenue de la Faiencerie, L-2311, Limpertsberg, Luxembourg."
+      },
+      {
+        "author_name": "Alexander Skupin",
+        "author_inst": "Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6, avenue du Swing, L-4367, Belvaux, Luxembourg"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "bioinformatics"
+  },
+  {
+    "rel_doi": "10.1101/2023.11.28.569052",
+    "rel_title": "copepodTCR: Identification of Antigen-Specific T Cell Receptors with combinatorial peptide pooling",
+    "rel_date": "2023-11-29",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.28.569052",
+    "rel_abs": "T cell receptor (TCR) repertoire diversity enables the orchestration of antigen-specific immune responses against the vast space of possible pathogens. Identifying TCR/antigen binding pairs from the large TCR repertoire and antigen space is crucial for biomedical research. Here, we introduce copepodTCR, an open-access tool for the design and interpretation of high-throughput experimental assays to determine TCR specificity. copepodTCR implements a combinatorial peptide pooling scheme for efficient experimental testing of T cell responses against large overlapping peptide libraries, useful for \"deorphaning\" TCRs of unknown specificity. The scheme detects experimental errors and, coupled with a hierarchical Bayesian model for unbiased results interpretation, identifies the response-eliciting peptide for a TCR of interest out of hundreds of peptides tested using a simple experimental set-up. We experimentally validated our approach on a library of 253 overlapping peptides covering the SARS-CoV-2 spike protein. We provide experimental guides for efficient design of larger screens covering thousands of peptides which will be crucial for the identification of antigen-specific T cells and their targets from limited clinical material.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Vasilisa A Kovaleva",
+        "author_inst": "Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA"
+      },
+      {
+        "author_name": "David J Pattinson",
+        "author_inst": "Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA"
+      },
+      {
+        "author_name": "Carl Barton",
+        "author_inst": "Birkbeck, University of London, WC1E 7HX London, UK"
+      },
+      {
+        "author_name": "Sarah R Chapin",
+        "author_inst": "Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA"
+      },
+      {
+        "author_name": "Anastasia A Minerva",
+        "author_inst": "Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA"
+      },
+      {
+        "author_name": "Katherine A Richards",
+        "author_inst": "David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642"
+      },
+      {
+        "author_name": "Andrea J Sant",
+        "author_inst": "David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642"
+      },
+      {
+        "author_name": "Paul G Thomas",
+        "author_inst": "Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA"
+      },
+      {
+        "author_name": "Mikhail V Pogorelyy",
+        "author_inst": "Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA"
+      },
+      {
+        "author_name": "Hannah V Meyer",
+        "author_inst": "Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
+  {
+    "rel_doi": "10.1101/2023.11.28.569051",
+    "rel_title": "Functional and antigenic characterization of SARS-CoV-2 spike fusion peptide by deep mutational scanning",
+    "rel_date": "2023-11-29",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.28.569051",
+    "rel_abs": "The fusion peptide of SARS-CoV-2 spike protein is functionally important for membrane fusion during virus entry and is part of a broadly neutralizing epitope. However, sequence determinants at the fusion peptide and its adjacent regions for pathogenicity and antigenicity remain elusive. In this study, we performed a series of deep mutational scanning (DMS) experiments on an S2 region spanning the fusion peptide of authentic SARS-CoV-2 in different cell lines and in the presence of broadly neutralizing antibodies. We identified mutations at residue 813 of the spike protein that reduced TMPRSS2-mediated entry with decreased virulence. In addition, we showed that an F823Y mutation, present in bat betacoronavirus HKU9 spike protein, confers resistance to broadly neutralizing antibodies. Our findings provide mechanistic insights into SARS-CoV-2 pathogenicity and also highlight a potential challenge in developing broadly protective S2-based coronavirus vaccines.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Ruipeng Lei",
+        "author_inst": "School of Molecular & Cellular Biology, College of Liberal Arts and Sciences, The University of Illinois at Urbana-Champaign"
+      },
+      {
+        "author_name": "Enya Qing",
+        "author_inst": "University of Illinois at Urbana Champaign"
+      },
+      {
+        "author_name": "Abby Odle",
+        "author_inst": "University of Iowa"
+      },
+      {
+        "author_name": "Meng Yuan",
+        "author_inst": "The Scripps Research Institute"
+      },
+      {
+        "author_name": "Timothy J.C. Tan",
+        "author_inst": "University of Illinois Urbana-Champaign"
+      },
+      {
+        "author_name": "Natalie So",
+        "author_inst": "University of Illinois at Urbana-Champaign"
+      },
+      {
+        "author_name": "Wenhao O Ouyang",
+        "author_inst": "University of Illinois at Urbana-Champaign"
+      },
+      {
+        "author_name": "Ian A. Wilson",
+        "author_inst": "The Scripps Research Institute"
+      },
+      {
+        "author_name": "Tom Gallagher",
+        "author_inst": "Loyola University Chicago"
+      },
+      {
+        "author_name": "Stanley Perlman",
+        "author_inst": "University of Iowa"
+      },
+      {
+        "author_name": "Nicholas C. Wu",
+        "author_inst": "University of Illinois at Urbana-Champaign"
+      },
+      {
+        "author_name": "Lok Yin Roy Wong",
+        "author_inst": "Rutgers Biomedical and Health Sciences"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
+  {
+    "rel_doi": "10.1101/2023.11.28.23299080",
+    "rel_title": "Unveiling Vulnerabilities in Maternal-Child Health amidst COVID-19: A Cross-Sectional Study on Food Insecurity and Socio-Demographic Disparities in the U.S.",
+    "rel_date": "2023-11-29",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.28.23299080",
+    "rel_abs": "Objective: Early infancy is a critical time of development when stresses, nutritional deficiencies, and other challenges have lifelong consequences. Social distancing regulations due to the COVID-19 pandemic in 2020 led to abrupt changes in work status, childcare accessibility, and food availability. Design: This cross-sectional study assessed responses regarding experiences during the COVID-19 pandemic, including food insecurity (validated two-question screener), WIC use, and changes in childcare accessibility and work status. Data were assessed using logistic regressions while controlling for sociodemographic factors. Setting: National U.S. online survey in July-August 2020. Participants: U.S. mothers (n=1861) with infants less than or equal to 12 months old. Results: We detected a 34% increase in perceived food insecurity during July-August 2020 compared to that before the pandemic. Hispanic mothers had 74% higher odds of becoming food insecure than non-Hispanic White mothers. Mothers with infants <9 weeks old had a 7% increase in WIC utilization, although no overall increase in WIC usage was detected. Most mothers (71%) reported moderate or extreme impacts from the pandemic, with higher odds associated with childcare interruptions, working from home, and identifying as Hispanic or non-Hispanic Black. Conclusions: Our findings reveal specific sociodemographic groups of mothers with infants who were especially vulnerable during the COVID-19 pandemic. These insights hold significant value for tailoring supportive programs, equipping these groups for potential socioeconomic upheavals, and aiding their transition into the post-pandemic world.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Zoe Henkes",
+        "author_inst": "Saint Louis University School of Medicine"
+      },
+      {
+        "author_name": "Maria Romo-Palafox",
+        "author_inst": "Saint Louis University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "nutrition"
+  },
+  {
+    "rel_doi": "10.1101/2023.11.27.23299097",
+    "rel_title": "Tracking the impact of government response to COVID-19 epidemic: Evidence from India",
+    "rel_date": "2023-11-29",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.27.23299097",
+    "rel_abs": "This paper tries to quantify the impact of government policy intervention on the death due to COVID-19 in India at national, regional and sub-national levels. The data used for this study are collected from the Oxford COVID-19 Government Response Tracker (OxCGRT), a longitudinal database of daily government response from Jan 28th, 2020, when the first COVID case was diagnosed in India till December 31st, 2022. Here, stringency measures, which gauge the severity of interventions such as lock-downs and travel restrictions, indicative of government control; and containment measures, representing a spectrum of actions aimed at preventing or limiting virus transmission and the overall government support, providing a holistic assessment of the government's efforts in mitigating the virus's spread. Using the Panel Corrected Standard Error (PCSE) method, this paper finds out that the stringency and overall government support interventions by the government have been successful in reducing the death counts by 25% and 23% respectively however the containment intervention alone has failed to reduce the death at all levels. Exploring regional variations, event study plots reveal nuanced temporal dynamics. The daily and 24-day lagged dependent variables, representing overall government response and stringency measures, reveal a consistent impact post-intervention at the all-India level. Both current and lagged variables show a reduction in COVID-19 deaths, with a more pronounced effect emerging after a four-day lag. Event-study plots with a 24-day lagged dependent variable confirm the anticipated negative impact of overall government response on deaths. However, the pattern diverges for stringency and overall government interventions compared to daily death counts.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Kaibalyapati Mishra",
+        "author_inst": "Institute for Social and Economic Change"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health economics"
+  },
+  {
+    "rel_doi": "10.1101/2023.11.27.23298847",
+    "rel_title": "SARS-CoV-2 Orphan Gene ORF10 Contributes to More Severe COVID-19 Disease",
+    "rel_date": "2023-11-29",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.27.23298847",
+    "rel_abs": "The orphan gene of SARS-CoV-2, ORF10, is the least stud- ied gene in the virus responsible for the COVID-19 pandemic. Recent experimentation indicated ORF10 expression moder- ates innate immunity in vitro. However, whether ORF10 af- fects COVID-19 in humans remained unknown. We determine that the ORF10 sequence is identical to the Wuhan-Hu-1 ances- tral haplotype in 95% of genomes across five variants of con- cern (VOC). Four ORF10 variants are associated with less vir- ulent clinical outcomes in the human host: three of these af- fect ORF10 protein structure, one affects ORF10 RNA struc- tural dynamics. RNA-Seq data from 2070 samples from di- verse human cells and tissues reveals ORF10 accumulation is conditionally discordant from that of other SARS-CoV-2 tran- scripts. Expression of ORF10 in A549 and HEK293 cells per- turbs immune-related gene expression networks, alters expres- sion of the majority of mitochondrially-encoded genes of oxida- tive respiration, and leads to large shifts in levels of 14 newly- identified transcripts. We conclude ORF10 contributes to more severe COVID-19 clinical outcomes in the human host.",
+    "rel_num_authors": 19,
+    "rel_authors": [
+      {
+        "author_name": "Jeffrey A Haltom",
+        "author_inst": "Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA"
+      },
+      {
+        "author_name": "Nidia S Trovao",
+        "author_inst": "Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892, USA"
+      },
+      {
+        "author_name": "Joseph Guarnieri",
+        "author_inst": "Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA"
+      },
+      {
+        "author_name": "Pan, Vincent",
+        "author_inst": "Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892, USA"
+      },
+      {
+        "author_name": "Urminder Singh",
+        "author_inst": "Bioinformatics and Computational Biology Program, and Genetics Program, Iowa State University, Ames, IA 50011, USA"
+      },
+      {
+        "author_name": "Sergey Tsoy",
+        "author_inst": "Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA"
+      },
+      {
+        "author_name": "Collin A O'Leary",
+        "author_inst": "Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA"
+      },
+      {
+        "author_name": "Yaron Bram",
+        "author_inst": "Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA"
+      },
+      {
+        "author_name": "Gabrielle A Widjaja",
+        "author_inst": "Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA"
+      },
+      {
+        "author_name": "Zimu Cen",
+        "author_inst": "Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA"
+      },
+      {
+        "author_name": "Robert, Meller",
+        "author_inst": "Morehouse School of Medicine, Atlanta, GA , 30310-1495, USA"
+      },
+      {
+        "author_name": "Stephen B Baylin",
+        "author_inst": "Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231"
+      },
+      {
+        "author_name": "Walter N Moss",
+        "author_inst": "Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA"
+      },
+      {
+        "author_name": "Basil J Nikolau",
+        "author_inst": "Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA"
+      },
+      {
+        "author_name": "Francisco J Enguita",
+        "author_inst": "Instituto de Medicina Molecular Joao Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal"
+      },
+      {
+        "author_name": "Douglas C Wallace",
+        "author_inst": "Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA"
+      },
+      {
+        "author_name": "Afshin Beheshti",
+        "author_inst": "COVID-19 International Research Team, Medford, MA 02155, USA"
+      },
+      {
+        "author_name": "Robert Schwartz",
+        "author_inst": "Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA"
+      },
+      {
+        "author_name": "Eve Syrkin Wurtele",
+        "author_inst": "Bioinformatics and Computational Biology Program, and Genetics Program, Iowa State University, Ames, IA 50011, USA"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health informatics"
+  },
   {
     "rel_doi": "10.1101/2023.11.28.23298927",
     "rel_title": "Social determinants of adult COVID-19 vaccine acceptance and uptake in a Brazilian urban informal community: a longitudinal time-to-event study",
@@ -73,6 +359,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "emergency medicine"
   },
+  {
+    "rel_doi": "10.1101/2023.11.28.568860",
+    "rel_title": "Expression and fusogenic activity of SARS CoV-2 Spike protein displayed in the HSV-1 Virion.",
+    "rel_date": "2023-11-28",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.28.568860",
+    "rel_abs": "Severe acute respiratory syndrome coronavirus (SARS-CoV) is a zoonotic pathogen that can cause severe respiratory disease in humans. The new SARS-CoV-2 is the cause of the current global pandemic termed coronavirus disease 2019 (COVID-19) that has resulted in many millions of deaths world-wide. The virus is a member of the Betacoronavirus family, its genome is a positive strand RNA molecule that encodes for many genes which are required for virus genome replication as well as for structural proteins that are required for virion assembly and maturation. A key determinant of this virus is the Spike (S) protein embedded in the virion membrane and mediates attachment of the virus to the receptor (ACE2). This protein also is required for cell-cell fusion (syncytia) that is an important pathogenic determinant. We have developed a pseudotyped herpes simplex virus type 1 (HSV-1) recombinant virus expressing S protein in the virion envelop. This virus has also been modified to express a Venus fluorescent protein fusion to VP16, a virion protein of HSV-1. The virus expressing Spike can enter cells and generates large multi-nucleated syncytia which are evident by the Venus fluorescence. The HSV-1 recombinant virus is genetically stable and virus amplification can be easily done by infecting cells. This recombinant virus provides a reproducible platform for Spike function analysis and thus adds to the repertoire of pseudotyped viruses expressing Spike.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Prashant J Desai",
+        "author_inst": "Johns Hopkins University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2023.11.24.568354",
     "rel_title": "Antiviral innate immune memory in alveolar macrophages following SARS-CoV-2 infection.",
@@ -142,7 +447,7 @@
     "rel_date": "2023-11-27",
     "rel_site": "bioRxiv",
     "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.25.568685",
-    "rel_abs": "The sex disparity in COVID-19 outcomes with males generally faring worse than females has been associated with the androgen-regulated expression of the protease TMPRSS2 and the cell receptor ACE2 in the lung and fueled interest in antiandrogens as potential antivirals. In this study, we explored enzalutamide, an antiandrogen used commonly against prostate cancer, as a potential antiviral against the human coronaviruses which cause seasonal respiratory infections (HCoV-NL63, -229E, and -OC43). Using lentivirus-pseudotyped and authentic HCoV, we report that enzalutamide reduced 229E and NL63 entry and replication in both TMPRSS2- and non-expressing immortalised cells, suggesting a TMPRSS2-independent mechanism. However, no effect was observed against OC43. To decipher this distinction, we performed RNA-sequencing analysis on 229E- and OC43-infected primary human airway cells. Our results show a significant induction of androgen-responsive genes by 229E compared to OC43 at 24 and 72h post-infection. The virus-mediated effect to AR signaling was further confirmed with a consensus androgen response element (ARE)-driven luciferase assay in androgen-depleted MRC-5 cells. Specifically, 229E induced luciferase reporter activity in the presence and absence of the synthetic androgen mibolerone, while OC43 inhibited induction. These findings highlight a complex interplay between viral infections and androgen signaling, offering insights for potential antiviral interventions.",
+    "rel_abs": "The sex disparity in COVID-19 outcomes with males generally faring worse than females has been associated with the androgen-regulated expression of the protease TMPRSS2 and the cell receptor ACE2 in the lung and fueled interest in antiandrogens as potential antivirals. In this study, we explored enzalutamide, an antiandrogen used commonly against prostate cancer, as a potential antiviral against the human coronaviruses which cause seasonal respiratory infections (HCoV-NL63, -229E, and -OC43). Using lentivirus-pseudotyped and authentic HCoV, we report that enzalutamide reduced 229E and NL63 entry and replication in both TMPRSS2- and non-expressing immortalised cells, suggesting a TMPRSS2-independent mechanism. However, no effect was observed against OC43. To decipher this distinction, we performed RNA-sequencing analysis on 229E-and OC43- infected primary human airway cells. Our results show a significant induction of androgen-responsive genes by 229E compared to OC43 at 24 and 72h post-infection. The virus-mediated effect to AR signaling was further confirmed with a consensus androgen response element (ARE)-driven luciferase assay in androgen-depleted MRC-5 cells. Specifically, 229E induced luciferase reporter activity in the presence and absence of the synthetic androgen mibolerone, while OC43 inhibited induction. These findings highlight a complex interplay between viral infections and androgen signaling, offering insights for potential antiviral interventions.",
     "rel_num_authors": 8,
     "rel_authors": [
       {
@@ -189,7 +494,7 @@
     "rel_date": "2023-11-27",
     "rel_site": "bioRxiv",
     "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.25.568642",
-    "rel_abs": "To better understand the role of pHsp90 adjuvant in immune response modulation, we proposed the use of the Receptor Binding Domain (RBD) of the Spike protein of SARS-CoV2, the principal candidate in the design of subunit vaccines. We evaluated the humoral and cellular immune responses against RBD through the strategy protein mixture (Adjuvant + Antigen). The rRBD adjuvanted with rAtHsp81.2 group showed a higher increase of the anti-rRBD IgG1, while the rRBD adjuvanted with rNbHsp90.3 group showed a significant increase of anti-rRBD IgG2b/2a. These results were consistent with the cellular immune response analysis. Spleen cell cultures from rRBD+rNbHsp90.3-immunized mice showed significantly increased IFN-{gamma} production. In contrast, spleen cell cultures from rRBD+rAtHsp81.2-immunized mice showed significant increased IL-4 levels. Finally, vaccines adjuvanted with rNbHsp90.3 induced higher neutralizing antibody responses compared to those adjuvanted with rAtHsp81.2. To know whether both chaperones must form complexes to generate an effective immune response, we performed co-immunoprecipitation (co-IP) assays. The results indicated that the greater neutralizing capacity observed in the rRBD adjuvanted with rNbHsp90.3 group would be given by the rRBD-rNbHsp90.3 interaction rather than by the quality of the immune response triggered by the adjuvants. These results, together with our previous results, provide a comparative benchmark of these two novel and safe vaccine adjuvants for their capacity to stimulate immunity to a subunit vaccine, demonstrating the capacity of adjuvanted SARS-CoV2 subunit vaccines. Furthermore, these results revealed differences in the ability to modulate the immune response between these two pHsp90s, highlighting the importance of adjuvant selection for future rational vaccine and adjuvant design.",
+    "rel_abs": "To better understand the role of pHsp90 adjuvant in immune response modulation, we proposed the use of the Receptor Binding Domain (RBD) of the Spike protein of SARS-CoV2, the principal candidate in the design of subunit vaccines. We evaluated the humoral and cellular immune responses against RBD through the strategy \"protein mixture\" (Adjuvant + Antigen). The rRBD adjuvanted with rAtHsp81.2 group showed a higher increase of the anti-rRBD IgG1, while the rRBD adjuvanted with rNbHsp90.3 group showed a significant increase of anti-rRBD IgG2b/2a. These results were consistent with the cellular immune response analysis. Spleen cell cultures from rRBD+rNbHsp90.3-immunized mice showed significantly increased IFN-{gamma} production. In contrast, spleen cell cultures from rRBD+rAtHsp81.2-immunized mice showed significant increased IL-4 levels. Finally, vaccines adjuvanted with rNbHsp90.3 induced higher neutralizing antibody responses compared to those adjuvanted with rAtHsp81.2. To know whether both chaperones must form complexes to generate an effective immune response, we performed co-immunoprecipitation (co-IP) assays. The results indicated that the greater neutralizing capacity observed in the rRBD adjuvanted with rNbHsp90.3 group would be given by the rRBD-rNbHsp90.3 interaction rather than by the quality of the immune response triggered by the adjuvants. These results, together with our previous results, provide a comparative benchmark of these two novel and safe vaccine adjuvants for their capacity to stimulate immunity to a subunit vaccine, demonstrating the capacity of adjuvanted SARS-CoV2 subunit vaccines. Furthermore, these results revealed differences in the ability to modulate the immune response between these two pHsp90s, highlighting the importance of adjuvant selection for future rational vaccine and adjuvant design.",
     "rel_num_authors": 11,
     "rel_authors": [
       {
@@ -248,7 +553,7 @@
     "rel_date": "2023-11-27",
     "rel_site": "bioRxiv",
     "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.25.568670",
-    "rel_abs": "Since the emergence of SARS-CoV-2 in Wuhan in 2019 its host reservoir has not been established. Phylogenetic analysis was performed on whole genome sequences (WGS) of 71 coronaviruses and a Breda virus. A subset comprising two SARS-CoV-2 Wuhan viruses and 8 of the most closely related coronavirus sequences were used for host reservoir analysis using Bayesian Evolutionary Analysis Sampling Trees (BEAST). Within these genomes, 20 core genome fragments were combined into 2 groups each with similar clock rates (5.9x10 -3 and 1.1x10 -3 subs/site/year). Pooling the results from these fragment groups yielded a most recent common ancestor (MRCA) shared between SARS-COV-2 and the bat isolate RaTG13 around 2007 (95% HPD: 2003, 2011). Further, the host of the MRCA was most likely a bat (probability 0.64 - 0.87). Hence, the spillover into humans must have occurred at some point between 2007 and 2019 and bats may have been the most likely host reservoir.",
+    "rel_abs": "1Since the emergence of SARS-CoV-2 in Wuhan in 2019 its host reservoir has not been established. Phylogenetic analysis was performed on whole genome sequences (WGS) of 71 coronaviruses and a Breda virus. A subset comprising two SARS-CoV-2 Wuhan viruses and 8 of the most closely related coronavirus sequences were used for host reservoir analysis using Bayesian Evolutionary Analysis Sampling Trees (BEAST). Within these genomes, 20 core genome fragments were combined into 2 groups each with similar clock rates (5.9x10-3 and 1.1x10-3 subs/site/year). Pooling the results from these fragment groups yielded a most recent common ancestor (MRCA) shared between SARS-COV-2 and the bat isolate RaTG13 around 2007 (95% HPD: 2003, 2011). Further, the host of the MRCA was most likely a bat (probability 0.64 - 0.87). Hence, the spillover into humans must have occurred at some point between 2007 and 2019 and bats may have been the most likely host reservoir.",
     "rel_num_authors": 3,
     "rel_authors": [
       {
@@ -322,7 +627,7 @@
     "rel_date": "2023-11-27",
     "rel_site": "bioRxiv",
     "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.27.568815",
-    "rel_abs": "Emerging viral infections, especially the global pandemic COVID-19, have had catastrophic impacts on public health worldwide. The culprit of this pandemic, SARS-CoV-2, continues to evolve, giving rise to numerous sublineages with distinct characteristics. The traditional post-hoc wet-lab approach is lagging behind, and it cannot quickly predict the evolutionary trends of the virus while consuming high costs. Capturing the evolutionary drivers of virus and predicting potential high-risk mutations has become an urgent and critical problem to address. To tackle this challenge, we introduce ProtFound-V, an evolution-inspired deep-learning framework designed to explore the mutational trajectory of virus. Take SARS-CoV-2 as an example, ProtFound-V accurately identifies the evolutionary advantage of Omicron and proposes evolutionary trends consistent with wet-lab experiments through in silico deep mutational scanning. This showcases the potential of deep learning predictions to replace traditional wet-lab experimental measurements. With the evolution-guided large language model, ProtFound-V presents a new state-of-the-art performance in key property predictions. Despite the challenge posed by epistasis to model generalization, ProtFound-V remains robust when extrapolating to lineages with different genetic backgrounds. Overall, this work paves the way for rapid responses to emerging viral infections, allowing for a plug-and-play approach to understanding and predicting virus evolution.",
+    "rel_abs": "Emerging viral infections, especially the global pandemic COVID-19, have had catastrophic impacts on public health worldwide. The culprit of this pandemic, SARS-CoV-2, continues to evolve, giving rise to numerous sublineages with distinct characteristics. The traditional post-hoc wet-lab approach is lagging behind, and it cannot quickly predict the evolutionary trends of the virus while consuming high costs. Capturing the evolutionary drivers of virus and predicting potential high-risk mutations has become an urgent and critical problem to address. To tackle this challenge, we introduce ProtFound-V, an evolution-inspired deeplearning framework designed to explore the mutational trajectory of virus. Take SARS-CoV-2 as an example, ProtFound-V accurately identifies the evolutionary advantage of Omicron and proposes evolutionary trends consistent with wetlab experiments through in silico deep mutational scanning. This showcases the potential of deep learning predictions to replace traditional wet-lab experimental measurements. With the evolution-guided large language model, ProtFound-V presents a new state-of-the-art performance in key property predictions. Despite the challenge posed by epistasis to model generalization, ProtFound-V remains robust when extrapolating to lineages with different genetic backgrounds. Overall, this work paves the way for rapid responses to emerging viral infections, allowing for a plug-and-play approach to understanding and predicting virus evolution.",
     "rel_num_authors": 13,
     "rel_authors": [
       {
@@ -543,7 +848,7 @@
     "rel_date": "2023-11-27",
     "rel_site": "medRxiv",
     "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.24.23298995",
-    "rel_abs": "Objectives: Substance use disorder has been associated with increased morbidity in COVID-19 infection. However, less is known about the impact of active substance use and medications for opioid use disorder (MOUD) on COVID-19 outcomes. We conducted a retrospective cohort study to evaluate the impact of substance use, namely cannabis, cocaine, alcohol, sedative and opioid use as well as buprenorphine or methadone = on COVID-19 morbidity and mortality. Methods: Using electronic-health record data at a large urban hospital system, patients who tested positive for COVID-19 between January 1, 2020 to December 31, 2021 were included. Substance use was identified from urine toxicology and MOUD prescriptions within 90 days prior to admission. COVID-19 outcomes included mortality, ICU admission, need for ventilatory support, number and duration of hospitalizations. Multivariable logistic regression was performed controlling for variables such as age, sex, medical comorbidity, tobacco use, and social disadvantage. Results: Among COVID-19 positive patients (n=17,423), sedative, cannabis, cocaine, and opioid use was associated with statistically significant increases in need for ICU care, need for ventilatory support, number of hospitalizations and duration of hospitalization. Substance use was not associated with an increase in all-cause mortality. There were no statistically significant differences between methadone, buprenorphine and other opioids on COVID-19 outcomes. Conclusions: Active substance use were associated with increased morbidity in COVID-19 infection. MOUD was not associated with worse COVID-19 outcomes compared to OUD. Future studies focused on MOUD treatments that reduce morbidity may help improve clinical outcomes in COVID-19.",
+    "rel_abs": "ObjectivesSubstance use disorder has been associated with increased morbidity in COVID-19 infection. However, less is known about the impact of active substance use and medications for opioid use disorder (MOUD) on COVID-19 outcomes. We conducted a retrospective cohort study to evaluate the impact of substance use, namely cannabis, cocaine, alcohol, sedative and opioid use as well as buprenorphine or methadone = on COVID-19 morbidity and mortality.\n\nMethodsUsing electronic-health record data at a large urban hospital system, patients who tested positive for COVID-19 between January 1, 2020 to December 31, 2021 were included. Substance use was identified from urine toxicology and MOUD prescriptions within 90 days prior to admission. COVID-19 outcomes included mortality, ICU admission, need for ventilatory support, number and duration of hospitalizations. Multivariable logistic regression was performed controlling for variables such as age, sex, medical comorbidity, tobacco use, and social disadvantage.\n\nResultsAmong COVID-19 positive patients (n=17,423), sedative, cannabis, cocaine, and opioid use was associated with statistically significant increases in need for ICU care, need for ventilatory support, number of hospitalizations and duration of hospitalization. Substance use was not associated with an increase in all-cause mortality. There were no statistically significant differences between methadone, buprenorphine and other opioids on COVID-19 outcomes.\n\nConclusionsActive substance use were associated with increased morbidity in COVID-19 infection. MOUD was not associated with worse COVID-19 outcomes compared to OUD. Future studies focused on MOUD treatments that reduce morbidity may help improve clinical outcomes in COVID-19.",
     "rel_num_authors": 3,
     "rel_authors": [
       {
@@ -824,7 +1129,7 @@
     "rel_date": "2023-11-27",
     "rel_site": "medRxiv",
     "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.24.23299005",
-    "rel_abs": "Background: Syndromic surveillance utilising primary health care (PHC) data is a valuable tool for early outbreak detection, as demonstrated in the potential to identify COVID-19 outbreaks. However, the potential of such an early warning system in the post-COVID-19 era remains largely unexplored. Methods: We analysed PHC encounter counts due to respiratory complaints registered in the Brazilian database of the Universal Health System between January and July 2023. We applied EARS (variation C1-C2-C3) and EVI to estimate the weekly thresholds. An alarm was determined when the number of encounters exceeded the week-specific threshold. We used data on hospitalisation due to respiratory disease to classify weeks in which the number of cases surpassed predetermined thresholds as anomalies. We compared EARS and EVI's efficacy in anticipating anomalies. Findings: A total of 119 anomalies were identified across 116 immediate regions during the study period. The EARS-C2 presented the highest early alarm rate, with 81/119 (68%) early alarms, and C1 the lowest, with 71 (60%) early alarms. The lowest true positivity was the EARS-C1 118/1354 (8.7%) and the highest EARS-C3 99/856 (11.6%). Conclusion: Routinely collected PHC data can be successfully used to detect respiratory disease outbreaks in Brazil. Syndromic surveillance enhances timeliness in surveillance strategies, albeit with lower specificity. A combined approach with other strategies is essential to strengthen accuracy, offering a proactive and effective public health response against future outbreaks.",
+    "rel_abs": "BackgroundSyndromic surveillance utilising primary health care (PHC) data is a valuable tool for early outbreak detection, as demonstrated in the potential to identify COVID-19 outbreaks. However, the potential of such an early warning system in the post-COVID-19 era remains largely unexplored.\n\nMethodsWe analysed PHC encounter counts due to respiratory complaints registered in the Brazilian database of the Universal Health System between January and July 2023. We applied EARS (variation C1-C2-C3) and EVI to estimate the weekly thresholds. An alarm was determined when the number of encounters exceeded the week-specific threshold. We used data on hospitalisation due to respiratory disease to classify weeks in which the number of cases surpassed predetermined thresholds as anomalies. We compared EARS and EVIs efficacy in anticipating anomalies.\n\nFindingsA total of 119 anomalies were identified across 116 immediate regions during the study period. The EARS-C2 presented the highest early alarm rate, with 81/119 (68%) early alarms, and C1 the lowest, with 71 (60%) early alarms. The lowest true positivity was the EARS-C1 118/1354 (8.7%) and the highest EARS-C3 99/856 (11.6%).\n\nConclusionRoutinely collected PHC data can be successfully used to detect respiratory disease outbreaks in Brazil. Syndromic surveillance enhances timeliness in surveillance strategies, albeit with lower specificity. A combined approach with other strategies is essential to strengthen accuracy, offering a proactive and effective public health response against future outbreaks.",
     "rel_num_authors": 10,
     "rel_authors": [
       {
@@ -1520,57 +1825,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "oncology"
   },
-  {
-    "rel_doi": "10.1101/2023.11.24.568532",
-    "rel_title": "Isogenic iPSC-derived proximal and distal lung-on-chip models: Tissue- and virus-specific immune responses in human lungs",
-    "rel_date": "2023-11-24",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.24.568532",
-    "rel_abs": "Micro-physiological systems (MPS) are set to play a vital role in preclinical studies, particularly in the context of future viral pandemics. Nonetheless, the development of MPS is often impeded by the scarcity of reliable cell sources, especially when seeking various organs or tissues from a single patient for comparative analysis of the host immune response. Herein, we developed human airway-on-chip and alveolus-on-chip models using induced pluripotent stem cell (iPSC)-derived isogenic lung progenitor cells. Both models demonstrated the replication of two different respiratory viruses, namely SARS-CoV-2 and Influenza, as well as related cellular damage and innate immune responses-on-chip. Our findings reveal distinct immune responses to SARS-CoV-2 in the proximal and distal lung-on-chip models. The airway chips exhibited a robust interferon (IFN)-dependent immune response, whereas the alveolus chips exhibited dysregulated IFN activation but a significantly upregulated chemokine pathway. In contrast, Influenza virus infection induced a more pronounced immune response and cellular damage in both chip models compared to SARS-CoV-2. Thus, iPSC-derived lung-on-chip models may aid in quickly gaining insights into viral pathology and screening potential drugs for future pandemics.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Sachin Yadav",
-        "author_inst": "Department of Micro Engineering, Kyoto University, Kyoto 615-8540, Japan;  CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan"
-      },
-      {
-        "author_name": "Kazuya Fujimoto",
-        "author_inst": "Department of Micro Engineering, Kyoto University, Kyoto 615-8540, Japan;  CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan"
-      },
-      {
-        "author_name": "Toru Takenaga",
-        "author_inst": "CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan; Institute of Frontier Life and Medical Science, Kyoto University, Kyoto 606-8507, Japan; Gr"
-      },
-      {
-        "author_name": "Senye Takahashi",
-        "author_inst": "CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan; Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan"
-      },
-      {
-        "author_name": "Yukiko Muramoto",
-        "author_inst": "CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan; Institute of Frontier Life and Medical Science, Kyoto University, Kyoto 606-8507, Japan; Gr"
-      },
-      {
-        "author_name": "Ryuta Mikawa",
-        "author_inst": "CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan; Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan; Depa"
-      },
-      {
-        "author_name": "Takeshi Noda",
-        "author_inst": "CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan; Institute of Frontier Life and Medical Science, Kyoto University, Kyoto 606-8507, Japan; Gr"
-      },
-      {
-        "author_name": "Shimpei Gotoh",
-        "author_inst": "CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan; Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan; Depa"
-      },
-      {
-        "author_name": "Ryuji Yokokawa",
-        "author_inst": "Department of Micro Engineering, Kyoto University, Kyoto 615-8540, Japan; CREST, Japan Science and Technology Agency, Saitama 332-0012, Japan"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "bioengineering"
-  },
   {
     "rel_doi": "10.1101/2023.11.22.568225",
     "rel_title": "Development of attenuated coxsackievirus B3 vectored intranasal pre-emptive pan-coronavirus vaccine",
@@ -1873,6 +2127,113 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2023.11.22.23298899",
+    "rel_title": "Quantitative susceptibility mapping at 7 Tesla in COVID-19: mechanistic and outcome associations",
+    "rel_date": "2023-11-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.22.23298899",
+    "rel_abs": "Post mortem studies have shown that patients dying from severe SARS-CoV-2 infection frequently have pathological changes in their central nervous system, particularly in the brainstem. Many of these changes are proposed to result from para-infectious and/or post-infection immune responses. Clinical symptoms such as fatigue, breathlessness, and chest pain are frequently reported in post-hospitalized COVID-19 patients. We propose that these symptoms are in part due to damage to key neuromodulatory brainstem nuclei. While brainstem involvement has been demonstrated in the acute phase of the illness, the evidence of long-term brainstem change on magnetic resonance imaging (MRI) is inconclusive. We therefore used ultra-high field (7T) quantitative susceptibility mapping (QSM) to test the hypothesis that brainstem abnormalities persist in post-COVID patients and that these are associated with persistence of key symptoms.\n\nWe used 7T QSM data from 30 patients, scanned 93 - 548 days after hospital admission for COVID-19 and compared them to 51 age-matched controls without prior history of COVID-19 infection. We correlated the patients QSM signals with disease severity (duration of hospital admission and COVID-19 severity scale), inflammatory response during the acute illness (C-reactive protein, D-Dimer and platelet levels), functional recovery (modified Rankin scale; mRS), depression (PHQ-9) and anxiety (GAD-7).\n\nIn COVID-19 survivors the MR susceptibility increased in the medulla, pons and midbrain regions of the brainstem. Specifically, there was increased susceptibility in the inferior medullary reticular formation and the raphe pallidus and obscurus. In these regions, patients with higher tissue susceptibility had worse acute disease severity, higher acute inflammatory markers, and significantly worse functional recovery.\n\nUsing non-invasive ultra-high field 7T MRI, we show evidence of brainstem pathophysiological changes associated with inflammatory processes in post-hospitalized COVID-19 survivors. This study contributes to understanding the mechanisms of long-term effects of COVID-19 and recovery.",
+    "rel_num_authors": 23,
+    "rel_authors": [
+      {
+        "author_name": "Catarina Rua",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Betty Raman",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Christopher T Rodgers",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Virginia F J Newcombe",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Anne Manktelow",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Doris A Chatfield",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Stephen J Sawcer",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Joanne G Outtrim",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Victoria C Lupson",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Emmanuel A Stamatakis",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Guy B Williams",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "William T Clarke",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Lin Qiu",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Martyn Ezra",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Rory McDonald",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Stuart Clare",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Mark Cassar",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Stefan Neubauer",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Karen D Ersche",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Edward T Bullmore",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "David K Menon",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Kyle Pattinson",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "James B Rowe",
+        "author_inst": "University of Cambridge"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "neurology"
+  },
   {
     "rel_doi": "10.1101/2023.11.22.23298851",
     "rel_title": "Wastewater monitoring of SARS-CoV-2 gene for COVID-19 epidemiological surveillance in Tucuman Argentina",
@@ -1899,7 +2260,7 @@
         "author_inst": "Laboratorio de Processamento de Sinais e Modelagem de Sistemas Biologicos. Nucleo de Pesquisas Tecnologicas. Universidade Mogi das Cruzes, Sao Paulo, Brasil."
       },
       {
-        "author_name": "Lucila Saavedra",
+        "author_name": "Maria Lucila Saavedra",
         "author_inst": "Centro de Referencia para Lactobacilos (CERELA-CONICET), Tucuman, Argentina"
       },
       {
@@ -1907,7 +2268,7 @@
         "author_inst": "Centro de Referencia para Lactobacilos (CERELA-CONICET), Tucuman, Argentina"
       },
       {
-        "author_name": "Alejandra Martinez",
+        "author_name": "Maria Alejandra Martinez",
         "author_inst": "Planta Piloto de Procesos Industriales Microbiologicos (PROIMI-CONICET), Tucuman, Argentina"
       },
       {
@@ -3222,45 +3583,6 @@
     "type": "new results",
     "category": "biophysics"
   },
-  {
-    "rel_doi": "10.1101/2023.11.20.23298760",
-    "rel_title": "Affect and post-COVID-19 symptoms in daily life: An exploratory experience sampling study",
-    "rel_date": "2023-11-21",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.20.23298760",
-    "rel_abs": "Insight into the daily life experiences of patients with post-COVID-19 syndrome is lacking. The current study explored temporal fluctuations of and associations between positive and negative affect and symptoms throughout the day in previously hospitalised post-COVID-19 patients using an experience sampling methodology. Ten participants (age: median = 60, interquartile range = 9 years; 50% women ; 80% [&ge;]1 comorbidity; 8-12 months since hospital discharge) filled out brief online questionnaires, six times a day for 14 consecutive days. Positive and negative affect, and self-reported symptoms (physical and mental fatigue, cognitive functioning, dyspnoea, and pain) were assessed in real-time. Primarily, graphs were analysed to assess the individual longitudinal courses of and (concurrent and time-lagged) associations between affect and symptoms. Secondly, correlations or multilevel linear regression models were used to support these interpretations. Visual assessment showed limited temporal fluctuation in affect and symptoms. All symptoms appeared to associate positively with each other (correlations between .26 and .85). Positive affect was associated with lower symptoms severity ({beta}s between -.28 and -.67), and negative affect with higher symptoms severity ({beta}s between .24 and .66). Time-lagged analyses showed that - adjusted for residual symptom severity of prior measurements - both types of affect predicted symptom severity two hours later ({beta}s between -.09 and -.31 for positive affect; between .09 and .28 for negative affect). These findings suggest that positive and negative affect may play important roles in post-COVID-19 symptom experience and temporal fluctuation.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Gerko Schaap",
-        "author_inst": "University of Twente Faculty of Behaviourial Management and Social sciences: Universiteit Twente Faculteit Behavioural Management and Social Sciences"
-      },
-      {
-        "author_name": "Marleen Wensink",
-        "author_inst": "University of Twente Faculty of Behaviourial Management and Social sciences: Universiteit Twente Faculteit Behavioural Management and Social Sciences"
-      },
-      {
-        "author_name": "Carine  J. M. Doggen",
-        "author_inst": "Universiteit Twente Technical Medical Centre"
-      },
-      {
-        "author_name": "Job van der Palen",
-        "author_inst": "Medisch Spectrum Twente"
-      },
-      {
-        "author_name": "Harald  E. Vonkeman",
-        "author_inst": "Medisch Spectrum Twente"
-      },
-      {
-        "author_name": "Christina Bode",
-        "author_inst": "University of Twente Faculty of Behaviourial Management and Social sciences: Universiteit Twente Faculteit Behavioural Management and Social Sciences"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2023.11.17.23298696",
     "rel_title": "Association Between COVID-19 During Pregnancy and Preterm Birth by Trimester of Infection: A Retrospective Cohort Study Using Longitudinal Social Media Data",
@@ -3535,7 +3857,7 @@
     "rel_date": "2023-11-20",
     "rel_site": "bioRxiv",
     "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.18.567675",
-    "rel_abs": "COVID-19 continues to spread today, leading to an accumulation of SARS-CoV-2 virus mutations in databases, and large amounts of genomic datasets are currently available. However, due to these large datasets, utilizing this amount of sequence data without random sampling is challenging. Major difficulties for downstream analyses include the increase in the dimension size along with the conversion of sequences into numerical values when using conventional amino acid representation methods, such as one-hot encoding and k-mer-based approaches that directly reflect sequences. Moreover, these sequences are deficient in physicochemical characteristics, such as structural information and hydrophilicity; hence, they fail to accurately represent the inherent function of the given sequences. In this study, we utilized the physicochemical properties of amino acids to develop a rapid and efficient approach for extracting feature parameters that are suitable for downstream processes of machine learning, such as clustering. A fixed-length feature vector representation of a spike sequence with reduced dimensionality was obtained by converting amino acid residues into physicochemical parameters. Next, t-distributed stochastic neighbor embedding (t-SNE), a method for dimensionality reduction and visualization of high-dimensional data, was performed, followed by density-based spatial clustering of applications with noise (DBSCAN). The results show that by using the physicochemical properties of amino acids rather than conventional methods that directly represent sequences into numerical values, SARS-CoV-2 spike sequences can be clustered with sufficient accuracy and a shorter runtime. Interestingly, the clusters obtained by using amino acid properties include subclusters that are distinct from those produced utilizing the method for the direct representation of amino acid sequences. A more detailed analysis indicated that the contributing parameters of this novel cluster identified exclusively when utilizing the physicochemical properties of amino acids significantly differ from one another. This suggests that representing amino acid sequences by physicochemical properties might enable the identification of clusters with enhanced sensitivity compared to conventional methods.",
+    "rel_abs": "COVID-19 continues to spread today, leading to an accumulation of SARS-CoV-2 virus mutations in databases, and large amounts of genomic datasets are currently available. However, due to these large datasets, utilizing this amount of sequence data without random sampling is challenging. Major difficulties for downstream analyses include the increase in the dimension size along with the conversion of sequences into numerical values when using conventional amino acid representation methods, such as one-hot encoding and k-mer-based approaches that directly reflect sequences. Moreover, these sequences are deficient in physicochemical characteristics, such as structural information and hydrophilicity; hence, they fail to accurately represent the inherent function of the given sequences. In this study, we utilized the physicochemical properties of amino acids to develop a rapid and efficient approach for extracting feature parameters that are suitable for downstream processes of machine learning, such as clustering. A fixed-length feature vector representation of a spike sequence with reduced dimensionality was obtained by converting amino acid residues into physicochemical parameters. Next, t-distributed stochastic neighbor embedding (t- SNE), a method for dimensionality reduction and visualization of high-dimensional data, was performed, followed by density-based spatial clustering of applications with noise (DBSCAN). The results show that by using the physicochemical properties of amino acids rather than conventional methods that directly represent sequences into numerical values, SARS-CoV-2 spike sequences can be clustered with sufficient accuracy and a shorter runtime. Interestingly, the clusters obtained by using amino acid properties include subclusters that are distinct from those produced utilizing the method for the direct representation of amino acid sequences. A more detailed analysis indicated that the contributing parameters of this novel cluster identified exclusively when utilizing the physicochemical properties of amino acids significantly differ from one another. This suggests that representing amino acid sequences by physicochemical properties might enable the identification of clusters with enhanced sensitivity compared to conventional methods.\n\nAuthor summaryOne of the major causes of the global threat of SARS-CoV-2 is the rapid emergence of its variants. While analyzing these variants is crucial for understanding the mechanism of outbreaks, the expansion of database size is becoming a barrier for effective analysis. In this study, we provide an approach that allows researchers without vast computational resources to comprehensively analyze the variants of SARS-CoV-2 spike by representing the sequences using the physicochemical properties of amino acids. The result of clusters derived using this method demonstrates not only an accuracy comparable to the conventional approaches of directly converting sequences into numerical values but also indicates the potential for more detailed clustering outcomes. The results suggest that our approach is valuable for the rapid identification of characteristic residues in new variants of SARS-CoV-2 and other viruses that may arise in the future.",
     "rel_num_authors": 8,
     "rel_authors": [
       {
@@ -3635,6 +3957,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2023.11.20.23298741",
+    "rel_title": "Increased Severity of New-onset Type 1 Diabetes in Children and Adolescents during the COVID-19 Pandemic: Experience from a Tertiary Care Center in Serbia",
+    "rel_date": "2023-11-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.20.23298741",
+    "rel_abs": "Background and objectivesPublic health measures, parental fear of infection, and redeployment of medical resources in response to the COVID-19 pandemic might have led to a decrease in pediatric healthcare access. As a result, a delay in type 1 diabetes diagnosis might have occurred, leading to the worsening of its clinical presentation in the pediatric population. This study aimed to examine the clinical and biochemical features of new-onset DM1 in children and adolescents during the COVID-19 pandemic, comparing it to the pre-pandemic period.\n\nMaterials and methodsThe clinical and biochemical features of diabetes observed during the COVID-19 period from April 1, 2020, until December 31, 2022, were compared with the period from April 1, 2017, until December 31, 2019. In the COVID-19 pandemic group, the clinical and biochemical features were compared between children with and without SARS-CoV-2 infection at diagnosis or before the diagnosis of DM1.\n\nResultsDuring the COVID-19 pandemic, observed frequencies of DKA and severe DKA at diagnosis were 47.6% and 20.7%, both significantly higher than during the pre-pandemic period (an absolute increase of 15% and 11.3%, respectively). In the COVID-19 group, blood pH levels were significantly lower than in the pre-pandemic group, while HbA1c levels were higher. Clinical and biochemical features of diabetes in children with SARS-CoV-2 infection at or before the diagnosis were not significantly different compared to children without an infection.\n\nConclusionWe report a significant worsening of the clinical presentation of new-onset type 1 diabetes and an increase in the frequency of DKA and severe DKA at diagnosis during the COVID-19 pandemic. Further studies are necessary to gain quantitative insight into pediatric healthcare availability in Serbia.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Damjan Jovanovic",
+        "author_inst": "Faculty of Medicine, University of Belgrade, Serbia"
+      },
+      {
+        "author_name": "Jelena Blagojevic",
+        "author_inst": "University Children's Hospital, Belgrade, Serbia"
+      },
+      {
+        "author_name": "Dejana Stanisavljevic",
+        "author_inst": "Faculty of Medicine, University of Belgrade, Serbia"
+      },
+      {
+        "author_name": "Maja Jesic",
+        "author_inst": "University Children's Hospital, Belgrade, Serbia"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "pediatrics"
+  },
   {
     "rel_doi": "10.1101/2023.11.20.23298335",
     "rel_title": "Associations between polygenic risk score and COVID-19 severity in Russian population using low-pass genome sequencing",
@@ -5128,57 +5481,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2023.11.14.567145",
-    "rel_title": "CCR5/CXCR3 antagonist TAK-779 prevents diffuse alveolar damage of the lung in murine model of the SARS-CoV-2-related acute respiratory distress syndrome",
-    "rel_date": "2023-11-15",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.14.567145",
-    "rel_abs": "The acute respiratory distress syndrome (ARDS) secondary to viral pneumonitis is one of the main causes of high mortality in patients with COVID-19 (novel coronavirus disease 2019) - ongoing SARS-CoV-2 infection, reached more than 0.7 billion registered cases. Recently we elaborated non- surgical and reproducible method of unilateral total diffuse alveolar damage (DAD) of the left lung in ICR mice - a publicly available imitation of the ARDS caused by SARS-CoV-2. Our data reads that two C-C chemokine receptor 5 (CCR5) ligands - macrophage inflammatory proteins (MIP) - (MIP-1/CCL3) and (MIP-1{beta}/CCL4) are upregulated in this DAD model up to three orders of magnitude compared to the background level. Here we showed that a nonpeptide compound TAK- 779, antagonist of CCR5/CXCR3, readily prevents DAD of the lung with a single injection of 2.5 mg/kg. Histological analysis revealed reduced peribronchial and perivascular mononuclear infiltration in the lung, and mononuclear infiltration of the wall and lumen of the alveoli in the TAK- 779-treated animals. Administration of the TAK-779 decreased 3-5-fold level of serum cytokines and chemokines in animals with DAD, including CCR5 ligands MIP-1/{beta}, MCP-1 and CCL5. Computed tomography revealed rapid recovery of the density and volume of the affected lung in TAK-779- treated animals. Our pre-clinical data suggest that TAK-779 is more effective than administration of dexamethasone or anti-IL6R therapeutic antibody tocilizumab, which brings novel therapeutic modality to TAK-779 and other CCR5 inhibitors recruited in ongoing clinical studies as a potential drugs for treatment of COVID19 and similar virus-induced inflammation syndromes.\n\nAbstract summaryThe pathogenesis of the SARS-CoV-2 infection is tightly linked with the cytokine storm resulting in the enormous release of cytokines and chemokines. Its clinical manifestation - the acute respiratory distress syndrome (ARDS), may be caused by self-sustaining hypersensitivity reactions leading to lung collapse even after virus clearance. Here we report that two macrophage inflammatory proteins, MIP-1/CCL3 and MIP-1{beta}/CCL4, seem to orchestrate mononuclear infiltration into the lungs during diffuse alveolar damage (DAD) in ICR mice - our murine model of ARDS caused by SARS-CoV-2. Inhibition of the C-C chemokine receptor 5 (CCR5) - parental receptor for MIP-1 and MIP-1{beta}, by nonpeptide antagonist TAK-779 results in significant amelioration of DAD in terms of reduced mononuclear infiltration into the lung, suppressed cytokine storm and restored physiology of affected lung according to computed tomography data. We suggest that targeted inhibition of CCR5 should be further elucidated as safe and effective approach to overcome severe viral pneumonia in humans.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Aleksandr Chernov",
-        "author_inst": "Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences: FBGUN Institut bioorganiceskoj himii im akademikov M M Semakina i U A Ovcin"
-      },
-      {
-        "author_name": "Maksim Rodionov",
-        "author_inst": "Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences: FBGUN Institut bioorganiceskoj himii im akademikov M M Semakina i U A Ovcin"
-      },
-      {
-        "author_name": "Vitaly Kazakov",
-        "author_inst": "IBCh RAS: FBGUN Institut bioorganiceskoj himii im akademikov M M Semakina i U A Ovcinnikova Rossijskoj akademii nauk"
-      },
-      {
-        "author_name": "Karina Ivanova",
-        "author_inst": "IBCh RAS: FBGUN Institut bioorganiceskoj himii im akademikov M M Semakina i U A Ovcinnikova Rossijskoj akademii nauk"
-      },
-      {
-        "author_name": "Fedor Mesheryakov",
-        "author_inst": "IBCh RAS: FBGUN Institut bioorganiceskoj himii im akademikov M M Semakina i U A Ovcinnikova Rossijskoj akademii nauk"
-      },
-      {
-        "author_name": "Anna Kudriaeva",
-        "author_inst": "IBCh RAS: FBGUN Institut bioorganiceskoj himii im akademikov M M Semakina i U A Ovcinnikova Rossijskoj akademii nauk"
-      },
-      {
-        "author_name": "Alexander Gabibov",
-        "author_inst": "IBCh RAS: FBGUN Institut bioorganiceskoj himii im akademikov M M Semakina i U A Ovcinnikova Rossijskoj akademii nauk"
-      },
-      {
-        "author_name": "Georgii Telegin",
-        "author_inst": "IBCh RAS: FBGUN Institut bioorganiceskoj himii im akademikov M M Semakina i U A Ovcinnikova Rossijskoj akademii nauk"
-      },
-      {
-        "author_name": "Alexey Belogurov",
-        "author_inst": "IBCh RAS: FBGUN Institut bioorganiceskoj himii im akademikov M M Semakina i U A Ovcinnikova Rossijskoj akademii nauk"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "pathology"
-  },
   {
     "rel_doi": "10.1101/2023.11.15.567102",
     "rel_title": "Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket",
@@ -5469,6 +5771,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2023.11.13.23298463",
+    "rel_title": "A SOLUTION TO THE KERMACK AND MCKENDRICK INTEGRO-DIFFERENTIAL EQUATIONS WHICH ACCURATELY PROJECTS COVID-19 CASE DATA USING GOOGLE MOBILITY DATA AS AN INPUT",
+    "rel_date": "2023-11-13",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.13.23298463",
+    "rel_abs": "In this manuscript, we derive a closed form solution to the full Kermack and McKendrick integro-differential equations (Kermack and McKendrick 1927) which we call the KMES. We demonstrate the veracity of the KMES using the Google Residential Mobility Measure to accurately project case data from the Covid 19 pandemic and we derive many useful, but previously unknown, analytical expressions for characterizing and managing an epidemic. These include expressions for the viral load, the final size, the effective reproduction number, and the time to the peak in infections. The KMES can also be cast in the form of a step function system response to the input of new infections; and that response is the time series of total infections.\n\nSince the publication of Kermack and McKendricks seminal paper (1927), thousands of authors have utilized the Susceptible, Infected, and Recovered (SIR) approximations; expressions putatively derived from the integro-differential equations to model epidemic dynamics. Implicit in the use of the SIR approximation are the beliefs that there is no closed form solution to the integro-differential equations, and that the approximation is a special case which adequately reproduces the dynamics of the integro-differential equations mapped onto the physical world. However, the KMES demonstrates that the SIR approximations are not adequate representations of the integro-differential equations, and we therefore suggest that the KMES obsoletes the need for the SIR approximations by providing not only a new mathematical perspective, but a new understanding of epidemic dynamics.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Theodore G Duclos",
+        "author_inst": "Ted Duclos Advisors"
+      },
+      {
+        "author_name": "Thomas Reichert",
+        "author_inst": "Entropy Research Institute"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2023.11.13.23298464",
     "rel_title": "Assessing the Impact of Mask Mandates on SARS-CoV-2 Transmission: A Case Study of Utah",
@@ -6978,11 +7303,11 @@
       },
       {
         "author_name": "Lei S. Qi",
-        "author_inst": "Stanford University"
+        "author_inst": "Department of Bioengineering & Sarafan ChEM-H, Stanford University"
       },
       {
         "author_name": "W.E. Moerner",
-        "author_inst": "Stanford University"
+        "author_inst": "Department of Bioengineering & Sarafan ChEM-H, Stanford University"
       }
     ],
     "version": "1",
@@ -6990,77 +7315,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2023.11.08.23297633",
-    "rel_title": "Standardization and Comparison of Emergency Use Authorized COVID-19 Assays and Testing Laboratories",
-    "rel_date": "2023-11-08",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.08.23297633",
-    "rel_abs": "SARS-CoV-2, the causal agent of the global COVID-19 pandemic, made its appearance at the end of 2019 and is still circulating in the population. The pandemic led to an urgent need for fast, reliable, and widely available testing. After December 2020, the emergence of new variants of SARS-CoV-2 led to additional challenges since new and existing tests had to detect variants to the same extent as the original Wuhan strain. When an antigen-based test is submitted to the Food and Drug Administration (FDA) for Emergency Use Authorization (EUA) consideration it is benchmarked against PCR comparator assays, which yield cycle threshold (CT) data as an indirect indicator of viral load - the lower the CT, the higher the viral load of the sample and the higher the CT, the lower the viral load. The FDA mandates that 10-20% of clinical samples used to evaluate the antigen test have to be low positive. Low positive, as defined by the FDA, are clinical samples in which the CT of the SARS-CoV-2 target gene is within 3 CT of the mean CT value of the approved comparator tests Limit of Detection (LOD). While all comparator tests are PCR-based, the results from different PCR assays used are not uniform. Results vary depending on assay platform, target gene, LOD and laboratory methodology. The emergence and dominance of the Omicron variant further challenged this approach as the fraction of low positive clinical samples dramatically increased as compared to earlier SARS-CoV-2 variants. This led to 20-40% of clinical samples having high CT values and therefore assays vying for an EUA were failing to achieve the 80% Percent Positive Agreement (PPA) threshold required. Here we describe the methods and statistical analyses used to establish a predefined cutoff, based on genome copies per ml (GE/ml) to classify samples as low positive (less than the cutoff GE/ml) or high positive (greater than the cutoff GE/mL). CT 30 for the E gene target using Cobas(R) SARS-CoV-2-FluA/B platform performed at TriCore Reference Laboratories, and this low positive cutoff value was used for two EUA authorizations. Using droplet digital PCR and methods described here, a value 49,447.72 was determined as the GE/ml equivalent for the low positive cutoff. The CT cutoff corresponding to 49447.72 GE/ml was determined across other platforms and laboratories. The methodology and statistical analysis described here can now be used for standardization of all comparators used for FDA submissions with a goal towards establishing uniform criteria for EUA authorization.\n\nMotivationThe motivation for this work was the need to establish a predefined cutoff based on genome copies per ml (GE/ml) rather than Ct, which can vary depending on the laboratory and assay used. A GE/ml-based threshold was necessary to define what constituted  low positives\" for samples that were included in data sets submitted to the FDA for emergency use approval for SARS-CoV-2 antigen tests.",
-    "rel_num_authors": 14,
-    "rel_authors": [
-      {
-        "author_name": "Anuradha Rao",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Jessica S Lin",
-        "author_inst": "Georgia Institute of Technology"
-      },
-      {
-        "author_name": "Richard S Parsons",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Morgan Greenleaf",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Adrianna Westbrook",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Eric Lai",
-        "author_inst": "Personalized Science, LLC"
-      },
-      {
-        "author_name": "Heather Bowers",
-        "author_inst": "Emory School of Medicine"
-      },
-      {
-        "author_name": "Kaleb Benjamin McLendon",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "William Henry O'Sick",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Tyler Baugh",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Markayla Sifford",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Julie Sullivan",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Wilbur A. Lam",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Leda Bassit",
-        "author_inst": "Emory University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2023.11.07.23297422",
     "rel_title": "The impact of SARS-CoV-2 variants on the likelihood of children identified as sources of infection in the NIH workforce: a cohort study",
@@ -7519,6 +7773,57 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2023.11.06.565757",
+    "rel_title": "Allosteric modulation by the fatty acid site in the glycosylated SARS-CoV-2 spike",
+    "rel_date": "2023-11-08",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.06.565757",
+    "rel_abs": "The trimeric spike protein plays an essential role in the SARS-CoV-2 virus lifecycle, facilitating virus entry through binding to the cellular receptor angiotensin-converting enzyme 2 (ACE2) and mediating viral and host membrane fusion. The SARS-CoV-2 spike contains an allosteric fatty acid (FA) binding site at the interface between two neighbouring receptor-binding domains. This site, also found in some other coronaviruses, binds free fatty acids such as linoleic and oleic acid, and other small molecules. Understanding allostery and how this site modulates the behaviour of different regions in this protein could potentiate the development of promising alternative strategies for new coronavirus therapies. Here, we apply dynamical nonequilibrium molecular dynamics (D-NEMD) simulations to investigate allosteric effects and identify the communication pathways in the fully glycosylated spike in the original SARS-CoV-2 ancestral variant. The results reveal the allosteric networks that connect the FA site to important functional regions of the protein, including some more than 40 [A] away. These regions include the receptor binding motif, an antigenic supersite in the N-terminal domain, the furin cleavage site, the regions surrounding the fusion peptide and a second allosteric site known to bind heme and biliverdin. The networks identified here highlight the complexity of the allosteric modulation in this protein and reveal a striking and unexpected connection between different allosteric sites. Notably, 65% of amino acid substitutions, deletions and insertions in the Alpha, Beta, Delta, Gamma and Omicron variants map onto or close to the identified allosteric pathways.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "A Sofia F Oliveira",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Fiona L Kearns",
+        "author_inst": "University of California San Diego"
+      },
+      {
+        "author_name": "Mia A Rosenfeld",
+        "author_inst": "University of California San Diego"
+      },
+      {
+        "author_name": "Lorenzo F Casalino",
+        "author_inst": "University of California San Diego"
+      },
+      {
+        "author_name": "Imre Berger",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Christiane Schaffitzel",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Andrew D Davidson",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Rommie E Amaro",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Adrian J Mulholland",
+        "author_inst": "University of Bristol"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "biochemistry"
+  },
   {
     "rel_doi": "10.1101/2023.11.07.566012",
     "rel_title": "Predicting human and viral protein variants affecting COVID-19 susceptibility and repurposing therapeutics",
@@ -8980,37 +9285,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2023.11.01.565087",
-    "rel_title": "Phylogenetic meta-analysis of chronic SARS-CoV-2 infections in immunocompromised patients shows no evidence of elevated evolutionary rates",
-    "rel_date": "2023-11-02",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.01.565087",
-    "rel_abs": "Genomic sequences from rapidly evolving pathogens, sampled over time, hold information on disease origin, transmission, and evolution. Together with their sampling times, sequences can be used to estimate the rates of molecular evolution and date evolutionary events through molecular tip-dating. The validity of this approach, however, depends on whether detectable levels of genetic variation have accumulated over the given sampling interval, generating temporal signal. Moreover, different molecular dating methods have demonstrated varying degrees of systematic biases under different biologically realistic scenarios, such as the presence of phylo-temporal clustering.\n\nChronic SARS-CoV-2 infection in immunocompromised patients has been linked to remarkably higher intra-host molecular rates than those of global lineages, facilitating the emergence of novel viral lineages. Yet, most studies reporting accelerated rates lack the evaluation of temporal signal or comparison of multiple methods of inference, both required to reliably estimate molecular rates. In this study, we use 26 previously published longitudinally sampled sequence series obtained from chronically infected immunocompromised patients to re-evaluate the rate of SARS-CoV-2 intrahost evolution. Using a range of methods, we analyse the strength of temporal signal and infer evolutionary rates from tip-calibrated phylogenies. Regardless of heterogeneity in rate estimates between sample series and methods, we find within-host rates to be in good agreement with rates derived from host-to-host transmission chains.\n\nOur findings suggest that when certain limitations of the methodology are disregarded, such as the underlying assumption of phylogenetic independence or the methods sensitivity to phylo- temporal grouping, evolutionary rates can be substantially overestimated. We demonstrate that estimating within-host rates is a challenging question necessitating careful interpretation of findings. While our results do not support faster evolution across the complete viral genome during chronic SARS-CoV-2 infection, prolonged viral shedding together with relapsing viral load dynamics may nevertheless promote the emergence of new viral variants in immunocompromised patients.\n\nAUTHOR SUMMARYThe evolutionary origin of SARS-CoV-2 variants of concern (VOC) is a longstanding point of controversy, with multiple proposed explanations. Observations of immunocompromised individuals being at a greater risk of developing a prolonged SARS-CoV-2 infection have led to the  Chronic infection hypothesis, suggesting that these cases may contribute to the emergence of VOCs. Correspondingly, many studies have reported accelerated viral evolution of SARS-CoV-2 within immunocompromised individuals with respect to the viral background population. However, many of these findings have not been validated with appropriate analytical methods. In this study we re-evaluate the rate of intrahost viral evolution of SARS- CoV-2 within immunocompromised patients utilising a range of methods. We assess the performance of different methodologies and compare our results to published estimates of SARS-CoV-2 evolutionary rates. Our systematic comparison showed no evidence supporting the previous claims of elevated levels of intrahost evolution in immunocompromised patients with chronic SARS-CoV-2. Instead, our findings exemplify the complexity of within-host viral dynamics, suggesting that a more comprehensive understanding of SARS-CoV-2 evolutionary processes would be derived from concurrent evaluation of viral genomic data together with patients clinical information.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Sanni Oversti",
-        "author_inst": "Max Planck Institute of Geoanthropology"
-      },
-      {
-        "author_name": "Emily Gaul",
-        "author_inst": "Eberhard Karls Universitat Tubingen"
-      },
-      {
-        "author_name": "Bjorn-Erik  Ole Jensen",
-        "author_inst": "Heinrich-Heine-Universitat Dusseldorf Medizinische Fakultat"
-      },
-      {
-        "author_name": "Denise Kuhnert",
-        "author_inst": "Max Planck Institute of Geoanthropology"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "evolutionary biology"
-  },
   {
     "rel_doi": "10.1101/2023.11.01.23297898",
     "rel_title": "Safety and immunogenicity of COReNAPCIN(R), a SARS-CoV-2 mRNA vaccine; a randomized, double-blind, placebo-controlled phase 1 clinical trial",
@@ -9361,6 +9635,49 @@
     "type": "new results",
     "category": "biochemistry"
   },
+  {
+    "rel_doi": "10.1101/2023.10.31.565042",
+    "rel_title": "SARS-CoV-2 infection leads to sustained testicular injury and functional impairments in K18 hACE2 mice",
+    "rel_date": "2023-11-01",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.31.565042",
+    "rel_abs": "Compromised male reproductive health is one of the symptoms of long COVID with a decrease in male fertility markers including testosterone levels and sperm count for months in recovering patients. However, the long-term impact of SARS-CoV-2 infection on testicular injury and underlying mechanisms remains unknown. We previously demonstrated a disrupted tissue architecture with no evidence of virus replication in the testis during the acute stage of the disease in K18-hACE2 mice. Here, we systematically delineate the consequences of SARS-CoV-2 infection on the testis injury and function both during the acute stage of the disease and up to 4 weeks after infection in survivor K18-hACE2 mice. The gross morphological defects included sloughing of healthy spermatids and spermatocytes into the lumen, lack of lumen, and increase in apoptotic cells that sustained for at least 2 weeks after infection. Testis injury correlated with systemic and testicular inflammation, and infiltration of immune cells in the interstitial space and seminiferous tubules. Transcriptomic analysis identified dysregulation of key pathways of testicular immune homeostasis, spermatogenesis, and cell death at the symptomatic and short-term recovery stages. Further, a significant reduction in testosterone levels was associated with transient reduction in sperm count and mouse fertility. Most of the testicular impairments except testosterone levels were resolved within 4 weeks, which is almost one spermatogenesis cycle in mice. These findings provide much-needed mechanistic insights beyond our current understanding of testicular pathogenesis, suggesting that recovering COVID-19 patients should be closely monitored to rescue the pathophysiological effects on male reproductive health.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Stefanos Giannakopoulos",
+        "author_inst": "Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA"
+      },
+      {
+        "author_name": "Monika A Ward",
+        "author_inst": "Institute for Biogenesis Research, John A Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA"
+      },
+      {
+        "author_name": "Jackson Bakse",
+        "author_inst": "Institute for Biogenesis Research, John A Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA"
+      },
+      {
+        "author_name": "Jin Hyuk Pak",
+        "author_inst": "Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA"
+      },
+      {
+        "author_name": "Vivek R Nerurkar",
+        "author_inst": "Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA"
+      },
+      {
+        "author_name": "Michelle D Tallquist",
+        "author_inst": "Center for Cardiovascular Research, John A. School of Medicine, University of Hawaii at Manoa, Honolulu, HI, USA"
+      },
+      {
+        "author_name": "Saguna Verma",
+        "author_inst": "Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2023.10.30.564631",
     "rel_title": "Patient phenotypes and their relation to TNF\u03b1 signaling and immune cell composition in critical illness and autoimmune disease",
@@ -10582,65 +10899,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2023.10.26.23297597",
-    "rel_title": "Complement dysregulation is a predictive and therapeutically amenable feature of long COVID",
-    "rel_date": "2023-10-28",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.26.23297597",
-    "rel_abs": "BackgroundLong COVID encompasses a heterogeneous set of ongoing symptoms that affect many individuals after recovery from infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The underlying biological mechanisms nonetheless remain obscure, precluding accurate diagnosis and effective intervention. Complement dysregulation is a hallmark of acute COVID-19 but has not been investigated as a potential determinant of long COVID.\n\nMethodsWe quantified a series of complement proteins, including markers of activation and regulation, in plasma samples from healthy convalescent individuals with a confirmed history of infection with SARS-CoV-2 and age/ethnicity/gender/infection/vaccine-matched patients with long COVID.\n\nFindingsMarkers of classical (C1s-C1INH complex), alternative (Ba, iC3b), and terminal pathway (C5a, TCC) activation were significantly elevated in patients with long COVID. These markers in combination had a receiver operating characteristic predictive power of 0.794. Other complement proteins and regulators were also quantitatively different between healthy convalescent individuals and patients with long COVID. Generalized linear modeling further revealed that a clinically tractable combination of just four of these markers, namely the activation fragments iC3b, TCC, Ba, and C5a, had a predictive power of 0.785.\n\nConclusionsThese findings suggest that complement biomarkers could facilitate the diagnosis of long COVID and further suggest that currently available inhibitors of complement activation could be used to treat long COVID.\n\nFundingThis work was funded by the National Institute for Health Research (COV-LT2-0041), the PolyBio Research Foundation, and the UK Dementia Research Institute.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Kirsten Baillie",
-        "author_inst": "Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Heath Park, Cardiff CF14 4XN, UK"
-      },
-      {
-        "author_name": "Helen E Davies",
-        "author_inst": "Department of Respiratory Medicine, University Hospital of Wales, Llandough, Penarth CF64 2XX, UK"
-      },
-      {
-        "author_name": "Samuel B K Keat",
-        "author_inst": "Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Heath Park, Cardiff CF14 4XN, UK"
-      },
-      {
-        "author_name": "Kristin Ladell",
-        "author_inst": "Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Heath Park, Cardiff CF14 4XN, UK"
-      },
-      {
-        "author_name": "Kelly L Miners",
-        "author_inst": "Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Heath Park, Cardiff CF14 4XN, UK"
-      },
-      {
-        "author_name": "Samantha A Jones",
-        "author_inst": "Department of Respiratory Medicine, University Hospital of Wales, Llandough, Penarth CF64 2XX, UK"
-      },
-      {
-        "author_name": "Ermioni Mellou",
-        "author_inst": "Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Heath Park, Cardiff CF14 4XN, UK"
-      },
-      {
-        "author_name": "Erik J M Toonen",
-        "author_inst": "Hycult Biotech, Frontstraat 2A, 5405 PB, Uden, The Netherlands"
-      },
-      {
-        "author_name": "David A Price",
-        "author_inst": "Division of Infection and Immunity & Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital of Wales, Heath Park, Cardi"
-      },
-      {
-        "author_name": "Bryan Paul Morgan",
-        "author_inst": "Division of Infection and Immunity & Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital of Wales, Heath Park, Cardi"
-      },
-      {
-        "author_name": "Wioleta M Zelek",
-        "author_inst": "Division of Infection and Immunity & Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital of Wales, Heath Park, Cardi"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2023.10.26.23297613",
     "rel_title": "Cost-effectiveness analysis of COVID-19 booster doses and oral antivirals in the Indo-Pacific",
@@ -10939,6 +11197,93 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
+  {
+    "rel_doi": "10.1101/2023.10.25.563967",
+    "rel_title": "Discovery of a novel inhibitor of macropinocytosis with antiviral activity",
+    "rel_date": "2023-10-26",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.25.563967",
+    "rel_abs": "Several viruses hijack various forms of endocytosis in order to infect host cells. Here, we report the discovery of a new molecule with antiviral properties that we named virapinib, which limits viral entry by macropinocytosis. The identification of virapinib derives from a chemical screen using High-Throughput Microscopy, where we identified new chemical entities capable of preventing infection with a pseudotype virus expressing the spike (S) protein from SARS-CoV-2. Subsequent experiments confirmed the capacity of virapinib to inhibit infection by SARS-CoV-2, as well as by additional viruses, such as Monkeypox virus and TBEV. Mechanistic analyses revealed that the compound inhibited macropinocytosis, limiting this entry route for the viruses. Importantly, virapinib has no significant toxicity to host cells. In summary, we present a new molecule that inhibits viral entry via the endocytic route, offering a new alternative to prevent viral infection.",
+    "rel_num_authors": 18,
+    "rel_authors": [
+      {
+        "author_name": "Bartlomiej Porebski",
+        "author_inst": "Karolinska Institute"
+      },
+      {
+        "author_name": "Wanda Christ",
+        "author_inst": "Karolinska Institute"
+      },
+      {
+        "author_name": "Alba Corman",
+        "author_inst": "Karolinska Institute"
+      },
+      {
+        "author_name": "Martin Haraldsson",
+        "author_inst": "Karolinska Institute"
+      },
+      {
+        "author_name": "Myriam Barz",
+        "author_inst": "Karolinska Institute"
+      },
+      {
+        "author_name": "Louise Lidemalm",
+        "author_inst": "Karolinska Institute"
+      },
+      {
+        "author_name": "Maria Haggblad",
+        "author_inst": "Karolinska Institute"
+      },
+      {
+        "author_name": "Juliana Illmain",
+        "author_inst": "NYU"
+      },
+      {
+        "author_name": "Shane Wright",
+        "author_inst": "Karolinska Institute"
+      },
+      {
+        "author_name": "Matilde Murga",
+        "author_inst": "CNIO"
+      },
+      {
+        "author_name": "Jan Schlegel",
+        "author_inst": "Karolinska Institute"
+      },
+      {
+        "author_name": "Erdinc Sezgin",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Gira Bhabha",
+        "author_inst": "NYU"
+      },
+      {
+        "author_name": "Volker M Lauschke",
+        "author_inst": "Karolinska Instituet"
+      },
+      {
+        "author_name": "Miguel Lafarga",
+        "author_inst": "University of Cantabria"
+      },
+      {
+        "author_name": "Jonas Klingstrom",
+        "author_inst": "Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden"
+      },
+      {
+        "author_name": "Daniela Huhn",
+        "author_inst": "Karolinska Institute"
+      },
+      {
+        "author_name": "Oscar Fernandez-Capetillo",
+        "author_inst": "CNIO/KI"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "pharmacology and toxicology"
+  },
   {
     "rel_doi": "10.1101/2023.10.25.564014",
     "rel_title": "Early antiviral CD4 and CD8 T cell responses are associated with upper respiratory tract clearance of SARS-CoV-2",
@@ -12704,37 +13049,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2023.10.24.23297475",
-    "rel_title": "Projections of the incidence of COVID-19 in Japan and the potential impact of a Fall 2023 COVID-19 Vaccine",
-    "rel_date": "2023-10-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.24.23297475",
-    "rel_abs": "BackgroundThe study objective was to estimate the incidence of COVID-19 infection, hospitalization, and deaths in Japan from September 2023 to August 2024 and potential impact of a Fall 2023 COVID-19 vaccine for adults [&ge;]18 years on these outcomes.\n\nMethodsA previously developed Susceptible-Exposed-Infected-Recovered model for the United States (US) was adapted to Japan. The numbers of symptomatic infections, COVID-19- related hospitalizations, and deaths were calculated. Given differences in vaccination coverage, masking practices and social mixing patterns between the US and Japan, all inputs were updated to reflect the Japanese context. Vaccine effectiveness (VE) values are hypothetical, but predicted based on existing VE values of bivalent BA.4/BA.5 boosters against BA.4/BA.5 in Japan, from the VERSUS test-negative case-control study. Sensitivity analyses were performed.\n\nResultsThe base case model predicts overall that there will be approximately 35.2 million symptomatic COVID-19 infections, 690,000 hospitalizations, and 62,000 deaths in Japan between September 2023 and August 2024. If an updated COVID-19 vaccine is offered to all adults aged 18 years and older in Fall 2023, the model predicts that 7.3 million infections, 275,000 hospitalizations and 26,000 deaths will be prevented. If vaccines are only given to those aged 65 years and older, only 2.9 million infections, 180,000 hospitalizations and 19,000 deaths will be prevented. Sensitivity analysis results suggest that hospitalizations and deaths prevented are most sensitive to initial vaccine effectiveness (VE) against infection and hospitalizations, and the waning rate associated with VE against infection. Symptomatic infections prevented was most sensitive to initial VE against infection and VE waning.\n\nConclusionsResults suggest that a Fall 2023 COVID-19 vaccine would reduce total numbers of COVID-19 related infections, hospitalizations, and deaths.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Michele Kohli",
-        "author_inst": "Quadrant Health Economics Inc."
-      },
-      {
-        "author_name": "Michael Maschio",
-        "author_inst": "Quadrant Health Economics Inc."
-      },
-      {
-        "author_name": "Amy Lee",
-        "author_inst": "Quadrant Health Economics Inc."
-      },
-      {
-        "author_name": "Ataru Igarashi",
-        "author_inst": "Yokohama City University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2023.10.24.23297454",
     "rel_title": "Inferring community transmission of SARS-CoV-2 in the United Kingdom using the ONS COVID-19 Infection Survey",
@@ -13109,6 +13423,77 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2023.10.23.563088",
+    "rel_title": "Nonspecific membrane bilayer perturbations by ivermectin underlie SARS-CoV-2 in vitro activity",
+    "rel_date": "2023-10-24",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.23.563088",
+    "rel_abs": "Since it was proposed as a potential host-directed antiviral agent for SARS-CoV-2, the antiparasitic drug ivermectin has been investigated thoroughly in clinical trials, which have provided insufficient support for its clinical efficacy. To examine the potential for ivermectin to be repurposed as an antiviral agent, we therefore undertook a series of preclinical studies. Consistent with early reports, ivermectin decreased SARS-CoV-2 viral burden in in vitro models at low micromolar concentrations, five-to ten-fold higher than the reported toxic clinical concentration. At similar concentrations, ivermectin also decreased cell viability and increased biomarkers of cytotoxicity and apoptosis. Further mechanistic and profiling studies revealed that ivermectin nonspecifically perturbs membrane bilayers at the same concentrations where it decreases the SARS-CoV-2 viral burden, resulting in nonspecific modulation of membrane-based targets such as G-protein coupled receptors and ion channels. These results suggest that a primary molecular mechanism for the in vitro antiviral activity of ivermectin may be nonspecific membrane perturbation, indicating that ivermectin is unlikely to be translatable into a safe and effective antiviral agent. These results and experimental workflow provide a useful paradigm for performing preclinical studies on (pandemic-related) drug repurposing candidates.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=61 SRC=\"FIGDIR/small/563088v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (18K):\norg.highwire.dtl.DTLVardef@a21f94org.highwire.dtl.DTLVardef@1c76751org.highwire.dtl.DTLVardef@500930org.highwire.dtl.DTLVardef@8b6c05_HPS_FORMAT_FIGEXP  M_FIG Graphical abstract C_FIG",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Richard T Eastman",
+        "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health"
+      },
+      {
+        "author_name": "Radda Rusinova",
+        "author_inst": "Weill Cornell Medicine"
+      },
+      {
+        "author_name": "Karl F Herold",
+        "author_inst": "Weill Cornell Medicine"
+      },
+      {
+        "author_name": "Xi-Ping Huang",
+        "author_inst": "University of North Carolina School of Medicine"
+      },
+      {
+        "author_name": "Patricia Dranchak",
+        "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health"
+      },
+      {
+        "author_name": "Ty C Voss",
+        "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health"
+      },
+      {
+        "author_name": "Sandeep Rana",
+        "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health"
+      },
+      {
+        "author_name": "Jonathan H Shrimp",
+        "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health"
+      },
+      {
+        "author_name": "Alex D White",
+        "author_inst": "University of California San Francisco"
+      },
+      {
+        "author_name": "Hugh C Hemmings Jr.",
+        "author_inst": "Weill Cornell Medicine"
+      },
+      {
+        "author_name": "Bryan L Roth",
+        "author_inst": "University of North Carolina School of Medicine"
+      },
+      {
+        "author_name": "James Inglese",
+        "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health"
+      },
+      {
+        "author_name": "Olaf S Andersen",
+        "author_inst": "Weill Cornell Medicine"
+      },
+      {
+        "author_name": "Jayme L Dahlin",
+        "author_inst": "National Center for Advancing Translational Sciences, National Institutes of Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc0",
+    "type": "new results",
+    "category": "pharmacology and toxicology"
+  },
   {
     "rel_doi": "10.1101/2023.10.24.563721",
     "rel_title": "Forecasting dominance of SARS-CoV-2 lineages by anomaly detection using deep AutoEncoders",
@@ -14606,69 +14991,6 @@
     "type": "new results",
     "category": "biophysics"
   },
-  {
-    "rel_doi": "10.1101/2023.10.20.23297300",
-    "rel_title": "Relative vaccine effectiveness of a CoronaVac booster dose in preventing symptomatic SARS-CoV-2 infection among healthcare workers during an Omicron period in Azerbaijan, January-August 2022",
-    "rel_date": "2023-10-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.20.23297300",
-    "rel_abs": "Among Azerbaijani healthcare workers (HCWs), compared to primary vaccine series, CoronaVac booster relative vaccine effectiveness was 60% (95% CI:25-79) and 79% (95% CI:44-92) against symptomatic and medically attended illness, respectively, during an Omicron BA.1/BA.2 period. Our results support timely CoronaVac booster uptake among Azerbaijani HCWs to reduce morbidity.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Iris Finci",
-        "author_inst": "World Health Organisation, Regional Office for Europe, Copenhagen, Denmark"
-      },
-      {
-        "author_name": "Madelyn Yiseth Rojas Castro",
-        "author_inst": "Epiconcept, Paris, France"
-      },
-      {
-        "author_name": "Nabil Seyidov",
-        "author_inst": "Public Health and Reforms Center, Ministry of Health, Baku, Azerbaijan Republic"
-      },
-      {
-        "author_name": "Samir Mehdiyev",
-        "author_inst": "Public Health and Reforms Center, Ministry of Health, Baku, Azerbaijan Republic"
-      },
-      {
-        "author_name": "C. Jason McKnight",
-        "author_inst": "World Health Organisation, Regional Office for Europe, Copenhagen, Denmark"
-      },
-      {
-        "author_name": "Barbara Muehlemann",
-        "author_inst": "Institute of Virology, Charite-Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute"
-      },
-      {
-        "author_name": "Christian Drosten",
-        "author_inst": "Institute of Virology, Charite-Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute"
-      },
-      {
-        "author_name": "Lindsey Duca",
-        "author_inst": "US Centers for Disease Control and Prevention, Atlanta, GA, US"
-      },
-      {
-        "author_name": "Richard Pebody",
-        "author_inst": "World Health Organisation, Regional Office for Europe, Copenhagen, Denmark"
-      },
-      {
-        "author_name": "Esther Kissling",
-        "author_inst": "Epiconcept, Paris, France"
-      },
-      {
-        "author_name": "Mark A Katz",
-        "author_inst": "World Health Organisation, Regional Office for Europe, Copenhagen, Denmark"
-      },
-      {
-        "author_name": "Gahraman Hagverdiyev",
-        "author_inst": "Public Health and Reforms Center, Ministry of Health, Baku, Azerbaijan Republic"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2023.10.18.563024",
     "rel_title": "Caveolin-1 mediates neuroinflammation and cognitive impairment in SARS-CoV-2 infection",
@@ -14903,6 +15225,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2023.10.17.23297174",
+    "rel_title": "Persistent high mortality rates for Diabetes Mellitus and Hypertension after excluding deaths associated with COVID-19 in Brazil, 2020-2022",
+    "rel_date": "2023-10-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.17.23297174",
+    "rel_abs": "BackgroundThe outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) posed a significant public health challenge globally, with Brazil being no exception. Excess mortality during this period reached alarming levels. Cardiovascular diseases (CVD), Systemic Hypertension (HTN), and Diabetes Mellitus (DM) were associated with increased mortality. However, the specific impact of DM and HTN on mortality during the pandemic remains poorly understood.\n\nMethodsThis study analyzed mortality data from Brazils mortality system, covering the period from 2015 to 2022. Data included all causes of death as listed on death certificates, categorized by International Classification of Diseases 10th edition (ICD-10) codes. Population data were obtained from the Brazilian Census. Mortality ratios (MRs) were calculated by comparing death rates in 2020, 2021, and 2022 to the average rates from 2015 to 2019. Adjusted MRs were calculated using Poisson models.\n\nResultsBetween 2015 and 2022, Brazil recorded a total of 11,423,288 deaths. Death rates remained relatively stable until 2019 but experienced a sharp increase in 2020 and 2021. In 2022, although a decrease was observed, it did not return to pre-pandemic levels. This trend persisted even when analyzing records mentioning DM, HTN, or CVD. Excluding death certificates mentioning COVID-19 codes, the trends still showed increases from 2020 through 2022, though less pronounced.\n\nConclusionThis study highlights the persistent high mortality rates for DM and HTN in Brazil during the years 2020-2022, even after excluding deaths associated with COVID-19. These findings emphasize the need for continued attention to managing and preventing DM and HTN as part of public health strategies, both during and beyond the COVID-19 pandemic. There are complex interactions between these conditions and the pandemics impact on mortality rates.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Rodrigo Moreira",
+        "author_inst": "Fundacao Oswaldo Cruz"
+      },
+      {
+        "author_name": "Leonardo  S Bastos",
+        "author_inst": "FIOCRUZ: Fundacao Oswaldo Cruz"
+      },
+      {
+        "author_name": "Luiz  Max Carvalho",
+        "author_inst": "Funda\u00e7\u00e3o Get\u00falio Vargas: Fundacao Getulio Vargas"
+      },
+      {
+        "author_name": "La\u00eds  Picinini Freitas",
+        "author_inst": "Universit\u00e9 de Montr\u00e9al \u00c9cole de Sant\u00e9 Publique: Universite de Montreal Ecole de Sante Publique"
+      },
+      {
+        "author_name": "Antonio  Guilherme Pacheco",
+        "author_inst": "FIOCRUZ: Fundacao Oswaldo Cruz"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2023.10.17.23297146",
     "rel_title": "The SHOW COVID-19 cohort: methods and rationale for examining the statewide impact of COVID-19 on the social determinants of health",
@@ -16340,25 +16697,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2023.10.12.23296888",
-    "rel_title": "Mathematical modeling of SARS-CoV-2 variant substitutions in European countries: Transmission dynamics and epidemiological insights",
-    "rel_date": "2023-10-13",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.12.23296888",
-    "rel_abs": "BackgroundCountries across Europe have faced similar evolutions of SARS-CoV-2 VOCs, including the Alpha, Delta, and Omicron variants.\n\nMaterials and MethodsWe used data from GISAID and applied a robust, automated mathematical substitution model to study the dynamics of COVID-19 variants across Europe over a period of more than two years, from late 2020 to early 2023. This model identifies variant substitution patterns and distinguishes between residual and dominant behavior. We used weekly sequencing data from 19 European countries to estimate the increase in transmissibility ({triangleup}{beta}) between consecutive SARS-CoV-2 variants. In addition, we focused on large countries with separate regional outbreaks and complex scenarios of multiple competing variants.\n\nResultsOur model accurately reproduced the observed substitution patterns between the Alpha, Delta, and Omicron major variants. We estimated the daily variant prevalence and calculated {triangleup}{beta} between variants, revealing that: (i) {triangleup}{beta} increased progressively from the Alpha to the Omicron variant; (ii) {triangleup}{beta} showed a high degree of variability within Omicron variants; (iii) a higher {triangleup}{beta} was associated with a later emergence of the variant within a country; (iv) a higher degree of immunization of the population against previous variants was associated with a higher {triangleup}{beta} for the Delta variant; (v) larger countries exhibited smaller {triangleup}{beta}, suggesting regionally diverse outbreaks within the same country; and finally (vi) the model reliably captures the dynamics of competing variants, even in complex scenarios.\n\nConclusionsThe use of mathematical models allows for the precise and reliable estimation of daily cases of each variant. By quantifying {triangleup}{beta}, we have tracked the spread of the different variants across Europe, highlighting a robust increase in transmissibility trend from Alpha to Omicron. On the other hand, we have shown that the country-level increases in transmissibility can always be influenced by the geographical characteristics of the country and the timing of the emergence of the variant.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Victor Lopez de Rioja",
-        "author_inst": "Universitat Politecnica de Catalunya"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2023.10.12.23296948",
     "rel_title": "A nationwide study of 331 rare diseases among 58 million individuals: prevalence, demographics, and COVID-19 outcomes",
@@ -16733,6 +17071,137 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2023.10.11.23296808",
+    "rel_title": "Safety of SARS-CoV-2 test-to-stay in daycare: a regression discontinuity in time analysis",
+    "rel_date": "2023-10-12",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.11.23296808",
+    "rel_abs": "Background and ObjectivesTest-to-stay concepts apply serial testing of children in daycare after exposure to SARS-CoV-2 without use of quarantine. This study aims to assess safety of a test-to-stay screening in daycare facilities.\n\nMethods714 daycare facilities and approximately 50,000 children [&le;]6 years in Cologne, Germany participated in a SARS-CoV-2 Pool-PCR screening from March 2021 to April 2022. The screening initially comprised post-exposure quarantine and was adapted to a test-to-stay approach during its course. To assess safety of the test-to-stay approach, we explored potential changes in frequencies of infections among children following the adaptation to the test-to-stay approach by applying regression discontinuity in time (RDiT) analyses. To this end, PCR-test data were linked with routinely collected data on reported infections in children and analyzed using ordinary least squares regressions.\n\nResults219,885 Pool-PCRs and 352,305 Single-PCRs were performed. 6,440 (2.93%) Pool-PCRs tested positive, and 17,208 infections in children were reported. We estimated that during a period of 30 weeks, the test-to-stay concept avoided between 7 and 20 days of quarantine per eligible daycare child. RDiT revealed a 26% reduction (Exp. Coef: 0.74, CI:0.52;1.06) in infection frequency among children and indicated no significant increase attributable to the test-to-stay approach. This result was not sensitive to adjustments for 7-day incidence, season, SARS-CoV-2 variant, and socioeconomic status.\n\nConclusionOur analyses provide evidence that suggest safety of the test-to-stay approach compared to traditional quarantine measures. This approach offers a promising option to avoid use of quarantine after exposure to respiratory pathogens in daycare settings.",
+    "rel_num_authors": 29,
+    "rel_authors": [
+      {
+        "author_name": "Felix Dewald",
+        "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany"
+      },
+      {
+        "author_name": "Gertrud Steger",
+        "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany"
+      },
+      {
+        "author_name": "Irina Fish",
+        "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany"
+      },
+      {
+        "author_name": "Ivonne Torre-Lage",
+        "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany"
+      },
+      {
+        "author_name": "Christina Hellriegel",
+        "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany"
+      },
+      {
+        "author_name": "Esther Milz",
+        "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany"
+      },
+      {
+        "author_name": "Anja Kolb-Bastigkeit",
+        "author_inst": "Youth Welfare Office of Cologne, Cologne, Germany"
+      },
+      {
+        "author_name": "Eva Heger",
+        "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany"
+      },
+      {
+        "author_name": "Mira Fries",
+        "author_inst": "Health department of Cologne, Cologne, Germany"
+      },
+      {
+        "author_name": "Michael Buess",
+        "author_inst": "Health department of Cologne, Cologne, Germany"
+      },
+      {
+        "author_name": "Niklas Marizy",
+        "author_inst": "Health department of Cologne, Cologne, Germany"
+      },
+      {
+        "author_name": "Barabara Michaelis",
+        "author_inst": "Health department of Cologne, Cologne, Germany"
+      },
+      {
+        "author_name": "Isabelle Suarez",
+        "author_inst": "Department I of Internal Medicine, Division of Infectious Diseases, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany"
+      },
+      {
+        "author_name": "Gibran Horemheb Rubio Quintanares",
+        "author_inst": "Virus security, Paul Ehrlich Institute, Langen, Germany"
+      },
+      {
+        "author_name": "Martin Pirkl",
+        "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany"
+      },
+      {
+        "author_name": "Annette Aigner",
+        "author_inst": "Institute of Biometry and Clinical Epidemiology, Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt Universitaet "
+      },
+      {
+        "author_name": "Max Obserste-Frielinghaus",
+        "author_inst": "Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany"
+      },
+      {
+        "author_name": "Martin Hellmich",
+        "author_inst": "Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany"
+      },
+      {
+        "author_name": "Anabelle Wong",
+        "author_inst": "Institute of Public Health, Charite - Universitaetsmedizin Berlin, Berlin, Germany"
+      },
+      {
+        "author_name": "Juan Camilo Orduz",
+        "author_inst": "juanitorduz@gmail.com, https://juanitorduz.github.io/"
+      },
+      {
+        "author_name": "Gerd Faetkenheuer",
+        "author_inst": "Department I of Internal Medicine, Division of Infectious Diseases, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany"
+      },
+      {
+        "author_name": "Joerg Doetsch",
+        "author_inst": "Department of Pediatrics, Faculty of Medicine, University Hospital Cologne, University of Cologne, Cologne, Germany"
+      },
+      {
+        "author_name": "Annelene Kossow",
+        "author_inst": "Health department of Cologne, Cologne, Germany"
+      },
+      {
+        "author_name": "Eva-Maria Moench",
+        "author_inst": "MVZ Labor Dr. Quade & Kollegen GmbH, Cologne, Germany"
+      },
+      {
+        "author_name": "Gustav Quade",
+        "author_inst": "MVZ Labor Dr. Quade & Kollegen GmbH, Cologne, Germany"
+      },
+      {
+        "author_name": "Udo Neumann",
+        "author_inst": "Youth Welfare Office of Cologne, Cologne, Germany"
+      },
+      {
+        "author_name": "Rolf Kaiser",
+        "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany"
+      },
+      {
+        "author_name": "Madlen Schranz",
+        "author_inst": "Charite-Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt Universitaet zu Berlin, Institute of Public Health, Berlin, Germ"
+      },
+      {
+        "author_name": "Florian Klein",
+        "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2023.10.10.23296845",
     "rel_title": "Availability of Essential Medicines During the COVID-19 Pandemic: A Qualitative Study Examining Experiences and Level of Preparedness in Kenya",
@@ -18222,101 +18691,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2023.10.08.23296718",
-    "rel_title": "Effects of COVID-19 mRNA vaccination on HIV viremia and reservoir size",
-    "rel_date": "2023-10-09",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.08.23296718",
-    "rel_abs": "ObjectiveThe immunogenic nature of COVID-19 mRNA vaccines led to some initial concern that these could stimulate the HIV reservoir. We analyzed changes in plasma HIV loads (pVL) and reservoir size following COVID-19 mRNA vaccination in 62 people with HIV (PWH) receiving antiretroviral therapy (ART), and analyzed province-wide trends in pVL before and after the mass vaccination campaign.\n\nDesignLongitudinal observational cohort and province-wide analysis.\n\nMethods62 participants were sampled pre-vaccination, and one month after their first and second COVID-19 immunizations. Vaccine-induced anti-SARS-CoV-2-Spike antibodies in serum were measured using the Roche Elecsys Anti-S assay. HIV reservoirs were quantified using the Intact Proviral DNA Assay; pVL were measured using the cobas 6800 (LLOQ:20 copies/mL). The province-wide analysis included all 290,401 pVL performed in British Columbia, Canada between 2012-2022.\n\nResultsPre-vaccination, the median intact reservoir size was 77 (IQR:20-204) HIV copies/million CD4+ T-cells, compared to 74 (IQR:27-212) and 65 (IQR:22-174) post-first and -second dose, respectively (all comparisons p>0.07). Pre-vaccination, 82% of participants had pVL<20 copies/mL (max:110 copies/mL), compared to 79% post-first dose (max:183 copies/mL) and 85% post-second dose (max:79 copies/mL) (p>0.4). The magnitude of the vaccine-elicited anti-SARS-CoV-2-Spike antibody response did not correlate with changes in reservoir size nor detectable pVL frequency (p>0.6). We found no evidence linking the COVID-19 mass vaccination campaign to population-level increases in detectable pVL frequency among all PWH in the province, nor among those who maintained pVL suppression on ART.\n\nConclusionWe found no evidence that COVID-19 mRNA vaccines induced changes in HIV reservoir size nor plasma viremia.",
-    "rel_num_authors": 20,
-    "rel_authors": [
-      {
-        "author_name": "Maggie C Duncan",
-        "author_inst": "Simon Fraser University"
-      },
-      {
-        "author_name": "F. Harrison Omondi",
-        "author_inst": "Simon Fraser University"
-      },
-      {
-        "author_name": "Natalie N Kinloch",
-        "author_inst": "Simon Fraser University"
-      },
-      {
-        "author_name": "Hope R Lapointe",
-        "author_inst": "British Columbia Centre for Excellence in HIV/AIDS"
-      },
-      {
-        "author_name": "Sarah Speckmaier",
-        "author_inst": "British Columbia Centre for Excellence in HIV/AIDS"
-      },
-      {
-        "author_name": "Nadia Moran Garcia",
-        "author_inst": "British Columbia Centre for Excellence in HIV/AIDS"
-      },
-      {
-        "author_name": "Tanya Lawson",
-        "author_inst": "St. Paul's Hospital"
-      },
-      {
-        "author_name": "Mari L DeMarco",
-        "author_inst": "Providence Health Care"
-      },
-      {
-        "author_name": "Janet Simons",
-        "author_inst": "Providence Health Care"
-      },
-      {
-        "author_name": "Daniel T Holmes",
-        "author_inst": "Providence Health Care"
-      },
-      {
-        "author_name": "Christopher F Lowe",
-        "author_inst": "St. Paul's Hospital"
-      },
-      {
-        "author_name": "Nic Bacani",
-        "author_inst": "British Columbia Centre for Excellence in HIV/AIDS"
-      },
-      {
-        "author_name": "Paul Sereda",
-        "author_inst": "British Columbia Centre for Excellence in HIV/AIDS"
-      },
-      {
-        "author_name": "Rolando Barrios",
-        "author_inst": "British Columbia Centre for Excellence in HIV/AIDS"
-      },
-      {
-        "author_name": "Marianne Harris",
-        "author_inst": "British Columbia Centre for Excellence in HIV/AIDS"
-      },
-      {
-        "author_name": "Marc G Romney",
-        "author_inst": "St. Pauls's Hospital"
-      },
-      {
-        "author_name": "Julio S G Montaner",
-        "author_inst": "British Columbia Centre for Excellence in HIV/AIDS"
-      },
-      {
-        "author_name": "Chanson J Brumme",
-        "author_inst": "British Columbia Centre for Excellence in HIV/AIDS"
-      },
-      {
-        "author_name": "Mark A Brockman",
-        "author_inst": "Simon Fraser University"
-      },
-      {
-        "author_name": "Zabrina L Brumme",
-        "author_inst": "Simon Fraser University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "hiv aids"
-  },
   {
     "rel_doi": "10.1101/2023.10.08.23296717",
     "rel_title": "Immunomodulators and risk for breakthrough infection after third COVID-19 mRNA vaccine among patients with rheumatoid arthritis: A cohort study",
@@ -18683,6 +19057,69 @@
     "type": "new results",
     "category": "biochemistry"
   },
+  {
+    "rel_doi": "10.1101/2023.10.05.561047",
+    "rel_title": "Fourth dose of Microneedle Array Patch of SARS-CoV-2 S1 Protein Subunit Vaccine Elicits Robust Long-lasting Humoral Responses in mice",
+    "rel_date": "2023-10-05",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.05.561047",
+    "rel_abs": "The COVID-19 pandemic has underscored the pressing need for safe and effective booster vaccines, particularly in considering the emergence of new SARS-CoV-2 variants and addressing vaccine distribution inequalities. Dissolving microneedle array patches (MAP) offer a promising delivery method, enhancing immunogenicity and improving accessibility through the skins immune potential. In this study, we evaluated a microneedle array patch-based S1 subunit protein COVID-19 vaccine candidate, which comprised a bivalent formulation targeting the Wuhan and Beta variant alongside a monovalent Delta variant spike proteins in a murine model. Notably, the second boost of homologous bivalent MAP-S1(WU+Beta) induced a 15.7-fold increase in IgG endpoint titer, while the third boost of heterologous MAP-S1RS09Delta yielded a more modest 1.6-fold increase. Importantly, this study demonstrated that the administration of four doses of the MAP vaccine induced robust and long-lasting immune responses, persisting for at least 80 weeks. These immune responses encompassed various IgG isotypes and remained statistically significant for one year. Furthermore, neutralizing antibodies against multiple SARS-CoV-2 variants were generated, with comparable responses observed against the Omicron variant. Overall, these findings emphasize the potential of MAP-based vaccines as a promising strategy to combat the evolving landscape of COVID-19 and to deliver a safe and effective booster vaccine worldwide.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Eun Kim",
+        "author_inst": "University of Pittsburgh"
+      },
+      {
+        "author_name": "Juyeop Shin",
+        "author_inst": "Raphas Co., Ltd."
+      },
+      {
+        "author_name": "Alessandro Ferrari",
+        "author_inst": "IRCCS Policlinico San Matteo"
+      },
+      {
+        "author_name": "Shaohua Huang",
+        "author_inst": "University of Pittsburgh"
+      },
+      {
+        "author_name": "Eunjin An",
+        "author_inst": "Raphas Co., Ltd."
+      },
+      {
+        "author_name": "Donghoon Han",
+        "author_inst": "Raphas Co., Ltd."
+      },
+      {
+        "author_name": "Muhammad Sohaib Khan",
+        "author_inst": "University of Pittsburgh"
+      },
+      {
+        "author_name": "Thomas W. Kenniston",
+        "author_inst": "University of Pittsburgh"
+      },
+      {
+        "author_name": "Irene Cassaniti",
+        "author_inst": "IRCCS Policlinico San Matteo"
+      },
+      {
+        "author_name": "Fausto Baldanti",
+        "author_inst": "Molecular Virology Unit, Microbiology and Virology Department, Foundation IRCCS Polyclinic San Matteo, Pavia, Italy"
+      },
+      {
+        "author_name": "Dohyeon Jeong",
+        "author_inst": "Raphas Co., Ltd."
+      },
+      {
+        "author_name": "Andrea Gambotto",
+        "author_inst": "University of Pittsburgh"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2023.10.05.23296592",
     "rel_title": "A mixed method study to assess behavioral and social predictors of parent/caregivers intention to vaccinate their children against COVID-19 disease in an Indian state marked by significant health disparities.",
@@ -20020,141 +20457,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2023.09.29.23296354",
-    "rel_title": "Suppressed IgG4 class switching in dupilumab- and TNF inhibitor-treated patients after repeated SARS-CoV-2 mRNA vaccination",
-    "rel_date": "2023-10-02",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.29.23296354",
-    "rel_abs": "BackgroundRepeated mRNA vaccination against SARS-CoV-2 has been shown to induce class switching to IgG4, a non-inflammatory human antibody subclass linked to tolerance. Although poorly understood, prolonged antigenic stimulation and IL-4 signalling may be instrumental in IgG4 switching. We and others have previously shown that widely used immunosuppressive drugs such as methotrexate (MTX) and TNF inhibitors (TNFi) have a minor inhibitory impact on humoral SARS-CoV-2 mRNA vaccination responses. However, the impact of such immunosuppressive drugs on IgG4 switching is unknown.\n\nAimTo study the impact of widely used immunosuppressive drugs (TNFi, MTX, or the IL-4 receptor-blocking antibody dupilumab on IgG4 skewing upon repeated SARS-CoV-2 mRNA vaccination.\n\nMethodsAntibody responses to the receptor-binding domain (RBD) of the spike protein upon repeated SARS-CoV-2 mRNA vaccination were measured in 604 individuals including patients with immune-mediated inflammatory diseases treated with TNFi and/or MTX, or dupilumab, as well as healthy controls and untreated patients.\n\nResultsWe observed a substantial increase in the proportion of RBD-specific IgG4 antibodies (median 21%) in healthy/untreated controls after a third mRNA vaccination. This IgG4 skewing was absent when primary vaccination was adenoviral vector-based and was profoundly reduced in both dupilumab- and TNFi-treated patients (<1%), but only moderately in patients treated with MTX (7%).\n\nConclusionOur results imply a major role for both IL-4/IL-13 as well as TNF in IgG4 class switching. These novel findings advance our understanding of IgG4 class switch dynamics, and may benefit future mRNA vaccine strategies, humoral tolerance induction, as well as treatment of IgG4 pathologies.",
-    "rel_num_authors": 30,
-    "rel_authors": [
-      {
-        "author_name": "Anika M. Valk",
-        "author_inst": "Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, Amsterdam, the Netherlands"
-      },
-      {
-        "author_name": "Jim B.D. Keijser",
-        "author_inst": "Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, Amsterdam, the Netherlands"
-      },
-      {
-        "author_name": "Koos van Dam",
-        "author_inst": "Academic Medical Center"
-      },
-      {
-        "author_name": "Eileen Stalman",
-        "author_inst": "Academic Medical Center"
-      },
-      {
-        "author_name": "Luuk Wieske",
-        "author_inst": "Academic Medical Center"
-      },
-      {
-        "author_name": "Maurice Steenhuis",
-        "author_inst": "Sanquin Blood Supply"
-      },
-      {
-        "author_name": "Laura Y.L. Kummer",
-        "author_inst": "Sanquin Blood Supply"
-      },
-      {
-        "author_name": "Phyllis I. Spuls",
-        "author_inst": "Department of Dermatology, Amsterdam Public Health/Infection and Immunology, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands"
-      },
-      {
-        "author_name": "Marcel W. Bekkenk",
-        "author_inst": "Department of Dermatology, Amsterdam Public Health/Infection and Immunology, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands"
-      },
-      {
-        "author_name": "Annelie H. Musters",
-        "author_inst": "Department of Dermatology, Amsterdam Public Health/Infection and Immunology, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands"
-      },
-      {
-        "author_name": "Nicoline F. Post",
-        "author_inst": "Department of Dermatology, Amsterdam Public Health/Infection and Immunology, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands"
-      },
-      {
-        "author_name": "Angela L. Bosma",
-        "author_inst": "Department of Dermatology, Amsterdam Public Health/Infection and Immunology, Amsterdam UMC, location AMC, University of Amsterdam, Amsterdam, the Netherlands"
-      },
-      {
-        "author_name": "Barbara Horvath",
-        "author_inst": "Department of Dermatology, UMCG Expertise Center for Blistering Diseases, University Medical Center Groningen, University of Groningen, Groningen, the Netherlan"
-      },
-      {
-        "author_name": "DirkJan Hijnen",
-        "author_inst": "Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands"
-      },
-      {
-        "author_name": "Corine R.G. Schreurs",
-        "author_inst": "Department of Dermatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands"
-      },
-      {
-        "author_name": "Zoe van Kempen",
-        "author_inst": "Department of Neurology, Amsterdam UMC, VU University Medical Center, Amsterdam, the Netherlands"
-      },
-      {
-        "author_name": "Joep Killestein",
-        "author_inst": "Amsterdam Free University"
-      },
-      {
-        "author_name": "Adriaan G. Volkers",
-        "author_inst": "Department of Gastroenterology and Hepatology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands"
-      },
-      {
-        "author_name": "Sander Tas",
-        "author_inst": "Academic Medical Center"
-      },
-      {
-        "author_name": "Laura Boekel",
-        "author_inst": "Reade"
-      },
-      {
-        "author_name": "Gertjan Wolbink",
-        "author_inst": "Reade"
-      },
-      {
-        "author_name": "Sofie Keijzer",
-        "author_inst": "Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, Amsterdam, the Netherlands"
-      },
-      {
-        "author_name": "Ninotska Derksen",
-        "author_inst": "Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, Amsterdam, the Netherlands"
-      },
-      {
-        "author_name": "Melanie van Deelen",
-        "author_inst": "University of Amsterdam"
-      },
-      {
-        "author_name": "Gerard van Mierlo",
-        "author_inst": "Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, Amsterdam, the Netherlands"
-      },
-      {
-        "author_name": "Taco W. Kuijpers",
-        "author_inst": "Department of Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands"
-      },
-      {
-        "author_name": "Filip Eftimov",
-        "author_inst": "Academic Medical Center"
-      },
-      {
-        "author_name": "Marieke van Ham",
-        "author_inst": "Sanquin Research"
-      },
-      {
-        "author_name": "Anja ten Brinke",
-        "author_inst": "Sanquin"
-      },
-      {
-        "author_name": "Theo Rispens",
-        "author_inst": "Sanquin Research"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "allergy and immunology"
-  },
   {
     "rel_doi": "10.1101/2023.09.29.23296359",
     "rel_title": "Dynamic Contact Networks of Residents of an Urban Jail in the Era of SARS-CoV-2",
@@ -20457,6 +20759,89 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2023.10.01.560365",
+    "rel_title": "Neutralisation of SARS-CoV-2 Omicron subvariants BA.2.86 and EG.5.1 by antibodies induced by earlier infection or vaccination",
+    "rel_date": "2023-10-02",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.01.560365",
+    "rel_abs": "Highly mutated SARS-CoV-2 Omicron subvariant BA.2.86 emerged in July 2023. We investigated the neutralisation of isolated virus by antibodies induced by earlier infection or vaccination. The neutralisation titres for BA.2.86 were comparable to those for XBB.1 and EG.5.1, by antibodies induced by XBB.1.5 or BA.4/5 breakthrough infection or BA.4/5 vaccination.",
+    "rel_num_authors": 17,
+    "rel_authors": [
+      {
+        "author_name": "Ria Lassauniere",
+        "author_inst": "Statens Serum Institut, Copenhagen, Denmark"
+      },
+      {
+        "author_name": "Charlotta Polacek",
+        "author_inst": "Statens Serum Institut, Copenhagen, Denmark"
+      },
+      {
+        "author_name": "Sharmin Baig",
+        "author_inst": "Statens Serum Institut, Copenhagen, Denmark"
+      },
+      {
+        "author_name": "Kirsten Ellegaard",
+        "author_inst": "Statens Serum Institut, Copenhagen, Denmark"
+      },
+      {
+        "author_name": "Leandro Andre Escobar-Herrera",
+        "author_inst": "Statens Serum Institut, Copenhagen, Denmark"
+      },
+      {
+        "author_name": "Anders Fomsgaard",
+        "author_inst": "Statens Serum Institut, Copenhagen, Denmark"
+      },
+      {
+        "author_name": "Katja Spiess",
+        "author_inst": "Statens Serum Institut, Copenhagen, Denmark"
+      },
+      {
+        "author_name": "Olivier Schwartz",
+        "author_inst": "Institut Pasteur, Paris, France"
+      },
+      {
+        "author_name": "Delphine Planas",
+        "author_inst": "Institut Pasteur, Paris, France"
+      },
+      {
+        "author_name": "Etienne Simon-Loriere",
+        "author_inst": "Institut Pasteur, Paris, France"
+      },
+      {
+        "author_name": "Uffe Vest Schneider",
+        "author_inst": "Statens Serum Institut, Copenhagen, Denmark"
+      },
+      {
+        "author_name": "Raphael Niklaus Sieber",
+        "author_inst": "Statens Serum Institut, Copenhagen, Denmark"
+      },
+      {
+        "author_name": "Marc Stegger",
+        "author_inst": "Statens Serum Institut, Copenhagen, Denmark"
+      },
+      {
+        "author_name": "Tyra Grove Krause",
+        "author_inst": "Statens Serum Institut, Copenhagen, Denmark"
+      },
+      {
+        "author_name": "Henrik Ullum",
+        "author_inst": "Statens Serum Institut, Copenhagen, Denmark"
+      },
+      {
+        "author_name": "Pikka Jokelainen",
+        "author_inst": "Statens Serum Institut, Copenhagen, Denmark"
+      },
+      {
+        "author_name": "Morten Rasmussen",
+        "author_inst": "Statens Serum Institut, Copenhagen, Denmark"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2023.09.28.559927",
     "rel_title": "Plasma of COVID-19 patients does not alter electrical resistance of human endothelial blood-brain barrier in vitro.",
@@ -21454,57 +21839,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2023.09.27.559660",
-    "rel_title": "p38-MAPK is prerequisite for the synthesis of SARS-CoV-2 protein",
-    "rel_date": "2023-09-27",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.27.559660",
-    "rel_abs": "The inhibition of p38 mitogen-activated protein kinase (p38-MAPK) by small molecule chemical inhibitors was previously shown to impair severe acute respiratory syndrome coronavirus 2 (SARS- CoV-2) replication, however, mechanisms underlying antiviral activity remains unexplored. In this study, reduced growth of SARS-CoV-2 in p38- knockout Vero cells, together with enhanced viral yield in cells transfected with construct expressing p38, suggested that p38-MAPK is essential for the propagation of SARS-CoV-2. The SARS-CoV-2 was also shown to induce phosphorylation (activation) of p38, at time when transcription/translational activities are considered to be at the peak levels. Further, we demonstrated that p38 supports viral RNA/protein synthesis without affecting viral attachment, entry, and budding in the target cells. In addition, we demonstrated that long-term culture of SARS-CoV-2 in the presence of p38 inhibitor SB203580 does not easily select resistant viral mutants. In conclusion, we provide mechanistic insights on the regulation of SARS-CoV-2 replication by p38 MAPK.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Priyasi Mittal",
-        "author_inst": "National Center for Veterinary Type Cultures  ICAR-NRC on Equines, Hisar and OM Sterling Global University, Hisar"
-      },
-      {
-        "author_name": "Nitin Khandelwal",
-        "author_inst": "National Center for Veterinary Type Cultures  ICAR-NRC on Equines, Hisar"
-      },
-      {
-        "author_name": "Yogesh Chander",
-        "author_inst": "National Center for Veterinary Type Cultures  ICAR-NRC on Equines, Hisar"
-      },
-      {
-        "author_name": "Assim Verma",
-        "author_inst": "National Center for Veterinary Type Cultures  ICAR-NRC on Equines, Hisar"
-      },
-      {
-        "author_name": "Ram Kumar",
-        "author_inst": "National Center for Veterinary Type Cultures  ICAR-NRC on Equines, Hisar"
-      },
-      {
-        "author_name": "Chayanika Putatunda",
-        "author_inst": "OM Sterling Global University, Hisar"
-      },
-      {
-        "author_name": "Sanjay Barua",
-        "author_inst": "National Center for Veterinary Type Cultures  ICAR-NRC on Equines, Hisar"
-      },
-      {
-        "author_name": "Baldev Raj Gulati",
-        "author_inst": "National Center for Veterinary Type Cultures  ICAR-NRC on Equines, Hisar"
-      },
-      {
-        "author_name": "Naveen Kumar",
-        "author_inst": "National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, India"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "confirmatory results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2023.09.27.559689",
     "rel_title": "Comparative Analysis of SARS-CoV-2 Antigenicity across Assays and in Human and Animal Model Sera",
@@ -22019,6 +22353,105 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2023.09.25.23289158",
+    "rel_title": "Recruitment, Consent and DNA Sample Acquisition in a U.S. Precision Health Cohort During the COVID-19 Pandemic",
+    "rel_date": "2023-09-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.25.23289158",
+    "rel_abs": "AimThe Yale Generations Project (YGP) is a precision health cohort initiative that began enrollment in New Haven Connecticut USA in July 2019. In March 2020, after nine months of operation, pandemic restrictions prompted abrupt changes to staff availability as well as changes to the projects recruitment, consenting, and sample acquisition. This manuscript describes the successful addition of remote recruitment, consenting, and DNA sampling to YGP workflows during the initial 27-months of pandemic restrictions ending June 30, 2022.\n\nMethodsThe initial YGP protocol established face-to-face workflow for recruiting, consenting and peripheral blood collection. A telemedicine consent protocol was initiated in April of 2020, and a remote saliva collection was established in October of 2020. De-identified data was extracted from YGP dataset and reported here.\n\nResultsAt the completion of YGPs initial 36 months (9-months pre-pandemic and 27-months pandemic) YGP enrolled N=4949 volunteers. There were N=1,950 (216.7 per month) volunteers consented pre-pandemic and N=2,999 (111.1 per month) during pandemic. The peak consenting month was February 2020 with N=428. DNA sample acquisition peaked in the pre-pandemic month of February 2020 with N=291 peripheral blood draws, and in the pandemic period the peak DNA acquisition month was November 2020 with N=176 (N=68 peripheral blood draws and N=108 saliva samples).\n\nConclusionThe YGP successfully transitioned from pre-pandemic recruiting, consenting and sample acquisition model that was exclusively face-to-face, to pandemic model that was predominantly remote. The added value of remote recruiting, consenting, and sampling has led to plans for an optimized hybrid model post-pandemic.",
+    "rel_num_authors": 21,
+    "rel_authors": [
+      {
+        "author_name": "Allyson M. Derry",
+        "author_inst": "Yale Center for Clinical Investigation, Yale School of Medicine"
+      },
+      {
+        "author_name": "Yvette Strong",
+        "author_inst": "Yale Center for Clinical Investigation, Yale School of Medicine"
+      },
+      {
+        "author_name": "Davia Schioppo",
+        "author_inst": "Yale Center for Clinical Investigation, Yale School of Medicine"
+      },
+      {
+        "author_name": "Joni Cotter",
+        "author_inst": "Yale Center for Clinical Investigation, Yale School of Medicine"
+      },
+      {
+        "author_name": "Geisa M. Wilkins",
+        "author_inst": "Yale Center for Clinical Investigation, Yale School of Medicine"
+      },
+      {
+        "author_name": "Laura I. Siquieros",
+        "author_inst": "Yale Center for Clinical Investigation, Yale School of Medicine"
+      },
+      {
+        "author_name": "Andrea Ouyang",
+        "author_inst": "Yale Center for Clinical Investigation, Yale School of Medicine"
+      },
+      {
+        "author_name": "Kathleen Hulseman",
+        "author_inst": "Yale Center for Clinical Investigation, Yale School of Medicine"
+      },
+      {
+        "author_name": "Joseph Petrosino",
+        "author_inst": "Yale Center for Clinical Investigation, Yale School of Medicine"
+      },
+      {
+        "author_name": "Lorrin Liang",
+        "author_inst": "Yale Center for Clinical Investigation, Yale School of Medicine"
+      },
+      {
+        "author_name": "Megan Stevenson",
+        "author_inst": "Yale Center for Clinical Investigation, Yale School of Medicine"
+      },
+      {
+        "author_name": "Tiffany Elianne Aguilera",
+        "author_inst": "Yale Center for Clinical Investigation, Yale School of Medicine"
+      },
+      {
+        "author_name": "Alexandria L. Soto",
+        "author_inst": "Department of Neurology, Yale School of Medicine"
+      },
+      {
+        "author_name": "Katherin Meurer",
+        "author_inst": "Department of Neurology, Yale School of Medicine"
+      },
+      {
+        "author_name": "Alison L. Herman",
+        "author_inst": "Department of Neurology, Yale School of Medicine"
+      },
+      {
+        "author_name": "Inessa Cohen",
+        "author_inst": "Department of Neurology, Yale School of Medicine"
+      },
+      {
+        "author_name": "Guido J. Falcone",
+        "author_inst": "Department of Neurology, Yale School of Medicine"
+      },
+      {
+        "author_name": "Erin E. Longbrake",
+        "author_inst": "Department of Neurology, Yale School of Medicine"
+      },
+      {
+        "author_name": "Cassius I. Ochoa Chaar",
+        "author_inst": "Division of Vascular Surgery, Department of Surgery Yale School of Medicine"
+      },
+      {
+        "author_name": "Kelly M. Anastasio",
+        "author_inst": "Yale Center for Clinical Investigation, Yale School of Medicine"
+      },
+      {
+        "author_name": "Michael F. Murray",
+        "author_inst": "Department of Genetics, Yale School of Medicine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "genetic and genomic medicine"
+  },
   {
     "rel_doi": "10.1101/2023.09.26.559506",
     "rel_title": "Metabolic and mitochondria alterations induced by SARS-CoV-2 accessory proteins ORF3a, ORF9b, ORF9c and ORF10",
@@ -22367,7 +22800,7 @@
     "rel_date": "2023-09-26",
     "rel_site": "medRxiv",
     "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.25.23296118",
-    "rel_abs": "Near-term forecasting of infectious disease incidence and consequent demand for acute healthcare services can support capacity planning and public health responses. Despite well-developed scenario modelling to support the Covid-19 response, Aotearoa New Zealand lacks advanced infectious disease forecasting capacity. We develop a model using Aotearoa New Zealands unique Covid-19 data streams to predict reported Covid-19 cases, hospital admissions and hospital occupancy. The method combines a semi-mechanistic model for disease transmission to predict cases with Gaussian process regression models to predict the fraction of reported cases that will require hospital treatment. We evaluate forecast performance against out-of-sample data over the period from 2 October 2022 to 23 July 2023. Our results show that forecast performance is reasonably good over a 1-3 week time horizon, although generally deteriorates as the time horizon is lengthened. The model has been operationalised to provide weekly national and regional forecasts in real-time. This study is an important step towards development of more sophisticated situational awareness and infectious disease forecasting tools in Aotearoa New Zealand.\n\nAuthor summaryThe emergency phase of the Covid-19 pandemic has ended, but Covid-19 continues to put significant additional load on stretched healthcare systems. Forecasting the number of hospital cases caused an infectious disease like Covid-19 over the next few weeks can help with effective planning and response. The ability to forecast reliably requires timely, high-quality data and accurate mathematical models. We have developed a model for forecasting the number of Covid-19 cases and hospitalisations in Aotearoa New Zealand. The model works in two stages: firstly predicting the number of new cases and secondly estimating the proportion of those cases that will need hospital treatment. The model produces a range of likely values, which is important because is impossible to predict with 100% accuracy. We show that the model does a reasonably good job of predicting hospitalisations up to 3 weeks ahead. The model has been used by public health agencies in Aotearoa New Zealand to help with healthcare capacity planning.",
+    "rel_abs": "Near-term forecasting of infectious disease incidence and consequent demand for acute healthcare services can support capacity planning and public health responses. Despite well-developed scenario modelling to support the Covid-19 response, Aotearoa New Zealand lacks advanced infectious disease forecasting capacity. We develop a model using Aotearoa New Zealand's unique Covid-19 data streams to predict reported Covid-19 cases, hospital admissions and hospital occupancy. The method combines a semi-mechanistic model for disease transmission to predict cases with Gaussian process regression models to predict the fraction of reported cases that will require hospital treatment. We evaluate forecast performance against out-of-sample data over the period from 2 October 2022 to 23 July 2023. Our results show that forecast performance is reasonably good over a 1-3 week time horizon, although generally deteriorates as the time horizon is lengthened. The model has been operationalised to provide weekly national and regional forecasts in real-time. This study is an important step towards development of more sophisticated situational awareness and infectious disease forecasting tools in Aotearoa New Zealand.",
     "rel_num_authors": 3,
     "rel_authors": [
       {
@@ -23114,7 +23547,7 @@
     "rel_date": "2023-09-25",
     "rel_site": "medRxiv",
     "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.22.23295541",
-    "rel_abs": "Our understanding of the quality of cellular and humoral immunity conferred by COVID-19 vaccination alone versus vaccination plus SARS-CoV-2 breakthrough (BT) infection remains incomplete. While the current (2023) SARS-CoV-2 immune landscape of Canadians is complex, in late 2021 most Canadians had either just received a third dose of COVID-19 vaccine, or had received their two dose primary series and then experienced an Omicron BT. Herein we took advantage of this coincident timing to contrast cellular and humoral immunity conferred by three doses of vaccine versus two doses plus BT. Our results show that mild BT infection induces cell-mediated immune responses to variants comparable to an intramuscular vaccine booster dose. In contrast, BT subjects had higher salivary IgG and IgA levels against the Omicron Spike and enhanced reactivity to the ancestral Spike for the IgA isotype, which also reacted with SARS-CoV-1. Serum neutralizing antibody levels against the ancestral strain and the variants were also higher after BT infection. Our results support the need for mucosal vaccines to emulate the enhanced mucosal and humoral immunity induced by Omicron without exposing individuals to the risks associated with SARS-CoV-2 infection.\n\nONE SENTENCE SUMMARYOmicron breakthrough elicits cross-reactive systemic and mucosal immune responses in fully vaccinated adults.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC=\"FIGDIR/small/23295541v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (27K):\norg.highwire.dtl.DTLVardef@13b8769org.highwire.dtl.DTLVardef@1373999org.highwire.dtl.DTLVardef@a6915corg.highwire.dtl.DTLVardef@1915447_HPS_FORMAT_FIGEXP  M_FIG C_FIG",
+    "rel_abs": "Our understanding of the quality of cellular and humoral immunity conferred by COVID-19 vaccination alone versus vaccination plus SARS-CoV-2 breakthrough (BT) infection remains incomplete. While the current (2023) SARS-CoV-2 immune landscape of Canadians is complex, in late 2021 most Canadians had either just received a third dose of COVID-19 vaccine, or had received their two dose primary series and then experienced an Omicron BT. Herein we took advantage of this coincident timing to contrast cellular and humoral immunity conferred by three doses of vaccine versus two doses plus BT. Our results show that mild BT infection induces cell-mediated immune responses to variants comparable to an intramuscular vaccine booster dose. In contrast, BT subjects had higher salivary IgG and IgA levels against the Omicron Spike and enhanced reactivity to the ancestral Spike for the IgA isotype, which also reacted with SARS-CoV-1. Serum neutralizing antibody levels against the ancestral strain and the variants were also higher after BT infection. Our results support the need for mucosal vaccines to emulate the enhanced mucosal and humoral immunity induced by Omicron without exposing individuals to the risks associated with SARS-CoV-2 infection.\n\nONE SENTENCE SUMMARYOmicron breakthrough elicits cross-reactive systemic and mucosal immune responses in fully vaccinated adults.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC=\"FIGDIR/small/23295541v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (27K):\norg.highwire.dtl.DTLVardef@39b305org.highwire.dtl.DTLVardef@183147org.highwire.dtl.DTLVardef@4b68e3org.highwire.dtl.DTLVardef@d326d3_HPS_FORMAT_FIGEXP  M_FIG C_FIG",
     "rel_num_authors": 22,
     "rel_authors": [
       {
@@ -23360,145 +23793,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2023.09.22.23295850",
-    "rel_title": "Group A streptococcal cases and treatments during the COVID-19 pandemic and 2022 outbreak: a retrospective cohort study in England using OpenSAFELY-TPP",
-    "rel_date": "2023-09-23",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.22.23295850",
-    "rel_abs": "ObjectiveTo investigate the impact of the COVID-19 pandemic on Group A streptococcal (GAS) cases and related antibiotic prescriptions.\n\nDesignA retrospective cohort study with supporting dashboards with the approval of NHS England.\n\nSettingPrimary care practices in England using TPP SystmOne software from January 2018 through March 2023.\n\nParticipantsPatients included were those registered at a TPP practice for each month of the study period. Patients with missing sex or age were excluded, resulting in a population of 23,816,470 in January 2018, increasing to 25,541,940 by March 2023.\n\nMain outcome measuresWe calculated monthly counts and crude rates of GAS cases (sore throat/tonsillitis, scarlet fever, invasive group A strep) and prescriptions linked with a GAS case, before (pre-April 2020), during and after (post-April 2021) COVID-19 restrictions. We calculated the maximum and minimum count and rate for each season (years running September-August), and the rate ratio (RR) of the 2022/23 season to the last comparably high season (2017/18).\n\nResultsRecording of GAS cases and antibiotic prescription linked with a GAS case peaked in December 2022, higher than the 2017/2018 peak. The peak rate of monthly sore throat/tonsillitis (possible group A strep throat) recording was 5.33 per 1,000 (RR 2022/23 versus 2017/18 1.39 (CI: 1.38 to 1.40)). Scarlet fever recording peaked at 0.51 per 1,000 (RR 2.68 (CI: 2.59 to 2.77)), and invasive group A streptococcal infection (iGAS) at 0.01 per 1,000 (RR 4.37 (CI: 2.94 to 6.48)). First line antibiotics with a record of a GAS infection peaked at 2.80 per 1,000 (RR 1.37 (CI:1.35 to 1.38)), alternative antibiotics at 2.03 per 1,000 (RR 2.30 (CI:2.26 to 2.34)), and reserved antibiotics at 0.09 per 1,000 (RR 2.42 (CI:2.24 to 2.61). For individual antibiotics, azithromycin with GAS indication showed the greatest relative increase (RR 7.37 (CI:6.22 to 8.74)).This followed a sharp drop in recording of cases and associated prescriptions during the period of COVID-19 restrictions where the maximum count and rates were lower than any pre COVID-19 minimum.\n\nMore detailed demographic breakdowns can be found in our regularly updated dashboard report.\n\nConclusionsRates of scarlet fever, sore throat/tonsillitis and iGAS recording and associated antibiotic prescribing peaked in December 2022. Primary care data can supplement existing infectious disease surveillance through linkages with relevant prescribing data and detailed clinical and demographic subgroups.\n\nWhat is knownDuring the COVID-19 pandemic there has been a substantial change to the pattern of circulating viruses and bacteria that cause illnesses. A spike in group A streptococcal infections in England starting December 2022 was associated with 426 deaths, including 48 children as of 7th May 2023. Increased demand for antibiotics in this period led to medicines shortages and the introduction of Serious Shortage Protocols (SSPs). Existing surveillance systems such as notifiable disease reports and GP in-hours surveillance bulletins describe clinical events, but they do not link to relevant prescribing data.\n\nWhat this study adds- This study supports the findings of routine surveillance reports which indicated a drop in GAS infections during the COVID-19 restrictions, followed by a spike in December 2022, demonstrating that the OpenSAFELY platform and primary care data can be used to rapidly describe not only clinical events but also relevant prescribing in the case of future outbreaks.\n- Antibiotic prescribing with a GAS indication, particularly for phenoxymethylpenicillin alternatives and reserved antibiotics, was higher in the December 2022 peak than in the 2017/2018 peak.",
-    "rel_num_authors": 31,
-    "rel_authors": [
-      {
-        "author_name": "Christine Cunningham",
-        "author_inst": "Bennett Institute for Applied Data Science, University of Oxford"
-      },
-      {
-        "author_name": "Louis Fisher",
-        "author_inst": "Bennett Institute for Applied Data Science, University of Oxford"
-      },
-      {
-        "author_name": "Christopher Wood",
-        "author_inst": "Bennett Institute for Applied Data Science, University of Oxford"
-      },
-      {
-        "author_name": "- The OpenSAFELY Collaborative",
-        "author_inst": "-"
-      },
-      {
-        "author_name": "Victoria Speed",
-        "author_inst": "Bennett Institute for Applied Data Science, University of Oxford"
-      },
-      {
-        "author_name": "Andrew D Brown",
-        "author_inst": "Bennett Institute for Applied Data Science, University of Oxford"
-      },
-      {
-        "author_name": "Helen J Curtis",
-        "author_inst": "Bennett Institute for Applied Data Science, University of Oxford"
-      },
-      {
-        "author_name": "Rose Higgins",
-        "author_inst": "Bennett Institute for Applied Data Science, University of Oxford"
-      },
-      {
-        "author_name": "Richard Croker",
-        "author_inst": "Bennett Institute for Applied Data Science, University of Oxford"
-      },
-      {
-        "author_name": "Ben FC Butler-Cole",
-        "author_inst": "Bennett Institute for Applied Data Science, University of Oxford"
-      },
-      {
-        "author_name": "David Evans",
-        "author_inst": "Bennett Institute for Applied Data Science, University of Oxford"
-      },
-      {
-        "author_name": "Peter Inglesby",
-        "author_inst": "Bennett Institute for Applied Data Science, University of Oxford"
-      },
-      {
-        "author_name": "Iain Dillingham",
-        "author_inst": "Bennett Institute for Applied Data Science, University of Oxford"
-      },
-      {
-        "author_name": "Sebastian CJ Bacon",
-        "author_inst": "Bennett Institute for Applied Data Science, University of Oxford"
-      },
-      {
-        "author_name": "Elizabeth Beech",
-        "author_inst": "NHS England"
-      },
-      {
-        "author_name": "Kieran Hand",
-        "author_inst": "NHS England"
-      },
-      {
-        "author_name": "Simon Davy",
-        "author_inst": "Bennett Institute for Applied Data Science, University of Oxford"
-      },
-      {
-        "author_name": "Tom Ward",
-        "author_inst": "Bennett Institute for Applied Data Science, University of Oxford"
-      },
-      {
-        "author_name": "George Hickman",
-        "author_inst": "Bennett Institute for Applied Data Science, University of Oxford"
-      },
-      {
-        "author_name": "Lucy Bridges",
-        "author_inst": "Bennett Institute for Applied Data Science, University of Oxford"
-      },
-      {
-        "author_name": "Tom O'Dwyer",
-        "author_inst": "Bennett Institute for Applied Data Science, University of Oxford"
-      },
-      {
-        "author_name": "Steven Maude",
-        "author_inst": "Bennett Institute for Applied Data Science, University of Oxford"
-      },
-      {
-        "author_name": "Rebecca M Smith",
-        "author_inst": "Bennett Institute for Applied Data Science, University of Oxford"
-      },
-      {
-        "author_name": "Amir Mehrkar",
-        "author_inst": "Bennett Institute for Applied Data Science, University of Oxford"
-      },
-      {
-        "author_name": "Liam C Hart",
-        "author_inst": "Bennett Institute for Applied Data Science, University of Oxford"
-      },
-      {
-        "author_name": "Chris Bates",
-        "author_inst": "TPP"
-      },
-      {
-        "author_name": "Jonathan Cockburn",
-        "author_inst": "TPP"
-      },
-      {
-        "author_name": "John Parry",
-        "author_inst": "TPP"
-      },
-      {
-        "author_name": "Frank Hester",
-        "author_inst": "TPP"
-      },
-      {
-        "author_name": "Ben Goldacre",
-        "author_inst": "Bennett Institute for Applied Data Science, University of Oxford"
-      },
-      {
-        "author_name": "Brian MacKenna",
-        "author_inst": "Bennett Institute for Applied Data Science, University of Oxford"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "primary care research"
-  },
   {
     "rel_doi": "10.1101/2023.09.21.23295904",
     "rel_title": "Impact of bivalent BA.4/5 BNT162b2 COVID-19 vaccine on acute symptoms, quality of life, work productivity and activity levels among symptomatic US adults testing positive for SARS-CoV-2 at a national retail pharmacy",
@@ -23881,6 +24175,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2023.09.19.23295768",
+    "rel_title": "COVID-19 VACCINE ACCEPTANCE AND HESITANCY IN GHANA: A SYSTEMATIC REVIEW",
+    "rel_date": "2023-09-21",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.19.23295768",
+    "rel_abs": "The propensity to accept vaccines and factors that affect vaccine acceptance and hesitancy will determine the overall success of the COVID-19 vaccination program. Therefore, it is essential for countries to understand the factors that influence vaccine acceptance and hesitancy in order to prevent further future shocks, and it is necessary to have a thorough understanding of these factors. This study, as a result, aims to review selected published works in the domain of study and conduct valuable analysis to determine the most influential factors in COVID-19 vaccine acceptance and hesitancy in Ghana. The review also explored the acceptance rate of COVID-19 vaccines in Ghana. We selected published works from 2021 to April 2023 and extracted, analyzed, and summarized the findings based on the key factors that influence COVID-19 vaccine acceptance and hesitancy in Ghana, the acceptance rate in Ghana, the demographic factors that are often examined, and the study approach used to examine these factors. The study found that positive vaccination perception, safety, belief in vaccine efficacy, knowledge of COVID-19, and a good vaccine attitude influence COVID-19 vaccine acceptance in Ghana. The negative side effects of the vaccines, mistrust in the vaccine, lack of confidence in the safety of the vaccines, fear, and spiritual and religious beliefs all played significant roles in the factors influencing COVID-19 vaccine hesitancy. The demographic parameters frequently included in these studies that have a significant impact include educational attainment, gender, religious affiliation, age, and marital status.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Godwin  Banafo Akrong",
+        "author_inst": "University of Electronic Science and Technology of China School of Economics and Management"
+      },
+      {
+        "author_name": "Rosemond  Akpene Hiadzi",
+        "author_inst": "University of Ghana College of Humanities"
+      },
+      {
+        "author_name": "Antonia  Bernadette Donkor",
+        "author_inst": "University of Ghana Balme Library"
+      },
+      {
+        "author_name": "Daniel  Kwasi Anafo",
+        "author_inst": "University of Ghana"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2023.09.20.558551",
     "rel_title": "COVID-19 ORF3a Viroporin Influenced Common and Unique Cellular Signalling Cascades in Lung, Heart and Brain Choroid Plexus Organoids with Additional Enriched MicroRNA Network Analyses for Lung and Brain Tissues",
@@ -25274,109 +25599,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2023.09.14.557399",
-    "rel_title": "Cooperativity and induced oligomerisation control the interaction of SARS- CoV-2 with its cellular receptor and patient-derived antibodies",
-    "rel_date": "2023-09-15",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.14.557399",
-    "rel_abs": "Viral entry is mediated by oligomeric proteins on the virus and cell surfaces. The association is therefore open to multivalent interactions between these proteins, yet such recognition is typically rationalised as affinity between monomeric equivalents. As a result, assessment of the thermodynamic mechanisms that control viral entry has been limited. Here, we use mass photometry to overcome the analytical challenges consequent to multivalency. Examining the interaction between the spike protein of SARS-CoV-2 and the ACE2 receptor, we find that ACE2 induces oligomerisation of spike in a variant-dependent fashion. We also demonstrate that patient-derived antibodies use induced-oligomerisation as a primary inhibition mechanism or to enhance the effects of receptor-site blocking. Our results reveal that naive affinity measurements are poor predictors of potency, and introduce a novel antibody-based inhibition mechanism for oligomeric targets.\n\nOne-Sentence SummaryMultivalent interactions between viral proteins, cell-surface receptors, and anti-viral antibodies regulate infection and inhibition.",
-    "rel_num_authors": 22,
-    "rel_authors": [
-      {
-        "author_name": "Roi Asor",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Anna Olerinyova",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Sean A Burnap",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Manish S Kushwah",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Fabian Soltermann",
-        "author_inst": "Oxford University"
-      },
-      {
-        "author_name": "Luca P Rudden",
-        "author_inst": "EPFL"
-      },
-      {
-        "author_name": "Mario Hensen",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Snezana Vasiljevic",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Julian Brun",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Michelle Hill",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Liu Chang",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Wanwisa Dejnirattisai",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Piyada Supasa",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Juthathip Mongkolsapaya",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Daming Zhou",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "David  I. Stuart",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Gavin Screaton",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Matteo Degiacomi",
-        "author_inst": "Durham University"
-      },
-      {
-        "author_name": "Nicole Zitzmann",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Justin LP Benesch",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Weston B Struwe",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Philipp Kukura",
-        "author_inst": "University of Oxford"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "biophysics"
-  },
   {
     "rel_doi": "10.1101/2023.09.14.557558",
     "rel_title": "MixOmics Integration of Biological Datasets Identifies Highly Correlated Key Variables of COVID-19 severity.",
@@ -25663,6 +25885,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2023.09.12.23294140",
+    "rel_title": "Effectiveness of Canadian travel restrictions in reducing burden of SARS-CoV-2 variants of concern",
+    "rel_date": "2023-09-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.12.23294140",
+    "rel_abs": "Evaluating travel restriction effectiveness in mitigating infectious disease burden is critical for informing public health policy. Here, we quantify where and when variants of SARS-CoV-2 were introduced into Canada to evaluate the extent to which travel restrictions averted viral introductions and COVID-19 case burden. Our results suggest that, across SARS-CoV-2 variants of concern subject to travel restrictions, at least 281 introductions were prevented, accounting for an averted burden of approximately 44,064 cases. This corresponds to approximately 441 averted hospitalizations, 24 averted deaths, and cost savings to Canadian health care systems of approximately 11.2 million Canadian dollars. Travel restrictions were found to be most effective when implemented rapidly during exponential case growth in the focal source and when global circulation was limited. Our analyses reveal that COVID-19 travel restrictions mitigated case burdens and highlight their value in future pandemic response.\n\nSummaryCOVID-19 travel restrictions against variants worked and were most effective when implemented rapidly and preceding new variants wider circulation.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Angela McLaughlin",
+        "author_inst": "Bioinformatics, University of British Columbia; British Columbia Centre for Excellence in HIV/AIDS"
+      },
+      {
+        "author_name": "Vincent Montoya",
+        "author_inst": "British Columbia Centre for Excellence in HIV/AIDS"
+      },
+      {
+        "author_name": "Rachel L Miller",
+        "author_inst": "British Columbia Centre for Excellence in HIV/AIDS"
+      },
+      {
+        "author_name": "- Canadian COVID-19 Genomics Network (CanCOGeN) Consortium",
+        "author_inst": "-"
+      },
+      {
+        "author_name": "Michael Worobey",
+        "author_inst": "Department of Ecology and Evolutionary Biology, University of Arizona"
+      },
+      {
+        "author_name": "Jeffrey B Joy",
+        "author_inst": "Department of Medicine, University of British Columbia; British Columbia Centre for Excellence in HIV/AIDS"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2023.09.13.557622",
     "rel_title": "Proximal immune-epithelial progenitor interactions drive chronic tissue sequelae post COVID-19",
@@ -26764,77 +27025,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2023.09.11.557206",
-    "rel_title": "Immune Evasion, Infectivity, and Fusogenicity of SARS-CoV-2 Omicron BA.2.86 and FLip Variants",
-    "rel_date": "2023-09-12",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.11.557206",
-    "rel_abs": "Evolution of SARS-CoV-2 requires the reassessment of current vaccine measures. Here, we characterized BA.2.86 and the XBB-lineage variant FLip by investigating their neutralization alongside D614G, BA.1, BA.2, BA.4/5, XBB.1.5, and EG.5.1 by sera from 3-dose vaccinated and bivalent vaccinated healthcare workers, XBB.1.5-wave infected first responders, and monoclonal antibody (mAb) S309. We assessed the biology of the variant Spikes by measuring viral infectivity and membrane fusogenicity. BA.2.86 is less immune evasive compared to FLip and other XBB variants, consistent with antigenic distances. Importantly, distinct from XBB variants, mAb S309 was unable to neutralize BA.2.86, likely due to a D339H mutation based on modeling. BA.2.86 had relatively high fusogenicity and infectivity in CaLu-3 cells but low fusion and infectivity in 293T-ACE2 cells compared to some XBB variants, suggesting a potentially differences conformational stability of BA.2.86 Spike. Overall, our study underscores the importance of SARS-CoV-2 variant surveillance and the need for updated COVID-19 vaccines.",
-    "rel_num_authors": 14,
-    "rel_authors": [
-      {
-        "author_name": "Panke Qu",
-        "author_inst": "The Ohio State University"
-      },
-      {
-        "author_name": "Kai Xu",
-        "author_inst": "The Ohio State University"
-      },
-      {
-        "author_name": "Julia N. Faraone",
-        "author_inst": "The Ohio State University"
-      },
-      {
-        "author_name": "Negin Goodarzi",
-        "author_inst": "The Ohio State University"
-      },
-      {
-        "author_name": "Yi-Min Zheng",
-        "author_inst": "The Ohio State University"
-      },
-      {
-        "author_name": "Claire Carlin",
-        "author_inst": "The Ohio State University"
-      },
-      {
-        "author_name": "Joseph S. Bednash",
-        "author_inst": "The Ohio State University"
-      },
-      {
-        "author_name": "Jeffrey C. Horowitz",
-        "author_inst": "The Ohio State University"
-      },
-      {
-        "author_name": "Rama K. Mallampalli",
-        "author_inst": "The Ohio State University"
-      },
-      {
-        "author_name": "Linda J. Saif",
-        "author_inst": "The Ohio State University"
-      },
-      {
-        "author_name": "Eugene M. Oltz",
-        "author_inst": "The Ohio State University"
-      },
-      {
-        "author_name": "Daniel Jones",
-        "author_inst": "The Ohio State University"
-      },
-      {
-        "author_name": "Richard J. Gumina",
-        "author_inst": "The Ohio State University"
-      },
-      {
-        "author_name": "Shan-Lu Liu",
-        "author_inst": "The Ohio State University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2023.09.11.557292",
     "rel_title": "WELPCR: Low-cost polymerase chain reaction (PCR) thermal cycler for nucleic acid amplification and sensing",
@@ -27113,6 +27303,121 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2023.09.12.23295384",
+    "rel_title": "Determinants of de novo B cell responses to drifted epitopes in post-vaccination SARS-CoV-2 infections",
+    "rel_date": "2023-09-12",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.12.23295384",
+    "rel_abs": "Vaccine-induced immunity may impact subsequent de novo responses to drifted epitopes in SARS-CoV-2 variants, but this has been difficult to quantify due to the challenges in recruiting unvaccinated control groups whose first exposure to SARS-CoV-2 is a primary infection. Through local, statewide, and national SARS-CoV-2 testing programs, we were able to recruit cohorts of individuals who had recovered from either primary or post-vaccination infections by either the Delta or Omicron BA.1 variants. Regardless of variant, we observed greater Spike-specific and neutralizing antibody responses in post-vaccination infections than in those who were infected without prior vaccination. Through analysis of variant-specific memory B cells as markers of de novo responses, we observed that Delta and Omicron BA.1 infections led to a marked shift in immunodominance in which some drifted epitopes elicited minimal responses, even in primary infections. Prior immunity through vaccination had a small negative impact on these de novo responses, but this did not correlate with cross-reactive memory B cells, arguing against competitive inhibition of naive B cells. We conclude that dampened de novo B cell responses against drifted epitopes are mostly a function of altered immunodominance hierarchies that are apparent even in primary infections, with a more modest contribution from pre-existing immunity, perhaps due to accelerated antigen clearance.",
+    "rel_num_authors": 25,
+    "rel_authors": [
+      {
+        "author_name": "Grace Quirk",
+        "author_inst": "University of Arizona"
+      },
+      {
+        "author_name": "Marta V Schoenle",
+        "author_inst": "University of Arizona"
+      },
+      {
+        "author_name": "Kameron L Peyton",
+        "author_inst": "University of Arizona"
+      },
+      {
+        "author_name": "Jennifer L Uhrlaub",
+        "author_inst": "University of Arizona"
+      },
+      {
+        "author_name": "Branden Lau",
+        "author_inst": "University of Arizona"
+      },
+      {
+        "author_name": "Jeffrey Burgess",
+        "author_inst": "University of Arizona"
+      },
+      {
+        "author_name": "Katherine Ellingson",
+        "author_inst": "University of Arizona"
+      },
+      {
+        "author_name": "Shawn Beitel",
+        "author_inst": "University of Arizona"
+      },
+      {
+        "author_name": "James Romine",
+        "author_inst": "University of Arizona"
+      },
+      {
+        "author_name": "Karen Lutrick",
+        "author_inst": "University of Arizona"
+      },
+      {
+        "author_name": "Ashley Fowlkes",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Amadea Britton",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Harmony Tyner",
+        "author_inst": "St. Luke's Regional Health Care System"
+      },
+      {
+        "author_name": "Alberto Caban-Martinez",
+        "author_inst": "University of Miami, Miller School of Medicine"
+      },
+      {
+        "author_name": "Allison Naleway",
+        "author_inst": "Kaiser Permanente Northwest Center for Health Research"
+      },
+      {
+        "author_name": "Manjusha Gaglani",
+        "author_inst": "Baylor Scott & White Health and Texas A and M University College of Medicine"
+      },
+      {
+        "author_name": "Sarang Yoon",
+        "author_inst": "University of Utah"
+      },
+      {
+        "author_name": "Laura Edwards",
+        "author_inst": "Abt Associates"
+      },
+      {
+        "author_name": "Lauren Olsho",
+        "author_inst": "Abt Associates"
+      },
+      {
+        "author_name": "Michael D Dake",
+        "author_inst": "University of Arizona"
+      },
+      {
+        "author_name": "Bonnie LaFleur",
+        "author_inst": "University of Arizona"
+      },
+      {
+        "author_name": "Janko Z Nikolich",
+        "author_inst": "University of Arizona"
+      },
+      {
+        "author_name": "Ryan Sprissler",
+        "author_inst": "University of Arizona"
+      },
+      {
+        "author_name": "Michael Worobey",
+        "author_inst": "University of Arizona"
+      },
+      {
+        "author_name": "Deepta Bhattacharya",
+        "author_inst": "University of Arizona"
+      }
+    ],
+    "version": "1",
+    "license": "cc0",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2023.09.11.23295394",
     "rel_title": "Sexual Gender-Based Violence among Adolescent Girls and Young Women during COVID-19 Pandemic, Mid-Eastern Uganda",
@@ -28606,61 +28911,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2023.09.07.554570",
-    "rel_title": "Stereotypic persistent B cell receptor clonotypes in Alzheimer's Disease",
-    "rel_date": "2023-09-08",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.07.554570",
-    "rel_abs": "We constructed B cell receptor (BCR) repertoires in silico using peripheral blood (PB) samples collected from 44 Alzheimers Disease (AD) patients at baseline and 37 patients at follow-up. For the control group (CG), we used BCR repertoire data from the chronologically collected PB samples of 55 healthy volunteers vaccinated with SARS-CoV-2 mRNA. The AD patients shared 3,983 stereotypic non-naive BCR clonotypes not found in CG, and their degree of overlap between patient pairs were significantly higher than that of CG pairs, even with the SARS-CoV-2 spike protein triggering a concerted BCR response. Twenty stereotypic non-naive AD patient-specific BCR clonotypes co-existed in more than four patients and persisted throughout two sampling points. One of these BCR clonotypes encoded an antibody reactive to the A{beta}42 peptide. Our findings strongly suggest that AD patients are exposed to common (auto)antigens associated with disease pathology, and their BCR repertoires show unique signatures with diagnostic potential.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Hyunji Yang",
-        "author_inst": "Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea"
-      },
-      {
-        "author_name": "Namphil Kim",
-        "author_inst": "Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea"
-      },
-      {
-        "author_name": "Yonghee Lee",
-        "author_inst": "Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea"
-      },
-      {
-        "author_name": "Duck Kyun Yoo",
-        "author_inst": "Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA"
-      },
-      {
-        "author_name": "Jinny Choi",
-        "author_inst": "Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea"
-      },
-      {
-        "author_name": "Kiwoong Kim",
-        "author_inst": "Department of Neuropsychiatry, Seoul National University Bundang Hospital, Gyeonggido, Republic of Korea"
-      },
-      {
-        "author_name": "Jongbin Bae",
-        "author_inst": "Department of Neuropsychiatry, Seoul National University Bundang Hospital, Gyeonggido, Republic of Korea"
-      },
-      {
-        "author_name": "Jiwon Han",
-        "author_inst": "Department of Neuropsychiatry, Seoul National University Bundang Hospital, Gyeonggido, Republic of Korea"
-      },
-      {
-        "author_name": "Sunghoon Kwon",
-        "author_inst": "Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea"
-      },
-      {
-        "author_name": "Junho Chung",
-        "author_inst": "Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2023.09.08.556788",
     "rel_title": "SARS-CoV-2 ORF8 modulates lung inflammation and clinical disease progression",
@@ -29167,6 +29417,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2023.09.08.23295177",
+    "rel_title": "Systematical assessment of the impact of single spike mutations of SARS-CoV-2 Omicron sub-variants on the neutralization capacity of post-vaccination sera",
+    "rel_date": "2023-09-08",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.08.23295177",
+    "rel_abs": "The evolution of novel SARS-CoV-2 variants significantly affects vaccine effectiveness. While these effects can only be studied retrospectively, neutralizing antibody titers are most used as correlates of protection. However, studies assessing neutralizing antibody titers often show heterogeneous data. To address this, we investigated assay variance and identified virus infection time and dose as factors affecting assay robustness. We next measured neutralization against Omicron sub-variants in cohorts with hybrid or vaccine induced immunity, identifying a gradient of immune escape potential. To evaluate the effect of individual mutations on this immune escape potential of Omicron variants, we systematically assessed the effect of each individual mutation specific to Omicron BA.1, BA.2, BA.2.12.1, and BA.4/5. We cloned a library of pseudo-viruses expressing spikes with single point mutations, and subjected it to pooled sera from vaccinated hosts, thereby identifying multiple mutations that independently affect neutralization potency. These data might help to predict antigenic features of novel viral variants carrying these mutations and support the development of broad monoclonal antibodies.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Maeva Katzmarzyk",
+        "author_inst": "Department of Viral Immunology; Helmholtz Centre for Infection Research; Braunschweig, 38124, Germany"
+      },
+      {
+        "author_name": "Denise Christine Clesle",
+        "author_inst": "Department of Viral Immunology; Helmholtz Centre for Infection Research; Braunschweig, 38124, Germany"
+      },
+      {
+        "author_name": "Joop van den Heuvel",
+        "author_inst": "Department of Recombinant Protein Expression; Helmholtz Centre for Infection Research; Braunschweig, 38124; Germany"
+      },
+      {
+        "author_name": "Markus Hoffmann",
+        "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung"
+      },
+      {
+        "author_name": "Henk Garritsen",
+        "author_inst": "Institute for Clinical Transfusion Medicine, Klinikum Braunschweig GmbH, Braunschweig, 38114 Germany and Fraunhofer Institute for Surface Engineering and Thin F"
+      },
+      {
+        "author_name": "Stefan Poehlmann",
+        "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung"
+      },
+      {
+        "author_name": "Henning Jacobsen",
+        "author_inst": "Department of Viral Immunology; Helmholtz Centre for Infection Research; Braunschweig, 38124, Germany"
+      },
+      {
+        "author_name": "Luka Cicin-Sain",
+        "author_inst": "Department of Viral Immunology; Helmholtz Centre for Infection Research; Braunschweig, 38124, Germany"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2023.09.07.23295183",
     "rel_title": "Comparison of Different PCR Methods for the Detection of SARS-CoV-2 RNA in Wastewater Based on the Reported Incidence of COVID-19 in Finland",
@@ -30568,49 +30865,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health economics"
   },
-  {
-    "rel_doi": "10.1101/2023.09.03.23294798",
-    "rel_title": "SARS-CoV-2 quarantine mandated by contact tracing: burden and infection rate among close contacts in Zurich, Switzerland, 2020-2021",
-    "rel_date": "2023-09-05",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.03.23294798",
-    "rel_abs": "ObjectivesBefore vaccines and effective treatments were available, quarantine of close contacts was important to limit the spread of SARS-CoV-2. To evaluate potential benefits and harms of quarantine, we aimed to estimate infection rates and describe experiences and mental health among persons in mandated quarantine during the early SARS-CoV-2 pandemic.\n\nMethodsWe invited adults in mandated quarantine after an exposure to SARS-CoV-2 identified through contact tracing of the Canton of Zurich, Switzerland, between August 2020 and January 2021. Participants completed two questionnaires and received up to two SARS-CoV-2 polymerase chain reaction tests, during and at the end of quarantine.\n\nResultsAmong 395 participants, quarantine duration ranged from 2 to 20 days. By day 11 since the last contact, 11.1% [95% CI 8.4%-14.7%] were infected with SARS-CoV-2. The proportion of participants with symptoms of depression doubled from 9.3% before quarantine to 18.9% during quarantine, and 12.1% reported quarantine was very or extremely difficult.\n\nConclusionsAlthough quarantine was only moderately burdensome for most participants, some experienced significant difficulties and burden. Policymakers need to balance infection control with potential harms placed on individuals.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "H\u00e9l\u00e8ne Eloise Aschmann",
-        "author_inst": "University of California, San Francisco"
-      },
-      {
-        "author_name": "Anja Domenghino",
-        "author_inst": "University Hospital Zurich, Department of Visceral and Transplantation Surgery"
-      },
-      {
-        "author_name": "Ruedi Jung",
-        "author_inst": "University of Zurich, Epidemiology, Biostatistics and Prevention Institute"
-      },
-      {
-        "author_name": "Tala Ballouz",
-        "author_inst": "University of Zurich, Epidemiology, Biostatistics and Prevention Institute"
-      },
-      {
-        "author_name": "Dominik Menges",
-        "author_inst": "University of Zurich, Epidemiology, Biostatistics and Prevention Institute"
-      },
-      {
-        "author_name": "Jan Fehr",
-        "author_inst": "University of Zurich, Epidemiology, Biostatistics and Prevention Institute"
-      },
-      {
-        "author_name": "Milo Alan Puhan",
-        "author_inst": "University of Zurich, Epidemiology, Biostatistics and Prevention Institute"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2023.08.28.555008",
     "rel_title": "Reference materials for SARS-CoV-2 molecular diagnostic: validation of encapsulated synthetic RNAs for room temperature storage and shipping",
@@ -30945,6 +31199,69 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2023.09.02.556038",
+    "rel_title": "Neutralization of SARS-CoV-2 EG.5/EG.5.1 by sera from ZF2001 RBD-dimer and its next-generation vaccines",
+    "rel_date": "2023-09-04",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.02.556038",
+    "rel_abs": "SARS-CoV-2 Omicron EG.5 and EG.5.1 are surging in several areas of the world, including China. Compared with XBB.1, EG.5 contains additional mutations of F456L and S486P in the spike protein receptor binding domain (RBD) and its subvariant EG.5.1 carries a further spike mutation Q52H. The immune escape potential of EG.5/EG.5.1 is of great concern. In this study, we evaluated the neutralization activities of sera from participants who received COVID-19 inactivated vaccines, protein subunit vaccine ZF2001 or a booster vaccination of Delta-BA.5 RBD-heterodimer protein vaccine, and participants who had a breakthrough infection during a wave of BF.7/BA.5.2 circulation in December 2022. Neutralization profiles elicited by bivalent RBD-heterodimer vaccine candidates containing XBB.1.5 antigen were evaluated in a murine model. We found that EG.5 and EG.5.1 displayed similar immune evasion potential to XBB.1 and XBB.1.5. The Delta-BA.5 RBD-heterodimer booster induced higher neutralizing titers against the tested XBB subvariants, including EG.5 and EG.5.1, than breakthrough infection by BF.7 or BA.5.2. In addition, Delta-XBB.1.5 and BQ.1.1-XBB.1.5 RBD-heterodimer vaccines induced high neutralizing activities against XBB sub-variants in a murine model, suggesting that next-generation COVID-19 vaccines with updated components must be developed to enhance the protection efficacy against the circulating SARS-CoV-2 strains.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Yaling An",
+        "author_inst": "Savaid Medical School, University of Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Xuemei Zhou",
+        "author_inst": "School of Life Sciences, Hebei University"
+      },
+      {
+        "author_name": "Lifeng Tao",
+        "author_inst": "Anhui Zhifei Longcom Biopharmaceutical Co. Ltd"
+      },
+      {
+        "author_name": "Haitang Xie",
+        "author_inst": "Yijishan Hospital of Wannan Medical College"
+      },
+      {
+        "author_name": "Chenxi Yang",
+        "author_inst": "Institute of Microbiology, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Dedong Li",
+        "author_inst": "College of Veterinary Medicine, China Agricultural University"
+      },
+      {
+        "author_name": "Ruyue Wang",
+        "author_inst": "Anhui Zhifei Longcom Biopharmaceutical Co. Ltd"
+      },
+      {
+        "author_name": "Hua Hu",
+        "author_inst": "Yijishan Hospital of Wannan Medical College"
+      },
+      {
+        "author_name": "Kefang Liu",
+        "author_inst": "Institute of Microbiology, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Lianpan Dai",
+        "author_inst": "Institute of Microbiology, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Kun Xu",
+        "author_inst": "Beijing Institutes of Life Science, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "George F. Gao",
+        "author_inst": "Institute of Microbiology Chinese Academy of Sciences"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2023.09.03.23295001",
     "rel_title": "COVID-19 vaccines and autoimmune disorders: A scoping review protocol",
@@ -32238,121 +32555,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2023.08.30.555211",
-    "rel_title": "Convergent evolution of SARS-CoV-2 XBB lineages on receptor-binding domain 455-456 enhances antibody evasion and ACE2 binding",
-    "rel_date": "2023-08-31",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.30.555211",
-    "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) XBB lineages have achieved dominance worldwide and keep on evolving. Convergent evolution of XBB lineages on the receptor-binding domain (RBD) L455F and F456L is observed, resulting in variants like EG.5, FL.1.5.1, XBB.1.5.70, and HK.3. Here, we show that neutralizing antibody (NAb) evasion drives the convergent evolution of F456L, while the epistatic shift caused by F456L enables the subsequent convergence of L455F through ACE2 binding enhancement and further immune evasion. L455F and F456L evade Class 1 NAbs, reducing the neutralization efficacy of XBB breakthrough infection (BTI) and reinfection convalescent plasma. Importantly, L455F single substitution significantly dampens receptor binding; however, the combination of L455F and F456L forms an adjacent residue flipping, which leads to enhanced NAbs resistance and ACE2 binding affinity. The perturbed receptor-binding mode leads to the exceptional ACE2 binding and NAb evasion, as revealed by structural analyses. Our results indicate the evolution flexibility contributed by epistasis cannot be underestimated, and the evolution potential of SARS-CoV-2 RBD remains high.",
-    "rel_num_authors": 25,
-    "rel_authors": [
-      {
-        "author_name": "Fanchong Jian",
-        "author_inst": "Peking University"
-      },
-      {
-        "author_name": "Leilei Feng",
-        "author_inst": "Institute of Biophysics, Chinese Academy of Sciences"
-      },
-      {
-        "author_name": "Sijie Yang",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Yuanling Yu",
-        "author_inst": "Changping Laboratory"
-      },
-      {
-        "author_name": "Lei Wang",
-        "author_inst": "Institute of Biophysics, Chinese Academy of Sciences"
-      },
-      {
-        "author_name": "Weiliang Song",
-        "author_inst": "Peking University"
-      },
-      {
-        "author_name": "Ayijiang Yisimayi",
-        "author_inst": "Peking University"
-      },
-      {
-        "author_name": "Xiaosu Chen",
-        "author_inst": "Nankai University"
-      },
-      {
-        "author_name": "Yanli Xu",
-        "author_inst": "Beijing Ditan Hospital"
-      },
-      {
-        "author_name": "Peng Wang",
-        "author_inst": "Changping Laboratory"
-      },
-      {
-        "author_name": "Lingling Yu",
-        "author_inst": "Changping Laboratory"
-      },
-      {
-        "author_name": "Jing Wang",
-        "author_inst": "Changping Laboratory"
-      },
-      {
-        "author_name": "Lu Liu",
-        "author_inst": "Changping Laboratory"
-      },
-      {
-        "author_name": "Xiao Niu",
-        "author_inst": "Peking University"
-      },
-      {
-        "author_name": "Jing Wang",
-        "author_inst": "Peking University"
-      },
-      {
-        "author_name": "Tianhe Xiao",
-        "author_inst": "Peking University"
-      },
-      {
-        "author_name": "Ran An",
-        "author_inst": "Changping Laboratory"
-      },
-      {
-        "author_name": "Yao Wang",
-        "author_inst": "Changping Laboratory"
-      },
-      {
-        "author_name": "Qingqing Gu",
-        "author_inst": "Changping Laboratory"
-      },
-      {
-        "author_name": "Fei Shao",
-        "author_inst": "Changping Laboratory"
-      },
-      {
-        "author_name": "Ronghua Jin",
-        "author_inst": "Beijing Ditan Hospital"
-      },
-      {
-        "author_name": "Zhongyang Shen",
-        "author_inst": "Nankai University"
-      },
-      {
-        "author_name": "Youchun Wang",
-        "author_inst": "Chinese Academy of Medical Science & Peking Union Medical College"
-      },
-      {
-        "author_name": "Xiangxi Wang",
-        "author_inst": "Institute of Biophysics, Chinese Academy of Sciences"
-      },
-      {
-        "author_name": "Yunlong Richard Cao",
-        "author_inst": "Peking University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2023.08.30.554497",
     "rel_title": "XBB.1.5 Spike Protein COVID-19 Vaccine Induces Broadly Neutralizing and Cellular Immune Responses Against EG.5.1 and Emerging XBB Variants",
@@ -32639,6 +32841,101 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2023.08.29.23293790",
+    "rel_title": "Outpatient treatment with concomitant vaccine-boosted convalescent plasma for patients with immunosuppression and COVID-19",
+    "rel_date": "2023-08-31",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.29.23293790",
+    "rel_abs": "Although severe coronavirus disease 19 (COVID-19) and hospitalization associated with COVID-19 are generally preventable among healthy vaccine recipients, patients with immunosuppression have poor immunogenic responses to COVID-19 vaccines and remain at high risk of infection with SARS-CoV-2 and hospitalization. Additionally, monoclonal antibody therapy is limited by the emergence of novel SARS-CoV-2 variants that have serially escaped neutralization. In this context, there is interest in understanding the clinical benefit associated with COVID-19 convalescent plasma collected from persons who have been both naturally infected with SARS-CoV-2 and vaccinated against SARS-CoV-2 (\"vax-plasma\"). Thus, we report the clinical outcome of 208 immunocompromised outpatients who were diagnosed with COVID-19 and who received contemporary COVID-19 specific therapeutics (standard of care group) and a subgroup who also received concomitant treatment with very high titer COVID-19 convalescent plasma (vax-plasma group) with a specific focus on hospitalization rates. The overall hospitalization rate was 1% (1 of 123 patients) in the vax-plasma group and 6% (5 of 85 patients) in the standard of care group, which corresponded to a relative risk reduction of 83%. Evidence of efficacy in nonvaccinated patients cannot be inferred from these data because 94% (196 of 208 patients) of patients were vaccinated. In vaccinated patients with immunosuppression and COVID-19, the addition of vax-plasma or very high titer COVID-19 convalescent plasma to COVID-19 specific therapies reduced the risk of disease progression leading to hospitalization.\n\nKey PointsO_LIAdministration of high-titer COVID-19 convalescent plasma was associated with a decreased incidence of hospitalization among immunocompromised outpatients who were diagnosed with COVID-19.\nC_LIO_LIHigh-titer COVID-19 convalescent plasma represents a promising therapeutic approach for patients with immunosuppression.\nC_LI",
+    "rel_num_authors": 20,
+    "rel_authors": [
+      {
+        "author_name": "Juan Ripoll Sanz",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Sidna Tulledge-Scheitel",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Shane Ford",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Marsha Pike",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Ellen K Gorman",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Sara N Hanson",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Justin E Juskewitch",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Raymund R Razonable",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Ravindra Ganesh",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Ryan T Hurt",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Erin N Fischer",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Amber N Derr",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Michelle R Eberle",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Jennifer J Larsen",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Christina M Carney",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Elitza S Theel",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Sameer A Parikh",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Neil E Kay",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Michael J Joyner",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Jonathon Senefeld",
+        "author_inst": "Mayo Clinic"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2023.08.28.23294715",
     "rel_title": "How much should we sequence? An analysis of the Swiss SARS- CoV-2 surveillance effort",
@@ -34208,109 +34505,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2023.08.27.23294704",
-    "rel_title": "Improvement of immune dysregulation and health-related quality of life in individuals with long COVID at 24-months following SARS-CoV-2 infection",
-    "rel_date": "2023-08-28",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.27.23294704",
-    "rel_abs": "This study investigated the humoral and cellular immune responses in individuals with long COVID (LC) compared to age and gender matched recovered COVID-19 controls (MC) over 24-months. LC participants showed elevated spike and nucleocapsid IgG levels, higher neutralizing capacity, and increased spike- and nucleocapsid-specific CD4+ T cells, PD-1, and TIM-3 expression on CD4+ and CD8+ T cells at 3- and 8-months, but these differences did not persist at 24-months. Some LC participants had detectable IFN-{gamma} and IFN-{beta}, that was attributed to reinfection and antigen re-exposure. Single-cell RNA sequencing at 24-month timepoint revealed similar immune cell proportions and reconstitution of naive T and B cell subsets in LC. No significant differences in exhaustion scores or antigen-specific T cell clones were observed. These findings suggest resolution of immune activation in LC and return to comparable immune responses between LC and MC over time. Improvement in self-reported health-related quality of life at 24-months was also evident in the majority of LC (62%). PTX3, CRP levels and platelet count were associated with improvements in health-related quality of life.",
-    "rel_num_authors": 22,
-    "rel_authors": [
-      {
-        "author_name": "Chansavath Phetsouphanh",
-        "author_inst": "The Kirby Institute, University of New South Wales"
-      },
-      {
-        "author_name": "Brendan Jacka",
-        "author_inst": "The Kirby Institute, UNSW"
-      },
-      {
-        "author_name": "Sara Ballouz",
-        "author_inst": "School of Computer Science and Engineering, Faculty of Engineering, University of New South Wales, Australia"
-      },
-      {
-        "author_name": "Katherine JL Jackson",
-        "author_inst": "Garvan Institute for Medical research, New South Wales, Australia"
-      },
-      {
-        "author_name": "Daniel B Wilson",
-        "author_inst": "The Kirby Institute, University of New South Wales, New South Wales, Australia"
-      },
-      {
-        "author_name": "Bikash Manandhar",
-        "author_inst": "The Kirby Institute, University of New South Wales, New South Wales, Australia"
-      },
-      {
-        "author_name": "Vera Klemm",
-        "author_inst": "The Kirby Institute, University of New South Wales, New South Wales, Australia"
-      },
-      {
-        "author_name": "Hyon-Xhi Tan",
-        "author_inst": "University of Melbourne, at The Peter Doherty Institute for Infection and Immunity"
-      },
-      {
-        "author_name": "Adam Wheatley",
-        "author_inst": "Department of Microbiology and Immunology, Peter Doherty Institute, University of Melbourne, Victoria, Australia"
-      },
-      {
-        "author_name": "Anupriya Aggarwal",
-        "author_inst": "The Kirby Institute, University of New South Wales, New South Wales, Australia"
-      },
-      {
-        "author_name": "Anouschka Akerman",
-        "author_inst": "The Kirby Institute, University of New South Wales, New South Wales, Australia"
-      },
-      {
-        "author_name": "Vanessa Milogiannakis",
-        "author_inst": "The Kirby Institute, University of New South Wales, New South Wales, Australia"
-      },
-      {
-        "author_name": "Mitchell Starr",
-        "author_inst": "St Vincents Centre for Applied Medical Research, Sydney, NSW, Australia"
-      },
-      {
-        "author_name": "Phillip Cunningham",
-        "author_inst": "St. Vincents Centre for Applied Medical Research, Sydney, NSW, Australia"
-      },
-      {
-        "author_name": "Stuart G Turville",
-        "author_inst": "The Kirby Institute, University of New South Wales, New South Wales, Australia"
-      },
-      {
-        "author_name": "Stephen J Kent",
-        "author_inst": "University of Melbourne"
-      },
-      {
-        "author_name": "Anthony Byrne",
-        "author_inst": "St. Vincents Hospital, Darlinghurst, New South Wales, Australia"
-      },
-      {
-        "author_name": "Bruce J Brew",
-        "author_inst": "St. Vincents Hospital, Darlinghurst, New South Wales, Australia"
-      },
-      {
-        "author_name": "David R Darley",
-        "author_inst": "St. Vincents Hospital, Darlinghurst, New South Wales, Australia"
-      },
-      {
-        "author_name": "Gregory J Dore",
-        "author_inst": "The Kirby Institute, University of New South Wales, New South Wales, Australia"
-      },
-      {
-        "author_name": "Anthony D Kelleher",
-        "author_inst": "University of New South Wales - Kensington Campus: University of New South Wales"
-      },
-      {
-        "author_name": "Gail V Matthews",
-        "author_inst": "University of New South Wales - Kensington Campus: University of New South Wales"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2023.08.27.23294685",
     "rel_title": "The well-being and work-related stress of senior school leaders in Wales and Northern Ireland during the COVID-19 pandemic: A cross-sectional descriptive study",
@@ -34641,6 +34835,53 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2023.08.24.554732",
+    "rel_title": "Mucosal antibody responses to SARS-CoV-2 booster vaccination and breakthrough infection",
+    "rel_date": "2023-08-25",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.24.554732",
+    "rel_abs": "Coronavirus disease 2019 (COVID-19) vaccines have saved millions of lives. However, variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged causing large numbers of breakthrough infections. These developments necessitated the rollout of COVID-19 vaccine booster doses. It has been reported that mucosal antibody levels in the upper respiratory tract, especially for secretory IgA (sIgA), correlate with protection from infection with SARS-CoV-2. However, it is still unclear how high levels of mucosal antibodies can be induced. In this study, we measured serum IgG, saliva IgG and saliva sIgA responses in individuals who received COVID-19 mRNA booster vaccinations or who experienced breakthrough infections. We found that mRNA booster doses could induce robust serum and saliva IgG responses, especially in individuals who had not experienced infections before, but saliva sIgA responses were weak. In contrast, breakthrough infections in individuals who had received the primary mRNA vaccination series induced robust serum and saliva IgG as well as saliva sIgA responses. Individuals who had received a booster dose and then had a breakthrough infection showed low IgG induction in serum and saliva but still responded with robust saliva sIgA induction. These data suggest that upper respiratory tract exposure to antigen is an efficient way of inducing mucosal sIgA while exposure via intramuscular injection is not.\n\nImportanceAntibodies on mucosal surfaces of the upper respiratory tract have been shown to be important for protection from infection with SARS-CoV-2. Here we investigate the induction of serum IgG, saliva IgG and saliva sIgA after COVID-19 mRNA booster vaccination or breakthrough infections.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Disha Bhavsar",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Gagandeep Singh",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Kaori Sano",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Charles Gleason",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Komal Srivastava",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Juan Manuel Carreno",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Viviana Simon",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Florian Krammer",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2023.08.24.554650",
     "rel_title": "Efficient Sequence Embedding For SARS-CoV-2 Variants Classification",
@@ -35750,41 +35991,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2023.08.22.23294419",
-    "rel_title": "Prediction of COVID-19 infection risk using personal mobile location data only",
-    "rel_date": "2023-08-24",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.22.23294419",
-    "rel_abs": "Predicting an individuals risk of infectious disease is a critical technology in infectious disease response. During the COVID-19 pandemic, identifying and isolating individuals at high risk of infection was an essential task for epidemic control. We introduce a new machine learning model that predicts the risk of COVID-19 infection using only individuals mobile cell tower location information. This model distinguishes the cell tower location information of an individual into residential and non-residential areas and calculates whether the cell tower locations overlapped with other individuals. It then generates various variables from the information of overlapping and predicts the possibility of COVID-19 infection using a machine learning algorithm. The predictive model we developed showed performance comparable to models using individuals clinical information. This predictive model, which can be used to predict infections of diseases with asymptomatic infections such as COVID-19, has the advantage of supplementing the limitations of existing infectious disease prediction models that use symptoms and other information.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Ahreum Jang",
-        "author_inst": "KT"
-      },
-      {
-        "author_name": "Sungtae Kim",
-        "author_inst": "KT"
-      },
-      {
-        "author_name": "Hyeongwoo Baek",
-        "author_inst": "KT"
-      },
-      {
-        "author_name": "Hyejung Kim",
-        "author_inst": "KT"
-      },
-      {
-        "author_name": "Hae-Lee Park",
-        "author_inst": "KT"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2023.08.24.554651",
     "rel_title": "Unveiling the Robustness of Machine Learning Models in Classifying COVID-19 Spike Sequences",
@@ -36219,6 +36425,93 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2023.08.24.554561",
+    "rel_title": "Rationally designed multimeric nanovaccines using icosahedral DNA origami for molecularly controlled display of SARS-CoV-2 receptor binding domain",
+    "rel_date": "2023-08-24",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.24.554561",
+    "rel_abs": "Multivalent antigen display on nanoparticles can enhance the immunogenicity of nanovaccines targeting viral moieties, such as the receptor binding domain (RBD) of SARS-CoV-2. However, particle morphology and size of current nanovaccines are significantly different from those of SARS-CoV-2. Additionally, surface antigen patterns are not controllable to enable the optimization of B cell activation. Herein, we employed an icosahedral DNA origami (ICO) as a display particle for SARS-CoV-2 RBD nanovaccines. The morphology and diameter of the particles were close to those of the virus (91 {+/-} 11 nm). The surface addressability of the DNA origami permitted facile modification of the ICO surface with numerous RBD antigen clusters (ICO-RBD) to form various antigen patterns. Using an in vitro screening system, we demonstrate that the antigen spacing, antigen copies within clusters and cluster number parameters of the surface antigen pattern all impact the ability of the nanovaccines to activate B cells. Importantly, the optimized ICO-RBD nanovaccines evoked stronger and more enduring humoral and T cell immune responses in mouse models compared to soluble RBD antigens. Our vaccines activated similar humoral immunity and slightly stronger cellular immunity compared to mRNA vaccines. These results provide reference principles for the rational design of nanovaccines and exemplify the utility of DNA origami as a display platform for vaccines against infectious disease.",
+    "rel_num_authors": 18,
+    "rel_authors": [
+      {
+        "author_name": "Qingqing Feng",
+        "author_inst": "National Center for Nanoscience and Technology of China"
+      },
+      {
+        "author_name": "Keman Cheng",
+        "author_inst": "National Center for Nanoscience and Technology of China"
+      },
+      {
+        "author_name": "Lizhuo Zhang",
+        "author_inst": "National Center for Nanoscience and Technology of China"
+      },
+      {
+        "author_name": "Xiaoyu Gao",
+        "author_inst": "National Center for Nanoscience and Technology of China"
+      },
+      {
+        "author_name": "Jie Liang",
+        "author_inst": "National Center for Nanoscience and Technology of China"
+      },
+      {
+        "author_name": "Guangna Liu",
+        "author_inst": "National Center for Nanoscience and Technology of China"
+      },
+      {
+        "author_name": "Nana Ma",
+        "author_inst": "National Center for Nanoscience and Technology of China"
+      },
+      {
+        "author_name": "Chen Xu",
+        "author_inst": "National Center for Nanoscience and Technology of China"
+      },
+      {
+        "author_name": "Ming Tang",
+        "author_inst": "National Center for Nanoscience and Technology of China"
+      },
+      {
+        "author_name": "Liting Chen",
+        "author_inst": "National Center for Nanoscience and Technology of China"
+      },
+      {
+        "author_name": "Xinwei Wang",
+        "author_inst": "National Center for Nanoscience and Technology of China"
+      },
+      {
+        "author_name": "Xuehui Ma",
+        "author_inst": "Institute of Microbiology, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Jiajia Zou",
+        "author_inst": "Beijing Intell Nanomedicine"
+      },
+      {
+        "author_name": "Quanwei Shi",
+        "author_inst": "Beijing Intell Nanomedicine"
+      },
+      {
+        "author_name": "Pei Du",
+        "author_inst": "Institute of Microbiology, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Qihui Wang",
+        "author_inst": "Institute of Microbiology, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Guangjun Nie",
+        "author_inst": "National Center for Nanoscience and Technology of China"
+      },
+      {
+        "author_name": "Xiao Zhao",
+        "author_inst": "National Center for Nanoscience and Technology of China"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "bioengineering"
+  },
   {
     "rel_doi": "10.1101/2023.08.17.23294204",
     "rel_title": "High proportions of post-exertional malaise and orthostatic intolerance in people living with post-COVID-19 condition: the PRIME post-COVID study",
@@ -37544,89 +37837,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2023.08.20.23294345",
-    "rel_title": "SARS-CoV-2 antibody response among COVID-19 patients is not affected by parasite co-infection",
-    "rel_date": "2023-08-21",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.20.23294345",
-    "rel_abs": "BackgroundB-cell hypo-responsiveness has been associated with intestinal parasitic co-infection. The effect of parasite co-infection on antibody response to SARS-CoV-2 is unknown. Here, we aimed to determine antibody response to SARS-CoV-2 among COVID-19 patients co-infected with intestinal parasites and those without parasite co-infection.\n\nMethodsIn this prospective cohort study, a total of 589 samples were serially collected from 72 RT-PCR-confirmed patients. Anti-SARS-CoV-2 nucleocapsid protein (NP) antibody titers were measured longitudinally during hospitalization. SARS-CoV-2 infection was confirmed by RT-PCR on samples obtained from nasopharyngeal swabs, while direct microscopic examination, modified Ritchie concentration, and Kato-Katz methods were used to identify parasites and ova from fresh stool samples. Data were analyzed using STATA version 14.\n\nResultsOf the 72 COVID-19 patients, 39 (54.2%) were co-infected with intestinal parasites while 33 (45.8%) had no parasitic co-infection. Overall, the median cut-off index (COI) for anti-NP antibody titer among COVID-19 patients co-infected with parasites was 6.91 (IQR: 0.55-40.7) compared to 7.51 (IQR: 0.21-59.21) in those without parasites (p=0.764). In addition, 174/261 [66.7% (95% CI: 60.68-72.16)] and 231/328 [70.4% (95% CI: 65.23-75.14)] specimens from COVID-19 patients with parasite co-infection and without parasites, respectively, had anti-SARS-CoV-2 antibody above the cut-off COI value (p=0.328). The positivity rate for anti-SARS-CoV-2 NP < 14 days after symptom onset was 66.3% (95% CI: 60.21-71.85) and 70.0% (95% CI: 64.72-74.74) for those not infected and co-infected with parasites, respectively (p=0.343). In addition, 31/72 (41.9%) of the patients who were negative at the time of enrollment were seroconverted. The trend in anti-NP antibodies among seroconverted individuals with and without parasites is also similar.\n\nConclusionsCo-infection with parasitic infection has very little effect on the anti-SARS-CoV-2 antibody immune response. Further studies on the profile of neutralizing antibodies in parasite-endemic areas are warranted to ascertain vaccine efficacy.\n\nAuthors summaryPre-existing co-infection with intestinal parasites has been shown to diminish antibody response to a multitude of heterologous pathogens or vaccines. However, the effect of parasite co-infection on antibody response to SARS-CoV-2 is unknown. We determined the anti-nucleocapsid protein (NP) antibody response to SARS-CoV-2 among COVID-19 patients co-infected with intestinal parasites and compared their response to those without parasites. There was no difference in anti-NP positivity rate, seroconversion, or titer level among COVID-19 patients with or without parasitic co-infection. Further studies on the profile of neutralizing antibodies in parasite-endemic areas are warranted to ascertain vaccine efficacy.",
-    "rel_num_authors": 17,
-    "rel_authors": [
-      {
-        "author_name": "Teklay Gebrecherkos",
-        "author_inst": "Mekelle University College of Health Sciences"
-      },
-      {
-        "author_name": "Yazezew Kebede",
-        "author_inst": "Mekelle University College of Health Sciences"
-      },
-      {
-        "author_name": "Feyissa Challa",
-        "author_inst": "EPHI: Ethiopian Public Health Institute"
-      },
-      {
-        "author_name": "Atsbeha Gebreegzabher",
-        "author_inst": "EPHI: Ethiopian Public Health Institute"
-      },
-      {
-        "author_name": "Saro Abdella",
-        "author_inst": "EPHI: Ethiopian Public Health Institute"
-      },
-      {
-        "author_name": "Dereje Leta",
-        "author_inst": "EPHI: Ethiopian Public Health Institute"
-      },
-      {
-        "author_name": "Abraham Desta",
-        "author_inst": "Tigray Health Research Institute"
-      },
-      {
-        "author_name": "Ataklti Hailu",
-        "author_inst": "Tigray Health Research Institute"
-      },
-      {
-        "author_name": "Geremew Tasew",
-        "author_inst": "EPHI: Ethiopian Public Health Institute"
-      },
-      {
-        "author_name": "Mahmud Abdulkadir",
-        "author_inst": "Mekelle University College of Health Sciences"
-      },
-      {
-        "author_name": "Masresha Tessema",
-        "author_inst": "EPHI: Ethiopian Public Health Institute"
-      },
-      {
-        "author_name": "Getachew Tollera",
-        "author_inst": "EPHI: Ethiopian Public Health Institute"
-      },
-      {
-        "author_name": "Zekarias Gessesse",
-        "author_inst": "Mekelle University College of Health Sciences"
-      },
-      {
-        "author_name": "Henk H DF Schallig",
-        "author_inst": "University of Amsterdam Faculty of Medicine: Amsterdam UMC Locatie AMC"
-      },
-      {
-        "author_name": "Britta C. Urban",
-        "author_inst": "Liverpool School of Tropical Medicine Department of Clinical Sciences"
-      },
-      {
-        "author_name": "Tobias Rinke de Wit",
-        "author_inst": "Amsterdam Institute for Global Health and Development"
-      },
-      {
-        "author_name": "Dawit Welday",
-        "author_inst": "Mekelle University College of Health Sciences"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2023.08.20.23294350",
     "rel_title": "Heterogeneous SARS-CoV-2 kinetics due to variable timing and intensity of immune responses",
@@ -37925,6 +38135,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2023.08.17.553661",
+    "rel_title": "Purification, crystallization, and preliminary structural analysis of multivalent immunogenic effector protein-anchored SARS-CoV-2 RBD",
+    "rel_date": "2023-08-18",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.17.553661",
+    "rel_abs": "The continuous spread of highly transmissible variants of concern and the potential diminished effectiveness of existing vaccines necessitate ongoing research and development of new vaccines. Immunogenic molecule-anchored antigen has demonstrated superior efficacy in subunit vaccination, primarily due to enhanced cellular uptake facilitated by the affinity between the surface of Immunogenic molecule and the cell membrane. Based on the Immunogenic recombinase B. malayi RecA (BmRecA), we have overexpressed the construct of BmRecA with SARS-CoV-2 RBD (BmRecA-RBD) that exists as a stable helical filament formation; it was purified and crystallized to obtain X-ray diffraction data at 2.7 [A], belonged to the hexagonal symmetry group P65 in the unit-cell parameters of a=b=122.12, c=75.55 and ={beta}=90{degrees}, {gamma}=120{degrees}. The Matthews coefficient was estimated to be 3.12 [A]3 Da-1, corresponding to solvent contents of 52.65.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Taek Hun Kwon",
+        "author_inst": "Baylor College of Medicine"
+      },
+      {
+        "author_name": "Tae Gyun Kim",
+        "author_inst": "Gyeongbuk Institute for Bio industry"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "biophysics"
+  },
   {
     "rel_doi": "10.1101/2023.08.17.553792",
     "rel_title": "How reliable are estimates of key parameters in viral dynamic models?",
@@ -39130,33 +39363,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2023.08.10.23293924",
-    "rel_title": "Published benefits of ivermectin use in Itajai, Brazil for COVID-19 infection, hospitalisation, and mortality are entirely explained by statistical artefacts",
-    "rel_date": "2023-08-15",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.10.23293924",
-    "rel_abs": "BackgroundTwo recent publications by Kerr et al. (Cureus 14(1):e21272; Cureus 14(8): e28624) reported dramatic effects of prophylactic ivermectin use for both prevention of COVID-19 and reduction of COVID-19-related hospitalisation and mortality, including a dose-dependent effect of ivermectin prophylaxis. These papers have gained an unusually large public influence: they were incorporated into debates around COVID-19 policies and may have contributed to decreased trust in vaccine efficacy and public health authorities more broadly. Both studies were based on retrospective observational analysis of city-wide registry data from the city of Itajai, Brazil from July-December 2020.\n\nMethodsStarting with initially identified sources of error, we conducted a revised statistical analysis of available data, including data made available with the original papers and public data from the Brazil Ministry of Health. We identified additional uncorrected sources of bias and errors from the original analysis, including incorrect subject exclusion and missing subjects, analysis of longitudinal data with cross-sectional design, an enrolment time bias, and multiple sources of immortal time bias. In models assuming no actual effect from ivermectin use, we conducted Monte Carlo simulations to estimate the contribution of these biases to any observed effect.\n\nResultsUntreated statistical artefacts and methodological errors alone lead to dramatic apparent risk reduction associated with ivermectin use in both studies. The magnitude of apparent risk reduction from these artefacts is comparable to the results reported by the studies themselves, including apparent protection from infection, hospitalisation, and death, and including the reported apparent dose-response relationship.\n\nConclusionsThe inference of ivermectin effect reported in both papers is unsupported, as the observed effects are entirely explained by untreated statistical artefacts and methodological errors. Our re-analysis calls for caution in interpreting highly publicised observational studies and highlights the importance of common sources of bias in clinical research.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Robin Mills",
-        "author_inst": "AI Horizon, The Netherlands"
-      },
-      {
-        "author_name": "Ana Carolina Pe\u00e7anha Antonio",
-        "author_inst": "Hospital de Cl\u00ednicas de Porto Alegre: Porto Alegre, BR"
-      },
-      {
-        "author_name": "Greg Tucker-Kellogg",
-        "author_inst": "National University of Singapore"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2023.08.11.23293971",
     "rel_title": "Individual level analysis of digital proximity tracing for COVID-19 in Belgium highlights major bottlenecks",
@@ -39471,6 +39677,37 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2023.08.14.553219",
+    "rel_title": "Transmission bottleneck size estimation from de novo viral genetic variation",
+    "rel_date": "2023-08-14",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.14.553219",
+    "rel_abs": "Sequencing of viral infections has become increasingly common over the last decade. Deep sequencing data in particular have proven useful in characterizing the roles that genetic drift and natural selection play in shaping within-host viral populations. They have also been used to estimate transmission bottleneck sizes from identified donor-recipient pairs. These bottleneck sizes quantify the number of viral particles that establish genetic lineages in the recipient host and are important to estimate due to their impact on viral evolution. Current approaches for estimating bottleneck sizes exclusively consider the subset of viral sites that are observed as polymorphic in the donor individual. However, allele frequencies can change dramatically over the course of an individuals infection, such that sites that are polymorphic in the donor at the time of transmission may not be polymorphic in the donor at the time of sampling and allele frequencies at donor-polymorphic sites may change dramatically over the course of a recipients infection. Because of this, transmission bottleneck sizes estimated using allele frequencies observed at a donors polymorphic sites may be considerable underestimates of true bottleneck sizes. Here, we present a new statistical approach for instead estimating bottleneck sizes using patterns of viral genetic variation that arose de novo within a recipient individual. Specifically, our approach makes use of the number of clonal viral variants observed in a transmission pair, defined as the number of viral sites that are monomorphic in both the donor and the recipient but carry different alleles. We first test our approach on a simulated dataset and then apply it to both influenza A virus sequence data and SARS-CoV-2 sequence data from identified transmission pairs. Our results confirm the existence of extremely tight transmission bottlenecks for these two respiratory viruses, using an approach that does not tend to underestimate transmission bottleneck sizes.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Teresa Shi",
+        "author_inst": "Emory University"
+      },
+      {
+        "author_name": "Jeremy Harris",
+        "author_inst": "Emory University"
+      },
+      {
+        "author_name": "Michael A Martin",
+        "author_inst": "Emory University"
+      },
+      {
+        "author_name": "Katia Koelle",
+        "author_inst": "Emory University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "new results",
+    "category": "evolutionary biology"
+  },
   {
     "rel_doi": "10.1101/2023.08.12.553079",
     "rel_title": "Pandemic preparedness through genomic surveillance: Overview of mutations in SARS-CoV-2 over the course of COVID-19 outbreak",
@@ -40444,37 +40681,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2023.08.05.23293695",
-    "rel_title": "Prevalence of Long COVID19 among paediatric age group in Duhok Kurdistan region, Iraq",
-    "rel_date": "2023-08-09",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.05.23293695",
-    "rel_abs": "BackgroundA range of persistent symptoms that can develop in some people after they have recovered from acute COVID-19, is known as Long COVI-19. It can affect people of all ages and severity of initial illness, including those who had mild or asymptomatic infections.. Dealing with Long COVID-19 can be challenging, and the best course of action will depend on the specific symptoms and individual needs of the patient. This study aims to detect the prevalence of long covid-19 among the children who tested positive for IgG test. If IgG antibodies are detected in a persons blood sample, it suggests that they have been infected with SARS-CoV-2 at some point in the past and their immune system has responded by producing antibodies against the virus.\n\nMaterial and MethodologyFrom (October 22nd till December 4th 2022) the data of this study had been collected through a face-to-face interview with withdrawing blood samples for serum Immunoglobin-G test in laboratory of (General zakho Teaching Hospital in Zakho) and (Hevi Pediatric Teaching Hospital in Duhok). A total number of 330 children aged between 5-12 ages participated in this study. Moreover, If IgG antibodies are detected in a persons blood sample, it suggests that they have been infected with SARS-CoV-2 at some point in the past and their immune system has responded by producing antibodies against the virus.\n\nResults(Fatigue 12/ 85.7%), (cough 10/ 71.4%), (post exertional malaise 5/ 35.7%) were the most detected symptoms among the 14 positive patients. Followed by (headache, dizziness, hair loss, loss of appetite, loss/change in smell and taste, difficulty in sleep, mood change, abdominal pain, change in bowel habits, chest pain) to lesser extent.\n\nConclusionlong-term sequelae of Covid-19 now is becoming a challenge that needs more continued research and collaboration among healthcare providers, researchers, and patients are essential. Long COVID-19 is a public health concern that requires ongoing attention and resources, as well as support for those who are experiencing its debilitating effects. Out of 330 children only 4.6% (14 children) were experiencing long covid-19 symptoms for more than 4 weeks after acute infections in Duhok city.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Rojeen Chalabi Khalid",
-        "author_inst": "University of Zakho"
-      },
-      {
-        "author_name": "Tamara Bassam Jamal",
-        "author_inst": "Department of biomolecular sciences, College of Medicine, University of Zakho, Kurdistan Region of Iraq"
-      },
-      {
-        "author_name": "Sara Ardalan Mahdi",
-        "author_inst": "Department of biomolecular sciences, College of Medicine, University of Zakho, Kurdistan Region of Iraq"
-      },
-      {
-        "author_name": "Abdullah Saeed Mustafa",
-        "author_inst": "Department of biomolecular sciences, College of Medicine, University of Zakho, Kurdistan Region of Iraq"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2023.08.06.23293725",
     "rel_title": "Predicting Clinical Outcomes of SARS-CoV-2 Infection During the Omicron Wave Using Machine Learning",
@@ -40881,6 +41087,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2023.08.08.552415",
+    "rel_title": "Antiviral efficacy of the SARS-CoV-2 XBB breakthrough infection sera against Omicron subvariants including EG.5",
+    "rel_date": "2023-08-08",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.08.552415",
+    "rel_abs": "As of July 2023, EG.5.1 (a.k.a. XBB.1.9.2.5.1), a XBB subvariant bearing the S:Q52H and S:F456L substitutions, alongside the S:F486P substitution (Figure S1A), has rapidly spread in some countries. On July 19, 2023, the WHO classified EG.5 as a variant under monitoring. First, we showed that EG.5.1 exhibits a higher effective reproduction number compared with XBB.1.5, XBB.1.16, and its parental lineage (XBB.1.9.2), suggesting that EG.5.1 will spread globally and outcompete these XBB subvariants in the near future. We then addressed whether EG.5.1 evades from the antiviral effect of the humoral immunity induced by breakthrough infection (BTI) of XBB subvariants and performed a neutralization assay using XBB BTI sera. However, the 50% neutralization titer (NT50) of XBB BTI sera against EG.5.1 was comparable to those against XBB.1.5/1.9.2 and XBB.1.16. Moreover, the sensitivity of EG.5.1 to convalescent sera of XBB.1- and XBB.1.5-infected hamsters was similar to those of XBB.1.5/1.9 and XBB.1.16. These results suggest that the increased Re of EG.5.1 is attributed to neither increased infectivity nor immune evasion from XBB BTI, and the emergence and spread of EG.5 is driven by the other pressures. We previously demonstrated that Omicron BTI cannot efficiently induce antiviral humoral immunity against the variant infected. In fact, the NT50s of the BTI sera of Omicron BA.1, BA.2, and BA.5 against the variant infected were 3.0-, 2.2-, and 3.4-fold lower than that against the ancestral B.1.1 variant, respectively. However, strikingly, we found that the NT50 of the BTI sera of XBB1.5/1.9 and XBB.1.16 against the variant infected were 8.7- and 8.3-fold lower than that against the B.1.1 variant. These results suggest that XBB BTI cannot efficiently induce antiviral humoral immunity against XBB subvariants.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=147 SRC=\"FIGDIR/small/552415v1_figs1.gif\" ALT=\"Figure 1\">\nView larger version (39K):\norg.highwire.dtl.DTLVardef@f95376org.highwire.dtl.DTLVardef@d66fa8org.highwire.dtl.DTLVardef@3c8841org.highwire.dtl.DTLVardef@15824c_HPS_FORMAT_FIGEXP  M_FIG O_FLOATNOFigure S1.C_FLOATNO Virological features of EG.5.1 and XBB BTI (A) Frequency of mutations of interest in the representative XBB sublineages. Only mutations with a frequency >0.5 in at least one but not all the representative sublineages are shown. Note that the S proteins of XBB.1.5 and XBB.1.9.2 are identical.\n\n(B) Estimated epidemic dynamics of the representative XBB sublineages in countries where >50 sequences of EG.5.1, XBB.1.5, XBB.1.9.2, and XBB.1.16 were detected from April 1, 2023 to July 13, 2023. Countries are ordered according to the number of detected sequences of EG.5.1. Line, posterior mean; ribbon, 95% Bayesian confidence interval. The dynamics for EG.5.1 is highlighted by a red arrowhead.\n\n(C) Estimated relative Re of the representative XBB sublineages in the six countries. The relative Re of XBB.1.5 is set to 1 (horizontal dashed line). Violin, posterior distribution; dot, posterior mean; line, 95% Bayesian confidence interval.\n\n(D) Lentivirus-based pseudovirus assay. HOS-ACE2-TMPRSS2 cells were infected with pseudoviruses bearing each S protein. The amount of input virus was normalized to the amount of HIV-1 p24 capsid protein. The percentage infectivity of XBB.1.5/1.9.2, XBB.1.5/1.9.2+Q52H, XBB.1.5/1.9.2+F456L, and EG.5.1 compared to that of XBB.1.5/1.9.2 are shown. The horizontal dash line indicates the mean value of the percentage infectivity of the XBB.1.5/1.9.2. Assays were performed in quadruplicate. The presented data are expressed as the average {+/-} SD. Each dot indicates the result of an individual replicate.\n\n(E-G) Neutralization assay. Assays were performed with pseudoviruses harboring the S proteins of B.1.1, BA.1, BA.2, BA.5, BQ.1.1, XBB.1, XBB.1.5/1.9.2, XBB.1.16, EG.5.1, XBB.1.5/1.9.2+Q52H, and XBB.1.5/1.9.2+F456L. The following sera were used: convalescent sera from fully vaccinated individuals who had been infected with XBB.1.5 (one 3-dose vaccinated. 1 donor in total), XBB.1.9 (one 3-dose vaccinated donor, one 4-dose vaccinated donor and one 5-dose vaccinated donor. 3 donors in total), and XBB.1.16 (one 2-dose vaccinated donor, two 3-dose vaccinated donors, and one 4-dose vaccinated donor. 4 donors in total) (E); sera from hamster infected with XBB.1 (left) or XBB.1.5 (right) (F); and convalescent sera from fully vaccinated individuals who had been infected with BA.1 (thirteen 2-dose vaccinated, 13 donors in total) (left)1, BA.2 (nine 2-dose vaccinated and four 3-dose vaccinated donors. 13 donors in total) (middle)19, and BA.5 (one 2-dose vaccinated, thirteen 3-dose vaccinated donors, and one 4-dose vaccinated. 15 donors in total) (right)19 (G). Each dot indicates the result of an individual replicate. Assays for each serum sample were performed in triplicate to determine the 50% neutralization titer (NT50). Each dot represents one NT50 value, and the geometric mean and 95% confidence interval are shown. The number in parenthesis indicates the mean of NT50 values. The horizontal dash line indicates the detection limit (120-fold).\n\nIn D, statistically significant differences (**, P < 0.001, ***, P < 0.0001) versus XBB.1.5/1.9.2 were determined by two-sided Students t tests. Blue asterisks indicate decreased percentage of infectivity.\n\nIn E and G, statistically significant differences versus B.1.1 were determined by two-sided Wilcoxon signed-rank tests. The fold change between B.1.1 and the variant indicated is shown in red. Background information on the convalescent donors is summarized in Table S1.\n\nIn F, statistically significant differences (*, P < 0.01, **, P < 0.001) between B.1.1 and XBB.1 (left) or XBB.1.5/1.9.2 (right) were determined by two-sided Wilcoxon signed-rank tests and indicated with asterisks. Red asterisks indicate decreased NT50s.\n\nC_FIG",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Yu Kaku",
+        "author_inst": "The University of Tokyo"
+      },
+      {
+        "author_name": "Yusuke Kosugi",
+        "author_inst": "The University of Tokyo"
+      },
+      {
+        "author_name": "Keiya Uriu",
+        "author_inst": "The University of Tokyo"
+      },
+      {
+        "author_name": "Jumpei Ito",
+        "author_inst": "The Institute of Medical Science, The University of Tokyo"
+      },
+      {
+        "author_name": "Jin Kuramochi",
+        "author_inst": "Interpark Kuramochi Clinic"
+      },
+      {
+        "author_name": "Kenji Sadamasu",
+        "author_inst": "Tokyo Metropolitan Institute of Public Health"
+      },
+      {
+        "author_name": "Kazuhisa Yoshimura",
+        "author_inst": "Tokyo Metropolitan Institute of Public Health"
+      },
+      {
+        "author_name": "Hiroyuki Asakura",
+        "author_inst": "Tokyo Metropolitan Institute of Public Health"
+      },
+      {
+        "author_name": "Mami Nagashima",
+        "author_inst": "Tokyo Metropolitan Institute of Public Health"
+      },
+      {
+        "author_name": "- The Genotype to Phenotype Japan (G2P-Japan) Consortium",
+        "author_inst": "-"
+      },
+      {
+        "author_name": "Kei Sato",
+        "author_inst": "Institute of Medical Science, The University of Tokyo"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2023.08.08.552503",
     "rel_title": "Within-host evolution of SARS-CoV-2: how often are mutations transmitted?",
@@ -42006,69 +42271,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2023.08.01.23293521",
-    "rel_title": "Diagnostic performance of LumiraDx SARS-CoV-2 rapid antigen test compared to PCR for diagnosis of COVID-19 in Liberia",
-    "rel_date": "2023-08-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.01.23293521",
-    "rel_abs": "BackgroundDiagnosis of SARS-CoV-2 infection in Liberia has primarily relied on polymerase chain reaction (PCR)-based testing at the countrys National Reference Laboratory. This centralized approach caused reporting delays, prompting evaluation of point-of-care antigen-based tests. We assessed the test performance of the LumiraDx SARS-CoV-2 Ag test (LumiraDx, London, UK) in this setting.\n\nMethodsWe tested ambulatory individuals screened for enrollment into an observational cohort study of COVID-19 sequelae in Monrovia in 2021. We compared the results of LumiraDx testing of anterior nasal swab specimens to the results of PCR BioFire(R) R2.1P (bioMerieux, Salt Lake City, Utah) on eluent from nasopharyngeal swabs.\n\nResultsWe evaluated 348 individuals. Among the 274 persons with symptoms, 49.3% were PCR-positive and 36.5% were antigen-positive. The sensitivity, specificity, negative predictive value (NPV), and positive predictive value (PPV) of LumiraDx in this group were 72.6% (95% CI: 64.3%-79.9%), 98.6% (95% CI: 94.9%-99.8%), 78.7% (CI: 71.9%-84.6%), and 98.0% (CI: 93.0%-99.8%), respectively. Among the 74 asymptomatic individuals, 12.2% were positive by PCR, and 5.5% by antigen testing, resulting in a sensitivity, specificity, NPV, and PPV of LumiraDx of 44.4% (95% CI: 13.7%-78.8%), 100% (95% CI: 94.5%-100%), 92.9% (CI: 84.1%-97.6%), and 100% (CI: 39.8%-100%), respectively.\n\nConclusionAlthough the specificity and PPV of LumiraDx for diagnosing SARS-CoV-2 were high among persons with and without symptoms, the sensitivity was unacceptably low in both groups, and much less than that reported by the manufacturer. Before new point-of-care diagnostics are adopted, test performance needs to be assessed in the local setting.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Mses Badio",
-        "author_inst": "Partnership for Research on Vaccines and Infectious Diseases in Liberia"
-      },
-      {
-        "author_name": "Christina Lindan",
-        "author_inst": "Department of Epidemiology and Biostatistics, University of California, San Francisco"
-      },
-      {
-        "author_name": "Kumblytee Johnson",
-        "author_inst": "Partnership for Research on Vaccines and Infectious Diseases In Liberia"
-      },
-      {
-        "author_name": "Cavan Reilly",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Julie Blie",
-        "author_inst": "Partnership for Research on Vaccines and Infectious Diseases in Liberia"
-      },
-      {
-        "author_name": "Katy Shaw-Saliba",
-        "author_inst": "National Institute of Allergy and Infectious Diseases, U.S. National Institutes of Health"
-      },
-      {
-        "author_name": "Tamba Fayiah",
-        "author_inst": "Partnership for Research on Vaccines and Infectious Diseases in Liberia"
-      },
-      {
-        "author_name": "John McCullough",
-        "author_inst": "Advanced BioMedical Laboratories"
-      },
-      {
-        "author_name": "J. Tanu Duworko",
-        "author_inst": "Partnership for Research on Vaccines and Infectious Diseases in Liberia"
-      },
-      {
-        "author_name": "Elizabeth Higgs",
-        "author_inst": "National Institute of Allergy and Infectious Diseases, U.S. National Institutes of Health"
-      },
-      {
-        "author_name": "Jeffrey Martin",
-        "author_inst": "Department of Epidemiology and Biostatistics, University of California"
-      },
-      {
-        "author_name": "Lisa Hensley",
-        "author_inst": "National Institute of Allergy and Infectious Diseases, U.S. National Institutes of Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2023.08.03.23293612",
     "rel_title": "Influence of Prior SARS-CoV-2 Infection on COVID-19 Severity: Evidence from the National COVID Cohort Collaborative",
@@ -42395,6 +42597,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2023.07.28.23293338",
+    "rel_title": "Systematic Review and Meta-Analysis Protocol of the Efficacy and Safety of COVID-19 Drug Candidates Targeting Host Enzymes Involved in Immune Response",
+    "rel_date": "2023-08-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.28.23293338",
+    "rel_abs": "IntroductionCOVID-19 is a rapidly spreading infectious disease caused by the SARS-CoV-2 virus. Although several therapeutic interventions have been developed, the mortality rate of the disease remains high, and effective treatment options are urgently needed. Host-directed therapies targeting enzymes involved in the immune response represent a promising strategy for the development of novel therapeutics against COVID-19. This study aims to conduct a systematic review and meta-analysis of the literature to evaluate the potential of drug candidates targeting host enzymes involved in the immune response for the treatment of COVID-19.\n\nMethods and analysisWe will conduct a systematic search of electronic databases including PubMed, Embase, and Cochrane Library, as well as preprint servers and clinical trial registries for relevant studies. We will include randomized controlled trials, observational studies, and preclinical studies evaluating the efficacy of drug candidates targeting host enzymes involved in the immune response in COVID-19. Two reviewers will independently screen articles, extract data, and assess study quality. The primary outcome will be the effect of drug candidates on mortality, while secondary outcomes will include time to recovery, adverse events, and changes in immune markers. A meta-analysis will be performed to estimate pooled effect sizes of the interventions, and a narrative synthesis will be conducted for studies that are not amenable to quantitative analysis. This study will provide a comprehensive evaluation of the potential of host-directed therapies targeting enzymes involved in the immune response for the treatment of COVID-19. The results of this study may guide the development of novel therapeutics against COVID-19 and inform clinical practice.\n\nEthics and disseminationThis study will review published data, and thus it is unnecessary to obtain ethical approval. The findings of this systematic review will be published in a peer-reviewed journal.\n\nPROSPERO registration numberCRD42023415110.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Aganze Gloire-Aime Mushebenge",
+        "author_inst": "University of KwaZulu-Natal"
+      },
+      {
+        "author_name": "Samuel Chima Ugbaja",
+        "author_inst": "University of KwaZulu-Natal"
+      },
+      {
+        "author_name": "Nonkululeko Avril Mbatha",
+        "author_inst": "University f KwaZulu Natal"
+      },
+      {
+        "author_name": "Manimani Ghislain Riziki",
+        "author_inst": "University of KwaZulu-Natal"
+      },
+      {
+        "author_name": "Tambwe Willy Muzumbukilwa",
+        "author_inst": "University of KwaZulu-Natal"
+      },
+      {
+        "author_name": "Mukanda Gedeon Kadima",
+        "author_inst": "University of KwaZulu-Natal"
+      },
+      {
+        "author_name": "Hezekiel M. Kumalo",
+        "author_inst": "University of KwaZulu-Natal"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2023.07.29.23293334",
     "rel_title": "CLINICAL AND SEROLOGICAL PREDICTORS OF POST COVID-19 CONDITION: FINDINGS FROM A CANADIAN PROSPECTIVE COHORT STUDY",
@@ -43652,61 +43897,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2023.07.30.23292881",
-    "rel_title": "Loss of severe respiratory syncytial virus infection-associated antibody function during the peak of the COVID-19 pandemic mitigation measures",
-    "rel_date": "2023-08-02",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.30.23292881",
-    "rel_abs": "Studies have linked reduced respiratory syncytial virus-specific Fc-mediated phagocytic function and complement deposition to more severe infection. This study shows a loss of these functions during the first year of COVID-19 pandemic. These findings corroborate other data supporting a general waning of RSV antibody functions in absence of viral circulation.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Bahaa Abu-Raya",
-        "author_inst": "University of British Columbia"
-      },
-      {
-        "author_name": "Frederic Reicherz",
-        "author_inst": "University of British Columbia"
-      },
-      {
-        "author_name": "Christina Michalski",
-        "author_inst": "University of British Columbia"
-      },
-      {
-        "author_name": "Abdelilah Majdoub",
-        "author_inst": "University of British Columbia"
-      },
-      {
-        "author_name": "Liam Golding",
-        "author_inst": "University of British Columbia"
-      },
-      {
-        "author_name": "Marina Vienta",
-        "author_inst": "University of British Columbia"
-      },
-      {
-        "author_name": "Madison Granoski",
-        "author_inst": "University of Alberta"
-      },
-      {
-        "author_name": "Aleksandra Stojic",
-        "author_inst": "University of Alberta"
-      },
-      {
-        "author_name": "David Marchant",
-        "author_inst": "University of Alberta"
-      },
-      {
-        "author_name": "Pascal M Lavoie",
-        "author_inst": "University of British Columbia"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2023.08.01.23293500",
     "rel_title": "Lower Urinary Tract Symptoms in a prospective cohort of COVID-19 survivors",
@@ -44157,6 +44347,105 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2023.08.01.551417",
+    "rel_title": "Phenotyping the virulence of SARS-CoV-2 variants in hamsters by digital pathology and machine learning",
+    "rel_date": "2023-08-01",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.01.551417",
+    "rel_abs": "SARS-CoV-2 has continued to evolve throughout the COVID-19 pandemic, giving rise to multiple variants of concern (VOCs) with different biological properties. As the pandemic progresses, it will be essential to test in near real time the potential of any new emerging variant to cause severe disease. BA.1 (Omicron) was shown to be attenuated compared to the previous VOCs like Delta, but it is possible that newly emerging variants may regain a virulent phenotype. Hamsters have been proven to be an exceedingly good model for SARS-CoV-2 pathogenesis. Here, we aimed to develop robust quantitative pipelines to assess the virulence of SARS-CoV-2 variants in hamsters. We used various approaches including RNAseq, RNA in situ hybridization, immunohistochemistry, and digital pathology, including software assisted whole section imaging and downstream automatic analyses enhanced by machine learning, to develop methods to assess and quantify virus-induced pulmonary lesions in an unbiased manner. Initially, we used Delta and Omicron to develop our experimental pipelines. We then assessed the virulence of recent Omicron sub-lineages including BA.5, XBB, BQ.1.18, BA.2 and BA.2.75. We show that in experimentally infected hamsters, accurate quantification of alveolar epithelial hyperplasia and macrophage infiltrates represent robust markers for assessing the extent of virus-induced pulmonary pathology, and hence virus virulence. In addition, using these pipelines, we could reveal how some Omicron sub-lineages (e.g., BA.2.75) have regained virulence compared to the original BA.1. Finally, to maximise the utility of the digital pathology pipelines reported in our study, we developed an online repository containing representative whole organ histopathology sections that can be visualised at variable magnifications (https://covid-atlas.cvr.gla.ac.uk). Overall, this pipeline can provide unbiased and invaluable data for rapidly assessing newly emerging variants and their potential to cause severe disease.",
+    "rel_num_authors": 21,
+    "rel_authors": [
+      {
+        "author_name": "Gavin R Meehan",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Vanessa Herder",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Jay Allan",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Xinyi Huang",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Karen Kerr",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Diogo  Correa Mendonca",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Georgios Ilia",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Derek Wright",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Kyriaki Nomikou",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Quan Gu",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Sergi  Molina Arias",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Giuditta De Lorenzo",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Vanessa Cowton",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Nicole Upfold",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Natasha Palmalux",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Jonathan  C Brown",
+        "author_inst": "Imperial College London"
+      },
+      {
+        "author_name": "Wendy Barclay",
+        "author_inst": "Imperial College London"
+      },
+      {
+        "author_name": "Ana  Da Silva Filipe",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Wilhelm Furnon",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Arvind Patel",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Massimo Palmarini",
+        "author_inst": "MRC-University of Glasgow Centre for Virus Research"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2023.07.28.551051",
     "rel_title": "Targeted Amplification and Genetic Sequencing of the Severe Acute Respiratory Syndrome Coronavirus 2 Surface Glycoprotein",
@@ -45618,81 +45907,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2023.07.24.23293091",
-    "rel_title": "Age- and sex-specific differences in immune responses to BNT162b2 COVID-19 and live-attenuated influenza vaccines in UK adolescents",
-    "rel_date": "2023-07-27",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.24.23293091",
-    "rel_abs": "Key to understanding COVID-19 correlates of protection is assessing vaccine-induced immunity in different demographic groups. Sex- and age-specific immune differences have a wide impact on outcomes from infections and immunisations. Typically, adult females make stronger immune responses and have better disease outcomes but suffer more adverse events following vaccination and are more prone to autoimmune disease. To understand better the mechanisms underlying these differences in vaccine responses, we studied immune responses to two doses of BNT162b2 Pfizer COVID-19 vaccine in an adolescent cohort (n=34, ages 12-16), an age group previously shown to make significantly greater immune responses to the same vaccine compared to young adults. At the same time, we were able to evaluate immune responses to the co-administered live attenuated influenza vaccine, which has been shown to induce stronger immune responses in adult females. Blood samples from 34 adolescents taken pre- and post-vaccination with COVID-19 and influenza vaccines were assayed for SARS-CoV-2-specific IgG and neutralising antibodies, and cellular immunity specific for SARS-CoV-2 and endemic betacoronaviruses. IgG targeting influenza lineages contained in the influenza vaccine was also assessed. As previously demonstrated, total IgG responses to SARS-CoV-2 Spike antigens were significantly higher among vaccinated adolescents compared to adults (aged 32-52) who received the BNT162b2 vaccine (comparing infection-naive, 49,696 vs 33,339; p=0.03; comparing SARS-CoV-2 previously-infected, 743,691 vs 269,985; p<0.0001) by MSD v-plex assay. However, unexpectedly, antibody responses to BNT162b2 and the live-attenuated influenza vaccine were not higher among female adolescents compared to males; among infection-naive adolescents, antibody responses to BNT162b2 were higher in males than females (62,270 vs 36,951 p=0.008). No sex difference was identified in vaccinated adults. These unexpected findings may result from the introduction of novel mRNA vaccination platforms, generating patterns of immunity divergent from established trends, and providing new insights into what might be protective following COVID-19 vaccination.",
-    "rel_num_authors": 15,
-    "rel_authors": [
-      {
-        "author_name": "Cecilia Jay",
-        "author_inst": "Nuffield Department of Medicine, University of Oxford"
-      },
-      {
-        "author_name": "Emily Adland",
-        "author_inst": "Department of Paediatrics, University of Oxford"
-      },
-      {
-        "author_name": "Anna Csala",
-        "author_inst": "Department of Paediatrics, University of Oxford"
-      },
-      {
-        "author_name": "Nicholas Lim",
-        "author_inst": "Department of Paediatrics, University of Oxford"
-      },
-      {
-        "author_name": "Stephanie Longet",
-        "author_inst": "Wellcome Centre for Human Genetics, University of Oxford"
-      },
-      {
-        "author_name": "Ane Ogbe",
-        "author_inst": "Nuffield Department of Medicine, University of Oxford"
-      },
-      {
-        "author_name": "Jeremy Ratcliff",
-        "author_inst": "Nuffield Department of Medicine, University of Oxford"
-      },
-      {
-        "author_name": "Oliver Sampson",
-        "author_inst": "Peter Medawar Building for Pathogen Research, University of Oxford"
-      },
-      {
-        "author_name": "Craig Thompson",
-        "author_inst": "Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Warwick, UK"
-      },
-      {
-        "author_name": "Lance Turtle",
-        "author_inst": "Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK"
-      },
-      {
-        "author_name": "Ellie Barnes",
-        "author_inst": "Nuffield Department of Medicine, University of Oxford"
-      },
-      {
-        "author_name": "Susanna Dunachie",
-        "author_inst": "Nuffield Department of Medicine, University of Oxford"
-      },
-      {
-        "author_name": "Paul Klenerman",
-        "author_inst": "Nuffield Department of Medicine, University of Oxford"
-      },
-      {
-        "author_name": "Miles Carroll",
-        "author_inst": "Wellcome Centre for Human Genetics, University of Oxford"
-      },
-      {
-        "author_name": "Philip Goulder",
-        "author_inst": "Department of Paediatrics, University of Oxford"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "pediatrics"
-  },
   {
     "rel_doi": "10.1101/2023.07.25.23293143",
     "rel_title": "The Cost of Keeping Patients Waiting: Retrospective Treatment-Control Study of Additional Healthcare Utilisation for UK Patients Awaiting Elective Treatment Following COVID-19",
@@ -46067,6 +46281,85 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2023.07.25.550460",
+    "rel_title": "Non-neutralizing SARS-CoV-2 N-terminal domain antibodies protect mice against severe disease using Fc-mediated effector functions",
+    "rel_date": "2023-07-26",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.25.550460",
+    "rel_abs": "Antibodies perform both neutralizing and non-neutralizing effector functions that protect against certain pathogen-induced diseases. A human antibody directed at the SARS-CoV-2 Spike N-terminal domain (NTD), DH1052, was recently shown to be non-neutralizing yet it protected mice and cynomolgus macaques from severe disease. The mechanisms of this non-neutralizing antibody-mediated protection are unknown. Here we show that Fc effector functions mediate non-neutralizing antibody (non-nAb) protection against SARS-CoV-2 MA10 viral challenge in mice. Though non-nAb infusion did not suppress infectious viral titers in the lung as potently as NTD neutralizing antibody (nAb) infusion, disease markers including gross lung discoloration were similar in nAb and non-nAb groups. Fc functional knockout substitutions abolished non-nAb protection and increased viral titers in the nAb group. Finally, Fc enhancement increased non-nAb protection relative to WT, supporting a positive association between Fc functionality and degree of protection in SARS-CoV-2 infection. This study demonstrates that non-nAbs can utilize Fc-mediated mechanisms to lower viral load and prevent lung damage due to coronavirus infection.\n\nAUTHOR SUMMARYCOVID-19 has claimed over 6.8 million lives worldwide and caused economic and social disruption globally. Preventing more deaths from COVID-19 is a principal goal of antibody biologic and vaccine developers. To guide design of such countermeasures, an understanding of how the immune system prevents severe COVID-19 disease is needed. We demonstrate here that antibody functions other than neutralization can contribute to protection from severe disease. Specifically, the functions of antibodies that rely on its Fc portion were shown to confer antibody-mediated protection of mice challenged with a mouse adapted version of SARS-CoV-2. Mice given an antibody that could not neutralize SARS-CoV-2 still showed a decrease in the amount of infectious virus in the lungs and less lung damage than mice given an irrelevant antibody. The decrease in infectious virus in the lungs was even larger when the non-neutralizing antibody was engineered to mediate non-neutralizing effector functions such as antibody-dependent cellular cytotoxicity more potently. Thus, in the absence of neutralization activity, non-neutralizing binding antibodies can contribute to the overall defense against SARS-CoV-2 infection and COVID-19 disease progression.",
+    "rel_num_authors": 16,
+    "rel_authors": [
+      {
+        "author_name": "Camille  N. Pierre",
+        "author_inst": "Duke University School of Medicine"
+      },
+      {
+        "author_name": "Lily  E. Adams",
+        "author_inst": "University of North Carolina Eshelman School of Pharmacy: The University of North Carolina at Chapel Hill Eshelman School of Pharmacy"
+      },
+      {
+        "author_name": "Kara Anasti",
+        "author_inst": "Duke University School of Medicine"
+      },
+      {
+        "author_name": "Derrick Goodman",
+        "author_inst": "Duke University School of Medicine"
+      },
+      {
+        "author_name": "Sherry Stanfield-Oakley",
+        "author_inst": "Duke University School of Medicine"
+      },
+      {
+        "author_name": "John  M. Powers",
+        "author_inst": "University of North Carolina Eshelman School of Pharmacy: The University of North Carolina at Chapel Hill Eshelman School of Pharmacy"
+      },
+      {
+        "author_name": "Dapeng Li",
+        "author_inst": "Duke University School of Medicine"
+      },
+      {
+        "author_name": "Wes Rountree",
+        "author_inst": "Duke University School of Medicine"
+      },
+      {
+        "author_name": "Yunfei Wang",
+        "author_inst": "Duke University School of Medicine"
+      },
+      {
+        "author_name": "Robert  J. Edwards",
+        "author_inst": "Duke University School of Medicine"
+      },
+      {
+        "author_name": "S.  Munir Alam",
+        "author_inst": "Duke University School of Medicine"
+      },
+      {
+        "author_name": "Guido Ferrari",
+        "author_inst": "Duke University School of Medicine"
+      },
+      {
+        "author_name": "Georgia  D. Tomaras",
+        "author_inst": "Duke University School of Medicine"
+      },
+      {
+        "author_name": "Barton  F. Haynes",
+        "author_inst": "Duke University School of Medicine"
+      },
+      {
+        "author_name": "Ralph  S. Baric",
+        "author_inst": "University of North Carolina Eshelman School of Pharmacy: The University of North Carolina at Chapel Hill Eshelman School of Pharmacy"
+      },
+      {
+        "author_name": "Kevin Saunders",
+        "author_inst": "Duke Human Vaccine Institute"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2023.07.21.23292937",
     "rel_title": "The Impact of the UK COVID-19 Lockdown on the Screening, Diagnostics and Incidence of Breast, Colorectal, Lung and Prostate Cancer in the UK: a Population-Based Cohort Study",
@@ -47224,45 +47517,6 @@
     "type": "new results",
     "category": "cell biology"
   },
-  {
-    "rel_doi": "10.1101/2023.07.20.23292951",
-    "rel_title": "Factors influencing COVID-19 vaccination decision-making among African American and Hispanic pregnant and postpartum women in Deep South",
-    "rel_date": "2023-07-24",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.20.23292951",
-    "rel_abs": "BackgroundCOVID-19 vaccination is vital for ending the pandemic but concerns about its safety among pregnant and postpartum women, especially among African American (AA) and Hispanic women, persist. This study aims to explore factors that influence vaccination decision-making among AA and Hispanic pregnant and postpartum women through womens experiences and maternal care providers (MCPs) observations.\n\nMethodsFrom January and August 2022, we conducted semi-structured interviews with AA and Hispanic women and MCPs. Participants were recruited from obstetric and pediatric clinics in South Carolina, and all births took place after March 2020. Thematic analysis was employed for data analysis.\n\nResultsThe study involved 19 AA and 20 Hispanic women, along with 9 MCPs, and revealed both barriers and facilitators to COVID-19 vaccination. The factors that influence pregnant and postpartum womens decision about COVID-19 vaccine uptake included: 1) awareness of health threats associated with COVID-19 vaccines, 2) vaccine availability and accessibility, 3) vaccine-related knowledge and exposure to misinformation, 4) concerns regarding pre-existing health conditions and potential side effects of COVID-19 vaccines, 5) emotional factors associated with vaccination decision-making processes, 6) concerns about the well-being of infants, 7) cultural perspectives, and 8) encouragement by trusted supporters.\n\nConclusionFindings suggest that reliable information, social support, and trusted doctors advice can motivate COVID-19 vaccination. However, barriers such as misinformation, mistrust in the health care system, and fears related to potential side effects impede vaccination uptake among AA and Hispanic pregnant and postpartum women. Future interventions should target these barriers, along with health disparities, involve trusted doctors in outreach, and initiate vaccine conversations to promote vaccination among this population.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Ran Zhang",
-        "author_inst": "University of South Carolina"
-      },
-      {
-        "author_name": "Tiffany Byrd",
-        "author_inst": "University of South Carolina Arnold School of Public Health"
-      },
-      {
-        "author_name": "Shan Qiao",
-        "author_inst": "University of South Carolina Arnold School of Public Health"
-      },
-      {
-        "author_name": "Myriam  E. Torres",
-        "author_inst": "University of South Carolina Arnold School of Public Health"
-      },
-      {
-        "author_name": "Xiaoming Li",
-        "author_inst": "University of South Carolina Arnold School of Public Health"
-      },
-      {
-        "author_name": "Jihong Liu",
-        "author_inst": "University of South Carolina Arnold School of Public Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2023.07.19.23292491",
     "rel_title": "High seroprevalence after the second wave of SARS-COV2 respiratory infection in a small settlement in the northern coastal of Peru.",
@@ -47613,6 +47867,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
+  {
+    "rel_doi": "10.1101/2023.07.21.23293001",
+    "rel_title": "Unraveling COVID-19 Relationship with Anxiety Disorders and Symptoms",
+    "rel_date": "2023-07-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.21.23293001",
+    "rel_abs": "BackgroundWhile COVID-19 outcomes are associated with increased anxiety, individuals affected by anxiety disorders are more likely to develop severe COVID-19 outcomes.\n\nMethodsWe used genome-wide data from UK Biobank (up to 420,531 participants), FinnGen Project (up to 329,077 participants), Million Veteran Program (175,163 participants), and COVID-19 Host Genetics Initiative (up to 122,616 cases and 2,475,240 controls) to investigate possible causal effects and shared genetic mechanisms linking COVID-19 outcomes to anxiety disorders and symptoms.\n\nResultsWe observed a strong genetic correlation of anxiety disorder with COVID-19 positive status (rg=0.35, p=2 x 10-4) and COVID-19 hospitalization (rg=0.31, p=7.2 x 10-4). Among anxiety symptoms, \"Tense, sore, or aching muscles during worst period of anxiety\" was genetically correlated with COVID-19 positive status (rg=0.33, p=0.001), while \"Frequent trouble falling or staying asleep during worst period of anxiety\" was genetically correlated with COVID-19 hospitalization (rg=0.24, p=0.004). Through a latent causal variable analysis, we observed that COVID-19 outcomes have statistically significant genetic causality proportion (gcp) on anxiety symptoms (e.g., COVID-19 positive status[-&gt;]\"Recent easy annoyance or irritability\" [boxv]gcp[boxv]=0.18, p=6.72 x 10-17). Conversely, anxiety disorders appear to have a possible causal effect on COVID-19 ([boxv]gcp[boxv]=0.38, p=3.17 x 10-9). Additionally, we also identified multiple loci with evidence of local genetic correlation between anxiety and COVID-19. These appear to be related to genetic effects shared with lung function, brain morphology, alcohol and tobacco use, and hematologic parameters.\n\nConclusionsThis study provided important insights into the relationship between COVID-19 and mental health, differentiating the dynamics linking anxiety disorders to COVID-19 from the effect of COVID-19 on anxiety symptoms.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Zeynep Asgel",
+        "author_inst": "Yale University"
+      },
+      {
+        "author_name": "Manuela Kouakou",
+        "author_inst": "Yale University"
+      },
+      {
+        "author_name": "Dora Koller",
+        "author_inst": "Yale University"
+      },
+      {
+        "author_name": "Gita A Pathak",
+        "author_inst": "Yale University"
+      },
+      {
+        "author_name": "Brenda Cabrera-Mendoza",
+        "author_inst": "Yale University"
+      },
+      {
+        "author_name": "Renato Polimanti",
+        "author_inst": "Yale University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "genetic and genomic medicine"
+  },
   {
     "rel_doi": "10.1101/2023.07.19.23292904",
     "rel_title": "Social Cohesion and Covid-19: an integrative review",
@@ -48902,49 +49195,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "intensive care and critical care medicine"
   },
-  {
-    "rel_doi": "10.1101/2023.07.16.23292747",
-    "rel_title": "Effects of nutritional supplements on antibody levels in pregnant women vaccinated with inactivated SARS-CoV-2 vaccines",
-    "rel_date": "2023-07-18",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.16.23292747",
-    "rel_abs": "BackgroundBecause of the significantly higher demand for nutrients during pregnancy, pregnant women are more likely to have nutrient deficiencies, which may adversely affect maternal and fetal health. The effect of nutritional supplements on the immune effects of inactivated SARS-CoV-2 vaccines during pregnancy is not clear.\n\nMethodsIn a multicenter cross-sectional study, we enrolled 873 pregnant women aged 18-45 y in Guangdong, China. The general demographic characteristics of pregnant women and their use of nutritional supplements were investigated, and the serum antibody levels induced by inactivated SARS-CoV-2 vaccines were measured. A logistic regression model was used to analyze the association between nutritional supplements and SARS-CoV-2 antibody levels.\n\nResultsOf the 873 pregnant women enrolled, 825 (94.5%) took folic acid during pregnancy, 165 (18.9%) took iron supplements, and 197 (22.6%) took DHA. All pregnant women received at least one dose of inactivated SARS-CoV-2 vaccine, and the positive rates of serum SARS-CoV-2 neutralizing antibodies (NAbs) and immunoglobulin G (IgG) antibodies were 44.7% and 46.4%, respectively. After adjustment for confounding factors, whether pregnant women took folic acid, iron supplements, or DHA did not influence NAb positivity or IgG positivity (P > 0.05).Compared with pregnant women who did not take folic acid, the odds ratios (ORs) for the presence of SARS-CoV-2 NAb and IgG antibody in pregnant women who took folic acid were 0.69 (P = 0.282; 95% CI, 0.35-1.35) and 1.31 (P = 0.456; 95% CI, 0.64-2.67), respectively. Compared with pregnant women who did not take iron supplements, the ORs for the presence of NAb and IgG antibody in pregnant women who took iron supplements were 1.22 (P = 0.336; 95% CI, 0.81-1.84) and 1.01 (P = 0.956; 95% CI, 0.66-1.54), respectively. Similarly, the ORs for NAb and IgG antibody were 0.74 (P = 0.125; 95% CI, 0.51-1.08) and 0.97 (P = 0.881; 95% CI, 0.66-1.44) in pregnant women who took DHA compared with those who did not.\n\nConclusionsNutritional supplementation with folic acid, iron, or DHA during pregnancy was not associated with antibody levels in pregnant women who received inactivated SARS-CoV-2 vaccines.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Xi Zhang",
-        "author_inst": "Guangdong Pharmaceutical University"
-      },
-      {
-        "author_name": "Xue Han",
-        "author_inst": "Guangdong Pharmaceutical University"
-      },
-      {
-        "author_name": "Baolan Chen",
-        "author_inst": "Guangdong Pharmaceutical University"
-      },
-      {
-        "author_name": "Xi Fu",
-        "author_inst": "Guangdong Pharmaceutical University"
-      },
-      {
-        "author_name": "Yajie Gong",
-        "author_inst": "Guangdong Pharmaceutical University"
-      },
-      {
-        "author_name": "Wenhan Yang",
-        "author_inst": "Guangdong Pharmaceutical University"
-      },
-      {
-        "author_name": "Qingsong CHEN",
-        "author_inst": "Guangdong Pharmaceutical University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2023.07.17.23292772",
     "rel_title": "Identification of COVID-19 Vaccine-Hesitancy Predictors in the United States",
@@ -49183,6 +49433,97 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2023.07.14.548971",
+    "rel_title": "Deep spatial proteomic exploration of severe COVID-19-related pulmonary injury in post-mortem specimens",
+    "rel_date": "2023-07-17",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.14.548971",
+    "rel_abs": "The lung, as a primary target of SARS-CoV-2, exhibits heterogeneous microenvironment accompanied by various histopathological changes following virus infection. However, comprehensive insight into the protein basis of COVID-19-related pulmonary injury with spatial resolution is currently deficient. Here, we generated a region-resolved quantitative proteomic atlas of seven major pathological structures within the lungs of COVID-19 victims by integrating histological examination, laser microdissection, and ultrasensitive proteomic technologies. Over 10,000 proteins were quantified across 71 dissected FFPE post-mortem specimens. By comparison with control samples, we identified a spectrum of COVID-19-induced protein and pathway dysregulations in alveolar epithelium, bronchial epithelium, and pulmonary blood vessels, providing evidence for the proliferation of transitional-state pneumocytes. Additionally, we profiled the region-specific proteomes of hallmark COVID-19 pulmonary injuries, including bronchiole mucus plug, pulmonary fibrosis, airspace inflammation, and hyperplastic alveolar type 2 cells. Bioinformatic analysis revealed the enrichment of cell-type and functional markers in these regions (e.g. enriched TGFBI in fibrotic region). Furthermore, we identified the up-regulation of proteins associated with viral entry, host restriction, and inflammatory response in COVID-19 lungs, such as FURIN and HGF. Collectively, this study provides spatial proteomic insights for understanding COVID-19-caused pulmonary injury, and may serve as a valuable reference for improving therapeutic intervention for severe pneumonia.",
+    "rel_num_authors": 19,
+    "rel_authors": [
+      {
+        "author_name": "Yiheng Mao",
+        "author_inst": "Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen"
+      },
+      {
+        "author_name": "Ying Chen",
+        "author_inst": "CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430030, China."
+      },
+      {
+        "author_name": "Yuan Li",
+        "author_inst": "Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen"
+      },
+      {
+        "author_name": "Longda Ma",
+        "author_inst": "Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China"
+      },
+      {
+        "author_name": "Xi Wang",
+        "author_inst": "Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen"
+      },
+      {
+        "author_name": "Qi Wang",
+        "author_inst": "CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430030, China."
+      },
+      {
+        "author_name": "An He",
+        "author_inst": "Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen"
+      },
+      {
+        "author_name": "Xi Liu",
+        "author_inst": "CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430030, China."
+      },
+      {
+        "author_name": "Tianyi Dong",
+        "author_inst": "CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430030, China."
+      },
+      {
+        "author_name": "Weina Gao",
+        "author_inst": "Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen"
+      },
+      {
+        "author_name": "Yanfen Xu",
+        "author_inst": "Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen"
+      },
+      {
+        "author_name": "Liang Liu",
+        "author_inst": "Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China"
+      },
+      {
+        "author_name": "Liang Ren",
+        "author_inst": "Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China"
+      },
+      {
+        "author_name": "Qian Liu",
+        "author_inst": "CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430030, China."
+      },
+      {
+        "author_name": "Peng Zhou",
+        "author_inst": "CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430030, China."
+      },
+      {
+        "author_name": "Ben Hu",
+        "author_inst": "CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430030, China."
+      },
+      {
+        "author_name": "Yiwu Zhou",
+        "author_inst": "Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China"
+      },
+      {
+        "author_name": "Ruijun Tian",
+        "author_inst": "Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, Shenzhen"
+      },
+      {
+        "author_name": "Zheng-Li Shi",
+        "author_inst": "CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430030, China."
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "systems biology"
+  },
   {
     "rel_doi": "10.1101/2023.07.16.23292735",
     "rel_title": "Causal association of COVID-19 with brain structure changes: Findings from a non-overlapping 2-sample Mendelian randomization study",
@@ -50472,33 +50813,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2023.07.12.23292582",
-    "rel_title": "A Population Level Study on the Determinants of COVID-19 Vaccine Hesitancy at the U.S. County Level",
-    "rel_date": "2023-07-13",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.12.23292582",
-    "rel_abs": "Multiple COVID-19 vaccines were proven to be safe and effective in curbing severe illness, but despite vaccine availability, uptake rates were relatively low in the United States (U.S.), primarily due to vaccine hesitancy. To better understand factors associated with COVID-19 vaccine hesitancy in the U.S., our study provides a comprehensive, data-driven population-level statistical analysis at the county level. We find that political affiliation, as determined by the proportion of votes received by the Republican candidate in the 2020 presidential election, has the strongest association with COVID-19 vaccine hesitancy. The next strongest association was median household income, which has a negative association. The percentage of Black people and the average number of vehicles per household are also positively associated with vaccine hesitancy. In contrast, COVID-19 infection rate, percentage of Hispanic people, postsecondary education percentage, median age, and prior non-COVID-19 childhood vaccination coverage are other factors negatively associated with vaccine hesitancy. Unlike previous studies, we do not find significant relationships between cable TV news viewership or Twitter misinformation variables with COVID-19 vaccine hesitancy. These results shed light on some factors that may impact vaccination choice in the U.S. and can be used to target specific populations for educational outreach and vaccine campaign strategies in efforts to reduce vaccine hesitancy.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Ensheng Dong",
-        "author_inst": "Johns Hopkins University"
-      },
-      {
-        "author_name": "Kristen Nixon",
-        "author_inst": "Johns Hopkins University"
-      },
-      {
-        "author_name": "Lauren Marie Gardner",
-        "author_inst": "Johns Hopkins University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2023.07.11.23292264",
     "rel_title": "Efficacy and Safety of 5-Day Oral Ensitrelvir for Patients With Mild-to-Moderate COVID-19: The SCORPIO-SR Randomized Clinical Trial",
@@ -50785,6 +51099,57 @@
     "type": "new results",
     "category": "cell biology"
   },
+  {
+    "rel_doi": "10.1101/2023.07.12.23292570",
+    "rel_title": "COVID-19 Case and Mortality Surveillance using Daily SARS-CoV-2 in Wastewater Samples adjusting for Meteorological Conditions and Sample pH",
+    "rel_date": "2023-07-12",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.12.23292570",
+    "rel_abs": "BackgroundWastewater monitoring is increasingly used for community surveillance of infectious diseases, especially after the COVID-19 pandemic as the genomic footprints of pathogens shed by infected individuals can be traced in the environment. However, detection and concentration of pathogens in the environmental samples and their efficacy in predicting infectious diseases can be influenced by meteorological conditions and quality of samples.\n\nObjectivesThis research examines whether meteorological conditions and sample pH affect SARS-CoV-2 concentrations in wastewater samples, and whether the association of SARS-CoV-2 with COVID-19 cases and mortality improves when adjusted for meteorological conditions and sample pH value in Miami-Dade County, FL.\n\nMethodsDaily wastewater samples were collected from Miami-Dade Wastewater Treatment Plant in Key Biscayne, Florida from August 2021 to August 2022. The samples were analyzed for pH and spiked with OC43. RNA was extracted from the concentrated wastewater sample and SARS-CoV-2 was quantified using qPCR. COVID-19 and mortality data were acquired from the Centers for Disease Control and Prevention (CDC) and meteorological data from the National Climatic Data Center. COVID-19 case and mortality rates were modelled with respect to time-lagged wastewater SARS-CoV-2 adjusting for meteorological conditions, and sample pH value and OC43 recovery.\n\nResultsTemperature, dew point, pH values and OC43 recovery showed significant associations with wastewater SARS-CoV-2. Time-lagged wastewater SARS-CoV-2 showed significant associations with COVID-19 case and mortality incidence rates. This association improved when wastewater SARS-CoV-2 levels were adjusted for (or instrumented on) meteorological conditions, OC43 recovery, and sample pH. A 0.47% change in COVID-19 case incidence rate was associated with 1% change in wastewater SARS-CoV-2 ({beta} [~] 0.47; 95% CI = 0.29 - 0.64; p < 0.001). A 0.12 % change in COVID-19 mortality rate was associated with 1 % change in SARS-CoV-2 in wastewater 44 days prior. A 0.07% decline in COVID-19 mortality rate was associated with a unit increase in ambient temperature 28 days prior.\n\nDiscussionTime lagged wastewater SARS-CoV-2 (and its adjustment for sample pH and RNA recovery) and meteorological conditions can be used for the surveillance of COVID-19 case and mortality. These findings can be extrapolated to improve the surveillance of other infectious diseases by proactive measurements of infectious agent(s) in the wastewater samples, adjusting for meteorological conditions and sample pH value.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Abelson Samantha",
+        "author_inst": "University of Miami"
+      },
+      {
+        "author_name": "Bader Alsuliman",
+        "author_inst": "University of Miami"
+      },
+      {
+        "author_name": "Jonathon Penso",
+        "author_inst": "University of Miami"
+      },
+      {
+        "author_name": "Kristina Babler",
+        "author_inst": "University of Miami"
+      },
+      {
+        "author_name": "Mark Sharkey",
+        "author_inst": "University of Miami"
+      },
+      {
+        "author_name": "Christopher Mason",
+        "author_inst": "Cornell University"
+      },
+      {
+        "author_name": "George S. Grills",
+        "author_inst": "University of Miami"
+      },
+      {
+        "author_name": "Helena Solo-Gabriele",
+        "author_inst": "University of Miami"
+      },
+      {
+        "author_name": "Naresh Kumar",
+        "author_inst": "University of Miami"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2023.07.12.23292559",
     "rel_title": "Risk Factors for Admission into COVID-19 General Wards, Sub-Intensive and Intensive Care Units among SARS-CoV-2 Positive Subjects in the Municipality of Bologna, Italy",
@@ -51711,7 +52076,7 @@
     "rel_date": "2023-07-09",
     "rel_site": "medRxiv",
     "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.08.23292389",
-    "rel_abs": "Antimicrobial peptides (AMPs) are a complex network of 10-100 amino acid sequence molecules, widely distributed in Nature. Even though more than 300 AMPs have been described in mammals, cathelicidins and defensins remain the most investigated to date.\n\nSome publications examined the role of AMPs in COVID-19, but the findings are preliminary and in vivo studies are still lacking. Here, we report the plasma levels of five AMPs (LL-37, -defensin 1, -defensin 3, {beta}-defensin 1 and {beta}-defensin 3) and five cytokines (tumor necrosis factor-, interleukin-1{beta}, interleukin-6, interleukin-10, interferon-{gamma} and monocyte chemoattractant protein-1), in 15 healthy volunteers, 36 COVID-19 patients without Acute Kidney Injury (AKI) and 17 COVID-19 patients with AKI, since AKI is a well-known marker of worse prognosis in Sars-CoV-2 infections.\n\nWe found increased levels of -defensin 1, -defensin 3 and {beta}-defensin 3, but not LL-37 or {beta}-defensin 3, in our COVID-19 population, when compared with the healthy controls, in conjunction with higher levels of interleukin-6, interleukin-10, interferon-{gamma} and monocyte chemoattractant protein-1, putting in evidence that these AMPs and cytokines may have an important role in the systemic inflammatory response and tissue damage that characterizes severe COVID-19.\n\nGraphic Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC=\"FIGDIR/small/23292389v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (45K):\norg.highwire.dtl.DTLVardef@1210150org.highwire.dtl.DTLVardef@1dd2dd1org.highwire.dtl.DTLVardef@1eb1204org.highwire.dtl.DTLVardef@1ebf9e8_HPS_FORMAT_FIGEXP  M_FIG C_FIG",
+    "rel_abs": "Antimicrobial peptides (AMPs) are a complex network of 10-100 amino acid sequence molecules, widely distributed in Nature. Even though more than 300 AMPs have been described in mammals, cathelicidins and defensins remain the most investigated to date.\n\nSome publications examined the role of AMPs in COVID-19, but the findings are preliminary and in vivo studies are still lacking. Here, we report the plasma levels of five AMPs (LL-37, -defensin 1, -defensin 3, {beta}-defensin 1 and {beta}-defensin 3) and five cytokines (tumor necrosis factor-, interleukin-1{beta}, interleukin-6, interleukin-10, interferon-{gamma} and monocyte chemoattractant protein-1), in 15 healthy volunteers, 36 COVID-19 patients without Acute Kidney Injury (AKI) and 17 COVID-19 patients with AKI, since AKI is a well-known marker of worse prognosis in Sars-CoV-2 infections.\n\nWe found increased levels of -defensin 1, -defensin 3 and {beta}-defensin 3, but not LL-37 or {beta}-defensin 3, in our COVID-19 population, when compared with the healthy controls, in conjunction with higher levels of interleukin-6, interleukin-10, interferon-{gamma} and monocyte chemoattractant protein-1, putting in evidence that these AMPs and cytokines may have an important role in the systemic inflammatory response and tissue damage that characterizes severe COVID-19.\n\nGraphic Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC=\"FIGDIR/small/23292389v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (45K):\norg.highwire.dtl.DTLVardef@1a06b38org.highwire.dtl.DTLVardef@df67eaorg.highwire.dtl.DTLVardef@11f3d54org.highwire.dtl.DTLVardef@1f35a79_HPS_FORMAT_FIGEXP  M_FIG C_FIG",
     "rel_num_authors": 5,
     "rel_authors": [
       {
@@ -52082,53 +52447,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2023.07.06.547955",
-    "rel_title": "Single cell susceptibility to SARS-CoV-2 infection is driven by variable cell states",
-    "rel_date": "2023-07-07",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.06.547955",
-    "rel_abs": "The ability of a virus to infect a cell type is at least in part determined by the presence of host factors required for the viral life cycle. However, even within cell types that express known factors needed for infection, not every cell is equally susceptible, suggesting that our knowledge of the full spectrum of factors that promote infection is incomplete. Profiling the most susceptible subsets of cells within a population may reveal additional factors that promote infection. However, because viral infection dramatically alters the state of the cell, new approaches are needed to reveal the state of these cells prior to infection with virus. Here, we used single-cell clone tracing to retrospectively identify and characterize lung epithelial cells that are highly susceptible to infection with SARS-CoV-2. The transcriptional state of these highly susceptible cells includes markers of retinoic acid signaling and epithelial differentiation. Loss of candidate factors identified by our approach revealed that many of these factors play roles in viral entry. Moreover, a subset of these factors exert control over the infectable cell state itself, regulating the expression of key factors associated with viral infection and entry. Analysis of patient samples revealed the heterogeneous expression of these factors across both cells and patients in vivo. Further, the expression of these factors is upregulated in particular inflammatory pathologies. Altogether, our results show that the variable expression of intrinsic cell states is a major determinant of whether a cell can be infected by SARS-CoV-2.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Sam Reffsin",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Jesse Miller",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Kasirajan Ayyanathan",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Margaret C Dunagin",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Naveen Jain",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "David C Schultz",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Sara Cherry",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Arjun Raj",
-        "author_inst": "University of Pennsylvania"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "bioengineering"
-  },
   {
     "rel_doi": "10.1101/2023.07.07.548077",
     "rel_title": "Novel Spike-stabilized trimers with improved production protect K18-hACE2 mice and golden Syrian hamsters from the highly pathogenic SARS-CoV-2 Beta variant.",
@@ -52523,6 +52841,81 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "respiratory medicine"
   },
+  {
+    "rel_doi": "10.1101/2023.07.05.23292278",
+    "rel_title": "Intracardiac Thrombus in COVID-19 Inpatients: A Nationwide Study of Incidence, Predictors and Outcomes",
+    "rel_date": "2023-07-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.05.23292278",
+    "rel_abs": "BackgroundCOronaVIrus Disease 2019 (COVID-19) has been observed to be associated with a hypercoagulable state. Intracardiac thrombosis is a serious complication but has seldom been evaluated in COVID-19 patients. We assessed the incidence, associated factors, and outcomes of COVID-19 patients with intracardiac thrombosis.\n\nMethodsCOVID-19 inpatients during 2020 were retrospectively identified from the national inpatient sample (NIS) database, and data retrieved regarding clinical characteristics, intracardiac thrombosis, and adverse outcomes. Multivariable logistic regression was performed to identify the clinical factors associated with intracardiac thrombosis and in-hospital mortality and morbidities.\n\nResultsA total of 1,683,785 COVID-19 inpatients were identified in 2020 from NIS, with a mean age of 63.8 {+/-} 1.6 years, and 32.2% females. Intracardiac thrombosis was present in 0.001% (1,830) patients. Overall, in-hospital outcomes include all-cause mortality 13.2% (222,695/1,683,785), cardiovascular mortality 3.5%, cardiac arrest 2.6%, acute coronary syndrome (ACS) 4.4%, heart failure 16.1%, stroke 1.3% and acute kidney injury (AKI) 28.3%. The main factors associated with intracardiac thrombosis were a history of congestive heart failure and coagulopathy. Intracardiac thrombosis was independently associated with a higher risk of in-hospital all-cause mortality (OR: 3.32, 95% CI: 2.42-4.54, p<0.001), cardiovascular mortality (OR: 2.95, 95% CI: 1.96-4.44, p<0.001), cardiac arrest (OR: 2.04, 95% CI: 1.22-3.43, p=0.006), ACS (OR: 1.62, 95% CI: 1.17-2.22, p=0.003), stroke (OR: 3.10, 95% CI: 2.11-4.56, p<0.001), and AKI (OR: 2.13 95% CI: 1.68-2.69, p<0.001), but not incident heart failure (p=0.27).\n\nConclusionAlthough intracardiac thrombosis is rare in COVID-19 inpatients, its presence was independently associated with higher risks of in-hospital mortality and most morbidities. Prompt investigations and treatments for intracardiac thrombosis are warranted when there is a high index of suspicion and a confirmed diagnosis respectively.",
+    "rel_num_authors": 15,
+    "rel_authors": [
+      {
+        "author_name": "Ankit Agrawal",
+        "author_inst": "Cleveland Clinic"
+      },
+      {
+        "author_name": "Suryansh Bajaj",
+        "author_inst": "University of Arkansas for Medical Sciences"
+      },
+      {
+        "author_name": "Umesh Bhagat",
+        "author_inst": "Cleveland Clinic Foundation"
+      },
+      {
+        "author_name": "Sanya Chandna",
+        "author_inst": "Cleveland Clinic Foundation"
+      },
+      {
+        "author_name": "Aro Daniela Arockiam",
+        "author_inst": "Cleveland Clinic Foundation"
+      },
+      {
+        "author_name": "Nicholas Chan",
+        "author_inst": "Columbia University Irving Medical Center, New York Presbyterian Hospital"
+      },
+      {
+        "author_name": "Elio Haroun",
+        "author_inst": "Cleveland Clinic Foundation"
+      },
+      {
+        "author_name": "Rahul Gupta",
+        "author_inst": "Lehigh Valley Health Network"
+      },
+      {
+        "author_name": "Osamah Badwan",
+        "author_inst": "Cleveland Clinic"
+      },
+      {
+        "author_name": "Shashank Shekhar",
+        "author_inst": "Cleveland Clinic"
+      },
+      {
+        "author_name": "Shivabalan Kathavarayan Ramu",
+        "author_inst": "Cleveland Clinic"
+      },
+      {
+        "author_name": "Divya Nayar",
+        "author_inst": "University of Arkansas for Medical Sciences"
+      },
+      {
+        "author_name": "Wael A. Jaber",
+        "author_inst": "The Cleveland Clinic"
+      },
+      {
+        "author_name": "Brian P. Griffin",
+        "author_inst": "Cleveland Clinic Foundation"
+      },
+      {
+        "author_name": "Tom Kai Ming Wang",
+        "author_inst": "Cleveland Clinic"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "cardiovascular medicine"
+  },
   {
     "rel_doi": "10.1101/2023.07.05.23291954",
     "rel_title": "Immunogenicity and safety of heterologous Omicron BA.1 and bivalent SARS-CoV-2 recombinant spike protein booster vaccines: a phase 3, randomized, clinical trial",
@@ -54064,61 +54457,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2023.06.29.23292037",
-    "rel_title": "Clinical Profile, Comorbidities, and Outcome of the Unvaccinated and Hospitalized for COVID-19 in Northern Brazil: Retrospective Cohort",
-    "rel_date": "2023-07-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.29.23292037",
-    "rel_abs": "Over the course of the pandemic, COVID-19 affected health, the economy and quality of life in Brazil. The worst years for the country were the first and second. There were delays in vaccine purchases for political reasons at the time. The northern region of the country had a higher mortality rate compared to other regions, associated with local vulnerabilities and fragility of surveillance due to geographic and population characteristics. This study aims to investigate the clinical profile, comorbidities, and outcome of unvaccinated people hospitalized for COVID-19 in the state of Para in 2022. Retrospective cohort epidemiological study, with data from the national epidemiological surveillance of acute and severe respiratory syndromes. Cases reported in 2022 with vaccinated yes or no field and completed doses were included. Only closed cases cure or death were included. We performed a chi-square test on categorical variables and a Mann-Whitney test on numerical variables. We compared vaccinated VS non-vaccinated; we performed the Odds Ratio in the significant variables. We used the SPSS 20.0 software. The study worked with 2,634 cases of COVID-19 hospitalized in the study period, confirmed by RT-PCR (851/32.30%) and (1,784/67.70%) rapid antigen test. The lethality was (778/29.53%), and those vaccinated with two doses were (1,473/55.90%) and those unvaccinated with no dose (1,162/44.10%). Death represents p-<0.001 (HR 1.306 - CI 1.124/1.517) higher risk of the event occurring in the unvaccinated cases, followed by male sex p-0.004 (HR 1.188 - CI 1.058/1.334).. The first cohort in Brazil and in the north of the country to evaluate the clinical profile, comorbidities, and outcome of COVID-19 in hospitalized patients in this Amazon region, which is a region characterized by local vulnerability factors unique to the other regions of Brazil, showed that the unvaccinated were males, younger, with fewer comorbidities, and that they were associated the deaths.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Ana Lucia da Silva Ferreira",
-        "author_inst": "UNIVERSIDADE DO ESTADO DO PARA"
-      },
-      {
-        "author_name": "Daniele Melo Sardinha",
-        "author_inst": "Instituto Evandro Chagas"
-      },
-      {
-        "author_name": "Daiane Cristina Viana de Moraes",
-        "author_inst": "UNIVERSIDADE DA AMAZONIA"
-      },
-      {
-        "author_name": "Maria Raimunda Rodrigues de Oliveira",
-        "author_inst": "UNIVERSIDADE DA AMAZONIA"
-      },
-      {
-        "author_name": "Mayara Carolina Frazao Viana",
-        "author_inst": "UNIVERSIDADE DA AMAZONIA"
-      },
-      {
-        "author_name": "Natasha Cristina Oliveira Andrade",
-        "author_inst": "UNIVERSIDADE DO ESTADO DO PARA"
-      },
-      {
-        "author_name": "Tamires de Nazare Soares",
-        "author_inst": "UNIVERSIDADE DO ESTADO DO PARA"
-      },
-      {
-        "author_name": "Ricardo Jose de Paula Souza e Guimaraes",
-        "author_inst": "INSTITUTO EVANDRO CHAGAS"
-      },
-      {
-        "author_name": "Luana Nepomuceno Gondim Costa Lima",
-        "author_inst": "UNIVERSIDADE DO ESTADO DO PARA"
-      },
-      {
-        "author_name": "Karla Valeria Batista Lima",
-        "author_inst": "UNIVERSIDADE DO ESTADO DO PARA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2023.06.29.23292056",
     "rel_title": "Genome-wide Association Study of Long COVID",
@@ -54785,6 +55123,129 @@
     "type": "new results",
     "category": "genomics"
   },
+  {
+    "rel_doi": "10.1101/2023.06.29.546885",
+    "rel_title": "Interaction between host G3BP and viral nucleocapsid protein regulates SARS-CoV-2 replication",
+    "rel_date": "2023-06-30",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.29.546885",
+    "rel_abs": "G3BP1/2 are paralogous proteins that promote stress granule formation in response to cellular stresses, including viral infection. G3BP1/2 are prominent interactors of the nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the functional consequences of the G3BP1-N interaction in the context of viral infection remain unclear. Here we used structural and biochemical analyses to define the residues required for G3BP1-N interaction, followed by structure-guided mutagenesis of G3BP1 and N to selectively and reciprocally disrupt their interaction. We found that mutation of F17 within the N protein led to selective loss of interaction with G3BP1 and consequent failure of the N protein to disrupt stress granule assembly. Introduction of SARS-CoV-2 bearing an F17A mutation resulted in a significant decrease in viral replication and pathogenesis in vivo, indicating that the G3BP1-N interaction promotes infection by suppressing the ability of G3BP1 to form stress granules.",
+    "rel_num_authors": 27,
+    "rel_authors": [
+      {
+        "author_name": "Zemin Yang",
+        "author_inst": "St. Jude Children's Research Hospital"
+      },
+      {
+        "author_name": "Bryan A. Johnson",
+        "author_inst": "University of Texas Medical Branch, Galveston"
+      },
+      {
+        "author_name": "Victoria A. Meliopoulos",
+        "author_inst": "St. Jude Children's Research Hospital"
+      },
+      {
+        "author_name": "Xiaohui Ju",
+        "author_inst": "Tsinghua University"
+      },
+      {
+        "author_name": "Peipei Zhang",
+        "author_inst": "St. Jude Children's Research Hospital"
+      },
+      {
+        "author_name": "Michael P. Hughes",
+        "author_inst": "St. Jude Children's Research Hospital"
+      },
+      {
+        "author_name": "Jinjun Wu",
+        "author_inst": "St. Jude Children's Research Hospital"
+      },
+      {
+        "author_name": "Kaitlin P. Koreski",
+        "author_inst": "St. Jude Children's Research Hospital"
+      },
+      {
+        "author_name": "Ti-Cheng Chang",
+        "author_inst": "St. Jude Children's Research Hospital"
+      },
+      {
+        "author_name": "Gang Wu",
+        "author_inst": "St Jude Children's Research Hospital"
+      },
+      {
+        "author_name": "Jeff Hixon",
+        "author_inst": "Faze Medicines"
+      },
+      {
+        "author_name": "Jay Duffner",
+        "author_inst": "Faze Medicines"
+      },
+      {
+        "author_name": "Kathy Wong",
+        "author_inst": "Faze Medicines"
+      },
+      {
+        "author_name": "Rene Lemieux",
+        "author_inst": "Faze Medicines"
+      },
+      {
+        "author_name": "Kumari G. Lokugamage",
+        "author_inst": "University of Texas Medical Branch, Galveston"
+      },
+      {
+        "author_name": "Rojelio E. Alvardo",
+        "author_inst": "University of Texas Medical Branch, Galveston"
+      },
+      {
+        "author_name": "Patricia A. Crocquet-Valdes",
+        "author_inst": "University of Texas Medical Branch, Galveston"
+      },
+      {
+        "author_name": "David H. Walker",
+        "author_inst": "University of Texas Medical Branch, Galveston"
+      },
+      {
+        "author_name": "Kenneth S. Plante",
+        "author_inst": "University of Texas Medical Branch, Galveston"
+      },
+      {
+        "author_name": "Jessica A. Plante",
+        "author_inst": "University of Texas Medical Branch, Galveston"
+      },
+      {
+        "author_name": "Scott C. Weaver",
+        "author_inst": "University of Texas Medical Branch, Galveston"
+      },
+      {
+        "author_name": "Hong Joo Kim",
+        "author_inst": "St. Jude Children's Research Hospital"
+      },
+      {
+        "author_name": "Rachel Meyers",
+        "author_inst": "Faze Medicines"
+      },
+      {
+        "author_name": "Stacey Schultz-Cherry",
+        "author_inst": "St. Jude Children's Research Hospital"
+      },
+      {
+        "author_name": "Qiang Ding",
+        "author_inst": "Tsinghua University"
+      },
+      {
+        "author_name": "Vineet D Menachery",
+        "author_inst": "University of Texas Medical Branch"
+      },
+      {
+        "author_name": "J Paul Taylor",
+        "author_inst": "St. Jude Children's Research Hospital"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "new results",
+    "category": "cell biology"
+  },
   {
     "rel_doi": "10.1101/2023.06.30.23292079",
     "rel_title": "Synthesis and new evidence from the PROTECT UK National Core Study: Determining occupational risks of SARS-CoV-2 infection and COVID-19 mortality",
@@ -56362,45 +56823,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2023.06.22.23291610",
-    "rel_title": "COVID-19 Impact in Crohn Disease Patients Underwent Autologous Hematopoietic Stem Cell Transplantation",
-    "rel_date": "2023-06-28",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.22.23291610",
-    "rel_abs": "SARS COV 2 is the virus responsible for COVID-19, a disease that has been blamed for inducing or exacerbating symptoms in patients with autoimmune diseases.\n\nCrohns disease (CD) is an inflammatory bowel disease that affects genetically susceptible patients who develop an abnormal mucosal immune response to the intestinal microbiota. Patients who underwent Hematopoietic Stem cell Transplantation are considered at risk for COVID-19.\n\nThe objective of this report was to describe for the first time the impact of COVID-19 in a group of 50 patients with Crohns Disease (CD, 28 females, and 22 male) with a mean age of 38 years, previously submitted to Autologous, non-myeloablative, Hematopoietic Stem Cell Transplantation (Auto HSCT) between 2013 and 2021. In this series, 19 patients were diagnosed with positive COVID-19. In two (2) patients there was a report of the occurrence of two infectious episodes. Parameters related to HSCT, such as time elapsed since the procedure, vaccination status, CD status before and after infection, and clinical manifestations resulting from COVID-19, were evaluated. Among the patients with COVID-19, in three, submitted to Auto HSCT less than six (6) months ago, there was a change in the CD status, and one of them, in addition to the CD symptoms, started to present thyroid impairment with positive anti-TPO. Only one of the patients required hospitalization for five days to treat COVID-19 and remained in CD clinical remission. Nine patients reported late symptoms that may be related to COVID-19. There were no deaths, and the statistical evaluation of the series of COVID-19 patients after HSCT and those who did not present an infectious episode did not present significant data regarding the analyzed parameters. Despite the change in CD status in three patients and the presence of nine patients with late symptoms, we can conclude that there was no significant adverse impact concerning COVID-19 in the evaluated patients who underwent HSCT to treat CD.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "MILTON ARTUR RUIZ",
-        "author_inst": "School of Medicine of the University of Sao Paulo"
-      },
-      {
-        "author_name": "Roberto Luiz Kaiser Junior Sr.",
-        "author_inst": "Kaiser Clinica and Hospital Dia. Sao Jose do Rio Preto, SP, Brazil"
-      },
-      {
-        "author_name": "Lilian Piron-Ruiz Sr.",
-        "author_inst": "Bone Marrow Transplantation Department, Associacao Portuguesa de Beneficencia, Sao Jose do Rio Preto, SP, Brazil"
-      },
-      {
-        "author_name": "Tainara Souza Pinho Sr.",
-        "author_inst": "Bone Marrow Transplantation Department, Associacao Portuguesa de Beneficencia, Sao Jose do Rio Preto, SP, Brazil"
-      },
-      {
-        "author_name": "Lilian Castiglioni Sr.",
-        "author_inst": "Epidemiology Health Department- FAMERP, Sao Jose do Rio Preto, SP, Brazil"
-      },
-      {
-        "author_name": "Luiz Gustavo De Quadros Sr.",
-        "author_inst": "Kaiser Clinica and Hospital Dia. Sao Jose do Rio Preto, SP, Brazil"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2023.06.26.23291907",
     "rel_title": "The effect of residential aged care facility COVID-19 lockdowns on resident mortality",
@@ -56711,6 +57133,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
+  {
+    "rel_doi": "10.1101/2023.06.27.23291947",
+    "rel_title": "Examining the inter-relationships between social isolation and loneliness and their correlates among older British adults before and during the COVID-19 lockdown: evidence from four British longitudinal studies",
+    "rel_date": "2023-06-28",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.27.23291947",
+    "rel_abs": "Background and ObjectivesUnprecedented social restrictions during the COVID-19 pandemic have provided a new lens for considering the inter-relationship between social isolation and loneliness in later life. We present these inter-relationships before and during the COVID-19 restrictions and investigate to what extent demographic, socio-economic, and health factors associated with such experiences differed during the pandemic.\n\nResearch Design and MethodWe used data from four British longitudinal population-based studies (1946 MRC NSHD, 1958 NCDS, 1970 BCS, and ELSA). Rates, co-occurrences, and correlates of social isolation and loneliness are presented prior to and during the early stage of the COVID-19 pandemic and the inter-relationships between these experiences are elucidated in both periods.\n\nResultsAcross the four studies, pre-pandemic proportions reporting social isolation ranged from 15 to 54%, with higher rates in older ages (e.g., 32% of 70-79 and 54% of those over 80). During the pandemic, the percentage of older people reporting both social isolation and loneliness and isolation only slightly increased. The inter-relationship between social isolation and loneliness did not change. Associations between socio-demographic and health characteristics and social isolation and loneliness also remained consistent, with greater burden among those with greater economic precarity (females, non-homeowners, unemployed, illness and greater financial stress).\n\nDiscussion and ImplicationsThere were already large inequalities in experiences of social isolation and loneliness and the pandemic had a small impact on worsening these inequalities. The concepts of loneliness and social isolation are not transferable and clarity is needed in how they are conceptualised, operationalised, and interpreted.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Rosie Mansfield",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Giorgio Di Gessa",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Kishan Patel",
+        "author_inst": "MRC LHA"
+      },
+      {
+        "author_name": "Eoin McElroy",
+        "author_inst": "Ulster University"
+      },
+      {
+        "author_name": "Jacques Wels",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Morag Henderson",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Jane Maddock",
+        "author_inst": "UCL"
+      },
+      {
+        "author_name": "Jean Stafford",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Andrew Steptoe",
+        "author_inst": "UCL: University College London"
+      },
+      {
+        "author_name": "Marcus Richards",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Praveetha Patalay",
+        "author_inst": "University College London"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2023.06.27.23291933",
     "rel_title": "mRNA-1273 vaccine effectiveness against symptomatic SARS-CoV-2 infection and COVID-19-related hospitalization in children aged 6 months to 5 years",
@@ -57744,101 +58225,6 @@
     "type": "new results",
     "category": "genomics"
   },
-  {
-    "rel_doi": "10.1101/2023.06.20.545832",
-    "rel_title": "Combination therapy with oral antiviral and anti-inflammatory drugs improves the efficacy of delayed treatment in severe COVID-19",
-    "rel_date": "2023-06-21",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.20.545832",
-    "rel_abs": "Pulmonary infection with SARS-CoV-2 stimulates host immune responses and can also result in the progression of dysregulated and critical inflammation. Throughout the pandemic, the management and treatment of COVID-19 has been continuously updated with a range of antiviral drugs and immunomodulators. Monotherapy with oral antivirals has proven to be effective in the treatment of COVID-19. However, the treatment should be initiated in the early stages of infection to ensure beneficial therapeutic outcomes, and there is still room for further consideration on therapeutic strategies using antivirals. Here, we show that the oral antiviral ensitrelvir combined with the anti-inflammatory corticosteroid methylprednisolone has higher therapeutic effects and better outcomes in a delayed dosing model of SARS-CoV-2 infected hamsters compared to the monotherapy with ensitrelvir or methylprednisolone alone. Combination therapy with these drugs improved respiratory conditions and the development of pneumonia in hamsters even when the treatment was started after 2 days post infection. The combination therapy led to a differential histological and transcriptomic pattern in comparison to either of the monotherapies, with reduced lung damage and down-regulated expressions of genes involved in inflammatory response. Furthermore, we found that the combination treatment is effective in infection with both highly pathogenic delta and circulating omicron variants. Our results demonstrate the advantage of combination therapy with antiviral and corticosteroid drugs in COVID-19 treatment. Since both drugs are available as oral medications, this combination therapy could provide a clinical and potent therapeutic option for COVID-19.",
-    "rel_num_authors": 20,
-    "rel_authors": [
-      {
-        "author_name": "Michihito Sasaki",
-        "author_inst": "International Institute for Zoonosis Control, Hokkaido University"
-      },
-      {
-        "author_name": "Shun Iida",
-        "author_inst": "National Institute of Infectious Diseases"
-      },
-      {
-        "author_name": "Yuichiro Hirata",
-        "author_inst": "National Institute of Infectious Diseases"
-      },
-      {
-        "author_name": "Shinji Kusakabe",
-        "author_inst": "Shionogi & Co., Ltd."
-      },
-      {
-        "author_name": "Kei Konishi",
-        "author_inst": "Shionogi & Co., Ltd."
-      },
-      {
-        "author_name": "Yukari Itakura",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Koshiro Tabata",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Mai Kishimoto",
-        "author_inst": "Osaka Metropolitan University"
-      },
-      {
-        "author_name": "Hiroko Kobayashi",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Takuma Ariizumi",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Kittiya Intaruck",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Haruaki Nobori",
-        "author_inst": "Shionogi & Co., Ltd."
-      },
-      {
-        "author_name": "Shinsuke Toba",
-        "author_inst": "Shionogi & Co., Ltd."
-      },
-      {
-        "author_name": "Akihiko Sato",
-        "author_inst": "Shionogi & Co., Ltd."
-      },
-      {
-        "author_name": "Keita Matsuno",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Junya Yamagishi",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Tadaki Suzuki",
-        "author_inst": "National Institute of Infectious Diseases"
-      },
-      {
-        "author_name": "William W Hall",
-        "author_inst": "University College of Dublin"
-      },
-      {
-        "author_name": "Yasuko Orba",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Hirofumi Sawa",
-        "author_inst": "Hokkaido University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2023.06.21.545910",
     "rel_title": "Spatial and Temporal Analysis of SARS-CoV-2 Genome Evolutionary Patterns",
@@ -58133,6 +58519,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2023.06.16.23291442",
+    "rel_title": "Vaccines at Velocity: Evaluating Potential Lives Saved by Earlier Vaccination in the COVID-19 Pandemic",
+    "rel_date": "2023-06-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.16.23291442",
+    "rel_abs": "Fast development of COVID-19 vaccines likely averted millions of deaths. We estimate how many more lives could have been saved if safe and effective vaccines were available earlier in the pandemic, in particular, before the epidemic waves in winter of 2020. We fit an epidemiological model informed by retrospective data and simulate counterfactual vaccination scenarios for the United Kingdom and the United States in which vaccines are available between 30 and 90 days earlier. We find that up to 1 July 2021 reductions in mortality range from 10,000 to 48,000 in the UK and 53,000 to 130,000 in the US, depending on when vaccinations start. This corresponds to a maximum of 7.1 and 4 deaths averted per 10,000 people in the UK and US respectively, or a reduction in overall deaths of 50% and 32%. We find that our model is sensitive to uncertain vaccine parameters and benefits depend on the time horizon of the analysis. However, the large average reductions we estimate suggests that it is highly cost-effective to make large investments in strategies to expedite vaccine availability.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Witold Wiecek",
+        "author_inst": "1Day Sooner, Delaware, United States"
+      },
+      {
+        "author_name": "David Johnston",
+        "author_inst": "1Day Sooner, Delaware, United States"
+      },
+      {
+        "author_name": "Tomas Dulka",
+        "author_inst": "1Day Sooner, Delaware, United States"
+      },
+      {
+        "author_name": "Danny Toomey",
+        "author_inst": "1Day Sooner, Delaware, United States"
+      },
+      {
+        "author_name": "Enlli Lewis",
+        "author_inst": "1Day Sooner, Delaware, United States"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2023.06.19.23291622",
     "rel_title": "Inpatient Antibacterial Drug Prescribing for Patients with COVID-19 in Hong Kong",
@@ -59726,65 +60147,6 @@
     "type": "new results",
     "category": "biochemistry"
   },
-  {
-    "rel_doi": "10.1101/2023.06.15.545129",
-    "rel_title": "Repurposing Remdesivir for COVID-19: Computational Drug Design Targeting SARS-CoV-2 RNA Polymerase and Main Protease using Molecular Dynamics Approach",
-    "rel_date": "2023-06-16",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.15.545129",
-    "rel_abs": "The coronavirus disease of 2019 (COVID-19) is a highly contagious respiratory illness that has become a global health crisis with new variants, an unprecedented number of infections, and deaths and demands urgent manufacturing of potent therapeutics. Despite the success of vaccination campaigns around the globe, there is no particular therapeutics approved to date for efficiently treating infected individuals. Repositioning or repurposing previously effective antivirals against RNA viruses to treat COVID-19 patients is a feasible option. Remdesivir is a broad-spectrum antiviral drug that the Food and Drug Administration (FDA) licenses for treating COVID-19 patients who are critically ill patients. Remdesivirs low efficacy, which has been shown in some clinical trials, possible adverse effects, and dose-related toxicities are issues with its use in clinical use. Our study aimed to design potent derivatives of remdesivir through the functional group modification of the parent drug targeting RNA-dependent RNA polymerase (RdRp) and main protease (MPro) of SARS-CoV-2. The efficacy and stability of the proposed derivatives were assessed by molecular docking and extended molecular dynamics simulation analyses. Furthermore, the pharmacokinetic activity was measured to ensure the safety and drug potential of the designed derivatives. The derivatives were non-carcinogenic, chemically reactive, highly interactive, and stable with the target proteins. D-CF3 is one of the designed derivatives that finally showed stronger interaction than the parent drug, according to the docking and dynamics simulation analyses, with both target proteins. However, in vitro and in vivo investigations are guaranteed to validate the findings in the future.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Mita Shikder",
-        "author_inst": "Bangabandhu Sheikh Mujibur Rahman Science and Technology University"
-      },
-      {
-        "author_name": "Kazi Ahsan Ahmed",
-        "author_inst": "Department of Biochemistry and Molecular Biology, Bangladesh Agricultural University, Mymensingh, Bangladesh"
-      },
-      {
-        "author_name": "Abu Tayab Moin",
-        "author_inst": "University of Chittagong Faculty of Biological Science"
-      },
-      {
-        "author_name": "Rajesh B. Patil",
-        "author_inst": "Sinhgad College of Pharmacy"
-      },
-      {
-        "author_name": "Tasnin Al Hasib",
-        "author_inst": "Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh"
-      },
-      {
-        "author_name": "Mohammad Imran Hossan",
-        "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh"
-      },
-      {
-        "author_name": "Deera Mahasin",
-        "author_inst": "Biotechnology Program, Department of Mathematics and Natural Sciences, School of Data and Sciences, BRAC University, Dhaka, Bangladesh"
-      },
-      {
-        "author_name": "Mohammad Najmul Sakib",
-        "author_inst": "University of Chittagong Faculty of Biological Science"
-      },
-      {
-        "author_name": "Iqrar Ahmed",
-        "author_inst": "Division of Computer-Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Maharashtra, Ind"
-      },
-      {
-        "author_name": "Harun Patel",
-        "author_inst": "Division of Computer-Aided Drug Design, Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Maharashtra, Ind"
-      },
-      {
-        "author_name": "Afrin Sultana Chowdhury",
-        "author_inst": "Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "bioinformatics"
-  },
   {
     "rel_doi": "10.1101/2023.06.13.23291332",
     "rel_title": "Omicron vs. the Rest: Assessing the Competitive Dynamics and Coinfection Scenarios of COVID-19 Strains on a Social Network",
@@ -60063,6 +60425,165 @@
     "type": "new results",
     "category": "biochemistry"
   },
+  {
+    "rel_doi": "10.1101/2023.06.14.544834",
+    "rel_title": "Immunogenicity of COVID-19 vaccines and their effect on the HIV reservoir in older people with HIV",
+    "rel_date": "2023-06-15",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.14.544834",
+    "rel_abs": "Older individuals and people with HIV (PWH) were prioritized for COVID-19 vaccination, yet comprehensive studies of the immunogenicity of these vaccines and their effects on HIV reservoirs are not available. We followed 68 PWH aged 55 and older and 23 age-matched HIV-negative individuals for 48 weeks from the first vaccine dose, after the total of three doses. All PWH were on antiretroviral therapy (cART) and had different immune status, including immune responders (IR), immune non-responders (INR), and PWH with low-level viremia (LLV). We measured total and neutralizing Ab responses to SARS-CoV-2 spike and RBD in sera, total anti-spike Abs in saliva, frequency of anti-RBD/NTD B cells, changes in frequency of anti-spike, HIV gag/nef-specific T cells, and HIV reservoirs in peripheral CD4+ T cells. The resulting datasets were used to create a mathematical model for within-host immunization. Various regimens of BNT162b2, mRNA-1273, and ChAdOx1 vaccines elicited equally strong anti-spike IgG responses in PWH and HIV- participants in serum and saliva at all timepoints. These responses had similar kinetics in both cohorts and peaked at 4 weeks post-booster (third dose), while half-lives of plasma IgG also dramatically increased post-booster in both groups. Salivary spike IgA responses were low, especially in INRs. PWH had diminished live virus neutralizing titers after two vaccine doses which were  rescued after a booster. Anti-spike T cell immunity was enhanced in IRs even in comparison to HIV- participants, suggesting Th1 imprinting from HIV, while in INRs it was the lowest. Increased frequency of viral  blips in PWH were seen post-vaccination, but vaccines did not affect the size of the intact HIV reservoir in CD4+ T cells in most PWH, except in LLVs. Thus, older PWH require three doses of COVID-19 vaccine to maximize neutralizing responses against SARS-CoV-2, although vaccines may increase HIV reservoirs in PWH with persistent viremia.",
+    "rel_num_authors": 36,
+    "rel_authors": [
+      {
+        "author_name": "Vitaliy A. Matveev",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Erik Z. Mihelic",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Erika Benko",
+        "author_inst": "Maple Leaf Medical Clinic"
+      },
+      {
+        "author_name": "Patrick Budylowski",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Sebastian Grocott",
+        "author_inst": "McGill University"
+      },
+      {
+        "author_name": "Terry Lee",
+        "author_inst": "CIHR Canadian HIV Trials Network (CTN)"
+      },
+      {
+        "author_name": "Chapin S. Korosec",
+        "author_inst": "York University"
+      },
+      {
+        "author_name": "Karen Colwill",
+        "author_inst": "Lunenfeld-Tanenbaum Research Institute"
+      },
+      {
+        "author_name": "Henry Stephenson",
+        "author_inst": "McGill University"
+      },
+      {
+        "author_name": "Ryan Law",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Lesley A. Ward",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Salma Sheikh-Mohamed",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Genevi\u00e8ve Mailhot",
+        "author_inst": "Lunenfeld-Tanenbaum Research Institute"
+      },
+      {
+        "author_name": "Melanie Delgado-Brand",
+        "author_inst": "Lunenfeld-Tanenbaum Research Institute"
+      },
+      {
+        "author_name": "Adrian Pasculescu",
+        "author_inst": "Lunenfeld-Tanenbaum Research Institute"
+      },
+      {
+        "author_name": "Jenny H. Wang",
+        "author_inst": "Lunenfeld-Tanenbaum Research Institute"
+      },
+      {
+        "author_name": "Freda Qi",
+        "author_inst": "Lunenfeld-Tanenbaum Research Institute"
+      },
+      {
+        "author_name": "Tulunay Tursun",
+        "author_inst": "Lunenfeld-Tanenbaum Research Institute"
+      },
+      {
+        "author_name": "Lela Kardava",
+        "author_inst": "National Institute of Allergy and Infectious Diseases (NIAID)"
+      },
+      {
+        "author_name": "Serena Chau",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Philip Samaan",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Annam Imran",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Dennis C. Copertino Jr.",
+        "author_inst": "Weill Cornell Medicine"
+      },
+      {
+        "author_name": "Gary Chao",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Yoojin Choi",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Robert J. Reinhard",
+        "author_inst": "Independent Public/Global Health Consultant"
+      },
+      {
+        "author_name": "Rupert Kaul",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Jane M. Heffernan",
+        "author_inst": "York University"
+      },
+      {
+        "author_name": "R. Brad Jones",
+        "author_inst": "Weill Cornell Medical College"
+      },
+      {
+        "author_name": "Tae-Wook Chun",
+        "author_inst": "National Institute of Allergy and Infectious Diseases"
+      },
+      {
+        "author_name": "Susan Moir",
+        "author_inst": "National Institute of Allergy and Infectious Diseases"
+      },
+      {
+        "author_name": "Joel Singer",
+        "author_inst": "The University of British Columbia"
+      },
+      {
+        "author_name": "Jen Gommerman",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Anne-Claude Gingras",
+        "author_inst": "Lunenfeld-Tanenbaum Research Institute"
+      },
+      {
+        "author_name": "Colin Kovacs",
+        "author_inst": "Maple Leaf Medical Clinic"
+      },
+      {
+        "author_name": "Mario Ostrowski",
+        "author_inst": "University of Toronto"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2023.06.14.23291388",
     "rel_title": "Association between vaccination rates and severe COVID-19 health outcomes in the United States: a population-level statistical analysis",
@@ -61432,101 +61953,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2023.06.08.23291159",
-    "rel_title": "Poor immunogenicity upon SARS-CoV-2 mRNA vaccinations in autoimmune SLE patients is associated with pronounced EF-mediated responses and anti-BAFF/Belimumab treatment.",
-    "rel_date": "2023-06-12",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.08.23291159",
-    "rel_abs": "Novel mRNA vaccines have resulted in a reduced number of SARS-CoV-2 infections and hospitalizations. Yet, there is a paucity of studies regarding their effectiveness on immunocompromised autoimmune subjects. In this study, we enrolled subjects naive to SARS-CoV-2 infections from two cohorts of healthy donors (HD, n=56) and systemic lupus erythematosus (SLE, n=69). Serological assessments of their circulating antibodies revealed a significant reduction of potency and breadth of neutralization in the SLE group, only partially rescued by a 3rd booster dose. Immunological memory responses in the SLE cohort were characterized by a reduced magnitude of spike-reactive B and T cell responses that were strongly associated with poor seroconversion.\n\nVaccinated SLE subjects were defined by a distinct expansion and persistence of a DN2 spike-reactive memory B cell pool and a contraction of spike-specific memory cTfh cells, contrasting with the sustained germinal center (GC)-driven activity mediated by mRNA vaccination in the healthy population. Among the SLE-associated factors that dampened the vaccine responses, treatment with the monoclonal antibody anti-BAFF/Belimumab (a lupus FDA-approved B cell targeting agent) profoundly affected the vaccine responsiveness by restricting the de novo B cell responses and promoting stronger extra-follicular (EF)-mediated responses that were associated with poor immunogenicity and impaired immunological memory.\n\nIn summary, this study interrogates antigen-specific responses and characterized the immune cell landscape associated with mRNA vaccination in SLE. The identification of factors associated with reduced vaccine efficacy illustrates the impact of SLE B cell biology on mRNA vaccine responses and provides guidance for the management of boosters and recall vaccinations in SLE patients according to their disease endotype and modality of treatment.",
-    "rel_num_authors": 20,
-    "rel_authors": [
-      {
-        "author_name": "Caterina E Faliti",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Fabliha Anam",
-        "author_inst": "Emory"
-      },
-      {
-        "author_name": "Narayanaiah Cheedarla",
-        "author_inst": "Emory"
-      },
-      {
-        "author_name": "Matthew Woodruff",
-        "author_inst": "Emory"
-      },
-      {
-        "author_name": "Sabeena Usman",
-        "author_inst": "Emory"
-      },
-      {
-        "author_name": "Martin Runnstrom",
-        "author_inst": "Emory"
-      },
-      {
-        "author_name": "Trinh Van",
-        "author_inst": "Emory"
-      },
-      {
-        "author_name": "Shuya Kyu",
-        "author_inst": "Emory"
-      },
-      {
-        "author_name": "Hasan Ahmed",
-        "author_inst": "Emory"
-      },
-      {
-        "author_name": "Andrea Morrison-Porter",
-        "author_inst": "Emory"
-      },
-      {
-        "author_name": "Hannah Quehl",
-        "author_inst": "Emory"
-      },
-      {
-        "author_name": "Natalie S. Haddad",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Weirong Chen",
-        "author_inst": "Emory"
-      },
-      {
-        "author_name": "Suneethamma Cheedarla",
-        "author_inst": "Emory"
-      },
-      {
-        "author_name": "Andrew Neish",
-        "author_inst": "Emory"
-      },
-      {
-        "author_name": "John D Roback",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Rustom Antia",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Arezou Khosroshahi",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Frances Eun-Hyung Lee",
-        "author_inst": "Emory"
-      },
-      {
-        "author_name": "Ignacio Sanz",
-        "author_inst": "Emory University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "allergy and immunology"
-  },
   {
     "rel_doi": "10.1101/2023.06.09.23290893",
     "rel_title": "Risk of Coronavirus Disease 2019 (COVID-19) among Those Up-to-Date and Not Up-to-Date on COVID-19 Vaccination",
@@ -61773,6 +62199,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "primary care research"
   },
+  {
+    "rel_doi": "10.1101/2023.06.07.23290927",
+    "rel_title": "SARS-CoV-2 infections among 12 000 pregnant women, 2020, Finland - cross-testing of neutralization assays",
+    "rel_date": "2023-06-12",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.07.23290927",
+    "rel_abs": "We studied the development of SARS-CoV-2 pandemic in Finland in 2020 and evaluated the performance of two surrogate immunoassays for detection of neutralizing antibodies (NAbs). The dataset consisted of 12000 retrospectively collected samples from pregnant women in their 1st trimester throughout 2020. All the samples were initially screened for IgG with SARS-CoV-2 spike antibody assay (EIM-S1, Euroimmun, Lubeck, Germany) followed by confirmation with nucleocapsid antibody assay (Architect SARS-CoV-2, Abbott, Illinois, USA). Samples that were reactive (positive or borderline) with both assays were subjected to testing with commercial surrogate immunoassays of NeutraLISA (EIM) and cPassTM (GenScript Biotech Corporation, Rijswijk, Netherlands) by using pseudoneutralization assay (PNAbA) as a golden standard. No seropositive cases were detected between January and March. Between April and December, IgG (EIM-S1 and Abbott positive) and NAb (PNAbA positive) seroprevalences were between 0.4-1.4%. NeutraLISA showed 90% and cPass 55% concordant results with PNAbA among PNAbA negative samples and 49% and 92% among PNAbA positive samples giving NeutraLISA better specificity but lower sensitivity than cPass. To conclude, seroprevalence in pregnant women reflected that of the general population but the variability of the performance of serological protocols needs to be taken into account in inter-study comparison.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Jenni Virtanen",
+        "author_inst": "University of Helsinki"
+      },
+      {
+        "author_name": "Essi M Korhonen",
+        "author_inst": "University of Helsinki"
+      },
+      {
+        "author_name": "Sami Salonen",
+        "author_inst": "University of Helsinki and Helsinki University Hospital"
+      },
+      {
+        "author_name": "Olli Vapalahti",
+        "author_inst": "University of Helsinki"
+      },
+      {
+        "author_name": "Tarja Sironen",
+        "author_inst": "Haartman Institute, University of Helsinki"
+      },
+      {
+        "author_name": "Anne J Jaaskelainen",
+        "author_inst": "University of Helsinki and Helsinki University Hospital"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2023.06.08.23291050",
     "rel_title": "Quantitatively assessing early detection strategies for mitigating COVID-19 and future pandemics",
@@ -63086,165 +63551,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2023.06.06.23290989",
-    "rel_title": "Metformin reduces SARS-CoV-2 in a Phase 3 Randomized Placebo Controlled Clinical Trial",
-    "rel_date": "2023-06-07",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.06.23290989",
-    "rel_abs": "Current antiviral treatment options for SARS-CoV-2 infections are not available globally, cannot be used with many medications, and are limited to virus-specific targets.1-3 Biophysical modeling of SARS-CoV-2 replication predicted that protein translation is an especially attractive target for antiviral therapy.4 Literature review identified metformin, widely known as a treatment for diabetes, as a potential suppressor of protein translation via targeting of the host mTor pathway.5 In vitro, metformin has antiviral activity against RNA viruses including SARS-CoV-2.6,7 In the COVID-OUT phase 3, randomized, placebo-controlled trial of outpatient treatment of COVID-19, metformin had a 42% reduction in ER visits/hospitalizations/death through 14 days; a 58% reduction in hospitalizations/death through 28 days, and a 42% reduction in Long COVID through 10 months.8,9 Here we show viral load analysis of specimens collected in the COVID-OUT trial that the mean SARS-CoV-2 viral load was reduced 3.6-fold with metformin relative to placebo (-0.56 log10 copies/mL; 95%CI, -1.05 to -0.06, p=0.027) while there was no virologic effect for ivermectin or fluvoxamine vs placebo. The metformin effect was consistent across subgroups and with emerging data.10,11 Our results demonstrate, consistent with model predictions, that a safe, widely available,12 well-tolerated, and inexpensive oral medication, metformin, can be repurposed to significantly reduce SARS-CoV-2 viral load.",
-    "rel_num_authors": 36,
-    "rel_authors": [
-      {
-        "author_name": "Carolyn T Bramante",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Kenneth B Beckman",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Tanvi Mehta",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Amy B Krager",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "David J Odde",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Christopher J Tignanelli",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "John B Buse",
-        "author_inst": "University of North Carolina"
-      },
-      {
-        "author_name": "Darnell M Johnson",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Ray H B Watson",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Jerry J Daniel",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "David M Liebovitz",
-        "author_inst": "Northwestern University"
-      },
-      {
-        "author_name": "Jacinda M Nicklas",
-        "author_inst": "University of Colorado"
-      },
-      {
-        "author_name": "Kenneth Cohen",
-        "author_inst": "Optum"
-      },
-      {
-        "author_name": "Michael A Puskarich",
-        "author_inst": "Hennepin Healthcare"
-      },
-      {
-        "author_name": "Hrishikesh K Belani",
-        "author_inst": "Olive View - UCLA Medical Center"
-      },
-      {
-        "author_name": "Lianne K Siegel",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Nichole R Klatt",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Blake Anderson",
-        "author_inst": "Emory School of Medicine"
-      },
-      {
-        "author_name": "Katrina M Hartman",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Via Rao",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Aubrey A Hagan",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Barkha Patel",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Sarah L Fenno",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Nandini Avula",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Neha V Reddy",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Spencer M Erickson",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Regina D Fricton",
-        "author_inst": "Northwestern University"
-      },
-      {
-        "author_name": "Samuel Lee",
-        "author_inst": "Northwestern University"
-      },
-      {
-        "author_name": "Gwendolyn Griffiths",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Matthew F Pullen",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Jennifer L Thompson",
-        "author_inst": "Vanderbilt University"
-      },
-      {
-        "author_name": "Nancy Sherwood",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Thomas A Murray",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Michael R Rose",
-        "author_inst": "Johns Hopkins University"
-      },
-      {
-        "author_name": "David R Boulware",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Jared D Huling",
-        "author_inst": "University of Minnesota"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2023.06.05.23290956",
     "rel_title": "How could a pooled testing policy have performed in managing the early stages of the COVID-19 pandemic? Results from a simulation study",
@@ -63439,6 +63745,77 @@
     "type": "new results",
     "category": "animal behavior and cognition"
   },
+  {
+    "rel_doi": "10.1101/2023.06.03.543589",
+    "rel_title": "A deep learning-based drug repurposing screening and validation for anti-SARS-CoV-2 compounds by targeting the cell entry mechanism",
+    "rel_date": "2023-06-05",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.03.543589",
+    "rel_abs": "The recent outbreak of Corona Virus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a severe threat to the global public health and economy, however, effective drugs to treat COVID-19 are still lacking. Here, we employ a deep learning-based drug repositioning strategy to systematically screen potential anti-SARS-CoV-2 drug candidates that target the cell entry mechanism of SARS-CoV-2 virus from 2,635 FDA-approved drugs and 1,062 active ingredients from Traditional Chinese Medicine herbs. In silico molecular docking analysis validates the interactions between the top compounds and host receptors or viral spike proteins. Using a SARS-CoV-2 pseudovirus system, we further identify several drug candidates including Fostamatinib, Linagliptin, Lysergol and Sophoridine that can effectively block the cell entry of SARS-CoV-2 variants into human lung cells even at a nanomolar scale. These efforts not only illuminate the feasibility of applying deep learning-based drug repositioning for antiviral agents by targeting a specified mechanism, but also provide a valuable resource of promising drug candidates or lead compounds to treat COVID-19.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Yingjia Yao",
+        "author_inst": "Northeastern University"
+      },
+      {
+        "author_name": "Yunhan Zhang",
+        "author_inst": "Northeastern University"
+      },
+      {
+        "author_name": "Zexu Li",
+        "author_inst": "Northeastern University"
+      },
+      {
+        "author_name": "Zhisong Chen",
+        "author_inst": "Northeastern University"
+      },
+      {
+        "author_name": "Xiaofeng Wang",
+        "author_inst": "Northeastern University"
+      },
+      {
+        "author_name": "Zihan Li",
+        "author_inst": "Northeastern University"
+      },
+      {
+        "author_name": "Li Yu",
+        "author_inst": "Northeastern University"
+      },
+      {
+        "author_name": "Xiaolong Cheng",
+        "author_inst": "Childrens National Hospital"
+      },
+      {
+        "author_name": "Wei Li",
+        "author_inst": "Childrens National Hospital"
+      },
+      {
+        "author_name": "Wen-Jie Jiang",
+        "author_inst": "Peking University"
+      },
+      {
+        "author_name": "Hua-Jun Wu",
+        "author_inst": "Peking University"
+      },
+      {
+        "author_name": "Zezhong Feng",
+        "author_inst": "Northeastern University"
+      },
+      {
+        "author_name": "Jinfu Sun",
+        "author_inst": "Institute of Biotechnology, College of Life and Health Sciences, Northeastern University"
+      },
+      {
+        "author_name": "Teng Fei",
+        "author_inst": "Northeastern University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2023.06.02.543458",
     "rel_title": "Machine Learning-Guided Antibody Engineering That Leverages Domain Knowledge To Overcome The Small Data Problem",
@@ -65288,45 +65665,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2023.05.29.23290677",
-    "rel_title": "Social inequalities in the misbelief of chloroquines protective effect against COVID-19: results from the EPICOVID-19 study in Brazil",
-    "rel_date": "2023-06-03",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.29.23290677",
-    "rel_abs": "Objectives: The aim of this study was to assess the spread of denialist messages regarding COVID-19 in Brazil, specifically examining how social inequalities contributed to the misconception of chloroquine having a protective effect against the virus.\n\nStudy design: Three countrywide population-based studies were conducted in 2020 (May 14-21, June 4-7, and June 21-24), including 133 Brazilian cities (n=88,772).\n\nMethods: Participants were asked whether they believed in chloroquines protective effect against infection with the SARS-CoV-2 virus (no/yes/dont know). A jeopardy index score to assess cumulative social deprivation was calculated based on gender, racial and socioeconomic variables. Descriptive analysis and inequality measures (Slope Index of Inequality - SII; and Concentration Index - CIX) were used to evaluate the main association under investigation. Multinomial logistic regression was used to evaluate 3-category outcome according to independent variables.\n\nResults: Overall, 47.9% of participants either believed that chloroquine prevented against COVID-19 or said, \"I dont know\". Misbelief and lack of knowledge about chloroquine were greater among the most vulnerable (lowest levels of education and socioeconomic status). Absolute and relative inequalities were observed according to jeopardy index. Lack of knowledge was 2.49 greater among women than among men. Race/ethnicity minorities, those with low education and low socioeconomic status were more likely to erroneously believe that chloroquine prevented against COVID-19. The highest absolute inequality was observed for the category \"I dont know\" (SII = -14.3).\n\nConclusions: Misbelief of chloroquines protective effect against the SARS-CoV-2 virus was high in Brazil. People with greater social vulnerability were more likely to wrongly believe chloroquine prevented against COVID-19",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Bruno Nunes",
-        "author_inst": "Federal University of Pelotas"
-      },
-      {
-        "author_name": "Inacio C Silva",
-        "author_inst": "Federal University of Pelotas"
-      },
-      {
-        "author_name": "Gregore I Mielke",
-        "author_inst": "Federal University of Pelotas"
-      },
-      {
-        "author_name": "Luis Paulo Vidaletti",
-        "author_inst": "International Center for Equity in Health"
-      },
-      {
-        "author_name": "Mariangela Freitas Silveira",
-        "author_inst": "Universidade Federal de Pelotas"
-      },
-      {
-        "author_name": "Pedro Hallal",
-        "author_inst": "UFPel"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2023.05.25.23290456",
     "rel_title": "Effectiveness of mRNA-1273 bivalent (Original and Omicron BA.4/BA.5) COVID-19 vaccine in preventing hospitalizations for COVID-19, medically attended SARS-CoV-2 infections, and hospital death in the United States",
@@ -65705,6 +66043,81 @@
     "type": "new results",
     "category": "biochemistry"
   },
+  {
+    "rel_doi": "10.1101/2023.05.31.543129",
+    "rel_title": "CD4+ T-cell immunity of SARS-CoV-2 patients determine pneumonia development",
+    "rel_date": "2023-06-01",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.31.543129",
+    "rel_abs": "Most humans infected with SARS-CoV-2 will recover without developing pneumonia. A few SARS-CoV-2 infected patients, however, develop pneumonia, and occasionally develop cytokine storms. In such cases, it is assumed that there is an inadequate immune response to eliminate viral infected cells and an excessive inappropriate immune response causing organ damage, but little is known about this mechanism. In this study, we used single cell RNA sequencing and mass cytometry to analyze peripheral blood T cells from patients hospitalized with proven COVID-19 infection in order to clarify the differences in host immune status among COVID-19 pneumonia cases, non-pneumonia cases, and healthy controls. The results showed that a specific CD4+ T cell cluster with chemokine receptor expression patterns, CXCR3+CCR4-CCR6+ (Th1/17), was less abundant in COVID-19 pneumonia patients. Interestingly, these CD4+ T-cell clusters were identical to those we have reported to correlate with antitumor immunity and predict programmed cell death (PD)-1 blockade treatment response in lung cancer. The Th1/17 cell percentages had biomarker performance in diagnosing pneumonia cases. In addition, CTLA-4 expression of type17 helper T cells (Th17) and regulatory T cells (Treg) was found to be significantly lower. This indicates that functional suppression of Th17 was less effective and Treg function was impaired in pneumonia cases. These results suggest that imbalance of CD4+ T-cell immunity generates excessive immunity that does not lead to viral eradication. This might be a potential therapeutic target mechanism to prevent severe viral infections.\n\nImportanceIn this observational study, 49 consecutive patients with SARS-CoV-2 infection confirmed by PCR testing and admitted to Saitama Medical University Hospital and Saitama Medical University International Medical Centre between December 4, 2020 and January 17, 2022 were included. Of these 49 patients, 29 were diagnosed with COVID-19 pneumonia by computed tomography (CT) scan (Table 1). The unique CD4+ T-cell immunity with less abundant Th1/17 CD4+ T-cell cluster and low expression of CTLA-4 in Th17 and Treg was consistently found in SARS-CoV-2 pneumonia patients on admission and 1-week of admission. The imbalance of CD4+ T-cell immunity may contribute to develop pneumonia in SARS-CoV-2 virus infected patients by delaying viral clearance and resulting in an excessive immune response.\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@1aac015org.highwire.dtl.DTLVardef@128c14dorg.highwire.dtl.DTLVardef@aacabaorg.highwire.dtl.DTLVardef@e39c8eorg.highwire.dtl.DTLVardef@13b439a_HPS_FORMAT_FIGEXP  M_TBL O_FLOATNOTable 1C_FLOATNO O_TABLECAPTIONPatient demographics\n\nC_TABLECAPTION C_TBL",
+    "rel_num_authors": 15,
+    "rel_authors": [
+      {
+        "author_name": "Erika Naito",
+        "author_inst": "Saitama Ika Daigaku"
+      },
+      {
+        "author_name": "Takahiro Uchida",
+        "author_inst": "Saitama Ika Daigaku"
+      },
+      {
+        "author_name": "Satoshi Yamasaki",
+        "author_inst": "Saitama Ika Daigaku Kokusai Iryo Center"
+      },
+      {
+        "author_name": "Kosuke Hashimoto",
+        "author_inst": "Saitama Ika Daigaku Kokusai Iryo Center"
+      },
+      {
+        "author_name": "Yu Miura",
+        "author_inst": "Saitama Ika Daigaku Kokusai Iryo Center"
+      },
+      {
+        "author_name": "Ayako Shiono",
+        "author_inst": "Saitama Medical University"
+      },
+      {
+        "author_name": "Takayuki Kawamura",
+        "author_inst": "Saitama Ika Daigaku Kokusai Iryo Center"
+      },
+      {
+        "author_name": "Atsuto Mouri",
+        "author_inst": "Saitama Ika Daigaku Kokusai Iryo Center"
+      },
+      {
+        "author_name": "Ou Yamaguchi",
+        "author_inst": "Saitama Ika Daigaku Kokusai Iryo Center"
+      },
+      {
+        "author_name": "Hisao Imai",
+        "author_inst": "Saitama Ika Daigaku Kokusai Iryo Center"
+      },
+      {
+        "author_name": "Kyoichi Kaira",
+        "author_inst": "Saitama Ika Daigaku Kokusai Iryo Center"
+      },
+      {
+        "author_name": "Manabu Nemoto",
+        "author_inst": "Saitama Medical University International Medical Center"
+      },
+      {
+        "author_name": "Kotaro Mitsutake",
+        "author_inst": "Tohoku Daigaku Daigakuin Igakukei Kenkyuka Igakubu"
+      },
+      {
+        "author_name": "Makoto Nagata",
+        "author_inst": "Saitama Medical University"
+      },
+      {
+        "author_name": "Hiroshi Kagamu",
+        "author_inst": "Saitama Ika Daigaku Kokusai Iryo Center"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2023.05.30.542314",
     "rel_title": "A semi-quantitative, rapid, point of care SARS-CoV-2 serologic assay predicts neutralizing antibody levels",
@@ -67026,841 +67439,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2023.05.26.23290475",
-    "rel_title": "Researching COVID to enhance recovery (RECOVER) adult study protocol: Rationale, objectives and design",
-    "rel_date": "2023-05-28",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.26.23290475",
-    "rel_abs": "ImportanceSARS-CoV-2 infection can result in ongoing, relapsing, or new symptoms or other health effects after the acute phase of infection; termed post-acute sequelae of SARS-CoV-2 infection (PASC), or long COVID. The characteristics, prevalence, trajectory and mechanisms of PASC are ill-defined. The objectives of the Researching COVID to Enhance Recovery (RECOVER) Multi-site Observational Study of PASC in Adults (RECOVER-Adult) are to: (1) characterize PASC prevalence; (2) characterize the symptoms, organ dysfunction, natural history, and distinct phenotypes of PASC; (3) identify demographic, social and clinical risk factors for PASC onset and recovery; and (4) define the biological mechanisms underlying PASC pathogenesis.\n\nMethodsRECOVER-Adult is a combined prospective/retrospective cohort currently planned to enroll 14,880 adults aged [&ge;]18 years. Eligible participants either must meet WHO criteria for suspected, probable, or confirmed infection; or must have evidence of no prior infection. Recruitment occurs at 86 sites in 33 U.S. states, Washington, DC and Puerto Rico, via facility- and community-based outreach. Participants complete quarterly questionnaires about symptoms, social determinants, vaccination status, and interim SARS-CoV-2 infections. In addition, participants contribute biospecimens and undergo physical and laboratory examinations at approximately 0, 90 and 180 days from infection or negative test date, and yearly thereafter. Some participants undergo additional testing based on specific criteria or random sampling. Patient representatives provide input on all study processes. The primary study outcome is onset of PASC, measured by signs and symptoms. A paradigm for identifying PASC cases will be defined and updated using supervised and unsupervised learning approaches with cross- validation. Logistic regression and proportional hazards regression will be conducted to investigate associations between risk factors, onset, and resolution of PASC symptoms.\n\nDiscussionRECOVER-Adult is the first national, prospective, longitudinal cohort of PASC among US adults. Results of this study are intended to inform public health, spur clinical trials, and expand treatment options.",
-    "rel_num_authors": 205,
-    "rel_authors": [
-      {
-        "author_name": "Leora I. Horwitz",
-        "author_inst": "Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA"
-      },
-      {
-        "author_name": "Tanayott Thaweethai",
-        "author_inst": "Department of Biostatistics, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Shari B. Brosnahan",
-        "author_inst": "Division of Pulmonary Critical Care and Sleep Medicine, NYU Langone Health, New York, NY, USA"
-      },
-      {
-        "author_name": "Mine S. Cicek",
-        "author_inst": "Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA"
-      },
-      {
-        "author_name": "Megan L. Fitzgerald",
-        "author_inst": "Patient Led Research Collaboration on COVID-19, Washington, DC, USA"
-      },
-      {
-        "author_name": "Jason D. Goldman",
-        "author_inst": "Division of Infectious Diseases, Providence Swedish Medical Center, Seattle, WA, USA"
-      },
-      {
-        "author_name": "Rachel Hess",
-        "author_inst": "Department of Population Health Sciences and Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT, USA"
-      },
-      {
-        "author_name": "S. L. Hodder",
-        "author_inst": "Department of Medicine, West Virginia University, Morgantown, WV, USA"
-      },
-      {
-        "author_name": "Vanessa L. Jacoby",
-        "author_inst": "Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA"
-      },
-      {
-        "author_name": "Michael R. Jordan",
-        "author_inst": "Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Medford, MA, USA"
-      },
-      {
-        "author_name": "Jerry A. Krishnan",
-        "author_inst": "Department of Medicine, University of Illinois Chicago, Chicago, IL, USA"
-      },
-      {
-        "author_name": "Adeyinka O. Laiyemo",
-        "author_inst": "Department of Medicine, Howard University, Washington DC, USA"
-      },
-      {
-        "author_name": "Torri D. Metz",
-        "author_inst": "Department of Obstetrics and Gynecology, University of Utah Health, Salt Lake City, UT, USA"
-      },
-      {
-        "author_name": "Lauren Nichols",
-        "author_inst": "Body Politic COVID-19 Support Group, Boston, MA, USA"
-      },
-      {
-        "author_name": "Rachel E. Patzer",
-        "author_inst": "Department of Medicine and Surgery, Health Services Research Center, Emory University School of Medicine, Atlanta, GA, USA"
-      },
-      {
-        "author_name": "Anisha Sekar",
-        "author_inst": "Patient Led Research Collaboration on COVID-19, Washington, DC, USA"
-      },
-      {
-        "author_name": "Nora G. Singer",
-        "author_inst": "Department of Medicine and Rheumatology, The MetroHealth Medical Center, Cleveland, OH, USA"
-      },
-      {
-        "author_name": "Lauren E. Stiles",
-        "author_inst": "Department of Neurology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY, USA"
-      },
-      {
-        "author_name": "Barbara S. Taylor",
-        "author_inst": "Department of Medicine, Division of Infectious Diseases and Infectious Diseases, Long School of Medicine, University of Texas Health Science Center San Antonio,"
-      },
-      {
-        "author_name": "Shifa Ahmed",
-        "author_inst": "Department of Biostatistics, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Heather A. Algren",
-        "author_inst": "Swedish Center for Research and Innovation, Providence Swedish Medical Center, Seattle, WA, USA"
-      },
-      {
-        "author_name": "Khamal Anglin",
-        "author_inst": "Department of Epidemiology and Biostatistics, University of California at San Francisco Institute of Global Health Sciences, San Francisco, San Francisco, CA, U"
-      },
-      {
-        "author_name": "Lisa Aponte-Soto",
-        "author_inst": "College of Science and Health, Department of Health Sciences, DePaul University, Chicago, IL, USA"
-      },
-      {
-        "author_name": "Hassan Ashktorab",
-        "author_inst": "Department of Medicine, Howard University, Washington DC, USA"
-      },
-      {
-        "author_name": "Ingrid V. Bassett",
-        "author_inst": "Medical Practice Evaluation Center, Department of Medicine, Massachusetts General"
-      },
-      {
-        "author_name": "Brahmchetna Bedi",
-        "author_inst": "Department of Medicine, Emory University, Atlanta, GA, USA"
-      },
-      {
-        "author_name": "Nahid Bhadelia",
-        "author_inst": "Center for Emerging Infectious Diseases Policy and Research, Boston University School of Medicine, Boston, MA, USA"
-      },
-      {
-        "author_name": "Christian Bime",
-        "author_inst": "Department of Medicine, University of Arizona, Tucson, AZ, USA"
-      },
-      {
-        "author_name": "Marie-Abele C. Bind",
-        "author_inst": "Department of Biostatistics, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Lora J. Black",
-        "author_inst": "Department of Clinical Research, Sanford Research, Sioux Falls, SD, USA"
-      },
-      {
-        "author_name": "Andra L. Blomkalns",
-        "author_inst": "Department of Emergency Medicine, Stanford University, Stanford, CA, USA"
-      },
-      {
-        "author_name": "Hassan Brim",
-        "author_inst": "Department of Pathology, Howard University, Washington, DC, USA"
-      },
-      {
-        "author_name": "Mario Castro",
-        "author_inst": "Division of Pulmonary and Critical Care, University of Kansas Medical Center, Kansas City, KS, USA"
-      },
-      {
-        "author_name": "James Chan",
-        "author_inst": "Department of Biostatistics, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Alexander W. Charney",
-        "author_inst": "Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA"
-      },
-      {
-        "author_name": "Benjamin K. Chen",
-        "author_inst": "Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA"
-      },
-      {
-        "author_name": "Li Qing Chen",
-        "author_inst": "Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Peter Chen",
-        "author_inst": "Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA"
-      },
-      {
-        "author_name": "David Chestek",
-        "author_inst": "Department of Emergency Medicine, University of Illinois Chicago, Chicago, IL, USA"
-      },
-      {
-        "author_name": "Lori B. Chibnik",
-        "author_inst": "Department of Neurology, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Dominic C. Chow",
-        "author_inst": "Department of Medicine, University of Hawaii at Manoa John A. Burns School of Medicine, Honolulu, HI, USA"
-      },
-      {
-        "author_name": "Helen Y. Chu",
-        "author_inst": "Department of Allergy & Infectious Diseases, University of Washington, Seattle, WA, USA"
-      },
-      {
-        "author_name": "Rebecca G. Clifton",
-        "author_inst": "Department of Biostatistics, George Washington University, Washington DC, USA"
-      },
-      {
-        "author_name": "Shelby Collins",
-        "author_inst": "Department of Medicine, Emory University, Atlanta, GA, USA"
-      },
-      {
-        "author_name": "Maged M. Costantine",
-        "author_inst": "Department of Obstetrics and Gynecology, The Ohio State University Hospital, Columbus, OH, USA"
-      },
-      {
-        "author_name": "Sushma K. Cribbs",
-        "author_inst": "Department of Medicine, Emory University, Atlanta, GA, USA"
-      },
-      {
-        "author_name": "Steven G. Deeks",
-        "author_inst": "Department of Medicine, University of California, San Francisco, San Francisco, CA, USA"
-      },
-      {
-        "author_name": "John D. Dickinson",
-        "author_inst": "Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA"
-      },
-      {
-        "author_name": "Sarah E. Donohue",
-        "author_inst": "Department of Research Services, University of Illinois College of Medicine, Peoria, IL, USA"
-      },
-      {
-        "author_name": "Matthew S. Durstenfeld",
-        "author_inst": "Department of Medicine, Division of Cardiology at Zuckerberg San Francisco General, University of California San Francisco, San Francisco, CA, USA"
-      },
-      {
-        "author_name": "Ivette F. Emery",
-        "author_inst": "MaineHealth Institute for Research, MaineHealth, Scarborough, ME, USA"
-      },
-      {
-        "author_name": "Kristine M. Erlandson",
-        "author_inst": "Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA"
-      },
-      {
-        "author_name": "Julio C. Facelli",
-        "author_inst": "Department of Biomedical Informatics and Clinical and Translational Science Institute, University of Utah, Salt Lake City, UT, USA"
-      },
-      {
-        "author_name": "Rachael Farah-Abraham",
-        "author_inst": "Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA"
-      },
-      {
-        "author_name": "Aloke V. Finn",
-        "author_inst": "Department of Pathology, CVPath Institute, Gaithersburg, MD, USA"
-      },
-      {
-        "author_name": "Melinda S. Fischer",
-        "author_inst": "Department of Medicine, Division of Infectious Diseases and Infectious Diseases, Long School of Medicine, University of Texas Health Science Center San Antonio,"
-      },
-      {
-        "author_name": "Valerie J. Flaherman",
-        "author_inst": "Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA"
-      },
-      {
-        "author_name": "Judes Fleurimont",
-        "author_inst": "Mile Square Health Center, University of Illinois Chicago, University of Illinois Chicago, IL, USA"
-      },
-      {
-        "author_name": "Vivian Fonseca",
-        "author_inst": "Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA"
-      },
-      {
-        "author_name": "Emily J. Gallagher",
-        "author_inst": "Department of Endocrinology, Diabetes and Bone Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA"
-      },
-      {
-        "author_name": "Jennifer C. Gander",
-        "author_inst": "Center for Research and Evaluation, Kaiser Permanente of Georgia, Atlanta, GA, USA"
-      },
-      {
-        "author_name": "Maria Laura Gennaro",
-        "author_inst": "Public Health Research Institute and Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA"
-      },
-      {
-        "author_name": "Kelly S. Gibson",
-        "author_inst": "Department of Obstetrics and Gynecology, MetroHealth System, Cleveland, OH, USA"
-      },
-      {
-        "author_name": "Minjoung Go",
-        "author_inst": "Department of Medicine, Stanford University, Stanford, CA, USA"
-      },
-      {
-        "author_name": "Steven N. Goodman",
-        "author_inst": "Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA"
-      },
-      {
-        "author_name": "Joey P. Granger",
-        "author_inst": "Department of Physiology & Biophysics, University of Mississippi Medical Center, Jackson, MS, USA"
-      },
-      {
-        "author_name": "Frank L. Greenway",
-        "author_inst": "Clinical Trials, Pennington Biomedical Research Center, Baton Rouge, LA, USA"
-      },
-      {
-        "author_name": "John W. Hafner",
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-        "author_inst": "Department of Arthritis & Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA"
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-        "author_inst": "Department of Family Medicine, Cambridge Health Alliance, Cambridge, MA, USA"
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-        "author_inst": "Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA"
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-        "author_inst": "Department of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA"
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-        "author_inst": "Department of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA"
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-        "author_inst": "Department of Obstetrics, Gynecology and Reproductive Sciences, University of Texas Health Science Center at Houston, Houston, TX, USA"
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-        "author_inst": "Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA"
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-        "author_inst": "Department of Neurology and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA"
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-        "author_inst": "Division of Cardiology, Kaiser Permanente of Georgia, Atlanta, GA, USA"
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-        "author_inst": "Department of Social, Statistical and Environmental Sciences, RTI International, Research Triangle Park, NC, USA"
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-        "author_inst": "Department of Biostatistics, Massachusetts General Hospital, Boston, MA, USA"
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-        "author_inst": "Department of Biostatistics, Massachusetts General Hospital, Boston, MA, USA"
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-        "author_name": "- Recover Initiative",
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-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2023.05.22.23290291",
     "rel_title": "Nurses' perceptions of videoconferencing telenursing: comparing frontal learning vs. online learning before and after the COVID-19 pandemic",
@@ -68175,6 +67753,101 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2023.05.25.542297",
+    "rel_title": "Multi-omic Profiling Reveals Early Immunological Indicators for Identifying COVID-19 Progressors",
+    "rel_date": "2023-05-26",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.25.542297",
+    "rel_abs": "The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to a rapid response by the scientific community to further understand and combat its associated pathologic etiology. A focal point has been on the immune responses mounted during the acute and post-acute phases of infection, but the immediate post-diagnosis phase remains relatively understudied. We sought to better understand the immediate post-diagnosis phase by collecting blood from study participants soon after a positive test and identifying molecular associations with longitudinal disease outcomes. Multi-omic analyses identified differences in immune cell composition, cytokine levels, and cell subset-specific transcriptomic and epigenomic signatures between individuals on a more serious disease trajectory (Progressors) as compared to those on a milder course (Non-progressors). Higher levels of multiple cytokines were observed in Progressors, with IL-6 showing the largest difference. Blood monocyte cell subsets were also skewed, showing a comparative decrease in non-classical CD14-CD16+ and intermediate CD14+CD16+ monocytes. Additionally, in the lymphocyte compartment, CD8+ T effector memory cells displayed a gene expression signature consistent with stronger T cell activation in Progressors. Importantly, the identification of these cellular and molecular immune changes occurred at the early stages of COVID-19 disease. These observations could serve as the basis for the development of prognostic biomarkers of disease risk and interventional strategies to improve the management of severe COVID-19.\n\nOne Sentence SummaryImmunological changes associated with COVID-19 progression can be detected during the early stages of infection.",
+    "rel_num_authors": 20,
+    "rel_authors": [
+      {
+        "author_name": "Katherine A Drake",
+        "author_inst": "Verily Life Sciences, South San Francisco, 94080, USA"
+      },
+      {
+        "author_name": "Dimitri Talantov",
+        "author_inst": "Janssen Research & Development, LLC, San Diego, 92121, USA"
+      },
+      {
+        "author_name": "Gary Tong",
+        "author_inst": "Verily Life Sciences, South San Francisco, 94080, USA"
+      },
+      {
+        "author_name": "Jack T Lin",
+        "author_inst": "Verily Life Sciences, South San Francisco, 94080, USA"
+      },
+      {
+        "author_name": "Simon Verheijden",
+        "author_inst": "Janssen Research & Development, Beerse, Belgium"
+      },
+      {
+        "author_name": "Samuel Katz",
+        "author_inst": "Verily Life Sciences, South San Francisco, 94080, USA"
+      },
+      {
+        "author_name": "Jacqueline M Leung",
+        "author_inst": "Verily Life Sciences, South San Francisco, 94080, USA"
+      },
+      {
+        "author_name": "Benjamin Yuen",
+        "author_inst": "Verily Life Sciences, South San Francisco, 94080, USA"
+      },
+      {
+        "author_name": "Vinod Krishna",
+        "author_inst": "Janssen Research & Development, LLC, San Diego, 92121, USA"
+      },
+      {
+        "author_name": "Michelle J Wu",
+        "author_inst": "Verily Life Sciences, South San Francisco, 94080, USA"
+      },
+      {
+        "author_name": "Alex Sutherland",
+        "author_inst": "Verily Life Sciences, South San Francisco, 94080, USA"
+      },
+      {
+        "author_name": "Sarah Short",
+        "author_inst": "Verily Life Sciences, South San Francisco, 94080, USA"
+      },
+      {
+        "author_name": "Pouya Kheradpour",
+        "author_inst": "Verily Life Sciences, South San Francisco, 94080, USA"
+      },
+      {
+        "author_name": "Maxwell R Mumbach",
+        "author_inst": "Verily Life Sciences, South San Francisco, 94080, USA"
+      },
+      {
+        "author_name": "Kate M Franz",
+        "author_inst": "Verily Life Sciences, South San Francisco, 94080, USA"
+      },
+      {
+        "author_name": "Vladimir Trifonov",
+        "author_inst": "Janssen Research & Development, LLC, San Diego, 92121, USA"
+      },
+      {
+        "author_name": "Molly V Lucas",
+        "author_inst": "Janssen Research & Development, LLC, New Jersey, 08933, USA"
+      },
+      {
+        "author_name": "James Merson",
+        "author_inst": "Janssen Research & Development, LLC, San Diego, 92121, USA"
+      },
+      {
+        "author_name": "Charles C Kim",
+        "author_inst": "Verily Life Sciences, South San Francisco, 94080, USA"
+      },
+      {
+        "author_name": "- The PRESCO Study Group",
+        "author_inst": ""
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2023.05.25.542331",
     "rel_title": "Evolution of transient RNA structure-RNA polymerase interactions in respiratory RNA virus genomes",
@@ -69712,61 +69385,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2023.05.19.541479",
-    "rel_title": "The COVID-19 mRNA vaccine Comirnaty induces anaphylactic shock in an anti-PEG hyperimmune large animal model: Role of complement in cardiovascular, hematological, and inflammatory mediator changes",
-    "rel_date": "2023-05-22",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.19.541479",
-    "rel_abs": "BackgroundComirnaty, Pfizer-BioNTechs polyethylene-glycol (PEG)-containing Covid-19 vaccine, can cause hypersensitivity reactions (HSRs) in a small fraction of immunized people which can, very rarely, culminate in life-threatening anaphylaxis. A role of anti-PEG antibodies (Abs) has been proposed, but causality has not yet been proven in an animal model. This study aimed to provide such evidence using anti-PEG hyperimmune pigs (i.e., pigs displaying very high levels of anti-PEG Abs). We also sought to find evidence for the role of complement (C) activation and thromboxane A2 (TXA2) release in blood as contributing effects to anaphylaxis.\n\nMethodsPigs (n=6) were immunized with 0.1 mg/kg PEGylated liposome (Doxebo) i.v. the rise of anti-PEG IgG and IgM was measured in serial blood samples with ELISA. After 2-3 weeks, during the height of seroconversion, the animals were injected i.v. with 1/3 human vaccine dose (HVD) of Comirnaty, and the hemodynamic (PAP, SAP), cardiopulmonary (HR, EtCO2,), hematological parameters (WBC, granulocyte, lymphocyte, and platelet counts) and blood immune mediators (anti-PEG IgM and IgG Abs, C3a and TXA2) were measured as endpoints of HSRs.\n\nResultsA week after immunization of 6 pigs with Doxebo, the level of anti-PEG IgM and IgG rose 5-10-thousands-fold in all animals, and they all developed anaphylactic shock to i.v. injection of 1/3 HVD of Comirnaty. The reaction, starting within 1 min, led to the abrupt decline of SAP along with maximal pulmonary hypertension, decreased pulse pressure amplitude, tachycardia, granulo- and thrombocytopenia, and paralleling rises of plasma C3a and TXB2 levels. These vaccine effects were not observed in non-immunized pigs.\n\nConclusionsConsistent with previous studies with PEGylated nano-liposomes, these data show a causal role of anti-PEG Abs in the anaphylaxis to Comirnaty. The reaction involves C activation, and, hence, it represents C activation-related pseudo-allergy (CARPA). The setup provides the first large-animal model for mRNA-vaccine-induced anaphylaxis in humans.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Balint A. Barta",
-        "author_inst": "Heart and Vascular Center, Semmelweis University, Budapest, Hungary"
-      },
-      {
-        "author_name": "Tamas Radovits",
-        "author_inst": "Heart and Vascular Center, Semmelweis University, Budapest, Hungary"
-      },
-      {
-        "author_name": "Attila B. Dobos",
-        "author_inst": "Heart and Vascular Center, Semmelweis University, Budapest, Hungary"
-      },
-      {
-        "author_name": "Gergely T. Kozma",
-        "author_inst": "Nanomedicine Research and Education Center, Department of Translational Medicine, Semmelweis University, Budapest, Hungary"
-      },
-      {
-        "author_name": "Tamas Meszaros",
-        "author_inst": "Nanomedicine Research and Education Center, Department of Translational Medicine, Semmelweis University, Budapest, Hungary"
-      },
-      {
-        "author_name": "Petra Berenyi",
-        "author_inst": "Nanomedicine Research and Education Center, Department of Translational Medicine, Semmelweis University, Budapest, Hungary"
-      },
-      {
-        "author_name": "Reka Facsko",
-        "author_inst": "Nanomedicine Research and Education Center, Department of Translational Medicine, Semmelweis University, Budapest, Hungary"
-      },
-      {
-        "author_name": "Tamas Gy. Fulop",
-        "author_inst": "TECOdevelopment GmbH, Rheinbach, Germany"
-      },
-      {
-        "author_name": "Bela Merkely",
-        "author_inst": "Heart and Vascular Center, Semmelweis University, Budapest, Hungary"
-      },
-      {
-        "author_name": "Janos Szebeni",
-        "author_inst": "Semmelweis University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "pharmacology and toxicology"
-  },
   {
     "rel_doi": "10.1101/2023.05.22.541294",
     "rel_title": "Breakthrough infections by SARS-CoV-2 variants boost cross-reactive hybrid immune responses in mRNA-vaccinated Golden Syrian Hamsters",
@@ -70061,6 +69679,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2023.05.19.23290234",
+    "rel_title": "Defining the Subtypes of Long COVID and Risk Factors for Prolonged Disease",
+    "rel_date": "2023-05-21",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.19.23290234",
+    "rel_abs": "ImportanceThere have been over 759 million confirmed cases of COVID-19 worldwide. A significant portion of these infections will lead to long COVID and its attendant morbidities and costs.\n\nObjectiveTo empirically derive a long COVID case definition consisting of significantly increased signs, symptoms, and diagnoses to support clinical, public health, research, and policy initiatives related to the pandemic.\n\nDesignCase-Crossover Population-based study.\n\nSettingVeterans Affairs (VA) medical centers across the United States between January 1, 2020 and August 18, 2022.\n\nParticipants367,148 individuals with positive COVID-19 tests and preexisting ICD-10-CM codes recorded in the VA electronic health record were enrolled.\n\nTriggerSARS-CoV-2 infection documented by positive laboratory test.\n\nCase WindowOne to seven months following positive COVID testing.\n\nMain Outcomes and MeasuresWe defined signs, symptoms, and diagnoses as being associated with long COVID if they had a novel case frequency of >= 1:1000 and they were significantly increased in our entire cohort after a positive COVID test when compared to case frequencies before COVID testing. We present odds ratios with confidence intervals for long COVID signs, symptoms, and diagnoses, organized by ICD-10-CM functional groups and medical specialty. We used our definition to assess long COVID risk based upon a patients demographics, Elixhauser score, vaccination status, and COVID disease severity.\n\nResultsWe developed a long COVID definition consisting of 323 ICD-10-CM diagnosis codes grouped into 143 ICD-10-CM functional groups that were significantly increased in our 367,148 patient post-COVID population. We define seventeen medical-specialty long COVID subtypes such as cardiology long COVID. COVID-19 positive patients developed signs, symptoms, or diagnoses included in our long COVID definition at a proportion of at least 59.7% (based on all COVID positive patients). Patients with more severe cases of COVID-19 and multiple comorbidities were more likely to develop long COVID.\n\nConclusions and RelevanceAn actionable, empirical definition for long COVID can help clinicians screen for and diagnose long COVID, allowing identified patients to be admitted into appropriate monitoring and treatment programs. An actionable long COVID definition can also support public health, research and policy initiatives. COVID patients with low oxygen saturation levels or multiple co-morbidities should be preferentially watched for the development of long COVID.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Skyler Resendez",
+        "author_inst": "University at Buffalo"
+      },
+      {
+        "author_name": "Steven H Brown",
+        "author_inst": "Department of Veterans Affairs"
+      },
+      {
+        "author_name": "Sebastian Ruiz",
+        "author_inst": "University at Bufalo"
+      },
+      {
+        "author_name": "Prahalad Rangan",
+        "author_inst": "University at Buffalo"
+      },
+      {
+        "author_name": "Jonathan K Nebeker",
+        "author_inst": "Department of Veterans Affairs"
+      },
+      {
+        "author_name": "Diane Montella",
+        "author_inst": "Department of Veterans Affairs"
+      },
+      {
+        "author_name": "Peter L Elkin",
+        "author_inst": "University at Buffalo"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health informatics"
+  },
   {
     "rel_doi": "10.1101/2023.05.20.23290269",
     "rel_title": "Evaluating the Association of Depressive Disorder Symptoms and Moral Injuries in Healthcare Workers during COVID-19 Pandemic",
@@ -71526,57 +71187,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2023.05.12.23289900",
-    "rel_title": "Absolute and relative excess mortality across demographic and clinical subgroups during the COVID-19 pandemic: an individual-level cohort study from a nationwide healthcare system of US Veterans",
-    "rel_date": "2023-05-16",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.12.23289900",
-    "rel_abs": "BackgroundMost analyses of excess mortality during the COVID-19 pandemic have employed aggregate data. Individual-level data from the largest integrated healthcare system in the US may enhance understanding of excess mortality.\n\nMethodsWe performed an observational cohort study following patients receiving care from the Department of Veterans Affairs (VA) between 1 March 2018 and 28 February 2022. We estimated excess mortality on an absolute scale (i.e., excess mortality rates, number of excess deaths), and a relative scale by measuring the hazard ratio (HR) for mortality comparing pandemic and pre-pandemic periods, overall, and within demographic and clinical subgroups. Comorbidity burden and frailty were measured using the Charlson Comorbidity Index and Veterans Aging Cohort Study Index, respectively.\n\nResultsOf 5,905,747 patients, median age was 65.8 years and 91% were men. Overall, the excess mortality rate was 10.0 deaths/1000 person-years (PY), with a total of 103,164 excess deaths and pandemic HR of 1.25 (95% CI 1.25-1.26). Excess mortality rates were highest among the most frail patients (52.0/1000 PY) and those with the highest comorbidity burden (16.3/1000 PY). However, the largest relative mortality increases were observed among the least frail (HR 1.31, 95% CI 1.30-1.32) and those with the lowest comorbidity burden (HR 1.44, 95% CI 1.43-1.46).\n\nConclusionsIndividual-level data offered crucial clinical and operational insights into US excess mortality patterns during the COVID-19 pandemic. Notable differences emerged among clinical risk groups, emphasising the need for reporting excess mortality in both absolute and relative terms to inform resource allocation in future outbreaks.\n\nKEY MESSAGESO_LIMost analyses of excess mortality during the COVID-19 pandemic have focused on evaluations of aggregate data, which may miss important individual-level drivers of excess mortality that may serve as future targets for improvement initiatives.\nC_LIO_LIUsing individual-level data from a national integrated healthcare system, we estimated absolute and relative excess mortality and number of excess deaths overall and within demographic and clinical subgroups.\nC_LIO_LIAbsolute rates of excess mortality were typically highest in groups where the baseline rate of mortality was higher; namely in older age groups and among those with more comorbidities and higher levels of physiologic frailty.\nC_LIO_LIRelative measures of excess mortality were typically greatest among younger age groups and among those with lower physiologic frailty and fewer comorbidities.\nC_LIO_LIRelative measures of excess mortality attenuated but remained elevated after censoring follow-up at first documented SARS-CoV-2 infection or COVID-19, suggesting that factors beyond SARS-CoV-2 infection contributed to the observed excess mortality during the pandemic.\nC_LI",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Daniel M. Weinberger",
-        "author_inst": "Yale School of Public Health"
-      },
-      {
-        "author_name": "Krishnan Bhaskaran",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Caroline Korves",
-        "author_inst": "White River Junction Veterans Affairs Medical Center"
-      },
-      {
-        "author_name": "Brian P. Lucas",
-        "author_inst": "White River Junction Veterans Affairs Medical Center, Geisel School of Medicine at Dartmouth"
-      },
-      {
-        "author_name": "Jesse A. Columbo",
-        "author_inst": "White River Junction Veterans Affairs Medical Center, Geisel School of Medicine at Dartmouth, Dartmouth Hitchcock Medical Center"
-      },
-      {
-        "author_name": "Anita Vashi",
-        "author_inst": "VA Palo Alto Health Care System, University of California San Francisco"
-      },
-      {
-        "author_name": "Louise Davies",
-        "author_inst": "White River Junction Veterans Affairs Medical Center, Geisel School of Medicine at Dartmouth"
-      },
-      {
-        "author_name": "Amy C. Justice",
-        "author_inst": "Yale School of Medicine, VA Connecticut Healthcare System, Yale School of Public Health"
-      },
-      {
-        "author_name": "Christopher T. Rentsch",
-        "author_inst": "US Department of Veterans Affairs, London School of Hygiene and Tropical Medicine, Yale School of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc0",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2023.05.12.23289872",
     "rel_title": "Regularized COVID-19 Forecast Ensemble Methods",
@@ -71879,6 +71489,57 @@
     "type": "new results",
     "category": "pharmacology and toxicology"
   },
+  {
+    "rel_doi": "10.1101/2023.05.10.23289325",
+    "rel_title": "Composite interventions on outcomes of severely and critically ill patients with COVID-19 in Shanghai, China",
+    "rel_date": "2023-05-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.10.23289325",
+    "rel_abs": "BackgroundThe sixty-day effects of initial composite interventions for the treatment of severely and critically ill patients with COVID-19 are not fully assessed.\n\nMethodsUsing a bayesian piecewise exponential model, we analyzed the 60-day mortality, health-related quality of life (HRQoL) and disability in 1082 severely and critically patients with COVID-19 between December 8, 2022 and February 9, 2023 in Shanghai, China. The final 60-day follow-up was completed on April 10, 2023.\n\nResultsAmong 1082 patients (mean age, 78.0 years), 421 [38.9%] women), 139 patients (12.9%) died within 60 days. Azvudine had a 99.8% probability of improving 2-month survival (adjusted HR, 0.44 [95% credible interval, 0.24-0.79]) and Paxlovid had a 91.9% probability of improving 2-month survival (adjusted HR, 0.71 [95% credible interval, 0.44-1.14]) compared with the control. IL-6 receptor antagonist, Baricitinib, and a-thymosin each had a high probability of benefit (99.5%, 99.4%, and 97.5%, respectively) compared to their controls, while the probability of trail-defined statistical futility (HR >0.83) was high for therapeutic anticoagulation (99.8%; HR, 1.64 [95% CrI, 1.06-2.50]), and glucocorticoid (91.4%; HR, 1.20 [95% CrI, 0.71-2.16]). Paxlovid, Azvudine and therapeutic anticoagulation showed significant reduction in disability (p<0.05)\n\nConclusionsAmong severely and critically ill patients with COVID-19 who received 1 or more therapeutic interventions, treatment with Azvudine had a high probability of improved 60-day mortality compared with the control, indicating its potential in resource-limited scenario. Treatment with IL-6 receptor antagonist, Baricitinib, and a-thymosin also had high probabilities of benefit of improving 2-month survival, among which a-thymosin could improve HRQoL. Treatment with Paxlovid, Azvudine and therapeutic anticoagulation could significantly reduce disability at day 60.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Jiasheng Shao",
+        "author_inst": "Department of Immunology and Rheumatology, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences"
+      },
+      {
+        "author_name": "Fan Rong",
+        "author_inst": "Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universitat Dresden"
+      },
+      {
+        "author_name": "Chengnan Guo",
+        "author_inst": "Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China"
+      },
+      {
+        "author_name": "Xuyuan Huang",
+        "author_inst": "Department of Urology, Renji Hospital, Shanghai JiaoTong University, Shanghai 200127, China"
+      },
+      {
+        "author_name": "Runsheng Guo",
+        "author_inst": "Department of General Surgery, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences"
+      },
+      {
+        "author_name": "Fengdi Zhang",
+        "author_inst": "Department of Infectious Disease, Shanghai East Hospital, Tongji University School of Medicine"
+      },
+      {
+        "author_name": "Jianrong Hu",
+        "author_inst": "Department of Respiratory Medicine, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences"
+      },
+      {
+        "author_name": "Gang Huang",
+        "author_inst": "Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences"
+      },
+      {
+        "author_name": "Liou Cao",
+        "author_inst": "Department of Nephrology, Molecular Cell Lab for Kidney Disease, Shanghai Peritoneal Dialysis Research Center, Ren Ji Hospital, Uremia Diagnosis and Treatment C"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2023.05.09.23289706",
     "rel_title": "Insight into risk associated phenotypes behind COVID-19 from phenotype genome-wide association studies",
@@ -73156,77 +72817,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2023.05.08.23289517",
-    "rel_title": "Persistent humoral immunity in children and adolescents throughout the COVID-19 pandemic (June 2020 to July 2022): a prospective school-based cohort study (Ciao Corona) in Switzerland",
-    "rel_date": "2023-05-10",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.08.23289517",
-    "rel_abs": "ObjectivesTo assess the longitudinal development of humoral immunity in children and adolescents during the COVID-19 pandemic, with a particular focus on how anti-spike IgG antibodies and neutralising response changed during the first Omicron peak (December 2021 to May 2022).\n\nDesignProspective school-based study during the COVID-19 pandemic (June 2020 to July 2022) including five testing rounds with corresponding cross-sectional cohorts and a longitudinal cohort who participated in at least four rounds.\n\nSetting55 randomly selected schools in the Canton of Zurich, Switzerland.\n\nParticipantsBetween 1875 to 2500 children and adolescents per testing round and 751 in the longitudinal cohort.\n\nMain outcome measuresDevelopment of SARS-CoV-2 seroprevalence, anti-spike IgG antibodies and neutralising antibody response over time, persistence of antibodies and variation of antibody levels in individuals only infected, vaccinated or with hybrid immunity during the early Omicron period.\n\nResultsBy July 2022 96.9% (95% credible interval [CrI] 95.2 to 98.1%) of children and adolescents had anti-spike IgG antibodies against SARS-CoV-2. The substantial increase in seroprevalence during the first peak of the Omicron wave was largely driven by primary infections in mostly unvaccinated children under the age of 12 (28.4% [95% CrI 24.2 to 33.2%] in December 2021, to 95.7% [95% CrI 93.4 to 97.4%] in July 2022). This stands in contrast to adolescents aged 12 years and older (69.4% [95% CrI 64.0 to 75.4%] in December 2021 to 98.4% [95% CrI 97.3 to 99.2%] in July 2022), who were eligible for vaccination since June 2021. Children and adolescents with hybrid immunity or immunity from vaccination had high anti-spike IgG titres (median Mean Fluorescence Intensity (MFI) ratio of 136.2 [Inter Quartile Range [IQR]: 121.9 to 154.3] and 127.6 [IQR: 114.1 to 151.0]) and strong neutralising responses (e.g., anti-Omicron 98.9% [95% Confidence Interval [CI] 96.0 to 99.7%] and 81.6% [95% CI 74.9 to 86.9%]). Meanwhile, infected but unvaccinated children and adolescents had substantially lower anti-spike IgG titres (median MFI ratio of 54.8 [IQR: 22.8 to 89.8]) and neutralising responses (e.g., anti-Omicron 64.9% [95% CI 59.8 to 69.7%]).\n\nConclusionThese findings show that the Omicron wave and the rollout of vaccines led to almost 100% seropositivity and boosted anti-spike IgG titres and neutralising capacity in children and adolescents. This was particularly driven by unvaccinated children (<12 years), who became seropositive due to the highly infectious Omicron variant. Nevertheless, during the entire study period parents of only one adolescent reported hospital stay of less than 24 hours related to a possible acute infection.",
-    "rel_num_authors": 14,
-    "rel_authors": [
-      {
-        "author_name": "Alessia Raineri",
-        "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland"
-      },
-      {
-        "author_name": "Thomas Radtke",
-        "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland"
-      },
-      {
-        "author_name": "Sonja Rueegg",
-        "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland"
-      },
-      {
-        "author_name": "Sarah R Haile",
-        "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland"
-      },
-      {
-        "author_name": "Dominik Menges",
-        "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich (UZH)"
-      },
-      {
-        "author_name": "Tala Ballouz",
-        "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland"
-      },
-      {
-        "author_name": "Agne Ulyte",
-        "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland"
-      },
-      {
-        "author_name": "Jan Fehr",
-        "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland"
-      },
-      {
-        "author_name": "Daniel L Cornejo",
-        "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland"
-      },
-      {
-        "author_name": "Giuseppe Pantaleo",
-        "author_inst": "Service of Immunology and Allergy, Departments of Medicine and Laboratory Medicine and Pathology, Lausanne University Hospital, University of Lausanne, Lausanne"
-      },
-      {
-        "author_name": "C\u00e9line Pellaton",
-        "author_inst": "Service of Immunology and Allergy, Departments of Medicine and Laboratory Medicine and Pathology, Lausanne University Hospital, University of Lausanne, Lausanne"
-      },
-      {
-        "author_name": "Craig Fenwick",
-        "author_inst": "Service of Immunology and Allergy, Departments of Medicine and Laboratory Medicine and Pathology, Lausanne University Hospital, University of Lausanne, Lausanne"
-      },
-      {
-        "author_name": "Milo A Puhan",
-        "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland"
-      },
-      {
-        "author_name": "Susi Kriemler",
-        "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2023.05.09.23289744",
     "rel_title": "Surveillance strategies for the detection of new SARS-CoV-2 variants across epidemiological contexts",
@@ -73513,6 +73103,61 @@
     "type": "new results",
     "category": "biochemistry"
   },
+  {
+    "rel_doi": "10.1101/2023.05.08.539929",
+    "rel_title": "Toll-like receptor 7 (TLR7)-mediated antiviral response protects mice from lethal SARS-CoV-2 infection",
+    "rel_date": "2023-05-09",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.08.539929",
+    "rel_abs": "SARS-CoV-2-induced impaired antiviral and excessive inflammatory responses cause fatal pneumonia. However, the key pattern recognition receptors that elicit effective antiviral and lethal inflammatory responses in-vivo are not well defined. CoVs possess single-stranded RNA (ssRNA) genome that is abundantly produced during infection and stimulates both antiviral interferon (IFN) and inflammatory cytokine/ chemokine responses. Therefore, in this study, using wild-type control and TLR7 deficient BALB/c mice infected with a mouse-adapted SARS-COV-2 (MA-CoV-2), we evaluated the role of TLR7 signaling in MA-CoV-2-induced antiviral and inflammatory responses and disease outcome. We show that TLR7-deficient mice are more susceptible to MA-CoV-2 infection as compared to infected control mice. Further evaluation of MA-CoV-2 infected lungs showed significantly reduced mRNA levels of antiviral type I (IFN/{beta}) and type III (IFN{lambda}) IFNs, IFN stimulated genes (ISGs, ISG15 and CXCL10), and several pro-inflammatory cytokines/chemokines in TLR7 deficient compared to control mice. Reduced lung IFN/ISG levels and increased morbidity/mortality in TLR7 deficient mice correlated with high lung viral titer. Detailed examination of total cells from MA-CoV-2 infected lungs showed high neutrophil count in TLR7 deficient mice compared to control mice. Additionally, blocking TLR7 activity post-MA-CoV-2 infection using a specific inhibitor also enhanced disease severity. In summary, our results conclusively establish that TLR7 signaling is protective during SARS-CoV-2 infection, and despite robust inflammatory response, TLR7-mediated IFN/ISG responses likely protect the host from lethal disease. Given similar outcomes in control and TLR7 deficient humans and mice, these results show that MA-CoV-2 infected mice serve as excellent model to study COVID-19.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Roshan Ghimire",
+        "author_inst": "Oklahoma State University"
+      },
+      {
+        "author_name": "Rakshya Shrestha",
+        "author_inst": "Oklahoma State University"
+      },
+      {
+        "author_name": "Radhika Amaradhi",
+        "author_inst": "Emory University"
+      },
+      {
+        "author_name": "Titus Patton",
+        "author_inst": "Oklahoma State University"
+      },
+      {
+        "author_name": "Cody Whitley",
+        "author_inst": "Oklahoma State University"
+      },
+      {
+        "author_name": "Debarati Chanda",
+        "author_inst": "Oklahoma State University"
+      },
+      {
+        "author_name": "Lin Liu",
+        "author_inst": "Oklahoma State University"
+      },
+      {
+        "author_name": "Sunil More",
+        "author_inst": "Oklahoma State University"
+      },
+      {
+        "author_name": "Thota Ganesh",
+        "author_inst": "Emory University"
+      },
+      {
+        "author_name": "Rudragouda Channappanavar",
+        "author_inst": "Oklahoma State University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2023.05.09.539943",
     "rel_title": "Dissecting the impact of somatic hypermutation on SARS-CoV-2 neutralization and viral escape",
@@ -74730,69 +74375,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "neurology"
   },
-  {
-    "rel_doi": "10.1101/2023.05.03.23289456",
-    "rel_title": "The plasma metabolome of long COVID-19 patients two years after infection",
-    "rel_date": "2023-05-05",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.03.23289456",
-    "rel_abs": "BackgroundOne of the major challenges currently faced by global health systems is the prolonged COVID-19 syndrome (also known as \"long COVID\") which has emerged as a consequence of the SARS-CoV-2 epidemic. The World Health Organization (WHO) recognized long COVID as a distinct clinical entity in 2021. It is estimated that at least 30% of patients who have had COVID-19 will develop long COVID. This has put a tremendous strain on still-overstretched healthcare systems around the world.\n\nMethodsIn this study, our goal was to assess the plasma metabolome in a total of 108 samples collected from healthy controls, COVID-19 patients, and long COVID patients recruited in Mexico between 2020 and 2022. A targeted metabolomics approach using a combination of LC-MS/MS and FIA MS/MS was performed to quantify 108 metabolites. IL-17 and leptin concentrations were measured in long COVID patients by immunoenzymatic assay.\n\nResultsThe comparison of paired COVID-19/post-COVID-19 samples revealed 53 metabolites that were statistically different (FDR < 0.05). Compared to controls, 29 metabolites remained dysregulated even after two years. Notably, glucose, kynurenine, and certain acylcarnitines continued to exhibit altered concentrations similar to the COVID-19 phase, while sphingomyelins and long saturated and monounsaturated LysoPCs, phenylalanine, butyric acid, and propionic acid levels normalized. Post-COVID-19 patients displayed a heterogeneous metabolic profile, with some showing no symptoms while others exhibiting a variable number of symptoms. Lactic acid, lactate/pyruvate ratio, ornithine/citrulline ratio, sarcosine, and arginine were identified as the most relevant metabolites for distinguishing patients with more complicated long COVID evolution. Additionally, IL-17 levels were significantly increased in these patients.\n\nConclusionsMitochondrial dysfunction, redox state imbalance, impaired energy metabolism, and chronic immune dysregulation are likely to be the main hallmarks of long COVID even two years after acute COVID-19 infection.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Yamile Lopez-Hernandez",
-        "author_inst": "National Council of Sciences and Technology"
-      },
-      {
-        "author_name": "Joel Monarrez-Aquino",
-        "author_inst": "Christus Muguerza del Parque Hospital, Chihuahua, Mexico"
-      },
-      {
-        "author_name": "David Alejandro Garcia-Lopez",
-        "author_inst": "Autonomous University of Zacatecas, Zacatecas, Mexico"
-      },
-      {
-        "author_name": "Jiamin Zheng",
-        "author_inst": "The Metabolomics Innovation Centre, Edmonton, Canada"
-      },
-      {
-        "author_name": "Juan Carlos Borrego",
-        "author_inst": "Departamento de Epidemiologia, Hospital General de Zona 1 Emilio Varela Lujan, Instituto Mexicano del Seguro Social, Zacatecas"
-      },
-      {
-        "author_name": "Claudia Torres-Calzada",
-        "author_inst": "The Metabolomics Innovation Centre, Edmonton, Canada"
-      },
-      {
-        "author_name": "Jose Pedro Elizalde-Diaz",
-        "author_inst": "Laboratory of Cell Communication and Extracellular Vesicles, Division of Basic Science, Instituto Nacional de Medicina Genomica, Ciudad de Mexico, 14610, Mexico"
-      },
-      {
-        "author_name": "Rupasri Mandal",
-        "author_inst": "The Metabolomics Innovation Centre, Edmonton, Canada"
-      },
-      {
-        "author_name": "Mark Berjanskii",
-        "author_inst": "The Metabolomics Innovation Centre, Edmonton, Canada"
-      },
-      {
-        "author_name": "Eduardo Martinez-Martinez",
-        "author_inst": "Laboratory of Cell Communication and Extracellular Vesicles, Division of Basic Science, Instituto Nacional de Medicina Genomica, Ciudad de Mexico, 14610, Mexico"
-      },
-      {
-        "author_name": "Jesus Adrian Lopez",
-        "author_inst": "MicroRNAs and Cancer Laboratory, Academic Unit of Biological Sciences, Autonomous University of Zacatecas, Zacatecas, 98000, Mexico"
-      },
-      {
-        "author_name": "David S Wishart",
-        "author_inst": "The Metabolomics Innovation Centre, Edmonton, Canada"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2023.05.04.23289498",
     "rel_title": "Excess Mortality Resulting from COVID-19 in Turkey during 2020-2021: Regional and Time-Based Analysis",
@@ -75075,6 +74657,109 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "ophthalmology"
   },
+  {
+    "rel_doi": "10.1101/2023.05.02.23289345",
+    "rel_title": "Persistent immune abnormalities discriminate post-COVID syndrome from convalescence",
+    "rel_date": "2023-05-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.02.23289345",
+    "rel_abs": "Innate lymphoid cells (ILCs) are key organizers of tissue immune responses and regulate tissue development, repair, and pathology. Persistent clinical sequelae beyond 12 weeks following acute COVID-19 disease, named post-COVID syndrome (PCS), are increasingly recognized in convalescent individuals. ILCs have been associated with the severity of COVID-19 symptoms but their role in the development of PCS remains poorly defined. Here we used multiparametric immune phenotyping, finding expanded circulating ILC precursors (ILCPs) and concurrent decreased group 2 innate lymphoid cells (ILC2s) in PCS patients compared to well-matched convalescent control groups at > 3 months after infection. Patients with PCS showed elevated expression of chemokines and cytokines associated with trafficking of immune cells (CCL19/MIP-3b, FLT3-ligand), endothelial inflammation and repair (CXCL1, EGF, RANTES, IL1RA, PDGF-AA). These results define immunological parameters associated with PCS and might help find biomarkers and disease-relevant therapeutic strategies.",
+    "rel_num_authors": 22,
+    "rel_authors": [
+      {
+        "author_name": "Julia Sbierski-Kind",
+        "author_inst": "Universitaetsklinikum Tuebingen"
+      },
+      {
+        "author_name": "Stephan Schlickeiser",
+        "author_inst": "Charite- Universitaetsmedizin Berlin"
+      },
+      {
+        "author_name": "Svenja Feldmann",
+        "author_inst": "LMU Munich"
+      },
+      {
+        "author_name": "Veronica Ober",
+        "author_inst": "LMU Munich"
+      },
+      {
+        "author_name": "Eva Gruener",
+        "author_inst": "LMU Munich"
+      },
+      {
+        "author_name": "Claire Pleimelding",
+        "author_inst": "LMU Munich"
+      },
+      {
+        "author_name": "Leonard Gilberg",
+        "author_inst": "LMU Munich"
+      },
+      {
+        "author_name": "Isabel Brand",
+        "author_inst": "LMU Munich"
+      },
+      {
+        "author_name": "Nikolas Weigl",
+        "author_inst": "LMU Munich"
+      },
+      {
+        "author_name": "Mohamed I.M. Ahmed",
+        "author_inst": "LMU Munich"
+      },
+      {
+        "author_name": "Gerardo Ibarra",
+        "author_inst": "LMU Munich"
+      },
+      {
+        "author_name": "Michael Ruzicka",
+        "author_inst": "LMU Munich"
+      },
+      {
+        "author_name": "Christopher Benesch",
+        "author_inst": "LMU Munich"
+      },
+      {
+        "author_name": "Anna Pernpruner",
+        "author_inst": "LMu Munich"
+      },
+      {
+        "author_name": "Elisabeth Valdinoci",
+        "author_inst": "LMU Munich"
+      },
+      {
+        "author_name": "Michael Hoelscher",
+        "author_inst": "LMU Medizinische Fakult\u00e4t: Ludwig-Maximilians-Universitat Munchen Medizinische Fakultat"
+      },
+      {
+        "author_name": "Kristina Adorjan",
+        "author_inst": "LMU Munich"
+      },
+      {
+        "author_name": "Hans Christian Stubbe",
+        "author_inst": "LMU Munich"
+      },
+      {
+        "author_name": "Michael Pritsch",
+        "author_inst": "LMU Munich"
+      },
+      {
+        "author_name": "Ulrich Seybold",
+        "author_inst": "LMU Munich"
+      },
+      {
+        "author_name": "Johannes Bogner",
+        "author_inst": "LMU Munich"
+      },
+      {
+        "author_name": "Julia Roider",
+        "author_inst": "LMU Munich"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "allergy and immunology"
+  },
   {
     "rel_doi": "10.1101/2023.05.03.23289472",
     "rel_title": "SARS-CoV-2 specific cellular and humoral immunity after bivalent BA.4/5 COVID-19 vaccination in previously infected and non-infected individuals",
@@ -76668,61 +76353,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
-  {
-    "rel_doi": "10.1101/2023.05.02.23289398",
-    "rel_title": "Did knowledge, attitudes, and practices matter during the second wave of COVID-19 pandemic in Bangladesh? Results from a web-based cross-sectional study",
-    "rel_date": "2023-05-02",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.02.23289398",
-    "rel_abs": "Globally, health promotion measures have been undertaken in preventing the emergence and spread of coronavirus disease 2019 (COVID-19). However, whether these measures influence public awareness and behaviors is unclear and evidence is limited in particular in low-and-middle income country. We conducted an online survey among internet users in Bangladesh to understand the status and attributes of their knowledge, attitudes and practices towards COVID-19 during second wave of the pandemic when COVID educational information was more accessible to the public. Survey data were analyzed using descriptive statistics, Chi-square tests, and multivariate logistic regression analysis. Of 964 respondents, 40.2%, 51.5%, and 64.3% had good knowledge, confident attitudes, and proper practices towards COVID-19, respectively. The multivariate regression analysis found that the knowledge and practice scores were associated (p<0.05) with gender, age, and occupation. Females had better knowledge and practices compared to males (p<0.05). There were major gaps in awareness, attitudes, and practices among internet users in particular males and elders that needs to be addressed to control the further spread of COVID-19 infections before at least COVID-19 vaccine become accessible at population level in Bangladesh.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Md. Robin Khan",
-        "author_inst": "University of Asia Pacific"
-      },
-      {
-        "author_name": "Md. Jamal Hossain",
-        "author_inst": "State University of Bangladesh"
-      },
-      {
-        "author_name": "Md. Ariful Islam",
-        "author_inst": "BCSIR: Bangladesh Council of Scientific and Industrial Research"
-      },
-      {
-        "author_name": "Shadid Uz Zaman",
-        "author_inst": "Northern University Bangladesh"
-      },
-      {
-        "author_name": "Mohammad Touhidul Islam",
-        "author_inst": "Daffodil International University"
-      },
-      {
-        "author_name": "Md. Anamul Haque",
-        "author_inst": "Daffodil International University"
-      },
-      {
-        "author_name": "Md. Rabiul Islam",
-        "author_inst": "University of Asia Pacific"
-      },
-      {
-        "author_name": "Farhana Alam Ripa",
-        "author_inst": "BRAC University"
-      },
-      {
-        "author_name": "Md. Monirul Islam",
-        "author_inst": "State University of Bangladesh"
-      },
-      {
-        "author_name": "Foyez Ahmmed",
-        "author_inst": "Comilla University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2023.05.01.23289358",
     "rel_title": "Association of SARS-CoV-2 Infection and Cardiopulmonary Long COVID with Exercise Capacity and Chronotropic Incompetence among People with HIV",
@@ -77581,6 +77211,69 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2023.04.28.23289257",
+    "rel_title": "The COV50 classifier predicts frailty and future death, independent from SARS-CoV-2 infection",
+    "rel_date": "2023-05-01",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.28.23289257",
+    "rel_abs": "BackgroundThere is evidence of pre-established vulnerability in individuals that increases the risk of their progression to severe disease or death, though the mechanisms that cause this are still not fully understood. Previous research has demonstrated that a urinary peptide classifier (COV50) predicts disease progression and death from SARS-CoV-2 at an early stage, indicating that the outcome prediction may be partly due to already present vulnerabilities. The aim of this study is to examine the ability of COV50 to predict future non-COVID-19-related mortality, and evaluate whether the pre-established vulnerability can be generic and explained on a molecular level by urinary peptides.\n\nMethodsUrinary proteomic data from 9193 patients (1719 patients sampled at intensive care unit (ICU) admission and 7474 patients with other diseases (non-ICU)) were extracted from the Human Urinary Proteome Database. The previously developed COV50 classifier, a urinary proteomics biomarker panel consisting of 50 peptides, was applied to all datasets. The association of COV50 scoring with mortality was evaluated.\n\nResultsIn the ICU group, an increase in the COV50 score of one unit resulted in a 20% higher relative risk of death (adj. HR 1{middle dot}2 [95% CI 1{middle dot}17-1{middle dot}24]). The same increase in COV50 in non-ICU patients resulted in a higher relative risk of 61% (adj. HR 1{middle dot}61 [95% CI 1{middle dot}47-1{middle dot}76]), in line with adjusted meta-analytic HR estimate of 1{middle dot}55. The most notable and significant changes associated with future fatal events were reductions of specific collagen fragments, most of collagen alpha I(I).\n\nConclusionThe COV50 classifier is predictive of death in the absence of SARS-CoV-2 infection, suggesting that it detects pre-existing vulnerability. Prediction is based mainly on collagen fragments, possibly reflecting disturbances in the integrity of the extracellular matrix. These data may serve as basis for proteomics guided intervention aiming towards manipulating/improving collagen turnover, thereby reducing the risk of death.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Felix Keller",
+        "author_inst": "Department of Internal Medicine IV (Nephrology and Hypertension), Medical University of Innsbruck, 6020 Innsbruck, Austria"
+      },
+      {
+        "author_name": "Joachim Beige",
+        "author_inst": "Hospital Sankt Georg"
+      },
+      {
+        "author_name": "Justyna Siwy",
+        "author_inst": "Mosaiques Diagnostics"
+      },
+      {
+        "author_name": "Alexandre Mebazaa",
+        "author_inst": "Department of Anaesthesiology and Intensive Care, Hospital Saint Louis-Lariboisiere, 75475 Paris Cedex 10, Paris, France"
+      },
+      {
+        "author_name": "De-Wei An",
+        "author_inst": "Non-Profit Research Institute Alliance for the Promotion of Preventive Medicine, 2800 Mechelen, Belgium"
+      },
+      {
+        "author_name": "Harald Mischak",
+        "author_inst": "Mosaiques Diagnostics"
+      },
+      {
+        "author_name": "Joost P Schanstra",
+        "author_inst": "Institut National de la Sante et de la Recherche Medicale, Institute of Cardiovascular and Metabolic Disease, UMRS 1297, 31432 Toulouse, France; Universite Toul"
+      },
+      {
+        "author_name": "Marika Mokou",
+        "author_inst": "Mosaiques Diagnostics"
+      },
+      {
+        "author_name": "Paul Perco",
+        "author_inst": "Department of Internal Medicine IV (Nephrology and Hypertension), Medical University of Innsbruck, 6020 Innsbruck, Austria"
+      },
+      {
+        "author_name": "Jan A Staessen",
+        "author_inst": "Non-Profit Research Institute Alliance for the Promotion of Preventive Medicine, 2800 Mechelen, Belgium"
+      },
+      {
+        "author_name": "Antonia Vlahou",
+        "author_inst": "Biomedical Research Foundation Academy of Athens"
+      },
+      {
+        "author_name": "Agnieszka Latosinska",
+        "author_inst": "Mosiaques Diagnostics GmbH"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "intensive care and critical care medicine"
+  },
   {
     "rel_doi": "10.1101/2023.04.28.23289271",
     "rel_title": "Effect of vaccination on time till Long COVID, a comparison of two ways to model effect of vaccination and two outcome definitions",
@@ -79258,49 +78951,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2023.04.26.23289142",
-    "rel_title": "A systematic review of the prevalence of persistent gastrointestinal symptoms and incidence of new gastrointestinal illness after acute SARS-CoV-2 infection",
-    "rel_date": "2023-04-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.26.23289142",
-    "rel_abs": "It is known that SARS-CoV-2 infection can result in gastrointestinal symptoms. For some, these symptoms may persist beyond acute infection, in what is known as  post-COVID syndrome. We conducted a systematic review to examine the prevalence of persistent gastrointestinal symptoms and the incidence of new gastrointestinal illness following acute SARS-CoV-2 infection. We searched scientific literature using MedLine, SCOPUS, Embase, Europe PubMed Central, medRxiv and Google Scholar from December 2019 to October 2022. Two reviewers independently identified 28 eligible articles which followed participants for various gastrointestinal outcomes after acute SARS-CoV-2 infection. Study quality was assessed using the Joanna Briggs Institute Critical Appraisal Tools. The weighted pooled prevalence for persistent gastrointestinal symptom of any nature and duration was 10.7%, compared to 4.9% in healthy controls. For six studies at a low risk of methodological bias, the symptom prevalence ranged from 0.2% to 24.1% with a median follow-up time of 13 weeks. We also identified the presence of functional gastrointestinal disorders in historically SARS-CoV-2 exposed individuals. Our review has shown that, from a limited pool of mostly low-quality studies, previous SARS-CoV-2 exposure may be associated with ongoing gastrointestinal symptoms and the development of functional gastrointestinal illness. Furthermore, we show the need for high-quality research to better understand the SARS-CoV-2 association with gastrointestinal symptoms, particularly as population exposure to enteric infections returns to pre-COVID-19-restriction levels.\n\nHighlightsO_LIAcute SARS-CoV-2 infection can result in gastrointestinal symptoms\nC_LIO_LIThe burden of gastrointestinal illness after acute SARS-CoV-2 infection is not known\nC_LIO_LIThis systematic review evaluates the evidence across 28 observational studies\nC_LIO_LIMost studies identified are at high risk of bias and of low quality\nC_LIO_LISARS-CoV-2 exposure may be associated with new post-infection gastrointestinal illness\nC_LI",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Michael J Hawkings",
-        "author_inst": "National Institute for Health and Care Research Health Protection Research Unit in Gastrointestinal Infections at University of Liverpool, Liverpool, L69 7BE, U"
-      },
-      {
-        "author_name": "N. Marcella Vaselli",
-        "author_inst": "Institute of Infection, Veterinary & Ecological Sciences, Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, L69"
-      },
-      {
-        "author_name": "Dimitrios Charalampopoulos",
-        "author_inst": "Institute of Population Health, Department of Public Health, Policy & Systems, University of Liverpool, Liverpool, L69 3GF, UK"
-      },
-      {
-        "author_name": "Liam Brierley",
-        "author_inst": "Institute of Population Health, Department of Health Data Science, University of Liverpool, Liverpool, L69 3GF, UK"
-      },
-      {
-        "author_name": "Alex J Elliot",
-        "author_inst": "Real-Time Syndromic Surveillance Team, Field Services, Health Protection Operations, UK Health Security Agency, Birmingham, B2 4BH, UK"
-      },
-      {
-        "author_name": "Iain Buchan",
-        "author_inst": "Institute of Population Health, Department of Public Health, Policy & Systems, University of Liverpool, Liverpool, L69 3GF, UK"
-      },
-      {
-        "author_name": "Daniel Hungerford",
-        "author_inst": "Institute of Infection, Veterinary & Ecological Sciences, Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, L69"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2023.04.25.23289110",
     "rel_title": "Comparative Cohort Study of Post-Acute Covid-19 Infection with a Nested, Randomized Controlled Trial of Ivabradine for Those With Postural Orthostatic Tachycardia Syndrome (The COVIVA Study)",
@@ -79591,6 +79241,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2023.04.24.23288921",
+    "rel_title": "Immune signature of patients with cardiovascular disease - in-depth immunophenotyping predicts increased risk for a severe course of COVID-19",
+    "rel_date": "2023-04-26",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.24.23288921",
+    "rel_abs": "ObjectiveSARS-CoV-2 infection can lead to life-threatening clinical manifestations. Patients with cardiovascular disease (CVD) are at higher risk for severe courses of COVID-19. However, strategies to predict the course of SARS-CoV-2 infection in CVD patients at hospital admission are still missing. Here, we investigated whether the severity of SARS-CoV-2 infection can be predicted by analyzing the immunophenotype in the blood of CVD patients.\n\nApproach and ResultsWe prospectively analyzed the peripheral blood of 94 participants, including CVD patients with acute SARS-CoV-2 infection, uninfected CVD patients, and healthy donors using a 36-color spectral flow cytometry panel. Clinical assessment included blood sampling, echocardiography, and electrocardiography. Patients were classified by their ISARIC WHO 4C-Mortality-Score on the day of admission into three subgroups of an expected mild, moderate, or severe course of COVID-19. Unsupervised data analysis revealed 40 clusters corresponding to major circulating immune cell populations. This revealed little differences between healthy donors and CVD patients, whereas the distribution of the cell populations changed dramatically in SARS-CoV-2-infected CVD patients. The latter had more mature NK cells, activated monocyte subsets, central memory CD4+ T cells, and plasmablasts than uninfected CVD patients. In contrast, fewer dendritic cells, CD16+ monocytes, innate lymphoid cells, and CD8+ T cell subsets were detected in SARS-CoV-2-infected CVD patients. We identified an immune signature characterized by low frequencies of MAIT and intermediate effector CD8+ T cells in combination with a high frequency of NKT cells that is predictive for CVD patients with a severe course of SARS-CoV-2 infection on hospital admission.\n\nConclusionAcute SARS-CoV-2 infected CVD patients revealed marked changes in abundance and phenotype of several immune cell populations associated with COVID-19 severity. Our data indicate that intensified immunophenotype analyses can help identify patients at risk of severe COVID-19 at hospital admission, improving clinical outcomes through specific treatment.\n\nHighlightsO_LIPatients with cardiovascular disease are at higher risk of severe courses of COVID-19 and may exhibit an altered immune response\nC_LIO_LIUnsupervised data analysis revealed that patients with cardiovascular disease and SARS-CoV-2 infection showed significant changes in the abundance and the phenotype of various immune cell populations\nC_LIO_LIWe identified a disease-related immune signature in patients with cardiovascular disease and SARS-CoV-2 infection associated with the severity of COVID-19\nC_LIO_LIIntensified immunophenotyping helps to identify cardiovascular patients at risk of a severe course of COVID-19 already at the early stages of the disease and might thereby improve clinical outcomes and specific treatment of COVID-19\nC_LI",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Manina Guenter",
+        "author_inst": "Deutsches Krebsforschungszentrum Heidelberg"
+      },
+      {
+        "author_name": "Karin Anne Lydia Mueller",
+        "author_inst": "Universitaetsklinikum Tuebingen"
+      },
+      {
+        "author_name": "Mathew James Salazar",
+        "author_inst": "DKFZ"
+      },
+      {
+        "author_name": "Sarah Gekeler",
+        "author_inst": "Universitaetsklinikum Tuebingen"
+      },
+      {
+        "author_name": "Carolin Prang",
+        "author_inst": "University Hospital Tuebingen"
+      },
+      {
+        "author_name": "Tobias Harm",
+        "author_inst": "Universitaetsklinikum Tuebingen"
+      },
+      {
+        "author_name": "Meinrad Gawaz",
+        "author_inst": "Universit\u00e4t T\u00fcbingen"
+      },
+      {
+        "author_name": "Stella E. Autenrieth",
+        "author_inst": "DKFZ"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2023.04.24.538130",
     "rel_title": "How Do Deer Respiratory Epithelial Cells Weather The Initial Storm of SARS-CoV-2?",
@@ -81104,49 +80801,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2023.04.18.23288060",
-    "rel_title": "Evaluation of coronavirus decay in French coastal water and application to SARS-CoV-2 risk evaluation using Porcine Epidemic Diarrhea Virus as surrogate.",
-    "rel_date": "2023-04-21",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.18.23288060",
-    "rel_abs": "SARS-CoV-2 in infected patient mainly display pulmonary and oronasal tropism however, the presence of the virus has also been demonstrated in stools of patients and consequently in wastewater treatment plant effluents, questioning the potential risk of environmental contamination (such as seawater contamination) through inadequately treated wastewater spill-over into surface or coastal waters. The environmental detection of RNA alone does not substantiate risk of infection, and evidence of an effective transmission is not clear where empirical observations are lacking.\n\nTherefore, here, we decided to experimentally evaluate the persistence and infectious capacity of the Porcine epidemic diarrhea virus (PEDv), considered as a coronavirus representative model and SARS-CoV-2 surrogate, in the coastal environment of France. Coastal seawater was collected, sterile-filtered, and inoculated with PEDv before incubation for 0-4 weeks at four temperatures representative of those measured along the French coasts throughout the year (4, 8, 15, and 24{degrees}C). The decay rate of PEDv was determined using mathematical modeling and was used to determine the half-life of the virus along the French coast in accordance with temperatures from 2000 to 2021.\n\nWe experimentally observed an inverse correlation between seawater temperature and the persistence of infectious viruses in seawater and confirm that the risk of transmission of infectious viruses from contaminated stool in wastewater to seawater during recreational practices is very limited. The present work represents a good model to assess the risk of transmission of not only SARS-CoV-2 but may also be used to model the risk of other coronaviruses, specifically enteric coronaviruses.\n\nImportanceThis present work is a follow up addressing the question of the persistence of coronavirus in marine environment owing to the fact that SARS-CoV-2 is regularly detected in wastewater treating plan and the coastal environment is particularly at risk since it is subjected to increasing anthropogenic pressure and is the final receiver of surface waters and treated or sometimes insufficiently depurated waste waters. Our findings are of interest to researchers and authorities seeking to monitor SARS-CoV-2 and also enteric coronaviruses in the environment, either in tourist areas or in regions of the world, where centralized systems for wastewater treatment are not implemented, and more broadly, to the scientific community involved in \"One Health\" approaches.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Maud Contrant",
-        "author_inst": "Anses Laboratoire de Ploufragan-Plouzane-Niort"
-      },
-      {
-        "author_name": "Lionel Bigault",
-        "author_inst": "Anses Ploufragan-Plouzane-Niort"
-      },
-      {
-        "author_name": "Mathieu Andraud",
-        "author_inst": "Anses Ploufragan-Plouzane-Niort"
-      },
-      {
-        "author_name": "Marion Desdouits",
-        "author_inst": "Ifremer"
-      },
-      {
-        "author_name": "Sophie Rocq",
-        "author_inst": "Ifremer Centre Atlantique"
-      },
-      {
-        "author_name": "Soizick F Le Guyader",
-        "author_inst": "IFREMER"
-      },
-      {
-        "author_name": "Yannick Blanchard",
-        "author_inst": "Anses Ploufragan-Plouzane-Niort"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2023.04.19.537521",
     "rel_title": "SARS-CoV-2 utilization of ACE2 from different bat species allows for virus entry and replication in vitro",
@@ -81697,6 +81351,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2023.04.18.23288715",
+    "rel_title": "Preliminary clinical characteristics of Pediatric Covid-19 cases during the ongoing Omicron XBB.1.16 driven surge in a north Indian city",
+    "rel_date": "2023-04-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.18.23288715",
+    "rel_abs": "India is experiencing a new surge in Covid-19 cases in most parts of the country. A new sub-variant of Omicron, XBB.1.16 which is far more aggressive and immune evasive than other sub-lineages of Omicron, is responsible for this outbreak. In this preliminary account, we describe key clinical characteristics of SARS-CoV-2 infected children, visiting an outdoor department of a pediatric hospital in a north Indian city. Our preliminary findings show a higher involvement of young infants than older children and mild respiratory illness predominates other presentations. One interesting finding was the presence of itchy, non-purulent conjunctivitis with mucoid discharge and stickiness of eyelids in 42.8% of positive infants. None of the children required hospitalization. All recovered with symptomatic treatment.\n\nKey findingsO_LIThe current ongoing XBB.1.16 driven surge of Covid-19 is causing mild febrile illness in children in India\nC_LIO_LIYoung infants are disproportionately more affected than older children.\nC_LIO_LIUnlike the previous BA.2 Omicron wave, respiratory symptoms are predominating the clinical presentation in young infants in the ongoing surge.\nC_LIO_LIConjunctival involvement is seen in 42.8% of affected infants.\nC_LI",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Vipin M Vashishtha",
+        "author_inst": "Mangla Hospital & Research Center"
+      },
+      {
+        "author_name": "Puneet Kumar",
+        "author_inst": "Clinician, Kumar Child clinic, KM Chowk, Sector 12, Dwarka, New Delhi, India"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2023.04.19.23288817",
     "rel_title": "Mortality among persons with HIV in the United States during the COVID-19 pandemic: a population-level analysis",
@@ -83422,81 +83099,6 @@
     "type": "new results",
     "category": "cell biology"
   },
-  {
-    "rel_doi": "10.1101/2023.04.14.533542",
-    "rel_title": "SARS-CoV-2 occurrence in white-tailed deer throughout their range in the conterminous United States",
-    "rel_date": "2023-04-17",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2023.04.14.533542",
-    "rel_abs": "Broad-scale data show SARS-CoV-2 occurrence in white-tailed deer throughout much of their range in the conterminous United States and reinforce findings of considerable SARS-CoV-2 infection and exposure. Results shed light on both current infections and prior exposure, with prevalence decreasing over time and seroprevalence increasing.\n\nOne-Sentence SummaryWhite-tailed deer are infected with, and have been exposed to, SARS-CoV-2 throughout their range in the conterminous US.",
-    "rel_num_authors": 15,
-    "rel_authors": [
-      {
-        "author_name": "Sarah Bevins",
-        "author_inst": "USDA/APHIS/National Wildlife Disease Program"
-      },
-      {
-        "author_name": "Newly Created",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Newly Created",
-        "author_inst": "<a href=\"/tracking/viewcorr?msid=BIORXIV/2023/533542&txn_name=notify_au_ms_will_close&txid=3503749049&roleName=staff\">[View Correspondence]</a>"
-      },
-      {
-        "author_name": "Converted",
-        "author_inst": "<a href=\"/tracking/viewcorr?msid=BIORXIV/2023/533542&txn_name=manuscript_converted&txid=3503757962&roleName=staff\">[View Correspondence]</a>"
-      },
-      {
-        "author_name": "New",
-        "author_inst": "<a href=\"/tracking/viewcorr?msid=BIORXIV/2023/533542&txn_name=new_submission&txid=3503757990&roleName=staff\">[View Correspondence]</a>"
-      },
-      {
-        "author_name": "New",
-        "author_inst": ""
-      },
-      {
-        "author_name": "New",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Assigned",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Assigned",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Assigned",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Assigned",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Final Decision",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Final Decision",
-        "author_inst": "<a href=\"/tracking/viewcorr?msid=BIORXIV/2023/533542&txn_name=send_accept_letter&txid=3503765502&roleName=staff\">[View Correspondence]</a>"
-      },
-      {
-        "author_name": "Final Decision",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Final Decision",
-        "author_inst": ""
-      }
-    ],
-    "version": "1",
-    "license": "cc0",
-    "type": "new results",
-    "category": "ecology"
-  },
   {
     "rel_doi": "10.1101/2023.04.16.23288641",
     "rel_title": "Prevention of cyclical resurgences of COVID-19-like pandemics in the long term: What are the trade-offs?",
@@ -83715,6 +83317,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2023.04.12.23288362",
+    "rel_title": "Bivalent COVID-19 booster vaccines induce cross-reactive but not BA.5-specific antibodies in polyclonal serum",
+    "rel_date": "2023-04-17",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.12.23288362",
+    "rel_abs": "The question if the bivalent mRNA COVID-19 booster vaccination, containing wild type and BA.5 spike, provides enhanced benefits against BA.5 and similar Omicron subvariants has been widely debated. One concern was an  original antigenic sin-like effect which may redirect immune responses to the bivalent vaccine towards the wild type spike and may block de novo generation of BA.5 specific antibodies. Here, we characterized the response to the bivalent vaccine and we performed antibody depletion experiments. Interestingly, when we depleted serum of all antibodies to wild type RBD, we also removed all reactivity to BA.5 RBD. This suggests that all antibodies induced by the bivalent vaccine - at least with the limit of detection of our assay in polyclonal serum - are in fact cross-reactive. This further suggests that, on a serum antibody level, the bivalent vaccine did not induce a de novo response to BA.5.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Juan Manuel Carreno Quiroz",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Gagandeep Singh",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Anass Abbad",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Temima Yellin",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Komal Srivastava",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Charles Gleason",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Harm van Bakel",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Viviana Simon",
+        "author_inst": "Icahn School of Medicine"
+      },
+      {
+        "author_name": "Florian Krammer",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2023.04.10.23288317",
     "rel_title": "Social dialogue quality and workers' health as perceived by Belgian trade union representatives during the COVID-19 pandemic.",
@@ -85059,53 +84712,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health economics"
   },
-  {
-    "rel_doi": "10.1101/2023.04.07.536037",
-    "rel_title": "SARS-CoV-2's evolutionary capacity is mostly driven by host antiviral molecules",
-    "rel_date": "2023-04-10",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2023.04.07.536037",
-    "rel_abs": "The COVID-19 pandemic has been characterised by sequential variant-specific waves shaped by viral, individual human and population factors. SARS-CoV-2 variants are defined by their unique combinations of mutations and there has been a clear adaptation to human infection since its emergence in 2019. Here we use machine learning models to identify shared signatures, i.e., common underlying mutational processes, and link these to the subset of mutations that define the variants of concern (VOCs). First, we examined the global SARS-CoV-2 genomes and associated metadata to determine how viral properties and public health measures have influenced the magnitude of waves, as measured by the number of infection cases, in different geographic locations using regression models. This analysis showed that, as expected, both public health measures and not virus properties alone are associated with the rise and fall of regional SARS-CoV-2 reported infection numbers. This impact varies geographically. We attribute this to intrinsic differences such as vaccine coverage, testing and sequencing capacity, and the effectiveness of government stringency. In terms of underlying evolutionary change, we used non-negative matrix factorisation to observe three distinct mutational signatures, unique in their substitution patterns and exposures from the SARS-CoV-2 genomes. Signatures 0, 1 and 3 were biased to C[-&gt;]T, T[-&gt;]C/A[-&gt;]G and G[-&gt;]T point mutations as would be expected of host antiviral molecules APOBEC, ADAR and ROS effects, respectively. We also observe a shift amidst the pandemic in relative mutational signature activity from predominantly APOBEC-like changes to an increasingly high proportion of changes consistent with ADAR editing. This could represent changes in how the virus and the host immune response interact, and indicates how SARS-CoV-2 may continue to accumulate mutations in the future. Linkage of the detected mutational signatures to the VOC defining amino acids substitutions indicates the majority of SARS-CoV-2s evolutionary capacity is likely to be associated with the action of host antiviral molecules rather than virus replication errors.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Kieran D Lamb",
-        "author_inst": "University of Glasgow"
-      },
-      {
-        "author_name": "Martha M Luka",
-        "author_inst": "University of Glasgow"
-      },
-      {
-        "author_name": "Megan Saathoff",
-        "author_inst": "University of Glasgow"
-      },
-      {
-        "author_name": "Richard Orton",
-        "author_inst": "University of Glasgow"
-      },
-      {
-        "author_name": "My Phan",
-        "author_inst": "MRC/UVRI & LSHTM Uganda Research Institute"
-      },
-      {
-        "author_name": "Matthew Cotten",
-        "author_inst": "MRC/UVRI & LSHTM Uganda Research Unit"
-      },
-      {
-        "author_name": "Ke Yuan",
-        "author_inst": "University of Glasgow"
-      },
-      {
-        "author_name": "David L Robertson",
-        "author_inst": "University of Glasgow"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "genomics"
-  },
   {
     "rel_doi": "10.1101/2023.04.08.536123",
     "rel_title": "Antibodies that neutralize all current SARS-CoV-2 variants of concern by conformational locking",
@@ -85684,6 +85290,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2023.04.07.23288300",
+    "rel_title": "Association between PM2.5 air pollution, temperature, and sunlight during different infectious stages with the case fatality of COVID-19 in the United Kingdom: a modeling study",
+    "rel_date": "2023-04-09",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.07.23288300",
+    "rel_abs": "Although the relationship between the environmental factors such as weather conditions and air pollution and COVID-19 case fatality rate (CFR) has been found, the impacts of these factors to which infected cases are exposed at different infectious stages (e.g., virus exposure time, incubation period, and at or after symptom onset) are still unknown. Understanding this link can help reduce mortality rates. During the first wave of COVID-19 in the United Kingdom (UK), the CFR varied widely between and among the four countries of the UK, allowing such differential impacts to be assessed.\n\nWe developed a generalized linear mixed-effect model combined with distributed lag nonlinear models to estimate the odds ratio of the weather factors (i.e., temperature, sunlight, relative humidity, and rainfall) and air pollution (i.e., ozone, NO2, SO2, CO, PM10 and PM2.5) using data between March 26, 2020 and May 12, 2020 in the UK. After retrospectively time adjusted CFR was estimated using back-projection technique, the stepwise model selection method was used to choose the best model based on Akaike information criteria (AIC) and the closeness between the predicted and observed values of CFR.\n\nWe found that the low temperature (8-11{degrees}C), prolonged sunlight duration (11-13hours) and increased PM2.5 (11-18 g/m3) after the incubation period posed a greater risk of death (measured by odds ratio (OR)) than the earlier infectious stages. The risk reached its maximum level when the low temperature occurred one day after (OR = 1.76; 95% CI: 1.10-2.81), prolonged sunlight duration 2-3 days after (OR = 1.50; 95% CI: 1.03-2.18) and increased P.M2.5 at the onset of symptom (OR =1.72; 95% CI: 1.30-2.26). In contrast, prolonged sunlight duration showed a protective effect during the incubation period or earlier.\n\nAfter reopening, many COVID-19 cases will be identified after their symptoms appear. The findings highlight the importance of designing different preventive measures against severe illness or death considering the time before and after symptom onset.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "M. Pear Hossain",
+        "author_inst": "City University of Hong Kong"
+      },
+      {
+        "author_name": "Wen Zhou",
+        "author_inst": "4. School of Energy and Environment, City University of Hong Kong, Hong Kong Special Administrative Region, China. 5. Department of Atmospheric and Oceanic Scie"
+      },
+      {
+        "author_name": "Marco Y. T. Leung",
+        "author_inst": "6. School of Marine Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China"
+      },
+      {
+        "author_name": "Hsiang-Yu Yuan",
+        "author_inst": "1. Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong Special Administrati"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2023.04.05.535806",
     "rel_title": "A new tractable method for generating Human Alveolar Macrophage Like cells in vitro to study lung inflammatory processes and diseases",
@@ -87141,169 +86778,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2023.04.03.23287902",
-    "rel_title": "Para-infectious brain injury in COVID-19 persists at follow-up despite attenuated cytokine and autoantibody responses",
-    "rel_date": "2023-04-04",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.03.23287902",
-    "rel_abs": "We measured brain injury markers, inflammatory mediators, and autoantibodies in 203 participants with COVID-19; 111 provided acute sera (1-11 days post admission) and 56 with COVID-19-associated neurological diagnoses provided subacute/convalescent sera (6-76 weeks post-admission). Compared to 60 controls, brain injury biomarkers (Tau, GFAP, NfL, UCH-L1) were increased in acute sera, significantly more so for NfL and UCH-L1, in patients with altered consciousness. Tau and NfL remained elevated in convalescent sera, particularly following cerebrovascular and neuroinflammatory disorders. Acutely, inflammatory mediators (including IL-6, IL-12p40, HGF, M-CSF, CCL2, and IL-1RA) were higher in participants with altered consciousness, and correlated with brain injury biomarker levels. Inflammatory mediators were lower than acute levels in convalescent sera, but levels of CCL2, CCL7, IL-1RA, IL-2R, M-CSF, SCF, IL-16 and IL-18 in individual participants correlated with Tau levels even at this late time point. When compared to acute COVID-19 patients with a normal GCS, network analysis showed significantly altered immune responses in patients with acute alteration of consciousness, and in convalescent patients who had suffered an acute neurological complication. The frequency and range of autoantibodies did not associate with neurological disorders. However, autoantibodies against specific antigens were more frequent in patients with altered consciousness in the acute phase (including MYL7, UCH-L1, GRIN3B, and DDR2), and in patients with neurological complications in the convalescent phase (including MYL7, GNRHR, and HLA antigens). In a novel low-inoculum mouse model of SARS-CoV-2, while viral replication was only consistently seen in mouse lungs, inflammatory responses were seen in both brain and lungs, with significant increases in CCL4, IFN{gamma}, IL-17A, and microglial reactivity in the brain. Neurological injury is common in the acute phase and persists late after COVID-19, and may be driven by a para-infectious process involving a dysregulated host response.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC=\"FIGDIR/small/23287902v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (43K):\norg.highwire.dtl.DTLVardef@1cd7473org.highwire.dtl.DTLVardef@198407corg.highwire.dtl.DTLVardef@b1ac7borg.highwire.dtl.DTLVardef@b2ebb4_HPS_FORMAT_FIGEXP  M_FIG (a) The acute cohort (days 1-11 post-hospitilisation) showed elevated pro-inflammatory cytokines, brain injury markers, and autoantibodies. The sub-acute/convalescent cohort (weeks to months post-COVID+ve test) retained elevated brain injury markers but lower proinflammatory cytokines and autoantibodies.\n\n(b) The mouse model of para-infectious brain with no active viral replication, had increased cytokines (IFN{gamma} and IL-17A) and microglia reactivity (increased Iba1 expression).\n\nCreated using Biorender.\n\nC_FIG",
-    "rel_num_authors": 37,
-    "rel_authors": [
-      {
-        "author_name": "Benedict D. Michael",
-        "author_inst": "Clinical Infection, Microbiology, and Immunology, University of Liverpool"
-      },
-      {
-        "author_name": "Cordelia Dunai",
-        "author_inst": "Clinical Infection, Microbiology, and Immunology, University of Liverpool"
-      },
-      {
-        "author_name": "Edward J. Needham",
-        "author_inst": "Clinical Neurosciences, University of Cambridge"
-      },
-      {
-        "author_name": "Kukatharmini Tharmaratnam",
-        "author_inst": "University of Liverpool"
-      },
-      {
-        "author_name": "Robyn Williams",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Yun Huang",
-        "author_inst": "Clinical Infection, Microbiology, and Immunology, University of Liverpool"
-      },
-      {
-        "author_name": "Sarah A. Boardman",
-        "author_inst": "Clinical Infection, Microbiology, and Immunology, University of Liverpool"
-      },
-      {
-        "author_name": "Jordan Clark",
-        "author_inst": "Infection Biology and Microbiomes, University of Liverpool"
-      },
-      {
-        "author_name": "Parul Sharma",
-        "author_inst": "Infection Biology and Microbiomes, University of Liverpool"
-      },
-      {
-        "author_name": "Krishanthi Subramaniam",
-        "author_inst": "Clinical Infection, Microbiology, and Immunology, University of Liverpool"
-      },
-      {
-        "author_name": "Greta K. Wood",
-        "author_inst": "Clinical Infection, Microbiology, and Immunology, University of Liverpool"
-      },
-      {
-        "author_name": "Ceryce Collie",
-        "author_inst": "Clinical Infection, Microbiology, and Immunology, University of Liverpool"
-      },
-      {
-        "author_name": "Richard Digby",
-        "author_inst": "Clinical Neurosciences, University of Cambridge"
-      },
-      {
-        "author_name": "Alexander Ren",
-        "author_inst": "Division of Anaesthesia, Department of Medicine, University of Cambridge"
-      },
-      {
-        "author_name": "Emma Norton",
-        "author_inst": "Clinical Neurosciences, University of Cambridge"
-      },
-      {
-        "author_name": "Maya Leibowitz",
-        "author_inst": "Clinical Neurosciences, University of Cambridge"
-      },
-      {
-        "author_name": "Soraya Ebrahimi",
-        "author_inst": "Clinical Neurosciences, University of Cambridge"
-      },
-      {
-        "author_name": "Andrew Fower",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Hannah Fox",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Esteban Tato",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Mark Ellul",
-        "author_inst": "Clinical Infection, Microbiology, and Immunology, University of Liverpool"
-      },
-      {
-        "author_name": "Geraint Sunderland",
-        "author_inst": "Clinical Infection, Microbiology, and Immunology, University of Liverpool"
-      },
-      {
-        "author_name": "Marie Held",
-        "author_inst": "University of Liverpool"
-      },
-      {
-        "author_name": "Claire Hetherington",
-        "author_inst": "Clinical Infection, Microbiology, and Immunology, University of Liverpool"
-      },
-      {
-        "author_name": "Franklyn Nkongho",
-        "author_inst": "Clinical Infection, Microbiology, and Immunology, University of Liverpool"
-      },
-      {
-        "author_name": "Alish Palmos",
-        "author_inst": "Translational and Neuropsychiatric Genetics Group, King's College London"
-      },
-      {
-        "author_name": "Alexander Grundmann",
-        "author_inst": "University of Southampton"
-      },
-      {
-        "author_name": "James P. Stewart",
-        "author_inst": "Infection Biology and Microbiomes, University of Liverpool"
-      },
-      {
-        "author_name": "Michael Griffiths",
-        "author_inst": "Clinical Infection, Microbiology, and Immunology, University of Liverpool"
-      },
-      {
-        "author_name": "Tom Solomon",
-        "author_inst": "Clinical Infection, Microbiology, and Immunology, University of Liverpool"
-      },
-      {
-        "author_name": "Gerome Breen",
-        "author_inst": "Translational and Neuropsychiatric Genetics Group, King's College London"
-      },
-      {
-        "author_name": "Alasdair Coles",
-        "author_inst": "Clinical Neurosciences, University of Cambridge"
-      },
-      {
-        "author_name": "Jonathan Cavanagh",
-        "author_inst": "Immunology and Infection, University of Glasgow"
-      },
-      {
-        "author_name": "Sarosh R. Irani",
-        "author_inst": "Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford"
-      },
-      {
-        "author_name": "Angela Vincent",
-        "author_inst": "Nuffield Department of Clinical Neurosciences, University of Oxford"
-      },
-      {
-        "author_name": "Leonie Taams",
-        "author_inst": "Department of Inflammation Biology, King's College London"
-      },
-      {
-        "author_name": "David K. Menon",
-        "author_inst": "Division of Anaesthesia, Department of Medicine, University of Cambridge"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2023.04.04.23288110",
     "rel_title": "Long-term outcomes of COVID-19 infection in children and young people: a systematic review and meta-analysis",
@@ -87694,6 +87168,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "primary care research"
   },
+  {
+    "rel_doi": "10.1101/2023.03.30.23287969",
+    "rel_title": "A Graph Embedding Approach for Deciphering the Longitudinal Associations of Global Mobility and COVID-19 Cases",
+    "rel_date": "2023-04-03",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.30.23287969",
+    "rel_abs": "The COVID-19 pandemic has highlighted the importance of monitoring mobility patterns and their impact on disease spread. This paper presents a methodology for developing effective pandemic surveillance systems by extracting scalable graph features from mobility networks. We utilized Metas \"Travel Patterns\" dataset to capture the daily number of individuals traveling between countries from March 2020 to April 2022. We have used an optimized node2vec algorithm to extract scalable features from the mobility networks. Our analysis revealed that movement embeddings accurately represented the movement patterns of countries, with geographically proximate countries exhibiting similar movement patterns. The temporal association dynamics between Global mobility and COVID-19 cases highlighted the significance of high-page rank centrality countries in mobility networks as a key intervention target in controlling infection spread. Our proposed methodology provides a useful approach for tracking the trajectory of infectious diseases and developing evidence-based interventions.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Raghav Awasthi",
+        "author_inst": "Indraprastha Institute of Information Technology, Delhi"
+      },
+      {
+        "author_name": "Meet Modi",
+        "author_inst": "Indraprastha Institute of Information Technology, Delhi"
+      },
+      {
+        "author_name": "Hardik Dudeja",
+        "author_inst": "Indraprastha Institute of Information Technology, Delhi"
+      },
+      {
+        "author_name": "Tanav Bajaj",
+        "author_inst": "Indian Institute of Information Technology, Bhopal"
+      },
+      {
+        "author_name": "Shruti Rastogi",
+        "author_inst": "BITS Pilani, K.K.Birla Goa Campus"
+      },
+      {
+        "author_name": "Tavpritesh Sethi",
+        "author_inst": "Indraprastha Institute of Information Technology, Delhi"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health informatics"
+  },
   {
     "rel_doi": "10.1101/2023.03.31.23288023",
     "rel_title": "Pharmaceutical and Non-Pharmaceutical Interventions for Controlling the COVID-19 Pandemic",
@@ -89015,73 +88528,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2023.03.29.534838",
-    "rel_title": "Improving mRNA vaccine safety and efficiency with cationized lipid nanoparticle formula",
-    "rel_date": "2023-03-30",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.29.534838",
-    "rel_abs": "The widespread use of Covid-19 mRNA vaccines has highlighted the need to address rare but concerning side effects. Systemic off-target gene expression has been identified as a primary cause of acute adverse reactions and side effects associated with nucleoside-modified mRNA vaccines. In this study, we incorporated the permanent cationic lipid Dotap component into the mRNA-LNP formula associated with the FDA-approved mRNA vaccine Comirnaty to create a novel positively charged LNP carrier for mRNA vaccine delivery. Using the optimized LNP formula to prepare SARS-Cov-2 Spike mRNA vaccines for immunogenicity testing, Balb/c mice exhibited improved immunogenicity kinetics with initial antibody titers being lower but showing a continuous upward trend, ultimately reaching levels comparable to those of control mRNA vaccines 8 weeks after boost immunization. The mRNA vaccines encapsulated in the modified LNPs have demonstrated a superior safety profile in respect to systemic delivery of LNP constituents, off-target gene expression, and the systemic pro-inflammatory stimulation. Consequently, it may represent a safer alternative of conventional mRNA-LNP vaccines.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Xu Peng Ph.D",
-        "author_inst": "The Laboratory Animal Center, Sichuan University, Chengdu, 610041, China"
-      },
-      {
-        "author_name": "Guangneng Liao",
-        "author_inst": "Animal experimental center of West China hospital, Sichuan University, Chengdu, 610041, China"
-      },
-      {
-        "author_name": "Dongsheng Ren Ph.D",
-        "author_inst": "Tibet Rhodiola Pharmaceutical Holding Co., Chengdu, Sichuan, 610000, China"
-      },
-      {
-        "author_name": "Yucheng Zhou",
-        "author_inst": "Tibet Rhodiola Pharmaceutical Holding Co., Chengdu, Sichuan, 610000, China"
-      },
-      {
-        "author_name": "Xiujin Wu",
-        "author_inst": "Chengdu Nuoen Genomics, Ltd., Chengdu, Sichuan, 610040, China"
-      },
-      {
-        "author_name": "Yingxue Lei",
-        "author_inst": "Chengdu Nuoen Genomics, Ltd., Chengdu, Sichuan, 610040, China"
-      },
-      {
-        "author_name": "Yan Zhang",
-        "author_inst": "Tibet Rhodiola Pharmaceutical Holding Co., Chengdu, Sichuan, 610000, China"
-      },
-      {
-        "author_name": "Liang Chen",
-        "author_inst": "Chengdu Nuoen Genomics, Ltd., Chengdu, Sichuan, 610040, China"
-      },
-      {
-        "author_name": "Chen He",
-        "author_inst": "Tibet Rhodiola Pharmaceutical Holding Co., Chengdu, Sichuan, 610000, China"
-      },
-      {
-        "author_name": "Yaoyi Zhang",
-        "author_inst": "Chengdu Nuoen Genomics, Ltd., Chengdu, Sichuan, 610040, China"
-      },
-      {
-        "author_name": "Hailin Yin",
-        "author_inst": "The Laboratory Animal Center, Sichuan University, Chengdu, 610041, China"
-      },
-      {
-        "author_name": "Guang Yang",
-        "author_inst": "Animal experimental center of West China hospital, Sichuan University, Chengdu, 610041, China"
-      },
-      {
-        "author_name": "Kai Xu",
-        "author_inst": "Chengdu Nuoen Genomics, Ltd., Chengdu, Sichuan, 610040, China"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "synthetic biology"
-  },
   {
     "rel_doi": "10.1101/2023.03.30.534873",
     "rel_title": "NETosis Induced by Serum of Patients with COVID-19 is Reduced with Reparixin or Antibodies Against DEK and IL-8",
@@ -89415,6 +88861,77 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2023.03.24.23287658",
+    "rel_title": "Safety and Immunogenicity of the NVX-CoV2373 Vaccine as a Booster in Adults Previously Vaccinated with the BBIBP-CorV Vaccine: An Interim Analysis",
+    "rel_date": "2023-03-29",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.24.23287658",
+    "rel_abs": "This phase 3 observer-blind, randomized, controlled study was conducted in adults [&ge;]18 years of age to assess the safety and immunogenicity of NVX-CoV2373 as a heterologous booster compared to BBIBP-CorV when utilized as a homologous booster. Approximately 1,000 participants were randomly assigned in a 1:1 ratio to receive a single dose of NVX-CoV2373 or BBIBP-CorV after prior vaccination with 2 or 3 doses of BBIBP-CorV. Solicited adverse events (AEs) were collected for 7 days after vaccination. Unsolicited AEs were collected for 28 days following the booster dose and serious adverse and adverse events of special interest (AESI) were collected throughout the study. For this interim analysis, anti-spike IgG and neutralizing antibodies against SARS-CoV-2 were measured at baseline, day 14, and day 28. The study achieved its primary non-inferiority endpoint and also demonstrated statistically higher neutralization responses of approximately 6-fold when NVX-CoV2373 was utilized as a heterologous booster compared with BBIBP-CorV as a homologous booster. Both vaccines had an acceptably low reactogenicity profile and no new safety concerns were found. Heterologous boosting with NVX-CoV2373 was a highly immunogenic and safe vaccine regimen in those previously vaccinated with BBIBP-CorV.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Seth Toback",
+        "author_inst": "Novavax Inc."
+      },
+      {
+        "author_name": "Anthony M. Marchese",
+        "author_inst": "Novavax Inc."
+      },
+      {
+        "author_name": "Brandy Warren",
+        "author_inst": "Novavax Inc."
+      },
+      {
+        "author_name": "Sondos Ayman",
+        "author_inst": "Insights Research Organization & Solutions"
+      },
+      {
+        "author_name": "Senka Zarkovic",
+        "author_inst": "Insights Research Organization & Solutions"
+      },
+      {
+        "author_name": "Islam ElTantawy",
+        "author_inst": "Insights Research Organization & Solutions"
+      },
+      {
+        "author_name": "Raburn M. Mallory",
+        "author_inst": "Novavax Inc."
+      },
+      {
+        "author_name": "Matthew Rousculp",
+        "author_inst": "Novavax Inc."
+      },
+      {
+        "author_name": "Fahed Almarzooqi",
+        "author_inst": "G42 Healthcare"
+      },
+      {
+        "author_name": "Bartlomiej Piechowski-Jozwiak",
+        "author_inst": "Cleveland Clinic Abu Dhabi"
+      },
+      {
+        "author_name": "Maria-Fernanda Bonilla",
+        "author_inst": "Cleveland Clinic Abu Dhabi"
+      },
+      {
+        "author_name": "Agyad Ebrahim Bakkour",
+        "author_inst": "Sheikh Khalifa Medical City"
+      },
+      {
+        "author_name": "Salah Eldin Hussein",
+        "author_inst": "Sheikh Khalifa Medical City"
+      },
+      {
+        "author_name": "Nawal Al Kaabi",
+        "author_inst": "Sheikh Khalifa Medical City; College of Medicine and Health Sciences, Khalifa University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2023.03.26.23287758",
     "rel_title": "Impact of opinion dynamics on the public health damage inflicted by COVID-19 in the presence of societal heterogeneities",
@@ -90472,89 +89989,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "sexual and reproductive health"
   },
-  {
-    "rel_doi": "10.1101/2023.03.25.23287718",
-    "rel_title": "Sequential viral introductions and spread of BA.1 drove the Omicron wave across Pakistani provinces",
-    "rel_date": "2023-03-27",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.25.23287718",
-    "rel_abs": "BackgroundCOVID-19 waves caused by specific SARS-CoV-2 variants have occurred globally at different times. We focused on Omicron variants to understand the genomic diversity and phylogenetic relatedness of SARS-CoV-2 strains in various regions of Pakistan.\n\nMethodsWe studied 276,525 COVID-19 cases and 1,041 genomes sequenced from December 2021 to August 2022. Sequences were analyzed and visualized using phylogenetic trees.\n\nResultsThe highest case numbers and deaths were recorded in Sindh and Punjab, the most populous provinces in Pakistan. Omicron variants comprised 95% of all genomes, with BA.2 (34.2%) and BA.5 (44.6%) predominating. The first Omicron wave was associated with the sequential identification of BA.1 in Sindh, then Islamabad Capital Territory, Punjab, Khyber Pakhtunkhwa (KP), Azad Jammu Kashmir (AJK), Gilgit-Baltistan (GB) and Balochistan. Phylogenetic analysis revealed Sindh to be the source of BA.1 and BA.2 introductions into Punjab and Balochistan during early 2022. BA.4 was first introduced in AJK and BA.5 in Punjab. Most recent common ancestor (MRCA) analysis revealed relatedness between the earliest BA.1 genome from Sindh with Balochistan, AJK, Punjab and ICT, and that of first BA.1 from Punjab with strains from KPK and GB.\n\nConclusionsPhylogenetic analysis provides insights into the introduction and transmission dynamics of the Omicron variant in Pakistan, identifying Sindh as a hotspot for viral dissemination. Such data linked with public health efforts can help limit surges of new infections.",
-    "rel_num_authors": 17,
-    "rel_authors": [
-      {
-        "author_name": "Sayed Ali Raza Shah Bukhari",
-        "author_inst": "Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi-74800, Pakistan"
-      },
-      {
-        "author_name": "Javaria Ashraf",
-        "author_inst": "Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi-74800, Pakistan"
-      },
-      {
-        "author_name": "Akbar Kanji",
-        "author_inst": "Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi-74800, Pakistan"
-      },
-      {
-        "author_name": "Yusra Rehman",
-        "author_inst": "Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi-74800, Pakistan"
-      },
-      {
-        "author_name": "Nidia S Trovao",
-        "author_inst": "Fogarty International Center, U.S. National Institutes of Health, 16 Center Drive, Bethesda, MD 20892, USA"
-      },
-      {
-        "author_name": "Peter M. Thielen",
-        "author_inst": "Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD 20723, USA"
-      },
-      {
-        "author_name": "Maliha Yameen",
-        "author_inst": "Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi-74800, Pakistan"
-      },
-      {
-        "author_name": "Samiah Kanwar",
-        "author_inst": "Department of Pediatrics and Child Health, Medical College, Aga Khan University, Karachi-74800, Pakistan"
-      },
-      {
-        "author_name": "Waqasuddin Khan",
-        "author_inst": "Department of Pediatrics and Child Health, Medical College, Aga Khan University, Karachi-74800, Pakistan"
-      },
-      {
-        "author_name": "Furqan Kabir",
-        "author_inst": "Department of Pediatrics and Child Health, Medical College, Aga Khan University, Karachi-74800, Pakistan"
-      },
-      {
-        "author_name": "M. Imran Nisar",
-        "author_inst": "Department of Pediatrics and Child Health, Medical College, Aga Khan University, Karachi-74800, Pakistan"
-      },
-      {
-        "author_name": "Brian Merritt",
-        "author_inst": "Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD 20723, USA"
-      },
-      {
-        "author_name": "Rumina Hasan",
-        "author_inst": "Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi-74800, Pakistan"
-      },
-      {
-        "author_name": "David Spiro",
-        "author_inst": "Fogarty International Center, U.S. National Institutes of Health, 16 Center Drive, Bethesda, MD 20892, USA"
-      },
-      {
-        "author_name": "Zeba Rasmussen",
-        "author_inst": "Fogarty International Center, U.S. National Institutes of Health, 16 Center Drive, Bethesda, MD 20892, USA"
-      },
-      {
-        "author_name": "Uzma Bashir",
-        "author_inst": "World Health Organization country office, Park Road, Chak Shahzad, Islamabad, Pakistan"
-      },
-      {
-        "author_name": "Zahra Hasan",
-        "author_inst": "Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi-74800, Pakistan"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2023.03.24.23287722",
     "rel_title": "Facility-based and virtual cardiac rehabilitation in young patients with heart disease during the COVID-19 era",
@@ -90929,6 +90363,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "occupational and environmental health"
   },
+  {
+    "rel_doi": "10.1101/2023.03.24.534062",
+    "rel_title": "Intra-Host Mutation Rate of Acute SARS-CoV-2 Infection During the Initial Pandemic Wave",
+    "rel_date": "2023-03-25",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.24.534062",
+    "rel_abs": "BackgroundOur understanding of SARS-CoV-2 evolution and mutation rate is limited. The rate of SARS-CoV-2 evolution is minimized through a proofreading function encoded by NSP-14 and may be affected by patient comorbidity. Current understanding of SARS-CoV-2 mutational rate is through population based analysis while intra-host mutation rate remains poorly studied.\n\nMethodsViral genome analysis was performed between paired samples and mutations quantified at allele frequencies (AF) [&ge;]0.25, [&ge;]0.5 and [&ge;]0.75. Mutation rate was determined employing F81 and JC69 evolution models and compared between isolates with ({Delta}NSP-14) and without (wtNSP-14) non-synonymous mutations in NSP-14 and by patient comorbidity.\n\nResultsForty paired samples with median interval of 13 days [IQR 8.5-20] were analyzed. The estimated mutation rate by F81 modeling was 93.6 (95%CI:90.8-96.4], 40.7 (95%CI:38.9-42.6) and 34.7 (95%CI:33.0-36.4) substitutions/genome/year at AF [&ge;]0.25, [&ge;]0.5, [&ge;]0.75 respectively. Mutation rate in {Delta}NSP-14 were significantly elevated at AF>0.25 vs wtNSP-14. Patients with immune comorbidities had higher mutation rate at all allele frequencies.\n\nDiscussionIntra-host SARS-CoV-2 mutation rates are substantially higher than those reported through population analysis. Virus strains with altered NSP-14 have accelerated mutation rate at low AF. Immunosuppressed patients have elevated mutation rate at all AF. Understanding intra-host virus evolution will aid in current and future pandemic modeling.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Thamali Madhu Adhikari",
+        "author_inst": "Case Western Reserve University"
+      },
+      {
+        "author_name": "Xiaoyi Leng",
+        "author_inst": "Case Western Reserve University"
+      },
+      {
+        "author_name": "Xiangyi Zhang",
+        "author_inst": "Case Western Reserve University"
+      },
+      {
+        "author_name": "Sarah Worley",
+        "author_inst": "Cleveland Clinic Foundation: Cleveland Clinic"
+      },
+      {
+        "author_name": "Jing Li",
+        "author_inst": "Case Western Reserve University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "new results",
+    "category": "evolutionary biology"
+  },
   {
     "rel_doi": "10.1101/2023.03.25.23287563",
     "rel_title": "Longitudinal wastewater surveillance addressed public health priorities during the transition from \"dynamic COVID-zero\" to \"opening up\" in China: a population-based study",
@@ -92206,69 +91675,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2023.03.22.533805",
-    "rel_title": "Evolving antibody evasion and receptor affinity of the Omicron BA.2.75 sublineage of SARS-CoV-2",
-    "rel_date": "2023-03-22",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.22.533805",
-    "rel_abs": "SARS-CoV-2 Omicron BA.2.75 has diversified into multiple subvariants with additional spike mutations, and several are expanding in prevalence, particularly CH.1.1 and BN.1. Here, we investigated the viral receptor affinities and neutralization evasion properties of major BA.2.75 subvariants actively circulating in different regions worldwide. We found two distinct evolutionary pathways and three newly identified mutations that shaped the virological features of these subvariants. One phenotypic group exhibited a discernible decrease in viral receptor affinities, but a noteworthy increase in resistance to antibody neutralization, as exemplified by CH.1.1, which is apparently as resistant as XBB.1.5. In contrast, a second group demonstrated a substantial increase in viral receptor affinity but only a moderate increase in antibody evasion, as exemplified by BN.1. We also observed that all prevalent SARS-CoV-2 variants in the circulation presently, except for BN.1, exhibit profound levels of antibody evasion, suggesting this is the dominant determinant of virus transmissibility today.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Zhiteng Li",
-        "author_inst": "Columbia University"
-      },
-      {
-        "author_name": "Yicheng Guo",
-        "author_inst": "Columbia University"
-      },
-      {
-        "author_name": "Ian A Mellis",
-        "author_inst": "Columbia University"
-      },
-      {
-        "author_name": "Sho Iketani",
-        "author_inst": "Columbia University"
-      },
-      {
-        "author_name": "Michael Liu",
-        "author_inst": "Columbia University"
-      },
-      {
-        "author_name": "Jian Yu",
-        "author_inst": "Columbia University"
-      },
-      {
-        "author_name": "Riccardo Valdez",
-        "author_inst": "University of Michigan"
-      },
-      {
-        "author_name": "Adam S Lauring",
-        "author_inst": "University of Michigan"
-      },
-      {
-        "author_name": "Zhizhang Sheng",
-        "author_inst": "Columbia University"
-      },
-      {
-        "author_name": "Aubree Gordon",
-        "author_inst": "University of Michigan"
-      },
-      {
-        "author_name": "Lihong Liu",
-        "author_inst": "Columbia University"
-      },
-      {
-        "author_name": "David D Ho",
-        "author_inst": "Columbia University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2023.03.21.533720",
     "rel_title": "BCG administration promotes the long-term protection afforded by a single-dose intranasal adenovirus-based SARS-CoV-2 vaccine",
@@ -92579,6 +91985,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2023.03.20.23287490",
+    "rel_title": "The Change of Screen Time and Screen Addiction, and their Association with Psychological Well-being During the COVID-19 Pandemic: An Analysis of US Country-Wide School-Age Children and Adolescents Between 2018 and 2020",
+    "rel_date": "2023-03-21",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.20.23287490",
+    "rel_abs": "Previous studies on screen use and childrens mental health during the Coronavirus Disease 2019 (COVID-19) pandemic either focused only on the timeframe during the pandemic, or only on children previously reporting COVID-related severe family economic hardship or worries. Instead, we used a large sample (n=63,211) of the National Survey of Childrens Health (NSCH) years 2018-20 to analyze changes in the trends of recreational screen device use before, versus during the COVID-19 pandemic, and associations with psychological well-being, widely among school-age children (6-17 year-olds) across the US. We assessed recreational screen use, instead of overall use including both instructional and recreational use, and developed psychological well-being issue scores to evaluate the associations among the pandemic, recreational screen use, and psychological well-being states. We found an increase in the prevalence of screen overuse/addiction and psychological well-being issues during the pandemic compared to the years prior, detected an association between the pandemic and psychological well-being issue scores (p <0.01 across all models), and observed increased magnitude of association between recreational screen overuse/addiction and mental health during the pandemic year (p <0.01 across all models). Further studies on elucidating and addressing the specific aspects of the pandemic that contribute to these associations are critical.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Helena T Wu",
+        "author_inst": "Massachusetts General Hospital"
+      },
+      {
+        "author_name": "Jiandong Li",
+        "author_inst": "Central University of Finance and Economics"
+      },
+      {
+        "author_name": "Amy Tsurumi",
+        "author_inst": "Massachusetts General Hospital"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2023.03.14.23287121",
     "rel_title": "First-in-human immunoPET imaging of COVID-19 convalescent patients using dynamic total-body PET and a CD8-targeted minibody",
@@ -94243,65 +93676,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pediatrics"
   },
-  {
-    "rel_doi": "10.1101/2023.03.15.23287287",
-    "rel_title": "Effect of Andrographis paniculata treatment for patients with early-stage COVID-19 on the prevention of pneumonia: A retrospective cohort study",
-    "rel_date": "2023-03-18",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.15.23287287",
-    "rel_abs": "There is a need for safe and cost-effective treatments for COVID-19. Andrographis paniculata (AP) is an herbal plant that has been used for centuries to treat upper respiratory tract infections. Andrographolide is the major active component of AP that inhibits intracellular SARS-CoV-2 replication and has anti-inflammatory action. We performed a retrospective cohort study to evaluate the therapeutic and adverse effects of oral AP-products on COVID-19 by using the risk of pneumonia diagnosed by chest radiography as an indicator. This study included patients 15 to 60 years of age with laboratory-confirmed early-stage (asymptomatic or mild) COVID-19 without comorbidities at seven hospitals in three adjacent provinces in Thailand, between December 2020 and March 2021. Patients were treated for five days with either AP-extract (60 mg andrographolide, 3 times daily) or crude-AP (48 mg andrographolide, 3 times daily), when available. Patient information was prospectively recorded in the structured medical records and retrospectively reviewed. All eligible patients who received AP-treatment were included and control patients who did not receive AP-treatment were randomly selected using a ratio of approximately 1:1. Pneumonia occurred in 1/243 AP-treatment patients and 69/285 control patients. The risks of pneumonia after adjusting for confounding effects were 0.3% (95%CI, 0%-0.9%) and 24.3% (95%CI, 19.0%-29.7%) in the AP-treatment and control groups, respectively. The number needed to treat to avoid pneumonia development in one patient was four (95% CI, 3-5). Eight patients developed mild adverse events. AP-treatment regimens are acceptably safe and associated with highly reduced rates of pneumonia for patients with early-stage COVID-19.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Amporn Benjaponpitak",
-        "author_inst": "Department of Thai Traditional and Alternative Medicine, Ministry of Public Health, Nonthaburi, Thailand"
-      },
-      {
-        "author_name": "Thiti Sawaengtham",
-        "author_inst": "Department of Thai Traditional and Alternative Medicine, Ministry of Public Health, Nonthaburi, Thailand"
-      },
-      {
-        "author_name": "Tewan Thaneerat",
-        "author_inst": "Department of Thai Traditional and Alternative Medicine, Ministry of Public Health, Nonthaburi, Thailand"
-      },
-      {
-        "author_name": "Kulthanit Wanaratna",
-        "author_inst": "Department of Thai Traditional and Alternative Medicine, Ministry of Public Health, Nonthaburi, Thailand"
-      },
-      {
-        "author_name": "Palang Chotsiri",
-        "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand"
-      },
-      {
-        "author_name": "Chalermquan Rungsawang",
-        "author_inst": "Department of Basic Medical Sciences, Faculty of Medicine, Siam University, Bangkok, Thailand"
-      },
-      {
-        "author_name": "Sakkarin Bhubhanilc",
-        "author_inst": "Department of Basic Medical Sciences, Faculty of Medicine, Siam University, Bangkok, Thailand"
-      },
-      {
-        "author_name": "Sataporn Charoensuk",
-        "author_inst": "Department of Basic Medical Sciences, Faculty of Medicine, Siam University, Bangkok, Thailand"
-      },
-      {
-        "author_name": "Suwat Benjaponpitak",
-        "author_inst": "Department of Basic Medical Sciences, Faculty of Medicine, Siam University, Bangkok, Thailand"
-      },
-      {
-        "author_name": "Sarawut Lapmanee",
-        "author_inst": "Department of Basic Medical Sciences, Faculty of Medicine, Siam University, Bangkok, Thailand"
-      },
-      {
-        "author_name": "Sayomporn Sirinavin",
-        "author_inst": "Faculty of Medicine Ramathibodi Hospital, Mahidol University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2023.03.15.23286981",
     "rel_title": "Impact of COVID-19 and effects of booster vaccination with BNT162b2 on six-month long COVID symptoms, quality of life, work productivity and activity impairment during Omicron",
@@ -94620,6 +93994,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "nephrology"
   },
+  {
+    "rel_doi": "10.1101/2023.03.16.23287360",
+    "rel_title": "Relative vaccine effectiveness (rVE) of mRNA COVID-19 boosters in the UK vaccination programme, during the Spring-Summer (monovalent vaccine) and Autumn-Winter 2022 (bivalent vaccine) booster campaigns: a prospective test negative case-control study",
+    "rel_date": "2023-03-17",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.16.23287360",
+    "rel_abs": "BackgroundUnderstanding the relative vaccine effectiveness (rVE) of new COVID-19 vaccine formulations against SARS-CoV-2 infection is an urgent public health priority. A precise analysis of the rVE of monovalent and bivalent boosters given during the 2022 Spring-Summer and Autumn-Winter campaigns, respectively, in a defined population has not been reported.\n\nAimWe therefore assessed rVE against hospitalisation for the Spring-Summer (fourth vs third monovalent mRNA vaccine doses) and Autumn-Winter (fifth BA.1/ancestral bivalent vs fourth monovalent mRNA vaccine dose) boosters.\n\nMethodsA prospective single-centre test-negative design case-control study of [&ge;]75 year-olds hospitalised with COVID-19 or other acute respiratory disease. We conducted regression analyses controlling for age, sex, socioeconomic status, patient comorbidities, community SARS-CoV-2 prevalence, vaccine brand and time between baseline dose and hospitalisation.\n\nResults682 controls and 182 cases were included in the Spring-Summer booster analysis; 572 controls and 152 cases for the Autumn-Winter booster analysis. A monovalent mRNA COVID-19 vaccine as fourth dose showed rVE 46{middle dot}6% (95% confidence interval [CI] 13{middle dot}9-67{middle dot}1) versus those not fully boosted. A bivalent mRNA COVID-19 vaccine as fifth dose had rVE 46{middle dot}7% (95%CI 18-65{middle dot}1), compared to a fourth monovalent mRNA COVID-19 vaccine dose.\n\nConclusionsBoth fourth monovalent and fifth BA.1/ancestral mRNA bivalent COVID-19 vaccine doses demonstrated benefit as a booster in older adults. Bivalent mRNA boosters offer similar protection against hospitalisation with Omicron infection to monovalent mRNA boosters given earlier in the year. These findings support immunisation programmes in several European countries that advised the use of BA.1/ancestral bivalent booster doses.",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Anastasia Chatzilena",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Catherine Hyams",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Robert Challen",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Robin Marlow",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Jade King",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "David Adegbite",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Jane Kinney",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Madeleine Clout",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Nick Maskell",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Jennifer Oliver",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Adam Finn",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Leon Danon",
+        "author_inst": "Department of Engineering Mathematics, University of Bristol, UK."
+      },
+      {
+        "author_name": "- The AvonCAP Research Group",
+        "author_inst": "-"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2023.03.17.533092",
     "rel_title": "Antibodies generated in vitro and in vivo elucidate design of a thermostable ADDomer COVID-19 nasal nanoparticle vaccine",
@@ -96145,41 +95586,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2023.03.15.23287285",
-    "rel_title": "Modeling COVID-19 vaccination strategies in LMICs considering uncertainty in viral evolution and immunity",
-    "rel_date": "2023-03-15",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.15.23287285",
-    "rel_abs": "Vaccines against the SARS-CoV-2 virus were developed in record time, but their distribution has been highly unequal. With demand saturating in high-income countries, many low- and middle-income countries (LMIC) finally have an opportunity to acquire COVID-19 vaccines. But the pandemic has taken its toll, and a majority of LMIC populations have partial immunity to COVID-19 disease due primarily to viral infection. This existing immunity, combined with resource limitations, raises the question of how LMICs should prioritize COVID-19 vaccines relative to other competing health priorities. We modify an established computational model, Covasim, to address these questions in four diverse country-like settings under a variety of viral evolution, vaccine delivery, and novel immunity scenarios. Under continued Omicron-like viral evolution and mid-level immunity assumptions, results show that COVID-19 vaccines could avert up to 2 deaths per 1,000 doses if administered to high-risk (60+) populations as prime+boost or annual boosting campaigns. Similar immunization efforts reaching healthy children and adults would avert less than 0.1 deaths per 1,000 doses. Together, these modeling results can help to support normative guidelines and programmatic decision making towards objectively maximizing population health.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Daniel J Klein",
-        "author_inst": "Bill & Melinda Gates Foundation"
-      },
-      {
-        "author_name": "Luojun Yang",
-        "author_inst": "Bill & Melinda Gates Foundation"
-      },
-      {
-        "author_name": "Cliff C Kerr",
-        "author_inst": "Bill & Melinda Gates Foundation"
-      },
-      {
-        "author_name": "Greer Fowler",
-        "author_inst": "Bill & Melinda Gates Foundation"
-      },
-      {
-        "author_name": "Jamie A Cohen",
-        "author_inst": "Bill & Melinda Gates Foundation"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2023.03.14.23287265",
     "rel_title": "Association of radiological severity with inflammatory biomarkers for prognostic prediction in patients with COVID-19",
@@ -96562,6 +95968,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health economics"
   },
+  {
+    "rel_doi": "10.1101/2023.03.11.23287138",
+    "rel_title": "How long is the long COVID? a retrospective analysis of football players in two major European Championships.",
+    "rel_date": "2023-03-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.11.23287138",
+    "rel_abs": "Objectivesthe goal of this study was to investigate the correlation between SARS-CoV-2 infection and muscle injuries among a large sample of professional soccer players.\n\nMethodsA retrospective cohort study was conducted on professional soccer players from the Serie A and LaLiga leagues during the 2019-2020 and 2020-2021 football seasons. The players were divided into two groups based on whether they contracted the Sars-CoV-2 infection (C+) or not (C-) during the 2020/2021 season. Data collection was conducted using the Transfermarkt24 site.\n\nResultsIn the 2019-2020 both championships showed non-significant differences in the average number of muscular injuries between the C+ group and the C- group (Serie A: p=0.194; 95%CI: - 0.044 to 0.215, LaLiga p=0.915; 95%CI: -0.123 to 0.137). In the 2020-2021 the C+ group had a significantly higher number of muscular injuries compared to the C- group in both championships (Serie A: p<0.001; 95%CI 0.731 to 1.038; LaLiga: p<0.001; 95%CI: 0.773 to 1.054). Multiple linear regression analysis confirmed that belonging to C+ in the season 2020/2021 was the variable that most strongly influenced the probability of having a muscle injury in both championships. Survival analysis revealed a hazard ratio of 3.73 (95%CI 3.018 to 4.628) and of 5.14 (95% CI 3.200 to 8.254) for Serie A and LaLiga respectively.\n\nConclusionsThis retrospective cohort study revealed a significant association between SARS-CoV-2 infection and increased risk of muscle injury, emphasizing the importance of carefully considering the infection in the decision-making process for determining athletes readiness to return to sport.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Sandra Miccinilli",
+        "author_inst": "Fondazione Policlinico Universitario Campus Bio-Medico"
+      },
+      {
+        "author_name": "Marco Bravi",
+        "author_inst": "Fondazione Policlinico Universitario Campus Bio-Medico"
+      },
+      {
+        "author_name": "Giorgio Conti",
+        "author_inst": "Fondazione Policlinico Universitario Campus Bio-Medico"
+      },
+      {
+        "author_name": "Federica Bressi",
+        "author_inst": "Fondazione Policlinico Universitario Campus Bio-Medico"
+      },
+      {
+        "author_name": "Silvia Sterzi",
+        "author_inst": "Fondazione Policlinico Universitario Campus Bio-Medico"
+      },
+      {
+        "author_name": "Fabio Santacaterina",
+        "author_inst": "Fondazione Policlinico Universitario Campus Bio-Medico"
+      },
+      {
+        "author_name": "Massimo Ciccozzi",
+        "author_inst": "Campus Biomedical University of Rome"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "sports medicine"
+  },
   {
     "rel_doi": "10.1101/2023.03.13.532446",
     "rel_title": "Murine Alveolar Macrophages Rapidly Accumulate Intranasally Administered SARS-CoV-2 Spike Protein leading to Neutrophil Recruitment and Damage",
@@ -97667,49 +97116,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "respiratory medicine"
   },
-  {
-    "rel_doi": "10.1101/2023.03.09.531948",
-    "rel_title": "Impaired potency of neutralizing antibodies against cell-cell fusion mediated by SARS-CoV-2",
-    "rel_date": "2023-03-10",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.09.531948",
-    "rel_abs": "The SARS-CoV-2 Omicron subvariants have dominated the pandemic due to their high transmissibility and immune evasion conferred by the spike mutations. The Omicron subvariants can spread by cell-free virus infection and cell-cell fusion, the latter of which is more effective but has not been extensively investigated. In this study, we developed a simple and high-throughput assay that provides a rapid readout to quantify cell-cell fusion mediated by the SARS-CoV-2 spike proteins without using live or pseudotyped virus. This assay can be used to identify variants of concern and to screen for prophylactic and therapeutic agents. We further evaluated a panel of monoclonal antibodies (mAbs) and vaccinee sera against D614G and Omicron subvariants, finding that cell-cell fusion is substantially more resistant to mAb and serum inhibition than cell-free virus infection. Such results have important implications for the development of vaccines and antiviral antibody drugs against cell-cell fusion induced by SARS-CoV-2 spikes.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Qian Wang",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Andre Yanchen Yeh",
-        "author_inst": "School of Medicine, National Taiwan University"
-      },
-      {
-        "author_name": "Yicheng Guo",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Hiroshi Mohri",
-        "author_inst": "Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Jian Yu",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "David D Ho",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Lihong Liu",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2023.03.09.531961",
     "rel_title": "SARS-CoV-2 protein structure and sequence mutations: evolutionary analysis and effects on virus variants SARS-CoV-2 protein structure and sequence mutations:",
@@ -98080,6 +97486,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2023.03.09.23287034",
+    "rel_title": "Real-world effectiveness of sotrovimab for the treatment of SARS-CoV-2 infection during Omicron BA.2 subvariant predominance: a systematic literature review",
+    "rel_date": "2023-03-10",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.09.23287034",
+    "rel_abs": "PurposeEmerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have impacted the in vitro activity of sotrovimab 500 mg, with reduced fold change in EC50 for the Omicron BA.2 sublineage and onward. The correlation between this reduction and clinical efficacy outcomes is unknown. In the absence of clinical trials assessing the efficacy of sotrovimab against emerging variants, real-world evidence becomes a critical source of information. A systematic literature review (SLR) of published observational studies was undertaken to evaluate the effectiveness of sotrovimab on severe clinical outcomes during the Omicron BA.2 subvariant predominance period.\n\nMethodsSearches of indexed electronic databases for peer-reviewed journals, preprint articles, and conference abstracts published between January 1, 2022 and November 3, 2022 were undertaken using a combination of search terms for COVID-19, sotrovimab, and observational study design. Study quality was assessed using the Newcastle Ottawa Scale (NOS).\n\nResultsFrom the 343 unique titles and abstracts identified, five studies were eligible for inclusion in the SLR. Included studies displayed heterogeneity in study design and population. The OpenSAFELY study, which received a high NOS score and had a sufficient sample of patients treated with sotrovimab during BA.2 predominance, demonstrated clinical effectiveness during both BA.1 (adjusted hazard ratio (HR) 0.54, 95% confidence interval (CI) 0.33-0.88; p = 0.014) and BA.2 (adjusted HR 0.44, 95% CI 0.27-0.71; p = 0.001) periods vs molnupiravir. Furthermore, a US-based study that also received a high NOS score reported that sotrovimab was associated with a lower risk of 30-day all-cause hospitalization or mortality compared with no monoclonal antibody treatment during the BA.2 subvariant surge in March (adjusted relative risk (RR) 0.41, 95% CI 0.27-0.62) and April 2022 (adjusted RR 0.54, 95% CI 0.08-3.54). Although only a limited number of studies evaluated sotrovimab during both the BA.1 and BA.2 periods, these demonstrated that clinical outcomes in patients with COVID-19 treated with sotrovimab were consistently low across both periods. One large study directly compared data from the two periods and found no evidence of a difference in the clinical outcomes of sotrovimab-treated patients with sequencing-confirmed BA.1 and BA.2 (HR 1.17, 95% CI 0.74-1.86).\n\nConclusionThe observational data presented in this SLR provide evidence that the effectiveness of sotrovimab (IV 500 mg) is maintained against Omicron BA.2 in both ecological and sequencing-confirmed studies, either through the demonstration of low and comparable rates of severe clinical outcomes between the Omicron BA.1 and BA.2 periods, or by comparison against an active comparator or no treatment within the Omicron BA.2 period.\n\nKey pointsO_ST_ABSWhy carry out this study?C_ST_ABSO_LIEmerging SARS-CoV-2 variants have impacted the in vitro activity of sotrovimab 500 mg, with reduced fold change in EC50 relative to wild-type for the Omicron BA.2 sublineage and onward; the clinical relevance of this difference on outcomes for BA.2 (and other variants) is unknown.\nC_LIO_LIGiven the complexity of generating formal clinical trial data in the context of the constantly evolving SARS-CoV-2 landscape, real-world evidence is a key source of information with which to assess the effectiveness of treatments such as sotrovimab on newly predominant or emerging variants.\nC_LIO_LIWe conducted a systematic literature review to evaluate the effectiveness of sotrovimab for the early treatment of COVID-19 on clinical outcomes during the period predominated by the Omicron BA.2 subvariant.\nC_LI\n\nWhat was learned from the study?O_LISotrovimab treatment was associated with low proportions of severe clinical outcomes (such as all-cause or COVID-19-related hospitalization or mortality) in patients infected during periods of Omicron BA.2 predominance, despite reduction in the in vitro neutralization activity of sotrovimab.\nC_LIO_LIThese data support continued clinical effectiveness of sotrovimab during Omicron BA.2 predominance.\nC_LI",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Myriam Drysdale",
+        "author_inst": "Value Evidence and Outcomes, GSK, Middlesex, UK"
+      },
+      {
+        "author_name": "Daniel C. Gibbons",
+        "author_inst": "Value Evidence and Outcomes, GSK, Middlesex, UK"
+      },
+      {
+        "author_name": "Moushmi Singh",
+        "author_inst": "Value Evidence and Outcomes, GSK, Middlesex, UK"
+      },
+      {
+        "author_name": "Catherine Rolland",
+        "author_inst": "Evidence Synthesis, Modelling and Communications, PPD Evidera, London, UK"
+      },
+      {
+        "author_name": "Louis Lavoie",
+        "author_inst": "Evidence Synthesis, Modelling and Communications, PPD Evidera, Montreal, Canada"
+      },
+      {
+        "author_name": "Andrew Skingsley",
+        "author_inst": "Clinical Research and Development, GSK, Middlesex, UK"
+      },
+      {
+        "author_name": "Emily J. Lloyd",
+        "author_inst": "Clinical Research and Development, GSK, Middlesex, UK"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2023.03.08.23286979",
     "rel_title": "Prevalence of IgG and IgM to SARS-CoV-2 and other human coronaviruses in The Democratic Republic of Congo, Sierra Leone and Uganda: A Longitudinal Study",
@@ -99501,61 +98950,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2023.03.07.23286963",
-    "rel_title": "Myocardial Infarction across COVID-19 Pandemic Phases: Insights from the Veterans Health Affairs System",
-    "rel_date": "2023-03-08",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.07.23286963",
-    "rel_abs": "BackgroundCardiovascular procedural treatments were deferred at scale during the COVID-19 pandemic, with unclear impact on patients presenting with Non-ST Elevation Myocardial Infarction (NSTEMI).\n\nMethodsIn a retrospective cohort study of all patients diagnosed with NSTEMI in the U.S. Veterans Affairs Healthcare System from 1/1/19 to 10/30/22 (n=67,125), procedural treatments and outcomes were compared between the pre-pandemic period and six unique pandemic phases (1: Acute phase, 2: Community spread, 3: First Peak, 4: Post-Vaccine, 5. Second Peak, 6. Recovery). Multivariable regression analysis was performed to assess association between pandemic phases and 30-day mortality.\n\nResultsNSTEMI volumes dropped significantly with the pandemic onset (62.7% of pre-pandemic peak) and did not revert to pre-pandemic levels in subsequent phases, even after vaccine availability. Percutaneous coronary intervention (PCI) and/or coronary artery bypass grafting (CABG) volumes declined proportionally. Compared to the pre-pandemic period, NSTEMI patients experienced higher 30-day mortality during Phase 2 and 3, even after adjustment for COVID-19 positive status, demographics, baseline comorbidities, and receipt of procedural treatment (adjusted OR for Phase 2-3 combined: 1.26 [95% CI 1.13-1.43], p<0.01). Patients receiving VA-paid community care had a higher adjusted risk of 30-day mortality compared to those at VA hospitals across all six pandemic phases.\n\nConclusionsHigher mortality after NSTEMI occurred during the initial spread and first peak of the pandemic, but resolved before the second, higher peak - suggesting effective adaptation of care delivery but a costly delay to implementation. Investigation into the vulnerabilities of the early pandemic spread are vital to informing future resource-constrained practices.\n\nClinical PerspectiveO_ST_ABSWhat is New?C_ST_ABSO_LIAfter the initial significant decline in NSTEMI presentations during the acute phase of the pandemic, volumes of NSTEMI presentations and procedural treatment have not reverted to pre-pandemic levels despite widespread availability of vaccines in the Veterans Health Administration.\nC_LIO_LICompared to the pre-pandemic period, 30-day mortality after NSTEMI increased during the initial spread and first pandemic peak (Phases 2 and 3) -- but resolved before the subsequent highest pandemic peak of Phase 5 -- suggesting a delay to implementation of adapted systems of cardiovascular care.\nC_LIO_LIThe increased mortality was not significantly mediated by the decline in procedural volumes, suggesting appropriate triage of procedural care during the pandemic.\nC_LI\n\nWhat are the Clinical Implications?O_LIThe COVID-19 pandemic appears to have had a lasting impact on health-seeking behaviors among NSTEMI patients, with unclear long-term effects of this increased threshold to obtain cardiovascular care.\nC_LIO_LIInvestigation into the vulnerabilities that occurred during initial phases of the pandemic are urgently needed to inform ongoing and future resource-constrained practices.\nC_LI",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Celina Mei Yong",
-        "author_inst": "Stanford University and Palo Alto Veterans Health Administration"
-      },
-      {
-        "author_name": "Laura Ansley Graham",
-        "author_inst": "VA Palo Alto Health Care System"
-      },
-      {
-        "author_name": "Tariku Beyene",
-        "author_inst": "VA Palo Alto Healthcare System"
-      },
-      {
-        "author_name": "Shirin Sadri",
-        "author_inst": "Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Juliette Hong",
-        "author_inst": "VA Palo Alto Healthcare System"
-      },
-      {
-        "author_name": "Thomas Allen Burdon",
-        "author_inst": "VA Palo Alto Healthcare System"
-      },
-      {
-        "author_name": "William F. F. Fearon",
-        "author_inst": "Stanford University Medical Center"
-      },
-      {
-        "author_name": "Steven M. Asch",
-        "author_inst": "VA Palo Alto Health Care System and Stanford University"
-      },
-      {
-        "author_name": "Mintu P Turakhia",
-        "author_inst": "VA Palo Alto Health Care System; Stanford University Department of Medicine; Center for Digital Health Stanford University"
-      },
-      {
-        "author_name": "Paul Heidenreich",
-        "author_inst": "VA Palo Alto Health Care System"
-      }
-    ],
-    "version": "1",
-    "license": "cc0",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "cardiovascular medicine"
-  },
   {
     "rel_doi": "10.1101/2023.03.07.23286949",
     "rel_title": "The external validity of machine learning-based prediction scores from hematological parameters of COVID-19: A study using hospital records from Brazil, Italy, and Western Europe",
@@ -99890,6 +99284,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2023.03.06.531252",
+    "rel_title": "Unraveling the Interactions between Human DPP4 Receptor, SARS-CoV-2 Variants, and MERS-CoV, converged for Pulmonary Disorders Integrating through Immunoinformatics and Molecular Dynamics",
+    "rel_date": "2023-03-07",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.06.531252",
+    "rel_abs": "Human coronaviruses like MERS CoV are known to utilize dipeptidyl peptidase 4 (DPP4), apart from angiotensin-converting enzyme 2(ACE2) as potential co-receptor for viral cell entry. DPP4, ubiquitous membrane-bound aminopeptidase is closely associated with elevation of disease severity in comorbidities. In SARS-CoV-2, there is inadequate evidence for combination of spike protein variants with DPP4, and underlying adversity in COVID19. To elucidate this mechanistic basis, we have investigated interaction of spike protein variants with DPP4 through molecular docking and simulation studies. The possible binding interactions between receptor binding domain (RBD) of different spike variants of SARS-CoV-2 and DPP4 have been compared with interactions observed in experimentally determined structure of complex of MERS-CoV with DPP4. Comparative binding affinity confers that Delta-CoV-2:DPP4 shows close proximity with MERS-CoV:DPP4, as depicted from accessible surface area, radius of gyration, number of hydrogen bonding and energy of interactions. Mutation in delta variant, L452R and T478K, directly participate in DPP4 interaction enhancing DPP4 binding. E484K in alpha and gamma variant of spike protein is also found to interact with DPP4. Hence, DPP4 interaction with spike protein gets more suitable due to mutation especially due to L452R, T478K and E484K. Furthermore, perturbation in the nearby residues Y495, Q474 and Y489 is evident due to L452R, T478K and E484K respectively. Virulent strains of spike protein are more susceptible to DPP4 interaction and are prone to be victimized in patients due to comorbidities. Our results will aid the rational optimization of DPP4 as a potential therapeutic target to manage COVID-19 disease severity.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Aayatti Mallick Gupta",
+        "author_inst": "S N Bose National Centre for Basic Sciences"
+      },
+      {
+        "author_name": "Pongali B Raghavendra",
+        "author_inst": "National Institute of Biomedical Genomics"
+      },
+      {
+        "author_name": "Arpan Narayan Roy",
+        "author_inst": "National Institute of Biomedical Genomics"
+      },
+      {
+        "author_name": "Deboshmita Banerjee",
+        "author_inst": "National Institute of Biomedical Genomics"
+      },
+      {
+        "author_name": "Jaydeb Chakrabarti",
+        "author_inst": "S N Bose National Centre for Basic Sciences"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "bioinformatics"
+  },
   {
     "rel_doi": "10.1101/2023.03.06.531431",
     "rel_title": "Genome-scale CRISPR-Cas9 screen identifies novel host factors as potential therapeutic targets for SARS-CoV-2 infection.",
@@ -101235,61 +100664,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2023.03.03.23286745",
-    "rel_title": "Decline in prevalence of tuberculosis following an intensive case-finding campaign and the COVID-19 pandemic in an urban Ugandan community",
-    "rel_date": "2023-03-05",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.03.23286745",
-    "rel_abs": "BackgroundSystematic screening is a potential tool for reducing the prevalence of tuberculosis and counteracting COVID-related disruptions in care. Repeated community-wide screening can also measure changes in the prevalence of tuberculosis over time.\n\nMethodsWe conducted serial, cross-sectional tuberculosis case-finding campaigns in one community in Kampala, Uganda, in 2019 and 2021. Both campaigns sought sputum for tuberculosis testing (Xpert MTB/RIF Ultra) from all adolescents and adults. We estimated the prevalence of tuberculosis among screening participants in each campaign and compared characteristics of people with tuberculosis across campaigns. We simultaneously enrolled and characterized community residents who were diagnosed with tuberculosis through routine care and assessed trends in facility-based diagnosis.\n\nResultsWe successfully screened 12,033 community residents (35% of the estimated adult/adolescent population) in 2019 and 11,595 (33%) in 2021. In 2019, 0.94% (95% CI 0.77-1.13%) of participants tested Xpert-positive (including trace). This proportion fell to 0.52% (95%CI 0.40-0.67%) in 2021; the prevalence ratio was 0.55 [95%CI: 0.40-0.75]). There was no change in the age (median 26 vs 26), sex (56% vs 59% female), or prevalence of chronic cough (49% vs 54%) among those testing positive. By contrast, the rate of routine facility-based diagnosis remained steady in the eight months before each campaign (210 [95%CI 155-279] vs. 240 [95%CI 181-312] per 100,000 per year).\n\nConclusionsFollowing an intensive initial case-finding campaign in an urban Ugandan community in 2019, the burden of prevalent tuberculosis as measured by systematic screening had decreased by 45% in 2021, despite the intervening COVID-19 pandemic.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Emily A Kendall",
-        "author_inst": "Johns Hopkins University School of Medicine, Baltimore, MD, USA"
-      },
-      {
-        "author_name": "Peter James Kitonsa",
-        "author_inst": "Makerere University College of Health Sciences, Kampala, Uganda"
-      },
-      {
-        "author_name": "Annet Nalutaaya",
-        "author_inst": "Uganda Tuberculosis Implementation Research Consortium, Walimu, Kampala, Uganda"
-      },
-      {
-        "author_name": "Katherine O Robsky",
-        "author_inst": "Georgetown University, Washington, DC, USA"
-      },
-      {
-        "author_name": "Kamoga Caleb Erisa",
-        "author_inst": "Uganda Tuberculosis Implementation Research Consortium, Walimu, Kampala, Uganda"
-      },
-      {
-        "author_name": "James Mukiibi",
-        "author_inst": "Uganda Tuberculosis Implementation Research Consortium, Walimu, Kampala, Uganda"
-      },
-      {
-        "author_name": "Adithya Cattamanchi",
-        "author_inst": "University of California Irvine, CA, USA"
-      },
-      {
-        "author_name": "Midori Kato-Maeda",
-        "author_inst": "University of California San Francisco, CA, USA"
-      },
-      {
-        "author_name": "Achilles Katamba",
-        "author_inst": "Makerere University College of Health Sciences, Kampala, Uganda"
-      },
-      {
-        "author_name": "David W Dowdy",
-        "author_inst": "Johns Hopkins University Bloomberg School of Public Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2023.03.03.23286750",
     "rel_title": "Detection of SARS-CoV-2 in Schools Using Built Environment Testing in Ottawa, Canada: A Multi-Facility Prospective Surveillance Study",
@@ -101708,6 +101082,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2023.03.02.23286686",
+    "rel_title": "Impact of COVID-19 pandemic on the etiology and characteristics of community-acquired pneumonia among children requiring bronchoalveolar lavage in northern China",
+    "rel_date": "2023-03-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.02.23286686",
+    "rel_abs": "BackgroundTo investigate the etiology and clinical characteristics of community-acquired pneumonia (CAP) among children requiring bronchoalveolar lavage (BAL) and analyze the impact of the coronavirus disease 2019 (COVID-19) pandemic on the pathogen spectrum and clinical manifestations.\n\nMethodsChildren <14 years old hospitalized with CAP requiring BLA were enrolled between February 2019 to January 2020 and August 2021 to July 2022. Multiplex reverse transcription polymerase chain reaction (mRT-PCR) was used for pathogen detection. The demographic and clinical characteristics were compared between different pathogen-type infection groups, and before and during the COVID-19 pandemic.\n\nResultsPathogen was detected in 91.66% (1363/1487) children. Mycoplasma pneumoniae, adenovirus and human rhinovirus were the most frequently detected pathogens. The frequency of detection of virus infections and co-infections was decreased during the pandemic, but the detection of atypical bacterial infections was increased. The clinical manifestations and the results of CT scans and fiberoptic bronchoscopy showed a significant difference between different types of pathogen infection, and lung inflammation was reduced during the COVID-19 pandemic compared with before the pandemic.\n\nConclusionsM. pneumoniae infection might be the greatest pediatric disease burden leading to CAP in northern China. Wearing masks and social distancing in public places during the COVID-19 pandemic effectively reduced the transmission of respiratory viruses, but it did not reduce the infection rate of M. pneumoniae. In addition, these interventions significantly reduced lung inflammation in children compared with before the pandemic.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Ruihan Liu",
+        "author_inst": "Affiliated Hospital of Jining Medical University"
+      },
+      {
+        "author_name": "Yuyan Zhang",
+        "author_inst": "Affiliated Hospital of Jining Medical University"
+      },
+      {
+        "author_name": "Zhouhua Lu",
+        "author_inst": "Affiliated Hospital of Jining Medical University"
+      },
+      {
+        "author_name": "Changqing Shen",
+        "author_inst": "Affiliated Hospital of Jining Medical University"
+      },
+      {
+        "author_name": "Jin Wang",
+        "author_inst": "Affiliated Hospital of Jining Medical University"
+      },
+      {
+        "author_name": "Qing Zhao",
+        "author_inst": "Affiliated Hospital of Jining Medical University"
+      },
+      {
+        "author_name": "Tongshu Hou",
+        "author_inst": "Binzhou Medical University - Yantai Campus"
+      },
+      {
+        "author_name": "Fenghai Niu",
+        "author_inst": "Affiliated Hospital of Jining Medical University"
+      },
+      {
+        "author_name": "Qingxia Kong",
+        "author_inst": "Affiliated Hospital of Jining Medical University"
+      },
+      {
+        "author_name": "Jun Ning",
+        "author_inst": "Affiliated Hospital of Jining Medical University"
+      },
+      {
+        "author_name": "Lei Yang",
+        "author_inst": "Affiliated Hospital of Jining Medical University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "pediatrics"
+  },
   {
     "rel_doi": "10.1101/2023.02.28.23286595",
     "rel_title": "SARS-CoV-2 post-vaccine surveillance studies in Australian children and adults with cancer: SerOzNET Quality of Life, Toxicity and Vaccine Beliefs Substudy Statistical Analysis Plan",
@@ -102937,129 +102370,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2023.02.28.23286559",
-    "rel_title": "Elevated symptoms of depression and anxiety among family members and friends of critically ill COVID-19 patients - An observational study of five cohorts across four countries",
-    "rel_date": "2023-03-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.28.23286559",
-    "rel_abs": "BackgroundLittle is known regarding the mental health impact of having a significant person (family member and/or close friend) with COVID-19 of different severity.\n\nMethodsThe study included five prospective cohorts from four countries (Iceland, Norway, Sweden, and the UK) with self-reported data on COVID-19 and symptoms of depression and anxiety during March 2020-March 2022. We calculated the prevalence ratio (PR) of depression and anxiety in relation to having a significant person with COVID-19 and performed a longitudinal analysis in the Swedish cohort to describe the temporal patterns of the results.\n\nResults162,237 and 168,783 individuals were included in the analysis of depression and anxiety, respectively, of whom 24,718 and 27,003 reported a significant person with COVID-19. Overall, the PR was 1.07 (95% CI: 1.05-1.10) for depression and 1.08 (95% CI: 1.03-1.13) for anxiety among significant others of COVID-19 patients. The respective PRs for depression and anxiety were 1.04 (95% CI: 1.01-1.07) and 1.03 (95% CI: 0.98-1.07) if the significant person was never hospitalized, 1.15 (95% CI: 1.08-1.23) and 1.24 (95% CI: 1.14-1.34) if the patient was hospitalized, 1.42 (95% CI: 1.27-1.57) and 1.45 (95% CI: 1.31-1.60) if admitted to the ICU, and 1.34 (95% CI: 1.22-1.46) and 1.36 (95% CI: 1.22-1.51) if the significant person died. Individuals of hospitalized, ICU admitted, or deceased patients showed higher prevalence of depression and anxiety during the entire 12 months after the COVID-19 diagnosis of the significant person.\n\nConclusionsClose friends and family members of critically ill COVID-19 patients show elevated prevalence of depression and anxiety throughout the first year after the diagnosis.",
-    "rel_num_authors": 27,
-    "rel_authors": [
-      {
-        "author_name": "Anik\u00f3 Lovik",
-        "author_inst": "Karolinska Institutet and Leiden University"
-      },
-      {
-        "author_name": "Juan Gonz\u00e1lez-Hij\u00f3n",
-        "author_inst": "Karolinska Institutet"
-      },
-      {
-        "author_name": "Asle Hoffart",
-        "author_inst": "University of Oslo"
-      },
-      {
-        "author_name": "Chloe Fawns-Ritchie",
-        "author_inst": "University of Edinburgh"
-      },
-      {
-        "author_name": "Ingibj\u00f6rg Magn\u00fasd\u00f3ttir",
-        "author_inst": "University of Iceland"
-      },
-      {
-        "author_name": "Li Lu",
-        "author_inst": "University of Oslo"
-      },
-      {
-        "author_name": "Anna B\u00e1ra Unnarsd\u00f3ttir",
-        "author_inst": "University of Iceland"
-      },
-      {
-        "author_name": "Anna K. K\u00e4hler",
-        "author_inst": "Karolinska Institutet"
-      },
-      {
-        "author_name": "Archie Campbell",
-        "author_inst": "University of Edinburgh"
-      },
-      {
-        "author_name": "Arna Hauksd\u00f3ttir",
-        "author_inst": "University of Iceland"
-      },
-      {
-        "author_name": "Charilaos Chourpiliadis",
-        "author_inst": "Karolinska Institutet"
-      },
-      {
-        "author_name": "Daniel L McCartney",
-        "author_inst": "University of Edinburgh"
-      },
-      {
-        "author_name": "Edda Bj\u00f6rk Thordard\u00f3ttir",
-        "author_inst": "University of Iceland"
-      },
-      {
-        "author_name": "Emily E. Joyce",
-        "author_inst": "Karolinska Institutet"
-      },
-      {
-        "author_name": "Emma M. Frans",
-        "author_inst": "Karolinska Institutet"
-      },
-      {
-        "author_name": "J\u00f3hanna Jakobsd\u00f3ttir",
-        "author_inst": "University of Iceland"
-      },
-      {
-        "author_name": "Lill Trogstad",
-        "author_inst": "Norwegian Institute of Public Health"
-      },
-      {
-        "author_name": "Ole A. Andreassen",
-        "author_inst": "University of Oslo"
-      },
-      {
-        "author_name": "Per Magnus",
-        "author_inst": "Norwegian Institute of Public Health"
-      },
-      {
-        "author_name": "Sverre Urnes Johnson",
-        "author_inst": "University of Oslo"
-      },
-      {
-        "author_name": "Patrick F. Sullivan",
-        "author_inst": "Karolinska Institutet"
-      },
-      {
-        "author_name": "Thor Aspelund",
-        "author_inst": "University of Iceland"
-      },
-      {
-        "author_name": "David J. Porteous",
-        "author_inst": "University of Edinburgh"
-      },
-      {
-        "author_name": "Helga Ask",
-        "author_inst": "University of Oslo"
-      },
-      {
-        "author_name": "Omid V. Ebrahimi",
-        "author_inst": "University of Oslo"
-      },
-      {
-        "author_name": "Unnur Anna Valdimarsd\u00f3ttir",
-        "author_inst": "Karolinska Institutet"
-      },
-      {
-        "author_name": "Fang Fang",
-        "author_inst": "Karolinska Institutet"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2023.02.27.530232",
     "rel_title": "SARS-CoV-2 ORF3c suppresses immune activation by inhibiting innate sensing",
@@ -103450,6 +102760,49 @@
     "type": "new results",
     "category": "biophysics"
   },
+  {
+    "rel_doi": "10.1101/2023.02.26.23286261",
+    "rel_title": "SARS-CoV-2 post-vaccine surveillance studies in Australian children and adults with cancer: SerOzNET Statistical Analysis Plan",
+    "rel_date": "2023-03-01",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.26.23286261",
+    "rel_abs": "COVID-19 disease is associated with higher morbidity and mortality in cancer patients. Our study aimed to characterize the optimal strategy to improve vaccine induced protection against COVID-19 in children and adolescents with cancer. Results from The SerOzNET study will contribute comprehensive data on serology, cellular immune correlates from functional T-cell assays, quality of life data, and associated toxicity in relation to COVID-19 vaccination in children and adults with cancer.\n\nIn this plan, we describe the statistics that will be used to report results of the SerOzNET study. SerOzNET examines COVID-19 vaccine response in children and adolescents with cancer.\n\nWe have no conflicts of interest to disclose.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Amy Louise Body",
+        "author_inst": "Monash University, Victoria, Australia"
+      },
+      {
+        "author_name": "Catherine Martin",
+        "author_inst": "Monash University, Victoria, Australia"
+      },
+      {
+        "author_name": "Lucy Busija",
+        "author_inst": "Monash University, Victoria, Australia"
+      },
+      {
+        "author_name": "Luxi Lal",
+        "author_inst": "Monash Health & Monash University, Victoria, Australia"
+      },
+      {
+        "author_name": "Elizabeth S Ahern",
+        "author_inst": "Monash Health/Monash University"
+      },
+      {
+        "author_name": "Raina C MacIntyre",
+        "author_inst": "The Kirby Institute @ The University of New South Wales, Australia"
+      },
+      {
+        "author_name": "Eva Segelov",
+        "author_inst": "University of Bern, Switzerland and Monash University, Victoria, Australia"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "oncology"
+  },
   {
     "rel_doi": "10.1101/2023.02.28.23286466",
     "rel_title": "COVID-19 or seasonal influenza? How to distinguish in people younger than 65 years old: A retrospective observational cohort study comparing the 2009 pandemic influenza A H1N1 with 2022 SARS-CoV-2 Omicron BA.2 outbreaks in China.",
@@ -104831,97 +104184,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2023.02.21.23286222",
-    "rel_title": "Genomic surveillance reveals early detection and transition of Delta to Omicron Lineages of SARS-CoV-2 Variants in wastewater treatment plants of Pune, India",
-    "rel_date": "2023-02-24",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.21.23286222",
-    "rel_abs": "The COVID-19 pandemic has emphasized the urgency for rapid public health surveillance methods in early detection and monitoring of the transmission of infectious diseases. The wastewater-based epidemiology (WBE) has emerged as a promising tool to analyze and enumerate the prevalence of infectious pathogens in a population ahead of time. In the present study, real time quantitative polymerase chain reaction (RT-qPCR) and Illumina sequencing was performed to determine the SARS-CoV-2 load trend and dynamics of variants over a longitudinal scale in 442 wastewater (WW) samples collected from 10 sewage treatment plants (STPs) of Pune city, India, during November 2021 to April-2022. In total 426 distinct lineages representing 17 highly transmissible variants of SARS-CoV-2 were identified. The SARS-CoV-2 Omicron variant fragments were detected in WW samples prior to its detection in clinical cases. Moreover, highly contagious sub-lineages of Omicron, such as BA.2.12 (0.8-0.25%), BA.2.38 (0.8-1.0%), BA.2.75 (0.01-0.02%), BA.3 (0.09-6.3%), BA.4 (0.24-0.29%), and XBB (0.01-13.7%) fragments were significantly detected. The longitudinal analysis also suggested the presence of the BA.5 lineage in November 2021, which was not reported in the clinical settings throughout the duration of this study, indicative of silent variant persistence. Overall, the present study demonstrated the practicality of WBE in early detection of SARS CoV-2 variants, which could be useful in tracking future outbreaks of SARS-CoV-2. Such approaches could be implicated in the monitoring of the infectious agents before they appear in clinical cases.\n\nHighlights{square} Omicron fragments were detected in the sewershed samples prior to clinical samples.\n{square}Omicron sub-lineages BA.2.12, BA.2.38, BA.2.75, BA.3, BA.4, and XBB were prevalent.\n{square}Lineage composition analysis indicated transition from Delta to Omicron variant indicated cause of third wave in India.\n{square}Overall, 426 lineages of 17 highly transmissible variants of SARS-CoV-2 were detected in the study.",
-    "rel_num_authors": 19,
-    "rel_authors": [
-      {
-        "author_name": "Vinay Rajput",
-        "author_inst": "CSIR-National Chemical Laboratory"
-      },
-      {
-        "author_name": "Rinka Pramanik",
-        "author_inst": "CSIR-National Chemical Laboratory"
-      },
-      {
-        "author_name": "Vinita Malik",
-        "author_inst": "CSIR-National Chemical Laboratory"
-      },
-      {
-        "author_name": "RakeshKumar Yadav",
-        "author_inst": "CSIR-National Chemical Laboratory"
-      },
-      {
-        "author_name": "Pradnya Kadam",
-        "author_inst": "Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 41108, Maharashtra, India"
-      },
-      {
-        "author_name": "Unnati Bhalerao",
-        "author_inst": "Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 41108, Maharashtra, India"
-      },
-      {
-        "author_name": "Manisha Tupekar",
-        "author_inst": "Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 41108, Maharashtra, India"
-      },
-      {
-        "author_name": "Dipti Deshpande",
-        "author_inst": "Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 41108, Maharashtra, India"
-      },
-      {
-        "author_name": "Priyanki Shah",
-        "author_inst": "The Pune Knowledge Cluster (PKC), Savitribai Phule Pune University (SPPU), Pune, Maharashtra, India"
-      },
-      {
-        "author_name": "LS Shashidhara",
-        "author_inst": "Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 41108, Maharashtra, India | The Pune Knowledge Cluster (PKC), Savitribai"
-      },
-      {
-        "author_name": "Radhika Boargaonkar",
-        "author_inst": "Ecosan Services Foundation (ESF), Pune 411030, Maharashtra,  India"
-      },
-      {
-        "author_name": "Dhawal Patil",
-        "author_inst": "Ecosan Services Foundation (ESF), Pune 411030, Maharashtra,  India"
-      },
-      {
-        "author_name": "Saurabh Kale",
-        "author_inst": "Ecosan Services Foundation (ESF), Pune 411030, Maharashtra,  India"
-      },
-      {
-        "author_name": "Asim Bhalerao",
-        "author_inst": "Fluid Robotics Private Limited (FRPL), Pune 411052, Maharashtra,  India"
-      },
-      {
-        "author_name": "Nidhi Jain",
-        "author_inst": "Fluid Robotics Private Limited (FRPL), Pune 411052, Maharashtra,  India"
-      },
-      {
-        "author_name": "Sanjay Kamble",
-        "author_inst": "Chemical Engineering and Process Development Division, CSIR-National Chemical Laboratory, Pune 411008, Maharashtra, India"
-      },
-      {
-        "author_name": "Syed Dastager",
-        "author_inst": "CSIR-National Chemical Laboratory"
-      },
-      {
-        "author_name": "Krishanpal Karmodiya",
-        "author_inst": "Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 41108, Maharashtra, India"
-      },
-      {
-        "author_name": "mahesh dharne",
-        "author_inst": "CSIR-National Chemical Laboratory"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2023.02.21.23286228",
     "rel_title": "Real-time forecasting of COVID-19-related hospital strain in France using a non-Markovian mechanistic model",
@@ -105228,6 +104490,109 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2023.02.16.23286009",
+    "rel_title": "Vaccine-induced correlate of protection against fatal COVID-19 in the old and frail during waves of neutralization resistant variants of concern.",
+    "rel_date": "2023-02-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.16.23286009",
+    "rel_abs": "BackgroundTo inform future preventive measures including repeated vaccinations, we have searched for a clinically useful immune correlate of protection against fatal Covid-19 among nursing homes residents.\n\nMethodsWe performed repeated capillary blood sampling with analysis of S-binding IgG in an open cohort study with inclusion of nursing home residents in Sweden. We analyzed immunological and registry data collected from September 2021 with end of follow-up 31 August 2022. The study period included implementation of the 3rd and 4th mRNA monovalent vaccine doses and Omicron virus waves.\n\nFindingsA total of 3012 nursing home residents with median age 86 were enrolled. The 3rd mRNA dose elicited a 99-fold relative increase of S-binding IgG among 2606 blood-sampled individuals and corresponding increase of neutralizing antibodies. The 4th mRNA vaccine dose boosted the levels 3.8-fold. Half-life of S-binding IgG was 72 days. A total 528 residents acquired their first SARS-CoV-2 infection after the 3rd or the 4th vaccine dose and the 30-day mortality was 9.1%. We found no indication that levels of vaccine-induced antibodies protected against infection with Omicron VOCs. In contrast, the risk of death was inversely correlated to levels of S-directed IgG below the 20th percentile. The risk plateaued at population average above lower 35th percentile of S-binding IgG.\n\nInterpretationIn the absence of neutralizing antibodies that protection from infection, quantification of S-binding IgG post vaccination may be useful to identify the most vulnerable for fatal Covid-19 among the oldest and frailest. This information is of importance for future strategies to protect vulnerable populations against neutralization resistant variants of concern.\n\nFundingSwedish Research Council, SciLife, Knut and Alice Wallenberg Foundation and Vinnova.",
+    "rel_num_authors": 22,
+    "rel_authors": [
+      {
+        "author_name": "Linnea Vikstrom",
+        "author_inst": "Umea University"
+      },
+      {
+        "author_name": "Peter Fjallstrom",
+        "author_inst": "Umea University"
+      },
+      {
+        "author_name": "Young-Dae Gwon",
+        "author_inst": "Umea University"
+      },
+      {
+        "author_name": "Daniel J Sheward",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Julia Wigren-Bystrom",
+        "author_inst": "Umea University"
+      },
+      {
+        "author_name": "Magnus Evander",
+        "author_inst": "Umea University"
+      },
+      {
+        "author_name": "Oscar Bladh",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Micael Widerstroem",
+        "author_inst": "Umea University"
+      },
+      {
+        "author_name": "Christian Molnar",
+        "author_inst": "Familjelakarna"
+      },
+      {
+        "author_name": "Gunlog Rasmussen",
+        "author_inst": "Region Orebro lan"
+      },
+      {
+        "author_name": "Louise Bennet",
+        "author_inst": "Lunds University"
+      },
+      {
+        "author_name": "Mikael Aberg",
+        "author_inst": "Uppsala University"
+      },
+      {
+        "author_name": "Jonas Bjork",
+        "author_inst": "Lund University"
+      },
+      {
+        "author_name": "Staffan Tevell",
+        "author_inst": "Region Varmland"
+      },
+      {
+        "author_name": "Charlotte Thalin",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Kim Blom",
+        "author_inst": "Swedish Public Health Agency"
+      },
+      {
+        "author_name": "Jonas Klingstrom",
+        "author_inst": "Linkopings University"
+      },
+      {
+        "author_name": "Benjamin Murrell",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Clas Ahlm",
+        "author_inst": "Umea University"
+      },
+      {
+        "author_name": "Johan Normark",
+        "author_inst": "Umea University"
+      },
+      {
+        "author_name": "Anders F Johansson",
+        "author_inst": "Umea University"
+      },
+      {
+        "author_name": "Mattias Forsell",
+        "author_inst": "Umea University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2023.02.15.23285958",
     "rel_title": "BRIEF COMMUNICATION High level of Anti SARS-Co-V2 RBD Antibody one year post booster vaccine hospital workers in Indonesia; Was second booster needed?",
@@ -106525,281 +105890,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2023.02.22.23286197",
-    "rel_title": "Peruvian National Survey of Mental Health and Service Utilization in the third year of the COVID-19 pandemic: Protocol for a nationally representative multistage survey",
-    "rel_date": "2023-02-23",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.22.23286197",
-    "rel_abs": "BackgroundPeru is the worst affected country by the COVID-19 pandemic showing the world highest mortality rate, thus triggering an increased mental health burden. Nevertheless, there are few population-based epidemiologic surveys of mental disorders in Peru; Therefore, nationally representative research is needed to understand the underlying population-based mental health burden and identify unmet care needs.\n\nObjectiveThe present study aims to estimate the prevalence and patterns of psychiatric disorders, mental health service use, and unmet mental health care needs\n\nMethodsThis cross-sectional study will collect information from a multistage random sample of 19,500 households. A child, an adolescent, an adult, and an older adult will be interviewed in the household. Trained staff will conduct face-to-face diagnostic interviews via the Preschool Age Psychiatric Assessment, the Child and Adolescent Psychiatric Assessment, the WHOs Composite International Diagnostic Interview, and the Alzheimer Disease 8 Scale. In addition, descriptive and inferential analysis for complex sampling will be performed to estimate the prevalence and correlates.\n\nEthics and disseminationIRB will approve the research protocol before the commencement of the study. Only respondents who signed their informed consents or assents will participate in the study; The parent or guardian will sign the consent for the participation of preschool children. The research findings will be disseminated in peer-reviewed publications, scientific reports, and presentations at national, and international meetings. In addition, de-identified data and study results will be posted on the Peruvian National Institute of Mental Health (PNIMH) website to be freely available to policymakers, researchers, and the general public.\n\nStrengths and LimitationsO_LIThis will be the first national survey on mental health and services use with a large probabilistic sample size, allowing to estimate the prevalence of psychiatric disorders and service use for the rural and urban areas of each of the 25 Peruvian regions.\nC_LIO_LIAt the national level, this survey will have enough power to estimate the prevalence of rare psychiatric disorders with a prevalence closest to one percent.\nC_LIO_LIResearchers aim to conduct a second interview among the participants after at least one year of performing the first evaluation to estimate the incidence of psychiatric disorders.\nC_LIO_LIResearchers are advocating among the Peruvian Ministry of Economics and Finance officers to conduct a national survey each year to evaluate the impact of mental health policies via the analysis of trends.\nC_LIO_LIThe principal limitation of this study is its cross-sectional design which does not allow to infer the temporality of associations.\nC_LI",
-    "rel_num_authors": 65,
-    "rel_authors": [
-      {
-        "author_name": "Victor Orlando Cruz",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Andres Pariamachi",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Nataly Napanga",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Brian Pena",
-        "author_inst": "Instituto Nacional de Salud Mental Honorio Delgado Hideyo Noguchi"
-      },
-      {
-        "author_name": "Lisette Gamboa",
-        "author_inst": "Instituto Nacional de Salud Mental Honorio Delgado - Hideyo Noguchi"
-      },
-      {
-        "author_name": "Caroline Gonzales",
-        "author_inst": "Instituto Nacional de Salud Mental Honorio Delgado - Hideyo Noguchi"
-      },
-      {
-        "author_name": "Paula Delgado",
-        "author_inst": "Instituto Nacional de Salud Mental Honorio Delgado - Hideyo Noguchi"
-      },
-      {
-        "author_name": "Paula Alejandra Burela",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Julio Villa-Palomino",
-        "author_inst": "Instituto Nacional de Salud Mental Honorio Delgado Hideyo Noguchi"
-      },
-      {
-        "author_name": "Liz Valentin",
-        "author_inst": "Instituto Nacional de Salud Mental Honorio Delgado Hideyo Noguchi"
-      },
-      {
-        "author_name": "Delia Zuniga",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Orlando Quispe",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Pedro Lopez",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Jessica Alcantara",
-        "author_inst": "Instituto Nacional de Salud Mental Honorio Delgado Hideyo Noguchi"
-      },
-      {
-        "author_name": "Nella Bonilla",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Sandra Anton",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Mirella Gutierrez",
-        "author_inst": "Instituto Nacional de Salud Mental Honorio Delgado Hideyo Noguchi"
-      },
-      {
-        "author_name": "Carlos Diaz",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Juan Claux",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Alberto Gonzales",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Roxana Vivar",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Gloria Lobe",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi"
-      },
-      {
-        "author_name": "Erika Contreras",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Blanca Mahr",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Milagros Pampamallco",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Silvia Salazar",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Merle Santos",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Veronica Valentin",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Jose P Arias",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Militza Alvarez",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Cindy Amaro",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Karla Calderon",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Jose Canchis",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Fanny Carbajal",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Jessica Chire",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Liany Correa",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Linnette Hermoza",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Giannina Moron",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Candy Palomino",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Rocio Ramirez",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Edelmira Rojas",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Mercedes Arevalo",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Cesar Arellano",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Vanessa Herrera",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Janet Ricardi",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Gloria Gupio",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Onesimo Jaramillo",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Carmen Clapes",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Esther Cerna",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Mariluz Antunez",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Fernando Luna",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Alfredo Saavedra",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Sara Carbajal",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Favio Vega",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Paulo Ruiz",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Javier Saavedra",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Elba Luna",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Javier Del-Campo",
-        "author_inst": "Instituto Nacional de Salud Mental \"Honorio Delgado - Hideyo Noguchi\""
-      },
-      {
-        "author_name": "Itziar Familiar-Lopez",
-        "author_inst": "Michigan State University College of Human Medicine"
-      },
-      {
-        "author_name": "Amantia A Ametaj",
-        "author_inst": "Harvard University T H Chan School of Public Health"
-      },
-      {
-        "author_name": "William E Copeland",
-        "author_inst": "Duke University School of Medicine"
-      },
-      {
-        "author_name": "Jim Anthony",
-        "author_inst": "Michigan State University, Epidemiology"
-      },
-      {
-        "author_name": "Raphael Nishimura",
-        "author_inst": "University of Michigan Institute for Social Research, Survey Research Center"
-      },
-      {
-        "author_name": "Henning Tiemeier",
-        "author_inst": "Harvard T.H. Chan School of Public Health"
-      },
-      {
-        "author_name": "Bizu Gelaye",
-        "author_inst": "Harvard T.H. Chan School of Public Health, Department of Epidemiology. Harvard Medical School, Psychiatry"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2023.02.23.23286343",
     "rel_title": "PREVALENCE OF DEPRESSION AND ANXIETY IN COLOMBIA: WHAT HAPPENED DURING COVID-19 PANDEMIC?",
@@ -107038,6 +106128,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2023.02.14.23285860",
+    "rel_title": "REAL-WORLD EFFECTIVENESS OF NIRMATRELVIR/RITONAVIR ON COVID-19-ASSOCIATED HOSPITALIZATION PREVENTION: A POPULATION-BASED COHORT STUDY IN THE PROVINCE OF QUEBEC, CANADA",
+    "rel_date": "2023-02-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.14.23285860",
+    "rel_abs": "IntroductionThe nirmatrelvir/ritonavir (PAXLOVID) is an antiviral blocking the replication of SARS-CoV-2. Early treatment with this antiviral has showed to reduce COVID-19 hospitalization and death in unvaccinated outpatients with mild-to-moderate COVID-19 and high risk of progression to severe disease with variants before Omicron. However, the current epidemiological context and the level of immunity in the population (vaccination and/or natural infection) have evolved considerably since the disclosure of these results. Thus, real-world evidence studies in vaccinated outpatients with lineage and sublineage of the variant are needed.\n\nObjectiveTo assess whether nirmatrelvir/ritonavir treatment reduces the risk of COVID-19-associated hospitalization among Quebec outpatients with mild-to-moderate COVID-19 at high risk of progression to severe disease in a real-world context, regardless of vaccination status and circulating variants, in the province of Quebec.\n\nMethodsThis was a retrospective cohort study of SARS-CoV-2-infected outpatients who received nirmatrelvir/ritonavir between March 15 and August 15, 2022, using data from the Quebec provincial clinico-administrative databases. Outpatients treated with nirmatrelvir/ritonavir were compared to unexposed ones. The treatment group was matched with controls using propensity-score matching in a ratio of 1:1. The outcome was COVID-19-associated hospitalization occurring within 30 days following the index date. Poisson regression with robust error variance was used to estimate the relative risk of hospitalization among the treatment group compared to the control group.\n\nResultsA total of 16,601 and 242,341 outpatients were eligible to be included in the treatment (nirmatrelvir/ritonavir) and control groups respectively. Among treated outpatients, 8,402 were matched to controls. Regardless of vaccination status, nirmatrelvir/ritonavir-treated outpatient status was associated with a 69% reduced relative risk of COVID-19-associated hospitalization (RR: 0.31 [95% CI: 0.28; 0.36]). The effect was more pronounced in outpatients without a complete primary vaccination course (RR: 0.04 [95% CI: 0.03; 0.06]), while treatment with nirmatrelvir/ritonavir was not associated with benefit when outpatients with a complete primary vaccination course were considered (RR: 0.93 [95% CI: 0.78; 1.08]) Subgroups analysis among outpatients with a primary vaccination course showed that nirmatrelvir/ritonavir treatment was associated with a significant decrease in relative risk of hospitalization in severely immunocompromised outpatients (RR: 0.66 [95% CI: 0.50; 0.89]) and in outpatients aged 70 years and older (RR: 0.50 [95% CI: 0.34; 0.74]) when the last dose of the vaccine was received more than six months before.\n\nConclusionsAmong SARS-CoV-2-infected outpatients at high risk for severe COVID-19 during Omicron BA.2 and BA.4/5 surges, treatment with nirmatrelvir/ritonavir was associated with a significant reduced relative risk of COVID-19-associated hospitalization. This effect was observed in outpatients with incomplete primary vaccination course and in outpatients who were severely immunocompromised. Except for severely immunocompromised outpatients, no evidence of benefit was found in any category of outpatient with a complete primary vaccination course whose last dose of COVID-19 vaccine was received within six months.",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Jean Luc Kabor\u00e9",
+        "author_inst": "Institut National d\u00b4Excellence en Sant\u00e9 et Services Sociaux (INESSS) du Qu\u00e9bec, Qu\u00e9bec, Canada"
+      },
+      {
+        "author_name": "Beno\u00eet Laffont",
+        "author_inst": "Institut National d\u00b4Excellence en Sant\u00e9 et Services Sociaux (INESSS) du Qu\u00e9bec, Qu\u00e9bec, Canada"
+      },
+      {
+        "author_name": "Mamadou Diop",
+        "author_inst": "Institut National d\u00b4Excellence en Sant\u00e9 et Services Sociaux (INESSS) du Qu\u00e9bec, Qu\u00e9bec, Canada"
+      },
+      {
+        "author_name": "Melanie R. Tardif",
+        "author_inst": "Institut National d\u00b4Excellence en Sant\u00e9 et Services Sociaux (INESSS) du Qu\u00e9bec, Qu\u00e9bec, Canada"
+      },
+      {
+        "author_name": "Alexis F. Turgeon",
+        "author_inst": "Department of Anesthesiology and Critical Care Medicine, Division of Critical Care Medicine, Universit\u00e9 Laval, Qu\u00e9bec City, Qu\u00e9bec, Canada"
+      },
+      {
+        "author_name": "Jeannot Dumaresq",
+        "author_inst": "Department of microbiology-infectiology and immunology, Faculty of Medicine, Universit\u00e9 Laval, Qu\u00e9bec City, Qu\u00e9bec, Canada"
+      },
+      {
+        "author_name": "Me-Linh Luong",
+        "author_inst": "Department of Medicine, Division of Infectious Diseases, CHUM, Montr\u00e9al, Qu\u00e9bec, Canada"
+      },
+      {
+        "author_name": "Michel Cauchon",
+        "author_inst": "Department of Family Practice and Emergency, Universit\u00e9 Laval, Qu\u00e9bec City, Qu\u00e9bec, Canada"
+      },
+      {
+        "author_name": "Hugo Chapdelaine",
+        "author_inst": "Department of medicine, Research Centre of Centre Hospitalier de l\u00b4Universit\u00e9 de Montr\u00e9al (CRCHUM), Montr\u00e9al, Qu\u00e9bec, Canada"
+      },
+      {
+        "author_name": "David Claveau",
+        "author_inst": "Departments of Emergency Medicine and Critical Care Medicine, Centre hospitalier affili\u00e9 universitaire r\u00e9gional, Trois-Rivi\u00e8res, Qu\u00e9bec, Canada"
+      },
+      {
+        "author_name": "Marc Brosseau",
+        "author_inst": "Department of Medicine, Faculty of Medicine, Universit\u00e9 de Montr\u00e9al, Montr\u00e9al, Qu\u00e9bec, Canada"
+      },
+      {
+        "author_name": "Elie Haddad",
+        "author_inst": "Department of Pediatrics, Universit\u00e9 de Montr\u00e9al, CHU Sainte-Justine, Montr\u00e9al, Qu\u00e9bec, Canada"
+      },
+      {
+        "author_name": "Mike Benigeri",
+        "author_inst": "Institut National d\u00b4Excellence en Sant\u00e9 et Services Sociaux (INESSS) du Qu\u00e9bec, Qu\u00e9bec, Canada"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "pharmacology and therapeutics"
+  },
   {
     "rel_doi": "10.1101/2023.02.19.23285730",
     "rel_title": "Dynamics of Influenza A and SARS-CoV-2 coinfections during the COVID-19 pandemic in India",
@@ -108219,37 +107376,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
-  {
-    "rel_doi": "10.1101/2023.02.13.23285842",
-    "rel_title": "Mortality by cause of death in Brazil: effects of the COVID-19 pandemic and contribution to changes in life expectancy at birth",
-    "rel_date": "2023-02-19",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.13.23285842",
-    "rel_abs": "We investigate the consequences of the COVID-19 pandemic on other underlying causes of death in Brazil in 2020 and 2021. We estimate monthly age-standardized mortality rates for 2010-2021 and decompose those time series into three additive components: trend, seasonality, and remainder. Given the long-term trend and historical seasonal fluctuations, we assume that any impact from the pandemic will be left on the remainder. We also decompose the contributions of COVID-19 deaths (direct effect) and those from other causes (indirect effects) to the annual change in life expectancy at birth (0) from 2017 to 2021. Broadly, the remainder mirrors the trajectory of pandemic waves. The impact of the COVID-19 pandemic on other causes of death was not limited to increases but also decreases. The direct effects of the pandemic reduced 0 by 1.89 years between 2019 and 2020 and 1.77 between 2020 and 2021. Indirect effects increased 0 by 0.44 between 2019 and 2020 and had virtually no impact on 0 between 2020 and 2021. Whether trajectories in mortality rates and annual gains in 0 will quickly return to pre-pandemic levels depends on governmental actions to mitigate the consequences of the COVID-19 pandemic.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Fernando Fernandes",
-        "author_inst": "Demography Department, Cedeplar, Universidade Federal de Minas Gerais, Belo Horizonte"
-      },
-      {
-        "author_name": "C\u00e1ssio M. Turra",
-        "author_inst": "Demography Department, Cedeplar, Universidade Federal de Minas Gerais, Belo Horizonte"
-      },
-      {
-        "author_name": "Giovanny V.A. Fran\u00e7a",
-        "author_inst": "Secretariat of Health Surveillance, Brazilian Ministry of Health"
-      },
-      {
-        "author_name": "Marcia C. Castro",
-        "author_inst": "Department of Global Health and Population, Harvard TH Chan School of Public Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2023.02.14.527605",
     "rel_title": "Protective effect of plasma neutralization from prior SARS-CoV-2 Omicron infection against BA.5 subvariant symptomatic reinfection",
@@ -108588,6 +107714,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2023.02.16.23286061",
+    "rel_title": "How well do we do social distancing?",
+    "rel_date": "2023-02-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.16.23286061",
+    "rel_abs": "During the pandemic of coronavirus disease 2019 (COVID-19), many jurisdictions around the world introduced a  social distance rule under which people are instructed to keep a certain distance from others. Generally, this rule is implemented simply by telling people how many metres or feet of separation should be kept, without giving them precise instructions as to how the specified distance can be measured. Consequently, the rule is effective only to the extent that people are able to gauge this distance through their space perception. To examine the effectiveness of the rule from this point of view, the present study empirically investigated how much distance people would leave from another person when they relied on their perception of this distance. Participants (N = 153) were asked to stand exactly 1.5-m away from a researcher, and resultant interpersonal distances showed that while their mean was close to the correct 1.5-m distance, they exhibited large individual differences. These results suggest that a number of people would not stay sufficiently away from others even when they intend to do proper social distancing. Given this outcome, it is suggested that official health advice include measures that compensate for this tendency.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Naohide Yamamoto",
+        "author_inst": "Queensland University of Technology"
+      },
+      {
+        "author_name": "Mia Nightingale",
+        "author_inst": "Queensland University of Technology"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2023.02.16.23286017",
     "rel_title": "Long-term outdoor air pollution and COVID-19 mortality in London: an individual-level analysis",
@@ -110125,61 +109274,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "intensive care and critical care medicine"
   },
-  {
-    "rel_doi": "10.1101/2023.02.14.23285921",
-    "rel_title": "Optimal Delivery Management for the Prevention of Early Neonatal SARS-CoV-2 Infection: Systematic review and Meta-analysis",
-    "rel_date": "2023-02-15",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.14.23285921",
-    "rel_abs": "ObjectiveReview how specific delivery management interventions (DMI) are associated with early neonatal SARS-CoV-2 infection (ENI) and neonatal death <28 days of life (ND).\n\nDesignSystematic review and meta-analysis of individual patient-specific data from articles published 1 January 2020 - 31 December 2021 from Cochrane review databases, Medline and Google Scholar.\n\nSettingInternational publications specifying DMI, ENI, and ND.\n\nPatientsPregnant women infected with SARS-CoV-2 and their infants\n\nMain outcome measuresArticle inclusion criteria: 1) mothers with SARS-CoV-2 PCR positive status within 10 days before delivery or symptomatic at delivery with a positive test within 48 hours after delivery, 2) delivery method described, 3) infant SARS-CoV-2 PCR result reported. Primary outcomes were 1) ENI confirmed by positive neonatal PCR and 2) ND.\n\nResultsAmong 11,075 screened publications, 117 publications containing data for 244 infants and 230 mothers were included. Maternal and infant characteristics were pooled using DerSimonian-Laird inverse variance method. Primary outcome analyses were completed using logit transformation and random effect. Heterogeneity of included studies was evaluated with I2 statistics.\n\nNo routine care was described so comparison of DMI combinations to routine care was not possible. Sample size for each combination was too small to conduct any valid comparison of different DMI combinations.\n\nConclusionSupport for specific DMI in SARS-CoV-2 infected mothers is lacking. This review highlights the need for rigorous and multinational studies on the guidelines best suited to prevent transmission from mother to neonate.\n\nKEY MESSAGESO_ST_ABSWhat is already known on this topicC_ST_ABSSeveral specific delivery management interventions (DMI) have been recommended for women with active SARS-CoV-2 to prevent early neonatal SARS-CoV-2 infection.\n\nWhat this study addsThis systematic review shows that support for specific DMI in SARS-CoV-2 infected mothers is lacking.\n\nHow this study might affect research, practice or policyThis review highlights the need for rigorous and multinational studies on the guidelines best suited to prevent transmission from mother to neonate.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Christina Snow Chan",
-        "author_inst": "Pediatrics / Division of Neonatal-Perinatal Medicine, University of Texas, Southwestern Medical Center, Dallas, Texas, USA"
-      },
-      {
-        "author_name": "Juin Yee Kong",
-        "author_inst": "Department of Neonatology, KK Women's and Children's Hospital, Singapore, Singapore"
-      },
-      {
-        "author_name": "Rehena Sultana",
-        "author_inst": "Duke - NUS Medical School, Singapore"
-      },
-      {
-        "author_name": "Vatsala Mundra",
-        "author_inst": "School of Medicine, University of Texas, Southwestern Medical Center, Dallas, Texas, USA"
-      },
-      {
-        "author_name": "Kikelomo Babata",
-        "author_inst": "Pediatrics / Division of Neonatal-Perinatal Medicine, University of Texas, Southwestern Medical Center, Dallas, Texas, USA"
-      },
-      {
-        "author_name": "Kelly Mazzarella",
-        "author_inst": "Pediatrics / Division of Neonatal-Perinatal Medicine, University of Texas, Southwestern Medical Center, Dallas, Texas, USA"
-      },
-      {
-        "author_name": "Emily Adhikari",
-        "author_inst": "Obstetrics and Gynecology, University of Texas, Southwestern Medical Center, Dallas, Texas, USA"
-      },
-      {
-        "author_name": "Kee Thai Yeo",
-        "author_inst": "Department of Neonatology, KK Women's and Children's Hospital, Singapore, Singapore"
-      },
-      {
-        "author_name": "Jean-Michel Hascoet",
-        "author_inst": "Lorraine University, DevAH, CHRU Nancy, France"
-      },
-      {
-        "author_name": "Luc P Brion",
-        "author_inst": "Pediatrics, Division of Neonatal-Perinatal Medicine, University of Texas, Southwestern Medical Center, Dallas, Texas, USA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "pediatrics"
-  },
   {
     "rel_doi": "10.1101/2023.02.15.528538",
     "rel_title": "Sotrovimab retains activity against SARS-CoV-2 Omicron variant BQ.1.1 in a non-human primate model",
@@ -110658,6 +109752,101 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2023.02.13.528235",
+    "rel_title": "P-Selectin promotes SARS-CoV-2 interactions with platelets and the endothelium",
+    "rel_date": "2023-02-14",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.13.528235",
+    "rel_abs": "COVID-19 causes a clinical spectrum of acute and chronic illness and host / virus interactions are not completely understood1,2. To identify host factors that can influence SARS-CoV-2 infection, we screened the human genome for genes that, when upregulated, alter the outcome of authentic SARS-CoV-2 infection. From this, we identify 34 new genes that can alter the course of infection, including the innate immune receptor P-selectin, which we show is a novel SARS-CoV-2 spike receptor. At the cellular level expression of P-selectin does not confer tropism for SARS-CoV-2, instead it acts to suppress infection. More broadly, P-selectin can also promote binding to SARS-CoV-2 variants, SARS-CoV-1 and MERS, acting as a general spike receptor for highly pathogenic coronaviruses. P-selectin is expressed on platelets and endothelium3, and we confirm SARS-CoV-2 spike interactions with these cells are P-selectin-dependent and can occur under shear flow conditions. In vivo, authentic SARS-CoV-2 uses P-selectin to home to airway capillary beds where the virus interacts with the endothelium and platelets, and blocking this interaction can clear vascular-associated SARS-CoV-2 from the lung. Together we show for the first time that coronaviruses can use the leukocyte recruitment system to control tissue localization, and this fundamental insight may help us understand and control highly pathogenic coronavirus disease progression.",
+    "rel_num_authors": 20,
+    "rel_authors": [
+      {
+        "author_name": "Cesar L Moreno",
+        "author_inst": "The Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life & Environmental Sciences, The University of Sydney, Sydney, N"
+      },
+      {
+        "author_name": "Fernanda V. S. Castanheira",
+        "author_inst": "Snyder Institute for Chronic Diseases, University of Calgary, Alberta T2N 4N1, Canada."
+      },
+      {
+        "author_name": "Alberto Ospina Stella",
+        "author_inst": "The Kirby Institute, University of New South Wales, New South Wales, Australia."
+      },
+      {
+        "author_name": "Felicity Chung",
+        "author_inst": "The Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life & Environmental Sciences, The University of Sydney, Sydney, N"
+      },
+      {
+        "author_name": "Anupriya Aggarwal",
+        "author_inst": "The Kirby Institute, University of New South Wales, New South Wales, Australia."
+      },
+      {
+        "author_name": "Alexander J Cole",
+        "author_inst": "Centenary Institute and Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia"
+      },
+      {
+        "author_name": "Lipin Loo",
+        "author_inst": "The Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre and School of Life & Environmental Sciences, The University of Sydney, Sydney, N"
+      },
+      {
+        "author_name": "Alexander Dupuy",
+        "author_inst": "Haematology Research Lab, Heart Research Institute, University of Sydney, Sydney, NSW 2042, Australia."
+      },
+      {
+        "author_name": "Yvonnne Kong",
+        "author_inst": "Haematology Research Lab, Heart Research Institute, University of Sydney, Sydney, NSW 2042, Australia."
+      },
+      {
+        "author_name": "Lejla Hagimola",
+        "author_inst": "Haematology Research Lab, Heart Research Institute, University of Sydney, Sydney, NSW 2042, Australia."
+      },
+      {
+        "author_name": "Jemma Fenwick",
+        "author_inst": "Haematology Research Lab, Heart Research Institute, University of Sydney, Sydney, NSW 2042, Australia."
+      },
+      {
+        "author_name": "Paul Coleman",
+        "author_inst": "Haematology Research Lab, Heart Research Institute, University of Sydney, Sydney, NSW 2042, Australia."
+      },
+      {
+        "author_name": "Michelle Wilson",
+        "author_inst": "Snyder Institute for Chronic Diseases, University of Calgary, Alberta T2N 4N1, Canada."
+      },
+      {
+        "author_name": "Maxwell Bui-Marinos",
+        "author_inst": "Snyder Institute for Chronic Diseases, University of Calgary, Alberta T2N 4N1, Canada."
+      },
+      {
+        "author_name": "Daniel Hesselson",
+        "author_inst": "Centenary Institute and Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia"
+      },
+      {
+        "author_name": "Jennifer Gamble",
+        "author_inst": "Vascular Biology Program Centenary Institute, The University of Sydney, Sydney, NSW, Australia."
+      },
+      {
+        "author_name": "Freda Passam",
+        "author_inst": "Haematology Research Lab, Heart Research Institute, University of Sydney, Sydney, NSW 2042, Australia."
+      },
+      {
+        "author_name": "Stuart Turville",
+        "author_inst": "The Kirby Institute, University of New South Wales, New South Wales, Australia."
+      },
+      {
+        "author_name": "Paul Kubes",
+        "author_inst": "Snyder Institute for Chronic Diseases, University of Calgary, Alberta T2N 4N1, Canada."
+      },
+      {
+        "author_name": "G Gregory Neely",
+        "author_inst": "The University of Sydney"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2023.02.14.528496",
     "rel_title": "Transcription regulation of SARS-CoV-2 receptor ACE2 by Sp1: a potential therapeutic target",
@@ -111887,49 +111076,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2023.02.08.527785",
-    "rel_title": "Functional comparisons of the virus sensor RIG-I from humans, the microbat Myotis daubentonii, and the megabat Rousettus aegyptiacus, and their response to SARS-CoV-2 infection",
-    "rel_date": "2023-02-11",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.08.527785",
-    "rel_abs": "Bats (order Chiroptera) are a major reservoir for emerging and re-emerging zoonotic viruses. Their tolerance towards highly pathogenic human viruses led to the hypothesis that bats may possess an especially active antiviral interferon (IFN) system. Here, we cloned and functionally characterized the virus RNA sensor, Retinoic Acid-Inducible Gene-I (RIG-I), from the \"microbat\" Myotis daubentonii (suborder Yangochiroptera) and the \"megabat\" Rousettus aegyptiacus (suborder Yinpterochiroptera), and compared them to the human ortholog. Our data show that the overall sequence and domain organization is highly conserved and that all three RIG-I orthologs can mediate a similar IFN induction in response to viral RNA at 37{degrees} and 39{degrees}C, but not at 30{degrees}C. Like human RIG-I, bat RIG-Is were optimally activated by double stranded RNA containing a 5-triphosphate end and required Mitochondrial Antiviral-Signalling Protein (MAVS) for antiviral signalling. Moreover, the RIG-I orthologs of humans and of R. aegyptiacus, but not of M. daubentonii, enable innate immune sensing of SARS-CoV-2 infection. Our results thus show that microbats and megabats express a RIG-I that is not substantially different from the human counterpart with respect to function, temperature dependency, antiviral signaling, and RNA ligand properties, and that human and megabat RIG-I are able to sense SARS-CoV-2 infection.\n\nIMPORTANCEA common hypothesis holds that bats (order Chiroptera) are outstanding reservoirs for zoonotic viruses because of a special antiviral interferon (IFN) system. However, functional studies about key components of the bat IFN system are rare. RIG-I is a cellular sensor for viral RNA signatures that activates the antiviral signalling chain to induce IFN. We cloned and functionally characterized RIG-I genes from representatives of the suborders Yangochiroptera and Yinpterochiroptera. The bat RIG-Is were conserved in their sequence and domain organization, and similar to human RIG-I in (i) mediating virus- and IFN-activated gene expression, (ii) antiviral signalling, (iii) temperature dependence, and (iv) recognition of RNA ligands. Moreover, RIG-I of Rousettus aegyptiacus (suborder Yinpterochiroptera) and of humans were found to recognize SARS-CoV-2 infection. Thus, members of both bat suborders encode RIG-Is that are comparable to their human counterpart. The ability of bats to harbour zoonotic viruses therefore seems due to other features.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Andreas Schoen",
-        "author_inst": "Justus-Liebig University"
-      },
-      {
-        "author_name": "Martin H\u00f6lzer",
-        "author_inst": "Robert-Kochs-Institute"
-      },
-      {
-        "author_name": "Marcel M\u00fcller",
-        "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin"
-      },
-      {
-        "author_name": "Christian Drosten",
-        "author_inst": "Charit\u00e9"
-      },
-      {
-        "author_name": "Manja Marz",
-        "author_inst": "Friedrich Schiller University Jena"
-      },
-      {
-        "author_name": "Benjamin Lamp",
-        "author_inst": "Institute for Virology, FB 10-Veterinary Medicine"
-      },
-      {
-        "author_name": "Friedemann Weber",
-        "author_inst": "Institute of Virology, FB10 - Veterinary Medicine of Justus Liebig University Gie\u00dfen"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2023.02.09.23285742",
     "rel_title": "Long COVID in Elderly Patients: An Epidemiologic Exploration Using a Medicare Cohort",
@@ -112168,6 +111314,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2023.02.08.23285589",
+    "rel_title": "Clinical severity prediction of COVID-19 admitted patients in Spain: SEMI and REDISSEC cohorts",
+    "rel_date": "2023-02-10",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.08.23285589",
+    "rel_abs": "This report addresses, from a machine learning perspective, a multi-class classification problem to predict the first deterioration level of a COVID-19 positive patient at the time of hospital admission. Socio-demographic features, laboratory tests and other measures are taken into account to learn the models. Our output is divided into 4 categories ranging from healthy patients, followed by patients requiring some form of ventilation (divided in 2 cate-gories) and finally patients expected to die. The study is conducted thanks to data provided by Sociedad Espanola de Medicina Interna (SEMI) and Red de Investigacion en Servicios de Salud de Enfermedades Cronicas (REDISSEC). Results show that logistic regression is the best method for identifying patients with clinical deterioration.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Mario Mart\u00ednez-Garc\u00eda",
+        "author_inst": "Basque Center for Applied Mathematics, BCAM, Bilbao, Spain"
+      },
+      {
+        "author_name": "Susana Garc\u00eda-Gutierrez",
+        "author_inst": "Galdakao Hospital, Osakidetza, Basque Country, Spain"
+      },
+      {
+        "author_name": "Lasai Barre\u00f1ada Taleb",
+        "author_inst": "Basque Center for Applied Mathematics, BCAM, Bilbao, Spain"
+      },
+      {
+        "author_name": "Rub\u00e9n Arma\u00f1anzas",
+        "author_inst": "Institute of Data Science and Artificial Intelligence, Universidad de Navarra, Pamplona, Spain"
+      },
+      {
+        "author_name": "Inaki Inza",
+        "author_inst": "University of the Basque Country UPV/EHU, Computer Science Faculty, San Sebasti\u00e1n, Spain"
+      },
+      {
+        "author_name": "Jose A. Lozano",
+        "author_inst": "Basque Center for Applied Mathematics, BCAM, Bilbao, Spain"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health informatics"
+  },
   {
     "rel_doi": "10.1101/2023.02.08.23285673",
     "rel_title": "Estimating serum cross-neutralizing responses to SARS-CoV-2 Omicron sub-lineages elicited by pre-Omicron or Omicron breakthrough infection with exposure interval compensation modeling",
@@ -113541,61 +112726,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2023.02.06.23285436",
-    "rel_title": "Mental distress among Norwegian adults during the Covid-19 pandemic: predictors of initial response and subsequent trajectories",
-    "rel_date": "2023-02-08",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.06.23285436",
-    "rel_abs": "BackgroundUnderstanding factors associated with mental distress during a pandemic is imperative for planning interventions to reduce the negative mental health impact of future crises. Our aim was to identify factors associated with change in levels of mental distress in the Norwegian adult population at the onset of the Covid-19 pandemic, relative to pre-pandemic levels, and with longitudinal changes in mental distress until vaccination against Covid-19 became widespread in Norway (the first 1.5 years of the pandemic).\n\nMethodsThe Norwegian Mother, Father and Child Cohort Study (MoBa) is a prospective longitudinal study with baseline recruitment from 1999-2009. Baseline characteristics and eight waves of data collection during the pandemic (between March 2020 and September 2021) were used for this analysis. Mental distress was measured with the 5-item version of Hopkins Symptoms Checklist (HSCL-5). A piecewise latent growth model was fitted to identify initial change in mental distress (March-early April 2020, adjusting for pre-pandemic mental distress measured during prior years of data collection) and longitudinal changes across the pandemic in three distinct periods.\n\nFindingsOur sample consisted of 105 972 adult participants (59.6% females). Mental distress levels peaked at the beginning of the pandemic. Several factors were associated with initial increases in distress: chronic medical conditions, living alone, history of psychiatric disorders, relatively lower educational background, female sex, younger age, and obesity. Several of these factors were also associated with long-term change. Being quarantined or having to isolate was associated with the likelihood of increasing distress during the pandemic. We observed a reduction in distress associated with Covid-19 vaccination status, while being infected with SARS-CoV-2 was associated with increasing distress late in the pandemic.\n\nInterpretationPre-pandemic vulnerability factors - like having a chronic disease - as well as Covid-19-related factors - like being quarantined or infected by SARS-CoV-2 - were associated with increased mental distress during the pandemic. This knowledge is important for planning of interventions to support vulnerable individuals during pandemics and other health crises.\n\nFundingThe Norwegian Ministry of Health, and Care Services and the Ministry of Education and Research. NordForsk, The Research Council of Norway, The South-Eastern Norway Regional Health Authority.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Li Lu",
-        "author_inst": "Health Management and Policy Institute, School of Public Policy and Administration, Xi'an Jiaotong University, Xi'an, China; NORMENT Centre, Institute of Clinic"
-      },
-      {
-        "author_name": "Laurie J Hannigan",
-        "author_inst": "Lovisenberg Diaconal Hospital, Oslo, Norway; Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway; Population Health Sciences, Bri"
-      },
-      {
-        "author_name": "Ragnhild E Brandlistuen",
-        "author_inst": "Department of Child Health and Development, Norwegian Institute of Public Health, Oslo, Norway; The Norwegian Mother, Father and Child Cohort Study (MoBa), Norw"
-      },
-      {
-        "author_name": "Ragnar Nesv\u00e5g",
-        "author_inst": "Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway"
-      },
-      {
-        "author_name": "Lill Trogstad",
-        "author_inst": "Division of Infection Control, Norwegian Institute of Public Health, Oslo, Norway"
-      },
-      {
-        "author_name": "Per Magnus",
-        "author_inst": "Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway"
-      },
-      {
-        "author_name": "Anna B\u00e1ra Unnarsd\u00f3ttir",
-        "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland."
-      },
-      {
-        "author_name": "Unnur A Valdimarsd\u00f3ttir",
-        "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.; Unit of Integrative Epidemiology, "
-      },
-      {
-        "author_name": "Ole A Andreassen",
-        "author_inst": "NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; NORMENT Centre, Division of Mental Health and Addiction, Oslo University Hospi"
-      },
-      {
-        "author_name": "Helga Ask",
-        "author_inst": "Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway; Department of Psychology, PROMENTA Research Center, University of Oslo, Oslo"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2023.02.08.23285565",
     "rel_title": "A Phase 2, Randomized, Double-blind, Placebo-controlled Study of oral RP7214, a DHODH inhibitor, in Patients with Symptomatic Mild SARS-CoV-2 Infection",
@@ -113914,6 +113044,89 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2023.02.02.23285352",
+    "rel_title": "Safety, Virology, Pharmacokinetics, and Clinical Experience of High-dose Intravenous Sotrovimab for the Treatment of Mild to Moderate COVID-19: An Open-label Clinical Trial",
+    "rel_date": "2023-02-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.02.23285352",
+    "rel_abs": "Background500 mg intravenous (IV) sotrovimab has been shown to be well tolerated and efficacious against pre-Omicron strains in treating patients with mild to moderate coronavirus disease 2019 (COVID-19) at high risk for disease progression.\n\nMethodsThis was an open-label, single-arm substudy of phase 3 COMET-TAIL (NCT04913675) assessing the safety and tolerability of a 2000 mg IV dose of sotrovimab. Symptomatic patients (aged [&ge;]18 years) with COVID-19 at high risk for progression were enrolled from June 30 through July 11, 2022, when Omicron BA.5, BA.2.12.1, and BA.4 were the predominant circulating variants in the United States. The primary endpoint was occurrence of adverse events (AEs), serious AEs (SAEs), AEs of special interest, and COVID-19 disease-related events (DREs) through Day 8. Safety, pharmacokinetics, viral load, and hospitalization >24 hours for acute management of illness or death through Day 29 were assessed.\n\nResultsAll participants (n=81) were Hispanic, 58% were female, and 51% were aged [&ge;]55 years. Through Day 8, no AEs, including infusion-related reactions or hypersensitivity, were reported; 2 participants reported DREs (mild cough, n=2). One SAE (acute myocardial infarction), which was considered unrelated to sotrovimab or COVID-19 by the investigator, occurred on Day 27 and was the only hospitalization reported. Maximum serum concentration (geometric mean) was 745.9 {micro}g/mL. Viral load decreased from baseline through Day 29; only 2 participants (3%) had persistently high viral load ([&ge;]4.1 log10 copies/mL) at Day 8.\n\nConclusions2000 mg IV sotrovimab was well tolerated, with no new unanticipated safety signals observed.\n\nKey points summaryIn participants with mild to moderate coronavirus disease 2019 at risk for progression to severe disease, a 2000 mg intravenous dose of sotrovimab had a low frequency of adverse events, with no hypersensitivity, infusion-related reactions, or deaths observed.",
+    "rel_num_authors": 17,
+    "rel_authors": [
+      {
+        "author_name": "Jaynier Moya",
+        "author_inst": "Pines Care Research Center"
+      },
+      {
+        "author_name": "Marisol Temech",
+        "author_inst": "Vir Biotechnology, Inc."
+      },
+      {
+        "author_name": "Sergio Parra",
+        "author_inst": "Vir Biotechnology, Inc."
+      },
+      {
+        "author_name": "Erick Juarez",
+        "author_inst": "Florida International Medical Research"
+      },
+      {
+        "author_name": "Reinaldo Hernandez-Loy",
+        "author_inst": "Dynamic Medical Research, LLC"
+      },
+      {
+        "author_name": "Juan C. Moises Gutierrez",
+        "author_inst": "Continental Clinical Research, LLC"
+      },
+      {
+        "author_name": "Jorge Diaz",
+        "author_inst": "Doral Medical Research"
+      },
+      {
+        "author_name": "Rubaba Hussain",
+        "author_inst": "RH Medical Urgent Care"
+      },
+      {
+        "author_name": "Scott Segal",
+        "author_inst": "GSK"
+      },
+      {
+        "author_name": "Claire Xu",
+        "author_inst": "GSK"
+      },
+      {
+        "author_name": "Andrew Skingsley",
+        "author_inst": "GSK"
+      },
+      {
+        "author_name": "Gretja Schnell",
+        "author_inst": "Vir Biotechnology, Inc."
+      },
+      {
+        "author_name": "Asma El-Zailik",
+        "author_inst": "Vir Biotechnology, Inc."
+      },
+      {
+        "author_name": "Jennnifer E. Sager",
+        "author_inst": "Vir Biotechnology, Inc."
+      },
+      {
+        "author_name": "Melissa Aldinger",
+        "author_inst": "Vir Biotechnology, Inc."
+      },
+      {
+        "author_name": "Elizabeth L. Alexander",
+        "author_inst": "Vir Biotechnology, Inc."
+      },
+      {
+        "author_name": "Gerard Acloque",
+        "author_inst": "Universal Medical and Research Center"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2023.02.02.23285391",
     "rel_title": "Longitudinal and Quantitative Fecal Shedding Dynamics of SARS-CoV-2, Pepper Mild Mottle Virus and CrAssphage",
@@ -115183,169 +114396,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2023.02.05.527215",
-    "rel_title": "Prior vaccination enhances immune responses during SARS-CoV-2 breakthrough infection with early activation of memory T cells followed by production of potent neutralizing antibodies",
-    "rel_date": "2023-02-06",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.05.527215",
-    "rel_abs": "SARS-CoV-2 infection of vaccinated individuals is increasingly common but rarely results in severe disease, likely due to the enhanced potency and accelerated kinetics of memory immune responses. However, there have been few opportunities to rigorously study early recall responses during human viral infection. To better understand human immune memory and identify potential mediators of lasting vaccine efficacy, we used high-dimensional flow cytometry and SARS-CoV-2 antigen probes to examine immune responses in longitudinal samples from vaccinated individuals infected during the Omicron wave. These studies revealed heightened Spike-specific responses during infection of vaccinated compared to unvaccinated individuals. Spike-specific CD4 T cells and plasmablasts expanded and CD8 T cells were robustly activated during the first week. In contrast, memory B cell activation, neutralizing antibody production, and primary responses to non-Spike antigens occurred during the second week. Collectively, these data demonstrate the functionality of vaccine-primed immune memory and highlight memory T cells as rapid responders during SARS-CoV-2 infection.",
-    "rel_num_authors": 37,
-    "rel_authors": [
-      {
-        "author_name": "Mark M. Painter",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Timothy S. Johnston",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Kendall A. Lundgreen",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Jefferson J.S. Santos",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Juliana S. Qin",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Rishi R. Goel",
-        "author_inst": "University of Pennsylvania, Perelman School of Medicine"
-      },
-      {
-        "author_name": "Sokratis A. Apostolidis",
-        "author_inst": "UPenn"
-      },
-      {
-        "author_name": "Divij Mathew",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Bria Fulmer",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Justine C. Williams",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Michelle L. McKeague",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Ajinkya Pattekar",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Ahmad Goode",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Sean Nasta",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Amy E. Baxter",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Josephine R. Giles",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Ashwin N. Skelly",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Laura E. Felley",
-        "author_inst": "University of Michigan"
-      },
-      {
-        "author_name": "Maura McLaughlin",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Joellen Weaver",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "- Penn Medicine BioBank",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Oliva Kuthuru",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Jeanette Dougherty",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Sharon Adamski",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Sherea Long",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Macy Kee",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Cynthia Clendenin",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Ricardo da Silva Antunes",
-        "author_inst": "La Jolla Institute for Immunology"
-      },
-      {
-        "author_name": "Alba Grifoni",
-        "author_inst": "La Jolla Institute for Immunology"
-      },
-      {
-        "author_name": "Daniela Weiskopf",
-        "author_inst": "La Jolla Institute For Allergy & Immunology"
-      },
-      {
-        "author_name": "Alessandro Sette",
-        "author_inst": "La Jolla Institute for Allergy & Immunology"
-      },
-      {
-        "author_name": "Alexander C. Huang",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Daniel J. Rader",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Scott E. Hensley",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Paul Bates",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Allison R. Greenplate",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "E. John Wherry",
-        "author_inst": "University of Pennsylvania"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2023.02.05.527216",
     "rel_title": "Bioinformatic analysis of the spike protein cleavage sites of coronaviruses in the mammalian order Eulipotyphla",
@@ -115604,6 +114654,77 @@
     "type": "new results",
     "category": "evolutionary biology"
   },
+  {
+    "rel_doi": "10.1101/2023.02.02.526749",
+    "rel_title": "Investigations on SARS-CoV-2 and other coronaviruses in mink farms in France at the end of the first year of COVID-19 pandemic",
+    "rel_date": "2023-02-02",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.02.526749",
+    "rel_abs": "Soon after the beginning of the COVID-19 pandemic in early 2020, the Betacoronavirus SARS-CoV-2 infection of several mink farms breeding American minks (Neovison vison) for fur was detected in several countries of Europe. The risk of a new reservoir formation and of a reverse zoonosis from minks was then a major concern. The aim of this study was to investigate the four French mink farms for the circulation of SARS-CoV-2 at the end of 2020. The investigations took place during the slaughtering period thus facilitating different types of sampling (swabs and blood). In one of the four mink farms, 96.6% of serum samples were positive in SARS-CoV-2 ELISA coated with purified N protein recombinant antigen and 54 out of 162 (33%) pharyngo-tracheal swabs were positive by RT-qPCR. The genetic variability among 12 SARS-CoV-2 genomes sequenced in this farm indicated the co-circulation of several lineages at the time of sampling. All SARS-CoV-2 genomes detected were nested within the 20A clade (Nextclade), together with SARS-CoV-2 genomes from humans sampled at the same period. The percentage of SARS-CoV-2 seropositivity by ELISA varied between 0.5 and 1.2% in the three other farms. Interestingly, among these three farms, 11 pharyngo-tracheal swabs and 3 fecal pools from two farms were positive by end-point RT-PCR for an Alphacoronavirus highly similar to a mink coronavirus sequence observed in Danish farms in 2015. In addition, a mink Caliciviridae was identified in one of the two positive farms for Alphacoronavirus. The clinical impact of these unapparent viral infections is not known. The co-infection of SARS-CoV-2 with other viruses in mink farms could contribute to explain the diversity of clinical symptoms noted in different infected farms in Europe. In addition, the co-circulation of an Alphacoronavirus and SARS-CoV-2 within a mink farm would increase potentially the risk of viral recombination between alpha and betacoronaviruses already suggested in wild and domestic animals, as well as in humans.\n\nAuthor summaryFrance is not a country of major mink fur production. Following the SARS-CoV-2 contamination of mink farms in Denmark and the Netherlands, the question arose for the four French farms.\n\nThe investigation conducted at the same time in the four farms revealed the contamination of one of them by a variant different from the one circulating at the same time in Denmark and the Netherlands mink farms.\n\nInvestigation of three other farms free of SARS-CoV-2 contamination revealed the circulation of other viruses including a mink Alphacoronavirus and Caliciviridae, which could modify the symptomatology of SARS-CoV-2 infection in minks.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Marine Wasniewski",
+        "author_inst": "Anses Laboratoire de la rage  et de la faune sauvage de Nancy"
+      },
+      {
+        "author_name": "Franck Bou\u00e9",
+        "author_inst": "Anses Laboratoire de la rage et de la faune sauvage de Nancy"
+      },
+      {
+        "author_name": "C\u00e9line Richomme",
+        "author_inst": "Anses Laboratoire de la rage et de la faune sauvage de Nancy"
+      },
+      {
+        "author_name": "Etienne Simon-Lori\u00e8re",
+        "author_inst": "Institut Pasteur"
+      },
+      {
+        "author_name": "Sylvie Van der Werf",
+        "author_inst": "Institut Pasteur"
+      },
+      {
+        "author_name": "Flora Donati",
+        "author_inst": "Institut Pasteur"
+      },
+      {
+        "author_name": "Vincent Enouf",
+        "author_inst": "Institut Pasteur"
+      },
+      {
+        "author_name": "Yannick Blanchard",
+        "author_inst": "Anses"
+      },
+      {
+        "author_name": "V\u00e9ronique Beven",
+        "author_inst": "Anses"
+      },
+      {
+        "author_name": "Estelle Leperchois",
+        "author_inst": "Normandie Universite"
+      },
+      {
+        "author_name": "Bryce Leterrier",
+        "author_inst": "Normandie Universite"
+      },
+      {
+        "author_name": "Meriadeg Le Gouil",
+        "author_inst": "Normandie Universite"
+      },
+      {
+        "author_name": "Elodie Monch\u00e2tre-Leroy",
+        "author_inst": "Anses Laboratoire de la rage et de la faune sauvage de Nancy"
+      },
+      {
+        "author_name": "Evelyne Picard-Meyer",
+        "author_inst": "Anses Laboratoire de la rage et de la faune sauvage de Nancy"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2023.02.01.526623",
     "rel_title": "Crystal Structures of Inhibitor-Bound Main Protease from Delta- and Gamma-Coronaviruses",
@@ -117121,53 +116242,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2023.01.30.23285170",
-    "rel_title": "Older age, lack of vaccination and infection with variants other than Omicron associated with severity of COVID-19 and in-hospital mortality in Pakistan",
-    "rel_date": "2023-02-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.30.23285170",
-    "rel_abs": "ObjectivesWe investigated factors associated with COVID-19 disease severity and in-hospital mortality in a low-middle income setting.\n\nMethodsRecords of 197 adult COVID-19 patients admitted to the Aga Khan University Hospital, Karachi between April 2021 and February 2022 were reviewed. Clinical data including, that of SARS-CoV-2 variants was collected.\n\nResultsThe median age of the patients was 55 years and 51.8% were males. 48.2 % of patients had non-severe disease, while 52.8% had severe/critical disease. Hypertension (48%) and diabetes mellitus (41.3%) were most common comorbid conditions. Omicron (55.3%), Beta (14.7%), Alpha (13.7%), Delta (12.7%) and Gamma (3.6%) were identified in patients. The risk of severe disease was higher in those aged above 50 years (OR 5.73; 95%CI [2.45-13.7]) and in diabetics (OR 4.24; 95% CI[1.82-9.85]). Full vaccination (OR 0.25; 95%CI [0.11-0.58]) or infection with Omicron variants (OR 0.42; 95% CI[0.23-0.74]) reduced disease severity. Age > 50 (OR 5.07; 95%CI [1.92-13.42]) and presence of myocardial infarction (OR 5.11; 95% CI[1.45-17.93]) was associated with increased mortality, but infection with Omicron (OR 0.22 95% CI 0.10-0.53]) reduced risk.\n\nConclusionsVaccination was found to protect against severe COVID-19 regardless of the infecting variant and is recommended especially, in those aged over 50 years and with co-morbid conditions.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Zain Mushtaq",
-        "author_inst": "Aga Khan University, Pakistan"
-      },
-      {
-        "author_name": "Nosheen Nasir",
-        "author_inst": "Aga Khan University"
-      },
-      {
-        "author_name": "Syed Faisal Mahmood",
-        "author_inst": "Aga Khan University, Pakistan"
-      },
-      {
-        "author_name": "Sara Khan",
-        "author_inst": "Aga Khan University, Pakistan"
-      },
-      {
-        "author_name": "Akbar Kanji",
-        "author_inst": "Aga Khan University, Pakistan"
-      },
-      {
-        "author_name": "Asghar Nasir",
-        "author_inst": "Aga Khan University, Pakistan"
-      },
-      {
-        "author_name": "Uzma Bashir Aamir",
-        "author_inst": "WHO,Pakistan"
-      },
-      {
-        "author_name": "Zahra Hasan",
-        "author_inst": "The Aga Khan University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2023.01.30.23285171",
     "rel_title": "Evaluation of a Commercially Available Rapid RT-PCR Assay's Detection of SARS-CoV-2 Novel Variants",
@@ -117626,6 +116700,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2023.01.30.526314",
+    "rel_title": "Fitness effects of mutations to SARS-CoV-2 proteins",
+    "rel_date": "2023-01-31",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.30.526314",
+    "rel_abs": "Knowledge of the fitness effects of mutations to SARS-CoV-2 can inform assessment of new variants, design of therapeutics resistant to escape, and understanding of the functions of viral proteins. However, experimentally measuring effects of mutations is challenging: we lack tractable lab assays for many SARS-CoV-2 proteins, and comprehensive deep mutational scanning has been applied to only two SARS-CoV-2 proteins. Here we develop an approach that leverages millions of publicly available SARS-CoV-2 sequences to estimate effects of mutations. We first calculate how many independent occurrences of each mutation are expected to be observed along the SARS-CoV-2 phylogeny in the absence of selection. We then compare these expected observations to the actual observations to estimate the effect of each mutation. These estimates correlate well with deep mutational scanning measurements. For most genes, synonymous mutations are nearly neutral, stop-codon mutations are deleterious, and amino-acid mutations have a range of effects. However, some viral accessory proteins are under little to no selection. We provide interactive visualizations of effects of mutations to all SARS-CoV-2 proteins (https://jbloomlab.github.io/SARS2-mut-fitness/). The framework we describe is applicable to any virus for which the number of available sequences is sufficiently large that many independent occurrences of each neutral mutation are observed.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Jesse D Bloom",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      },
+      {
+        "author_name": "Richard A Neher",
+        "author_inst": "University of Basel"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "new results",
+    "category": "evolutionary biology"
+  },
   {
     "rel_doi": "10.1101/2023.01.30.526101",
     "rel_title": "A comprehensive survey of coronaviral main protease active site diversity in 3D: Identifying and analyzing drug discovery targets in search of broad specificity inhibitors for the next coronavirus pandemic",
@@ -119083,81 +118180,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health systems and quality improvement"
   },
-  {
-    "rel_doi": "10.1101/2023.01.24.23284913",
-    "rel_title": "Longitudinal home self-collection of capillary blood using homeRNA correlates interferon and innate viral defense pathways with SARS-CoV-2 viral clearance",
-    "rel_date": "2023-01-28",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.24.23284913",
-    "rel_abs": "Blood transcriptional profiling is a powerful tool to evaluate immune responses to infection; however, blood collection via traditional phlebotomy remains a barrier to precise characterization of the immune response in dynamic infections (e.g., respiratory viruses). Here we present an at-home self-collection methodology, homeRNA, to study the host transcriptional response during acute SARS-CoV-2 infections. This method uniquely enables high frequency measurement of the host immune kinetics in non-hospitalized adults during the acute and most dynamic stage of their infection. COVID-19+ and healthy participants self-collected blood every other day for two weeks with daily nasal swabs and symptom surveys to track viral load kinetics and symptom burden, respectively. While healthy uninfected participants showed remarkably stable immune kinetics with no significant dynamic genes, COVID-19+ participants, on the contrary, depicted a robust response with over 418 dynamic genes associated with interferon and innate viral defense pathways. When stratified by vaccination status, we detected distinct response signatures between unvaccinated and breakthrough (vaccinated) infection subgroups; unvaccinated individuals portrayed a response repertoire characterized by higher innate antiviral responses, interferon signaling, and cytotoxic lymphocyte responses while breakthrough infections portrayed lower levels of interferon signaling and enhanced early cell-mediated response. Leveraging cross-platform longitudinal sampling (nasal swabs and blood), we observed that IFI27, a key viral response gene, tracked closely with SARS-CoV-2 viral clearance in individual participants. Taken together, these results demonstrate that at-home sampling can capture key host antiviral responses and facilitate frequent longitudinal sampling to detect transient host immune kinetics during dynamic immune states.\n\nOne Sentence SummarySelf-blood collection using homeRNA captures temporal dynamics in host transcriptional immune response during acute SARS-CoV-2 infection.",
-    "rel_num_authors": 15,
-    "rel_authors": [
-      {
-        "author_name": "Fang Yun Lim",
-        "author_inst": "Fred Hutchinson Cancer Center, University of Washington"
-      },
-      {
-        "author_name": "Soo-Young Kim",
-        "author_inst": "Fred Hutchinson Cancer Center"
-      },
-      {
-        "author_name": "Karisma N. Kulkarni",
-        "author_inst": "Fred Hutchinson Cancer Center"
-      },
-      {
-        "author_name": "Rachel L. Blazevic",
-        "author_inst": "Fred Hutchinson Cancer Center"
-      },
-      {
-        "author_name": "Louise E. Kimball",
-        "author_inst": "Fred Hutchinson Cancer Center"
-      },
-      {
-        "author_name": "Hannah G. Lea",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Amanda J. Haack",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Maia S. Gower",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Terry Stevens-Ayers",
-        "author_inst": "Fred Hutchinson Cancer Center"
-      },
-      {
-        "author_name": "Lea M. Starita",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Michael Boeckh",
-        "author_inst": "Fred Hutchinson Cancer Center, University of Washington"
-      },
-      {
-        "author_name": "Joshua T. Schiffer",
-        "author_inst": "Fred Hutchinson Cancer Center, University of Washington"
-      },
-      {
-        "author_name": "Ollivier Hyrien",
-        "author_inst": "Fred Hutchinson Cancer Center"
-      },
-      {
-        "author_name": "Ashleigh B. Theberge",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Alpana Waghmare",
-        "author_inst": "Fred Hutchinson Cancer Research Center, University of Washington, Seattle Children's Research Institute"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2023.01.24.23284952",
     "rel_title": "Exploring the Transmission Dynamics of the COVID-19 Outbreaks after Dec. 2022 in Shaanxi Province, China: Analysis of Baseline Data from A Large Scale Cohort",
@@ -119484,6 +118506,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
+  {
+    "rel_doi": "10.1101/2023.01.24.23284885",
+    "rel_title": "Impact of vaccination and risk factors on COVID-19 mortality amid delta surge in Libya: a single centre cohort study",
+    "rel_date": "2023-01-28",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.24.23284885",
+    "rel_abs": "BackgroundThe Delta variant has led to a surge in COVID-19 cases in Libya, making it crucial to investigate the impact of vaccination on mortality rates among hospitalized patients and critically ill.\n\nAimsTo study risk factors and COVID-19 mortality rates among unvaccinated and vaccinated adults during delta wave at a single COVID-19 care centre in Tripoli, Libya.\n\nMethodsThe study involved two independent cohorts (n=341). One cohort was collected retrospectively from May 2021-August 2021 and the second cohort was prospectively collected from August 2021-October 2021 and most of them were during the Delta wave. The two cohorts were merged and analysed as one group.\n\nResultsMost patients were male (60.5%) and 53.3% were >60 years. The vast majority of admitted patients did not have previous COVID-19 infection (98.9%) and were unvaccinated (90.3%). Among vaccinated, 30 patients had one dose and only 3 had two doses. Among patients who received one dose, 58.1% (18/31) died and 41.9% (13/31) survived. Most patients (72.2%) had a pre-existing medical condition. Multivariable prediction model showed that age >60 years was significantly associated with death (odds ratio=2.328, CI 1.456-3.724, p-value=<0.0001).\n\nConclusionPrevious infection or full vaccination against COVID-19 significantly reduces hospitalization and death, as most admitted patients were unvaccinated and not previously infected. However, a single vaccine dose may not be adequate, especially for older individuals and those with underlying medical conditions. High-risk older patients with comorbidities should be fully vaccinated and offered up to date bivalent COVID-19 booster doses.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Inas Mohamed Alhudiri",
+        "author_inst": "Biotechnology Research center"
+      },
+      {
+        "author_name": "Zakarya Suleiman ABUSREWIL",
+        "author_inst": "University of Tripoli"
+      },
+      {
+        "author_name": "Omran Dakhil",
+        "author_inst": "Souq Thullatha Isolation Centre, Tripoli, Libya"
+      },
+      {
+        "author_name": "Mosab Ali Zwaik",
+        "author_inst": "Souq Thullatha Isolation Centre, Tripoli, Libya"
+      },
+      {
+        "author_name": "Mohammed Ammar Awn",
+        "author_inst": "Souq Thullatha Isolation Centre, Tripoli, Libya"
+      },
+      {
+        "author_name": "Mwada Jallul",
+        "author_inst": "Libyan Biotechnology Research Centre, Tripoli, Libya"
+      },
+      {
+        "author_name": "Aimen Ibrahim Ahmed",
+        "author_inst": "National Migration Health, International Organization for Migration, Tripoli, Libya"
+      },
+      {
+        "author_name": "Rasha Abugrara",
+        "author_inst": "National Migration Health, International Organization for Migration, Tripoli, Libya"
+      },
+      {
+        "author_name": "Adam Ibrahim Elzagheid",
+        "author_inst": "Libyan Biotechnology Research Center, Tripoli, Libya"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2023.01.25.23284996",
     "rel_title": "Bioinformatics and system biology approach to identify the influences of COVID-19 on metabolic unhealthy obese patients",
@@ -120953,45 +120026,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2023.01.23.23284902",
-    "rel_title": "COVID-19 in Pakistan: A national analysis of five pandemic waves",
-    "rel_date": "2023-01-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.23.23284902",
-    "rel_abs": "ObjectivesThe COVID-19 pandemic showed distinct waves where cases ebbed and flowed. While each country had slight, nuanced differences, lessons from each wave with country-specific details provides important lessons for prevention, understanding medical outcomes and the role of vaccines. This paper compares key characteristics from the five different COVID-19 waves in Pakistan.\n\nMethodsWe used specific criteria to define COVID-19 waves, and key variables such as COVID-19 tests, cases, and deaths with their rates of change to the peak and then to the trough were used to draw descriptive comparisons. Additionally, a linear regression model estimated daily new COVID-19 deaths in Pakistan.\n\nResultsPakistan saw five distinct waves, each of which displayed the typical topology of a complete infectious disease epidemic. The time from wave-start to peak became progressively shorter, and from wave-peak to trough, progressively longer. Each wave appears to also be getting shorter, except for wave 4, which lasted longer than wave 3. A one percent increase in vaccinations increased daily new COVID-19 deaths by 0.10% (95% CI: 0.01, 0.20) in wave 4 and decreased deaths by 0.38% (95% CI: -0.67, -0.08) in wave 5.\n\nConclusionEach wave displayed distinct characteristics that must be interpreted in the context of the level of response and the variant driving the epidemic. Key indicators suggest that COVID-19 preventive measures kept pace with the disease. Waves 1 and 2 were mainly about prevention and learning how to clinically manage patients. Vaccination started late during Wave 3 and its impact became apparent on hospitalizations and deaths in Wave 5. The impact of highly virulent strains Alpha/B1.1.7 and Delta/B.1.617.2 variants during Wave 3 and milder but more infectious Omicron/BA.5.2.1.7 are apparent.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Taimoor Ahmad",
-        "author_inst": "Akhter Hameed Khan Foundation"
-      },
-      {
-        "author_name": "Mujahid Abdullah",
-        "author_inst": "Akhter Hameed Khan Foundation"
-      },
-      {
-        "author_name": "Abdul Mueed",
-        "author_inst": "Akhter Hameed Khan Foundation"
-      },
-      {
-        "author_name": "Faisal Sultan",
-        "author_inst": "Shaukat Khanum Memorial Cancer Hospital and Research Centre"
-      },
-      {
-        "author_name": "Ayesha Khan",
-        "author_inst": "Akhter Hameed Khan Foundation"
-      },
-      {
-        "author_name": "Adnan  Ahmad Khan",
-        "author_inst": "Research and Development Solutions"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2023.01.25.525485",
     "rel_title": "Long-term respiratory mucosal immune memory to SARS-CoV-2 after infection and vaccination",
@@ -121390,6 +120424,61 @@
     "type": "new results",
     "category": "molecular biology"
   },
+  {
+    "rel_doi": "10.1101/2023.01.24.525203",
+    "rel_title": "Multimodal characterization of antigen-specific CD8+ T cells across SARS-CoV-2 vaccination and infection.",
+    "rel_date": "2023-01-24",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.24.525203",
+    "rel_abs": "The human immune response to SARS-CoV-2 antigen after infection or vaccination is defined by the durable production of antibodies and T cells. Population-based monitoring typically focuses on antibody titer, but there is a need for improved characterization and quantification of T cell responses. Here, we utilize multimodal sequencing technologies to perform a longitudinal analysis of circulating human leukocytes collected before and after BNT162b2 immunization. Our data reveal distinct subpopulations of CD8+ T cells which reliably appear 28 days after prime vaccination (7 days post boost). Using a suite of cross-modality integration tools, we define their transcriptome, accessible chromatin landscape, and immunophenotype, and identify unique biomarkers within each modality. By leveraging DNA-oligo-tagged peptide-MHC multimers and T cell receptor sequencing, we demonstrate that this vaccine-induced population is SARS-CoV-2 antigen-specific and capable of rapid clonal expansion. Moreover, we also identify these CD8+ populations in scRNA-seq datasets from COVID-19 patients and find that their relative frequency and differentiation outcomes are predictive of subsequent clinical outcomes. Our work contributes to our understanding of T cell immunity, and highlights the potential for integrative and multimodal analysis to characterize rare cell populations.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Bingjie Zhang",
+        "author_inst": "1 New York Genome Center, New York, NY, USA. 2 Center for Genomics and Systems Biology, New York University, New York, NY, USA. 3 Department of Cell Biology and"
+      },
+      {
+        "author_name": "Rabi Upadhyay",
+        "author_inst": "3 Department of Cell Biology and Regenerative Medicine, New York University Grossman School of Medicine, New York, NY, USA. 4 Perlmutter Cancer Center, New York"
+      },
+      {
+        "author_name": "Yuhan Hao",
+        "author_inst": "1 New York Genome Center, New York, NY, USA. 2 Center for Genomics and Systems Biology, New York University, New York, NY, USA."
+      },
+      {
+        "author_name": "Marie I. Samanovic",
+        "author_inst": "5 Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA. 6 New York University Langone Vaccine Center, New York, NY, USA."
+      },
+      {
+        "author_name": "Ramin S. Herati",
+        "author_inst": "5 Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA. 6 New York University Langone Vaccine Center, New York, NY, USA."
+      },
+      {
+        "author_name": "John Blair",
+        "author_inst": "1 New York Genome Center, New York, NY, USA. 2 Center for Genomics and Systems Biology, New York University, New York, NY, USA."
+      },
+      {
+        "author_name": "Jordan Axelrad",
+        "author_inst": "5 Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA."
+      },
+      {
+        "author_name": "Mark J Mulligan",
+        "author_inst": "5 Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA. 6 New York University Langone Vaccine Center, New York, NY, USA."
+      },
+      {
+        "author_name": "Dan R Littman",
+        "author_inst": "3 Department of Cell Biology and Regenerative Medicine, New York University Grossman School of Medicine, New York, NY, USA. 4 Perlmutter Cancer Center, New York"
+      },
+      {
+        "author_name": "Rahul Satija",
+        "author_inst": "1 New York Genome Center, New York, NY, USA. 2 Center for Genomics and Systems Biology, New York University, New York, NY, USA."
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "genomics"
+  },
   {
     "rel_doi": "10.1101/2023.01.24.23284869",
     "rel_title": "A Randomized Trial Comparing Omicron-Containing Boosters with the Original Covid-19 Vaccine mRNA-1273",
@@ -122767,41 +121856,6 @@
     "type": "new results",
     "category": "developmental biology"
   },
-  {
-    "rel_doi": "10.1101/2023.01.19.23284772",
-    "rel_title": "Estimating The Uncertain Effect of the COVID Pandemic on Drug Overdoses",
-    "rel_date": "2023-01-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.19.23284772",
-    "rel_abs": "ObjectiveU.S. drug-related overdose deaths and Emergency Department (ED) visits rose in 2020 and again in 2021. Multiple studies and the news media attributed this rise primarily to increased drug use resulting from the societal disruptions related to the coronavirus (COVID-19) pandemic. A competing explanation is that higher overdose deaths and ED visits may instead have been a continuation of pre-pandemic trends in synthetic-opioid deaths. We assess the evidence on whether increases in overdose deaths and ED visits are likely to be causally related to the COVID-19 pandemic, increased synthetic-opioid use, or some of both.\n\nMethodsWe use national data from the Centers for Disease Control and Prevention (CDC) on rolling 12-month drug-related deaths (2015-2021); CDC data on monthly ED visits (2019-September 2020); and ED visit data across 21states from a national ED group (January 2016-June 2022). We study drug overdose deaths per 100,000 persons during the pandemic period, and ED visits for drug overdoses, compared to predicted levels based on pre-pandemic trends.\n\nResultsO_ST_ABSMortalityC_ST_ABSNational overdose mortality increased from 21/100,000 in 2019 to 26/100,000 in 2020 and 30/100,000 in 2021. The 2020 increase is well-predicted by models that extrapolate pre-pandemic trends for rolling 12-month mortality to the pandemic period, consistent with higher mortality reflecting continuation of those trends. Placebo analyses (which assume the pandemic started earlier or later than March 2020) do not provide evidence for a change in trend in or soon after March 2020. State-level analyses of actual-minus-predicted mortality, relative to pre-pandemic trends, show no consistent pattern. The state-level results support state heterogeneity in overdose mortality trends, and do not support the pandemic being a major driver of overdose mortality.\n\nED visitsED overdose visits rose during our sample period, reflecting a worsening opioid epidemic, but rose at similar rates during the pre-pandemic and pandemic periods.\n\nConclusionThe causes of rising overdose mortality in 2020 and 2021 cannot be definitely determined, but the observed increases can be largely explained by a continuation of pre-pandemic trends in synthetic-opioid deaths, principally fentanyl. In contrast to prior studies, we do not find support for the pandemic having been a principal driver of rising mortality. Policymakers need to directly address the synthetic opioid epidemic, and not expect a respite as the pandemic recedes.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Ali Moghtaderi",
-        "author_inst": "George Washington University School of Public Health and Health Services: The George Washington University Milken Institute of Public Health"
-      },
-      {
-        "author_name": "Mark Zocchi",
-        "author_inst": "Brandeis University Heller School for Social Policy and Management"
-      },
-      {
-        "author_name": "Jesse Pines",
-        "author_inst": "Allegheny Health Network"
-      },
-      {
-        "author_name": "Arvind Venkat",
-        "author_inst": "Allegheny Health Network"
-      },
-      {
-        "author_name": "Bernard Black",
-        "author_inst": "Northwestern University School of Law"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health policy"
-  },
   {
     "rel_doi": "10.1101/2023.01.19.524762",
     "rel_title": "Induction of SARS-CoV-2 N-specific CD8+ T cell immunity in lungs by engineered extracellular vesicles associates with strongly impaired viral replication",
@@ -123164,6 +122218,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2023.01.20.23284812",
+    "rel_title": "Immunogenicity, Safety and Effectiveness of COVID-19 Pfizer-BioNTech (BNT162b2) mRNA Vaccination in Immunocompromised Adolescents and Young Adults: A systematic Review and Meta-Analyses",
+    "rel_date": "2023-01-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.20.23284812",
+    "rel_abs": "People with weak immune systems are more likely to develop severe COVID-19, less likely to be included in vaccine controlled studies but more likely to be under-vaccinated. We review post-marketing studies to examine the immunogenicity, safety and effectiveness of BNT162b2 vaccine in immunocompromised adolescents and young adults (AYA). We searched more than three international databases from 2020 to 30 May 2022 and used the ROBINS-I for bias assessment. Random effect model was used to estimate pooled proportion, log RR, and mean difference. Eggers regression and Beggs rank correlation were used to examine publication bias. 47 full texts were reviewed, and nine were included. Conditions studied were rheumatic diseases, diabetes mellitus, Down syndrome, solid tumours, neurodisability, and cystic fibrosis. Eight studies used cohort designs and one used cross-sectional designs. Europe led most of the investigations. Most studies had unclear risk of bias and none could rule out selection bias, ascertainment bias, or selective outcome reporting. The overall estimated proportion of combined local and systemic reactions after the first BNT162b2 vaccination was 30%[95% CI: 17-42%] and slightly rose to 32% [95% CI: 19-44%] after the second dose. Rheumatic illnesses had the highest rate of AEFI (40%[95% CI: 16-65%]), while cystic fibrosis had the lowest (27%[95% CI: 17%-38%]). Hospitalizations for AEFIs were rare. Healthy controls exhibited higher levels of neutralizing antibodies and measured IgG than immunocompromised AYA, although pooled estimations did not demonstrate a statistically significant difference after primary dose. BNT162b2 is safe and effective in immunocompromised AYA, with no significant difference to healthy controls. However, current evidence is low to moderate due to high RoB. Our research advocates for improving methodology in studies including specific AYA population.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Patrick DMC Katoto",
+        "author_inst": "South African Medical Research Council"
+      },
+      {
+        "author_name": "Mireille AM Kakubu",
+        "author_inst": "Ministry of Health and Social Services of Namibia, Windhoek, Namibia"
+      },
+      {
+        "author_name": "Jacques L Tamuzi",
+        "author_inst": "Stellenbosch University"
+      },
+      {
+        "author_name": "Amanda S Brand",
+        "author_inst": "Centre for Evidence-based Health Care, Division of Epidemiology and Biostatistics, Department of Global Health, Faculty of Medicine and Health Sciences, Stellen"
+      },
+      {
+        "author_name": "Adaeze Ayuk",
+        "author_inst": "Department of Paediatrics and Child Health, University of Nigeria Teaching Hospital, Enugu, Nigeria"
+      },
+      {
+        "author_name": "Liliane N. Byamungu",
+        "author_inst": "Department of Paediatric, Faculty of Medicine and Health Sciences, University of KwaZulu-Natal, Durban, South Africa"
+      },
+      {
+        "author_name": "Charles Shey Wiysonge",
+        "author_inst": "South African Medical Research Council"
+      },
+      {
+        "author_name": "Glenda Gray",
+        "author_inst": "Office of the President and CEO, South African Medical Research Council, Cape Town, South Africa"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2023.01.20.23284814",
     "rel_title": "Frequency and Clinical Characteristics of Breakthrough Cases Post COVID-19 Vaccine and Predictive Risk Factors in College Students",
@@ -124613,57 +123714,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2023.01.17.23284684",
-    "rel_title": "Who is most at risk of dying if infected with SARS-CoV-2? A mortality risk factor analysis using machine learning of COVID-19 patients over time in a large Mexican population.",
-    "rel_date": "2023-01-18",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.17.23284684",
-    "rel_abs": "BackgroundCOVID-19 would kill fewer people if health programs can predict who is at higher risk of mortality because resources can be targeted to protect those people from infection. We predict mortality in a very large population in Mexico with machine learning using demographic variables and pre-existing conditions.\n\nMethodsWe conducted a population-based cohort study with over 1.4 million laboratory-confirmed COVID-19 patients using the Mexican social security database. Analysis is performed on data from March 2020 to November 2021 and over three phases: (1) from March to October in 2020, (2) from November 2020 to March 2021, and (3) from April to November 2021. We predict mortality using an ensemble machine learning method, super learner, and independently estimate the adjusted mortality relative risk of each pre-existing condition using targeted maximum likelihood estimation.\n\nResultsSuper learner fit has a high predictive performance (C-statistic: 0.907), where age is the most predictive factor for mortality. After adjusting for demographic factors, renal disease, hypertension, diabetes, and obesity are the most impactful pre-existing conditions. Phase analysis shows that the adjusted mortality risk decreased over time while relative risk increased for each pre-existing condition.\n\nConclusionsWhile age is the most important predictor of mortality, younger individuals with hypertension, diabetes and obesity are at comparable mortality risk as individuals who are 20 years older without any of the three conditions. Our model can be continuously updated to identify individuals who should most be protected against infection as the pandemic evolves.\n\nKey messagesO_ST_ABSWhat is already known on this topicC_ST_ABSStudies for Mexico and other countries have suggested that pre-existing conditions such as renal disease, diabetes, hypertension, and obesity are strongly associated with COVID-19 mortality. While age and the presence of pre-existing conditions have been shown to predict mortality, other studies have typically used less powerful statistical approaches, have had smaller sample sizes, and have not been able to describe changes over time.\n\nWhat this study addsThis study examines mortality risk in a very large population (> 60 M); it uses powerful ensemble machine learning methods that outperform regression analyses; and it demonstrates marked changes over time in the degree to which different risk factors predict mortality.\n\nHow this study might affect research, practice or policyBecause we show an important improvement in predictive performance over traditional regression analyses, and the ability to update estimates as the pandemic evolves, we argue that these methods should be much more widely used to inform national programming in Mexico and elsewhere. Programs that assume that predictive models dont change over time as variants emerge and as pre-existing immunity evolves due to vaccination and prior infection will not accurately predict mortality risk.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Lauren D. Liao",
-        "author_inst": "University of California, Berkeley"
-      },
-      {
-        "author_name": "Alan E Hubbard",
-        "author_inst": "University of California, Berkeley"
-      },
-      {
-        "author_name": "Juan Pablo Gutierrez",
-        "author_inst": "Universidad Nacional Aut\u00f3noma de M\u00e9xico"
-      },
-      {
-        "author_name": "Arturo Juarez Flores",
-        "author_inst": "Universidad Nacional Aut\u00f3noma de M\u00e9xico"
-      },
-      {
-        "author_name": "Kendall Kikkawa",
-        "author_inst": "Micron Technology"
-      },
-      {
-        "author_name": "Ronit Gupta",
-        "author_inst": "University of California, Berkeley"
-      },
-      {
-        "author_name": "Yana Yarmolich",
-        "author_inst": "University of California, Berkeley"
-      },
-      {
-        "author_name": "Iv\u00e1n de Jes\u00fas Ascencio-Montiel",
-        "author_inst": "Instituto Mexicano del Seguro Social"
-      },
-      {
-        "author_name": "Stefano M. Bertozzi",
-        "author_inst": "University of Washington, University of California, Berkeley, and Instituto Nacional de Salud P\u00fablica"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2023.01.16.23284640",
     "rel_title": "Post-pandemic modeling of COVID-19: Waning immunity determines recurrence frequency",
@@ -124990,6 +124040,93 @@
     "type": "new results",
     "category": "cell biology"
   },
+  {
+    "rel_doi": "10.1101/2023.01.17.524469",
+    "rel_title": "A Systematic Survey of Reversibly Covalent Dipeptidyl Inhibitors of the SARS-CoV-2 Main Protease",
+    "rel_date": "2023-01-18",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.17.524469",
+    "rel_abs": "SARS-CoV-2 is the coronavirus pathogen of the currently prevailing COVID-19 pandemic. It relies on its main protease (MPro) for replication and pathogenesis. MPro is a demonstrated target for the development of antivirals for SARS-CoV-2. Past studies have systematically explored tripeptidyl inhibitors such as nirmatrelvir as MPro inhibitors. However, dipeptidyl inhibitors especially those with a spiro residue at their P2 position have not been systematically investigated. In this work, we synthesized about 30 reversibly covalent dipeptidyl MPro inhibitors and characterized them on in vitro enzymatic inhibition potency, structures of their complexes with MPro, cellular MPro inhibition potency, antiviral potency, cytotoxicity, and in vitro metabolic stability. Our results indicated that MPro has a flexible S2 pocket that accommodates dipeptidyl inhibitors with a large P2 residue and revealed that dipeptidyl inhibitors with a large P2 spiro residue such as (S)-2-azaspiro[4,4]nonane-3-carboxylate and (S)-2-azaspiro[4,5]decane-3-carboxylate have optimal characteristics. One compound MPI60 containing a P2 (S)-2-azaspiro[4,4]nonane-3-carboxylate displayed high antiviral potency, low cellular cytotoxicity, and high in vitro metabolic stability and can be potentially advanced to further preclinical tests.",
+    "rel_num_authors": 18,
+    "rel_authors": [
+      {
+        "author_name": "Zhi Zachary Geng",
+        "author_inst": "Texas A M University"
+      },
+      {
+        "author_name": "Sandeep Atla",
+        "author_inst": "Texas AM University, Department of Chemistry"
+      },
+      {
+        "author_name": "Namir Shaabani",
+        "author_inst": "Sorrento Therapeutics"
+      },
+      {
+        "author_name": "Veerabhadra R Vulupara",
+        "author_inst": "Texas AM University, Department of Chemistry"
+      },
+      {
+        "author_name": "Kai S Yang",
+        "author_inst": "Texas AM University, Department of Chemistry"
+      },
+      {
+        "author_name": "Yugendar R Alugubelli",
+        "author_inst": "Texas AM University, Department of Chemistry"
+      },
+      {
+        "author_name": "Kaustav Khatua",
+        "author_inst": "Texas AM University, Department of Chemistry"
+      },
+      {
+        "author_name": "Peng-Hsun Chase Chen",
+        "author_inst": "Texas AM University, Department of Chemistry"
+      },
+      {
+        "author_name": "Jing Xiao",
+        "author_inst": "Texas AM University, Department of Chemistry"
+      },
+      {
+        "author_name": "Lauren R Blankenship",
+        "author_inst": "Texas AM University, Department of Chemistry"
+      },
+      {
+        "author_name": "Xinyu R Ma",
+        "author_inst": "Texas AM University, Department of Chemistry"
+      },
+      {
+        "author_name": "Erol Can Vatansever",
+        "author_inst": "Texas AM University, Department of Chemistry"
+      },
+      {
+        "author_name": "Chia-Chuan Cho",
+        "author_inst": "Texas AM University, Department of Chemistry"
+      },
+      {
+        "author_name": "Yuying Ma",
+        "author_inst": "Texas AM University, Department of Chemistry"
+      },
+      {
+        "author_name": "Robert Allen",
+        "author_inst": "Sorrento Therapeutics"
+      },
+      {
+        "author_name": "Henry Ji",
+        "author_inst": "Sorrento Therapeutics"
+      },
+      {
+        "author_name": "Shiqing Xu",
+        "author_inst": "Texas AM University"
+      },
+      {
+        "author_name": "Wenshe R Liu",
+        "author_inst": "Texas AM Drug Discovery Laboratory, Department of Chemistry, Texas AM University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "biochemistry"
+  },
   {
     "rel_doi": "10.1101/2023.01.17.524492",
     "rel_title": "Discovery of highly potent small molecule pan-coronavirus fusion inhibitors",
@@ -126519,29 +125656,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2023.01.13.22274536",
-    "rel_title": "Occupational Determinants of COVID-19 Cumulative Incidence and Vaccination Rate in the United States",
-    "rel_date": "2023-01-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.13.22274536",
-    "rel_abs": "ObjectiveWe aim to study the relationship between occupation distribution within each county and COVID-19 cumulative incidence and vaccination rate in the United States.\n\nMethodsWe collected county-level data from January 22, 2020 up to December 25, 2021. We fit multivariate linear models to find the relationship of the percentage of people employed by 23 main occupations.\n\nResultsCounties with more health-related jobs, office support roles, community service, sales, production and material moving occupations had higher COVID-19 cumulative incidence. During the uptick of the \"Delta\" COVID variant (stratified period July 1-Dec 25), counties with more transportation occupations had significantly more COVID-19 cumulative incidence than before.\n\nSignificanceUnderstanding the association between occupations and COVID-19 cumulative incidence on an ecological level can provide information for precision public health strategies for prevention and protecting vulnerable workers.\n\nImpact StatementWe used data from US Census and COVID-19 data to explore the association between occupations and COVID-19 cumulative incidence and vaccination rate on an ecological level, which can provide information for precision public health strategies for prevention of spread of disease and protecting vulnerable workers.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "John S. Ji",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Dustin T. Duncan",
-        "author_inst": "Columbia University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2023.01.13.23284467",
     "rel_title": "Coverage of primary and booster vaccination against COVID-19 by socioeconomic level: A nationwide cross-sectional registry study",
@@ -126860,6 +125974,25 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2023.01.12.23284481",
+    "rel_title": "Data-driven Targeting of COVID-19 Vaccination Programs: An Analysis of the Evidence on Impact, Implementation, Ethics and Equity",
+    "rel_date": "2023-01-13",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.12.23284481",
+    "rel_abs": "The data-driven targeting of COVID-19 vaccination programs is a major determinant of the ongoing toll of COVID-19. Targeting of access to, outreach about and incentives for vaccination can reduce total deaths by 20-50 percent relative to a first-come-first-served allocation. This piece performs a systematic review of the modeling literature on the relative benefits of targeting different groups for vaccination and evaluates the broader scholarly evidence - including analyses of real-world challenges around implementation, equity, and other ethical considerations - to guide vaccination targeting strategies. Three-quarters of the modeling studies reviewed concluded that the most effective way to save lives, reduce hospitalizations and mitigate the ongoing toll of COVID-19 is to target vaccination program resources to high-risk people directly rather than reducing transmission by targeting low-risk people. There is compelling evidence that defining vulnerability based on a combination of age, occupation, underlying medical conditions and geographic location is more effective than targeting based on age alone. Incorporating measures of economic vulnerability into the prioritization scheme not only reduces mortality but also improves equity. The data-driven targeting of COVID-19 vaccination program resources benefits everyone by efficiently mitigating the worst effects of the pandemic until the threat of COVID-19 has passed.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Zoe M McLaren",
+        "author_inst": "University of Maryland Baltimore County"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health policy"
+  },
   {
     "rel_doi": "10.1101/2023.01.13.23284524",
     "rel_title": "The COVID-19 antibody responses, isotypes and glycosylation: Why SARS-CoV-2 Spike protein complex binding of IgG3 is potentiated in some and immuno-pathologies manifest.",
@@ -128185,69 +127318,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2023.01.11.23284424",
-    "rel_title": "Country Learning on Maintaining Quality Essential Health Services (EHS) during COVID-19 in Timor-Leste: A mixed methods qualitative analysis",
-    "rel_date": "2023-01-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.11.23284424",
-    "rel_abs": "ObjectiveThis research study examines the enabling factors, strengths, and challenges experienced by the Timor-Leste health system as it sought to maintain quality essential health services (EHS) during the COVID-19 pandemic.\n\nDesignA mixed methods qualitative analysis\n\nSettingNational, municipal, facility levels in Baucau, Dili and Ermera Municipalities in TLS\n\nParticipantsKey informant interviews (n=40) and focus group discussions (n=6) working to maintain quality EHS in TLS.\n\nResultsA reduction in people accessing general health services was observed in 2020, reportedly due to fears of contracting COVID-19 in healthcare settings, limited resources (eg. human resources, personal protective equipment, clinical facilities, etc) and closure of health services. However, improvements in maternal child health services simultaneously improved in the areas of skilled birth attendants, prenatal coverage, and vitamin A distribution, for example. Five themes emerged as enabling factors for maintaining quality EHS including 1) high level strategy for maintaining quality EHS, 2) implementation of quality activities across the three levels of the health system, 3) measurement for quality and factors affecting service utilization 4) the positive impact of quality improvement leadership in health facilities during COVID-19, and 5) learning from each other for maintaining quality EHS now and for the future. Other countries may benefit from the challenges, strengths and enablers found on planning for quality.\n\nConclusionThe maintenance of quality essential health services (EHS) is critical to mitigate adverse health effects from the COVID-19 pandemic. When quality health services are delivered prior to and maintained during public health emergencies, they build trust within the health system and promote healthcare seeking behavior. Planning for quality as part of emergency preparedness can facilitate a high standard of care by ensuring health services continue to provide a safe environment, reduce harm, improve clinical care, and engage patients, facilities, and communities.\n\nDATA SHARINGAll data is kept with MBK and GR and is available upon request. The dataset analysis is available from the corresponding author upon reasonable request.\n\nQUALITATIVE CHECKLISTThe Standards for Reporting Qualitative Research (SRQR) checklist was used for this original research.\n\nSTRENGTHS AND LIMITATIONS OF THIS STUDYO_LIThe qualitative data gave detailed insights to the operationalization of key strategic COVID-19 emergency documents and the national quality implementation strategy.\nC_LIO_LIData collection was performed in three out of thirteen municipalities, including the largest metropolitan city of Dili.\nC_LIO_LIThe qualitative research was conducted in the participants native language (Tetum).\nC_LIO_LINot all pre-identified national level KII participants were available to provide feedback.\nC_LI",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Melissa Kleine Bingham Ms",
-        "author_inst": "World Health Organization"
-      },
-      {
-        "author_name": "Gregorio Rangel Mr",
-        "author_inst": "World Health Organization"
-      },
-      {
-        "author_name": "Diana Sarakbi Ms",
-        "author_inst": "Queens University"
-      },
-      {
-        "author_name": "Treasa Kelleher Dr",
-        "author_inst": "World Health Organization"
-      },
-      {
-        "author_name": "Nana Mensah Abrampah Ms",
-        "author_inst": "The London School of Hygiene & Tropical Medicine"
-      },
-      {
-        "author_name": "Matthew Neilson Dr",
-        "author_inst": "World Health Organization"
-      },
-      {
-        "author_name": "Oriane Bodson Ms",
-        "author_inst": "World Health Organization"
-      },
-      {
-        "author_name": "Philippa White Dr",
-        "author_inst": "World Health Organization"
-      },
-      {
-        "author_name": "Vinay Bothra Dr",
-        "author_inst": "World Health Organization"
-      },
-      {
-        "author_name": "Helder M. de Carvalho Dr",
-        "author_inst": "Ministerio da Saude de Timor-Leste"
-      },
-      {
-        "author_name": "Feliciano da C.A. Pinto Dr",
-        "author_inst": "Ministerio da Saude de Timor-Leste"
-      },
-      {
-        "author_name": "Shamsuzzoha Babar Syed Dr",
-        "author_inst": "World Health Organization"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2023.01.11.23284437",
     "rel_title": "A cross sectional survey examining the association of clinician characteristics with perceived changes in cervical cancer screening and colposcopy practice during the COVID-19 pandemic",
@@ -128594,6 +127664,97 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2023.01.11.23284427",
+    "rel_title": "Genetic determinants of severe COVID-19 in young Asian and Middle Eastern patients",
+    "rel_date": "2023-01-11",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.11.23284427",
+    "rel_abs": "Studies of genetic factors associated with severe COVID-19 in young adults have been limited in non-Caucasian populations. Here, we use whole exome sequencing to characterize the genetic landscape of severe COVID-19 in a well phenotyped cohort of otherwise healthy, young adults (N=55; mean age 34.1 {+/-} SD 5.0 years) representing 16 countries in Asia, the Middle East, and North Africa. Our findings show enrichment of rare, likely deleterious missense and truncating variants in interferon-mediated and bacterial infection-susceptibility genes, when compared to control, mildly affected, or asymptomatic COVID-19 patients (N = 25), or to general populations representing Asia and the Middle East. Genetic variants tended to associate with mortality, intensive care admission, and ventilation support. Our findings confirm the association of interferon pathway genes with severe COVID-19 and highlight the importance of extending genetic studies to diverse populations given implications for pan-ethnic therapeutic and genetic screening options.\n\nAuthor SummaryBased on the hypothesis that rare monogenic variants contribute to the severity of SARS-CoV-2 infection outcomes, we performed whole exome sequencing in young, previously healthy patients with severe COVID-19 of Asian or Middle Eastern origins. We found an enrichment of rare missense and truncating variants in immune-related genes, mainly associated with interferon pathways and susceptibility to bacterial infections, which can be therapeutic targets. Genetic findings tended to correlate with mortality, intensive care unit (ICU) admission, high dependency unit (HDU) admission, and invasive ventilation.",
+    "rel_num_authors": 19,
+    "rel_authors": [
+      {
+        "author_name": "Beshr Badla",
+        "author_inst": "Mohammed Bin Rashid University of Medicine and Health Sciences Hamdan Bin Mohammed College of Dental Medicine"
+      },
+      {
+        "author_name": "Mohamed Hanifa",
+        "author_inst": "Mohammed Bin Rashid University of Medicine and Health Sciences"
+      },
+      {
+        "author_name": "Ruchi Jain",
+        "author_inst": "Al Jalila Children's Specialty Hospital"
+      },
+      {
+        "author_name": "Maha El Naofal",
+        "author_inst": "Al Jalila Children's Specialty Hospital"
+      },
+      {
+        "author_name": "Nour Halabi",
+        "author_inst": "Al Jalila Children's Specialty Hospital"
+      },
+      {
+        "author_name": "Sawsan Yaslam",
+        "author_inst": "Al Jalila Children's Specialty Hospital"
+      },
+      {
+        "author_name": "Sathishkumar Ramaswamy",
+        "author_inst": "Al Jalila Children's Specialty Hospital"
+      },
+      {
+        "author_name": "Alan Taylor",
+        "author_inst": "Al Jalila Children's Specialty Hospital"
+      },
+      {
+        "author_name": "Roudha Al Falasi",
+        "author_inst": "Al Jalila Children's Specialty Hospital"
+      },
+      {
+        "author_name": "Shruti Shenbagam",
+        "author_inst": "Al Jalila Children's Specialty Hospital"
+      },
+      {
+        "author_name": "Hamda Khansaheb",
+        "author_inst": "Dubai Health Authority"
+      },
+      {
+        "author_name": "Hanan Al Suwaidi",
+        "author_inst": "Mohammed Bin Rashid University of Medicine and Health Sciences"
+      },
+      {
+        "author_name": "Norbert Nowotny",
+        "author_inst": "University of Veterinary Medicine Vienna: Veterinarmedizinische Universitat Wien"
+      },
+      {
+        "author_name": "Rizwana Popatia",
+        "author_inst": "Mohammed Bin Rashid University of Medicine and Health Sciences"
+      },
+      {
+        "author_name": "Alawi Alsheikh-Ali",
+        "author_inst": "Mohammed Bin Rashid University of Medicine and Health Sciences Hamdan Bin Mohammed College of Dental Medicine"
+      },
+      {
+        "author_name": "Abdulla Al Khayat",
+        "author_inst": "Al Jalila Children's Specialty Hospital"
+      },
+      {
+        "author_name": "Tom Loney",
+        "author_inst": "Mohammed Bin Rashid University of Medicine and Health Sciences"
+      },
+      {
+        "author_name": "Laila Al Dabal",
+        "author_inst": "Dubai Health Authority"
+      },
+      {
+        "author_name": "Ahamd  N Abou Tayoun",
+        "author_inst": "Al Jalila Children's Specialty Hospital"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "genetic and genomic medicine"
+  },
   {
     "rel_doi": "10.1101/2023.01.03.22277971",
     "rel_title": "Impact of COVID-19 pandemic on cancer screening in Denmark: A register-based study",
@@ -129839,37 +129000,6 @@
     "type": "new results",
     "category": "ecology"
   },
-  {
-    "rel_doi": "10.1101/2023.01.09.523246",
-    "rel_title": "Unique amino acid substitution in RBD region of SARS-CoV-2 Omicron XAY.2",
-    "rel_date": "2023-01-09",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.09.523246",
-    "rel_abs": "We attempted to explain the rare mutation at the receptor binding domain of the spike protein in the XAY.2 variant of SARS-CoV-2 from the perspective of hydrophobic interactions. We propose that decreasing hydrophobicity at position 446 and 486 of the RBD region of the spike protein might affect the infectivity of SARS-CoV-2. We also estimated the probable mutations at the 446 and 486 position the virus may acquire, leading to a decreased hydrophobicity.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Lekha Salsekar",
-        "author_inst": "Council of Scientific and Industrial Research-National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, India."
-      },
-      {
-        "author_name": "Shefali Rahangdale",
-        "author_inst": "Council of Scientific and Industrial Research-National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, India."
-      },
-      {
-        "author_name": "Ekant Tamboli",
-        "author_inst": "Council of Scientific and Industrial Research-National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, India."
-      },
-      {
-        "author_name": "Krishna Khairnar",
-        "author_inst": "Council of Scientific and Industrial Research-National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, India."
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "genomics"
-  },
   {
     "rel_doi": "10.1101/2023.01.06.23284223",
     "rel_title": "Nursing Intervention Analysis in COVID-19 Negative Pressure Isolation Wards and General Wards: Observational study",
@@ -130316,6 +129446,77 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
+  {
+    "rel_doi": "10.1101/2023.01.05.23284247",
+    "rel_title": "Identification of differences in the magnitude and specificity of SARS-CoV-2 nucleocapsid antibody responses in naturally infected and vaccinated individuals",
+    "rel_date": "2023-01-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.05.23284247",
+    "rel_abs": "BackgroundAs there are limited data on B cell epitopes for the nucleocapsid protein in SARS-CoV-2, we sought to identify the immunodominant regions within the N protein, recognized by patients with varying severity of natural infection with the Wuhan strain (WT), delta, omicron and in those who received the Sinopharm vaccines, which is an inactivated, whole virus vaccine.\n\nMethodsUsing overlapping peptides representing the N protein, with an in-house ELISA, we mapped the immunodominant regions within the N protein, in seronegative (n=30), WT infected (n=30), delta infected (n=30), omicron infected+vaccinated (n=20) and Sinopharm (BBIBP-CorV) vaccinees (n=30). We then investigated the sensitivity and specificity of these immunodominant regions and analysed their conservation with other SARS-CoV-2 variants of concern, seasonal human coronaviruses and bat Sarbecoviruses. We then investigated the kinetics of responses to these regions in those with varying severity of acute COVID-19.\n\nResultsWe identified four immunodominant regions aa 29-52, aa 155-178, aa 274 to 297 and aa 365 to 388, were highly conserved within SARS-CoV-2 and the bat coronaviruses. The magnitude of responses to these regions varied based on the infecting SARS-CoV-2 variants, with WT infected individuals predominantly recognizing aa155 to 178 regions, delta infected individuals and vaccinated+omicron infected individuals predominantly recognizing regions aa 29 to 52 and aa 274 to 294 regions. Sinopharm vaccinees recognized all four regions, with the magnitude of responses significantly lower than other groups. >80% of individuals gave responses above the positive cut-off threshold to many of the four regions, with some differences with individuals who were infected with different VoCs. These regions were found to be 100% specific, as none of the seronegative individuals gave any responses.\n\nConclusionsN-protein specific responses appear to be detectable in over 90% of those who were naturally infected or vaccinated with a whole virus inactivated vaccine, with responses mainly directed against four regions of the protein, which were highly conserved. As these regions were highly specific with high sensitivity, they have a potential to be used to develop diagnostic assays and to be used in development of vaccines.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Pradeep D Pushpakumara",
+        "author_inst": "University of Sri Jayewardenepura"
+      },
+      {
+        "author_name": "Chandima Jeewandara",
+        "author_inst": "University of Sri Jayewardenepura"
+      },
+      {
+        "author_name": "Farha Bary",
+        "author_inst": "University of Sri Jayewardenepura"
+      },
+      {
+        "author_name": "Deshan Madushanka",
+        "author_inst": "University of Sri Jayewardenepura"
+      },
+      {
+        "author_name": "Lahiru Perera",
+        "author_inst": "University of Sri Jayewardenepura"
+      },
+      {
+        "author_name": "Inoka S Aberathna",
+        "author_inst": "University of Sri Jayewardenepura"
+      },
+      {
+        "author_name": "Thashmi Nimasha",
+        "author_inst": "University of Sri Jayewardenepura"
+      },
+      {
+        "author_name": "Jeewantha Jayamali",
+        "author_inst": "University of Sri Jayewardenepura"
+      },
+      {
+        "author_name": "Thushali Ranasinghe",
+        "author_inst": "University of Sri Jayewardenepura"
+      },
+      {
+        "author_name": "Heshan Kuruppu",
+        "author_inst": "University of Sri Jayewardenepura Faculty of Medical Sciences"
+      },
+      {
+        "author_name": "Saubhagya Danasekara",
+        "author_inst": "University of Sri Jayewardenepura"
+      },
+      {
+        "author_name": "Ananda Wijewickrama",
+        "author_inst": "National Institute of infectious diseases"
+      },
+      {
+        "author_name": "Graham Ogg",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Gathsaurie Neelika Malavige",
+        "author_inst": "University of Sri Jayewardenepura"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2023.01.06.23284283",
     "rel_title": "Impact of the COVID-19 pandemic on food safety inspection outcomes in Toronto, Canada: a Bayesian interrupted time series analysis",
@@ -131977,61 +131178,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2023.01.05.522853",
-    "rel_title": "The SARS-CoV-2 Spike protein induces long-term transcriptional perturbations of mitochondrial metabolic genes, causes cardiac fibrosis, and reduces myocardial contractile in obese mice",
-    "rel_date": "2023-01-05",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.05.522853",
-    "rel_abs": "BackgroundAs the pandemic evolves, post-acute sequelae of CoV-2 (PACS) including cardiovascular manifestations have emerged as a new health threat. This study aims to study whether the Spike protein plus obesity can exacerbate PACS-related cardiomyopathy.\n\nMethodsA Spike protein-pseudotyped (Spp) virus with the proper surface tropism of SARS-CoV-2 was developed for viral entry assay in vitro and administration into high fat diet (HFD)-fed mice. The systemic viral loads and cardiac transcriptomes were analyzed at 2 and 24 hrs, 3, 6, and 24 weeks post introducing (wpi) Spp using RNA-seq or real time RT-PCR. Echocardiography was used to monitor cardiac functions.\n\nResultsLow-density lipoprotein cholesterol enhanced viral uptake in endothelial cells, macrophages, and cardiomyocyte-like H9C2 cells. Selective cardiac and adipose viral depositions were observed in HFD mice but not in normal-chow-fed mice. The cardiac transcriptional signatures in HFD mice at 3, 6, and 24 wpi showed systemic suppression of mitochondria respiratory chain genes including ATP synthases and nicotinamide adenine dinucleotide:ubiquinone oxidoreductase gene members, upregulation of stress pathway-related crucial factors such as nuclear factor-erythroid 2-related factor 1 and signal transducer and activator of transcription 5A, and increases in expression of glucose metabolism-associated genes. As compared with the age-matched HFD control mice, cardiac ejection fraction and fractional shortening were significantly decreased, while left ventricular end-systolic diameter and volume were significantly elevated, and cardiac fibrosis was increased in HFD mice at 24 wpi.\n\nConclusionOur data demonstrated that the Spike protein could induce long-term transcriptional suppression of mitochondria metabolic genes and cause cardiac fibrosis and myocardial contractile impairment, providing mechanistic insights to PACS-related cardiomyopathy.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Xiaoling Cao",
-        "author_inst": "University of South Carolina"
-      },
-      {
-        "author_name": "Vi Nguyen",
-        "author_inst": "University of South Carolina"
-      },
-      {
-        "author_name": "Joseph Tsai",
-        "author_inst": "UC San Diego School of Medicine"
-      },
-      {
-        "author_name": "Chao Gao",
-        "author_inst": "University of South Carolina"
-      },
-      {
-        "author_name": "Yan Tian",
-        "author_inst": "Central South University"
-      },
-      {
-        "author_name": "Yuping Zhang",
-        "author_inst": "Central South University"
-      },
-      {
-        "author_name": "Wayne Carver",
-        "author_inst": "University of South Carolina"
-      },
-      {
-        "author_name": "Hippokratis Kiaris",
-        "author_inst": "University of South Carolina"
-      },
-      {
-        "author_name": "Taixing Cui",
-        "author_inst": "University of South Carolina"
-      },
-      {
-        "author_name": "Wenbin Tan",
-        "author_inst": "University of South Carolina, School of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2023.01.03.22284042",
     "rel_title": "SARS-CoV-2 Reinfection is Preceded by Unique Biomarkers and Related to Initial Infection Timing and Severity: an N3C RECOVER EHR-Based Cohort Study",
@@ -132538,6 +131684,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2023.01.02.23284120",
+    "rel_title": "The time between vaccination and infection impacts immunity against SARS-CoV-2 variants",
+    "rel_date": "2023-01-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.02.23284120",
+    "rel_abs": "As the COVID-19 pandemic continues, long-term immunity against SARS-CoV-2 will be globally important. Official weekly cases have not dropped below 2 million since September of 2020, and continued emergence of novel variants have created a moving target for our immune systems and public health alike. The temporal aspects of COVID-19 immunity, particularly from repeated vaccination and infection, are less well understood than short-term vaccine efficacy. In this study, we explore the impact of combined vaccination and infection, also known as hybrid immunity, and the timing thereof on the quality and quantity of antibodies produced by a cohort of 96 health care workers. We find robust neutralizing antibody responses among those with hybrid immunity against all variants, including Omicron BA.2, and we further found significantly improved neutralizing titers with longer vaccine-infection intervals up to 400 days. These results indicate that anti-SARS-CoV-2 antibody responses undergo continual maturation following primary exposure by either vaccination or infection for at least 400 days after last antigen exposure. We show that neutralizing antibody responses improved upon secondary boosting with greater impact seen after extended intervals. Our findings may also extend to booster vaccine doses, a critical consideration in future vaccine campaign strategies.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Timothy A. Bates",
+        "author_inst": "Oregon Health & Science University"
+      },
+      {
+        "author_name": "Hans C. Leier",
+        "author_inst": "Oregon Health & Science University"
+      },
+      {
+        "author_name": "Savannah K. McBride",
+        "author_inst": "Oregon Health & Science University"
+      },
+      {
+        "author_name": "Devin Schoen",
+        "author_inst": "Oregon Health & Science University"
+      },
+      {
+        "author_name": "Zoe L. Lyski",
+        "author_inst": "Oregon Health & Science University"
+      },
+      {
+        "author_name": "David X. Lee",
+        "author_inst": "Oregon Health & Science University"
+      },
+      {
+        "author_name": "William B. Messer",
+        "author_inst": "Immunology, Oregon Health & Science University"
+      },
+      {
+        "author_name": "Marcel E. Curlin",
+        "author_inst": "Oregon Health & Science University"
+      },
+      {
+        "author_name": "Fikadu G. Tafesse",
+        "author_inst": "Oregon Health & Science University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2023.01.03.23284130",
     "rel_title": "A Phase 2/3 observer-blind, randomized, controlled study to determine the safety and immunogenicity of SARS-CoV-2 recombinant spike protein vaccine in Indian children and adolescents aged 2 to 17 years",
@@ -134019,37 +133216,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2023.01.01.522435",
-    "rel_title": "L-shape distribution of the relative substitution rate (c micro) observed for SARS-COV-2 genome, inconsistent with the selectionist theory, the neutral theory and the nearly neutral theory but a near-neutral balanced selection theory: implication on neutralist-selectionist debate",
-    "rel_date": "2023-01-03",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.01.522435",
-    "rel_abs": "The genomic substitution rate (GSR) of SARS-CoV-2 exhibits a molecular clock feature and does not change under fluctuating environmental factors such as the infected human population (100-107), vaccination etc.. The molecular clock feature is believed to be inconsistent with the selectionist theory (ST). The GSR shows lack of dependence on the effective population size, suggesting Ohtas nearly neutral theory (ONNT) is not applicable to this virus. Big variation of the substitution rate within its genome is also inconsistent with Kimuras neutral theory (KNT). Thus, all three existing evolution theories fail to explain the evolutionary nature of this virus. In this paper, we proposed a Segment Substitution Rate Model (SSRM) under non-neutral selections and pointed out that a balanced mechanism between negative and positive selection of some segments that could also lead to the molecular clock feature. We named this hybrid mechanism as near-neutral balanced selection theory (NNBST) and examined if it was followed by SARS-CoV-2 using the three independent sets of SARS-CoV-2 genomes selected by the Nextstrain team. Intriguingly, the relative substitution rate of this virus exhibited an L-shaped probability distribution consisting with NNBST rather than Poisson distribution predicted by KNT or an asymmetric distribution predicted by ONNT in which nearly neutral sites are believed to be slightly deleterious only, or the distribution that is lack of nearly neutral sites predicted by ST. The time-dependence of the substitution rates for some segments and their correlation with the vaccination were observed, supporting NNBST. Our relative substitution rate method provides a tool to resolve the long standing \"neutralist-selectionist\" controversy. Implications of NNBST in resolving Lewontins Paradox is also discussed.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Chun Wu",
-        "author_inst": "Rowan University"
-      },
-      {
-        "author_name": "Nicholas Paradis",
-        "author_inst": "Rowan University"
-      },
-      {
-        "author_name": "Phillip Lakernick",
-        "author_inst": "Rowan University"
-      },
-      {
-        "author_name": "Mariya Hryb",
-        "author_inst": "Rowan University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "evolutionary biology"
-  },
   {
     "rel_doi": "10.1101/2022.12.31.522389",
     "rel_title": "Nirmatrelvir Resistance in SARS-CoV-2 Omicron_BA.1 and WA1 Replicons and Escape Strategies",
@@ -134428,6 +133594,69 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.12.27.22283698",
+    "rel_title": "Safety and Effectiveness of SA58 Nasal Spray against COVID-19 Infection in Medical Personnel\uff1aAn Open-label, Blank-controlled Study",
+    "rel_date": "2022-12-31",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.27.22283698",
+    "rel_abs": "Approved COVID-19 vaccines to date have limited effectiveness in protecting infection and blocking transmission. A nasal spray of broad-spectrum antibody against COVID-19 (SA58 Nasal Spray) has recently been developed by Sinovac Life Sciences Co., Ltd.. From October 31 to November 30, 2022, an open-label, blank controlled study on the SA58 Nasal Spray against COVID-19 infection was conducted with the medical personnel working in the designated COVID-19 hospitals and Fangcang shelter hospitals (alternate care sites) of COVID-19 cases in Hohhot city, the Inner Mongolia Autonomous Region. A total of 6662 medical personnel were involved in this study: 3368 used SA58 Nasal Spray from the drug group, and 3294 not used from blank control group. The medication was self-administered intranasally 1[~]2 times per day with an interval of 6 hours for 30 days.. The safety results indicated that the SA58 Nasal Spray was well tolerant. The incidence of adverse events (AEs) was 28.6% (497/1736), and the majority of the AEs were mild and from administrative site. 135 COVID-19 cases were identified for SARS-CoV-2 by RT-PCR during the 30-day observation. The cumulative incidence of COVID-19 in the drug group and the control group were 0.026% and 0.116%, respectively. The effectiveness of the SA58 Nasal Spray for preventing COVID-19 infection among medical personnel was evaluated as 77.7% (95% CI: 52.2% - 89.6%). In conclusion, the SA58 Nasal Spray is well-tolerant and highly effective against COVID-19 infection.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Shujie Si",
+        "author_inst": "Inner Mongolia Fourth Hospital"
+      },
+      {
+        "author_name": "Canrui Jin",
+        "author_inst": "Sinovac Biotech Co., Ltd."
+      },
+      {
+        "author_name": "Yunlong Richard Cao",
+        "author_inst": "Peking University"
+      },
+      {
+        "author_name": "Jianping Li",
+        "author_inst": "Sinovac Biotech Co., Ltd."
+      },
+      {
+        "author_name": "Biao Kan",
+        "author_inst": "Chinese Center for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Feng Xue",
+        "author_inst": "Sinovac Life Sciences Co., Ltd."
+      },
+      {
+        "author_name": "Xiaoliang Sunny Xie",
+        "author_inst": "Peking University"
+      },
+      {
+        "author_name": "Liang Fang",
+        "author_inst": "Sinovac Biotech Co., Ltd."
+      },
+      {
+        "author_name": "Gang Zeng",
+        "author_inst": "Sinovac Biotech Co., Ltd."
+      },
+      {
+        "author_name": "Shuo Zhang",
+        "author_inst": "Inner Mongolia Blood Center"
+      },
+      {
+        "author_name": "Yaling Hu",
+        "author_inst": "Sinovac Life Sciences Co., Ltd."
+      },
+      {
+        "author_name": "Xiaoping Dong",
+        "author_inst": "Chinese Center for Disease Control and Prevention"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.12.28.22283986",
     "rel_title": "Cost-effectiveness of the second COVID-19 booster vaccination in the United States",
@@ -135625,173 +134854,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2022.12.27.521990",
-    "rel_title": "An alpaca-derived nanobody neutralizes the SARS-CoV-2 omicron variant",
-    "rel_date": "2022-12-27",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.27.521990",
-    "rel_abs": "The SARS-CoV2 Omicron variant sub-lineages spread rapidly through the world, mostly due to their immune-evasive properties. This has put a significant part of the population at risk for severe disease and underscores the need for anti-SARS-CoV-2 agents that are effective against emergent strains in vulnerable patients. Camelid nanobodies are attractive therapeutic candidates due to their high stability, ease of large-scale production and potential for delivery via inhalation. Here, we characterize the RBD-specific nanobody W25, which we previously isolated from an alpaca, and show superior neutralization activity towards Omicron lineage BA.1 in comparison to all other SARS-CoV2 variants. Structure analysis of W25 in complex with the SARS-CoV2 spike surface glycoprotein shows that W25 engages an RBD epitope not covered by any of the antibodies previously approved for emergency use. Furthermore, we show that W25 also binds the spike protein from the emerging, more infectious Omicron BA.2 lineage with picomolar affinity. In vivo evaluation of W25 prophylactic and therapeutic treatments across multiple SARS-CoV-2 variant infection models, together with W25 biodistribution analysis in mice, demonstrates favorable pre-clinical properties. Together, these data endorse prioritization of W25 for further clinical development.",
-    "rel_num_authors": 38,
-    "rel_authors": [
-      {
-        "author_name": "Naphak Modhiran",
-        "author_inst": "School of Chemistry and Molecular Bioscience, the University of Queensland; Brisbane, Australia. Australian Institute for Bioengineering and Nanotechnology; Bri"
-      },
-      {
-        "author_name": "Simon Malte Lauer",
-        "author_inst": "Charite Universitatsmedizin Berlin, corporate member of Freie Universitat Berlin and Humboldt-Universitat zu Berlin, Institute of Medical Physics and Biophysics"
-      },
-      {
-        "author_name": "Alberto A Amarilla",
-        "author_inst": "School of Chemistry and Molecular Bioscience, the University of Queensland; Brisbane, Australia"
-      },
-      {
-        "author_name": "Peter Hewins",
-        "author_inst": "Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA"
-      },
-      {
-        "author_name": "Sara Irene Lopes van den Broek",
-        "author_inst": "Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen; Jagtvej 160, 2100 Copenhagen, Denmark"
-      },
-      {
-        "author_name": "Yu Shang Low",
-        "author_inst": "School of Chemistry and Molecular Bioscience, the University of Queensland; Brisbane, Australia"
-      },
-      {
-        "author_name": "Nazia Thakur",
-        "author_inst": "The Pirbright Institute; Pirbright, United Kingdom"
-      },
-      {
-        "author_name": "Benjamin Liang",
-        "author_inst": "School of Chemistry and Molecular Bioscience, the University of Queensland; Brisbane, Australia"
-      },
-      {
-        "author_name": "Guillermo Valenzuela Nieto",
-        "author_inst": "Institute of Medicine, Faculty of Medicine & Center for Interdisciplinary Studies on the Nervous System, CISNE, Universidad Austral de Chile; Valdivia, Chile"
-      },
-      {
-        "author_name": "James Jung",
-        "author_inst": "School of Chemistry and Molecular Bioscience, the University of Queensland; Brisbane, Australia"
-      },
-      {
-        "author_name": "Devina Paramitha",
-        "author_inst": "School of Chemistry and Molecular Bioscience, the University of Queensland; Brisbane, Australia"
-      },
-      {
-        "author_name": "Ariel Isaacs",
-        "author_inst": "School of Chemistry and Molecular Bioscience, the University of Queensland; Brisbane, Australia"
-      },
-      {
-        "author_name": "Julian de Sng",
-        "author_inst": "School of Chemistry and Molecular Bioscience, the University of Queensland; Brisbane, Australia"
-      },
-      {
-        "author_name": "David Song",
-        "author_inst": "Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA"
-      },
-      {
-        "author_name": "Jesper Jorgensen",
-        "author_inst": "Department of Clinical Physiology, Nuclear Medicine & PET, Copenhagen University Hospital, Rigshospitalet  Blegdamsvej 9, 2100 Copenhagen, Denmark. Cluster for "
-      },
-      {
-        "author_name": "Yorka Cheuquemilla",
-        "author_inst": "Institute of Medicine, Faculty of Medicine & Center for Interdisciplinary Studies on the Nervous System, CISNE, Universidad Austral de Chile; Valdivia, Chile"
-      },
-      {
-        "author_name": "Jorg Burger",
-        "author_inst": "Charite Universitatsmedizin Berlin, corporate member of Freie Universitat Berlin and Humboldt-Universitat zu Berlin, Institute of Medical Physics and Biophysics"
-      },
-      {
-        "author_name": "Ida Vang Andersen",
-        "author_inst": "Department of Microbiology, University of Pennsylvania; Philadelphia, PA, USA"
-      },
-      {
-        "author_name": "Johanna Himelreichs",
-        "author_inst": "Institute of Medicine, Faculty of Medicine & Center for Interdisciplinary Studies on the Nervous System, CISNE, Universidad Austral de Chile; Valdivia, Chile"
-      },
-      {
-        "author_name": "Ronald Jara",
-        "author_inst": "Institute of Medicine, Faculty of Medicine & Center for Interdisciplinary Studies on the Nervous System, CISNE, Universidad Austral de Chile; Valdivia, Chile"
-      },
-      {
-        "author_name": "Ronan MacLoughlin",
-        "author_inst": "Research and Development, Science and Emerging Technologies, Aerogen Limited; Galway Business Park, H91 HE94 Galway, Ireland"
-      },
-      {
-        "author_name": "Zaray Miranda-Chacon",
-        "author_inst": "Institute of Medicine, Faculty of Medicine & Center for Interdisciplinary Studies on the Nervous System, CISNE, Universidad Austral de Chile; Valdivia, Chile"
-      },
-      {
-        "author_name": "Pedro Chana-Cuevas",
-        "author_inst": "CETRAM & Faculty of Medical Science Universidad de Santiago de Chile; Chile"
-      },
-      {
-        "author_name": "Vasko Kramer",
-        "author_inst": "PositronPharma SA, Santiago, Chile."
-      },
-      {
-        "author_name": "Christian M.T. Spahn",
-        "author_inst": "Charite Universitatsmedizin Berlin, corporate member of Freie Universitat Berlin and Humboldt-Universitat zu Berlin, Institute of Medical Physics and Biophysics"
-      },
-      {
-        "author_name": "Thorsten Mielke",
-        "author_inst": "Microscopy and Cryo-Electron Microscopy Service Group, Max-Planck-Institute for Molecular Genetics, Berlin, Germany"
-      },
-      {
-        "author_name": "Alexander A Khromykh",
-        "author_inst": "School of Chemistry and Molecular Bioscience, the University of Queensland; Brisbane, Australia. Australian Infectious Diseases Research Centre, Global Virus Ne"
-      },
-      {
-        "author_name": "Trent Munro",
-        "author_inst": "Australian Institute for Bioengineering and Nanotechnology; Brisbane, Australia"
-      },
-      {
-        "author_name": "Martina Jones",
-        "author_inst": "Australian Institute for Bioengineering and Nanotechnology; Brisbane, Australia"
-      },
-      {
-        "author_name": "Paul R Young",
-        "author_inst": "School of Chemistry and Molecular Bioscience, the University of Queensland; Brisbane, Australia. Australian Institute for Bioengineering and Nanotechnology; Bri"
-      },
-      {
-        "author_name": "Keith Chappell",
-        "author_inst": "School of Chemistry and Molecular Bioscience, the University of Queensland; Brisbane, Australia. Australian Institute for Bioengineering and Nanotechnology; Bri"
-      },
-      {
-        "author_name": "Dalan Bailey",
-        "author_inst": "The Pirbright Institute; Pirbright, United Kingdom"
-      },
-      {
-        "author_name": "Andreas Kjaer",
-        "author_inst": "Department of Clinical Physiology, Nuclear Medicine & PET, Copenhagen University Hospital, Rigshospitalet; Blegdamsvej 9, 2100 Copenhagen, Denmark"
-      },
-      {
-        "author_name": "Matthias Manfred Herth",
-        "author_inst": "Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen; Jagtvej 160, 2100 Copenhagen, Denmark. Department "
-      },
-      {
-        "author_name": "Kellie Ann Jurado",
-        "author_inst": "Department of Microbiology, University of Pennsylvania; Philadelphia, PA, USA"
-      },
-      {
-        "author_name": "David Schwefel",
-        "author_inst": "Charite Universitatsmedizin Berlin, corporate member of Freie Universitat Berlin and Humboldt-Universitat zu Berlin, Institute of Medical Physics and Biophysics"
-      },
-      {
-        "author_name": "Alejandro Rojas-Fernandez",
-        "author_inst": "Institute of Medicine, Faculty of Medicine & Center for Interdisciplinary Studies on the Nervous System, CISNE, Universidad Austral de Chile; Valdivia, Chile. B"
-      },
-      {
-        "author_name": "Daniel Watterson",
-        "author_inst": "School of Chemistry and Molecular Bioscience, the University of Queensland; Brisbane, Australia. Australian Institute for Bioengineering and Nanotechnology; Bri"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2022.12.27.521979",
     "rel_title": "Tissue protective role of Ganetespib in SARS-CoV-2-infected Syrian golden hamsters",
@@ -136150,6 +135212,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
+  {
+    "rel_doi": "10.1101/2022.12.24.22283835",
+    "rel_title": "Literature analysis of the efficacy of COVID-19 vaccinations",
+    "rel_date": "2022-12-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.24.22283835",
+    "rel_abs": "The COVID-19 pandemic is the largest epidemic of the 21st century so far. Over 650 million people have already been infected with the SARS-CoV-2 virus. One of the ways to stop this pandemic, is to vaccinate the population and gain herd immunity. Many different vaccines are being used around the world, with differing efficacy. This review summarizes the 79 publications on the efficacy of the currently existing COVID-19 vaccines. It shows that there are eleven vaccines that have efficacy data published in a PubMed-indexed scientific journal. Most research has been done on the Pfizer/BioNTech BNT162B2 vaccine, and the eleven vaccines generally have a high efficacy in preventing illness. The Pfizer (86%-100%), Moderna (93.2%-94.1%), Sputnik-V (91.6%) and Novavax ([~]90%) vaccines show the highest efficacy, followed by the Sinovac (83.5%), QazCovid-in 82%) and Covaxin (77.8%) vaccines. The Oxford/AstraZeneca (69% - 81.5%) and Johnson & Johnson (66%) vaccines have lower efficacy in preventing illness. This overview also shows efficacies other than in preventing illness (e.g. asymptomatic, severe illness, hospitalization, death) in some cases. The results also show that the vaccines have specific effects on specific age groups (e.g. adolescents, adults, elderly) and people with diseases (e.g. leukemia, other cancers, HIV). Future research in this area will mostly focus on vaccine efficacy on specific strains of the SARS-CoV-2 virus (such as the Omicron variant) as well as the efficacy of booster vaccinations.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Tim Hulsen",
+        "author_inst": "Philips Research"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.12.25.22283940",
     "rel_title": "Clinical Virology and Effect of Vaccination and Monoclonal Antibodies against SARS-CoV-2 Omicron Sub variant BF.7 (BA.5.2.1.7) : A systematic review",
@@ -137891,61 +136972,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.12.22.521646",
-    "rel_title": "Glyco-engineered pentameric SARS-CoV-2 IgMs show superior activities compared to IgG1 orthologues",
-    "rel_date": "2022-12-23",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.22.521646",
-    "rel_abs": "Immunoglobulin M (IgM) is the largest antibody isotype with unique features like extensive glycosylation and oligomerization. Major hurdles in characterizing its properties are difficulties in the production of well-defined multimers. Here we report the expression of two SARS-CoV-2 neutralizing monoclonal antibodies in glycoengineered plants. Isotype switch from IgG1 to IgM resulted in the production of pentameric IgMs, comprising of correctly assembled 21 human protein subunits. All four recombinant monoclonal antibodies carried a highly reproducible human-type N-glycosylation profile, with a single dominant N-glycan species at each glycosite. Both pentameric IgMs exhibited increased antigen binding and virus neutralization potency, up to 390-fold, compared to the parental IgG1. Collectively, the results may impact on the future design of vaccines, diagnostics and antibody-based therapies and emphasize the versatile use of plants for the expression of highly complex human proteins with targeted posttranslational modifications.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Somanath Kallolimath",
-        "author_inst": "University of Natural Resources and Life Sciences Vienna"
-      },
-      {
-        "author_name": "Roman Palt",
-        "author_inst": "University of Natural Resources and Life Sciences Vienna"
-      },
-      {
-        "author_name": "Esther F\u00f6derl-H\u00f6benreich",
-        "author_inst": "Medical University of Graz"
-      },
-      {
-        "author_name": "Lin Sun",
-        "author_inst": "BOKU University"
-      },
-      {
-        "author_name": "Qiang Chen",
-        "author_inst": "Arizona State University"
-      },
-      {
-        "author_name": "Florian Pruckner",
-        "author_inst": "University of Southern Denmark"
-      },
-      {
-        "author_name": "Lukas Eidenberger",
-        "author_inst": "University of Natural Resources and Life Sciences Vienna"
-      },
-      {
-        "author_name": "Richard Strasser",
-        "author_inst": "University of Natural Resources and Life Sciences Vienna"
-      },
-      {
-        "author_name": "Kurt Zatloukal",
-        "author_inst": "Medical University Graz"
-      },
-      {
-        "author_name": "Herta Steinkellner",
-        "author_inst": "University of Natural Resources and Life Sciences Vienna"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "molecular biology"
-  },
   {
     "rel_doi": "10.1101/2022.12.20.22283750",
     "rel_title": "Monkeypox Post COVID19: Knowledge, Worrying, and Vaccine Adoption of the Arabic General Population",
@@ -138364,6 +137390,25 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2022.12.22.22283830",
+    "rel_title": "To test or not to test? A new behavioral epidemiology framework for COVID-19",
+    "rel_date": "2022-12-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.22.22283830",
+    "rel_abs": "Recent clinical research finds that rapid transmission of SARS-CoV-2 is facilitated by substantial undocumented asymptomatic infections. Asymptomatic infections have implications for behavioral response to voluntary testing. The paper argues that a substantial proportion of SARS-CoV-2 infections are hidden due to rational test avoidance behavior, especially among those without perceptible disease symptoms. However, if perception of disease threat is prevalence dependent, testing compliance increases in response to reported infection prevalence rate in the population. This behavior, in turn, affects infection and mortality dynamics. This paper proposes an analytical framework that explicitly incorporates prevalence-dependent testing behavior in a standard epidemiological model, generating distinctive equilibrium epidemiological outcomes with significant policy implications. Numerical simulations show that failure to consider endogenous testing behavior among asymptomatic individuals leads to over- and underestimation of infection rates at the peaks and troughs, respectively, thereby distorting the disease containment policies. The results underscore the importance of augmenting testing capacity as an effective mitigation policy for COVID-19 and similar infectious diseases.\n\nJEL CodesI12, I18",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Jayanta Sarkar",
+        "author_inst": "Queensland University of Technology"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2022.12.21.22283809",
     "rel_title": "Wastewater monitoring of SARS-CoV-2 RNA at K-12 schools: Comparison to pooled clinical testing data",
@@ -139525,81 +138570,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2022.12.20.521139",
-    "rel_title": "Altered somatic hypermutation patterns in COVID-19 patients classifies disease severity",
-    "rel_date": "2022-12-21",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.20.521139",
-    "rel_abs": "The success of the human body in fighting SARS-CoV-2 infection relies on lymphocytes and their antigen receptors. Identifying and characterizing clinically relevant receptors is of utmost importance. We report here the application of a machine learning approach, utilizing B cell receptor repertoire sequencing data from severely and mildly infected individuals with SARS-CoV-2 compared with uninfected controls. In contrast to previous studies, our approach successfully stratifies non-infected from infected individuals, as well as disease level of severity. The features that drive this classification are based on somatic hypermutation patterns, and point to alterations in the somatic hypermutation process in COVID-19 patients. These features may be used to build and adapt therapeutic strategies to COVID-19, in particular to quantitatively assess potential diagnostic and therapeutic antibodies. These results constitute a proof of concept for future epidemiological challenges.",
-    "rel_num_authors": 15,
-    "rel_authors": [
-      {
-        "author_name": "Modi Safra",
-        "author_inst": "Bar Ilan University, Ramat Gan, Israel"
-      },
-      {
-        "author_name": "Zvi Tamari",
-        "author_inst": "Bar Ilan University, Ramat Gan, Israel"
-      },
-      {
-        "author_name": "Pazit Polak",
-        "author_inst": "Bar Ilan University, Ramat Gan, Israel"
-      },
-      {
-        "author_name": "Shachaf Shiber",
-        "author_inst": "Tel Aviv University, Tel Aviv, Israel"
-      },
-      {
-        "author_name": "Moshe Matan",
-        "author_inst": "Baruch Padeh Medical Center, Poriya, Israel"
-      },
-      {
-        "author_name": "Hani Karameh",
-        "author_inst": "Hebrew University School of Medicine, Jerusalem, Israel"
-      },
-      {
-        "author_name": "Yigal Helviz",
-        "author_inst": "Hebrew University School of Medicine, Jerusalem, Israel"
-      },
-      {
-        "author_name": "Adva Levy-Barda",
-        "author_inst": "Rabin Medical Center- Belinson campus, Petah Tikva, Israel"
-      },
-      {
-        "author_name": "Vered Yahalom",
-        "author_inst": "Tel Aviv University, Tel Aviv, Israel"
-      },
-      {
-        "author_name": "Avi Peretz",
-        "author_inst": "Bar-Ilan University, Safed, Israel"
-      },
-      {
-        "author_name": "Eli Ben-Chetrit",
-        "author_inst": "Hebrew University School of Medicine, Jerusalem, Israel"
-      },
-      {
-        "author_name": "Baruch Brenner",
-        "author_inst": "Rabin Medical Center- Belinson campus, Petah Tikva, Israel"
-      },
-      {
-        "author_name": "Tamir Tuller",
-        "author_inst": "Tel Aviv University, Tel Aviv, Israel"
-      },
-      {
-        "author_name": "Meital Gal-Tanamy",
-        "author_inst": "Bar-Ilan University, Safed, Israel"
-      },
-      {
-        "author_name": "Gur Yaari",
-        "author_inst": "Bar Ilan University, Ramat Gan, Israel"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2022.12.21.521388",
     "rel_title": "SARS-CoV-2 variant-specific differences in inhibiting the effects of the PKR-activated integrated stress response",
@@ -139822,6 +138792,181 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
+  {
+    "rel_doi": "10.1101/2022.12.20.22282909",
+    "rel_title": "The onset of late severe lung impairment in COVID-19 is associated with high inflammation markers at admission and metabolic syndrome markers",
+    "rel_date": "2022-12-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.20.22282909",
+    "rel_abs": "BackgroundCOVID-19 severity is mainly related to lung impairment. However, preexisting patient characteristics and biomarkers at admission associated with this event are not precisely known.\n\nMethodsWe report 205 patients admitted for a proven COVID-19 in our institution between March 7 and April 22, 2020, particularly their comorbidities, respiratory severity, immune profile, and metabolic profile.\n\nFindingsMedian age was 70 years [interquartile range (IQR) 25-75: 60;79]; 115 (56{middle dot}1%) patients were men. Oxygen supplementation of >2L/min was required in 107 patients (52{middle dot}2%) after a median time of 8 days [IQR: 6;10] after the first symptoms; 67 (32{middle dot}7%) patients were admitted to the intensive care unit (ICU), almost exclusively due to severe hypoxia. Patients requiring >2L/min oxygen therapy and/or ICU admission were older and more frequently males, with a significantly higher body mass index (BMI), a significantly higher total cholesterol (TC) / HDL cholesterol ratio, and higher triglycerides. They also had higher plasma levels of C-reactive protein (CRP) and interleukin 6 (IL-6); IL-6 >20 ng/L and CRP >70 mg/L were significantly associated with ICU admission and/or (for patients with a decision of limitation of life-support therapy) death. Higher BMI and TC/HDL-c ratio were associated with higher CRP and IL-6 levels. Steroid therapy was performed in 61 patients; while its clinical impact was inconclusive due to heterogeneous situations, IL-6 levels decreased significantly more in these patients.\n\nInterpretationSevere COVID-19 mostly relates to late-onset pneumonia associated with preexisting metabolic syndrome markers and a surge in inflammatory markers, allowing the early identification of at-risk patients.\n\nFundingThis work was supported by Foundation University of Grenoble Alpes.",
+    "rel_num_authors": 40,
+    "rel_authors": [
+      {
+        "author_name": "Olivier EPAULARD",
+        "author_inst": "Infectious Diseases Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Audrey LE GOUELLEC",
+        "author_inst": "Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP*, TIMC-IMAG, Grenoble, France"
+      },
+      {
+        "author_name": "Marion LE MARECHAL",
+        "author_inst": "Infectious Diseases Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Benjamin NEMOZ",
+        "author_inst": "Institut de Biologie Structurale, UMR 5075 CEA-CNRS-UGA, Grenoble, France"
+      },
+      {
+        "author_name": "Anne Laure BOREL",
+        "author_inst": "Nutrition Department, Grenoble-Alpes University Hospital, Grenoble, France; Hypoxia pathophysiology laboratory INSERM U1042, Grenoble Alpes University"
+      },
+      {
+        "author_name": "Anais DARTEVEL",
+        "author_inst": "Medical Intensive Care Unit, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Hubert GHEERBRANT",
+        "author_inst": "Pneumology Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Marie Christine HERAULT",
+        "author_inst": "Department of Anaesthesia and Intensive Care Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Annick BOSSERAY",
+        "author_inst": "Internal Medicine Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Giovanna CLAVARINO",
+        "author_inst": "Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP*, TIMC-IMAG, Grenoble, France"
+      },
+      {
+        "author_name": "Julien LUPO",
+        "author_inst": "Institut de Biologie Structurale, UMR 5075 CEA-CNRS-UGA, Grenoble, France"
+      },
+      {
+        "author_name": "Damien VIGLINO",
+        "author_inst": "Emergency Department, Grenoble-Alpes University Hospital, Grenoble, France; Hypoxia pathophysiology laboratory INSERM U1042, Grenoble Alpes University"
+      },
+      {
+        "author_name": "Fanny QUENARD",
+        "author_inst": "Infectious Diseases Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Clara CANDILLE",
+        "author_inst": "Medical Intensive Care Unit, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Boubou CAMARA",
+        "author_inst": "Pneumology Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Michel DURAND",
+        "author_inst": "Department of Anaesthesia and Intensive Care Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Patrice FAURE",
+        "author_inst": "Biochemistry Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Dorra GUERGOUR",
+        "author_inst": "Biochemistry Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Elena CHIDLOVSKI",
+        "author_inst": "Internal Medicine Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Marie Christine JACOB",
+        "author_inst": "Immunology Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Sylvie LARRAT",
+        "author_inst": "Institut de Biologie Structurale, UMR 5075 CEA-CNRS-UGA, Grenoble, France"
+      },
+      {
+        "author_name": "Marie FROIDURE",
+        "author_inst": "Infectious Diseases Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Nicolas TERZI",
+        "author_inst": "Medical Intensive Care Unit, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Sebastien QUETANT",
+        "author_inst": "Pneumology Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Jean Francois PAYEN",
+        "author_inst": "Department of Anaesthesia and Intensive Care Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Barbara COLOMBE",
+        "author_inst": "Internal Medicine Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Tatiana RASKOVALOVA",
+        "author_inst": "Immunology Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Patrice MORAND",
+        "author_inst": "Institut de Biologie Structurale, UMR 5075 CEA-CNRS-UGA, Grenoble, France"
+      },
+      {
+        "author_name": "Isabelle PIERRE",
+        "author_inst": "Infectious Diseases Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Carole SCHWEBEL",
+        "author_inst": "Medical Intensive Care Unit, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Rebecca HAMIDFAR",
+        "author_inst": "Pneumology Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Laurence BOUILLET",
+        "author_inst": "Internal Medicine Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Jean Paul BRION",
+        "author_inst": "Infectious Diseases Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Candice TROCME",
+        "author_inst": "Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP*, TIMC-IMAG, Grenoble, France"
+      },
+      {
+        "author_name": "Sylvie BERTHIER",
+        "author_inst": "Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP*, TIMC-IMAG, Grenoble, France"
+      },
+      {
+        "author_name": "Carole CHIRICA",
+        "author_inst": "Biochemistry Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Anne Laure MOUNAYAR",
+        "author_inst": "Infectious Diseases Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Myriam BLANC",
+        "author_inst": "Infectious Diseases Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Patricia PAVESE",
+        "author_inst": "Infectious Diseases Department, Grenoble-Alpes University Hospital, Grenoble, France"
+      },
+      {
+        "author_name": "Bertrand TOUSSAINT",
+        "author_inst": "Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP*, TIMC-IMAG, Grenoble, France"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.12.18.22281291",
     "rel_title": "A prospective evaluation of three saliva qualitative antigen testing kits for the detection of SARS-CoV-2 in Japan",
@@ -141311,325 +140456,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pharmacology and therapeutics"
   },
-  {
-    "rel_doi": "10.1101/2022.12.17.520865",
-    "rel_title": "A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms",
-    "rel_date": "2022-12-19",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.17.520865",
-    "rel_abs": "The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. Community-driven and highly interdisciplinary, the project is collaborative and supports community standards, open access, and the FAIR data principles. The coordination of community work allowed for an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework links key molecules highlighted from broad omics data analysis and computational modeling to dysregulated pathways in a cell-, tissue- or patient-specific manner. We also employ text mining and AI-assisted analysis to identify potential drugs and drug targets and use topological analysis to reveal interesting structural features of the map. The proposed framework is versatile and expandable, offering a significant upgrade in the arsenal used to understand virus-host interactions and other complex pathologies.",
-    "rel_num_authors": 76,
-    "rel_authors": [
-      {
-        "author_name": "Anna Niarakis",
-        "author_inst": "University of Paris Saclay, Laboratoire Europeen de Recherche pour la Polyarthrite rhumatoide, Genhotel, Univ Evry, Evry, France and Lifeware Group, Inria, Sacl"
-      },
-      {
-        "author_name": "Marek Ostaszewski",
-        "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg"
-      },
-      {
-        "author_name": "Alexander Mazein",
-        "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg"
-      },
-      {
-        "author_name": "Inna Kuperstein",
-        "author_inst": "Institut Curie, PSL Research University, F 75005 Paris, France INSERM, U900, F 75005 Paris, France MINES ParisTech, PSL Research University, CBIO Centre for Com"
-      },
-      {
-        "author_name": "Marc E. Gillespie",
-        "author_inst": "Ontario Institute for Cancer Research, Toronto, ON, Canada, M5G 0A3 9)"
-      },
-      {
-        "author_name": "Martina Kutmon",
-        "author_inst": "Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, PO Box 616, 6200 MD, Maastricht, the Netherlands"
-      },
-      {
-        "author_name": "Akira Funahashi",
-        "author_inst": "Department of Biosciences and Informatics, Keio University, Kanagawa 223-8522, Japan"
-      },
-      {
-        "author_name": "Marcio Luis Acencio",
-        "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg"
-      },
-      {
-        "author_name": "Ahmed Hemedan",
-        "author_inst": "Bioinformatics core unit. Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg"
-      },
-      {
-        "author_name": "Michael Aichem",
-        "author_inst": "Department of Computer and Information Science, University of Konstanz, Universitatsstr. 10, 78464 Konstanz, Germany"
-      },
-      {
-        "author_name": "Karsten Klein",
-        "author_inst": "Department of Computer and Information Science, University of Konstanz, Universitatsstr. 10, 78464 Konstanz, Germany"
-      },
-      {
-        "author_name": "Tobias Czauderna",
-        "author_inst": "Faculty of Applied Computer Sciences & Biosciences, University of Applied Sciences Mittweida, Technikumplatz 17, 09648 Mittweida, Germany"
-      },
-      {
-        "author_name": "Felicia Burtscher",
-        "author_inst": "Bioinformatics core unit. Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg"
-      },
-      {
-        "author_name": "Takahiro G. Yamada",
-        "author_inst": "Department of Biosciences and Informatics, Keio University, Kanagawa 223-8522, Japan"
-      },
-      {
-        "author_name": "Yusuke Hiki",
-        "author_inst": "Center for Biosciences and Informatics, Graduate School of Fundamental Science and Technology, Keio University, Kanagawa 223-8522, Japan"
-      },
-      {
-        "author_name": "Noriko F. Hiroi",
-        "author_inst": "Faculty of Creative Engineering, Kanagawa Institute of Technology, Kanagawa 243-0292, Japan Keio University School of Medicine, Tokyo, 160-0016, Japan"
-      },
-      {
-        "author_name": "Finterly Hu",
-        "author_inst": "Department of Bioinformtatics - BiGCaT, NUTRIM, Maastricht University, PO Box 616, 6200 MD, Maastricht, the Netherlands  Maastricht Centre for Systems Biology ("
-      },
-      {
-        "author_name": "Nhung Pham",
-        "author_inst": "Department of Bioinformtatics - BiGCaT, NUTRIM, Maastricht University, PO Box 616, 6200 MD, Maastricht, the Netherlands  Maastricht Centre for Systems Biology ("
-      },
-      {
-        "author_name": "Friederike Ehrhart",
-        "author_inst": "Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, PO Box 616, 6200 MD, Maastricht, the Netherlands"
-      },
-      {
-        "author_name": "Egon L. Willighagen",
-        "author_inst": "Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, PO Box 616, 6200 MD, Maastricht, the Netherlands"
-      },
-      {
-        "author_name": "Alberto Valdeolivas",
-        "author_inst": "Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Aurelien Dugourd",
-        "author_inst": "Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, BIOQUANT-Center"
-      },
-      {
-        "author_name": "Francesco Messina",
-        "author_inst": "National Instritute for Infectious Diseases \"L. Spallanzani\" - IRCCS"
-      },
-      {
-        "author_name": "Marina Esteban-Medina",
-        "author_inst": "Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013, Sevilla, Spain. Computational Systems Medicine, Institute of Biome"
-      },
-      {
-        "author_name": "Maria Pena-Chilet",
-        "author_inst": "Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013, Sevilla, Spain. Computational Systems Medicine, Institute of Biome"
-      },
-      {
-        "author_name": "Kinza Rian",
-        "author_inst": "Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013, Sevilla, Spain."
-      },
-      {
-        "author_name": "Sylvain Soliman",
-        "author_inst": "Inria Saclay: Inria Centre de Recherche Saclay-Ile-de-France"
-      },
-      {
-        "author_name": "Sara Sadat Aghamiri",
-        "author_inst": "Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA"
-      },
-      {
-        "author_name": "Bhanwar Lal Puniya",
-        "author_inst": "Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA"
-      },
-      {
-        "author_name": "Tomas Helikar",
-        "author_inst": "Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA"
-      },
-      {
-        "author_name": "Vidisha Singh",
-        "author_inst": "University of Paris Saclay, Laboratoire Europeen de Recherche pour la Polyarthrite rhumatoide, Genhotel, Univ Evry, Evry, France."
-      },
-      {
-        "author_name": "Marco Farinas Fernandez",
-        "author_inst": "Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway"
-      },
-      {
-        "author_name": "Viviam Bermudez",
-        "author_inst": "Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway"
-      },
-      {
-        "author_name": "Eirini Tsirvouli",
-        "author_inst": "Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway"
-      },
-      {
-        "author_name": "Arnau Montagud",
-        "author_inst": "Barcelona Supercomputing Center (BSC)"
-      },
-      {
-        "author_name": "Vincent Noel",
-        "author_inst": "Institut Curie, PSL Research University, F 75005 Paris, France INSERM, U900, F 75005 Paris, France MINES ParisTech, PSL Research University, CBIO Centre for Com"
-      },
-      {
-        "author_name": "Miguel Ponce de Leon",
-        "author_inst": "Barcelona Supercomputing Center (BSC)"
-      },
-      {
-        "author_name": "Dieter Maier",
-        "author_inst": "Biomax Informatics AG"
-      },
-      {
-        "author_name": "Angela Bauch",
-        "author_inst": "Biomax Informatics"
-      },
-      {
-        "author_name": "Benjamin M Gyori",
-        "author_inst": "Harvard Medical School"
-      },
-      {
-        "author_name": "John A. Bachman",
-        "author_inst": "Harvard Medical School"
-      },
-      {
-        "author_name": "Agustin Luna",
-        "author_inst": "cBio Center, Divisions of Biostatistics and Computational Biology, Department of Data Sciences, Dana Farber Cancer Institute, Boston, MA, 02215, US Department o"
-      },
-      {
-        "author_name": "Janet Pinero",
-        "author_inst": "Medbioinformatics Solutions SL, Carrer dels Almogavers 165, 08018 Barcelona, Spain Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical"
-      },
-      {
-        "author_name": "Laura Furlong",
-        "author_inst": "Medbioinformatics Solutions SL, Carrer dels Almogavers 165, 08018 Barcelona, Spain Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical"
-      },
-      {
-        "author_name": "Irina Balaur",
-        "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg"
-      },
-      {
-        "author_name": "Adrien Rougny",
-        "author_inst": "National Institute of Advanced Industrial Science and Technology"
-      },
-      {
-        "author_name": "Yohan Jarosz",
-        "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg"
-      },
-      {
-        "author_name": "Rupert W. Overall",
-        "author_inst": "Institute for Biology, Humboldt University of Berlin, 10115 Berlin, Germany"
-      },
-      {
-        "author_name": "Robert Phair",
-        "author_inst": "Integrative Bioinformatics, Inc., 346 Paul Ave, Mountain View, CA, USA"
-      },
-      {
-        "author_name": "Livia Perfetto",
-        "author_inst": "Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, Italy"
-      },
-      {
-        "author_name": "Lisa Matthews",
-        "author_inst": "Department of Biochemistry & Molecular Pharmacology, NYU Langone Medical Center, New York NY 10016 USA"
-      },
-      {
-        "author_name": "Devasahayam Arokia Balaya Rex",
-        "author_inst": "Centre for Integrative Omics Data Science, Yenepoya, Derlakatte, Mangalore: 575018"
-      },
-      {
-        "author_name": "Marija Orlic-Milacic",
-        "author_inst": "Ontario Institute for Cancer Research, Toronto, ON, Canada, M5G 0A3, ORCID: 0000-0002-3218-5631"
-      },
-      {
-        "author_name": "Luis Cristobal Monraz Gomez",
-        "author_inst": "Institut Curie, PSL Research University, F 75005 Paris, France INSERM, U900, F 75005 Paris, France MINES ParisTech, PSL Research University, CBIO-Centre for Com"
-      },
-      {
-        "author_name": "Bertrand De Meulder",
-        "author_inst": "Association EISBM"
-      },
-      {
-        "author_name": "Jean Marie Ravel",
-        "author_inst": "Institut Curie, PSL Research University, F 75005 Paris, France INSERM, U900, F 75005 Paris, France MINES ParisTech, PSL Research University, CBIO-Centre for Com"
-      },
-      {
-        "author_name": "Bijay Jassal",
-        "author_inst": "Ontario Institute for Cancer Research"
-      },
-      {
-        "author_name": "Venkata P. Satagopam",
-        "author_inst": "Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg"
-      },
-      {
-        "author_name": "Guanming Wu",
-        "author_inst": "Oregon Health Sciences University, Portland, OR 97239, USA"
-      },
-      {
-        "author_name": "Martin Golebiewski",
-        "author_inst": "Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany"
-      },
-      {
-        "author_name": "Piotr Gawron",
-        "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg"
-      },
-      {
-        "author_name": "Laurence Calzone",
-        "author_inst": "Institut Curie, PSL Research University, F 75005 Paris, France INSERM, U900, F 75005 Paris, France MINES ParisTech, PSL Research University, CBIO-Centre for Com"
-      },
-      {
-        "author_name": "Jacques Beckmann",
-        "author_inst": "University of Lausanne, Lausanne, Switzerland"
-      },
-      {
-        "author_name": "Chris Evelo",
-        "author_inst": "Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, PO Box 616, 6200 MD, Maastricht, the Netherlands"
-      },
-      {
-        "author_name": "Falk Schreiber",
-        "author_inst": "Department of Computer and Information Science, University of Konstanz, Universitatsstr. 10, 78464 Konstanz, Germany  Faculty of Information Technology, Monash "
-      },
-      {
-        "author_name": "Julio Saez-Rodriguez",
-        "author_inst": "Institute for Computational Biomedicine, Heidelberg University, Faculty of Medicine, Heidelberg University Hospital, Bioquant, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Joaquin Dopazo",
-        "author_inst": "Computational Medicine Platform, Andalusian Public Foundation Progress and Health-FPS, 41013, Sevilla, Spain. Computational Systems Medicine, Institute of Biome"
-      },
-      {
-        "author_name": "Martin Kuiper",
-        "author_inst": "Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway"
-      },
-      {
-        "author_name": "Alfonso Valencia",
-        "author_inst": "Barcelona Supercomputing Center (BSC),  ICREA, Pg. Lluis Companys 23, 08010 Barcelona, Spain"
-      },
-      {
-        "author_name": "Olaf Wolkenhauer",
-        "author_inst": "Dept of Systems Biology & Bioinformatics, University of Rostock  Leibniz Institute for Food Systems Biology, at the Technical University Munich"
-      },
-      {
-        "author_name": "Hiroaki Kitano",
-        "author_inst": "The Systems Biology Institute"
-      },
-      {
-        "author_name": "Emmanuel Barillot",
-        "author_inst": "Institut Curie, PSL Research University, F 75005 Paris, France INSERM, U900, F 75005 Paris, France MINES ParisTech, PSL Research University, CBIO-Centre for Com"
-      },
-      {
-        "author_name": "Charles Auffray",
-        "author_inst": "Association EISBM"
-      },
-      {
-        "author_name": "Rudi Balling",
-        "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg"
-      },
-      {
-        "author_name": "Reinhard Schneider",
-        "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg"
-      },
-      {
-        "author_name": "- the COVID-19 Disease Map Community",
-        "author_inst": "-"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "systems biology"
-  },
   {
     "rel_doi": "10.1101/2022.12.16.520835",
     "rel_title": "High-Throughput Discovery and Characterization of Viral Transcriptional Effectors in Human Cells",
@@ -141904,6 +140730,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.12.19.22283668",
+    "rel_title": "A retrospective analysis of COVID-19 non-pharmaceutical interventions for Mexico and Peru: a modeling study",
+    "rel_date": "2022-12-19",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.19.22283668",
+    "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWWe model the observed dynamics of COVID-19 in Mexico and Peru and explore the impact of hypothetical non-pharmaceutical interventions applied on key days of civic, religious, or political nature that increased contacts and transmission events. Using as a baseline the observed epidemic curve, we apply hypothetical reductions in the contact rates during the first year of the pandemic: i) near the beginning, ii) at the beginning of the second outbreak, and iii) end of the year. The effects of the interventions are different for Mexico and Peru but underlie the fact that strong early interventions do reduce the prevalence and, in general, allow for an epidemic evolution of relatively lower prevalence than interventions applied once the epidemic is underway. We provide evidence that key calendar days are good approximations of times when contact rates change and, therefore, are efficient periods for effective interventions particularly in places with low testing and lack of contact tracing. This has helped us to recreate different outbreaks of the COVID-19 disease dynamics in Mexico and Peru and explore the impact of hypothetical interventions that reduce the contact rate.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "M. Adrian Acuna-Zegarra",
+        "author_inst": "Universidad de Sonora"
+      },
+      {
+        "author_name": "Mario Santana-Cibrian",
+        "author_inst": "UNAM ENES: Universidad Nacional Autonoma de Mexico - Escuela Nacional de Estudios Superiores Unidad Juriquilla"
+      },
+      {
+        "author_name": "Carlos E. Rodriguez Hernandez-Vela",
+        "author_inst": "UNAM IIMAS: Universidad Nacional Autonoma de Mexico Instituto de Investigaciones en Matematicas Aplicadas y Sistemas"
+      },
+      {
+        "author_name": "Ramses H. Mena",
+        "author_inst": "UNAM IIMAS: Universidad Nacional Autonoma de Mexico Instituto de Investigaciones en Matematicas Aplicadas y Sistemas"
+      },
+      {
+        "author_name": "Jorge X. Velasco-Hernandez",
+        "author_inst": "UNAM IMATE: Universidad Nacional Autonoma de Mexico, Campus Juriquilla - Instituto de Matematicas"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2022.12.17.520843",
     "rel_title": "Transgenic Mouse Models Establish a Protective Role of Type 1 IFN Response in SARS-CoV-2 infection-related Immunopathology",
@@ -143249,37 +142110,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.12.16.520684",
-    "rel_title": "Structural basis for the assembly of the DNA polymerase holoenzyme from a monkeypox virus variant",
-    "rel_date": "2022-12-16",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.16.520684",
-    "rel_abs": "The ongoing pandemic caused by a monkeypox virus (MPXV) variant has spread all over the world and raised great public health concerns. The DNA polymerase F8 of MPXV, associated with its processivity factors A22 and E4, is responsible for viral genome replication in the perinuclear sites of the infected cells as well as a critical target for developing antiviral drugs. However, the assembly and working mechanism for the DNA polymerase holoenzyme of MPXV remains elusive. Here, we present the cryo-EM structure of the DNA polymerase holoenzyme F8/A22/E4 from the 2022 West African strain at an overall resolution of 3.5 [A] and revealed the precise spatial arrangement. Surprisingly, unlike any other previously reported B-family DNA polymerase, the holoenzyme complex is assembled as a dimer of heterotrimers, of which the extra interface between the thumb domain of F8 and A22 shows a clash between A22 and substrate DNA, suggesting an auto-inhibition state. Supplying an exogenous double-stranded DNA could notably shift the hexameric form into a trimeric form, which exposes the DNA binding site of thumb domain and might represent a more active state. The structures provide a molecular basis for the design of new antiviral therapeutics that target the MPXV DNA polymerase holoenzyme.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Renhong Yan",
-        "author_inst": "School of Life Sciences, Westlake University; School of Medicine, Southern University of Science and Technology"
-      },
-      {
-        "author_name": "Yaning Li",
-        "author_inst": "School of Life Sciences, Westlake University; School of Life Sciences, Tsinghua University"
-      },
-      {
-        "author_name": "Yaping Shen",
-        "author_inst": "School of Life Sciences, Westlake University"
-      },
-      {
-        "author_name": "Ziwei Hu",
-        "author_inst": "School of Medicine, Southern University of Science and Technology"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "biochemistry"
-  },
   {
     "rel_doi": "10.1101/2022.12.15.520606",
     "rel_title": "Identification of broad, potent antibodies to functionally constrained regions of SARS-CoV-2 spike following a breakthrough infection",
@@ -143562,6 +142392,89 @@
     "type": "new results",
     "category": "biophysics"
   },
+  {
+    "rel_doi": "10.1101/2022.12.14.520265",
+    "rel_title": "COVID-19 Associated Pulmonary Aspergillosis isolates are genomically diverse but similar to each other in their responses to infection-relevant stresses",
+    "rel_date": "2022-12-15",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.14.520265",
+    "rel_abs": "Secondary infections caused by the pulmonary fungal pathogen Aspergillus fumigatus are a significant cause of mortality in patients with severe Coronavirus Disease 19 (COVID-19). Even though epithelial cell damage and aberrant cytokine responses have been linked with susceptibility to COVID-19 associated pulmonary aspergillosis (CAPA), little is known about the mechanisms underpinning co-pathogenicity. Here, we analysed the genomes of 11 A. fumigatus isolates from patients with CAPA in three centres from different European countries. CAPA isolates did not cluster based on geographic origin in a genome-scale phylogeny of representative A. fumigatus isolates. Phenotypically, CAPA isolates were more similar to the A. fumigatus A1160 reference strain than to the Af293 strain when grown in infection-relevant stresses; except for interactions with human immune cells wherein macrophage responses were similar to those induced by the Af293 reference strain. Collectively, our data indicates that CAPA isolates are genomically diverse but are more similar to each other in their responses to infection-relevant stresses. A larger number of isolates from CAPA patients should be studied to identify genetic drivers of co-pathogenicity in patients with COVID-19.\n\nImportanceCoronavirus disease 2019 (COVID-19)-associated pulmonary aspergillosis (CAPA) has been globally reported as a life-threatening complication in some patients with severe COVID-19. Most of these infections are caused by the environmental mould Aspergillus fumigatus which ranks third in the fungal pathogen priority list of the WHO. However, little is known about the molecular epidemiology of Aspergillus fumigatus CAPA strains. Here, we analysed the genomes of 11 A. fumigatus isolates from patients with CAPA in three centres from different European countries and, carried out phenotypic analyses with a view to understand the pathophysiology of the disease. Our data indicates that A. fumigatus CAPA isolates are genomically diverse but are more similar to each other in their responses to infection-relevant stresses.",
+    "rel_num_authors": 17,
+    "rel_authors": [
+      {
+        "author_name": "Matthew E Mead",
+        "author_inst": "Vanderbilt University, Nashville, Tennessee, USA"
+      },
+      {
+        "author_name": "Patricia Alves de Castro",
+        "author_inst": "Universidade de Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "Jacob B Steenwyk",
+        "author_inst": "Vanderbilt University, Nashville, Tennessee, USA"
+      },
+      {
+        "author_name": "Jean-Pierre Gangneux",
+        "author_inst": "Univ Rennes, CHU Rennes,"
+      },
+      {
+        "author_name": "Martin Hoenigl",
+        "author_inst": "Medical University of Graz, Graz, Austria"
+      },
+      {
+        "author_name": "Juergen Prattes",
+        "author_inst": "Medical University of Graz, Graz, Austria"
+      },
+      {
+        "author_name": "Riina Rautemaa-Richardson",
+        "author_inst": "The University of Manchester, Manchester, UK"
+      },
+      {
+        "author_name": "Helene Guegan",
+        "author_inst": "Univ Rennes, CHU Rennes,"
+      },
+      {
+        "author_name": "Caroline B Moore",
+        "author_inst": "The University of Manchester, Manchester, UK"
+      },
+      {
+        "author_name": "Cornelia Lass-Floerl",
+        "author_inst": "Medical University of Innsbruck, Austria"
+      },
+      {
+        "author_name": "Florian Reizine",
+        "author_inst": "Medical Intensive Care Unit , Rennes University Hospital, 35000 Rennes."
+      },
+      {
+        "author_name": "Clara Valero",
+        "author_inst": "The University of Manchester, Manchester, UK"
+      },
+      {
+        "author_name": "Norman van Rhijn",
+        "author_inst": "The University of Manchester, Manchester, UK"
+      },
+      {
+        "author_name": "Mike J Bromley",
+        "author_inst": "The University of Manchester, Manchester, UK"
+      },
+      {
+        "author_name": "Antonis Rokas",
+        "author_inst": "Vanderbilt University, Nashville, Tennessee, USA"
+      },
+      {
+        "author_name": "Gustavo H Goldman",
+        "author_inst": "Universidade de Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "Sara Gago",
+        "author_inst": "The University of Manchester, Manchester, UK"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "cell biology"
+  },
   {
     "rel_doi": "10.1101/2022.12.15.22283503",
     "rel_title": "Long-term neutralizing antibody dynamics against SARS-CoV-2 in symptomatic and asymptomatic infections: a systematic review and meta-analysis",
@@ -145183,77 +144096,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2022.12.09.22283280",
-    "rel_title": "Identification of a protein expression signature distinguishing early from organising diffuse alveolar damage in COVID-19 patients.",
-    "rel_date": "2022-12-13",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.09.22283280",
-    "rel_abs": "Diffuse alveolar damage (DAD) is a histopathological finding associated with severe viral infections, including SARS-CoV-2. However, the mechanisms mediating progression of DAD are poorly understood. Applying protein digital spatial profiling to lung tissue obtained from a cohort of 27 COVID-19 autopsy cases from the UK, we identified a protein signature (ARG1, CD127, GZMB, IDO1, Ki67, phospho-PRAS40 (T246), and VISTA that distinguishes early / exudative DAD from late / organising DAD with good predictive accuracy. These proteins warrant further investigation as potential immunotherapeutic targets to modulate DAD progression and improve patient outcome.",
-    "rel_num_authors": 14,
-    "rel_authors": [
-      {
-        "author_name": "Helen Ashwin",
-        "author_inst": "University of York"
-      },
-      {
-        "author_name": "Luke Milross",
-        "author_inst": "Newcastle University"
-      },
-      {
-        "author_name": "Julie Wilson",
-        "author_inst": "University of York"
-      },
-      {
-        "author_name": "Joaquim Majo",
-        "author_inst": "Newcastle upon Tyne Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Jimmy T. H. Lee",
-        "author_inst": "Sanger Institute"
-      },
-      {
-        "author_name": "Grant Calder",
-        "author_inst": "University of York"
-      },
-      {
-        "author_name": "Bethany Hunter",
-        "author_inst": "Newcastle University"
-      },
-      {
-        "author_name": "Sally James",
-        "author_inst": "University of York"
-      },
-      {
-        "author_name": "Dimitris Lagos",
-        "author_inst": "University of York"
-      },
-      {
-        "author_name": "Nathalie Signoret",
-        "author_inst": "University of York"
-      },
-      {
-        "author_name": "Andrew Filby",
-        "author_inst": "Newcastle University"
-      },
-      {
-        "author_name": "Omer Ali Bayraktar",
-        "author_inst": "Sanger Institute"
-      },
-      {
-        "author_name": "Andrew J Fisher",
-        "author_inst": "Newcastle University"
-      },
-      {
-        "author_name": "Paul M Kaye",
-        "author_inst": "University of York"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "pathology"
-  },
   {
     "rel_doi": "10.1101/2022.12.12.22283381",
     "rel_title": "Identifying and preventing fraudulent responses in online public health surveys: Lessons learned during the COVID-19 pandemic",
@@ -145563,6 +144405,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.12.10.22283298",
+    "rel_title": "The Use and Safety Risk of Repurposed Drugs for COVID-19 patients: Lessons Learned Utilizing the Food and Drug Administrations Adverse Event Reporting System",
+    "rel_date": "2022-12-13",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.10.22283298",
+    "rel_abs": "ObjectivesThis study was designed to assess the disproportionality analyses of adverse drug reactions (ADRs) related to hydroxychloroquine and remdesivir and how ADR reporting fluctuated during the COVID-19 pandemic.\n\nMethodsA retrospective observational study was conducted utilizing the Food and Drug Administrations Adverse Event Reporting System (FAERS) data between 2019 and 2021. The study was conducted in two phases. In the first phase, all reports associated with the drugs of interest were evaluated to assess all related adverse drug reactions. In the second phase, specific outcomes of interest (i.e., QT prolongation and renal and hepatic events) were determined to study their association with the drugs of interest. A descriptive analysis was conducted for all adverse reactions related to the drugs being studied. In addition, disproportionality analyses were conducted to compute the reporting odds ratio, the proportional reporting ratio, the information component, and the empirical Bayes geometric mean. All analyses were conducted using RStudio.\n\nResultsA total of 9,443 ADR reports related to hydroxychloroquine; 6,160 (71.49) patients were female, and higher percentage of patients of both sexes were over the age of 65 years. QT prolongation (1.48%), pain (1.38%), and arthralgia (1.25%) were most frequently reported ADRs during the COVID-19 pandemic. The association of QT prolongation with use of hydroxychloroquine was statistically significant (ROR 47.28 [95% CI 35.95-62.18]; PRR 42.41 [95% CI 32.25-55.78]; EBGM 16.08; IC 4.95) compared with fluoroquinolone. The outcome was serious medical events in 48.01% of ADR reports; 27.42% required hospitalization and 8.61% resulted in death. Of 6,673 ADR reports related to remdesivir, 3,928 (61.13%) patients were male. During 2020, the top three ADR reports were elevated liver function tests (17.26%), acute kidney injury (5.95%) and death (2.84%). Additionally, 42.71% of ADR reports indicated serious medical events; 19.69% resulted in death and 11.71% indicated hospitalization. The ROR and PRR of hepatic and renal events associated with remdesivir were statistically significant, (4.81 [95% CI 4.46-5.19] and 2.96 [95% CI 2.66-3.29], respectively.\n\nConclusionOur study showed that several serious ADRs were reported with the use of hydroxychloroquine, which resulted in hospitalization and death. Trends with the use of remdesivir were similar, but to a lesser extent. Therefore, this study showed us that off-label use should be based on thorough evidence-based evaluation.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Deemah S Alsuhaibani",
+        "author_inst": "Pharmaceutical Care Department, Medical Services for Armed Forces, Ministry of Defense, Riyadh, Saudi Arabia"
+      },
+      {
+        "author_name": "Heba H Edrees",
+        "author_inst": "Harvard T.H. Chan School of Public Health, Boston, MA"
+      },
+      {
+        "author_name": "Thamir M Alshammari",
+        "author_inst": "Medication Safety Research Chair, King Saud University, Riyadh, Saudi Arabia"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.12.11.22283166",
     "rel_title": "Safety and Immunogenicity of an Omicron BA.4/BA.5 Bivalent Vaccine against Covid-19",
@@ -146960,61 +145829,6 @@
     "type": "new results",
     "category": "molecular biology"
   },
-  {
-    "rel_doi": "10.1101/2022.12.11.519990",
-    "rel_title": "Immunogenic fusion proteins induce neutralizing SARS-CoV-2 antibodies in the serum and milk of sheep",
-    "rel_date": "2022-12-12",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.11.519990",
-    "rel_abs": "Antigen-specific polyclonal immunoglobulins derived from the serum, colostrum, or milk of immunized ruminant animals have potential as scalable therapeutics for the control of viral diseases such as COVID-19. Enhancing the efficacy of vaccine antigens to induce robust and specific antibody responses remains central to developing highly effective formulations. The direct fusion of immunoglobulin (IgG) Fc domains or other immune-stimulating proteins to antigens has shown promise in several mammalian species but has not yet been tested and optimized in commercially-relevant ruminant species. Here we show that the immunization of sheep with fusions of the receptor binding domain (RBD) of SARS-CoV-2 to ovine IgG2a Fc domains promotes significantly higher levels of antigen-specific antibodies compared to native RBD or full-length spike antigens. This antibody population was shown to contain elevated levels of neutralizing antibodies that suppress binding between the RBD and soluble hACE2 receptors in vitro. The parallel evaluation of a second immune-stimulating fusion candidate, Granulocyte-macrophage colony-stimulating factor (GM-CSF), induced high neutralizing responses in select animals but narrowly missed achieving significance at the group level. Furthermore, we demonstrate that the antibodies induced by these fusion antigens are transferred from maternal serum into colostrum/milk. These antibodies also demonstrate cross-neutralizing activity against diverse SARS-CoV-2 variants including delta and omicron. Our findings highlight a new pathway for recombinant antigen design in ruminant animals with applications in immune milk production and animal health.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Gregory Jacobson",
-        "author_inst": "The University of Waikato"
-      },
-      {
-        "author_name": "Kirsty Kraakman",
-        "author_inst": "Ruakura Technologies Ltd"
-      },
-      {
-        "author_name": "Olivia Wallace",
-        "author_inst": "Ruakura Technologies Ltd"
-      },
-      {
-        "author_name": "Jolyn Pan",
-        "author_inst": "The University of Waikato"
-      },
-      {
-        "author_name": "Adele Williamson",
-        "author_inst": "The University of Waikato"
-      },
-      {
-        "author_name": "Alex Hennebry",
-        "author_inst": "Ruakura Technologies Ltd"
-      },
-      {
-        "author_name": "Grant Smolenski",
-        "author_inst": "Ruakura Technologies Ltd"
-      },
-      {
-        "author_name": "Ray Cursons",
-        "author_inst": "The University of Waikato"
-      },
-      {
-        "author_name": "Steve Hodgkinson",
-        "author_inst": "Ruakura Technologies Ltd"
-      },
-      {
-        "author_name": "William Kelton",
-        "author_inst": "The University of Waikato"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "new results",
-    "category": "bioengineering"
-  },
   {
     "rel_doi": "10.1101/2022.12.10.519730",
     "rel_title": "Dynamical nonequilibrium molecular dynamics simulations identify allosteric sites and positions associated with drug resistance in the SARS-CoV-2 main protease",
@@ -147269,6 +146083,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2022.12.08.22283272",
+    "rel_title": "Duration of viral shedding of the Omicron variant in asymptomatic and mild COVID-19 cases from Shanghai, China",
+    "rel_date": "2022-12-09",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.08.22283272",
+    "rel_abs": "BackgroundThe Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), designated as a variant of concern by the World Health Organization, spreads globally and was confirmed as the cause of the Omicron wave of the coronavirus disease 2019 (COVID-19) pandemic in Shanghai, China. The viral shedding duration of Omicron variants needs to be determined.\n\nMethodsWe retrospectively analyzed 382 patients admitted to a shelter hospital for COVID-19. Of the patients, 8 patients were referred to a designated hospital, 100 were infected asymptomatic patients, and 274 patients had mild COVID-19.\n\nResultsThe vaccination rates (including fully and boosted) in the asymptomatic and mild COVID-19 patients were 92.00% and 94.16%, respectively. Majority of the studied population showed a first reverse transcription-polymerase chain reaction cycle threshold (Ct) value of 20. For 2565 nasopharyngeal swabs from close or sub-close contacts, the Ct value gradually increased to 35 for 8 days, and the median duration of viral shedding time was 10 days after the first positive detection of the SARS-CoV-2 nuclei acid.\n\nConclusionsQuantitative viral RNA load assays in COVID-19 (BA.2.2.1) close or sub-closed contacts could be used to prevent transmissions and control precautions.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Weijie Sun",
+        "author_inst": "Department of Clinical Laboratory, Ningbo First Hospital, University of Ningbo, Zhejiang Province, China"
+      },
+      {
+        "author_name": "Naibin Yang",
+        "author_inst": "Department of Infectious Diseases, Ningbo First Hospital, University of Ningbo, Zhejiang Province, China"
+      },
+      {
+        "author_name": "Yang Mao",
+        "author_inst": "Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China"
+      },
+      {
+        "author_name": "Danying Yan",
+        "author_inst": "Department of Infectious Diseases, Ningbo First Hospital, University of Ningbo, Zhejiang Province, China"
+      },
+      {
+        "author_name": "Qifa Song",
+        "author_inst": "Medical Data Centre, Ningbo First Hospital, University of Ningbo, Zhejiang Province, China"
+      },
+      {
+        "author_name": "Guoqing Qian Sr.",
+        "author_inst": "Department of Infectious Diseases, Ningbo First Hospital, University of Ningbo, Zhejiang Province, China"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.12.08.22283268",
     "rel_title": "Respiratory Virus Circulation during the First Year of the COVID-19 Pandemic in the Household Influenza Vaccine Evaluation (HIVE) Cohort",
@@ -148814,37 +147667,6 @@
     "type": "new results",
     "category": "scientific communication and education"
   },
-  {
-    "rel_doi": "10.1101/2022.12.02.22283013",
-    "rel_title": "Impact of COVID-19 Vaccinations in India - A Statewise Analysis",
-    "rel_date": "2022-12-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.02.22283013",
-    "rel_abs": "ObjectiveThe COVID-19 vaccination program in India started after the first wave of infections had almost subsided. In this work, the objective is to perform a statewise analysis to assess the impact of vaccination during the second COVID-19 wave in India. A total of 21 states are chosen for the analysis encompassing 97% of the Indian population.\n\nMethodsWe use the generalized Gompertz curve to study the COVID-19 outbreak. The generalized Gompertz model is then modified to study the impact of vaccination. The modified model considers the cumulative daily number of individuals having the first and second shots of the vaccine in each state as explanatory variables.\n\nResultsWe observe that, out of 21 states, 16 states show the effectiveness of vaccines in curbing the spread of COVID-19. However, in states like Telangana, West Bengal, Tamil Nadu, Rajasthan, and Kerala, we do not conclusively observe the impact of vaccination during the study period.\n\nConclusionsThe effectiveness of COVID-19 vaccine depends on many factors. Some of them are not directly measurable. Using only COVID-19 infection cases and the vaccination data, we conclude that overall the vaccination program was effective in curbing the spread of COVID-19 in India.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Abhigayan Adhikary",
-        "author_inst": "Economic Research Unit, Indian Statistical Institute, Kolkata"
-      },
-      {
-        "author_name": "Manoranjan Pal",
-        "author_inst": "Economic Research Unit, Indian Statistical Institute, Kolkata"
-      },
-      {
-        "author_name": "Raju Maiti",
-        "author_inst": "Economic Research Unit, Indian Statistical Institute, Kolkata"
-      },
-      {
-        "author_name": "Palash Ghosh",
-        "author_inst": "Indian Institute of Technology Guwahati"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2022.12.05.22283130",
     "rel_title": "Utilization of Cycle Threshold Values of RTPCR SARS-Cov-2 Among Admitted Patients in a Public Hospital",
@@ -149099,6 +147921,85 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.12.04.22282996",
+    "rel_title": "COVID-19 vaccine coverage targets to inform reopening plans in a low incidence setting",
+    "rel_date": "2022-12-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.04.22282996",
+    "rel_abs": "Since the emergence of SARS-CoV-2 in 2019 through to mid-2021, much of the Australian population lived in a COVID-19 free environment. This followed the broadly successful implementation of a strong suppression strategy, including international border closures. With the availability of COVID-19 vaccines in early 2021, the national government sought to transition from a state of minimal incidence and strong suppression activities to one of high vaccine coverage and reduced restrictions but with still-manageable transmission. This transition is articulated in the national \"re-opening\" plan released in July 2021. Here we report on the dynamic modelling study that directly informed policies within the national re-opening plan including the identification of priority age groups for vaccination, target vaccine coverage thresholds and the anticipated requirements for continued public health measures -- assuming circulation of the Delta SARS-CoV-2 variant. Our findings demonstrated that adult vaccine coverage needed to be at least 70% to minimise public health and clinical impacts following the establishment of community transmission. They also supported the need for continued application of test-trace-isolate-quarantine and social measures during the vaccine roll-out phase and beyond.",
+    "rel_num_authors": 16,
+    "rel_authors": [
+      {
+        "author_name": "Eamon Conway",
+        "author_inst": "Walter and Eliza Hall Institute"
+      },
+      {
+        "author_name": "Camelia Walker",
+        "author_inst": "The University of Melbourne"
+      },
+      {
+        "author_name": "Chris Baker",
+        "author_inst": "The University of Melbourne"
+      },
+      {
+        "author_name": "Michael Lydeamore",
+        "author_inst": "Monash University"
+      },
+      {
+        "author_name": "Gerard E Ryan",
+        "author_inst": "Telethon Kids Institute; The University of Melbourne"
+      },
+      {
+        "author_name": "Trish Campbell",
+        "author_inst": "The University of Melbourne; The Peter Doherty Institute for Infection and Immunity"
+      },
+      {
+        "author_name": "Joel C Miller",
+        "author_inst": "La Trobe University"
+      },
+      {
+        "author_name": "Max Yeung",
+        "author_inst": "Quantium"
+      },
+      {
+        "author_name": "Greg Kabashima",
+        "author_inst": "Quantium"
+      },
+      {
+        "author_name": "James Wood",
+        "author_inst": "University of New South Wales"
+      },
+      {
+        "author_name": "Nic Rebuli",
+        "author_inst": "University of New South Wales"
+      },
+      {
+        "author_name": "James M McCaw",
+        "author_inst": "The University of Melbourne"
+      },
+      {
+        "author_name": "Jodie McVernon",
+        "author_inst": "The Peter Doherty Institute for Infection and Immunity"
+      },
+      {
+        "author_name": "Nick Golding",
+        "author_inst": "Telethon Kids Institute and Curtin University"
+      },
+      {
+        "author_name": "David J Price",
+        "author_inst": "The University of Melbourne; The Peter Doherty Institute for Infection and Immunity"
+      },
+      {
+        "author_name": "Freya M Shearer",
+        "author_inst": "The University of Melbourne"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2022.12.05.519191",
     "rel_title": "A screen for modulation of nucleocapsid protein condensation identifies small molecules with anti-coronavirus activity",
@@ -150448,157 +149349,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2022.12.05.519085",
-    "rel_title": "Convergent evolution of the SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant",
-    "rel_date": "2022-12-05",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.05.519085",
-    "rel_abs": "In late 2022, although the SARS-CoV-2 Omicron subvariants have highly diversified, some lineages have convergently acquired amino acid substitutions at five critical residues in the spike protein. Here, we illuminated the evolutionary rules underlying the convergent evolution of Omicron subvariants and the properties of one of the latest lineages of concern, BQ.1.1. Our phylogenetic and epidemic dynamics analyses suggest that Omicron subvariants independently increased their viral fitness by acquiring the convergent substitutions. Particularly, BQ.1.1, which harbors all five convergent substitutions, shows the highest fitness among the viruses investigated. Neutralization assays show that BQ.1.1 is more resistant to breakthrough BA.2/5 infection sera than BA.5. The BQ.1.1 spike exhibits enhanced binding affinity to human ACE2 receptor and greater fusogenicity than the BA.5 spike. However, the pathogenicity of BQ.1.1 in hamsters is comparable to or even lower than that of BA.5. Our multiscale investigations provide insights into the evolutionary trajectory of Omicron subvariants.",
-    "rel_num_authors": 34,
-    "rel_authors": [
-      {
-        "author_name": "Jumpei Ito",
-        "author_inst": "University of Tokyo"
-      },
-      {
-        "author_name": "Rigel Suzuki",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Keiya Uriu",
-        "author_inst": "University of Tokyo"
-      },
-      {
-        "author_name": "Yukari Itakura",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Jiri Zahradnik",
-        "author_inst": "Weizmann Institute of Science"
-      },
-      {
-        "author_name": "Sayaka Deguchi",
-        "author_inst": "Kyoto University"
-      },
-      {
-        "author_name": "Lei Wang",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Spyos Lytras",
-        "author_inst": "University of Glasgow"
-      },
-      {
-        "author_name": "Tomokazu Tamura",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Izumi Kida",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Hesham Nasser",
-        "author_inst": "Kumamoto University"
-      },
-      {
-        "author_name": "Maya Shofa",
-        "author_inst": "University of Miyazaki"
-      },
-      {
-        "author_name": "MST Monira Begum",
-        "author_inst": "Kumamoto University"
-      },
-      {
-        "author_name": "Masumi Tsuda",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Yoshikata Oda",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Shigeru Fujita",
-        "author_inst": "University of Tokyo"
-      },
-      {
-        "author_name": "Kumiko Yoshimatsu",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Hayato Ito",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Naganori Nao",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Hiroyuki Asakura",
-        "author_inst": "Tokyo Metropolitan Institute of Public Health"
-      },
-      {
-        "author_name": "Mami Nagashima",
-        "author_inst": "Tokyo Metropolitan Institute of Public Health"
-      },
-      {
-        "author_name": "Kenji Sadamasu",
-        "author_inst": "Tokyo Metropolitan Institute of Public Health"
-      },
-      {
-        "author_name": "Kazuhisa Yoshimura",
-        "author_inst": "Tokyo Metropolitan Institute of Public Health"
-      },
-      {
-        "author_name": "Yuki Yamamoto",
-        "author_inst": "HiLung Inc."
-      },
-      {
-        "author_name": "Tetsuharu Nagamoto",
-        "author_inst": "HiLung Inc."
-      },
-      {
-        "author_name": "Gideon Schreiber",
-        "author_inst": "Weizmann Institute of Science"
-      },
-      {
-        "author_name": "- The Genotype to Phenotype Japan (G2P-Japan) Consortium",
-        "author_inst": "-"
-      },
-      {
-        "author_name": "Akatsuki Saito",
-        "author_inst": "University of Miyazaki"
-      },
-      {
-        "author_name": "Keita Matsuno",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Kazuo Takayama",
-        "author_inst": "Kyoto University"
-      },
-      {
-        "author_name": "Shinya Tanaka",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Takasuke Fukuhara",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Terumasa Ikeda",
-        "author_inst": "Kumamoto University"
-      },
-      {
-        "author_name": "Kei Sato",
-        "author_inst": "Institute of Medical Science, The University of Tokyo"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2022.12.05.519151",
     "rel_title": "Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane",
@@ -150961,6 +149711,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.11.30.22282946",
+    "rel_title": "Discovering Social Determinants of Health from Case Reports using Natural Language Processing: Algorithmic Development and Validation",
+    "rel_date": "2022-12-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.30.22282946",
+    "rel_abs": "BackgroundSocial determinants of health are non-medical factors that influence health outcomes (SDOH). There is a wealth of SDOH information available in electronic health records, clinical reports, and social media data, usually in free text format. Extracting key information from free text poses a significant challenge and necessitates the use of natural language processing (NLP) techniques to extract key information.\n\nObjectiveThe objective of this research is to advance the automatic extraction of SDOH from clinical texts.\n\nSetting and DataThe case reports of COVID-19 patients from the published literature are curated to create a corpus. A portion of the data is annotated by experts to create ground truth labels, and semi-supervised learning method is used for corpus re-annotation.\n\nMethodsAn NLP framework is developed and tested to extract SDOH from the free texts. A two-way evaluation method is used to assess the quantity and quality of the methods.\n\nResultsThe proposed NER implementation achieves an accuracy (F1-score) of 92.98% on our test set and generalizes well on benchmark data. A careful analysis of case examples demonstrates the superiority of the proposed approach in correctly classifying the named entities.\n\nConclusionsNLP can be used to extract key information, such as SDOH factors from free texts. A more accurate understanding of SDOH is needed to further improve healthcare outcomes.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Shaina Raza",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Elham Dolatabadi",
+        "author_inst": "Vector Institute"
+      },
+      {
+        "author_name": "Nancy Ondrusek",
+        "author_inst": "OAHPP"
+      },
+      {
+        "author_name": "Laura Rosella",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Brian Schwartz",
+        "author_inst": "University of Toronto"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health informatics"
+  },
   {
     "rel_doi": "10.1101/2022.12.01.22282963",
     "rel_title": "Perceptions, readiness and recommendations of traditional herbalists to integrate traditional and modern medicine in controlling COVID-19 epidemics in Northeast Ethiopia: An interpretive qualitative study",
@@ -152626,33 +151411,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.11.30.22282924",
-    "rel_title": "Trends in patients' willingness for cancer care and the number of registered cancer cases in Ehime Prefecture during the COVID-19 pandemic",
-    "rel_date": "2022-12-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.30.22282924",
-    "rel_abs": "BackgroundThe COVID-19 pandemic has reduced diagnosed cancer cases worldwide. This study aimed to elucidate the recovery of cancer care from the COVID-19 pandemic in Ehime Prefecture, Japan.\n\nMethodsThis study collected data from the hospital-based cancer registry (HBCR) as well as the number of outpatients, medical information provision fee payments (MIP2), and second opinion patients (SOP) from the Council of Ehime Cancer Care Hospitals (ECCH). Then cancer care and patient requests for hospital transfers before and during the COVID-19 pandemic were analyzed.\n\nResultThe HBCR from the ECCH comprises >80% of cancer cases in Ehime Prefecture. In 2020, the numbers of all registered cases, first-line treatment cases, and cases detected by cancer screening in the HBCR decreased from those in 2018-2019. In 2021, they increased to almost the same levels as those in 2020. In contrast, the number of registered patients that changed hospitals (hospital-change cases) after first-line treatments, patients who lived outside the metropolitan area of Ehime but registered in metropolitan hospitals, MIP2, and SOP remained low in 2021 after decreasing in 2020. Furthermore, using the Wilcoxon rank sum test, the monthly numbers of hospital-change cases, MIP2, and SOP were significantly smaller in 2021 than in 2018-2019.\n\nConclusionThe assessed indicators suggest that the willingness of cancer patients to improve and/or advance cancer care had not returned to pre-pandemic levels by 2021. Hence, psychological measures in society and support for patient caregivers are necessary to prevent self-restraint in patients receiving cancer care.\n\nMini-abstractThe number of registered cases in hospital-based cancer registries returned to pre-COVID-19 levels by 2021, cancer patients willingness to further their care did not return to pre-pandemic levels.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Norihiro Teramoto",
-        "author_inst": "National Hospital Organization Shikoku Cancer Center"
-      },
-      {
-        "author_name": "Natsumi Yamashita",
-        "author_inst": "National Hospital Organization Shikoku Cancer Center"
-      },
-      {
-        "author_name": "Yutsuko Ohira",
-        "author_inst": "National Hospital Organization Shikoku Cancer Center"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2022.12.01.22282978",
     "rel_title": "Pilot Study Demonstrates Benefits of Nursing Home Air Purification on COVID-19 Outcomes",
@@ -152907,6 +151665,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "allergy and immunology"
   },
+  {
+    "rel_doi": "10.1101/2022.11.30.22282922",
+    "rel_title": "Epidemiological impact of a large number of incorrect negative SARS-CoV-2 test results in South West England during September and October 2021",
+    "rel_date": "2022-11-30",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.30.22282922",
+    "rel_abs": "BackgroundIn England, free testing for COVID-19 was widely available from early in the pandemic until 1 April 2022. Based on apparent differences in the rate of positive PCR tests at a single laboratory compared to the rest of the laboratory network, we hypothesised that a substantial number of UK PCR tests processed during September and October 2021 may have been incorrectly reported as negative, compared with the rest of the laboratory network. We investigate the epidemiological impact of this incident.\n\nMethodsWe estimate the additional number of COVID-19 cases that would have been reported had the sensitivity of the laboratory test procedure not dropped for the period 2 September to 12 October. In addition, by making comparisons between the most affected local areas and comparator populations, we estimate the number of additional infections, cases, hospitalisations and deaths that could have occurred as a result of increased transmission due to the misclassification of tests.\n\nResultsWe estimate that around 39,000 tests may have been incorrectly classified during this period and, as a direct result of this incident, the most affected areas in the South West could have experienced between 6,000 and 34,000 additional reportable cases, with a central estimate of around 24,000 additional reportable cases. Using modelled relationships between key variables, we estimate that this central estimate could have translated to approximately 55,000 additional infections, which means that each incorrect negative test likely led to just over two additional infections. In those same geographical areas, our results also suggest an increased number of admissions and deaths.\n\nConclusionThe incident is likely to have had a measurable impact on cases and infections in the affected areas in the South West of England.",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Luke Hounsome",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Daniel Herr",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Ruby Bryant",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Robert Smith",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Leo Loman",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Joshua Harris",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Urslaan Youhan",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Evija Dzene",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Pantelis Hadjipantelis",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Harry Long",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Timothy Laurence",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Steven Riley",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Fergus Cumming",
+        "author_inst": "UK Health Security Agency"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2022.11.26.518005",
     "rel_title": "An Optimized Circular Polymerase Extension Reaction-based Method for Functional Analysis of SARS-CoV-2",
@@ -154180,61 +153005,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health systems and quality improvement"
   },
-  {
-    "rel_doi": "10.1101/2022.11.28.22282830",
-    "rel_title": "Mortality due to SARS COV-2 And its Associated Factors in East Shewa Zone Treatment Centers, Ethiopia, 2022: A retrospective cross-sectional study",
-    "rel_date": "2022-11-29",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.28.22282830",
-    "rel_abs": "BackgroundCoronavirus disease (COVID-19) is an infectious disease that is caused by the SARS-CoV-2virus. The objective of this study was to determine SARS COV-2 Mortality and its associated factors in East Shewa Zone Treatment centers, Oromia, Ethiopia, 2022. The study of these types of viral infection will add new insight into the most common causes of mortality in SARS-CoV-2infection and the most common co-morbidities associated with the disease in the East Shewa Zone.\n\nMethodsThe study was conducted on patients who were admitted to Adama Hospital medical college and Modjo Primary Hospital for SARS-COV 2 treatment. Data used for the study were collected from March 2020-April 2022 GC. The study population was SARS-COV 2 patients who come to Adama Hospital and Medical College and Modjo Primary Hospital for treatment. All eligible SARS-CoV-2 patients data were collected from Both Adama and Modjo treatment center SARS-CoV-2 accession registration book and medical record card.\n\nResultA total of 409 patient data were collected from which 199 were from Adama Hospital and Medical College and 210 samples were collected from Modjo Primary Hospital Treatment center. The study design was a retrospective Cross-sectional study. The most affected age group in terms of mortality was the age group between 60-69 years old which suffers a 45.28% death rate. The major sign symptoms identified include cough (80.4%), Shortness of breath (66.7%) followed by fever (43.2%). SARS-CoV-2 Comorbidity was detected in 152 (37.2%) patients. Pneumonia was identified as the major comorbid disease to be recorded with 89(21.8%) cases. Other major comorbidities include Hypertension (16.9%) and Diabetes Mellites (13.9%). The least identified comorbidities were anemia (0.2%), Rectal cancer (0.2%), breast cancer (0.5%), and Chronic liver disease.\n\nConclusionNearly one in four (22.7%) SARS-COV 2 patients admitted for treatment to Adama Hospital and Medical College and Modjo Primary Hospital did not make their way out of treatment Hospitals alive. Pneumonia was identified as the major comorbid disease to be recorded with 89(21.8%) cases",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Jemal  Hassen Ali",
-        "author_inst": "Adama Public Health Research and Referral Laboratory Center"
-      },
-      {
-        "author_name": "Tewodros Getinet",
-        "author_inst": "St Paul's Hospital Millennium Medical College"
-      },
-      {
-        "author_name": "Abera Botore",
-        "author_inst": "Oromia Regional Health Bureau"
-      },
-      {
-        "author_name": "Mesfin Bekele",
-        "author_inst": "Adama Public Health Research and Referral Laboratory Center"
-      },
-      {
-        "author_name": "Bayisa Bekele",
-        "author_inst": "Adama Public Health Research and Referral Laboratory Center"
-      },
-      {
-        "author_name": "Firaol Jalata",
-        "author_inst": "Adama Public Health Research and Referral Laboratory Center"
-      },
-      {
-        "author_name": "Wake Abebe",
-        "author_inst": "Adama Public Health Research and Referral Laboratory Center"
-      },
-      {
-        "author_name": "Mekdes Sisay",
-        "author_inst": "Adama Public Health Research and Referral Laboratory Center"
-      },
-      {
-        "author_name": "Asnakech Getahun",
-        "author_inst": "Adama Public Health Research and Referral Laboratory Center"
-      },
-      {
-        "author_name": "Tadesse Ligdi",
-        "author_inst": "Adama Public Health Research and Referral Laboratory Center"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.11.24.22282643",
     "rel_title": "Wastewater genomic surveillance captures early detection of Omicron in Utah",
@@ -154477,6 +153247,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.11.29.518406",
+    "rel_title": "Atomic-level characterization of the conformational transition pathways in SARS-CoV-1 and SARS-CoV-2 spike proteins",
+    "rel_date": "2022-11-29",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.29.518406",
+    "rel_abs": "Severe acute respiratory syndrome (SARS) coronaviruses 1 and 2 (SARS-CoV-1 and SARS-CoV-2) derive transmissibility from spike protein activation in the receptor binding domain (RBD) and binding to the host cell angiotensin converting enzyme 2 (ACE2). However, the mechanistic details that describe the large-scale conformational changes associated with spike protein activation or deactivation are still somewhat unknown. Here, we have employed an extensive set of nonequilibrium all-atom molecular dynamics (MD) simulations, utilizing a novel protocol, for the SARS-CoV-1 (CoV-1) and SARS-CoV-2 (CoV-2) prefusion spike proteins in order to characterize the conformational pathways associated with the active-to-inactive transition. Our results indicate that both CoV-1 and CoV-2 spike proteins undergo conformational transitions along pathways unique to each protein. We have identified a number of key residues that form various inter-domain saltbridges, suggesting a multi-stage conformational change along the pathways. We have also constructed the free energy profiles along the transition pathways for both CoV-1 and CoV-2 spike proteins. The CoV-2 spike protein must overcome larger free energy barriers to undergo conformational changes towards protein activation or deactivation, when compared to CoV-1.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Dylan S Ogden",
+        "author_inst": "University of Arkansas"
+      },
+      {
+        "author_name": "Mahmoud Moradi",
+        "author_inst": "University of Arkansas"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "biophysics"
+  },
   {
     "rel_doi": "10.1101/2022.11.28.22282858",
     "rel_title": "Trajectories of host-response biomarkers and inflammatory subphenotypes in COVID-19 patients across the spectrum of respiratory support.",
@@ -156238,49 +155031,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.11.23.22282679",
-    "rel_title": "Substance use, psychiatric symptoms, personal mastery, and social support among COVID-19 long haulers: A compensatory model",
-    "rel_date": "2022-11-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.23.22282679",
-    "rel_abs": "BackgroundSubstance use has become a critical health concern during the COVID-19 pandemic, and emerging attention has been paid to people with the persistent symptoms of COVID-19 (COVID-19 long haulers) due to their high vulnerability. However, scant research has investigated their substance use and relevant psychosocial factors. The current study was to (1) examine substance use behaviors (i.e., legal drug use, illicit drug use, and non-medical use of prescription drugs); and (2) assessed their associations with psychiatric symptoms (i.e., depression, anxiety, and post-traumatic stress disorder) and psychosocial factors (i.e., personal mastery and social support) among COVID-19 long haulers.\n\nMethodsIn January - March 2022, 460 COVID-19 long haulers (50% female), with an average age of 32, completed online surveys regarding their demographics, substance use, psychiatric symptoms, and psychosocial factors.\n\nResultsIn the past three months, the most commonly used or non-medically used substances were tobacco (82%) for legal drugs, cocaine (53%) for illicit drugs, and prescription opioids (67%) for prescription drugs. Structural equation modeling suggested that psychiatric symptoms were positively associated with substance use behaviors ({beta}s = .38 to .68, ps < .001), while psychosocial factors were negatively associated with substance use behaviors ({beta}s = -.61 to -.43, ps < .001).\n\nConclusionSubstance use is common in COVID-19 long haulers and psychiatric symptoms are the risk factors. Personal mastery and social support appear to offer protection offsetting the psychiatric influences. Substance use prevention and mental health services for COVID-19 long haulers should attend to personal mastery and social support.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Cheuk Chi Tam",
-        "author_inst": "University of South Carolina"
-      },
-      {
-        "author_name": "Shan Qiao",
-        "author_inst": "University of South Carolina"
-      },
-      {
-        "author_name": "Camryn Garrett",
-        "author_inst": "University of South Carolina"
-      },
-      {
-        "author_name": "Ran Zhang",
-        "author_inst": "University of South Carolina"
-      },
-      {
-        "author_name": "Atefeh Aghaei",
-        "author_inst": "University of South Carolina"
-      },
-      {
-        "author_name": "Abhishek Aggarwal",
-        "author_inst": "University of South Carolina"
-      },
-      {
-        "author_name": "Xiaoming Li",
-        "author_inst": "University of South Carolina"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "addiction medicine"
-  },
   {
     "rel_doi": "10.1101/2022.11.22.22282637",
     "rel_title": "Prediction of Covid-19 vaccine effectiveness in adult populations and in clinically-vulnerable subgroups",
@@ -156571,6 +155321,101 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.11.23.22282648",
+    "rel_title": "An Early SARS-CoV-2 Omicron Outbreak in a Dormitory in Saint-Petersburg, Russia",
+    "rel_date": "2022-11-24",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.23.22282648",
+    "rel_abs": "The Omicron variant of SARS-CoV-2 has rapidly spread globally in late 2021 - early 2022, displacing the previously prevalent Delta variant. Before December 16, 2021, community transmission had already been observed in tens of countries globally. However, in Russia, the majority of reported cases at that time had been sporadic and associated with travel. Here, we report an Omicron outbreak at a student dormitory in Saint Petersburg between December 16 - 29, 2021, which was the earliest known instance of large-scale community transmission in Russia. Out of the 465 sampled residents of the dormitory, 180 (38.7%) tested PCR positive. Among the 118 residents for whom the variant has been tested by whole-genome sequencing, 111 (94.1%) carried the Omicron variant. Among these 111 residents, 60 (54.1%) were vaccinated or had reported previous COVID-19. Phylogenetic analysis confirmed that the outbreak was caused by a single introduction of the BA.1.1 sublineage of Omicron. The dormitory-derived clade constituted a significant proportion of BA.1.1 samples in Saint-Petersburg and has spread to other regions of Russia and other countries. The rapid spread of Omicron in a population with preexisting immunity to previous variants underlines its propensity for immune evasion.",
+    "rel_num_authors": 20,
+    "rel_authors": [
+      {
+        "author_name": "Galya V. Klink",
+        "author_inst": "IITP RAS"
+      },
+      {
+        "author_name": "Daria M. Danilenko",
+        "author_inst": "Smorodintsev Research Institute of Influenza"
+      },
+      {
+        "author_name": "Andrey B. Komissarov",
+        "author_inst": "Smorodintsev Research Institute for Influenza"
+      },
+      {
+        "author_name": "Nikita Yolshin",
+        "author_inst": "Smorodintsev Research Institute of Influenza"
+      },
+      {
+        "author_name": "Olga V. Shneider",
+        "author_inst": "Smorodintsev Research Institute of Influenza"
+      },
+      {
+        "author_name": "Sergey Shcherbak",
+        "author_inst": "City Hospital 40"
+      },
+      {
+        "author_name": "Elena Nabieva",
+        "author_inst": "IITP RAS"
+      },
+      {
+        "author_name": "Nikita Shvyrev",
+        "author_inst": "HSE University"
+      },
+      {
+        "author_name": "Nadezhda Konovalova",
+        "author_inst": "Smorodintsev Research Institute of Influenza"
+      },
+      {
+        "author_name": "Alyona Zheltukhina",
+        "author_inst": "Smorodintsev Research Institute of Influenza"
+      },
+      {
+        "author_name": "Artem Fadeev",
+        "author_inst": "Smorodintsev Research Institute of Influenza"
+      },
+      {
+        "author_name": "Kseniya Komissarova",
+        "author_inst": "Smorodintsev Research Institute of Influenza"
+      },
+      {
+        "author_name": "Andrey Ksenafontov",
+        "author_inst": "Smorodintsev Research Institute of Influenza"
+      },
+      {
+        "author_name": "Tamila Musaeva",
+        "author_inst": "Smorodintsev Research Institute of Influenza"
+      },
+      {
+        "author_name": "Veronica Eder",
+        "author_inst": "Smorodintsev Research Institute of Influenza"
+      },
+      {
+        "author_name": "Maria Pisareva",
+        "author_inst": "Smorodintsev Research Institute of Influenza"
+      },
+      {
+        "author_name": "Petr Nekrasov",
+        "author_inst": "Smorodintsev Research Institute of Influenza"
+      },
+      {
+        "author_name": "Vladimir Shchur",
+        "author_inst": "HSE University"
+      },
+      {
+        "author_name": "Georgii A Bazykin",
+        "author_inst": "Skoltech"
+      },
+      {
+        "author_name": "Dmitry Lioznov",
+        "author_inst": "Smorodintsev Research Institute of Influenza"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2022.11.23.517678",
     "rel_title": "An FcRn-targeted mucosal vaccine against SARS-CoV-2 infection and transmission",
@@ -157984,37 +156829,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2022.11.19.517207",
-    "rel_title": "Evolution of the SARS-CoV-2 mutational spectrum",
-    "rel_date": "2022-11-21",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.19.517207",
-    "rel_abs": "SARS-CoV-2 evolves rapidly in part because of its high mutation rate. Here we examine whether this mutational process itself has changed during viral evolution. To do this, we quantify the relative rates of different types of single nucleotide mutations at four-fold degenerate sites in the viral genome across millions of human SARS-CoV-2 sequences. We find clear shifts in the relative rates of several types of mutations during SARS-CoV-2 evolution. The most striking trend is a roughly two-fold decrease in the relative rate of G[-&gt;]T mutations in Omicron versus early clades, as was recently noted by Ruis et al (2022). There is also a decrease in the relative rate of C[-&gt;]T mutations in Delta, and other subtle changes in the mutation spectrum along the phylogeny. We speculate that these changes in the mutation spectrum could arise from viral mutations that affect genome replication, packaging, and antagonization of host innate-immune factors--although environmental factors could also play a role. Interestingly, the mutation spectrum of Omicron is more similar than that of earlier SARS-CoV-2 clades to the spectrum that shaped the long-term evolution of sarbecoviruses. Overall, our work shows that the mutation process is itself a dynamic variable during SARS-CoV-2 evolution, and suggests that human SARS-CoV-2 may be trending towards a mutation spectrum more similar to that of other animal sarbecoviruses.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Jesse D Bloom",
-        "author_inst": "Fred Hutchinson Cancer Research Center"
-      },
-      {
-        "author_name": "Annabel C Beichman",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Richard A Neher",
-        "author_inst": "University of Basel"
-      },
-      {
-        "author_name": "Kelley Harris",
-        "author_inst": "University of Washington"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "evolutionary biology"
-  },
   {
     "rel_doi": "10.1101/2022.11.20.517236",
     "rel_title": "Polymorphic regions in BA.2.12.1, BA.4 and BA.5 likely implicated in immunological evasion of Omicron subvariant BQ.1.1",
@@ -158329,6 +157143,41 @@
     "type": "new results",
     "category": "genomics"
   },
+  {
+    "rel_doi": "10.1101/2022.11.21.517338",
+    "rel_title": "Ultrasound treatment inhibits SARS-CoV-2 in vitro infectivity",
+    "rel_date": "2022-11-21",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.21.517338",
+    "rel_abs": "BackgroundCOVID-19 (coronavirus disease 2019) is a disease caused by infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), affecting millions of people worldwide, with a high rate of deaths. The present study aims to evaluate ultrasound (US) as a physical method for virus inactivation.\n\nMaterials and methodsThe US-transductor was exposed to the SARS-CoV-2 viral solution for 30 minutes. Vero-E6 cells were infected with medium exposure or not with the US, using 3-12, 5-10, or 6-18MHz as frequencies applied. We performed confocal microscopy to determine virus infection and replicative process. Moreover, we detected the virus particles with a titration assay.\n\nResultsWe observed an effective infection of SARS-CoV-2 Wuhan, Delta, and Gamma strains in comparison with mock, an uninfected experimental group. The US treatment was able to inhibit the Wuhan strain in all applied frequencies. Interestingly, 3-12 and 6-18MHz did not inhibit SARS-CoV-2 delta and gamma variants infection, on the other hand, 5-10MHz was able to abrogate infection and replication in all experimental conditions.\n\nConclusionsThese results show that SARS-CoV-2 is susceptible to US exposure at a specific frequency 5-10MHz and could be a novel tool for reducing the incidence of SARS-CoV-2 infection.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Flavio Protasio Veras",
+        "author_inst": "University of Sao Paulo"
+      },
+      {
+        "author_name": "Ronaldo Martins",
+        "author_inst": "University of Sao Paulo"
+      },
+      {
+        "author_name": "Eurico Arruda",
+        "author_inst": "University of Sao Paulo"
+      },
+      {
+        "author_name": "Fernando Q Cunha",
+        "author_inst": "University of Sao Paulo"
+      },
+      {
+        "author_name": "Odemir M Bruno",
+        "author_inst": "University of Sao Paulo"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "biophysics"
+  },
   {
     "rel_doi": "10.1101/2022.11.19.22282551",
     "rel_title": "Serologic Responses to COVID-19 Vaccination in Children with History of Multisystem Inflammatory Syndrome (MIS-C)",
@@ -159718,53 +158567,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2022.11.18.517035",
-    "rel_title": "Design and validation of an exposure system for efficient inter-animal SARS-CoV-2 airborne transmission in Syrian hamsters",
-    "rel_date": "2022-11-18",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.18.517035",
-    "rel_abs": "SARS-CoV-2 is a highly transmissible respiratory pathogen whose main transmission route is airborne. Development of an animal model and exposure system that recapitulates airborne transmission of SARS-CoV-2 is integral for understanding the dynamics of SARS-CoV-2 spread in individuals and populations. Here we designed, built, and characterized a hamster transmission caging and exposure system that allows for efficient SARS-CoV-2 airborne transmission from an infected index animal to naive recipients under unidirectional airflow, without contribution from fomite or direct contact transmission. To validate our system, we assessed a 1:1 or 1:4 ratio of infected index to naive recipient hamsters and compared their virological and clinical measurements after eight hours of airborne exposure. Airborne exposure concentrations and pulmonary deposited dose of SARS-CoV-2 in index and naive hamsters, respectively, were similar in both groups. Daily nasal viral RNA levels, and terminal (day 5) lung viral RNA and infectious virus, and fecal viral RNA levels were statistically similar among 1:1 and 1:4 naive animals. However, virological measurements in the 1:4 naive animals were more variable than the 1:1 naive animals, likely due to hamster piling behavior creating uneven SARS-CoV-2 exposure during the grouped 1:4 airborne exposure. This resulted in slight, but not statistically significant, changes in daily body weights between the 1:1 and 1:4 naive groups. Our report describes a multi-chamber caging and exposure system that allowed for efficient SARS-CoV-2 airborne transmission in single and grouped hamsters. This system can be used to better define airborne transmission dynamics and test transmission-blocking therapeutic strategies against SARS-CoV-2.\n\nImportanceThe main route of SARS-CoV-2 transmission is airborne. However, there are few experimental systems that can assess airborne transmission dynamics of SARS-CoV-2 in vivo. Here, we designed, built, and characterized a hamster transmission caging and exposure system that allows for efficient SARS-CoV-2 airborne transmission in Syrian hamsters, without contributions from fomite or direct contact transmission. We successfully measured SARS-CoV-2 viral RNA in aerosols and demonstrated that SARS-CoV-2 is transmitted efficiently at either a 1:1 or 1:4 infected index to naive recipient hamster ratio. This is meaningful as a 1:4 infected index to naive hamster ratio would allow for simultaneous comparisons of various interventions in naive animals to determine their susceptibility of infection by aerosol transmission of SARS-CoV-2. Our SARS-CoV-2 exposure system allows for testing viral airborne transmission dynamics and transmission-blocking therapeutic strategies against SARS-CoV-2 in Syrian hamsters.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Philip J Kuehl",
-        "author_inst": "Lovelace Biomedical"
-      },
-      {
-        "author_name": "Justin Dearing",
-        "author_inst": "Lovelace Biomedical"
-      },
-      {
-        "author_name": "Adam Werts",
-        "author_inst": "Lovelace Biomedical"
-      },
-      {
-        "author_name": "Jason Cox",
-        "author_inst": "Lovelace Biomedical"
-      },
-      {
-        "author_name": "Hammad Irshad",
-        "author_inst": "Lovelace Biomedical"
-      },
-      {
-        "author_name": "Edward G Barrett",
-        "author_inst": "Lovelace Biomedical"
-      },
-      {
-        "author_name": "Sean Tucker",
-        "author_inst": "Vaxart"
-      },
-      {
-        "author_name": "Stephanie N. Langel",
-        "author_inst": "Case Western Reserve University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2022.11.18.517047",
     "rel_title": "Innate immune response to SARS-1 CoV-2 infection contributes to neuronal damage in human iPSC-derived peripheral neurons",
@@ -160135,6 +158937,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2022.11.16.22282406",
+    "rel_title": "Special Olympics global report on COVID-19 vaccination and reasons not to vaccinate among adults with intellectual disabilities",
+    "rel_date": "2022-11-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.16.22282406",
+    "rel_abs": "IntroductionThe COVID-19 pandemic has disproportionately affected people with intellectual disabilities worldwide. The objective of this study was to identify global rates of COVID-19 vaccination and reasons not to vaccinate among adults with intellectual disabilities (ID) associated with country economic income levels.\n\nMethodsThe Special Olympics COVID-19 online survey was administered in January-February 2022 to adults with ID from 138 countries. Descriptive analyses of survey responses include 95% margins of error. Logistic regression and Pearson Chi-squared tests were calculated to assess associations with predictive variables for vaccination using R 4.1.2 software.\n\nResultsParticipants (n=3560) represented 18 low (n=410), 35 lower-middle (n=1182), 41 upper-middle (n=837), and 44 high (n=1131) income countries. Globally, 76% (74.8-77.6%) received a COVID-19 vaccination while 49.5% (47.9-51.2%) received a COVID-19 booster. Upper-middle (93% (91.2-94.7%)) and high-income country (94% (92.1-95.0%)) participants had the highest rates of vaccination while low-income countries had the lowest rates (38% (33.3-42.7%)). In multivariate regression models, country economic income level (OR = 3.12, 95% CI [2.81, 3.48]), age (OR = 1.04, 95% CI [1.03, 1.05]), and living with family (OR = 0.70, 95% CI [0.53, 0.92]) were associated with vaccination. Among LLMICs, the major reason for not vaccinating was lack of access (41.2% (29.5-52.9%)). Globally, concerns about side effects (42%, (36.5-48.1%)) and parent/guardian not wanting the adult with ID to vaccinate (32% (26.1-37.0%)) were the most common reasons for not vaccinating.\n\nConclusionAdults with ID from low and low-middle income countries reported fewer COVID-19 vaccinations, suggesting reduced access and availability of resources in these countries. Globally, COVID-19 vaccination levels among adults with ID were higher than the general population. Interventions should address the increased risk of infection for those in congregate living situations and family caregiver apprehension to vaccinate this high-risk population.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Andrew  Ethan Lincoln",
+        "author_inst": "Georgetown University Medical Center"
+      },
+      {
+        "author_name": "Alicia  M Dixon-Ibarra",
+        "author_inst": "Special Olympics"
+      },
+      {
+        "author_name": "John  P Hanley",
+        "author_inst": "Special Olympics"
+      },
+      {
+        "author_name": "Ashlyn  L Smith",
+        "author_inst": "Special Olympics"
+      },
+      {
+        "author_name": "Kiki Martin",
+        "author_inst": "Special Olympics"
+      },
+      {
+        "author_name": "Alicia Bazzano",
+        "author_inst": "Special Olympics"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.11.18.22282501",
     "rel_title": "Long-term temporal trends in incidence rate and case fatality of sepsis and COVID-19-related sepsis: nationwide registry study",
@@ -161488,29 +160329,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.11.14.22282323",
-    "rel_title": "Sensible Long-lead Forecast of COVID-19 Epidemic Outcomes",
-    "rel_date": "2022-11-15",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.14.22282323",
-    "rel_abs": "Coronavirus disease 2019 (COVID-19) will likely remain a major public health burden; accurate forecast of COVID-19 epidemic outcomes several months into the future is needed to support more proactive planning. Here, we propose strategies to address three major forecast challenges, i.e., error growth, the emergence of new variants, and infection seasonality. Using these strategies in combination we generate retrospective predictions of COVID-19 cases and deaths 6 months in the future for 10 representative US states. Tallied over >25,000 retrospective predictions through September 2022, the forecast approach using all three strategies consistently outperformed a baseline forecast approach without these strategies across different variant waves and locations, for all forecast targets. Overall, probabilistic forecast accuracy improved by 64% and 38% and point prediction accuracy by 133% and 87% for cases and deaths, respectively. Real-time 6-month lead predictions made in early October 2022 suggested large attack rates in most states but a lower burden of deaths than previous waves during October 2022 - March 2023; these predictions are in general accurate compared to reported data. The superior skill of the forecast methods developed here demonstrate means for generating more accurate long-lead forecast of COVID-19 and possibly other infectious diseases.\n\nAuthor SummaryInfectious disease forecast aims to reliably predict the most likely future outcomes during an epidemic. To date, reliable COVID-19 forecast remains elusive and is needed to support more proactive planning. Here, we pinpoint the major challenges facing COVID-19 forecast and propose three strategies. Comprehensive testing shows the forecast approach using all three strategies consistently outperforms a baseline approach without these strategies across different variant waves and locations in the United States for all forecast targets, improving the probabilistic forecast accuracy by [~]50% and point prediction accuracy by [~]100%. The superior skills of the forecast methods developed here demonstrate means for generating more accurate long-lead COVID-19 forecasts. The methods may be also applicable to other infectious diseases.\n\nOne sentence summaryTo support more proactive planning, we develop COVID-19 forecast methods that substantially improve accuracy with lead time up to 6 months.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Wan Yang",
-        "author_inst": "Columbia University"
-      },
-      {
-        "author_name": "Jeffrey Shaman",
-        "author_inst": "Columbia University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.11.14.22282128",
     "rel_title": "Assessment of level of depression and associated factors among COVID-19 recovered patients: a cross sectional study",
@@ -161953,6 +160771,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "rehabilitation medicine and physical therapy"
   },
+  {
+    "rel_doi": "10.1101/2022.11.11.22282032",
+    "rel_title": "COVID Seq as Laboratory Developed Test (LDT) for diagnosis of SARS-CoV-2 Variants of Concern (VOC)",
+    "rel_date": "2022-11-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.11.22282032",
+    "rel_abs": "Rapid classification and detection of SARS-CoV-2 variants have been critical in comprehending the viruss transmission dynamics. Clinical manifestation of the infection is influenced by comorbidities such as age, immune status, diabetes, and the infecting variant. Thus, clinical management may differ for new variants. For example, some monoclonal antibody treatments are variant-specific. Yet, an FDA-approved test for detecting the SARS-CoV-2 variant is unavailable. A laboratory-developed test (LDT) remains a viable option for reporting the infecting variant for clinical intervention or epidemiological purposes. Accordingly, we have validated the Illumina COVID-Seq assay as an LDT according to the guidelines prescribed by the College of American Pathologists (CAP) and Clinical Laboratory Improvement Amendments (CLIA). The limit of detection (LOD) of this test is Ct<30 ([~]15 viral copies) and >200X genomic coverage, and the test is 100% specific in the detection of existing variants. The test demonstrated 100% precision in inter-day, intra-day, and intra-laboratory reproducibility studies. It is also 100% accurate, defined by reference strain testing and split sample testing with other CLIA laboratories. Advanta Genetics LDT COVID Seq has been reviewed by CAP inspectors and is under review by FDA for Emergency Use Authorization.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Rob E. Carpenter",
+        "author_inst": "University of Texas at Tyler, 3900 University Boulevard, Tyler, Texas 75799, USA"
+      },
+      {
+        "author_name": "Vaibhav Kumar Tamrakar",
+        "author_inst": "ICMR-National Institute of Research in Tribal Health, Jabalpur M.P. India"
+      },
+      {
+        "author_name": "Emily Brown",
+        "author_inst": "Advanta Genetics, 10935 CR 159 Tyler, Texas 75703, USA"
+      },
+      {
+        "author_name": "Sadia Almas",
+        "author_inst": "Advanta Genetics, 10935 CR 159 Tyler, Texas 75703, USA"
+      },
+      {
+        "author_name": "Rahul Sharma",
+        "author_inst": "Advanta Genetics, 10935 CR 159 Tyler, Texas 75703, USA"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "genetic and genomic medicine"
+  },
   {
     "rel_doi": "10.1101/2022.11.07.22281957",
     "rel_title": "Clinical Evaluation of the GeneXpert(R) Xpert(R) Xpress SARS-CoV-2/Flu/RSV PLUS Combination Test",
@@ -163470,137 +162323,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2022.11.11.516111",
-    "rel_title": "Attenuated humoral responses in HIV infection after SARS-CoV-2 vaccination are linked to global B cell defects and cellular immune profiles",
-    "rel_date": "2022-11-11",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.11.516111",
-    "rel_abs": "People living with HIV (PLWH) on suppressive antiretroviral therapy (ART) can have residual immune dysfunction and often display poorer responses to vaccination. We assessed in a cohort of PLWH (n=110) and HIV negative controls (n=64) the humoral and spike-specific B-cell responses following 1, 2 or 3 SARS-CoV-2 vaccine doses. PLWH had significantly lower neutralizing antibody (nAb) titers than HIV-negative controls at all studied timepoints. Moreover, their neutralization breadth was reduced with fewer individuals developing a neutralizing response against the Omicron variant (BA.1) relative to controls. We also observed a delayed development of neutralization in PLWH that was underpinned by a reduced frequency of spike-specific memory B cells (MBCs) and pronounced B cell dysfunction. Improved neutralization breadth was seen after the third vaccine dose in PLWH but lower nAb responses persisted and were associated with global, but not spike-specific, MBC dysfunction. In contrast to the inferior antibody responses, SARS-CoV-2 vaccination induced robust T cell responses that cross-recognized variants in PLWH. Strikingly, a subset of PLWH with low or absent neutralization had detectable functional T cell responses. These individuals had reduced numbers of circulating T follicular helper cells and an enriched population of CXCR3+CD127+CD8+ T cells after two doses of SARS-CoV-2 vaccination, which may compensate for sub-optimal serological responses in the event of infection. Therefore, normalisation of B cell homeostasis could improve serological responses to vaccines in PLWH and evaluating T cell immunity could provide a more comprehensive immune status profile in these individuals and others with B cell imbalances.",
-    "rel_num_authors": 29,
-    "rel_authors": [
-      {
-        "author_name": "Emma Touizer",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Aljawharah Alrubbayi",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Rosemarie Ford",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Noshin Hussain",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Pehu\u00e9n Pereyra Gerber",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Hiu-Long Shum",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Chloe Rees-Spear",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Luke Muir",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Ester Gea-Mallorqu\u00ed",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Jakub Kopycinski",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Dylan Jankovic",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Christopher Pinder",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Thomas A Fox",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Ian Williams",
-        "author_inst": "Central and North West London NHS Trust"
-      },
-      {
-        "author_name": "Claire Mullender",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Irfaan Maan",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Laura Waters",
-        "author_inst": "Central and North West London NHS Trust"
-      },
-      {
-        "author_name": "Margaret Johnson",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Sara Madge",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Michael Youle",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Tristan Barber",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Fiona Burns",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Sabine Kinloch",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Sarah Rowland-Jones",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Richard Gilson",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Nicholas J Matheson",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Emma Morris",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Dimitra Peppa",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Laura E McCoy",
-        "author_inst": "University College London"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2022.11.11.516107",
     "rel_title": "Crystal structure and activity profiling of deubiquitinating inhibitors-bound to SARS-CoV-2 papain like protease revealed new allosteric sites for antiviral therapies",
@@ -163875,6 +162597,69 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "allergy and immunology"
   },
+  {
+    "rel_doi": "10.1101/2022.11.07.22282030",
+    "rel_title": "Neurologic sequalae of COVID-19 are determined by immunologic imprinting from previous Coronaviruses.",
+    "rel_date": "2022-11-10",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.07.22282030",
+    "rel_abs": "Coronavirus disease 2019 (COVID-19), which is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains a global public health emergency. Although SARS-CoV-2 is primarily a respiratory pathogen, extra-respiratory organs, including the central nervous system (CNS), can also be affected. Neurologic symptoms have been observed not only during acute SARS-CoV-2 infection, but also at distance from respiratory disease, also known as long-COVID or neurological post-acute sequelae of COVID-19 (neuroPASC). The pathogenesis of neuroPASC is not well understood, but hypotheses include SARS-CoV-2-induced immune dysfunctions, hormonal dysregulations, and persistence of SARS-CoV-2 reservoirs. In this study, we used a high throughput systems serology approach to dissect the humoral response to SARS-CoV-2 (and other common Coronaviruses - 229E, HKU1, NL63, OC43) in the serum and cerebrospinal fluid (CSF) from 112 infected individuals who developed or did not develop neuroPASC. Unique SARS-CoV-2 humoral profiles were observed in the CSF of neuroPASC. All antibody isotypes (IgA, IgM, IgA) and subclasses (IgA1-2; IgG1-4) were detected in serum, whereas CSF was characterized by focused IgG1 (and absence of IgM). These data argue in favor of compartmentalized brain-specific responses against SARS-CoV-2 through selective transfer of antibodies from the serum to the CSF across the blood-brain-barrier, rather than intrathecal synthesis, where more diversity in antibody classes/subclasses would be expected. Moreover, compared to individuals who did not develop post-acute neurological complications following infection (n=94), those with neuroPASC (n=18) exhibited attenuated systemic antibody responses against SARS-CoV-2, characterized by decreased capacity to activate antibody-dependent complement deposition (ADCD), NK cell activation (ADNKA) and to bind Fc{gamma} receptors. However, surprisingly, neuroPASC showed significantly expanded antibody responses to other common Coronaviruses, including 229E, HKU1, NL63, and OC43. This biased humoral activation across coronaviruses was particularly enriched in neuroPASC individuals with poor outcome, suggesting an original antigenic sin (or immunologic imprinting), where pre-existing immune responses against related viruses shape the response to current infection, as a key prognostic marker of neuroPASC disease. Overall, these findings point to a pathogenic role for compromised anti-SARS-CoV-2 responses in the CSF, likely resulting in incomplete virus clearance from the brain and persistent neuroinflammation, in the development of post-acute neurologic complications of SARS-CoV-2 infection.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Marianna Spatola",
+        "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge, USA"
+      },
+      {
+        "author_name": "Nadege Nziza",
+        "author_inst": "Ragon Institute of MGH, MIT and Harvard"
+      },
+      {
+        "author_name": "Yixiang Deng",
+        "author_inst": "Ragon Institute of mGH, MIT and Harvard; Massachusetts Institute of Technology"
+      },
+      {
+        "author_name": "Wonyeong Jung",
+        "author_inst": "Ragon Institute of MGH, MIT and Harvard; Massachusetts Institute of Technology"
+      },
+      {
+        "author_name": "Dansu Yuan",
+        "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge, USA"
+      },
+      {
+        "author_name": "Alessandro Dinoto",
+        "author_inst": "Neurology Unit, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona"
+      },
+      {
+        "author_name": "Silvia Bozzetti",
+        "author_inst": "Neurology Unit, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona"
+      },
+      {
+        "author_name": "Vanessa Chiodega",
+        "author_inst": "Neurology Unit, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona; Department of Neurology/Stroke Unit, San Maurizio hospital,"
+      },
+      {
+        "author_name": "Sergio Ferrari",
+        "author_inst": "Neurology Unit, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona"
+      },
+      {
+        "author_name": "Douglas A Lauffenburger",
+        "author_inst": "Massachusetts Institute of Technology, Cambridge, MA, USA"
+      },
+      {
+        "author_name": "Sara Mariotto",
+        "author_inst": "Neurology Unit, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona"
+      },
+      {
+        "author_name": "Galit Alter",
+        "author_inst": "Ragon Institute of MGH, MIT and Harvard"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "allergy and immunology"
+  },
   {
     "rel_doi": "10.1101/2022.11.08.22282097",
     "rel_title": "The interface between SARS-CoV-2 and non-communicable diseases (NCDs) in a high HIV/TB burden district level hospital setting, Cape Town, South Africa",
@@ -165204,41 +163989,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2022.11.07.515545",
-    "rel_title": "Optimization of the Illumina COVIDSeq\u2122 protocol for decentralized, cost-effective genomic surveillance",
-    "rel_date": "2022-11-08",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.07.515545",
-    "rel_abs": "A decentralized surveillance system to identify local outbreaks and monitor SARS-CoV-2 Variants of Concern is one of the primary strategies for the pandemics containment. Although next-generation sequencing (NGS) is a gold standard for genomic surveillance and variant discovery, the technology is still cost-prohibitive for decentralized sequencing, particularly in small independent labs with limited resources. We have optimized the Illumina COVID-seq protocol to reduce cost without compromising accuracy. 90% of genomic coverage was achieved for 142/153 samples analyzed in this study. The lineage was correctly assigned to all samples (152/153) except for one. This modified protocol can help laboratories with constrained resources contribute to decentralized SARS-CoV-2 surveillance in the post-vaccination era.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Rob E. Carpenter",
-        "author_inst": "University of Texas at Tyler, 3900 University Boulevard, Tyler, Texas 75799, USA"
-      },
-      {
-        "author_name": "Vaibhav K Tamrakar",
-        "author_inst": "ICMR-National Institute of Research in Tribal Health, Jabalpur"
-      },
-      {
-        "author_name": "Sadia Almas",
-        "author_inst": "Advanta Genetics, 10935 CR 159 Tyler, Texas 75703, USA"
-      },
-      {
-        "author_name": "Chase Rowan",
-        "author_inst": "Advanta Genetics, 10935 CR 159 Tyler, Texas 75703, USA"
-      },
-      {
-        "author_name": "Rahul Sharma",
-        "author_inst": "Advanta Genetics, 10935 CR 159 Tyler, Texas 75703, USA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "genomics"
-  },
   {
     "rel_doi": "10.1101/2022.11.08.515673",
     "rel_title": "Prediction of Transport, Deposition, and Resultant Immune Response of Nasal Spray Vaccine Droplets using a CFPD-HCD Model in a 6-Year-Old Upper Airway Geometry to Potentially Prevent COVID-19",
@@ -165529,6 +164279,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.11.04.22281943",
+    "rel_title": "Fine scale human mobility changes in 26 US cities in 2020 in response to the COVID-19 pandemic were associated with distance and income",
+    "rel_date": "2022-11-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.04.22281943",
+    "rel_abs": "Human mobility patterns changed greatly due to the COVID-19 pandemic. Despite many analyses investigating general mobility trends, there has been less work characterising changes in mobility on a fine spatial scale and developing frameworks to model these changes. We analyse zip code-level mobility data from 26 US cities between February 2 - August 31, 2020. We use Bayesian models to characterise the initial decrease in mobility and mobility patterns between June - August at this fine spatial scale. There were similar temporal trends across cities but large variations in the magnitude of mobility reductions. Long-distance routes and higher-income subscribers, but not age, were associated with greater mobility reductions. At the city level, mobility rates around early April, when mobility was lowest, and over summer showed little association with non-pharmaceutical interventions or case rates. Changes in mobility patterns lasted until the end of the study period, despite overall numbers of trips recovering to near baseline levels in many cities.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Rohan Arambepola",
+        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
+      },
+      {
+        "author_name": "Kathryn L Schaber",
+        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
+      },
+      {
+        "author_name": "Catherine Schluth",
+        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
+      },
+      {
+        "author_name": "Angkana T Huang",
+        "author_inst": "Department of Genetics, Cambridge University"
+      },
+      {
+        "author_name": "Alain B Labrique",
+        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
+      },
+      {
+        "author_name": "Shruti H Mehta",
+        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
+      },
+      {
+        "author_name": "Sunil S Solomon",
+        "author_inst": "Johns Hopkins University School of Medicine"
+      },
+      {
+        "author_name": "Derek A T Cummings",
+        "author_inst": "Department of Biology and the Emerging Pathogens Institute, University of Florida"
+      },
+      {
+        "author_name": "Amy Wesolowski",
+        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2022.11.06.22281984",
     "rel_title": "The relationship between controllability, optimal testing resource allocation, and incubation-latent period mismatch as revealed by COVID-19",
@@ -166750,73 +165551,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2022.10.31.513793",
-    "rel_title": "Antiviral effect of candies containing persimmon-derived tannin against SARS-CoV-2 delta strain",
-    "rel_date": "2022-11-04",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.31.513793",
-    "rel_abs": "Inactivation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the mouth has the potential to reduce the spread of coronavirus disease 2019 (COVID-19) because the virus is readily transmitted by dispersed saliva. Persimmon-derived tannin has strong antioxidant and antimicrobial activity owing to its strong adhesiveness to proteins, and it also exhibited antiviral effects against non-variant and alpha variant SARS-CoV-2 in our previous study. In this report, we first demonstrated the antiviral effects of persimmon-derived tannin against the delta variant of SARS-CoV-2 in vitro via the plaque assay method. We then examined the effects of candy containing persimmon-derived tannin. Our plaque assay results show that saliva samples provided by healthy volunteers while they were eating tannin-containing candy remarkably suppressed the virus titers of the SARS-CoV-2 delta variant. In addition, we found that the SARS-CoV-2 viral load in saliva from patients with COVID-19 that was collected immediately after they had eaten the tannin-containing candy was below the level of detection by PCR for SARS-CoV-2. These data suggest that adding persimmon-derived tannin to candy and holding such candy in the mouth is an effective method by which to inactivate the SARS-CoV-2 in saliva, and the application of this approach has potential for inhibiting the transmission of COVID-19.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Ryutaro Furukawa",
-        "author_inst": "Nara Medical University"
-      },
-      {
-        "author_name": "Masahiro Kitabatake",
-        "author_inst": "Nara Medical University"
-      },
-      {
-        "author_name": "Noriko Ouji-Sageshima",
-        "author_inst": "Nara Medical University"
-      },
-      {
-        "author_name": "Dai Tomita",
-        "author_inst": "National Hospital Organization Nara Medical Center"
-      },
-      {
-        "author_name": "Makiko Kumamoto",
-        "author_inst": "National Hospital Organization Nara Medical Center"
-      },
-      {
-        "author_name": "Yuki Suzuki",
-        "author_inst": "Nara Medical University"
-      },
-      {
-        "author_name": "Akiyo Nakano",
-        "author_inst": "Nara Medical University"
-      },
-      {
-        "author_name": "Ryuichi Nakano",
-        "author_inst": "Nara Medical University"
-      },
-      {
-        "author_name": "Yoko Matsumura",
-        "author_inst": "Kio University"
-      },
-      {
-        "author_name": "Shin-ichi Kayano",
-        "author_inst": "Kio University"
-      },
-      {
-        "author_name": "Hisakazu Yano",
-        "author_inst": "Nara Medical University"
-      },
-      {
-        "author_name": "Shinji Tamaki",
-        "author_inst": "National Hospital Organization Nara Medical Center"
-      },
-      {
-        "author_name": "Toshihiro Ito",
-        "author_inst": "Nara Medical University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2022.11.01.22281746",
     "rel_title": "Population-based sero-epidemiological estimates of real-world vaccine effectiveness against Omicron infection in an infection-naive population, Hong Kong, January to July 2022",
@@ -167131,6 +165865,81 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.11.02.22281821",
+    "rel_title": "Screening COVID-19 by Swaasa AI Platform using cough sounds: A cross-sectional study",
+    "rel_date": "2022-11-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.02.22281821",
+    "rel_abs": "The Advent of Artificial Intelligence (AI) has led to the use of auditory data for detecting various diseases, including COVID-19. SARS-CoV-2 infection has claimed more than 6 million lives till date and hence, needs a robust screening technique to control the disease spread. In the present study we developed and validated the Swaasa AI platform for screening and prioritizing COVID-19 patients based on the signature cough sound and the symptoms presented by the subjects. The cough data records collected from 234 COVID-19 suspects were subjected to validate the convolutional neural network (CNN) architecture and tabular features-based algorithm. The likelihood of the disease was predicted by combining the final output obtained from both the models. In the clinical validation phase, Swaasa was found to be 75.54% accurate in detecting the likely presence of COVID-19 with 95.45% sensitivity and 73.46% specificity. The pilot testing of Swaasa was carried out on 183 presumptive COVID subjects, out of which 82 subjects were found to be positive for the disease by Swaasa. Among them, 58 subjects were truly COVID-19 positive, which corresponds to a Positive Predictive Value of 70.73%. The currently available rapid screening methods are very costly and require technical expertise, therefore a cost effective, remote monitoring tool would be very beneficial for preliminary screening of the potential COVID-19 subject.",
+    "rel_num_authors": 15,
+    "rel_authors": [
+      {
+        "author_name": "Padmalatha P",
+        "author_inst": "Andhra Medical College"
+      },
+      {
+        "author_name": "Gowrisree Rudraraju",
+        "author_inst": "Salcit Technologies"
+      },
+      {
+        "author_name": "Narayana Rao Sripada",
+        "author_inst": "Salcit Technologies"
+      },
+      {
+        "author_name": "Baswaraj Mamidgi",
+        "author_inst": "Salcit Technologies"
+      },
+      {
+        "author_name": "Charishma Gottipulla",
+        "author_inst": "Salcit Technologies"
+      },
+      {
+        "author_name": "Charan Jalukuru",
+        "author_inst": "Salcit Technologies"
+      },
+      {
+        "author_name": "ShubhaDeepti Palreddy",
+        "author_inst": "Salcit Technologies"
+      },
+      {
+        "author_name": "Nikhil kumar Reddy Bhoge",
+        "author_inst": "Salcit technologies"
+      },
+      {
+        "author_name": "Priyanka Firmal",
+        "author_inst": "Salcit Technologies"
+      },
+      {
+        "author_name": "Venkat Yechuri",
+        "author_inst": "Salcit Technologies"
+      },
+      {
+        "author_name": "P V Sudhakar",
+        "author_inst": "Andhra Medical College"
+      },
+      {
+        "author_name": "Devi Madhavi B",
+        "author_inst": "Andhra Medical College"
+      },
+      {
+        "author_name": "Srinivas S",
+        "author_inst": "Andhra Medical  College"
+      },
+      {
+        "author_name": "K L Prasad K",
+        "author_inst": "Guntur Medical College"
+      },
+      {
+        "author_name": "Niranjan Joshi",
+        "author_inst": "C-Camp"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "respiratory medicine"
+  },
   {
     "rel_doi": "10.1101/2022.10.31.22281769",
     "rel_title": "Time intervals between COVID-19 cases, and more severe outcomes",
@@ -168278,20 +167087,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2022.10.31.22281766",
-    "rel_title": "Effectiveness of mRNA COVID-19 vaccine booster doses against Omicron severe outcomes",
-    "rel_date": "2022-11-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.31.22281766",
-    "rel_abs": "BackgroundTo inform planning for further booster doses of COVID-19 vaccines, we estimated the effectiveness of monovalent mRNA vaccines against Omicron-associated severe outcomes in adults over time.\n\nMethodsWe used a test-negative design and multivariable logistic regression to estimate vaccine effectiveness (VE; 2, 3, or 4 doses compared to unvaccinated individuals) and marginal effectiveness (3 or 4 doses compared to 2 doses) against Omicron-associated hospitalization or death among community-dwelling adults aged [&ge;]50 years who were tested for SARS-CoV-2 between January 2, 2022 and October 1, 2022 in Ontario, Canada, stratified by age group and time since vaccination. We also compared VE during periods of Omicron BA.1/BA.2 and BA.4/BA.5 sublineage predominance.\n\nResultsWe included 11,160 cases of Omicron-associated severe outcomes and 62,880 test-negative symptomatic controls. Depending on the age group, compared to unvaccinated individuals, VE was 91-98% 7-59 days after a third dose, waned to 76-87% after [&ge;]240 days, was restored to 92-97% 7-59 days after a fourth dose, and waned to 86-89% after [&ge;]120 days. Trends in marginal effectiveness were consistent with VE estimates. VE was lower during the BA.4/BA.5-predominant period compared to the BA.1/BA.2-predominant period based on the same intervals since vaccination.\n\nConclusionOur findings suggest that 1 or 2 booster doses of monovalent mRNA COVID-19 vaccines initially restored very strong protection against Omicron-associated severe outcomes in all age groups, but VE subsequently declined over time with some age-related differences, and particularly so during a period of BA.4/BA.5 predominance.",
-    "rel_num_authors": 0,
-    "rel_authors": null,
-    "version": "1",
-    "license": "",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2022.10.26.22281561",
     "rel_title": "FULL-SCALE DEEPLY SUPERVISED ATTENTION NETWORK FOR SEGMENTING COVID-19 LESIONS",
@@ -168376,6 +167171,77 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.10.28.22281588",
+    "rel_title": "A novel hospital-at-home model for patients with COVID-19 built by a team of local primary care clinics and clinical outcomes: A multi-center retrospective cohort study",
+    "rel_date": "2022-10-31",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.28.22281588",
+    "rel_abs": "BackgroundHospital-at-home (HaH) care has been proposed as an alternative to inpatient care for patients with COVID-19. Previous reports were hospital-led and involved patients triaged at the hospitals. To reduce the burden on hospitals, we constructed a novel HaH care model organised by a team of local primary care clinics.\n\nMethodsWe conducted a multi-center retrospective cohort study of the COVID-19 patients who received our HaH care from Jan 1st to Mar 31st, 2022. Patients who were not able to be triaged for the need for hospitalization by the Health Center solely responsible for the management of COVID-19 patients in Osaka City were included. The primary outcome was receiving medical care beyond the HaH care defined as a composite outcome of any medical consultation, hospitalization, or death within 30 days from the initial treatment.\n\nResultsOf 382 eligible patients, 34 (9%) were triaged for hospitalization immediately after the initial visit. Of the remaining 348 patients followed up, 37 (11%) developed the primary outcome, while none died. Obesity, fever, and gastrointestinal symptoms at baseline were independently associated with an increased risk of needing medical care beyond the HaH care. A further 129 (37%) patients were managed online alone without home visit, and 170 (50%) required only one home visit in addition to online treatment.\n\nConclusionsThe HaH care model with a team of primary care clinics was able to triage patients with COVID-19 who needed immediate hospitalization without involving hospitals, and treated most of the remaining patients at home.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Yasushi Tsujimoto",
+        "author_inst": "Oku Medical Clinic"
+      },
+      {
+        "author_name": "Masanori Kobayashi",
+        "author_inst": "Kassai Medical Clinic"
+      },
+      {
+        "author_name": "Tomohisa Oku",
+        "author_inst": "Oku Medical Clinic"
+      },
+      {
+        "author_name": "Takahisa Ogawa",
+        "author_inst": "Oku Medical Clinic"
+      },
+      {
+        "author_name": "Shinichi Yamadera",
+        "author_inst": "Nanohana Clinic"
+      },
+      {
+        "author_name": "Masako Tsukamoto",
+        "author_inst": "Sagisu Naka Clinic"
+      },
+      {
+        "author_name": "Noriya Matsuda",
+        "author_inst": "Matsuda Clinic"
+      },
+      {
+        "author_name": "Morikazu Nishihira",
+        "author_inst": "Nishihira Clinic"
+      },
+      {
+        "author_name": "Yu Terauchi",
+        "author_inst": "Terauchi Clinic"
+      },
+      {
+        "author_name": "Takahiro Tanaka",
+        "author_inst": "Minato Clinic"
+      },
+      {
+        "author_name": "Yoshitaka Kawabata",
+        "author_inst": "Hinata Medical Clinic"
+      },
+      {
+        "author_name": "Yuki Miyamoto",
+        "author_inst": "Yoshiki Home Care Clinic"
+      },
+      {
+        "author_name": "Yoshiki Morikami",
+        "author_inst": "Yoshiki Home Care Clinic"
+      },
+      {
+        "author_name": "- The KISA2-Tai Osaka",
+        "author_inst": ""
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "primary care research"
+  },
   {
     "rel_doi": "10.1101/2022.10.30.22281600",
     "rel_title": "The impact of the COVID-19 pandemic on the reporting of violence against children",
@@ -169653,85 +168519,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
-  {
-    "rel_doi": "10.1101/2022.10.25.22281427",
-    "rel_title": "Viral load of SARS-CoV-2 Omicron BA.5 is lower than that of BA.2 despite the higher infectivity of BA.5",
-    "rel_date": "2022-10-28",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.25.22281427",
-    "rel_abs": "Sublineage BA.5 of the SARS-CoV-2 Omicron variant rapidly spread and replaced BA.2 in July 2022 in Tokyo. A high viral load can be a possible cause of high transmissibility. Therefore, the copy numbers of SARS-CoV-2 in nasopharyngeal swab samples obtained from all patients visiting the hospital where this research was conducted were measured using quantitative polymerase chain reaction (qPCR). Viral genotypes were determined using PCR-based melting curve analysis. Next, whole-genome sequencing was performed using approximately one-fifth of the samples to verify the viral genotypes determined using PCR. Then, the copy numbers of the BA.1, BA.2, and BA.5 cases were compared. Contrary to expectations, the copy numbers of the BA.5 cases (median 4.7 x 104 copies/L, n = 290) were significantly (p = 0.001) lower than those of BA.2 cases (median 1.1 x 105 copies/L, n = 184). There was no significant difference between the BA.5 and BA.1 cases (median, 3.1 x 104 copies/L; n = 215). The results presented here suggest that the increased infectivity of BA.5 is not caused by higher viral loads, but presumably by other factors such as increased affinity to human cell receptors or immune escape due to its L452R mutation.",
-    "rel_num_authors": 16,
-    "rel_authors": [
-      {
-        "author_name": "Yuna Takatsuki",
-        "author_inst": "Tokyo Medical and Dental University"
-      },
-      {
-        "author_name": "Yuta Takahashi",
-        "author_inst": "Tokyo Medical and Dental University"
-      },
-      {
-        "author_name": "Jun Nakajima",
-        "author_inst": "Tokyo Medical and Dental University"
-      },
-      {
-        "author_name": "Yumi Iwasaki",
-        "author_inst": "Tokyo Medical and Dental University"
-      },
-      {
-        "author_name": "Katsutoshi Nagano",
-        "author_inst": "Tokyo Medical and Dental University"
-      },
-      {
-        "author_name": "Chihiro Tani-Sassa",
-        "author_inst": "Tokyo Medical and Dental University"
-      },
-      {
-        "author_name": "Sonoka Yuasa",
-        "author_inst": "Tokyo Medical and Dental University"
-      },
-      {
-        "author_name": "Saki Kanehira",
-        "author_inst": "Tokyo Medical and Dental University"
-      },
-      {
-        "author_name": "Kazunari Sonobe",
-        "author_inst": "Tokyo Medical and Dental University"
-      },
-      {
-        "author_name": "Yoko Nukui",
-        "author_inst": "Tokyo Medical and Dental University"
-      },
-      {
-        "author_name": "Hiroaki Takeuchi",
-        "author_inst": "Tokyo Medical and Dental University"
-      },
-      {
-        "author_name": "Kousuke Tanimoto",
-        "author_inst": "Tokyo Medical and Dental University"
-      },
-      {
-        "author_name": "Yukie Tanaka",
-        "author_inst": "Tokyo Medical and Dental University"
-      },
-      {
-        "author_name": "Akinori Kimura",
-        "author_inst": "Tokyo Medical and Dental University"
-      },
-      {
-        "author_name": "Naoya Ichimura",
-        "author_inst": "Tokyo Medical and Dental University"
-      },
-      {
-        "author_name": "Shuji Tohda",
-        "author_inst": "Tokyo Medical and Dental University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.10.27.514070",
     "rel_title": "A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients",
@@ -170418,6 +169205,101 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "radiology and imaging"
   },
+  {
+    "rel_doi": "10.1101/2022.10.26.22278866",
+    "rel_title": "Experiences in the use of multiple doses of convalescent plasma in critically ill patients with COVID-19",
+    "rel_date": "2022-10-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.26.22278866",
+    "rel_abs": "At the beginning of the SARS-CoV-2 pandemic, transfusion of COVID-19 convalescent plasma (CCP) was considered as one of the possibilities to help severe patients to overcome COVID-19 disease. The use of CCP has been controversial as its effectiveness depends on many variables from the plasma donor and the COVID-19 patient, for example, time of convalescence or symptoms onset. This was a feasibility study assessing the safety of multiple doses of CCP in mechanically ventilated intubated patients with respiratory failure due to COVID-19. Thirty (30) patients with severe respiratory failure, in ICU, with invasive mechanical ventilation received up to 5 doses of 300 to 600 ml of CP on alternate days (0,2,4,6 and 8) until extubation, futility, or death. Nineteen patients received five doses, seven received four, and four had 2 or 3 doses. On day 28 of follow-up, 57% of patients recovered and were at home and the long-term mortality observed was 27%. The ten severe adverse events reported in the study were unrelated to CCP transfusion. This study suggests that transfusion of multiple doses of convalescent plasma (CP) is safe. This strategy may represent an option to use in new studies, given the potential benefit of CCP transfusions in the early stage of infection in unvaccinated populations and in settings where monoclonal antibodies or antivirals are contraindicated or not available.\n\nSummary boxO_LITransfusion of multiple doses (up to 5 doses) of 300-600 ml of convalescent plasma from COVID-19 recovered patients is safe as it does not induce more severe effects than a single dose.\nC_LIO_LIIndependent of the number of transfused doses, most patients had detectable levels of total and neutralizing antibodies in plasma.\nC_LIO_LIFuture studies are needed to determine if multiple transfusion doses are more efficient in preventing severity than a single dose.\nC_LI",
+    "rel_num_authors": 20,
+    "rel_authors": [
+      {
+        "author_name": "Ricardo Aguilar",
+        "author_inst": "Complejo Hospitalario Metropolitano Arnulfo Arias Madrid, Caja de Seguro Social, Panama, Panama"
+      },
+      {
+        "author_name": "Sandra L Lopez-Verges",
+        "author_inst": "Gorgas Memorial Institute of Health Studies"
+      },
+      {
+        "author_name": "Anarellys Quintana",
+        "author_inst": "Hospital Santo Tomas, Panama, Panama"
+      },
+      {
+        "author_name": "Johanna Morris",
+        "author_inst": "Sociedad Panamena de Hematologia, Panama, Panama"
+      },
+      {
+        "author_name": "Lineth Lopez",
+        "author_inst": "Complejo Hospitalario Metropolitano, Caja de Seguro Social, Panama, Panama"
+      },
+      {
+        "author_name": "Ana Cooke",
+        "author_inst": "Complejo Hospitalario Metropolitano, Caja de Seguro Social, Panama, Panama"
+      },
+      {
+        "author_name": "Dimas Quiel",
+        "author_inst": "Complejo Hospitalario Metropolitano, Caja de Seguro Social, Panama, Panama"
+      },
+      {
+        "author_name": "Nathalie Buitron",
+        "author_inst": "Hospital Punta Pacifica"
+      },
+      {
+        "author_name": "Yaseikiry Perez",
+        "author_inst": "Complejo Hospitalario Metropolitano, Caja de Seguro Social, Panama, Panama"
+      },
+      {
+        "author_name": "Lesbia Lobo",
+        "author_inst": "Complejo Hospitalario Metropolitano, Caja de Seguro Social"
+      },
+      {
+        "author_name": "Yaneth Pitti",
+        "author_inst": "Gorgas Memorial Institute of Health Studies"
+      },
+      {
+        "author_name": "Yamilka Yamiselle Diaz",
+        "author_inst": "Gorgas Memorial Institute for Health Studies"
+      },
+      {
+        "author_name": "Lisseth Saenz",
+        "author_inst": "Gorgas Memorial Institute of Health Studies"
+      },
+      {
+        "author_name": "Danilo Franco",
+        "author_inst": "Gorgas Memorial Institute of Health Studies"
+      },
+      {
+        "author_name": "Daniel Castillo",
+        "author_inst": "Gorgas Memorial Institute of Health Studies"
+      },
+      {
+        "author_name": "Elimelec Valdespino",
+        "author_inst": "Gorgas Memorial Institute of Health Studies"
+      },
+      {
+        "author_name": "Isabel Blanco",
+        "author_inst": "Pacifica Salud, Centro de Investigacion Medica, Panama, PANAMA."
+      },
+      {
+        "author_name": "Emilio Romero",
+        "author_inst": "Universidad de Panama"
+      },
+      {
+        "author_name": "Alcibiades Villarreal",
+        "author_inst": "Instituto de Investigaciones Cientificas y Servicios de Alta Tecnologia INDICASAT-AIP, City of Knowledge, PANAMA."
+      },
+      {
+        "author_name": "Idalina Cubilla-Batista",
+        "author_inst": "Hospital Regional Dr. Rafael Estevez, Caja de Seguro Social, Panama, PANAMA"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "hematology"
+  },
   {
     "rel_doi": "10.1101/2022.10.26.513886",
     "rel_title": "Complex changes in serum protein levels upon recovery from SARS-CoV2 infection",
@@ -172031,53 +170913,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2022.10.21.22281363",
-    "rel_title": "COVID-19 vaccine equity and the right to health for displaced Venezuelans in Latin America",
-    "rel_date": "2022-10-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.21.22281363",
-    "rel_abs": "Given the magnitude of Venezuelan displacement in Latin America, there is a need to assess how migrants were, and will continue to be, addressed in COVID-19 vaccination policies. To explore migration status as a dimension of vaccine equity in Latin America and in relation to international human rights, we assessed national vaccination plans, peer-reviewed, and gray literature published between January 2020 and June 2021. Three key rights-related concerns were found to restrict the health rights of migrants in the region: 1) lack of prioritization of migrants in vaccine distribution; 2) onerous documentation requirements to be eligible for COVID-19 vaccination; and (3) how pervasive anti-migrant discrimination limited equitable health care access. While international human rights law prohibits against discrimination based on migration status, few countries analyzed realized their obligations to provide equal access to COVID-19 vaccines to non-citizens, including displaced Venezuelans. Especially for migrants and displaced people, effective and sustainable vaccination strategies for COVID-19 and future pandemics in Latin America must be guided not only by epidemiological risk but also seek to align with human rights obligations. To achieve this, States must also take special measures to facilitate vaccine access for communities facing systemic discrimination, exclusion, and marginalization.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "David Hill",
-        "author_inst": "University of Toronto Dalla Lana School of Public Health"
-      },
-      {
-        "author_name": "Zafiro Andrade-Romo",
-        "author_inst": "University of Toronto Dalla Lana School of Public Health"
-      },
-      {
-        "author_name": "Karla Solari",
-        "author_inst": "Universidad Peruana Cayetano Heredia"
-      },
-      {
-        "author_name": "Ellithia Adams",
-        "author_inst": "University of Toronto Dalla Lana School of Public Health"
-      },
-      {
-        "author_name": "Lisa Forman",
-        "author_inst": "University of Toronto Dalla Lana School of Public Health"
-      },
-      {
-        "author_name": "Daniel Grace",
-        "author_inst": "University of Toronto Dalla Lana School of Public Health"
-      },
-      {
-        "author_name": "Alfonso Silva-Santisteban",
-        "author_inst": "Universidad Peruana Cayetano Heredia"
-      },
-      {
-        "author_name": "Amaya Perez-Brumer",
-        "author_inst": "University of Toronto Dalla Lana School of Public Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2022.10.21.22281271",
     "rel_title": "NC-COVID: A Time-Varying Compartmental Model for Estimating SARS-CoV-2 Infection Dynamics in North Carolina, US",
@@ -172832,6 +171667,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.10.24.513610",
+    "rel_title": "Fever temperatures modulate intraprotein dynamics and enhance the binding affinity between monoclonal antibodies and the Spike protein from SARS-CoV-2",
+    "rel_date": "2022-10-25",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.24.513610",
+    "rel_abs": "Fever is a typical symptom of most infectious diseases. While prolonged fever may be clinically undesirable, mild reversible fever (< 39{degrees}C, 312K) can potentiate the immune responses against pathogens. Here, using molecular dynamics, we investigated the effect of febrile temperatures (38{degrees}C to 40{degrees}C, 311K to 313K) on the immune complexes formed by the SARS-CoV-2 spike protein with two neutralizing antibodies. We found that, at mild fever temperatures (311-312K), the binding affinities of the two antibodies improve when compared to the physiological body temperature (37{degrees}C, 310K). Furthermore, only at 312K, antibodies exert distinct mechanical effects on the receptor binding domains of the spike protein that may hinder SARS-CoV-2 infectivity. Enhanced antibody binding affinity may thus be obtained using appropriate temperature conditions.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Dong Gun Kim",
+        "author_inst": "Korea Advanced Institute of Science and Technology"
+      },
+      {
+        "author_name": "Hak Sung Kim",
+        "author_inst": "Korea Advanced Institute of Science and Technology"
+      },
+      {
+        "author_name": "Yoonjoo Choi",
+        "author_inst": "Chonnam National University Medical School"
+      },
+      {
+        "author_name": "Razvan Costin Stan",
+        "author_inst": "Chonnam National University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "bioinformatics"
+  },
   {
     "rel_doi": "10.1101/2022.10.24.513619",
     "rel_title": "Immunogenicity of the BA.5 Bivalent mRNA Vaccine Boosters",
@@ -174373,41 +173239,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health systems and quality improvement"
   },
-  {
-    "rel_doi": "10.1101/2022.10.20.22281311",
-    "rel_title": "Meeting the 2030 End TB goals in the wake of COVID-19: a modelling study of countries in the USAID TB portfolio",
-    "rel_date": "2022-10-21",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.20.22281311",
-    "rel_abs": "Progress towards the 2030 End TB goals has seen severe setbacks due to disruptions arising from the COVID-19 pandemic. For governments and international partner organizations supporting the global TB response, there is a need to assess what level of effort is now needed to reach these goals. Using mathematical modelling, we addressed this question for the countries being supported by the United States Agency for International Development (USAID). We aggregated the 24 countries in the USAID portfolio into three geographical country groups: South Asia; sub-Saharan Africa; and Central Asian Republics/Europe (CAR/EU). From 2023 onwards we modelled a combination of interventions acting at different stages of the care cascade, including improved diagnostics; reducing the patient care seeking delay; and the rollout of a disease-preventing vaccine from 2025 onwards. We found that in all three country groups, meeting the End TB goals by 2030 will require a combination of interventions acting at stages of the TB care cascade. Specific priorities may depend on country settings, for example with public-private mix playing an important role in countries in South Asia and elsewhere. When a vaccine becomes available, its required coverage to meet the 2030 goals will vary by setting, depending on the amount of preventive therapy that has already been implemented. Monitoring the number-needed-to-test to identify 1 person with TB in community settings can provide a useful measure of progress towards the End TB goals.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Nimalan Arinaminpathy",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Ya Diul Mukadi",
-        "author_inst": "USAID"
-      },
-      {
-        "author_name": "Amy Bloom",
-        "author_inst": "USAID"
-      },
-      {
-        "author_name": "Cheri Vincent",
-        "author_inst": "USAID"
-      },
-      {
-        "author_name": "Sevim Ahmedov",
-        "author_inst": "USAID"
-      }
-    ],
-    "version": "1",
-    "license": "cc0",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.10.18.22281237",
     "rel_title": "Did Risk-based or Age-based Vaccine Prioritization for Covid-19 Save More Lives?",
@@ -174758,6 +173589,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2022.10.20.22281317",
+    "rel_title": "The COVID-19 burnout scale: Development and initial validation",
+    "rel_date": "2022-10-21",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.20.22281317",
+    "rel_abs": "We developed and validated a self-assessment instrument to measure COVID-19 pandemic-related burnout in the general population. We assessed the psychometric properties of the COVID-19 burnout scale (COVID-19-BS). Exploratory and confirmatory factor analysis identified three factors for the COVID-19-BS; emotional exhaustion, physical exhaustion, and exhaustion due to measures against the COVID-19. Cronbach s alpha coefficients for the three factors and the COVID-19-BS ranged from 0.860 to 0.921. Kaiser-Meyer-Olkin value was 0.945 and p-value for Bartlett test was <0.001 indicating highly acceptable values. Convergent validity results indicated a significant positive correlation between COVID-19-BS and anxiety and depression. Known-groups analysis identified the ability of COVID-19-BS to discriminate groups according to gender, chronic condition, and health status. Our findings indicate that the final 13-item model of COVID-19-BS is a brief, easy to administer, valid and reliable scale for assessing COVID-19-related burnout in the general public.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Petros A Galanis",
+        "author_inst": "Faculty of Nursing, National and Kapodistrian University of Athens"
+      },
+      {
+        "author_name": "Aglaia Katsiroumpa",
+        "author_inst": "Faculty of Nursing, National and Kapodistrian University of Athens"
+      },
+      {
+        "author_name": "Panayota Sourtzi",
+        "author_inst": "Faculty of Nursing, National and Kapodistrian University of Athens"
+      },
+      {
+        "author_name": "Olga Siskou",
+        "author_inst": "University of Piraeus"
+      },
+      {
+        "author_name": "Olympia Konstantakopoulou",
+        "author_inst": "Faculty of Nursing, National and Kapodistrian University of Athens"
+      },
+      {
+        "author_name": "Daphne Kaitelidou",
+        "author_inst": "Faculty of Nursing, National and Kapodistrian University of Athens"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2022.10.20.22281334",
     "rel_title": "Prediction of COVID-19 Diagnosis from Healthy and Pneumonia CT scans using Convolutional Neural Networks",
@@ -176483,69 +175353,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "genetic and genomic medicine"
   },
-  {
-    "rel_doi": "10.1101/2022.10.14.22280869",
-    "rel_title": "MULTISYSTEM INFLAMMATORY SYNDROME IN CHILDREN COURSE AMID COVID-19 PANDEMIC IN THE REBUBLIC OF BELARUS",
-    "rel_date": "2022-10-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.14.22280869",
-    "rel_abs": "ResumeIn first two years of COVID-19 pandemic, children usually had a mild or asymptomatic form of the disease. However, in rare cases, after suffering COVID-19, children had clinical manifestations similar to incomplete Kawasaki Disease (CD) or toxic shock syndrome. This condition is known as multisystem inflammatory syndrome in children (MIS-C).\n\nThe purposeof this research was to study clinical and laboratory features and outcomes of multisystem inflammatory syndrome in children who were hospitalized during COVID-19 pandemic.\n\nMaterials and methodsIn 19 months (May 2020 - December 2021) 63 patients with a diagnosis of \"Multisystem inflammatory syndrome in children\" (MIS-C) associated with COVID-19 were observed in the departments of Anesthesiology and Intensive Care of the Healthcare Institution \"City Childrens Infectious Clinical Hospital\" in Minsk, Republic of Belarus. MIS-C was diagnosed on criteria of CDC/WHO, 2020. All calculations were carried out in the statistical package R, version 4.1. The results of the analysis were considered statistically significant with p<0,05.\n\nThe results of the studyAll of 63 children with MIS-C didnt have an acute coronavirus infection. Therefore, it was impossible to determine which strain of SARS-CoV-2 patient exactly had. However, we formed 3 groups of patients based on circulation of the dominant strain of SARS-CoV-2 in Belarus at different times. The 1st group included 40 patients (63,5%) received treatment from 05.25.2020 to 02.21.2021 (\"wuhan strains\"); the 2nd group - 9 children (14,3%) from 02.23.2021 to 06.13.2021 (\"alpha\"); the 3rd group - 14 children (22,2%) from 07.01.2021 to 11.19.2021 (\"delta\"). 47 (74,6%) patients had complete and incomplete Kawasaki Disease phenotype of MIS-C. Nonspecific phenotype was observed in 16 (25,4%) children. It manifested as signs of shock. The mean age didnt differ in study groups. It was 7{+/-}2,5; 9,4{+/-}4,2; 7,9{+/-}5 years respectively. All children had hyperthermic syndrome. Fever reached febrile numbers 3-4 times a day. Average fever duration was 3,2 [1-15] days. The course of MIS-C in children also didnt depend on the circulating strain of the virus. For instance, gastrointestinal dysfunction was observed in all three groups with equal frequency (73%, 78% and 57%, respectively). The only a statistically significant increase was in the number of children with cheilitis. In the 2nd group 8 children (89%) and the 3rd group 13 children (93%) had cheilitis, respectively, p=0,002. Neurological disorders such as headache, hyperesthesia, hallucinations, photophobia were more often observed in the 1st group of children - 19 (48%) cases and less frequently in the 2nd and 3rd group (in 11% and 14% of cases), p=0,022. Pathological blood flow regurgitation was the most common disorder (68-71%). Several biochemical markers of inflammation levels, such as C-reactive protein (CRP) and procalcitonin (PCT), were high. CRP levels were 162 mg/l [130; 245]; 130 mg/l [90; 160]; 130 mg/l [106; 149] in 3 study groups, respectively. In children of the 1st group CRP level was significantly higher, p=0.052. PCT level was higher in patients of the 3rd group (4.2 ng/ml [2,4; 8,8]; 3.9 ng/ml [3,2; 11,9]; 8.7 ng/ml [3,4; 14,1], p=0.625).\n\nConclusionAs a result of the research there wasnt found notable connection between clinical or laboratory features of MIS-C and the dominant circulating strain of SARS-CoV-2 in given time periods. During the circulation of \"alpha\" and \"delta\" strains, the only significant differences were decrease of the number of patients with neurological disorders and increase in the frequency of cheilitis, p=0,002. The remaining indicators of organ dysfunction were similar in three groups of children. There was 1 (1,6%) fatal outcome in our study.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Oksana Romanova",
-        "author_inst": "State Educational Belarusian State Medical University, Minsk, Belarus"
-      },
-      {
-        "author_name": "Natalia Kolomiets",
-        "author_inst": "State Educational Establishment Belarusian Medical Academy of Postgraduate Education, Minsk, Republic of Belarus"
-      },
-      {
-        "author_name": "Dzianis Savitski",
-        "author_inst": "City Children's Infectious Diseases Clinical Hospital, Minsk, Belarus"
-      },
-      {
-        "author_name": "Ala M Dashkevich",
-        "author_inst": "State Institution Republican Centre of Hygiene, Epidemiology and Public Health, Minsk, Republic of Belarus"
-      },
-      {
-        "author_name": "Olga Krasko",
-        "author_inst": "The State Scientific Institution \"The United Institute of Informatics Problems of the National Academy of Sciences of Belarus\", Minsk, Belarus"
-      },
-      {
-        "author_name": "Galina Batyan",
-        "author_inst": "State Educational Belarusian State Medical University, Minsk, Belarus"
-      },
-      {
-        "author_name": "Anna Kluchareva",
-        "author_inst": "State Educational Establishment Belarusian Medical Academy of Postgraduate Education, Minsk, Republic of Belarus"
-      },
-      {
-        "author_name": "Marina Sokolova",
-        "author_inst": "City Children's Infectious Diseases Clinical Hospital, Minsk, Belarus"
-      },
-      {
-        "author_name": "Ekaterina Sergienko",
-        "author_inst": "State Educational Belarusian State Medical University, Minsk, Belarus"
-      },
-      {
-        "author_name": "Oksana Hanenko",
-        "author_inst": "State Educational Establishment Belarusian Medical Academy of Postgraduate Education, Minsk, Republic of Belarus"
-      },
-      {
-        "author_name": "Lydia Matush",
-        "author_inst": "State Educational Belarusian State Medical University, Minsk, Belarus"
-      },
-      {
-        "author_name": "Uladislava Senkevich",
-        "author_inst": "City Children's Infectious Diseases Clinical Hospital, Minsk, Belarus"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.10.18.22281212",
     "rel_title": "ALCOHOLIC LIVER BIOMARKERS: DETERMINANTS FOR ADMISSION TO REHABILITATION CENTRES DURING THE COVID 19 PERIOD IN KENYA",
@@ -176860,6 +175667,189 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.10.17.22281161",
+    "rel_title": "Clinical antiviral efficacy of remdesivir and casirivimab/imdevimab against the SARS-CoV-2 Delta and Omicron variants",
+    "rel_date": "2022-10-19",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.17.22281161",
+    "rel_abs": "BackgroundUncertainty over the therapeutic benefit provided by parenteral remdesivir in COVID-19 has resulted in varying treatment guidelines. Early in the pandemic the monoclonal antibody cocktail, casirivimab/imdevimab, proved highly effective in clinical trials but because of weak or absent in vitro activity against the SARS-CoV-2 Omicron BA.1 subvariant, it is no longer recommended.\n\nMethodsIn a multicenter open label, randomized, controlled adaptive platform trial, low-risk adult patients with early symptomatic COVID-19 were randomized to one of eight treatment arms including intravenous remdesivir (200mg followed by 100mg daily for five days), casirivimab/imdevimab (600mg/600mg), and no study drug. The primary outcome was the viral clearance rate in the modified intention-to-treat population derived from daily log10 viral densities (days 0-7) in standardized duplicate oropharyngeal swab eluates. This ongoing adaptive trial is registered at ClinicalTrials.gov (NCT05041907).\n\nResultsAcceleration in mean estimated SARS-CoV-2 viral clearance, compared with the contemporaneous no study drug arm (n=64), was 42% (95%CI 18 to 73%) for remdesivir (n=67). Acceleration with casirivimab/imdevimab was 58% (95%CI: 10 to 120) in Delta (n=13), and 20% (95%CI: 3 to 43) in Omicron variant (n=61) infections compared with contemporaneous no study drug arm (n=84). In a post hoc subgroup analysis viral clearance was accelerated by 8% in BA.1 (95%CI: -21 to 59) and 23% (95%CI: 3 to 49) in BA.2 and BA.5 Omicron subvariants.\n\nConclusionsParenteral remdesivir accelerates viral clearance in early symptomatic COVID-19. Despite substantially reduced in vitro activities, casirivimab/imdevimab retains in vivo antiviral activity against COVID-19 infections caused by currently prevalent Omicron subvariants.\n\nBrief summaryIn early symptomatic COVID-19 remdesivir accelerated viral clearance by 42% while the monoclonal antibody cocktail casirivimab/imdevimab accelerated clearance by approximately 60% in SARS-CoV-2 Delta variant infections, and by approximately 25% in infections with Omicron subvariants BA.2 and BA.5.",
+    "rel_num_authors": 42,
+    "rel_authors": [
+      {
+        "author_name": "Podjanee Jittamala",
+        "author_inst": "Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "William Henry Keith Schilling",
+        "author_inst": "Mahidol Oxford Tropical Medicine Research Unit (MORU)"
+      },
+      {
+        "author_name": "James A Watson",
+        "author_inst": "Mahidol Oxford Tropical Medicine Research Unit"
+      },
+      {
+        "author_name": "Viravarn Luvira",
+        "author_inst": "Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Tanaya Siripoon",
+        "author_inst": "Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Thundon Ngamprasertchai",
+        "author_inst": "Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Pedro J Almeida",
+        "author_inst": "Clinical Research Unit, Center for Advanced and Innovative Therapies, Universidade Federal de Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Maneerat Ekkapongpisit",
+        "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Cintia Cruz",
+        "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "James J Callery",
+        "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Simon Boyd",
+        "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Orawan Anunsittichai",
+        "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Maliwan Hongsuwan",
+        "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Yutaritat Singhaboot",
+        "author_inst": "Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Watcharee Pagornrat",
+        "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Runch Tuntipaiboontana",
+        "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Varaporn Kruabkontho",
+        "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Thatsanun Ngernseng",
+        "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Jaruwan Tubprasert",
+        "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Mohammad Yazid Abdad",
+        "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Srisuda Keayarsa",
+        "author_inst": "Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Wanassanan Madmanee",
+        "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Renato S Aguiar",
+        "author_inst": "Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Universidade Federal de Minas Gerais"
+      },
+      {
+        "author_name": "Franciele M Santos",
+        "author_inst": "Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Universidade Federal de Minas Gerais"
+      },
+      {
+        "author_name": "Elizabeth M Batty",
+        "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Pongtorn Hanboonkunupakarn",
+        "author_inst": "Bangplee Hospital, Ministry of Public Health, Thailand"
+      },
+      {
+        "author_name": "Borimas Hanboonkunupakarn",
+        "author_inst": "Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Sakol Sookprome",
+        "author_inst": "Bangplee Hospital, Ministry of Public Health, Thailand"
+      },
+      {
+        "author_name": "Kittiyod Poovorawan",
+        "author_inst": "Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Mallika Imwong",
+        "author_inst": "Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Walter RJ Taylor",
+        "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Vasin Chotivanich",
+        "author_inst": "Faculty of Medicine, Navamindradhiraj University, Thailand"
+      },
+      {
+        "author_name": "Chunlanee Sangketchon",
+        "author_inst": "Faculty of Science and Health Technology, Navamindradhiraj University, Thailand"
+      },
+      {
+        "author_name": "Wiroj Ruksakul",
+        "author_inst": "Faculty of Medicine, Navamindradhiraj University, Thailand"
+      },
+      {
+        "author_name": "Kesinee Chotivanich",
+        "author_inst": "Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Sasithon Pukrittayakamee",
+        "author_inst": "Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Arjen M Dondorp",
+        "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Nicholas  PJ Day",
+        "author_inst": "Mahidol Oxford Tropical Medicine Research Unit"
+      },
+      {
+        "author_name": "Mauro M Teixeira",
+        "author_inst": "Clinical Research Unit, Center for Advanced and Innovative Therapies, Universidade Federal de Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Watcharapong Piyaphanee",
+        "author_inst": "Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Weerapong Phumratanaprapin",
+        "author_inst": "Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Thailand"
+      },
+      {
+        "author_name": "Nicholas J White",
+        "author_inst": "Faculty of Tropical Medicine, Mahidol University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.10.17.22280652",
     "rel_title": "Effects of return-to-office, public schools reopening, and vaccination mandates on COVID-19 cases among municipal employee residents of New York City",
@@ -178441,61 +177431,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2022.10.15.22281123",
-    "rel_title": "Investigating the cause of a 2021 winter wave of COVID-19 in a border region in Eastern Germany: a mixed-methods study, August to November 2021",
-    "rel_date": "2022-10-17",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.15.22281123",
-    "rel_abs": "In winter 2020 and 2021 many countries worldwide experienced a COVID-19 pandemic wave which led to severe burdens on healthcare systems and huge economic losses. Yet, it remains unclear how the winter waves started and many debates are ongoing about actions necessary to prevent future winter waves. In this study we deciphered the dynamic course of a winter wave in 2021 in Saxony, a state in Eastern Germany neighboring Czech Republic and Poland. The information we achieved might help future pandemic prevention.\n\nThe dynamic course of the 2021 winter wave in Saxony was investigated through integration of multiple virus genomic epidemiology approaches and functional evaluations of locally circulating variants. Through international collaborations, we performed genomic epidemiology analysis on a weekly base with samples from Saxony and also from one neighbor region in the Czech Republic. Phylogeny analyses were used to track transmission chains, monitor virus genetic changes and identify emerging variants. Phylodynamic approaches have been applied to track the dynamic changes of transmission clusters. For identified local variants of interest, active viruses were isolated and functional evaluations were performed.\n\nGenomic epidemiology studies revealed multiple long-lasting community transmission clusters acting as the major driving forces for the winter wave 2021. Analysis of the dynamic courses of two representative long-lasting community transmission clusters indicated similar dynamic changes. In the first 6-8 weeks, the relevant variant was mainly circulating in a small region among young and middle-aged people; after eight weeks, the ratio of people aged above 60 years in the infected population markedly increased, and the virus got more widely spread to distant regions. On the other hand, the transmission cluster caused by a locally occurring variant showed a different transmission pattern. It got geographically widely distributed within six weeks, with many people aged above 60 years being infected since the beginning of the cluster, indicating a higher risk for escalating healthcare burdens. This variant displayed a relative growth advantage compared to co-circulating Delta sub-lineages. Functional analyses revealed a replication advantage, but no advantage in immune evasion ability.\n\nThis study indicated that long-lasting community transmission clusters starting between August and October caused by imported variants as well as locally occurring variants all contributed to the development of the 2021 winter wave in Saxony. In particular, the cluster derived from a locally occurring variant with certain growth advantage might have stressed local healthcare systems.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Buqing Yi",
-        "author_inst": "Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Saxony, Germany"
-      },
-      {
-        "author_name": "Alexa Laubner",
-        "author_inst": "Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Saxony, Germany"
-      },
-      {
-        "author_name": "Marlena Stadtmueller",
-        "author_inst": "Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Saxony, Germany"
-      },
-      {
-        "author_name": "Eva Patrasova",
-        "author_inst": "Department of Epidemiology, Regional Public Health Authority for Ustecky Kraj, Usti nad Labem, Czech Republic; Third Faculty of Medicine, Charles University in "
-      },
-      {
-        "author_name": "Lenka Simunkova",
-        "author_inst": "Department of Epidemiology, Regional Public Health Authority for Ustecky Kraj, Usti nad Labem, Czech Republic"
-      },
-      {
-        "author_name": "Fabian Rost",
-        "author_inst": "DRESDEN concept Genome Center, TU Dresden, Dresden, Saxony, Germany; Center for Regenerative Therapies Dresden, TU Dresden, Dresden, Saxony, Germany"
-      },
-      {
-        "author_name": "Sylke Winkler",
-        "author_inst": "Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany and DRESDEN concept Genome Center, TU Dresden, Dresden, Saxony, Germany"
-      },
-      {
-        "author_name": "Susanne Reinhardt",
-        "author_inst": "DRESDEN concept Genome Center, TU Dresden, Dresden, Saxony, Germany"
-      },
-      {
-        "author_name": "Andreas Dahl",
-        "author_inst": "DRESDEN concept Genome Center, TU Dresden, Dresden, Saxony, Germany"
-      },
-      {
-        "author_name": "Alexander H. Dalpke",
-        "author_inst": "Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Saxony, Germany"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.10.17.22281058",
     "rel_title": "Eleven key measures for monitoring general practice clinical activity during COVID-19 using federated analytics on 48 million adults' primary care records through OpenSAFELY",
@@ -178894,6 +177829,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.10.14.512325",
+    "rel_title": "The impact of the ABO/Rh blood group on susceptibility and severity among COVID-19 patients in Luanda, Angola",
+    "rel_date": "2022-10-17",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.14.512325",
+    "rel_abs": "SARS-CoV-2 is a public health concern worldwide. Identification of biological factors that could influence transmission and worsen the disease has been the subject of extensive investigation. Herein, we investigate the impact of the ABO/Rh blood group on susceptibility and severity among COVID-19 patients in Luanda, Angola. This was a multicentric cohort study conducted with 101 COVID-19 patients. Chi-square and logistic regression were calculated to check factors related to the worsening of the disease and deemed significant when p<0.05. Blood type O (51.5%) and Rh-positive (93.1%) were the most frequent. Patients from blood type O had a high risk to severe disease [OR: 1.33 (95% CI: 0.42 - 4.18), p=0.630] and hospitalization [OR: 2.59 (95% CI: 0.84 - 8.00), p=0.099]. Also, Rh-positive blood type presented a high risk for severe disease (OR: 10.6, p=0.007) and hospitalization (OR: 6.04, p=0.026). We find a high susceptibility, severity, hospitalization, and mortality, respectively, among blood group O and Rh-positive patients, while blood group AB presented a low susceptibility, severity, hospitalization, and mortality, respectively. Our findings add to the body of evidence suggesting that ABO/Rh blood groups play an important role in the course of SARS-CoV-2 infection.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Cruz  S. Sebasti\u00e3o",
+        "author_inst": "Centro de Investiga\u00e7\u00e3o em Sa\u00fade de Angola (CISA), Caxito, Angola"
+      },
+      {
+        "author_name": "Alice Teixeira",
+        "author_inst": "Cl\u00ednica Girassol"
+      },
+      {
+        "author_name": "Ana Lu\u00edsa",
+        "author_inst": "Instituto Nacional de Investiga\u00e7\u00e3o em Sa\u00fade (INIS), Luanda, Angola"
+      },
+      {
+        "author_name": "Margarete Arrais",
+        "author_inst": "Centro de Investiga\u00e7\u00e3o em Sa\u00fade de Angola (CISA), Caxito, Angola"
+      },
+      {
+        "author_name": "Chissengo Tchonhi",
+        "author_inst": "Centro de Investiga\u00e7\u00e3o em Sa\u00fade de Angola (CISA), Caxito, Angola"
+      },
+      {
+        "author_name": "Adis Cogle",
+        "author_inst": "Cl\u00ednica Girassol"
+      },
+      {
+        "author_name": "Euclides Sacomboio",
+        "author_inst": "Instituto nacional de investiga\u00e7\u00e3o em sa\u00fade (INIS), Luanda, Angola"
+      },
+      {
+        "author_name": "Bruno Cardoso",
+        "author_inst": "Cl\u00ednica Girassol"
+      },
+      {
+        "author_name": "Joana Morais",
+        "author_inst": "Inistituto Nacional de Investiga\u00e7\u00e3o em sa\u00fade (INIS), Luanda, Angola"
+      },
+      {
+        "author_name": "Jocelyne Vasconcelos",
+        "author_inst": "Centro de Investiga\u00e7\u00e3o em sa\u00fade de Angola (CISA), Caxito, Angola"
+      },
+      {
+        "author_name": "Miguel Brito",
+        "author_inst": "Centro de Investiga\u00e7\u00e3o em Sa\u00fade de Angola (CISA), Caxito, Angola"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "new results",
+    "category": "genetics"
+  },
   {
     "rel_doi": "10.1101/2022.10.15.512291",
     "rel_title": "Diet Induced Obesity and Diabetes Enhance Mortality and Reduces Vaccine Efficacy for SARS-CoV-2",
@@ -180559,45 +179553,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2022.10.12.22280917",
-    "rel_title": "Evaluating an epidemiologically motivated surrogate model of a multi-model ensemble",
-    "rel_date": "2022-10-13",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.12.22280917",
-    "rel_abs": "Multi-model and multi-team ensemble forecasts have become widely used to generate reliable short-term predictions of infectious disease spread. Notably, various public health agencies have used them to leverage academic disease modelling during the COVID-19 pandemic. However, ensemble forecasts are difficult to interpret and require extensive effort from numerous participating groups as well as a coordination team. In other fields, resource usage has been reduced by training simplified models that reproduce some of the observed behaviour of more complex models. Here we used observations of the behaviour of the European COVID-19 Forecast Hub ensemble combined with our own forecasting experience to identify a set of properties present in current ensemble forecasts. We then developed a parsimonious forecast model intending to mirror these properties. We assess forecasts generated from this model in real time over six months (the 15th of January 2022 to the 19th of July 2022) and for multiple European countries. We focused on forecasts of cases one to four weeks ahead and compared them to those by the European forecast hub ensemble. We find that the surrogate model behaves qualitatively similarly to the ensemble in many instances, though with increased uncertainty and poorer performance around periods of peak incidence (as measured by the Weighted Interval Score). The performance differences, however, seem to be partially due to a subset of time points, and the proposed model appears better probabilistically calibrated than the ensemble. We conclude that our simplified forecast model may have captured some of the dynamics of the hub ensemble, but more work is needed to understand the implicit epidemiological model that it represents.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Sam Abbott",
-        "author_inst": "London School of Hygiene & Tropical Medicine"
-      },
-      {
-        "author_name": "Katharine Sherratt",
-        "author_inst": "London School of Hygiene & Tropical Medicine"
-      },
-      {
-        "author_name": "Nikos Bosse",
-        "author_inst": "London School of Hygiene & Tropical Medicine"
-      },
-      {
-        "author_name": "Hugo Gruson",
-        "author_inst": "London School of Hygiene & Tropical Medicine"
-      },
-      {
-        "author_name": "Johannes Bracher",
-        "author_inst": "Karlsruhe Institute of Technology"
-      },
-      {
-        "author_name": "Sebastian Funk",
-        "author_inst": "London School of Hygiene & Tropical Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.10.12.22280997",
     "rel_title": "Utility of human judgment ensembles during times of pandemic uncertainty: A case study during the COVID-19 Omicron BA.1 wave in the USA",
@@ -180852,6 +179807,49 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2022.10.12.512011",
+    "rel_title": "Laboratory evaluation of a quaternary ammonium compound (QAC)-based antimicrobial coating used in public transport during the COVID-19 pandemic",
+    "rel_date": "2022-10-13",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.12.512011",
+    "rel_abs": "The virucidal activity of a quaternary ammonium compound (QAC)-based antimicrobial coating used by the UK rail industry during the COVID-19 pandemic was evaluated using the bacteriophage {phi}6 as a surrogate for SARS-CoV-2. Immediately after application and in the absence of interfering substance, the product showed efficacy (>3 log10 reduction) on some materials typically used in rail carriages (stainless steel, high pressure laminate and plastic), variable efficacy on glass and no efficacy (<3 log10 reduction) on a train armrest made of Terluran 22. If, after application of the product, the surfaces remained undisturbed, the antimicrobial coating retained its efficacy for at least 28 days on all materials where it was effective immediately after application. However, regardless of the material coated or time since application, the presence of organic debris (fetal bovine serum) significantly reduced the viricidal activity of the coating. Wiping the surface with a wetted cloth after organic debris deposition was not sufficient to restore efficacy. We conclude that the product is likely to be of limited effectiveness in a busy multi-user environment such as public transport.\n\nImportanceThis study evaluated the performance of a commercially available antimicrobial coating used by the transport industry in the UK during the COVID-19 pandemic. While the product initially showed efficacy against {phi}6 when applied to some materials, when organic debris was subsequently deposited, the efficacy was severely diminished and could not be recovered through wiping (cleaning) the surface. This highlights the importance of including relevant materials and conditions when evaluating antimicrobial coatings in the laboratory. Further efforts are required to identify suitable infection prevention and control practices for the transport industry.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Paz Aranega-Bou",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Natalie Brown",
+        "author_inst": "University of Surrey"
+      },
+      {
+        "author_name": "Abigail Stigling",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Neville Q Verlander",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Thomas Pottage",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Allan Bennett",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Ginny Moore",
+        "author_inst": "UK Health Security Agency"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2022.10.12.22280904",
     "rel_title": "Residential clustering of COVID-19 cases and efficiency of building-wide compulsory testing notices as a transmission control measure in Hong Kong",
@@ -182341,109 +181339,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
-  {
-    "rel_doi": "10.1101/2022.10.08.22280863",
-    "rel_title": "A Third Dose COVID-19 Vaccination in Allogeneic Hematopoietic Stem Cell Transplantation Patients",
-    "rel_date": "2022-10-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.08.22280863",
-    "rel_abs": "We previously reported that a second dose of COVID-19 mRNA vaccine was safe and effective for allogeneic hematopoietic stem cell transplantation (HSCT) patients. However, some of these patients did not achieve seroconversion. Here, we investigated the safety and efficacy of a third dose of COVID-19 mRNA vaccine in Japanese allogeneic HSCT patients. Antibody titers against the S1 spike protein were measured using the QuaResearch COVID-19 Human IgM IgG ELISA kit. The previous study included 25 allogeneic HSCT patients who received two doses of COVID-19 mRNA vaccine. Following the exclusion of three patients because of the development of COVID-19 (n = 2) and loss to follow-up (n = 1), the study evaluated 22 allogeneic HSCT patients who received a third dose of COVID-19 mRNA vaccine (BNT162b2 [n = 15] and mRNA-1273 [n = 7]). Median age at the time of the first vaccination was 56 (range, 23-71) years. Median time from HSCT to the third vaccination and from the second to the third vaccination was 1842 (range, 378-4279) days and 219 (range, 194-258) days, respectively. Five patients were receiving immunosuppressants at the third vaccination, namely calcineurin inhibitors (CI) alone (n = 1), steroids alone (n = 2), or CI combined with steroids (n = 2). Median optical density of S1 IgG titers before and after the third dose was 0.099 (range, 0.001-0.713) and 1.315 (range, 0.006-1.730), respectively. Among 22 evaluable patients, 21 (95%) seroconverted after the third dose. Four of the five patients treated with steroids or CI seroconverted after the third vaccination. One patient with a serum IgG level of 173 mg/dL who received steroids did not achieve seroconversion. On one-week follow-up, none of our patients had > grade 3 or serious adverse events, new-onset graft-versus-host disease (GVHD), or GVHD exacerbation after vaccination. The most frequent adverse event was mild pain at the injection site. A third dose of the BNT162b2 and mRNA-1273 COVID-19 vaccines was safe and effective for allogeneic HSCT patients.",
-    "rel_num_authors": 22,
-    "rel_authors": [
-      {
-        "author_name": "Marika Watanabe",
-        "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan"
-      },
-      {
-        "author_name": "Kimikazu Yakushijin",
-        "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan"
-      },
-      {
-        "author_name": "Yohei Funakoshi",
-        "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan"
-      },
-      {
-        "author_name": "Goh Ohji",
-        "author_inst": "Division of Infectious Disease Therapeutics, Department of Microbiology and Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan"
-      },
-      {
-        "author_name": "Hiroya Ichikawa",
-        "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan"
-      },
-      {
-        "author_name": "Hironori Sakai",
-        "author_inst": "R&D, Cellspect Co., Ltd., Morioka, Iwate, Japan"
-      },
-      {
-        "author_name": "Wataru Hojo",
-        "author_inst": "R&D, Cellspect Co., Ltd., Morioka, Iwate, Japan"
-      },
-      {
-        "author_name": "Miki Saeki",
-        "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan"
-      },
-      {
-        "author_name": "Yuri Hirakawa",
-        "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan"
-      },
-      {
-        "author_name": "Sakuya Matsumoto",
-        "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan"
-      },
-      {
-        "author_name": "Rina Sakai",
-        "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan"
-      },
-      {
-        "author_name": "Shigeki Nagao",
-        "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan"
-      },
-      {
-        "author_name": "Akihito Kitao",
-        "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan"
-      },
-      {
-        "author_name": "Yoshiharu Miyata",
-        "author_inst": "BioResource Center, Kobe University Hospital, Kobe, Japan"
-      },
-      {
-        "author_name": "Taiji Koyama",
-        "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan"
-      },
-      {
-        "author_name": "Yasuyuki Saito",
-        "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan"
-      },
-      {
-        "author_name": "Shinichiro Kawamoto",
-        "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan"
-      },
-      {
-        "author_name": "Katsuya Yamamoto",
-        "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan"
-      },
-      {
-        "author_name": "Mitsuhiro Ito",
-        "author_inst": "Laboratory of Hematology, Division of Medical Biophysics, Kobe University Graduate School of Health Sciences, Kobe, Japan"
-      },
-      {
-        "author_name": "Tohru Murayama",
-        "author_inst": "Department of Hematology, Hyogo Cancer Center, Akashi, Japan"
-      },
-      {
-        "author_name": "Hiroshi Matsuoka",
-        "author_inst": "BioResource Center, Kobe University Hospital, Kobe, Japan"
-      },
-      {
-        "author_name": "Hironobu Minami",
-        "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.10.11.22280953",
     "rel_title": "CoViD-19 rRT-PCR Testing Capacity in Ghana; Indications of Preparedness for Marburg virus Outbreak?",
@@ -182834,6 +181729,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.10.09.22280878",
+    "rel_title": "Associations Between Reported Post-COVID-19 Symptoms and Subjective Well-Being, Israel, July 2021 -April 2022",
+    "rel_date": "2022-10-10",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.09.22280878",
+    "rel_abs": "The impact of individual symptoms reported post-COVID-19 on subjective well-being (SWB) is unknown. We described associations between SWB and selected reported symptoms following SARS-CoV-2 infection. We analysed reported symptoms and subjective well being from 2295 participants (of which 576 reporting previous infection) in an ongoing longitudinal cohort study taking place in Israel. We estimated changes in SWB associated with reported selected symptoms at three follow-up time points (3-6, 6-12, and 12-18 months post infection) among participants reporting previous SARS-CoV-2 infection, adjusted for key demographic variables, using linear regression. Our results suggest that the biggest and most sustained changes in SWB stems from non-specific symptoms (fatigue -7.7 percentage points (pp), confusion/ lack of concentration -10.7 pp, and sleep disorders -11.5pp, p<0.005), whereas the effect of system-specific symptoms, such as musculoskeletal symptoms (weakness in muscles and muscle pain) on SWB, are less profound and more transient. Taking a similar approach for other symptoms and following individuals over time to describe trends in SWB changes attributable to specific symptoms will help understand the post-acute phase of COVID-19 and how it should be defined and better managed.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Yanay Gorelik",
+        "author_inst": "Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel"
+      },
+      {
+        "author_name": "Amiel A Dror",
+        "author_inst": "Galilee Medical Center, Azrieli Faculty of Medicine Bar-Ilan University"
+      },
+      {
+        "author_name": "Hiba Zayyad",
+        "author_inst": "Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel; Baruch Padeh Poriya Medical Center, Poriya, Israel"
+      },
+      {
+        "author_name": "Ofir Wertheim",
+        "author_inst": "Baruch Padeh Poriya Medical Center, Poriya, Israel"
+      },
+      {
+        "author_name": "Kamal Abu Jabal",
+        "author_inst": "Azrieli Faculty of Medicine, Safed, Israel; Ziv medical Centre, Safed, israel"
+      },
+      {
+        "author_name": "Nazzal Saleh",
+        "author_inst": "Baruch Padeh Poriya Medical Center, Poriya, Israel"
+      },
+      {
+        "author_name": "Paul Kuodi",
+        "author_inst": "The Azrieli Faculty of Medicine, Bar Ilan University, Tzfat, Israel"
+      },
+      {
+        "author_name": "Jelte Elsinga",
+        "author_inst": "The Azrieli Faculty of Medicine, Bar Ilan University, Tzfat, Israel"
+      },
+      {
+        "author_name": "Daniel Glikman",
+        "author_inst": "The Azrieli Faculty of Medicine, Bar Ilan University, Tzfat, Israel; Baruch Padeh Poriya Medical Center, Poriya, Israel"
+      },
+      {
+        "author_name": "Michael Edelstein",
+        "author_inst": "Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel; Ziv Medical Centre, Safed, Israel"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2022.10.07.22280827",
     "rel_title": "Mitigating the Severity of COVID-19 Illness in the Primary Care Patient Population through Early Identification and Close Monitoring of Underlying Comorbidities",
@@ -184323,49 +183273,6 @@
     "type": "new results",
     "category": "evolutionary biology"
   },
-  {
-    "rel_doi": "10.1101/2022.10.07.511263",
-    "rel_title": "Neutralization of SARS-CoV-2 Omicron BA.4/BA.5 subvariant by a booster dose of bivalent adjuvanted subunit vaccine containing Omicron BA.4/BA.5 and BA.1 subvariants",
-    "rel_date": "2022-10-07",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.07.511263",
-    "rel_abs": "The dominance of SARS-CoV-2 variants of concern (VoC), such as the Omicron subvariants, is a threat to the current vaccination scheme due to increased resistance to immune neutralization and greater transmissibility. To develop the next generation of prefusion SARS-CoV-2 spike protein (S-2P) subunit vaccine adjuvanted with CpG1018 and aluminum hydroxide, mice immunized with two doses of the adjuvanted ancestral Wuhan strain (W) followed by the third dose of the W or Omicron variants (BA.1 or BA.4/BA.5) S-2P, or a combination of the above bivalent S-2Ps. Antisera from mice were tested against pseudovirus neutralization assay of ancestral SARS-CoV-2 (WT) and Omicron BA.4/BA.5 subvariant. Boosting with bivalent mixture of Omicron BA.4/BA.5 and W S-2P achieved the highest neutralizing antibody titers against BA.4/BA.5 subvariant pseudovirus compared to other types of S-2P as boosters.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Tsun-Yung Kuo",
-        "author_inst": "Medigen Vaccine Biologics Corporation"
-      },
-      {
-        "author_name": "Chia En Lien",
-        "author_inst": "Medigen Vaccine Biologics Corporation"
-      },
-      {
-        "author_name": "Yi-Jiun Lin",
-        "author_inst": "Medigen Vaccine Biologics Corporation"
-      },
-      {
-        "author_name": "Meei-Yun Lin",
-        "author_inst": "Medigen Vaccine Biologics Corporation"
-      },
-      {
-        "author_name": "Luke Tzu-Chi Liu",
-        "author_inst": "Medigen Vaccine Biologics Corporation"
-      },
-      {
-        "author_name": "Chung-Chin Wu",
-        "author_inst": "Medigen Vaccine Biologics Corporation"
-      },
-      {
-        "author_name": "Wei-Hsuan Tang",
-        "author_inst": "Medigen Vaccine Biologics Corporation"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2022.10.07.511319",
     "rel_title": "Development of SARS-CoV-2 mRNA vaccines encoding spike N-terminal and receptor binding domains",
@@ -184756,6 +183663,61 @@
     "type": "new results",
     "category": "scientific communication and education"
   },
+  {
+    "rel_doi": "10.1101/2022.10.03.22280660",
+    "rel_title": "Effectiveness and duration of a second COVID-19 vaccine booster",
+    "rel_date": "2022-10-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.03.22280660",
+    "rel_abs": "Using a prospective national cohort of 3.75 million individuals aged 20 or older, we evaluated the effectiveness against COVID-19 related ICU admissions and death of mRNA-based second vaccine boosters for four different three-dose background regimes: BNT162b2 primary series plus a homologous booster, and CoronaVac primary series plus an mRNA booster, a homologous booster, and a ChAdOx-1 booster. We estimated the vaccine effectiveness weekly from February 14 to August 15, 2022, by estimating hazard ratios of immunization over non-vaccination, accounting for relevant confounders. The overall adjusted effectiveness of a second mRNA booster shot was 88.2% (95%CI, 86.2-89.9) and 90.5% (95%CI 89.4-91.4) against ICU admissions and death, respectively. Vaccine effectiveness showed a mild decrease for all regimens and outcomes, probably associated with the introduction of BA.4 and BA.5 Omicron sub-lineages and immunity waning. The duration of effectiveness suggests that no additional boosters are needed six months following a second booster shot.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Alejandro Jara",
+        "author_inst": "Pontificia Universidad Catolica de Chile"
+      },
+      {
+        "author_name": "Cristobal Cuadrado",
+        "author_inst": "Ministerio de Salud Chile"
+      },
+      {
+        "author_name": "Eduardo A Undurraga",
+        "author_inst": "Pontificia Universidad Catolica de Chile"
+      },
+      {
+        "author_name": "Christian Garcia",
+        "author_inst": "Ministerio de Salud Chile"
+      },
+      {
+        "author_name": "Manuel Najera",
+        "author_inst": "Ministerio de Salud Chile"
+      },
+      {
+        "author_name": "Maria Paz Bertoglia",
+        "author_inst": "Ministerio de Salud Chile"
+      },
+      {
+        "author_name": "Veronica Vergara",
+        "author_inst": "Ministerio de Salud Chile"
+      },
+      {
+        "author_name": "Jorge Fernandez",
+        "author_inst": "Ministerio de Salud Chile"
+      },
+      {
+        "author_name": "Heriberto Garcia",
+        "author_inst": "Ministerio de Salud Chile"
+      },
+      {
+        "author_name": "Rafael Araos",
+        "author_inst": "Universidad del Desarrollo Clinica Alemana"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.10.04.22280542",
     "rel_title": "Key performance indicators of COVID-19 contact tracing in Belgium from September 2020 to December 2021",
@@ -186293,117 +185255,6 @@
     "type": "new results",
     "category": "systems biology"
   },
-  {
-    "rel_doi": "10.1101/2022.09.27.22280428",
-    "rel_title": "Impact of Fluvoxamine on outpatient treatment of COVID-19 in Honduras",
-    "rel_date": "2022-10-04",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.27.22280428",
-    "rel_abs": "BackgroundCOVID-19 pandemic has impacted lives globally. While COVID-19 did not discriminate against developed or developing nations, it has been a significant challenge for third world countries like Honduras to have widespread availability of advanced therapies. The concept of early treatment was almost unheard-of when early outpatient treatment with repurposed drugs in Latin American countries showed promising results. One such drug is fluvoxamine, that has shown tremendous potential in two major studies, following which fluvoxamine was added to the standard of care in Honduras.\n\nMethodsThis is a prospective observational study performed at the Hospital Centro Medico Sanpedrano (CEMESA) in San Pedro Sula, Cortes, Honduras in the COVID-19 outpatient clinic. All patients fifteen years of age or older, with mild or moderate signs and symptoms of COVID-19, and a positive SARS-CoV-2 antigen or Reverse Transcription Polymerase Chain Reaction (RT-PCR) were included in the study and prescribed fluvoxamine. Cohort of patients who decided to take fluvoxamine were compared to the cohort who did not take fluvoxamine for mortality risk and risk of hospitalization as primary endpoints. Patient were monitored for 30 days with first follow up at 7 days and second follow up at 10-14 days of symptom onset. Categorical variables were compared by Pearson Chi-square test. The Odds ratio was calculated using univariate and multivariate logistic regression. Continuous variables were compared by t-test and Wilcoxon rank-sum tests.\n\nResultsOf 657 total COVID-19 cases, 594 patients took fluvoxamine and 63 did not. A total of five patients (0.76 percent) died, of which only one death occurred in the fluvoxamine group. Patients who did not receive fluvoxamine had a significantly higher mortality (OR 24, p0.005, CI 2.6 to 233.5). Odds ratio of hospitalization in patients who did not take fluvoxamine was 2.38 (30 vs 10 hospitalizations, p 0.040, CI 1.04-5.47). The odds ratio of requiring oxygen in patients in the non-fluvoxamine group was 5.08 (p<0.001, CI 2.18-11.81). Mean lymphocytes count on the first follow-up visit was significantly higher in the fluvoxamine group (1.72 vs. 1.38, {Delta} 0.33, p 0.007, CI 0.09 to 0.58).\n\nConclusionThe results of our study suggest lowers odds of mortality and hospitalization in patients who took fluvoxamine vs fluvoxamine non-takers. Non-fluvoxamine group had higher odds of oxygen requirement than fluvoxamine group as well.",
-    "rel_num_authors": 24,
-    "rel_authors": [
-      {
-        "author_name": "Estela Pineda",
-        "author_inst": "Department of Internal Medicine, Hospital CEMESA Cortes, San Pedro Sula, Honduras"
-      },
-      {
-        "author_name": "Jarmanjeet Singh",
-        "author_inst": "Cardiovascular Medicine, University of California Riverside, United States of America"
-      },
-      {
-        "author_name": "Miguel Fernando Vargas Pineda",
-        "author_inst": "Department of Internal Medicine, Hospital Nacional Mario Catarino Rivas, San Pedro Sula, Honduras"
-      },
-      {
-        "author_name": "Jose Rodolfo Garay Umanzor",
-        "author_inst": "Department of Obstetrics & Gynaecology, Hospital Nacional Mario Catarino Rivas, San Pedro Sula, Honduras"
-      },
-      {
-        "author_name": "Fernando Baires",
-        "author_inst": "Universidad Nacional Autonoma de Honduras UNAH, Tegucigalpa, Honduras"
-      },
-      {
-        "author_name": "Luis Benitez",
-        "author_inst": "Universidad Nacional Autonoma de Honduras UNAH, Tegucigalpa, Honduras"
-      },
-      {
-        "author_name": "Cesar Burgos",
-        "author_inst": "Universidad Nacional Autonoma de Honduras UNAH, Tegucigalpa, Honduras"
-      },
-      {
-        "author_name": "Anupamjeet Kaur Sekhon",
-        "author_inst": "Sleep Medicine, Kaiser Permanente, Fontana, California, United States of America"
-      },
-      {
-        "author_name": "Nicole Crisp",
-        "author_inst": "Wound Care Department, El Campo Memorial Hospital, United States of America"
-      },
-      {
-        "author_name": "Anita S Lewis",
-        "author_inst": "Pharmacy Department, El Campo Memorial Hospital, United States of America"
-      },
-      {
-        "author_name": "Jana Radwanski",
-        "author_inst": "PharmD, Citizens Hospital Department of Pharmacy"
-      },
-      {
-        "author_name": "Marco Bermudez",
-        "author_inst": "Medicine Department , SBH Health System , Bronx , NY"
-      },
-      {
-        "author_name": "Karen Sanchez Barjun",
-        "author_inst": "Department of Internal Medicine Hospital Mario Catarino Rivas, San Pedro Sula, Cortes, Honduras"
-      },
-      {
-        "author_name": "Oscar Diaz",
-        "author_inst": "Department of Critical Care Hospital Regional del Norte Instituto Hondureno de Seguridad Social, San Pedro Sula, Cortes, Honduras"
-      },
-      {
-        "author_name": "Elsa Palou",
-        "author_inst": "Internal Medicine Department, Facultad de Ciencias Medicas, Universidad Nacional Autonoma de Honduras, Tegucigalpa, Honduras"
-      },
-      {
-        "author_name": "Rossany E Escalante",
-        "author_inst": "Department of Medicine, Facultad de Ciencas Medicas, Universidad Nacional Autonoma de Honduras, Tegucigalpa, Honduras"
-      },
-      {
-        "author_name": "Carlos Isai Hernandez",
-        "author_inst": "HEME Clinic, Choluteca, Choluteca, Honduras"
-      },
-      {
-        "author_name": "Mark L Stevens",
-        "author_inst": "Research Department, Texas A&M College of Medicine, Detar Family Medicine Residency Program, Victoria, TX, United States of America"
-      },
-      {
-        "author_name": "Deke Eberhard",
-        "author_inst": "Research Department, Texas A&M College of Medicine, Detar Family Medicine Residency Program, Victoria, TX, United States of America"
-      },
-      {
-        "author_name": "Manuel Sierra",
-        "author_inst": "Universidad Tecnologica Centroamericana, Tegucigalpa, Honduras"
-      },
-      {
-        "author_name": "Tito Alvarado",
-        "author_inst": "Infectiology Department, Facultad de Ciencias Medicas, Universidad Nacional Autonoma de Honduras, Tegucigalpa, Honduras"
-      },
-      {
-        "author_name": "Omar Videa",
-        "author_inst": "Clinica de Atencion Medica Integral CAMI, Tegucigalpa, Honduras"
-      },
-      {
-        "author_name": "Miguel Sierra-Hoffman",
-        "author_inst": "Research and Infectious Disease Department, Texas A&M College of Medicine"
-      },
-      {
-        "author_name": "Fernando Ramon Valerio",
-        "author_inst": "Department of Critical Care, Hospital CEMESA Cortes, San Pedro Sula,  Honduras"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.10.04.510657",
     "rel_title": "Relevance of the viral Spike protein/cellular Estrogen Receptor-\u03b1 interaction for endothelial-based coagulopathy induced by SARS-CoV-2",
@@ -186794,6 +185645,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2022.10.02.22280627",
+    "rel_title": "Dynamics of Vaccine-Hesitant Parents' Considerations Regarding Covid-19 Vaccination",
+    "rel_date": "2022-10-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.02.22280627",
+    "rel_abs": "IntroductionMost studies present a snapshot of hesitant parents decisions and thinking concerning COVID-19 vaccination, but for many it is a dynamic rather than a stable process. We examined the considerations of a group of vaccine hesitant parents (VHPs) with respect to COVID-19 vaccinations for their children before, during and after the main vaccination campaign for the 12 to15-year-old age group in Israel, over a six-month period.\n\nMethodsDigital surveys were administered to 1118 Israeli parents. After VHPs were identified, three surveys were conducted to evaluate considerations that discourage or encourage vaccination. A logistic regression was carried out on sixteen models; of these, six were found to be statistically significant.\n\nResults456 parents data were analyzed. Parents intentions to vaccinate prior to the vaccination campaign were a good predictor of their actual behavior, (rp=.497, p<.001). We divided the parents into four groups: consistently pro-vaccine (39.4%), consistently anti-vaccine (15.2%), pro-vaccine parents who did not vaccinate (17.6%), and anti-vaccine parents who did vaccinate (27.9%). We identified eight considerations that were significant in VHPs vaccination behavior: trust in scientists, doctors and drug companies, childrens preferences, spread of COVID, social responsibility, childrens characteristics, the vaccines speed of development and its side effects.\n\nDiscussionGreater vaccine uptake for teenagers may depend on the attitudes and perceptions of their parents. We identified encouraging and discouraging considerations that may make potential targets for public health officials when communicating about vaccines.\n\nArticle SummaryEncouraging and discouraging considerations re COVID-19 vaccination are explored and identified in vaccine hesitant parents.\n\nWhats known on this subjectMost studies found that vaccine uptake is improved among well-to-do or highly educated parents. Severity of the disease and safety of the vaccination are the main factors influencing the decision.\n\nWhat this study addsThe dynamics of attitude change toward vaccination among VHPs may be affected by several different factors. Chief are childrens preferences and individual health characteristics, side effects and speed of vaccine development",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Erga Atad",
+        "author_inst": "Reichman University"
+      },
+      {
+        "author_name": "Itamar Netzer",
+        "author_inst": "Clalit Healthcare"
+      },
+      {
+        "author_name": "Orr Peleg",
+        "author_inst": "Technion, Israel Institute of Technology"
+      },
+      {
+        "author_name": "Keren Landsman",
+        "author_inst": "Mida'at, for Informed Health (RA)"
+      },
+      {
+        "author_name": "Keren Dalyot",
+        "author_inst": "Technion, Israel Institute of Technology"
+      },
+      {
+        "author_name": "Shanny Edan-Reuvan",
+        "author_inst": "Technion, Israel Institute of Technology"
+      },
+      {
+        "author_name": "Eyal Nitzani",
+        "author_inst": "Amazon"
+      },
+      {
+        "author_name": "Ayelet Baram-Tsabari",
+        "author_inst": "Technion, Israel Institute of Technology"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2022.10.03.22280639",
     "rel_title": "Evaluation of primary allied healthcare in patients recovering from COVID-19: first results after six months follow-up in a Dutch nationwide prospective cohort study",
@@ -188407,49 +187305,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2022.09.29.22280448",
-    "rel_title": "Retrospective and prospective studies evaluating the performance of the SARS-Cov-2 \"AQ+ COVID-19 Ag Rapid Test\" from InTec on symptomatic and non-symptomatic patients",
-    "rel_date": "2022-09-30",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.29.22280448",
-    "rel_abs": "For the last two years, the SARS-CoV-2 virus spread all around the world and led to the COVID-19 pandemic. The need of methods to control the pandemic and to propose rapid and efficient diagnostic tools has emerged. In this perspective, SARS-CoV-2 rapid antigen detection tests (RADT) have been developed. We performed a retrospective study on 638 collected nasopharyngeal samples used for reference RT-qPCR diagnosis to compare the AQ+ COVID-19 Ag Rapid Test\" from InTec (AQ+ InTec test) performance with other commercially available RADT. We analysed the sensitivity and specificity of the different tests and showed a better overall performance of the AQ+ InTec test, which was confirmed on the SARS-Cov-2 Omicron variant. We then conducted a prospective study on 1428 patients, to evaluate the sensitivity and specificity of the AQ+ InTec test on nasal and nasopharyngeal samples in a point of care setting. We showed that sensitivity and specificity reach acceptable criteria regarding the official recommendations of the MDCG 2021-21 in both symptomatic and asymptomatic patients. Overall, the results of these two studies confirm that the AQ+ InTec test is a valuable tool for testing in a pandemic context with a high proportion of asymptomatic patients who are potential carriers for the SARS-CoV-2 virus and is performant on the most current circulating variant Omicron.\n\nHighlightsO_LIThe sensitivity of the AQ+ COVID-19 Ag Rapid Test from InTec reaches 94.4% on nasal samples and 97.4% on nasopharyngeal samples.\nC_LIO_LIThe performance of the test remains high on asymptomatic patients with a sensitivity of 89.2% on nasal samples and 97.0% on nasopharyngeal samples.\nC_LIO_LIProspective study in a point of care setting revealed a better sensitivity compared with other commercially available rapid antigen detection tests\nC_LI",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Thierry Prazuck",
-        "author_inst": "CHR Orleans"
-      },
-      {
-        "author_name": "Raphael Serreau",
-        "author_inst": "PsycoMADD, CHU Paul Brousse, APHP, Universite Paris Saclay"
-      },
-      {
-        "author_name": "Aurelie Theillay",
-        "author_inst": "Service des maladies infectieuses, CHR Orleans, France"
-      },
-      {
-        "author_name": "Sandra Pallay",
-        "author_inst": "Service des maladies infectieuses, CHR Orleans, France"
-      },
-      {
-        "author_name": "Daniela Pires-Roteia",
-        "author_inst": "Service des maladies infectieuses, CHR Orleans, France"
-      },
-      {
-        "author_name": "Fanny Prazuck",
-        "author_inst": "Service des maladies infectieuses, CHR Orleans, France"
-      },
-      {
-        "author_name": "Fabien Lesne",
-        "author_inst": "Laboratoire de biologie moleculaire, CHR Orleans, France"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.09.28.22280467",
     "rel_title": "The impact of a home-based personalized computerized training program on cognitive dysfunction associated with Long COVID: a before-and-after feasibility study",
@@ -188876,6 +187731,25 @@
     "type": "new results",
     "category": "pharmacology and toxicology"
   },
+  {
+    "rel_doi": "10.1101/2022.09.28.22280472",
+    "rel_title": "Covid-19: Qualitative Change in the Behavior of the \"Virus vs Human\" System - From Limit Cycle to Sustained Focus",
+    "rel_date": "2022-09-30",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.28.22280472",
+    "rel_abs": "AnnotationThe high contagiousness of the latest strains of Covid-19 qualitatively changes the behavior of the \"virus vs human\" system. Numerical experiments with a model of the Covid-19 epidemic in Moscow have shown that a reproduction number R0 of about 4 is critical, defining a qualitative change in the dynamics of the epidemic. Below this value (observed until 2022), the long-term forecast tends to undamped oscillations; above this value, it is described by damped oscillations: amplitudes of the epidemic waves get smaller and smaller, with a constant, very high background level of morbidity (or high-intensity vaccination) that maintains the state of natural immunity at a level close to 100% (reaching 93.7% for the current R0 value of about 16). At the limit, the system tends to a stable equilibrium point. Here we consider a reduced model of epidemic dynamics. Its study (search for equilibrium solutions, analysis of their stability, construction a bifurcation diagram and a phase portrait) confirms the presence of points of qualitative change in the behavior of the \"virus vs human\" system (bifurcation points). Some practical results for Moscow are given. A further increase in the contagiousness of the virus does not change the picture significantly, thus more infectious strains are not to be feared. The key parameter of the study is the function of the immunity level depending on the time after the disease. The damping of omicron waves (oscillations), observed recently in many countries, is a confirmation of the correctness of the accepted hypotheses.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Alexander Sokolov",
+        "author_inst": "Institute for information transmission problem RAS"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2022.09.29.22280508",
     "rel_title": "When Case Reporting Becomes Untenable: Can Sewer Networks Tell Us Where COVID-19 Transmission Occurs?",
@@ -190409,37 +189283,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.09.26.22280293",
-    "rel_title": "Long-term mental health outcomes after SARS-CoV-2 infection: prospective cohort study",
-    "rel_date": "2022-09-27",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.26.22280293",
-    "rel_abs": "Despite previous evidence from retrospective cohorts suggest that survivors of COVID-19 may be at increased risk of psychiatric sequelae, questions remain on the incidence and absolute risk of psychiatric outcomes, and on the potential protective effect of vaccination. Addressing these knowledge gaps will help public health and clinical service planning during the ongoing pandemic. Based on UK Biobank prospective data, we constructed a SARS-CoV-2 infection cohort including participants with a positive PCR test for SARS-CoV-2 between March 1, 2020 and September 30, 2021; a contemporary control cohort with no evidence of SARS-CoV-2, and a historical control cohort predating the COVID-19 pandemic. Additional control cohorts were constructed for benchmarking, including participants diagnosed with other respiratory tract infection, or with a negative SARS-CoV-2 test. We used propensity score weighting using predefined (clinically informed) and data-driven covariates to minimize confounding. We then estimated incidence rates and risk of first psychiatric disorders diagnosed by ICD-10 codes and psychotropic prescriptions after SARS-CoV-2 infection using cause-specific Cox models.\n\nIn this prospective cohort including 406,579 adults (224,681 women, 181,898 men; mean [SD] age 66.1 [8.4] years), 26,181 had a SARS-CoV-2 infection. Compared with contemporary controls (n=380,398), COVID-19 survivors had increased risks of subsequent psychiatric diagnoses (HR: 2.02, 95% CI 1.85-2.21; difference in incidence rate: 24.85, 95 CI 20.69-29.39 per 1000 person-years) and psychotropic prescriptions (HR: 1.61, 95% CI 1.48-1.75; difference in incidence rate: 21.77, 95% CI 16.59-27.54 per 1000 person-years). Regarding individual mental health related outcomes, the SARS-CoV-2 infection cohort showed an increased risk of psychotic disorders (2.26, 1.28-3.98), mood disorders (2.19, 1.92-2.50), anxiety disorders (2.08, 1.82-2.38), substance use disorders (1.59, 1.34-1.90), sleep disorders (1.95, 1.60-2.39); and prescriptions for antipsychotics (3.78, 2.74-5.21), antidepressants (1.55, 1.29-1.87), benzodiazepines (1.82, 1.58-2.11), and opioids (1.40, 1.26-1.55). Overall, the risk of any mental health outcome was increased with a HR of 1.58, 95% CI 1.47-1.70; and difference in incidence rate of 32.04, 25.76-38.81 per 1000 person-years. These results were consistent when comparing to a historical control cohort. Additionally, mental health risks were increased even further in participants who tested positive in hospital settings. Finally, participants who were fully vaccinated had a lower risk of mental health outcomes compared to those infected when unvaccinated or partially vaccinated. All observed risks of mental health outcomes were attenuated or even lower after SARS-CoV-2 infection compared with those with other respiratory infections, or with participants in the test-negative control cohort.\n\nIn this prospective cohort study, people who survived COVID-19 were at increased risk of psychiatric outcomes and related psychotropic medications. These risks were higher in those with more severe disease, treated in hospital settings, and were significantly reduced in fully vaccinated people. Of note, compared to participants with other respiratory infections or with only negative testing results, those infected with SARS-CoV-2 had an even lower risk of mental health outcomes, warranting further research into causation. The early identification and treatment of psychiatric disorders among survivors of COVID-19 should be a priority in the long-term management of COVID-19. Particular attention might be needed for those with severe (hospitalized) disease and those who were not fully vaccinated at the time of infection.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Yunhe Wang",
-        "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom"
-      },
-      {
-        "author_name": "Junqing Xie",
-        "author_inst": "Centre for Statistics in Medicine and NIHR Biomedical Research Centre Oxford, NDORMS, University of Oxford, Oxford, United Kingdom"
-      },
-      {
-        "author_name": "GARCIA CLEMENTE",
-        "author_inst": "CIBERSAM, ISCIII, Madrid, Spain"
-      },
-      {
-        "author_name": "DANIEL PRIETO-ALHAMBRA",
-        "author_inst": "Centre for Statistics in Medicine and NIHR Biomedical Research Centre Oxford, NDORMS, University of Oxford, Oxford, United Kingdom"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.09.27.22280400",
     "rel_title": "Direct modelling from GPS data reveals daily-activity-dependency of effective reproduction number in COVID-19 pandemic",
@@ -190838,6 +189681,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pediatrics"
   },
+  {
+    "rel_doi": "10.1101/2022.09.22.22280262",
+    "rel_title": "Development and validation of a methodology to measure exhaled carbon dioxide (CO2) and control indoor air renewal",
+    "rel_date": "2022-09-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.22.22280262",
+    "rel_abs": "The measurement of CO2 has positioned itself as a low-cost and straightforward technique to indirectly control indoor air quality, allowing the reduction of the concentration of potentially pathogen-loaded aerosols to which we are exposed. However, on numerous occasions, bad practice limits the technique for CO2 level interpreting and does not apply methodologies that guarantee air renewal. This work proposes a new methodology for measuring and controlling CO2 levels for indoor air in shared spaces. The proposed methodology is based on three stages: diagnosis, correction protocols, and monitoring/control/surveillance (MCS). The procedure is explained using a cultural center as an actual base case study. Additionally, the procedure was validated by implementing 40 voluntary commercial spaces in Zaragoza (Spain). Standardization of methods is suggested so that the measurement of CO2 becomes an effective strategy to control the airborne transmission of pathogens and thus prevent future Covid-19 outbreaks and novel pandemics.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Marta Baselga",
+        "author_inst": "Institute for Health Research Aragon (IIS Aragon)"
+      },
+      {
+        "author_name": "Juan J Alba",
+        "author_inst": "University of Zaragoza"
+      },
+      {
+        "author_name": "Alberto J Schuhmacher",
+        "author_inst": "Institute for Health Research Aragon (IIS Aragon)"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2022.09.27.22280425",
     "rel_title": "Association of IFNAR2 rs2236757 and OAS3 rs10735079 polymorphisms with susceptibility to COVID-19 infection and severity",
@@ -192267,205 +191137,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2022.09.22.22280247",
-    "rel_title": "Abatacept for Treatment of Adults Hospitalized with Moderate or Severe Covid-19",
-    "rel_date": "2022-09-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.22.22280247",
-    "rel_abs": "BackgroundWe investigated whether abatacept, a selective costimulation modulator, provides additional benefit when added to standard-of-care for patients hospitalized with Covid-19.\n\nMethodsWe conducted a master protocol to investigate immunomodulators for potential benefit treating patients hospitalized with Covid-19 and report results for abatacept. Intravenous abatacept (one-time dose 10 mg/kg, maximum dose 1000 mg) plus standard of care (SOC) was compared with shared placebo plus SOC. Primary outcome was time-to-recovery by day 28. Key secondary endpoints included 28-day mortality.\n\nResultsBetween October 16, 2020 and December 31, 2021, a total of 1019 participants received study treatment (509 abatacept; 510 shared placebo), constituting the modified intention-to-treat cohort. Participants had a mean age 54.8 (SD 14.6) years, 60.5% were male, 44.2% Hispanic/Latino and 13.7% Black. No statistically significant difference for the primary endpoint of time-to-recovery was found with a recovery-rate-ratio of 1.14 (95% CI 1.00-1.29; p=0.057) compared with placebo. We observed a substantial improvement in 28-day all-cause mortality with abatacept versus placebo (11.0% vs. 15.1%; odds ratio [OR] 0.62 [95% CI 0.41- 0.94]), leading to 38% lower odds of dying. Improvement in mortality occurred for participants requiring oxygen/noninvasive ventilation at randomization. Subgroup analysis identified the strongest effect in those with baseline C-reactive protein >75mg/L. We found no statistically significant differences in adverse events, with safety composite index slightly favoring abatacept. Rates of secondary infections were similar (16.1% for abatacept; 14.3% for placebo).\n\nConclusionsAddition of single-dose intravenous abatacept to standard-of-care demonstrated no statistically significant change in time-to-recovery, but improved 28-day mortality.\n\nTrial registrationClinicalTrials.gov (NCT04593940).",
-    "rel_num_authors": 46,
-    "rel_authors": [
-      {
-        "author_name": "Emily R Ko",
-        "author_inst": "Duke University Medical Center"
-      },
-      {
-        "author_name": "Kevin J Anstrom",
-        "author_inst": "University of North Carolina"
-      },
-      {
-        "author_name": "Reynold A Panettieri Jr.",
-        "author_inst": "Robert Wood Johnson Medical School"
-      },
-      {
-        "author_name": "Anne M Lachiewicz",
-        "author_inst": "University of North Carolina"
-      },
-      {
-        "author_name": "Martin Maillo",
-        "author_inst": "Sanatorio Diagnostico"
-      },
-      {
-        "author_name": "Jane O'Halloran",
-        "author_inst": "Washington University in St. Louis School of Medicine"
-      },
-      {
-        "author_name": "Cynthia Boucher",
-        "author_inst": "National Center for Advancing Translational Sciences"
-      },
-      {
-        "author_name": "P. Brian Smith",
-        "author_inst": "Duke Clinical Research Institute, Duke University School of Medicine"
-      },
-      {
-        "author_name": "Matthew W McCarthy",
-        "author_inst": "Weill Cornell Medicine"
-      },
-      {
-        "author_name": "Patricia Segura Nunez",
-        "author_inst": "Hospital Nacional Hipolito Unanue"
-      },
-      {
-        "author_name": "Sabina Mendivil Tuchia de Tai",
-        "author_inst": "Hospital Central de la Fuerza Aerea del Peru"
-      },
-      {
-        "author_name": "Akram Khan",
-        "author_inst": "Oregon Health and Science University"
-      },
-      {
-        "author_name": "Alfredo J Mena Lora",
-        "author_inst": "University of Illinois at Chicago"
-      },
-      {
-        "author_name": "Matthias Salathe",
-        "author_inst": "University of Kansas Medical Center, Kansas City"
-      },
-      {
-        "author_name": "Eyal Kedar",
-        "author_inst": "St. Lawrence Health System"
-      },
-      {
-        "author_name": "Gerardo Capo",
-        "author_inst": "Trinitas Hospital"
-      },
-      {
-        "author_name": "Daniel Rodriguez Gonzalez",
-        "author_inst": "Nuevo Hospital Civil de Guadalajara Juan I. Menchaca"
-      },
-      {
-        "author_name": "Thomas F Patterson",
-        "author_inst": "University of Texas Health Science Center at San Antonio"
-      },
-      {
-        "author_name": "Christopher Palma",
-        "author_inst": "University of Rochester Medical School Medicine and Dentistry"
-      },
-      {
-        "author_name": "Horacio Ariza",
-        "author_inst": "Clinica Central S.A., Villa Regina"
-      },
-      {
-        "author_name": "Maria Patelli Lima",
-        "author_inst": "Hospital e Maternidade Celso Pierro-PUC Campinas"
-      },
-      {
-        "author_name": "John Blamoun",
-        "author_inst": "MidMichigan Medical Center"
-      },
-      {
-        "author_name": "Esteban Nannini",
-        "author_inst": "Departamento de Enfermedades Infecciosas, Sanatorio Britanico"
-      },
-      {
-        "author_name": "Eduardo Sprinz",
-        "author_inst": "Hospital de Clinicas de Porto Alegre HCPA"
-      },
-      {
-        "author_name": "Analia Mykietiuk",
-        "author_inst": "Instituto Medico Platense"
-      },
-      {
-        "author_name": "Jennifer P Wang",
-        "author_inst": "University of Massachusetts Medical Center"
-      },
-      {
-        "author_name": "Luis Parra-Rodriguez",
-        "author_inst": "Washington University St. Louis"
-      },
-      {
-        "author_name": "Tatyana Der",
-        "author_inst": "Duke University Medical Center"
-      },
-      {
-        "author_name": "Kate Willsey",
-        "author_inst": "Weill Cornell Medicine"
-      },
-      {
-        "author_name": "Daniel K Benjamin Jr.",
-        "author_inst": "Duke Clinical Research Institute, Duke University School of Medicine"
-      },
-      {
-        "author_name": "Jun Wen",
-        "author_inst": "Duke Clinical Research Institute, Duke University School of Medicine"
-      },
-      {
-        "author_name": "Pearl Zakroysky",
-        "author_inst": "Duke Clinical Research Institute, Duke University School of Medicine"
-      },
-      {
-        "author_name": "Susan Halabi",
-        "author_inst": "Duke Clinical Research Institute, Duke University School of Medicine"
-      },
-      {
-        "author_name": "Adam Silverstein",
-        "author_inst": "Duke Clinical Research Institute, Duke University School of Medicine"
-      },
-      {
-        "author_name": "Steven E McNulty",
-        "author_inst": "Duke Clinical Research Institute, Duke University School of Medicine"
-      },
-      {
-        "author_name": "Sean M O'Brien",
-        "author_inst": "Duke Clinical Research Institute, Duke University School of Medicine"
-      },
-      {
-        "author_name": "Hussein R Al-Khalidi",
-        "author_inst": "Duke Clinical Research Institute, Duke University School of Medicine"
-      },
-      {
-        "author_name": "Sandra Butler",
-        "author_inst": "Technical Resources International"
-      },
-      {
-        "author_name": "Jane Atkinson",
-        "author_inst": "National Center for Advancing Translational Sciences"
-      },
-      {
-        "author_name": "Stacey J Adam",
-        "author_inst": "Foundation for the National Institutes of Health"
-      },
-      {
-        "author_name": "Soju Chang",
-        "author_inst": "National Center for Advancing Translational Sciences"
-      },
-      {
-        "author_name": "Michael A Maldonado",
-        "author_inst": "Bristol Myers Squibb"
-      },
-      {
-        "author_name": "Michael Proscham",
-        "author_inst": "National Institute of Allergy and Infectious Diseases"
-      },
-      {
-        "author_name": "Lisa LaVange",
-        "author_inst": "University of North Carolina"
-      },
-      {
-        "author_name": "Samuel A Bozzette",
-        "author_inst": "National Center for Advancing Translational Sciences"
-      },
-      {
-        "author_name": "William  G. Powderly",
-        "author_inst": "Washington University in St Louis School of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.09.26.509485",
     "rel_title": "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease",
@@ -192904,6 +191575,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "occupational and environmental health"
   },
+  {
+    "rel_doi": "10.1101/2022.09.23.22279458",
+    "rel_title": "Pan-Canadian survey on the impact of the COVID-19 pandemic on cervical cancer screening and management",
+    "rel_date": "2022-09-25",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.23.22279458",
+    "rel_abs": "BackgroundThe COVID-19 pandemic has caused disruptions to cancer care by delaying diagnoses and treatment, presenting challenges and uncertainties for both patients and physicians. We conducted a nationwide online survey to investigate the effects of the pandemic and capture modifications, prompted by pandemic-related control measures, on cervical cancer screening-related activities from mid-March to mid-August 2020, across Canada.\n\nMethodsThe survey consisted of 61 questions related to the continuum of care in cervical cancer screening and treatment: appointment scheduling, tests, colposcopy, follow-up, treatment of pre-cancerous lesions/cancer, and telemedicine. We piloted the survey with 21 Canadian experts in cervical cancer prevention and care. We partnered with the Society of Canadian Colposcopists, Society of Gynecologic Oncology of Canada, Canadian Association of Pathologists, and Society of Obstetricians and Gynecologists of Canada, which distributed the survey to their members via email. We reached out to family physicians and nurse practitioners via MDBriefCase. The survey was also posted on McGill Channels (Department of Family Medicine News and Events) and social media platforms. The data were analyzed descriptively.\n\nResultsUnique responses were collected from 510 participants (16 November 2020 - 28 February 2021), representing 418 fully- and 92 partially-completed surveys. Responses were from Ontario (41.0%), British Columbia (21.0%), and Alberta (12.8%), and mostly comprised family physicians/general practitioners (43.7%), and gynecologist/obstetrician professionals (21.6%). Cancelled screening appointments were mainly reported by family physicians/general practitioners (28.3%), followed by gynecologist/obstetrician professionals (19.8%), and primarily occurred in private clinics (30.5%). Decreases in the number of screening Pap tests and colposcopy procedures were consistently observed across Canadian provinces. About 90% reported that their practice/institution adopted telemedicine to communicate with patients.\n\nConclusionsThe area most severely impacted by the pandemic was appointment scheduling, with an important level of cancellations reported. Survey results may inform resumptions of various fronts in cervical cancer screening and management.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Mariam El-Zein",
+        "author_inst": "Division of Cancer Epidemiology, McGill University, Montreal, Quebec, Canada"
+      },
+      {
+        "author_name": "Rami Ali",
+        "author_inst": "Division of Cancer Epidemiology, McGill University, Montreal, Quebec, Canada"
+      },
+      {
+        "author_name": "Eliya Farah",
+        "author_inst": "Division of Cancer Epidemiology, McGill University, Montreal, Quebec, Canada"
+      },
+      {
+        "author_name": "Sarah Botting-Provost",
+        "author_inst": "Division of Cancer Epidemiology, McGill University, Montreal, Quebec, Canada"
+      },
+      {
+        "author_name": "Eduardo L. Franco",
+        "author_inst": "Division of Cancer Epidemiology, McGill University, Montreal, Quebec, Canada"
+      },
+      {
+        "author_name": "- Survey Study Group",
+        "author_inst": ""
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "oncology"
+  },
   {
     "rel_doi": "10.1101/2022.09.24.22280269",
     "rel_title": "Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria.",
@@ -194933,37 +193643,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.09.20.22276701",
-    "rel_title": "Dose of approved COVID-19 vaccines is based on weak evidence: a review of early-phase, dose-finding trials",
-    "rel_date": "2022-09-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.20.22276701",
-    "rel_abs": "Although over 12 billion COVID-19 vaccine doses have been administered globally, the important issue of whether the optimal doses are being used has been relatively neglected. To address this question, we reviewed the reports of early-phase dose-finding trials of the nine COVID-19 vaccines approved by World Health Organization (and one additional vaccine which showed partial clinical efficacy), extracting information on study design and findings on reactogenicity and early humoral immune response. The number of different doses evaluated per vaccine varied widely (range 1-7), as did the number of subjects studied per dose (range 15-190). As expected, the frequency and severity of adverse reactions generally increased at higher doses, although most were clinically tolerable. Higher doses also tended to elicit better immune responses, but differences between the maximum dose and the second-highest dose evaluated were small, typically less than 1.6-fold for both binding antibody concentration and neutralising antibody titre. All of the trials had at least one important design limitation: few doses evaluated, large gaps between adjacent doses, or an inadequate sample size. In general, it is therefore uncertain whether the single dose taken into clinical efficacy trials, and subsequently authorised by regulatory agencies, was optimal. In particular, the recommended doses for some vaccines appear to be unnecessarily high. Although reduced dosing for booster injections is an active area of research, the priming dose is equally deserving of study. We conclude by suggesting some ways in which the design of future trials of candidate COVID-19 vaccines could be improved.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "David Dunn",
-        "author_inst": "UCL"
-      },
-      {
-        "author_name": "Richard Gilson",
-        "author_inst": "UCL"
-      },
-      {
-        "author_name": "Sheena McCormack",
-        "author_inst": "UCL"
-      },
-      {
-        "author_name": "Laura McCoy",
-        "author_inst": "UCL"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.09.21.508922",
     "rel_title": "Evolution of antibody immunity following Omicron BA.1 breakthrough infection",
@@ -195378,6 +194057,49 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2022.09.22.508999",
+    "rel_title": "Triple COVID-19 vaccination induces humoral and cellular immunity to SARS-CoV-2 with cross-recognition of the Omicron variant and IgA secretion",
+    "rel_date": "2022-09-22",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.22.508999",
+    "rel_abs": "COVID-19 vaccination is the leading strategy to prevent severe courses after SARS-CoV-2 infection. In our study, we analyzed humoral and cellular immune responses in detail to three consecutive homologous or heterologous COVID-19 vaccinations. All individuals (n=20) responded to vaccination with increasing S1- /RBD-/S2-specific IgG levels, whereas specific plasma IgA displayed individual variability. The third dose increased antibody inhibitory capacity (AIC) against immune-escape variants Beta and Omicron independently from age. The mRNA-primed vaccination induced IgG and IgA immunity more efficiently, whereas vector-primed individuals displayed higher levels of memory T and B cells. Vaccinees showed a SARS-CoV-2-specific T cell responses, which were further improved and specified after Omicron breakthrough infections in parallel to appearance of new variant-specific antibodies. In conclusion, the third vaccination was essential to increase IgG levels, mandatory to boost AIC against immune-escape variants and induced SARS-CoV-2-specific T cells. Breakthrough infection with Omicron generates additional spike specificities covering all known variants.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Louisa Ruhl",
+        "author_inst": "Hannover Medical School"
+      },
+      {
+        "author_name": "Jenny F Kuehne",
+        "author_inst": "Hannover Medical School"
+      },
+      {
+        "author_name": "Kerstin Beushausen",
+        "author_inst": "Hannover Medical School"
+      },
+      {
+        "author_name": "Jana Keil",
+        "author_inst": "Hannover Medical School"
+      },
+      {
+        "author_name": "Stella Christoph",
+        "author_inst": "Hannover Medical School"
+      },
+      {
+        "author_name": "Jasper Sauer",
+        "author_inst": "Hannover Medical School"
+      },
+      {
+        "author_name": "Christine S Falk",
+        "author_inst": "Hannover Medical School"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2022.09.20.22279832",
     "rel_title": "Simplified Within Host and Dose-response Models of SARS-CoV-2",
@@ -196927,33 +195649,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2022.09.18.508442",
-    "rel_title": "HCR Lateral Flow Assays for Amplified Instrument-Free At-Home SARS-CoV-2 Testing",
-    "rel_date": "2022-09-19",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.18.508442",
-    "rel_abs": "The lateral flow assay format enables rapid, instrument-free, at-home testing for SARS-CoV-2. Due to the absence of signal amplification, this simplicity comes at a cost in sensitivity. Here, we enhance sensitivity by developing an amplified lateral flow assay that incorporates isothermal, enzyme-free signal amplification based on the mechanism of hybridization chain reaction (HCR). The simplicity of the user experience is maintained using a disposable 3-channel lateral flow device to automatically deliver reagents to the test region in three successive stages without user interaction. To perform a test, the user loads the sample, closes the device, and reads the result by eye after 60 minutes. Detecting gamma-irradiated SARS-CoV-2 virions in a mixture of saliva and extraction buffer, the current amplified HCR lateral flow assay achieves a limit of detection of 200 copies/L using available antibodies to target the SARS-CoV-2 nucleocapsid protein. By comparison, five commercial unamplified lateral flow assays that use proprietary antibodies exhibit limits of detection of 500 copies/L, 1000 copies/L, 2000 copies/L, 2000 copies/L, and 20,000 copies/L. By swapping out antibody probes to target different pathogens, amplified HCR lateral flow assays offer a platform for simple, rapid, and sensitive at-home testing for infectious disease. As an alternative to viral protein detection, we further introduce an HCR lateral flow assay for viral RNA detection.\n\nHCR lateral flow assayO_LIAmplified\nC_LIO_LIInstrument-free\nC_LIO_LIAt-home\nC_LIO_LI60 min\nC_LIO_LINaked eye\nC_LIO_LISARS-CoV-2\nC_LIO_LI200 copies/L\nC_LI\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=166 SRC=\"FIGDIR/small/508442v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (23K):\norg.highwire.dtl.DTLVardef@a04874org.highwire.dtl.DTLVardef@f4ba0borg.highwire.dtl.DTLVardef@e2445corg.highwire.dtl.DTLVardef@f63411_HPS_FORMAT_FIGEXP  M_FIG C_FIG",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Samuel J. Schulte",
-        "author_inst": "California Institute of Technology"
-      },
-      {
-        "author_name": "Jining Huang",
-        "author_inst": "California Institute of Technology"
-      },
-      {
-        "author_name": "Niles A. Pierce",
-        "author_inst": "California Institute of Technology"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "bioengineering"
-  },
   {
     "rel_doi": "10.1101/2022.09.18.22279896",
     "rel_title": "Application of the SEIR Model to a Logistic Formula and the Basic Reproduction Number of COVID-19 in Japan",
@@ -197352,6 +196047,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.09.19.22280079",
+    "rel_title": "The impact of prior COVID-19 on vaccine response and the resultant hybrid immunity are age-dependent",
+    "rel_date": "2022-09-19",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.19.22280079",
+    "rel_abs": "BackgroundMore people with a history of prior infection are receiving SARS-CoV-2 vaccines. Understanding the magnitude of protectivity granted by  hybrid immunity, the combined response of infection- and vaccine-induced immunity, may impact vaccination strategies.\n\nMethodsA total of 36 synchronously infected ( prior infection) and, 33 SARS-CoV-2 naive ( naive) individuals participated. Participants provided sera six months after completing a round of BNT162b2 vaccination, to be processed for anti-spike antibody measurements and neutralization assays. The relationships between antibody titer, groups and age were explored.\n\nResultsAnti-spike antibody titers at 6 months post-vaccination were significantly higher, reaching 13- to 17-fold, in the  prior infection group. Linear regression models showed that the enhancement in antibody titer attributable to positive infection history increased from 8.9- to 9.4- fold at age 30 to 19- to 32-fold at age 60. Sera from the  prior infection group showed higher neutralizing capacity against all six analyzed strains, including the Omicron variant.\n\nConclusionsPrior COVID-19 led to establishing enhanced humoral immunity at 6 months after vaccination. Antibody fold-difference attributed to positive COVID-19 history increased with age, possibly because older individuals are prone to symptomatic infection accompanied by potentiated immune responses. Durable protection of hybrid immunity deserves reflection in vaccination campaigns.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Sachie Nakagama",
+        "author_inst": "Osaka Metropolitan University"
+      },
+      {
+        "author_name": "Yu Nakagama",
+        "author_inst": "Osaka Metropolitan University"
+      },
+      {
+        "author_name": "Yuko Komase",
+        "author_inst": "St.Mariannna University, Yokohama Seibu Hospital"
+      },
+      {
+        "author_name": "Masaharu Kudo",
+        "author_inst": "Osaka Metropolitan University"
+      },
+      {
+        "author_name": "Takumi Imai",
+        "author_inst": "Osaka Metropolitan University"
+      },
+      {
+        "author_name": "Yuko Nitahara",
+        "author_inst": "Osaka Metropolitan University"
+      },
+      {
+        "author_name": "Natsuko Kaku",
+        "author_inst": "Osaka Metropolitan University"
+      },
+      {
+        "author_name": "Evariste Tshibangu-Kabamba",
+        "author_inst": "Osaka Metropolitan University"
+      },
+      {
+        "author_name": "Yasutoshi Kido",
+        "author_inst": "Osaka Metropolitan University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.09.13.22279673",
     "rel_title": "Social Media Data for Omicron Detection from Unscripted Voice Samples",
@@ -198821,65 +197567,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2022.09.16.508299",
-    "rel_title": "Omicron sublineage BA.2.75.2 exhibits extensive escape from neutralising antibodies",
-    "rel_date": "2022-09-16",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.16.508299",
-    "rel_abs": "Several sublineages of omicron have emerged with additional mutations that may afford further antibody evasion. Here, we characterise the sensitivity of emerging omicron sublineages BA.2.75.2, BA.4.6, and BA.2.10.4 to antibody-mediated neutralisation, and identify extensive escape by BA.2.75.2. BA.2.75.2 was resistant to neutralisation by Evusheld (tixagevimab + cilgavimab), but remained sensitive to bebtelovimab. In recent serum samples from blood donors in Stockholm, Sweden, BA.2.75.2 was neutralised, on average, at titers approximately 6.5-times lower than BA.5, making BA.2.75.2 the most neutralisation resistant variant evaluated to date. These data raise concerns that BA.2.75.2 may effectively evade humoral immunity in the population.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Daniel J Sheward",
-        "author_inst": "Karolinska Institutet"
-      },
-      {
-        "author_name": "Changil Kim",
-        "author_inst": "Karolinska Institutet"
-      },
-      {
-        "author_name": "Julian Fischbach",
-        "author_inst": "Karolinska Institutet"
-      },
-      {
-        "author_name": "Sandra Muschiol",
-        "author_inst": "Karolinska Institutet"
-      },
-      {
-        "author_name": "Roy A Ehling",
-        "author_inst": "ETH Zurich"
-      },
-      {
-        "author_name": "Niklas K Bj\u00f6rkstr\u00f6m",
-        "author_inst": "Karolinska Institutet"
-      },
-      {
-        "author_name": "Gunilla B Karlsson Hedestam",
-        "author_inst": "Karolinska Institutet"
-      },
-      {
-        "author_name": "Sai T Reddy",
-        "author_inst": "ETH Zurich"
-      },
-      {
-        "author_name": "Jan Albert",
-        "author_inst": "Karolinska Institutet"
-      },
-      {
-        "author_name": "Thomas P Peacock",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Ben Murrell",
-        "author_inst": "Karolinska Institutet"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2022.09.16.508278",
     "rel_title": "Semantic and population analysis of the genetic targets related to COVID-19 and its association with genes and diseases",
@@ -199270,6 +197957,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "neurology"
   },
+  {
+    "rel_doi": "10.1101/2022.09.09.22279763",
+    "rel_title": "COVID-19 induced birth sex ratio changes in England and Wales",
+    "rel_date": "2022-09-15",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.09.22279763",
+    "rel_abs": "BackgroundThe sex ratio at birth (male live births divided by total live births) may be a sentinel health indicator. Stressful events reduce this ratio 3-5 months later by increasing male fetal loss. This ratio can also change 9 months after major population events that are linked to an increase or decrease in the frequency of sexual intercourse at the population level, with the ratio either rising or falling respectively after the event. We postulated that stress caused by the COVID-19 pandemic may have affected the ratio in England and Wales.\n\nMethodsPublicly available, monthly live birth data for England and Wales was obtained from the Office for National Statistics up to December 2020. The sex ratio at birth for 2020 (global COVID-19 onset) was predicted using data from 2012-2019. Observed and predicted values were compared.\n\nResultsThree months after COVID-19 was declared pandemic (March 2020), there was a significant fall in the sex ratio at birth to 0.5100 in June 2020 which was below the 95% prediction interval of 0.5102-0.5179. Nine months after the pandemic declaration, (December 2020), there was a significant rise to 0.5171 (95% prediction interval 0.5085-0.5162). However, December 2020 had the lowest number of live births of any month from 2012 to 2020.\n\nConclusionsGiven that June 2020 falls within the crucial window when population stressors are known to affect the sex ratio at birth, these findings imply that the start of the COVID-19 pandemic caused population stress with notable effects on those who were already pregnant by causing a disproportionate loss of male fetuses. The finding of a higher sex ratio at birth in December 2020, i.e., 9 months after COVID-19 was declared a pandemic, suggests that lockdown restrictions initially spurred more sexual activity in a subset of the population in March 2020.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Gwinyai Masukume",
+        "author_inst": "Independent Researcher, Munster, Ireland"
+      },
+      {
+        "author_name": "Margaret Ryan",
+        "author_inst": "Trinity College Dublin, Dublin, Ireland"
+      },
+      {
+        "author_name": "Rumbidzai Masukume",
+        "author_inst": "Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa"
+      },
+      {
+        "author_name": "Dorota Zammit",
+        "author_inst": "National Statistics Office, Valletta, Malta"
+      },
+      {
+        "author_name": "Victor Grech",
+        "author_inst": "Academic Department of Paediatrics, Medical School, Mater Dei Hospital, Msida, Malta"
+      },
+      {
+        "author_name": "Witness Mapanga",
+        "author_inst": "Division of Medical Oncology, Department of Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, So"
+      },
+      {
+        "author_name": "Yosuke Inoue",
+        "author_inst": "Department of Epidemiology and Prevention, Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "obstetrics and gynecology"
+  },
   {
     "rel_doi": "10.1101/2022.09.09.22279765",
     "rel_title": "SDG5 Gender Equality and the COVID-19 pandemic: a rapid assessment of health system responses in selected upper-middle and high-income countries",
@@ -200767,53 +199497,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2022.09.12.22279862",
-    "rel_title": "The epidemiology of long COVID in US adults two years after the start of the US SARS-CoV-2 pandemic",
-    "rel_date": "2022-09-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.12.22279862",
-    "rel_abs": "ObjectivesTo characterize prevalence and impact of long COVID.\n\nMethodsWe conducted a population-representative survey, June 30-July 2, 2022, of a random sample of 3,042 United States adults. Using questions developed by the United Kingdoms Office of National Statistics, we estimated the prevalence by sociodemographics, adjusting for gender and age.\n\nResultsAn estimated 7.3% (95% CI: 6.1-8.5%) of all respondents reported long COVID, approximately 18,533,864 adults. One-quarter (25.3% [18.2-32.4%]) of respondents with long COVID reported their day-to-day activities were impacted  a lot and 28.9% had SARS-CoV-2 infection >12 months ago. The prevalence of long COVID was higher among respondents who were female (aPR: 1.84 [1.40-2.42]), had comorbidities (aPR: 1.55 [1.19-2.00]) or were not (versus were) boosted (aPR: 1.67 [1.19-2.34]) or not vaccinated (versus boosted) (aPR: 1.41 (1.05-1.91)).\n\nConclusionsWe observed a high burden of long COVID and substantial variability in prevalence of SARS-CoV-2. Population-based surveys are an important surveillance tool and supplement to ongoing efforts to monitor long COVID.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "McKaylee Robertson",
-        "author_inst": "CUNY ISPH"
-      },
-      {
-        "author_name": "Saba Qasmieh",
-        "author_inst": "City University of New York School of Public Health and Health Policy"
-      },
-      {
-        "author_name": "Sarah Kulkarni",
-        "author_inst": "CUNY ISPH"
-      },
-      {
-        "author_name": "Chloe A Teasdale",
-        "author_inst": "CUNY Graduate School of Public Health and Health Policy"
-      },
-      {
-        "author_name": "Heidi E Jones",
-        "author_inst": "CUNY School of Public Health"
-      },
-      {
-        "author_name": "Margaret McNairy",
-        "author_inst": "Center for Global Health and Division of General Internal Medicine, Weill Cornell Medicine, New York, NY, USA"
-      },
-      {
-        "author_name": "Luisa N Borrell",
-        "author_inst": "CUNY Graduate School of Public Health"
-      },
-      {
-        "author_name": "Denis Nash",
-        "author_inst": "CUNY Graduate School of Public Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.09.12.22279850",
     "rel_title": "SARS-CoV-2 containment was achievable during the early stage of the pandemic: a retrospective modelling study of the Xinfadi outbreak in Beijing",
@@ -201172,6 +199855,41 @@
     "type": "new results",
     "category": "bioengineering"
   },
+  {
+    "rel_doi": "10.1101/2022.09.14.507985",
+    "rel_title": "Analysis and comprehensive lineage identification for SARS-CoV-2 genomes through scalable learning methods",
+    "rel_date": "2022-09-14",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.14.507985",
+    "rel_abs": "Since its emergence in late 2019, SARS-CoV-2 has diversified into a large number of lineages and globally caused multiple waves of infection. Novel lineages have the potential to spread rapidly and internationally if they have higher intrinsic transmissibility and/or can evade host immune responses, as has been seen with the Alpha, Delta, and Omicron variants of concern (VoC). They can also cause increased mortality and morbidity if they have increased virulence, as was seen for Alpha and Delta, but not Omicron. Phylogenetic methods provide the gold standard for representing the global diversity of SARS-CoV-2 and to identify newly emerging lineages. However, these methods are computationally expensive, struggle when datasets get too large, and require manual curation to designate new lineages. These challenges together with the increasing volumes of genomic data available provide a motivation to develop complementary methods that can incorporate all of the genetic data available, without down-sampling, to extract meaningful information rapidly and with minimal curation. Here, we demonstrate the utility of using algorithmic approaches based on word-statistics to represent whole sequences, bringing speed, scalability, and interpretability to the construction of genetic topologies, and while not serving as a substitute for current phylogenetic analyses the proposed methods can be used as a complementary approach to identify and confirm new emerging variants.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Roberto Cahuantzi",
+        "author_inst": "Univeristy of Manchester"
+      },
+      {
+        "author_name": "Katrina Lythgoe",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Ian Hall",
+        "author_inst": "University of Manchester"
+      },
+      {
+        "author_name": "Lorenzo Pellis",
+        "author_inst": "University of Manchester"
+      },
+      {
+        "author_name": "Thomas A House",
+        "author_inst": "University of Manchester"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "new results",
+    "category": "bioinformatics"
+  },
   {
     "rel_doi": "10.1101/2022.09.13.22279868",
     "rel_title": "Excess mortality in the general population versus Veterans Healthcare System during the first year of the COVID-19 pandemic in the United States",
@@ -202565,81 +201283,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.09.09.22279771",
-    "rel_title": "THE EFFECT OF THE MEASLES, MUMPS AND RUBELLA VACCINE ON INNATE AND ADAPTIVE IMMUNE RESPONSES IN PERSONS RECEIVING A SARS-COV-2 mRNA VACCINE.A SUB-STUDY OF THE CROWN CORONATION TRIAL",
-    "rel_date": "2022-09-10",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.09.22279771",
-    "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWVaccination elicits a complex combination of immune responses. Immune memory formation is observed not only in the antibody responses of B-cells, but also in the T-cell response. Moreover, some live attenuated vaccines such as measles-containing vaccines can induces heterologous protection, likely through induction of memory characteristics in the innate immune response. Little is known about the immunological interaction that may occur when different vaccines are administered soon after one another, especially in relation to the novel COVID-19 vaccines.\n\nThe aim of this study was to compare the innate and adaptive immune responses between persons randomized to receive either a MMR or a placebo (0.9% NaCl) injection prior to their SARS-CoV-2 mRNA vaccination. We compared: i) the cytokine and chemokine production (tumor necrosis factor [TNF]-, interleukin [IL]-1{beta}, IL-6, IL-10, IL-17, IL-22, interferon [IFN]- and IFN-{gamma}) after in-vitro stimulation of peripheral blood mononuclear cells (PBMCs) with heterologous stimuli (severe acute respiratory syndrome coronavirus [SARS-CoV]-2, measles mumps and rubella [MMR] vaccine, Toll-like receptor [TLR]-3 ligand, TLR-7/8 ligand, or TLR-4 ligand), and ii) the SARS-CoV-2 neutralizing antibody responses.\n\nNinety-five participants in the CROWN CORONATION trial (NCT04333732; a randomized control trial comparing MMR to placebo for prevention of COVID-19) agreed to an additional single blood sample collection for this immunological study. Samples were collected around 196 (SD 22) days after administration of MMR or placebo, and around 105 (SD 27) days after their second SARS-CoV-2 mRNA vaccine injection.\n\nTwenty-four percent of participants were older than fifty and sixty-seven percent were female. The median TNF- response to stimulation with MMR was 8315.3 pg/mL in the MMR group and 4340.5 pg/mL in the placebo group; adjusted median difference (95% CI) 3012.5 (-4734.1; -323.5); p=0.017. No other significant differences were noted in the cytokine and chemokine responses between treatment groups. The SARS-CoV-2 neutralization assay geometric mean (SD) IC50 in the MMR group was 507.6 (2.6) and in the placebo group was 515.7 (2.2); ratio of geometric means (95% CI) 1.0 (0.7; 1.5).\n\nPre-exposure to MMR vaccine was generally not associated with changes in cytokine and chemokine responses of stimulated PBMCs at 105 (27) days after SARS-CoV-2 mRNA vaccination. MMR vaccination led only to an increase of TNF- production in response to an additional ex-vivo stimulation with the MMR vaccine. The SARS-CoV-2 neutralization IC50 values did not differ between MMR and placebo groups. Further studies using a repeated measures design would be better suited to explore or rule-out any short-lived vaccine response and vaccine-vaccine immunological interaction.",
-    "rel_num_authors": 15,
-    "rel_authors": [
-      {
-        "author_name": "Leon du Toit",
-        "author_inst": "Department of Anesthesia, Washington University School of Medicine, Saint Louis, MO, USA and Department of Anaesthesia and Perioperative Medicine, University of"
-      },
-      {
-        "author_name": "Ananya Gupta",
-        "author_inst": "Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO, USA"
-      },
-      {
-        "author_name": "Hakim-Moulay Dehbi",
-        "author_inst": "Comprehensive Clinical Trials Unit, Institute of Clinical Trials and Methodology, UCL, London, UK"
-      },
-      {
-        "author_name": "Tamarand L Darling",
-        "author_inst": "Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA"
-      },
-      {
-        "author_name": "Darya V Urusova",
-        "author_inst": "Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO, USA"
-      },
-      {
-        "author_name": "Shyamala Thirunavukkarasu",
-        "author_inst": "Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO, USA"
-      },
-      {
-        "author_name": "Adrianus CM Boon",
-        "author_inst": "Department of Molecular Microbiology,  Department of Medicine, and Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis"
-      },
-      {
-        "author_name": "Erik R Dubberke",
-        "author_inst": "Division of Infectious Diseases, Washington University School of Medicine, Saint Louis, MO, USA"
-      },
-      {
-        "author_name": "Linda Yun",
-        "author_inst": "Department of Anesthesia, Washington University School of Medicine, Saint Louis, MO, USA"
-      },
-      {
-        "author_name": "Sherry McKinnon",
-        "author_inst": "Department of Anesthesia, Washington University School of Medicine, Saint Louis, MO, USA"
-      },
-      {
-        "author_name": "Anne K DeSchryver",
-        "author_inst": "Department of Anesthesia, Washington University School of Medicine, Saint Louis, MO, USA"
-      },
-      {
-        "author_name": "Ben Swan",
-        "author_inst": "Department of Anesthesia, Washington University School of Medicine, Saint Louis, MO, USA"
-      },
-      {
-        "author_name": "Mihai G Netea",
-        "author_inst": "Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands and Department of Immun"
-      },
-      {
-        "author_name": "Shabaana Khader",
-        "author_inst": "Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO, USA"
-      },
-      {
-        "author_name": "Michael S Avidan",
-        "author_inst": "Department of Anesthesia, Washington University School of Medicine, Saint Louis, MO, USA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "allergy and immunology"
-  },
   {
     "rel_doi": "10.1101/2022.09.08.22279459",
     "rel_title": "Population Normalization in SARS-CoV-2 Wastewater-Based Epidemiology: Implications from Statewide Wastewater Monitoring in Missouri",
@@ -203214,6 +201857,149 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "genetic and genomic medicine"
   },
+  {
+    "rel_doi": "10.1101/2022.09.08.22279729",
+    "rel_title": "Image-based and machine learning-guided multiplexed serology test for SARS-CoV-2",
+    "rel_date": "2022-09-09",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.08.22279729",
+    "rel_abs": "Here, we describe a scalable and automated, high-content microscopy -based mini-immunofluorescence assay (mini-IFA) for serological testing i.e., detection of antibodies. Unlike conventional IFA, which often relies on the use of cells infected with the target pathogen, our assay employs transfected cells expressing individual viral antigens. The assay builds on a custom neural network-based image analysis pipeline for the automated and multiplexed detection of immunoglobulins (IgG, IgA, and IgM) in patient samples. As a proof-of-concept, we employed high-throughput equipment to set up the assay for measuring antibody response against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection with spike (S), membrane (M), and nucleo (N) proteins, and the receptor-binding domain (R) as the antigens. We compared the automated mini-IFA results from hundreds of patient samples to the visual observations of human experts and to the results obtained with conventional ELISA. The comparisons demonstrated a high correlation to both, suggesting high sensitivity and specificity of the mini-IFA. By testing pre-pandemic samples and those collected from patients with RT-PCR confirmed SARS-CoV-2 infection, we found mini-IFA to be most suitable for IgG and IgA detection. The results demonstrated N and S proteins as the ideal antigens, and the use of these antigens can serve to distinguish between vaccinated and infected individuals. The assay principle described enables detection of antibodies against practically any pathogen, and none of the assay steps require high biosafety level environment. The simultaneous detection of multiple Ig classes allows for distinguishing between recent and past infection.\n\nPublic abstractThe manuscript describes a miniaturized immunofluorescence assay (mini-IFA) for measuring antibody response in patient blood samples. The automated method builds on machine-learning -guided image analysis with SARS-CoV-2 as the model pathogen. The method enables simultaneous measurement of IgM, IgA, and IgG responses against different virus antigens in a high throughput manner. The assay relies on antigens expressed through transfection and allows for differentiation between vaccine-induced and infection-induced antibody responses. The transfection-based antigen expression enables performing the assay at a low biosafety level laboratory and allows fast adaptation of the assay to emerging pathogens. Our results provide proof-of-concept for the approach, demonstrating fast and accurate measurement of antibody responses in a clinical and research set-up.",
+    "rel_num_authors": 32,
+    "rel_authors": [
+      {
+        "author_name": "Vilja Pietiainen",
+        "author_inst": "Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland"
+      },
+      {
+        "author_name": "Minttu Polso",
+        "author_inst": "Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland"
+      },
+      {
+        "author_name": "Ede Migh",
+        "author_inst": "Laboratory of Microscopic Image Analysis and Machine Learning, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary"
+      },
+      {
+        "author_name": "Christian Guckelsberger",
+        "author_inst": "Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland; Department of Computer"
+      },
+      {
+        "author_name": "Maria Harmati",
+        "author_inst": "Laboratory of Microscopic Image Analysis and Machine Learning, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary"
+      },
+      {
+        "author_name": "Akos Diosdi",
+        "author_inst": "Laboratory of Microscopic Image Analysis and Machine Learning, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary"
+      },
+      {
+        "author_name": "Laura Turunen",
+        "author_inst": "Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland"
+      },
+      {
+        "author_name": "Antti Hassinen",
+        "author_inst": "Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland"
+      },
+      {
+        "author_name": "Swapnil Potdar",
+        "author_inst": "Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland"
+      },
+      {
+        "author_name": "Annika Koponen",
+        "author_inst": "Minerva Foundation Institute for Medical Research, Helsinki, Finland; Department of Anatomy, Faculty of Medicine, University of Helsinki, Helsinki, Finland"
+      },
+      {
+        "author_name": "Edina Gyukity-Sebestyen",
+        "author_inst": "Laboratory of Microscopic Image Analysis and Machine Learning, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary"
+      },
+      {
+        "author_name": "Ferenc Kovacs",
+        "author_inst": "Laboratory of Microscopic Image Analysis and Machine Learning, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary; Single-Cell Technologies "
+      },
+      {
+        "author_name": "Andras Kriston",
+        "author_inst": "Laboratory of Microscopic Image Analysis and Machine Learning, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary; Single-Cell Technologies "
+      },
+      {
+        "author_name": "Reka Hollandi",
+        "author_inst": "Laboratory of Microscopic Image Analysis and Machine Learning, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary"
+      },
+      {
+        "author_name": "Katalin Burian",
+        "author_inst": "Department of Medical Microbiology, Faculty of Medicine, University of Szeged, Szeged, Hungary"
+      },
+      {
+        "author_name": "Gabriella Terhes",
+        "author_inst": "Department of Medical Microbiology, Faculty of Medicine, University of Szeged, Szeged, Hungary"
+      },
+      {
+        "author_name": "Adam Visnyovszki",
+        "author_inst": "1st Department of Internal Medicine, Faculty of Medicine, University of Szeged, Szeged, Hungary"
+      },
+      {
+        "author_name": "Eszter Fodor",
+        "author_inst": "Department of Sports Physiology, Inst. Sports and Health Sciences, University of Physical Education, Budapest, Hungary"
+      },
+      {
+        "author_name": "Zsombor Lacza",
+        "author_inst": "Department of Sports Physiology, Inst. Sports and Health Sciences, University of Physical Education, Budapest, Hungary"
+      },
+      {
+        "author_name": "Anu Kantele",
+        "author_inst": "Meilahti Infectious Diseases and Vaccine Research Center, MeiVac, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Human Microbiome R"
+      },
+      {
+        "author_name": "Pekka Kolehmainen",
+        "author_inst": "Institute of Biomedicine, University of Turku, Turku, Finland"
+      },
+      {
+        "author_name": "Laura Kakkola",
+        "author_inst": "Institute of Biomedicine, University of Turku, Turku, Finland"
+      },
+      {
+        "author_name": "Tomas Strandin",
+        "author_inst": "Department of Virology, Medicum, University of Helsinki, Helsinki, Finland"
+      },
+      {
+        "author_name": "Lev Levanov",
+        "author_inst": "Department of Virology, Medicum, University of Helsinki, Helsinki, Finland"
+      },
+      {
+        "author_name": "Olli Kallioniemi",
+        "author_inst": "Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland;Department of Oncology-"
+      },
+      {
+        "author_name": "Lajos Kemeny",
+        "author_inst": "HCEMM-USZ Skin Research Group, Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary"
+      },
+      {
+        "author_name": "Ilkka Julkunen",
+        "author_inst": "Institute of Biomedicine, University of Turku, Turku, Finland; Turku University Hospital, Turku, Finland"
+      },
+      {
+        "author_name": "Olli Vapalahti",
+        "author_inst": "Department of Virology, Medicum, University of Helsinki, Helsinki, Finland; Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland; HUS"
+      },
+      {
+        "author_name": "Krisztina Buzas",
+        "author_inst": "Laboratory of Microscopic Image Analysis and Machine Learning, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary; Department of Immunology,"
+      },
+      {
+        "author_name": "Lassi Paavolainen",
+        "author_inst": "Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland"
+      },
+      {
+        "author_name": "Peter Horvath",
+        "author_inst": "Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland; Laboratory of Microsco"
+      },
+      {
+        "author_name": "Jussi Hepojoki",
+        "author_inst": "Department of Virology, Medicum, University of Helsinki, Helsinki, Finland; University of Zurich, Vetsuisse Faculty, Institute of Veterinary Pathology, Zurich, "
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.09.07.22279662",
     "rel_title": "The aerobiology of SARS-CoV-2 in UK hospitals and the impact of aerosol generating procedures",
@@ -204687,53 +203473,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2022.09.09.22279754",
-    "rel_title": "Contact patterns of UK home delivery drivers and their use of protective measures during the COVID-19 pandemic: a cross-sectional study",
-    "rel_date": "2022-09-09",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.09.22279754",
-    "rel_abs": "ObjectivesTo quantify contact patterns of UK home delivery drivers and identify protective measures adopted during the pandemic.\n\nMethodsWe conducted a cross-sectional online survey to measure the interactions of 170 UK delivery drivers during a working shift between 7 December 2020 and 31 March 2021.\n\nResultsDelivery drivers had a mean number of 71.6 (95% Confidence Interval (CI) 61.0 to 84.1) customer contacts per shift and 15.0 (95%CI 11.19 to 19.20) depot contacts per shift. Maintaining physical distancing with customers was more common than at delivery depots. Prolonged contact (more than 5 minutes) with customers was reported by 5.4% of drivers on their last shift. We found 3.0% of drivers had tested positive for SARS-CoV-2 since the start of the pandemic and 16.8% of drivers had self-isolated due to a suspected or confirmed case of COVID-19. Additionally, 5.3% (95%CI 2.3% to 10.2%) of participants reported having worked whilst ill with COVID-19 symptoms, or with a member of their household having a suspected or confirmed case of COVID-19.\n\nConclusionDelivery drivers had a large number of face-to-face customer and depot contacts per shift compared to other working adults during this time. However, transmission risk may be curtailed as contact with customers was of short duration. Most drivers were unable to maintain physical distance with customers and at depots at all times. Usage of protective items such as face masks and hand sanitizer was widespread.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Jessica R E Bridgen",
-        "author_inst": "Lancaster University"
-      },
-      {
-        "author_name": "Hua Wei",
-        "author_inst": "The University of Manchester"
-      },
-      {
-        "author_name": "Carl A Whitfield",
-        "author_inst": "University of Manchester"
-      },
-      {
-        "author_name": "Yang Han",
-        "author_inst": "University of Manchester"
-      },
-      {
-        "author_name": "Ian Hall",
-        "author_inst": "University of Manchester"
-      },
-      {
-        "author_name": "Chris Jewell",
-        "author_inst": "Lancaster University"
-      },
-      {
-        "author_name": "Martie JA van Tongeren",
-        "author_inst": "University of Manchester"
-      },
-      {
-        "author_name": "Jonathan M Read",
-        "author_inst": "Lancaster University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "occupational and environmental health"
-  },
   {
     "rel_doi": "10.1101/2022.09.04.22279016",
     "rel_title": "The Most Cost-Efficient And Effective Set Of COVID-19 Policies To Reduce Monthly COVID-19 Case Increase Rates",
@@ -205132,6 +203871,69 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2022.09.09.507257",
+    "rel_title": "Cellular stress modulates severity of the acute respiratory distress syndrome in COVID-19",
+    "rel_date": "2022-09-09",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.09.507257",
+    "rel_abs": "Inflammation is a central pathogenic feature of the acute respiratory distress syndrome (ARDS) in COVID-19. Previous pathologies such as diabetes, autoimmune or cardiovascular diseases become risk factors for the severe hyperinflammatory syndrome. A common feature among these risk factors is the subclinical presence of cellular stress, a finding that has gained attention after the discovery that BiP (GRP78), a master regulator of stress, participates in the SARS-CoV-2 recognition. Here, we show that BiP serum levels are higher in COVID-19 patients who present certain risk factors. Moreover, early during the infection, BiP levels predict severe pneumonia, supporting the use of BiP as a prognosis biomarker. Using a mouse model of pulmonary inflammation, we demonstrate that cell surface BiP (cs-BiP) responds by increasing its levels in leukocytes. Neutrophiles show the highest levels of cs-BiP and respond by increasing their population, whereas alveolar macrophages increase their levels of cs-BiP. The modulation of cellular stress with the use of a clinically approved drug, 4-PBA, resulted in the amelioration of the lung hyperinflammatory response, supporting the anti-stress therapy as a valid therapeutic strategy for patients developing ARDS. Finally, we identified stress-modulated proteins that shed light into the mechanism underlying the cellular stress-inflammation network in lungs.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Gustavo Rico-Llanos",
+        "author_inst": "CIBER-BBN"
+      },
+      {
+        "author_name": "Oscar Porras",
+        "author_inst": "IBIMA"
+      },
+      {
+        "author_name": "Sandra Escalante",
+        "author_inst": "University of Malaga"
+      },
+      {
+        "author_name": "Daniel Vazquez",
+        "author_inst": "University of Malaga"
+      },
+      {
+        "author_name": "Lucia Valiente",
+        "author_inst": "IBIMA"
+      },
+      {
+        "author_name": "Maria Castillo",
+        "author_inst": "IBIMA"
+      },
+      {
+        "author_name": "Jose Miguel Perez-Tejeiro",
+        "author_inst": "University of Malaga"
+      },
+      {
+        "author_name": "David Baglietto",
+        "author_inst": "University of Malaga"
+      },
+      {
+        "author_name": "Jose Becerra",
+        "author_inst": "University of Malaga"
+      },
+      {
+        "author_name": "Jose Maria Reguera",
+        "author_inst": "IBIMA"
+      },
+      {
+        "author_name": "Ivan Duran",
+        "author_inst": "University of Malaga"
+      },
+      {
+        "author_name": "Fabiana Csukasi",
+        "author_inst": "University of Malaga"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "cell biology"
+  },
   {
     "rel_doi": "10.1101/2022.09.07.506979",
     "rel_title": "A novel biopolymer for mucosal adjuvant against respiratory pathogens",
@@ -206569,49 +205371,6 @@
     "type": "confirmatory results",
     "category": "systems biology"
   },
-  {
-    "rel_doi": "10.1101/2022.09.06.22279606",
-    "rel_title": "The COVID-19 Pandemic as an Opportunity for Unravelling the Causative Association between Respiratory Viruses and Pneumococcus-Associated Disease in Young Children: A Prospective Cohort Study",
-    "rel_date": "2022-09-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.06.22279606",
-    "rel_abs": "BACKGROUNDIn young children, rates of lower respiratory infections (LRI) and invasive pneumococcal disease (IPD) have been associated with respiratory syncytial virus (RSV), human metapneumovirus (hMPV), influenza (flu), and parainfluenza (PIV) (collectively termed here as pneumonia and pneumococcal disease-associated viruses [PDA-viruses]). However, their contribution to the pathogenesis of these disease endpoints has not yet been elucidated. The COVID-19 pandemic provided a unique opportunity to examine the question.\n\nMETHODSThis prospective study comprised all children <5 years, living in southern Israel, during 2016 through 2021. The data were previously collected in multiple ongoing prospective surveillance programs and include: hospital visits for community-acquired alveolar pneumonia (CAAP), non-CAAP LRI; nasopharyngeal pneumococcal carriage (<3 years of age); respiratory virus activity; and nationwide, all-ages COVID-19 episodes and IPD in children <5 years. A hierarchical statistical model was developed to estimate the proportion of the different clinical endpoints attributable to each virus from monthly time series data, stratified by age and ethnicity. A separate model was fit for each endpoint, with covariates that included a linear time trend, 12-month harmonic variables to capture unexplained seasonal variations, and the proportion of tests positive for each virus in that month.\n\nFINDINGSDuring 2016 through 2021, 3,204, 26,695, 257, and 619 episodes of CAAP, non-CAAP LRI, pneumococcal bacteremic pneumonia and non-pneumonia IPD, respectively, were reported. Compared to 2016-2019, broad declines in the disease endpoints were observed shortly after the pandemic surge, coincident with a complete disappearance of all PDA-viruses and continued circulation of rhinovirus (RhV) and adenovirus (AdV). From April 2021, off-season and abrupt surges of all disease endpoints occurred, associated with similar dynamics among the PDA-viruses, which re-emerged sequentially. Using our model fit to the entire 2016-2021 period, 82% (95% CI, 75-88%) of CAAP episodes in 2021 were attributable to the common respiratory viruses, as were 22%-31% of the other disease endpoints. Virus-specific contributions to CAAP were: RSV, 49% (95% CI, 43-55%); hMPV, 13% (10-17%); PIV, 11% (7-15%); flu, 7% (1-13%). RhV and AdV did not contribute. RSV was the main contributor in all endpoints, especially in infants. Pneumococcal carriage prevalence remained largely stable throughout the study.\n\nINTERPRETATIONRSV and hMPV play a critical role in the burden of CAAP and pneumococcal disease in children. Interventions targeting these viruses could have a secondary effect on the burden of disease typically attributed to bacteria.\n\nFUNDINGThere was no funding for this study.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSLower respiratory infections (LRI) and invasive pneumococcal disease (IPD) in young children, have often been associated with specific respiratory viruses, namely respiratory syncytial virus (RSV), human metapneumovirus (hMPV) influenza viruses (flu), and parainfluenza viruses (PIV) (termed in the current article pneumonia and pneumococcal disease-associated viruses [PDA-viruses]). However, their causative role as co-pathogens has not yet been fully elucidated. There is already ample evidence that bacteria and viruses interact to cause severe disease. This could be seen after the introduction of pneumococcal conjugate vaccines (PCVs), when there was a significant reduction in hospitalisation for viral lower respiratory infections (LRIs). This suggests that viral-pneumococcal coinfections are common and play a role in the pathogenesis of pneumococcal respiratory infections. To demonstrate the contribution of viruses to the burden of pneumococcal disease specifically, and pneumonia in general, it would be necessary to eliminate one or more of the respiratory viruses. Shortly after the start of the COVID-19 pandemic, multiple reports demonstrated reduced IPD and LRI rates among young children, coincident with dramatically reduced rates of the PDA-viruses globally. Initially, the reduced rates of pneumococcal disease were attributed to non-pharmaceutical interventions that might reduce pneumococcal transmission in the community. However, continuous, virtually unchanged pneumococcal carriage rates were reported in multiple studies, strongly suggesting the reduced circulation of S. pneumoniae was not significantly contributing to disease reduction. Surprisingly, pneumococcus-associated diseases and PDA-viruses simultaneously re-emerged in 2021 during the off-season. In contrast to PDA-viruses, other viruses, such as adenovirus and rhinovirus did not show any of the patterns discussed above. We searched PubMed on June 1st, 2022, for studies since 2020 using the following terms: (\"COVID-19\" or \"SARS-Cov-2\") and (\"S. pneumoniae\" or \"pneumococcus\" or \"IPD\" or \"respiratory virus\" or respiratory syncytial virus\" or \"hMPV\" or \"influenza\" or \"parainfluenza\" or \"adenovirus\" or \"rhinovirus\" or \"lower respiratory infection\"). The search was for English literature and unrestricted by date.\n\nAdded value of this studyThree unique characteristics of the COVID-19 pandemic-induced abnormal dynamics, coupled with multiple ongoing cohort studies in young children, contributed to the historic opportunity to model and quantify the attributable role of the various common respiratory viruses to four pneumococcus-associated disease endpoints (in particular community-acquired alveolar pneumonia (CAAP), non-CAAP LRIs, pneumococcal bacteremic pneumonia and non-pneumonia IPD): First, the full seasonal disappearance of all PDA-viruses shortly after the start of the pandemic, in the presence of continuous, uninterrupted pneumococcal carriage and continuous unchanged rhinovirus and adenovirus activity. Second, the off-season resurgence of the PDA-viruses in 2021. Third, the sequential, rather than simultaneous, re-emergence of the PDA-viruses. The analysis in this study suggests that several of the respiratory viruses, particularly RSV and hMPV, play an important causative role in the pathogenesis of pneumococcal diseases and other respiratory infections. Furthermore, the proportion attributable to each of the PDA-viruses for each of the four studied disease endpoints, and each of the age groups (<1, 1, and 2-4 years of age) could be estimated.\n\nImplication of all the available findingsOur findings add evidence about the absolute and relative contribution of common respiratory viruses to the burden of pneumonia and pneumococcal diseases and related conditions in young children. The strong contribution of RSV to disease burden compared to other viruses in all studied disease endpoints suggests that interventions that target viruses could have secondary effects on the burden of diseases typically attributed to bacteria.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Ron Dagan",
-        "author_inst": "Ben-Gurion University of the Negev"
-      },
-      {
-        "author_name": "Bart Adriaan van der Beek",
-        "author_inst": "Ben Gurion University"
-      },
-      {
-        "author_name": "Shalom Ben-Shimol",
-        "author_inst": "Ben Gurion University"
-      },
-      {
-        "author_name": "David Greenberg",
-        "author_inst": "Ben Gurion University"
-      },
-      {
-        "author_name": "Yonat Shemer Avni",
-        "author_inst": "Ben Gurion University"
-      },
-      {
-        "author_name": "Daniel M. Weinberger",
-        "author_inst": "Yale School of Public Health"
-      },
-      {
-        "author_name": "Dana Danino",
-        "author_inst": "Ben Gurion University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.09.05.22279572",
     "rel_title": "Distinct immune signatures discriminate SARS-CoV-2 vaccine combinations",
@@ -207270,6 +206029,25 @@
     "type": "new results",
     "category": "evolutionary biology"
   },
+  {
+    "rel_doi": "10.1101/2022.09.02.22279526",
+    "rel_title": "Spatial determination of COVID-19 mortality",
+    "rel_date": "2022-09-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.02.22279526",
+    "rel_abs": "COVID-19 has affected at the global scale. However, its impacts are not evenly distributed. The article aims to explore the spatial determination of the COVID-19 related death. The data for the analysis has been accessed from the World Health Organization (WHO). Both descriptive and statistical analysis has been done to assess the COVID-19 related death and spatial explanation. The regression models suggested the explanatory power of spatial difference in the COVID-19 related death. However, further addition of various COVID-19 vaccine did not produce expected result.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Arun GC",
+        "author_inst": "Tribhuvan University Central Department of Economics"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health economics"
+  },
   {
     "rel_doi": "10.1101/2022.09.02.22279519",
     "rel_title": "Metagenomic next-generation sequencing to characterize etiologies of non-malarial fever in a cohort living in a high malaria burden area of Uganda",
@@ -208687,33 +207465,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "nephrology"
   },
-  {
-    "rel_doi": "10.1101/2022.08.31.22279422",
-    "rel_title": "Zero-COVID policy or Living-with-COVID policy? Analysis Based on Percent Excess Mortality",
-    "rel_date": "2022-09-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.31.22279422",
-    "rel_abs": "IntroductionWith the economic recession and pandemic fatigue, milder viral variants and higher vaccine coverage along the time lay the basis for lifting anti-COVID policies to restore COVID-19 normalcy. However, when and how to adjust the anti-COVID policies remain under debate in many countries.\n\nMethodsIn this study, four countries (Singapore, South Korea, Australia, and New Zealand) and one region (Hong Kong SAR), that have shifted from the zero-COVID (ZC) policy to or close to the living-with-COVID (LWC) during or after the Omicron outbreak, were selected as research objects. All-cause mortality data were collected for these objects from 2009-2019. The expected mortality was estimated by a simple linear regression method. Excess mortality over time was calculated as the difference between the expected mortality and the observed mortality. Finally, percent excess mortality (PEM) was calculated as the excess mortality divided by the expected mortality.\n\nResultsIn the examined four countries, PEM fluctuated around 0% and was lower than 10% most of the time under the ZC policy before 2022. After shifting to the LWC policy, all the examined countries increased the PEM. Briefly, countries with high population density (Singapore and South Korea) experienced an average PEM of 20-40% during the first half of 2022, and followed by a lower average PEM of 15-18% during the second half of 2022. For countries with low population density under the LWC policy, Australia experienced an average PEM of 39.85% during the first half of 2022, while New Zealand was the only country in our analysis that achieved no more than 10% in average PEM all the time. On the contrary, Hong Kong SAR under their ZC policy attained an average PEM of 71.14% during the first half of 2022, while its average PEM decreased to 9.19% in the second half of 2022 with LWC-like policy.\n\nConclusionPEM under different policies within each country/region overtime demonstrated that the mortality burden caused by COVID-19 had been reduced overtime. Moreover, anti-COVID policies are suggested to control the excess mortality to achieve as low as 10% in PEM.\n\nContribution to the fieldO_LIThis study compared excess mortality within the same country/region, instead of among countries, thus, PEM during the outbreaks of different SARS-cov-2 variants overtime could reflect the effectiveness of regional specific anti-pandemic policies in protecting the lives of citizens locally.\nC_LIO_LIOur analysis demonstrated that Singapore, South Korea and Australia might implement the LWC policy without sufficient preparation, which resulted in a very high mortality burden during the first half of 2022.\nC_LIO_LIThe reduced PEM in late 2022 in the examined countries/regions suggested that the mortality burden caused by COVID-19 was reduced overtime, laying a great foundation to call for a further relief of LWC policy in the world in the near future.\nC_LIO_LIThis study delineated a threshold of percent excess mortality, which is 10%, as a criterion to assess the effectiveness of anti-COVID policies.\nC_LI",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Xiaohan Cao",
-        "author_inst": "Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China"
-      },
-      {
-        "author_name": "Yunlong Zi",
-        "author_inst": "Thrust of Sustainable Energy and Environment, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou, Guangdong 511400, China"
-      },
-      {
-        "author_name": "Yuyan Zhu",
-        "author_inst": "Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.08.30.22279409",
     "rel_title": "Racism and Racial Injustice During COVID-19: Impact on University Student Mental Health",
@@ -208984,6 +207735,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.08.31.22279444",
+    "rel_title": "Effectiveness of the COVID-19 vaccines against severe disease with Omicron sub-lineages BA.4 and BA.5 in England",
+    "rel_date": "2022-09-01",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.31.22279444",
+    "rel_abs": "The Omicron sub-lineages BA.4 and BA.5 were first detected in England in April 2022. A case surge followed despite England having recently experienced waves with BA.1 and BA.2. This study used a whole population test-negative case-control study design to estimate the effectiveness of the vaccines currently in use as part of the UK COVID-19 vaccination programme against hospitalisation following infection with BA.4 and BA.5 as compared to BA.2 during a period of co-circulation. Incremental VE was estimated in those vaccinated with either a third or fourth dose as compared to individuals with waned immunity who had received their second dose at least 25 weeks prior. Vaccination status was included as an independent variable and effectiveness was defined as 1-odds of vaccination in cases/odds of vaccination in controls. During the study period, there were 32,845 eligible tests from hospitalised individuals. Of these, 25,862 were negative (controls), 3,432 were BA.2, 273 were BA.4, 947 were BA.5 and 2,331 were either BA.4 or BA.5 cases. There was no evidence of reduced VE against hospitalisation for BA.4 or BA.5 as compared to BA.2. The incremental VE was 56.8% (95% C.I.; 24.0-75.4%), 59.9% (95% C.I.; 45.6-70.5%) and 52.4% (95% C.I.; 43.2-60.1%) for BA.4, BA.5 and BA.2, respectively, at 2 to 14 weeks after a third or fourth dose. VE against hospitalisation with BA.4/5 or BA.2 was slightly higher for the mRNA-1273 booster than the BNT162b2 booster at all time-points investigated, but confidence intervals overlapped. These data provide reassuring evidence of the protection conferred by the current vaccines against severe disease with BA.4 and BA.5.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Freja Kirsebom",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Nick Andrews",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Julia Stowe",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Mary Ramsay",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Jamie Lopez Bernal",
+        "author_inst": "UK Health Security Agency"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2022.08.31.22279428",
     "rel_title": "Effects of inbound attendees of a mass gathering event on the COVID-19 epidemic using individual-based simulations",
@@ -210341,61 +209127,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "respiratory medicine"
   },
-  {
-    "rel_doi": "10.1101/2022.08.26.22279232",
-    "rel_title": "UB-612 Multitope Vaccine Targeting SARS-CoV-2 Spike and Non-Spike Proteins Provides Broad and Durable Immune Responses",
-    "rel_date": "2022-08-30",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.26.22279232",
-    "rel_abs": "The SARS-CoV-2 non-Spike (S) structural protein targets of nucleocapsid (N), membrane (M) and envelope (E), critical in the host cell interferon response and memory T-cell immunity, have been grossly overlooked since the inception of COVID vaccine development. To pursue a universal (pan-sarbecovirus) vaccine against ever-emergent future mutants, we explored booster immunogenicity of UB-612, a multitope-vaccine that contains S1-RBD-sFc protein and sequence-conserved rationally designed promiscuous Th and CTL epitope peptides on the Sarbecovirus N, M and S2 proteins. To a subpopulation of infection-free participants (aged 18-85 years) involved in a two-dose Phase-2 trial, a UB-612 booster (third dose) was administered 6-8 months after the second dose. The immunogenicity was evaluated at 14 days post-booster with overall safety monitored until the end of study. The booster induced high viral-neutralizing antibodies against live Wuhan WT (VNT50, 1,711) and Delta (VNT50, 1,282); and against pseudovirus WT (pVNT50, 11,167) vs. Omicron BA.1/BA.2/BA.5 variants (pVNT50, 2,314/1,890/854), respectively. The lower primary neutralizing antibodies in the elderly were uplifted upon boosting to approximately the same high level in young adults. UB-612 also induced potent, durable Th1-oriented (IFN-{gamma}+-) responses (peak/pre-boost/post-boost SFU/106 PBMCs, 374/261/444) along with robust presence of cytotoxic CD8+ T cells (peak/pre-boost/post-boost CD107a+-Granzyme B+, 3.6%/1.8%/1.8%). Booster vaccination is safe and well tolerated without SAEs. By recognition against epitopes on Spike (S1-RBD and S2) and non-Spike (N and M) structure proteins, UB-612 provides potent, broad and long-lasting B-cell and T-cell memory immunity and offers a potential as a universal vaccine to fend off Omicrons and new VoCs.\n\nSIGNIFICANCE STATEMENTThe Omicron has swept the globe with a rapid succession of dominating sublineages from BA.1, BA.2, to the current BA.5 with increasing infectivity and antibody evasion. Concerningly, the non-Spike structure proteins that promote T-cell immunity are grossly overlooked in vaccine development. Looking beyond short-interval booster jabs and omicron-updated vaccines, a pragmatic approach to curbing ever-emergent new mutants would be \"universal (pan-Sarbecovirus) vaccines\" targeting conserved nonmutable epitopes on coronavirus. UB-612, a multitope-vaccine armed with Spike (S1-RBD and S2) and non-Spike targets (Nucleocapsid N and Membrane M), allows booster vaccination to elicit potent, broadly-recognizing, durable B- and T-cell memory immunity. Sequence-conserved epitope peptides were rationally-designed from S2, N and M proteins to synergistically enhance memory helper and cytotoxic T-cell immunity and B-cell immunity.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Chang Yi Wang",
-        "author_inst": "UBI Asia"
-      },
-      {
-        "author_name": "Wen-Jiun Peng",
-        "author_inst": "UBI Asia"
-      },
-      {
-        "author_name": "Be-Sheng Kuo",
-        "author_inst": "UBI Asia"
-      },
-      {
-        "author_name": "Hope Liu",
-        "author_inst": "UBI Asia"
-      },
-      {
-        "author_name": "Yu-Hsin Ho",
-        "author_inst": "UBI Asia"
-      },
-      {
-        "author_name": "Min-Sheng Wang",
-        "author_inst": "UBI Asia"
-      },
-      {
-        "author_name": "Ya-Ting Yang",
-        "author_inst": "UBI Asia"
-      },
-      {
-        "author_name": "Po-Yen Chang",
-        "author_inst": "UBI Asia"
-      },
-      {
-        "author_name": "Yea-Huei Shen",
-        "author_inst": "StatPlus Inc."
-      },
-      {
-        "author_name": "Kao-Pin Hwang",
-        "author_inst": "School of Medicine, College of Medicine, China Medical University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.08.29.22279351",
     "rel_title": "Insights into COVID-19 epidemiology and control from temporal changes in serial interval distributions in Hong Kong",
@@ -210794,6 +209525,53 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2022.08.29.22279161",
+    "rel_title": "Organizational impact of an ID NOW COVID-19 point-of-care testing for SARS-CoV2 detection in a maternity ward",
+    "rel_date": "2022-08-30",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.29.22279161",
+    "rel_abs": "BackgroundSARS-CoV-2 has been responsible for more than 550 million cases of COVID-19 worldwide. RT-PCR is considered the \"gold standard\" for the diagnosis of patients suspected of having COVID-19. During the heightened waves of the pandemic, more rapid tests have been required. Point-of-care tests (POCT) for COVID-19 include antigen tests, serological tests, and other molecular-based platforms. The ID NOW COVID-19 assay (Abbott) performs an isothermal gene amplification of a target encoding the RNA-dependent RNA polymerase of SARSCoV-2. The main objective of this study was to evaluate the organizational impact following the implementation of a POC testing platform ID NOW in a maternity ward.\n\nMaterials and MethodsThis retrospective study included pregnant women admitted for Groupe Hospitalier Paris Saint-Joseph Paris. The study was conducted over 2 periods lasting 6 months each. The first period (P1) corresponded to the 2nd wave in France (July to December 2020) whereas the second (P2) period focused on the 3rd wave (February to July 2021). During P1, viral detection was performed by RT-PCR at the hospitals laboratory. During P2, it was performed with the ID NOW COVID-19 test directly in the delivery room by nursing staff after training and certification. Our primary endpoint was the length of time in the birth room from admission to discharge in the postpartum period.\n\nResults2447 pregnant women were included, 1053 during P1 and 1394 during P2. The median age, percentage of singleton pregnancies, mean gestational age, percentage of nulliparous individuals, percentage of vaginal deliveries, and COVID19 positivity rate were comparable between the two periods. During P2, the length of stay in the delivery room was significantly shorter than during P1 (17.9 vs 14.7 hours, p<0.001).\n\nConclusionAnalysis of the data from this study following the implementation of the ID NOW POCT in the maternity ward indicates a significant decrease in the length of stay in the birth room. This outcome needs to be confirmed in a multicenter cohort, in particular to precise the specific impact of COVID-19 care on delays.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Jean-Claude Nguyen Van",
+        "author_inst": "Groupe Hospitalier Paris Saint-Joseph"
+      },
+      {
+        "author_name": "Benoit Pilmis",
+        "author_inst": "Groupe Hospitalier Paris Saint-Joseph"
+      },
+      {
+        "author_name": "Amir Khaterchi",
+        "author_inst": "Groupe Hospitalier Paris Saint-Joseph"
+      },
+      {
+        "author_name": "Olivier Billuart",
+        "author_inst": "Groupe Hospitalier Paris Saint-Joseph"
+      },
+      {
+        "author_name": "Gauthier Pean de Ponfilly",
+        "author_inst": "Groupe Hospitalier Paris Saint-Joseph"
+      },
+      {
+        "author_name": "Alban Le Monnier",
+        "author_inst": "Groupe Hospitalier Paris Saint-Joseph"
+      },
+      {
+        "author_name": "Elie Azria",
+        "author_inst": "Groupe Hospitalier Paris Saint-Joseph"
+      },
+      {
+        "author_name": "Assaf Mizrahi",
+        "author_inst": "Groupe Hospitalier Paris Saint-Joseph"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "obstetrics and gynecology"
+  },
   {
     "rel_doi": "10.1101/2022.08.30.22279383",
     "rel_title": "Polygenic Risk Scores for Asthma and Allergic Disease Predict COVID-19 Severity in 9/11 Responders",
@@ -212235,125 +211013,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.08.25.505316",
-    "rel_title": "Enhancer deregulation in TET2 Mutant Clonal Hematopoiesis is associated with increased COVID-19 related inflammation severity and mortality",
-    "rel_date": "2022-08-26",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.25.505316",
-    "rel_abs": "Coronavirus disease 2019 (COVID-19) is associated with significant morbidity and mortality, albeit with considerable heterogeneity among affected individuals. It remains unclear which factors determine severity of illness and long-term outcomes. Emerging evidence points towards an important role of preexisting host factors, such as a deregulated inflammatory response at the time of infection. Here, we demonstrate the negative impact of clonal hematopoiesis, a prevalent clonal disorder of ageing individuals, on COVID-19-related cytokine release severity and mortality. We show that mutations in the gene coding for the methylcytosine dioxygenase TET2 promotes amplification of classical and intermediate monocyte subsets. Using single cell multiomic sequencing approaches, we identify cell-specific gene expression changes associated with the loss of TET2 and significant epigenomic deregulation affecting enhancer accessibility of a subset of transcription factors involved in monocyte differentiation. We further identify EGR1 down-regulation secondary to TET2-mediated hypermethylation, resulting in overexpression of MALAT1, a lncRNA that plays a role in hematopoietic stem cell differentiation and monocyte lineage commitment. Together, these data provide a mechanistic insight to the poor prognostic value of clonal hematopoiesis in patients infected with Sars-COV2.",
-    "rel_num_authors": 26,
-    "rel_authors": [
-      {
-        "author_name": "Moritz Binder",
-        "author_inst": "Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, United States;  Epigenomics Program, Center for Individualized Medici"
-      },
-      {
-        "author_name": "Terra L. Lasho",
-        "author_inst": "Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, United States"
-      },
-      {
-        "author_name": "Wazim Mohammed Ismail",
-        "author_inst": "Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, United States; Department of Laboratory Medicine and Pathology, Mayo "
-      },
-      {
-        "author_name": "Nana A. Ben-Crentsil",
-        "author_inst": "H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, United States"
-      },
-      {
-        "author_name": "Jenna A. Fernandez",
-        "author_inst": "Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, United States"
-      },
-      {
-        "author_name": "Minsuk Kim",
-        "author_inst": "Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, United States"
-      },
-      {
-        "author_name": "Susan M. Geyer",
-        "author_inst": "Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, United States"
-      },
-      {
-        "author_name": "Amelia Mazzone",
-        "author_inst": "Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, United States; Department of Laboratory Medicine and Pathology, Mayo "
-      },
-      {
-        "author_name": "Christy M. Finke",
-        "author_inst": "Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, United States"
-      },
-      {
-        "author_name": "Abhishek A. Mangaonkar",
-        "author_inst": "Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, United States"
-      },
-      {
-        "author_name": "Jeong-Heon Lee",
-        "author_inst": "Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, United States"
-      },
-      {
-        "author_name": "Kwan Hyun Kim",
-        "author_inst": "Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, United States"
-      },
-      {
-        "author_name": "Vernadette A. Simon",
-        "author_inst": "Medical Genome Facility, Genome Analysis Core, Mayo Clinic, Rochester, MN 55905, United States"
-      },
-      {
-        "author_name": "Fariborz Rakhshan Rohakthar",
-        "author_inst": "Medical Genome Facility, Genome Analysis Core, Mayo Clinic, Rochester, MN 55905, United States"
-      },
-      {
-        "author_name": "Amik Munankarmy",
-        "author_inst": "Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, United States"
-      },
-      {
-        "author_name": "Susan M. Schwager",
-        "author_inst": "Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, United States"
-      },
-      {
-        "author_name": "Jonathan J. Harrington",
-        "author_inst": "Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, United States"
-      },
-      {
-        "author_name": "Melissa R. Snyder",
-        "author_inst": "Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, United States"
-      },
-      {
-        "author_name": "Nathalie M. Droin",
-        "author_inst": "INSERM U1287, Gustave Roussy Cancer Center, 94805 Villejuif, France"
-      },
-      {
-        "author_name": "Eric Solary",
-        "author_inst": "INSERM U1287, Gustave Roussy Cancer Center, 94805 Villejuif, France"
-      },
-      {
-        "author_name": "Keith D. Robertson",
-        "author_inst": "Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, United States; Department of Molecular Pharmacology and Experimental "
-      },
-      {
-        "author_name": "Eric D. Wieben",
-        "author_inst": "Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, United States"
-      },
-      {
-        "author_name": "Eric Padron",
-        "author_inst": "H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, United States"
-      },
-      {
-        "author_name": "Nicholas Chia",
-        "author_inst": "Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, United States"
-      },
-      {
-        "author_name": "Alexandre Gaspar-Maia",
-        "author_inst": "Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, United States; Department of Laboratory Medicine and Pathology, Mayo "
-      },
-      {
-        "author_name": "Mrinal M. Patnaik",
-        "author_inst": "Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, United States;  Epigenomics Program, Center for Individualized Medici"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "genetics"
-  },
   {
     "rel_doi": "10.1101/2022.08.26.505450",
     "rel_title": "Characterization of SARS-CoV-2 Omicron BA.2.75 clinical isolates",
@@ -212716,6 +211375,129 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.08.24.22279159",
+    "rel_title": "Dynamics of anti-S IgG antibodies titers after the second dose of COVID 19 mRNA and non-mRNA vaccines in the manual and craft worker population of Qatar",
+    "rel_date": "2022-08-25",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.24.22279159",
+    "rel_abs": "BackgroundThere is limited seroepidemiological evidence on the magnitude and long-term durability of antibody titers of mRNA and non-mRNA vaccines in the Qatari population. This study was conducted to generate evidence on long-term anti-S IgG antibodies titers and their dynamics in individuals who have completed a primary COVID-19 vaccination schedule.\n\nMethodsA total of 300 participants who received any of the following vaccines BNT162b2/Comirnaty or mRNA-1273 or ChAdOx1-S/Covishield or COVID-19 Vaccine Janssen/Johnson or BBIBP-CorV or Covaxin were enrolled in our study. All sera samples were tested by chemiluminescent microparticle immunoassay (CMIA) for the quantitative determination of IgG antibodies to SARS-CoV-2, receptor-binding domain (RBD) of the S1 subunit of the spike protein of SARS-CoV-2. Antibodies against SARS-CoV-2 nucleocapsid (SARS-CoV-2 N-protein IgG) were also determined. Kaplan-Meier survival curves were used to compare the time from the last dose of the primary vaccination schedule to the time by which anti-S IgG antibodies titers fell into the lowest quartile (range of values collected) for the mRNA and non-mRNA vaccines.\n\nResultsParticipants vaccinated with mRNA vaccines had higher median anti-S IgG antibody titers. Participants vaccinated with the mRNA-1273 vaccine had the highest median anti-S-antibody level of 13720.9 AU/mL (IQR 6426.5 to 30185.6 AU/mL) followed by BNT162b2 (median, 7570.9 AU/ml; IQR, 3757.9 to 16577.4 AU/mL); while the median anti-S antibody titer for non-mRNA vaccinated participants was 3759.7 AU/mL (IQR, 2059.7-5693.5 AU/mL). The median time to reach the lowest quartile was 3.53 months (IQR, 2.2-4.5 months) and 7.63 months (IQR, 6.3-8.4 months) for the non-mRNA vaccine recipients and Pfizer vaccine recipients, respectively. However, more than 50% of the Moderna vaccine recipients did not reach the lowest quartile by the end of the follow-up period.\n\nConclusionsThis evidence on anti-S IgG antibody titers, their durability and decay over time should be considered for the utility of these assays in transmission dynamics after the full course of primary vaccination.",
+    "rel_num_authors": 27,
+    "rel_authors": [
+      {
+        "author_name": "Devendra Bansal",
+        "author_inst": "Health Protection and Communicable Disease Control, Ministry of Public Health, Doha 42, Qatar"
+      },
+      {
+        "author_name": "Hassan Atia",
+        "author_inst": "Health Protection and Communicable Disease Control, Ministry of Public Health, Doha 42, Qatar"
+      },
+      {
+        "author_name": "Mashael Al Badr",
+        "author_inst": "National Reference Laboratory, Ministry of Public Health, Doha 42, Qatar"
+      },
+      {
+        "author_name": "Mohamed Nour",
+        "author_inst": "Health Protection and Communicable Disease Control, Ministry of Public Health, Doha 42, Qatar"
+      },
+      {
+        "author_name": "Jazeel Abdulmajeed",
+        "author_inst": "Primary Health Care Corporation"
+      },
+      {
+        "author_name": "Amal Hasan",
+        "author_inst": "Health Protection and Communicable Disease Control, Ministry of Public Health, Doha 42, Qatar"
+      },
+      {
+        "author_name": "Noora Al-Hajri",
+        "author_inst": "National Reference Laboratory, Ministry of Public Health, Doha 42, Qatar"
+      },
+      {
+        "author_name": "Lina Ahmed",
+        "author_inst": "Health Protection and Communicable Disease Control, Ministry of Public Health, Doha 42, Qatar"
+      },
+      {
+        "author_name": "Rumissa Ibrahim",
+        "author_inst": "Health Protection and Communicable Disease Control, Ministry of Public Health, Doha 42, Qatar"
+      },
+      {
+        "author_name": "Reham Zamel",
+        "author_inst": "Health Protection and Communicable Disease Control, Ministry of Public Health, Doha 42, Qatar"
+      },
+      {
+        "author_name": "Almuthana Mohamed",
+        "author_inst": "Health Protection and Communicable Disease Control, Ministry of Public Health, Doha 42, Qatar"
+      },
+      {
+        "author_name": "Hamad Pattalaparambil",
+        "author_inst": "Health Protection and Communicable Disease Control, Ministry of Public Health, Doha 42, Qatar"
+      },
+      {
+        "author_name": "Faisal Daraan",
+        "author_inst": "Health Protection and Communicable Disease Control, Ministry of Public Health, Doha 42, Qatar"
+      },
+      {
+        "author_name": "Adil Chaudhry",
+        "author_inst": "Health Protection and Communicable Disease Control, Ministry of Public Health, Doha 42, Qatar"
+      },
+      {
+        "author_name": "Sahar Oraby",
+        "author_inst": "Health Protection and Communicable Disease Control, Ministry of Public Health, Doha 42, Qatar"
+      },
+      {
+        "author_name": "Sahar El-Saleh",
+        "author_inst": "Health Protection and Communicable Disease Control, Ministry of Public Health, Doha 42, Qatar"
+      },
+      {
+        "author_name": "Sittana S El-Shafie",
+        "author_inst": "National Reference Laboratory, Ministry of Public Health, Doha 42, Qatar"
+      },
+      {
+        "author_name": "Affra Faiz Al-Farsi",
+        "author_inst": "Laboratory Section, Medical Commission Department, Ministry of Public Health, Doha 42, Qatar"
+      },
+      {
+        "author_name": "Jiji Paul",
+        "author_inst": "Laboratory Section, Medical Commission Department, Ministry of Public Health, Doha 42, Qatar"
+      },
+      {
+        "author_name": "Ahmed Ismail",
+        "author_inst": "Laboratory Section, Medical Commission Department, Ministry of Public Health, Doha 42, Qatar"
+      },
+      {
+        "author_name": "Hamad E. Al-Romaihi",
+        "author_inst": "Health Protection and Communicable Disease Control, Ministry of Public Health, Doha 42, Qatar"
+      },
+      {
+        "author_name": "Mohammed H Al-Thani",
+        "author_inst": "Health Protection and Communicable Disease Control, Ministry of Public Health, Doha 42, Qatar"
+      },
+      {
+        "author_name": "Suhail A.R. Doi",
+        "author_inst": "Department of Population Medicine, College of Medicine, Q U Health, Qatar University, Doha, Qatar"
+      },
+      {
+        "author_name": "Susu M Zughaier",
+        "author_inst": "Department of Basic Medical Sciences, College of Medicine, Q U Health, Qatar University, Doha, Qatar"
+      },
+      {
+        "author_name": "Farhan Cyprian",
+        "author_inst": "Department of Basic Medical Sciences, College of Medicine, Q U Health, Qatar University, Doha, Qatar"
+      },
+      {
+        "author_name": "Elmobashar Farag",
+        "author_inst": "Health Protection and Communicable Disease Control, Ministry of Public Health, Doha 42, Qatar"
+      },
+      {
+        "author_name": "Habib Hasan Farooqui",
+        "author_inst": "Department of Population Medicine, College of Medicine, Q U Health, Qatar University, Doha, Qatar"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.08.24.22279197",
     "rel_title": "TRENDS IN CASES, HOSPITALISATION AND MORTALITY RELATED TO THE OMICRON BA.4/BA.5 SUB-VARIANTS IN SOUTH AFRICA",
@@ -213985,113 +212767,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.08.23.22279026",
-    "rel_title": "Immune protection against SARS-CoV-2 re-reinfection and immune imprinting",
-    "rel_date": "2022-08-24",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.23.22279026",
-    "rel_abs": "We investigated epidemiological evidence for immune imprinting by comparing incidence of re-reinfection in the national cohort of individuals with a documented Omicron (BA.1/BA.2) reinfection after a pre-Omicron primary infection (designated as the reinfection cohort), to incidence of reinfection in the national cohort of individuals with a documented Omicron (BA.1/BA.2) primary infection (designated as the primary-infection cohort). This was done using a matched, retrospective cohort study that emulated a randomized \"target trial\". Vaccinated individuals were excluded. Associations were estimated using Cox proportional-hazard regression models. Cumulative incidence of infection was 1.1% (95% CI: 0.8-1.4%) for the reinfection cohort and 2.1% (95% CI: 1.8-2.3%) for the primary-infection cohort, 135 days after the start of follow-up. The adjusted hazard ratio (aHR) for infection was 0.52 (95% CI: 0.40-0.68), comparing incidence in the reinfection cohort to that in the primary-infection cohort. The aHR was 0.59 (95% CI: 0.40-0.85) in a subgroup analysis in which primary infection in the reinfection cohort was restricted to only the index virus or Alpha variant. In the first 70 days of follow-up, when incidence was dominated by BA.2, the aHR was 0.92 (95% CI: 0.51-1.65). However, cumulative incidence curves diverged when BA.4/BA.5 subvariants dominated incidence (aHR, 0.46 (95% CI: 0.34-0.62)). There was no evidence that immune imprinting compromises protection against Omicron subvariants. However, there was evidence that having two infections, one with a pre-Omicron variant followed by one with an Omicron subvariant, elicits stronger protection against future Omicron-subvariant reinfection than having had only one infection with an Omicron subvariant.",
-    "rel_num_authors": 23,
-    "rel_authors": [
-      {
-        "author_name": "Hiam Chemaitelly",
-        "author_inst": "Weill Cornell Medicine-Qatar"
-      },
-      {
-        "author_name": "Houssein Ayoub",
-        "author_inst": "Qatar University"
-      },
-      {
-        "author_name": "Patrick Tang",
-        "author_inst": "Sidra Medicine"
-      },
-      {
-        "author_name": "Mohammad R. Hasan",
-        "author_inst": "Sidra Medicine"
-      },
-      {
-        "author_name": "Peter Coyle",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "HADI M. YASSINE",
-        "author_inst": "Qatar University"
-      },
-      {
-        "author_name": "Hebah A. Al-Khatib",
-        "author_inst": "Qatar University"
-      },
-      {
-        "author_name": "Maria K Smatti",
-        "author_inst": "Qatar University"
-      },
-      {
-        "author_name": "Zaina Al-Kanaani",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Einas Al-Kuwari",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Andrew Jeremijenko",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Anvar Hassan Kaleeckal",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Ali Nizar Latif",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Riyazuddin Mohammad Shaik",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Hanan F. Abdul-Rahim",
-        "author_inst": "Qatar University"
-      },
-      {
-        "author_name": "Gheyath Nasrallah",
-        "author_inst": "Qatar University"
-      },
-      {
-        "author_name": "Mohamed Ghaith Al-Kuwari",
-        "author_inst": "Primary Health Care Corporation"
-      },
-      {
-        "author_name": "Adeel A Butt",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Hamad Eid Al-Romaihi",
-        "author_inst": "MoPH: Ministry of Public Health Qatar"
-      },
-      {
-        "author_name": "Mohammed H. Al-Thani",
-        "author_inst": "MoPH: Ministry of Public Health Qatar"
-      },
-      {
-        "author_name": "Abdullatif Al-Khal",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Roberto Bertollini",
-        "author_inst": "MoPH: Ministry of Public Health Qatar"
-      },
-      {
-        "author_name": "Laith J Abu-Raddad",
-        "author_inst": "Weill Cornell Medicine-Qatar"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.08.23.22279058",
     "rel_title": "Knowledge, attitude, and practices of ward attendant and housekeeping staffs towards dead body care of COVID-19 patients at tertiary care hospital : A cross sectional study",
@@ -214510,6 +213185,69 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.08.22.22279079",
+    "rel_title": "Assessing Vulnerability to COVID-19 in High-Risk Populations: The Role of SARS-CoV-2 Spike-Targeted Serology",
+    "rel_date": "2022-08-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.22.22279079",
+    "rel_abs": "ImportanceIndividuals at increased risk for severe outcomes from COVID-19, due to compromised immunity or other risk factors, would benefit from objective measures of vulnerability to infection based on prior infection and/or vaccination. We reviewed published data to identify a specific role and interpretation of SARS-CoV-2 spike-targeted serology testing for such individuals. We also provide real-world evidence of spike-targeted antibody test results, identifying the seronegativity rate across the United States from March 2021 through June 2022. Analysis of antibody test results were compared between post-transplant (ie, immunocompromised) and all other patients tested in the first half of 2022. Finally, specific recommendations are provided for an evidence-based and clinically useful interpretation of spike-targeted serology to identify vulnerability to infection and potential subsequent adverse outcomes.\n\nObservationsDecreased vaccine effectiveness among immunocompromised individuals is linked to correspondingly high rates of breakthrough infections. Evidence indicates that negative results on SARS-CoV-2 antibody tests are associated with increased risk for subsequent infection. Results from widely available, laboratory-based tests do not provide a direct measure of protection but appear to correlate well with the presence of surrogate pseudovirus-neutralizing antibodies. The results of SARS-CoV-2 semiquantitative tests have also been associated with vaccine effectiveness and the likelihood of breakthrough infection. The data suggest that \"low-positive\" results on semiquantitative SARS-CoV-2 spike-targeted antibody tests may help identify persons at increased relative risk for breakthrough infection leading to adverse outcomes. In an analysis of data from large national laboratories during the COVID-19 Omicron-related surge in 2022, results from SARS-CoV-2 spike-targeted antibody tests were negative in 16.6% (742/4459) of solid organ transplant recipients tested compared to only 11.0% (47,552/432,481) of the remaining tested population.\n\nConclusions and RelevanceStandardized semiquantitative and quantitative SARS-CoV-2 spike-targeted antibody tests may provide objective information on risk of SARS-CoV-2 infection and associated adverse outcomes. This holds especially for high-risk populations, including transplant recipients, who demonstrate a relatively higher rate of seronegativity. The widespread availability of such tests presents an opportunity to refine risk assessment for individuals with suboptimal SARS-CoV-2 antibody levels and to promote effective interventions. Interim federal guidance would support physicians and patients while additional investigations are pursued.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Harvey W Kaufman",
+        "author_inst": "Quest Diagnostics"
+      },
+      {
+        "author_name": "William A Meyer",
+        "author_inst": "Quest Diagnostics"
+      },
+      {
+        "author_name": "Nigel J Clarke",
+        "author_inst": "Quest Diagnostics"
+      },
+      {
+        "author_name": "William A Meyer",
+        "author_inst": "Quest Diagnostics"
+      },
+      {
+        "author_name": "Christopher M Rank",
+        "author_inst": "Roche Diagnostics"
+      },
+      {
+        "author_name": "James Freeman",
+        "author_inst": "Siemens Healthineers"
+      },
+      {
+        "author_name": "Marcia Eisenberg",
+        "author_inst": "LabCorp"
+      },
+      {
+        "author_name": "Laura Gillim",
+        "author_inst": "LabCorp"
+      },
+      {
+        "author_name": "William G Morice",
+        "author_inst": "Mayo Medical Laboratories"
+      },
+      {
+        "author_name": "David M Briscoe",
+        "author_inst": "Boston Children's Hospital"
+      },
+      {
+        "author_name": "David S Perlin",
+        "author_inst": "Center for Discovery and Innovation, Hackensack Meridian Health"
+      },
+      {
+        "author_name": "Jay G Wohlgemuth",
+        "author_inst": "Quest Diagnostics"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.08.22.22279060",
     "rel_title": "Omicron B.1.1.529 variant infections associated with severe disease are uncommon in a COVID-19 under-vaccinated, high SARS-CoV-2 seroprevalence population in Malawi",
@@ -215743,109 +214481,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.08.21.22278552",
-    "rel_title": "Neutralizing Antibody to Omicron BA.1, BA.2 and BA.5 in COVID-19 Patients",
-    "rel_date": "2022-08-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.21.22278552",
-    "rel_abs": "Neutralizing antibody plays a key role in protective immunity against COVID-19. As increasingly distinct variants circulate, debate continues regarding the value of adding novel variants to SARS-CoV-2 vaccines. In this study, we have analyzed live virus neutralization titers against WA1, Delta, BA.1, BA.2, and BA.5 in 187 hospitalized patients infected with Delta or Omicron strains. This information will be useful in selection of the SARS-CoV-2 strains to include in an updated vaccine. Our results show that unvaccinated Delta infected patients made a highly biased neutralizing antibody response towards the infecting Delta strain with slightly lower responses against the WA1 strain, but with strikingly lower titers against BA.1, BA.2, and BA.5. Delta infected patients that had been previously vaccinated with the WA1 containing COVID vaccine made equivalent responses to WA1 and Delta strains, but still had very low neutralizing antibody responses to Omicron strains. In striking contrast, both unvaccinated and vaccinated Omicron patients exhibited a more balanced ratio of Omicron virus neutralization compared to neutralization of ancestral strains. Interestingly, Omicron patients infected with BA.1 or BA.2 had detectable neutralizing antibody titers to BA.5, but these titers were lower than neutralization titers to BA.1 and BA.2. Taken together, these results suggest that inclusion of the Omicron BA.5 strain in a SARS-CoV-2 vaccine would be beneficial in protection against the widely circulating BA.5 variant.\n\nDisclaimerThe findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention.",
-    "rel_num_authors": 22,
-    "rel_authors": [
-      {
-        "author_name": "Susanne L Linderman",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Lilin Lai",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Estefany L Bocangel Gamarra",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Nicholas M. Mohr",
-        "author_inst": "University of Iowa Carver College of Medicine"
-      },
-      {
-        "author_name": "Kevin W Gibbs",
-        "author_inst": "Wake Forest School of Medicine"
-      },
-      {
-        "author_name": "Jay S Steingrub",
-        "author_inst": "Baystate Medical Center"
-      },
-      {
-        "author_name": "Matthew C Exline",
-        "author_inst": "The Ohio State University"
-      },
-      {
-        "author_name": "Nathan I Shapiro",
-        "author_inst": "Beth Israel Deaconess Medical Center"
-      },
-      {
-        "author_name": "Anne E Frosch",
-        "author_inst": "Hennepin County Medical Center"
-      },
-      {
-        "author_name": "Nida Qadir",
-        "author_inst": "University of California Los Angeles"
-      },
-      {
-        "author_name": "Srilatha Edupuganti",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Diya Surie",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Mark W Tenforde",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Meredith E Davis Gardner",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "James D Chappell",
-        "author_inst": "Vanderbilt University Medical Center"
-      },
-      {
-        "author_name": "Max SY Lau",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "M. Juliana McElrath",
-        "author_inst": "Fred Hutchinson Cancer Research Center"
-      },
-      {
-        "author_name": "Adam S. Lauring",
-        "author_inst": "University of Michigan"
-      },
-      {
-        "author_name": "Mehul S Suthar",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Manish M Patel",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Wesley H. Self",
-        "author_inst": "Vanderbilt University Medical Center"
-      },
-      {
-        "author_name": "Rafi Ahmed",
-        "author_inst": "Emory University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "allergy and immunology"
-  },
   {
     "rel_doi": "10.1101/2022.08.19.22278966",
     "rel_title": "Seasonal variations in social contact patterns in a rural population in north India: Implications for pandemic control",
@@ -216264,6 +214899,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "transplantation"
   },
+  {
+    "rel_doi": "10.1101/2022.08.20.22279023",
+    "rel_title": "Brain microstructural changes and fatigue after COVID-19",
+    "rel_date": "2022-08-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.20.22279023",
+    "rel_abs": "BackgroundFatigue and cognitive complaints are the most frequent persistent symptoms in patients after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. This study aimed to assess fatigue and neuropsychological performance and investigate changes in the thickness and volume of gray matter (GM) and microstructural abnormalities in the white matter (WM) in a group of patients with mild-to-moderate coronavirus disease 2019 (COVID-19).\n\nMethodsWe studied 56 COVID-19 patients and 37 matched controls using magnetic resonance imaging (MRI). Cognition was assessed using Montreal Cognitive Assessment and Cambridge Neuropsychological Test Automated Battery, and fatigue was assessed using Chalder Fatigue Scale (CFQ-11). T1-weighted MRI was used to assess GM thickness and volume. Fiber-specific apparent fiber density (FD), free water index, and diffusion tensor imaging data were extracted using diffusion-weighted MRI (d-MRI). d-MRI data were correlated with clinical and cognitive measures using partial correlations and general linear modeling.\n\nResultsCOVID-19 patients had mild-to-moderate acute illness (95% non-hospitalized). The average period between real-time quantitative reverse transcription polymerase chain reaction-based diagnosis and clinical/MRI assessments was 93.3 ({+/-}26.4) days. The COVID-19 group had higher CFQ-11 scores than the control group (p < 0.001). There were no differences in neuropsychological performance between groups. The COVID-19 group had lower FD in the association, projection, and commissural tracts, but no change in GM. The corona radiata, corticospinal tract, corpus callosum, arcuate fasciculus, cingulate, fornix, inferior fronto-occipital fasciculus, inferior longitudinal fasciculus, superior longitudinal fasciculus, and uncinate fasciculus were involved. CFQ-11 scores correlated with microstructural changes in patients with COVID-19.\n\nConclusionsQuantitative d-MRI detected changes in the WM microstructure of patients recovering from COVID-19. This study suggests a possible brain substrate underlying the symptoms caused by SARS-CoV-2 during medium- to long-term recovery.\n\nKey pointsO_LIPatients with COVID-19 had microstructural changes in the WM at a mean follow-up of 3 months.\nC_LIO_LIThere is a possible brain substrate underlying the symptoms caused by SARS-CoV-2 during medium- to long-term recovery.\nC_LIO_LIA serial d-MRI study following up on a non-hospitalized sample of patients with milder COVID-19 forms is warranted.\nC_LI",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Diogenes Diego de Carvalho Bispo",
+        "author_inst": "Brasilia University Hospital, University of Brasilia"
+      },
+      {
+        "author_name": "Pedro Renato de Paula Brandao",
+        "author_inst": "Hospital Sirio Libanes (Brasilia)"
+      },
+      {
+        "author_name": "Danilo Assis Pereira",
+        "author_inst": "Brazilian Institute of Neuropsychology and Cognitive Sciences"
+      },
+      {
+        "author_name": "Fernando Bisinoto Maluf",
+        "author_inst": "Department of Radiology, Hospital Santa Marta"
+      },
+      {
+        "author_name": "Bruna Arrais Dias",
+        "author_inst": "Department of Radiology, Hospital Santa Marta"
+      },
+      {
+        "author_name": "Hugo Rafael Paranhos",
+        "author_inst": "Department of Radiology, Hospital Santa Marta"
+      },
+      {
+        "author_name": "Felipe von Glehn",
+        "author_inst": "Faculty of Medicine, University of Brasilia"
+      },
+      {
+        "author_name": "Augusto Cesar Penalva de Oliveira",
+        "author_inst": "Instituto de Infectologia Emilio Ribas"
+      },
+      {
+        "author_name": "Neysa Aparecida Tinoco Regattieri",
+        "author_inst": "Faculty of Medicine, University of Brasilia"
+      },
+      {
+        "author_name": "Lucas Scardua Silva",
+        "author_inst": "Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), University of Campinas"
+      },
+      {
+        "author_name": "Clarissa Lin Yasuda",
+        "author_inst": "Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), University of Campinas"
+      },
+      {
+        "author_name": "Alexandre Anderson de Sousa Munhoz Soares",
+        "author_inst": "Faculty of Medicine, University of Brasilia"
+      },
+      {
+        "author_name": "Maxime Descoteaux",
+        "author_inst": "Sherbrooke Connectivity Imaging Lab, University of Sherbrooke"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "neurology"
+  },
   {
     "rel_doi": "10.1101/2022.08.20.22279020",
     "rel_title": "Clinical Study to Evaluate the Possible Efficacy and Safety of Antibodies Combination (casirivimab and imdevimab) versus standard antiviral therapy as antiviral agent against Corona virus 2 infection in hospitalized COVID-19 patients",
@@ -217569,57 +216271,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2022.08.17.22278898",
-    "rel_title": "Within-host genetic diversity of SARS-CoV-2 in the context of large-scale hospital-associated genomic surveillance",
-    "rel_date": "2022-08-19",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.17.22278898",
-    "rel_abs": "The COVID-19 pandemic has resulted in extensive surveillance of the genomic diversity of SARS-CoV-2. Sequencing data generated as part of these efforts can also capture the diversity of the SARS-CoV-2 virus populations replicating within infected individuals. To assess this within-host diversity of SARS-CoV-2 we quantified low frequency (minor) variants from deep sequence data of thousands of clinical samples collected by a large urban hospital system over the course of a year. Using a robust analytical pipeline to control for technical artefacts, we observe that at comparable viral loads, specimens from patients hospitalized due to COVID-19 had a greater number of minor variants than samples from outpatients. Since individuals with highly diverse viral populations could be disproportionate drivers of new viral lineages in the patient population, these results suggest that transmission control should pay special attention to patients with severe or protracted disease to prevent the spread of novel variants.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Alexandra Mushegian",
-        "author_inst": "National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Scott Wesley Long",
-        "author_inst": "Houston Methodist Hospital"
-      },
-      {
-        "author_name": "Randall James Olsen",
-        "author_inst": "Houston Methodist Research Institute"
-      },
-      {
-        "author_name": "Paul James Christensen",
-        "author_inst": "Houston Methodist Hospital"
-      },
-      {
-        "author_name": "Sishir Subedi",
-        "author_inst": "Houston Methodist Research Institute"
-      },
-      {
-        "author_name": "Matthew Chung",
-        "author_inst": "National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "James Davis",
-        "author_inst": "Argonne National Laboratory"
-      },
-      {
-        "author_name": "James Musser",
-        "author_inst": "Houston Methodist Research Hospital"
-      },
-      {
-        "author_name": "Elodie Ghedin",
-        "author_inst": "National Institutes of Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc0",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.08.18.22278963",
     "rel_title": "Relative contributions of vaccination and previous infection to population-level SARS-CoV-2 immunity over time: a simulation modelling study",
@@ -217970,6 +216621,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.08.17.22278893",
+    "rel_title": "Uptake of Sotrovimab for prevention of severe COVID-19 and its safety in the community in England",
+    "rel_date": "2022-08-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.17.22278893",
+    "rel_abs": "Sotrovimab is a neutralising monoclonal antibody (nMAB), currently administrated in England to treat extremely clinically vulnerable COVID-19 patients. Trials have shown it to have mild or moderate side effects, however safety in real-world settings has not been yet evaluated. We used national databases to investigate its uptake and safety in community patients across England. We used a cohort study to describe uptake and a self-controlled case series design to evaluate the risks of 49 pre-specified suspected adverse events in the 2-28 days post-treatment. Between December 11, 2021 and May 24, 2022, there were 172,860 COVID-19 patients eligible for treatment. Of the 22,815 people who received Sotrovimab, 21,487 (94.2%) had a positive SARS-CoV-2 test and 5,999 (26.3%) were not on the eligible list. Between treated and untreated eligible individuals, the mean age (54.6, SD: 16.1 vs 54.1, SD: 18.3) and sex distribution (women: 60.9% vs 58.1%; men: 38.9% vs 41.1%) were similar. There were marked variations in uptake between ethnic groups, which was higher amongst Indian (15.0%; 95%CI 13.8, 16.3), Other Asian (13.7%; 95%CI 11.9, 15.8), White (13.4%; 95%CI 13.3, 13.6), and Bangladeshi (11.4%; 95%CI 8.8, 14.6); and lower amongst Black Caribbean individuals (6.4%; 95%CI 5.4, 7.5) and Black Africans (4.7%; 95%CI 4.1, 5.4). We found no increased risk of any of the suspected adverse events in the overall period of 2-28 days post-treatment, but an increased risk of rheumatoid arthritis (IRR 3.08, 95% CI 1.44, 6.58) and of systematic lupus erythematosus (IRR 5.15, 95% CI 1.60, 16.60) in the 2-3 days post-treatment, when we narrowed the risk period.\n\nFundingNational Institute of Health Research (Grant reference 135561)",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Martina Patone",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Holly Tibble",
+        "author_inst": "University of Edinburgh"
+      },
+      {
+        "author_name": "Andrew JHL Snelling",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Carol Coupland",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Aziz Sheikh",
+        "author_inst": "University of Edinburgh"
+      },
+      {
+        "author_name": "Julia Hippisley-Cox",
+        "author_inst": "University of Oxford"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2022.08.17.22278896",
     "rel_title": "Impact of the COVID-19 Pandemic on Personal Networks and Neurological Outcomes of People with Multiple Sclerosis: A Case-Control Cross-sectional and Longitudinal Analysis",
@@ -219315,41 +218005,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.08.13.22278733",
-    "rel_title": "QCovid 4 - Predicting risk of death or hospitalisation from COVID-19 in adults testing positive for SARS-CoV-2 infection during the Omicron wave in England",
-    "rel_date": "2022-08-16",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.13.22278733",
-    "rel_abs": "ObjectivesTo (a) derive and validate risk prediction algorithms (QCovid4) to estimate risk of COVID-19 mortality and hospitalisation in UK adults with a SARS-CoV-2 positive test during the  Omicron pandemic wave in England and (b) evaluate performance with earlier versions of algorithms developed in previous pandemic waves and the high-risk cohort identified by NHS Digital in England.\n\nDesignPopulation-based cohort study using the QResearch database linked to national data on COVID-19 vaccination, high risk patients prioritised for COVID-19 therapeutics, SARS-CoV-2 results, hospitalisation, cancer registry, systemic anticancer treatment, radiotherapy and the national death registry.\n\nSettings and study period1.3 million adults in the derivation cohort and 0.15 million adults in the validation cohort aged 18-100 years with a SARS-CoV-2 positive test between 11th December 2021 and 31st March 2022 with follow up to 30th June 2022.\n\nMain outcome measuresOur primary outcome was COVID-19 death. The secondary outcome of interest was COVID-19 hospital admission. Models fitted in the derivation cohort to derive risk equations using a range of predictor variables. Performance evaluated in a separate validation cohort.\n\nResultsOf 1,297,984 people with a SARS-CoV-2 positive test in the derivation cohort, 18,756 (1.45%) had a COVID-19 related hospital admission and 3,878 (0.3%) had a COVID-19 death during follow-up. Of the 145,404 people in the validation cohort, there were 2,124 (1.46%) COVID-19 admissions and 461 (0.3%) COVID-19 deaths.\n\nThe COVID-19 mortality rate in men increased with age and deprivation. In the QCovid4 model in men hazard ratios were highest for those with the following conditions (for 95% CI see Figure 1): kidney transplant (6.1-fold increase); Downs syndrome (4.9-fold); radiotherapy (3.1-fold); type 1 diabetes (3.4-fold); chemotherapy grade A (3.8-fold), grade B (5.8-fold); grade C (10.9-fold); solid organ transplant ever (2.4-fold); dementia (1.62-fold); Parkinsons disease (2.2-fold); liver cirrhosis (2.5-fold). Other conditions associated with increased COVID-19 mortality included learning disability, chronic kidney disease (stages 4 and 5), blood cancer, respiratory cancer, immunosuppressants, oral steroids, COPD, coronary heart disease, stroke, atrial fibrillation, heart failure, thromboembolism, rheumatoid/SLE, schizophrenia/bipolar disease sickle cell/HIV/SCID; type 2 diabetes. Results were similar in the model in women.\n\nO_FIG O_LINKSMALLFIG WIDTH=100 HEIGHT=200 SRC=\"FIGDIR/small/22278733v1_fig1.gif\" ALT=\"Figure 1\">\nView larger version (35K):\norg.highwire.dtl.DTLVardef@4e93b7org.highwire.dtl.DTLVardef@c3e600org.highwire.dtl.DTLVardef@1311bd4org.highwire.dtl.DTLVardef@11a3246_HPS_FORMAT_FIGEXP  M_FIG O_FLOATNOFigure 1C_FLOATNO QCOVID4 (mortality): Adjusted hazard ratios for COVID-19 death in men mutually adjusted and also adjusted for fractional polynomial terms for age and BMI\n\nC_FIG COVID-19 mortality risk was lower among those who had received COVID-19 vaccination compared with unvaccinated individuals with evidence of a dose response relationship. The reduced mortality rates associated with prior SARS-CoV-2 infection were similar in men (adjusted hazard ratio (HR) 0.51 (95% CI 0.40, 0.64)) and women (adjusted HR 0.55 (95%CI 0.45, 0.67)).\n\nThe QCOVID4 algorithm explained 76.6% (95%CI 74.4 to 78.8) of the variation in time to COVID-19 death (R2) in women. The D statistic was 3.70 (95%CI 3.48 to 3.93) and the Harrells C statistic was 0.965 (95%CI 0.951 to 0.978). The corresponding results for COVID-19 death in men were similar with R2 76.0% (95% 73.9 to 78.2); D statistic 3.65 (95%CI 3.43 to 3.86) and C statistic of 0.970 (95%CI 0.962 to 0.979). QCOVID4 discrimination for mortality was slightly higher than that for QCOVID1 and QCOVID2, but calibration was much improved.\n\nConclusionThe QCovid4 risk algorithm modelled from data during the UKs Omicron wave now includes vaccination dose and prior SARS-CoV-2 infection and predicts COVID-19 mortality among people with a positive test. It has excellent performance and could be used for targeting COVID-19 vaccination and therapeutics. Although large disparities in risks of severe COVID-19 outcomes among ethnic minority groups were observed during the early waves of the pandemic, these are much reduced now with no increased risk of mortality by ethnic group.\n\nWhat is knownO_LIThe QCOVID risk assessment algorithm for predicting risk of COVID-19 death or hospital admission based on individual characteristics has been used in England to identify people at high risk of severe COVID-19 outcomes, adding an additional 1.5 million people to the national shielded patient list in England and in the UK for prioritising people for COVID-19 vaccination.\nC_LIO_LIThere are ethnic disparities in severe COVID-19 outcomes which were most marked in the first pandemic wave in 2020.\nC_LIO_LICOVID-19 vaccinations and therapeutics (monoclonal antibodies and antivirals) are available but need to be targeted to those at highest risk of severe outcomes.\nC_LI\n\nWhat this study addsO_LIThe QCOVID4 risk algorithm using data from the Omicron wave now includes number of vaccination doses and prior SARS-CoV-2 infection. It has excellent performance both for ranking individuals (discrimination) and predicting levels of absolute risk (calibration) and can be used for targeting COVID-19 vaccination and therapeutics as well as individualised risk assessment.\nC_LIO_LIQCOVID4 more accurately identifies individuals at highest levels of absolute risk for targeted interventions than the  conditions-based approach adopted by NHS Digital based on relative risk of a list of medical conditions.\nC_LIO_LIAlthough large disparities in risks of severe COVID-19 outcomes among ethnic minority groups were observed during the early waves of the pandemic, these are much reduced now with no increased risk of mortality by ethnic group.\nC_LI",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Julia Hippisley-Cox",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Kamlesh Khunti",
-        "author_inst": "University of Leicester"
-      },
-      {
-        "author_name": "Aziz Sheikh",
-        "author_inst": "University of Edinburgh"
-      },
-      {
-        "author_name": "Jonathan Nguyen-Van-Tam",
-        "author_inst": "University of Nottingham"
-      },
-      {
-        "author_name": "Carol Coupland",
-        "author_inst": "University of Oxford"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.08.16.504085",
     "rel_title": "Synchronicity of viral shedding in molossid bat maternity colonies",
@@ -219620,6 +218275,49 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2022.08.12.503822",
+    "rel_title": "The Spike protein of SARS-coV2 19B (S) clade mirrors critical features of viral adaptation and coevolution",
+    "rel_date": "2022-08-15",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.12.503822",
+    "rel_abs": "Pathogens including viruses evolve in tandem with diversity in their animal and human hosts. For SARS-coV2, the focus is generally for understanding such coevolution on the virus spike protein since it demonstrates high mutation rates compared to other genome regions, particularly in the receptor-binding domain (RBD).\n\nViral sequences of the SARS-coV2 19B (S) clade and variants of concern from different continents, were investigated, with a focus on the A.29 lineage which presented with different mutational patterns within the 19B (S) lineages in order to learn more about how SARS-coV2 may have evolved and adapted to widely diverse populations globally.\n\nResults indicated that SARS-coV2 went through evolutionary constrains and intense selective pressure, particularly in Africa. This was manifested in a departure from neutrality with excess nonsynonymous mutations and a negative Tajima D consistent with rapid expansion and directional selection as well as deletion and deletion-frameshifts in the N-terminal domain (NTD region) of the spike protein.\n\nIn conclusion, viral transmission during epidemics through population of diverse genomic structure and marked complexity may be a significant factor for the virus to acquire distinct patterns of mutations within these populations in order to ensure its survival and fitness, hence in the emergence of novel variants and strains.\n\nImportanceIn this study, we justify the fact that the viruss evolution varies across continents, with each continent showing different amounts and patterns of mutations and deletions, which was manifested in the 19B (S) clade of SARS-coV2, particularly in areas with high population complexity, such as Africa, despite the low rate of sampling and data sharing. The findings show that SARS-coV2 was subject to evolutionary constraints and intense selective pressure. This study will contribute to the scanty amount of research on the SARS-coV2 coevolution and adaptation, in which the host variation is of great significance in understanding the intricacies of viral host coevolution.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Bidour K. Hussein",
+        "author_inst": "Institute of Endemic Diseases, UofK"
+      },
+      {
+        "author_name": "Omnia M. Ibrahium",
+        "author_inst": "University of Khartoum, Faculty of science"
+      },
+      {
+        "author_name": "Marwa F. Alamin",
+        "author_inst": "Institute of Endemic Diseases, UofK"
+      },
+      {
+        "author_name": "Lamees A.M Ahmed",
+        "author_inst": "Institute of Endemic Diseases, UofK"
+      },
+      {
+        "author_name": "Safa A.E Abuswar",
+        "author_inst": "Institute of Endemic Diseases, UofK"
+      },
+      {
+        "author_name": "Mohammed H. Abdelraheem",
+        "author_inst": "Institute of Endemic Diseases, UofK"
+      },
+      {
+        "author_name": "Muntaser E. Ibrahim",
+        "author_inst": "Institute of Endemic Diseases, UofK"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "new results",
+    "category": "evolutionary biology"
+  },
   {
     "rel_doi": "10.1101/2022.08.14.503921",
     "rel_title": "Evasion of Neutralizing Antibody Response by the SARS-CoV-2 BA.2.75 Variant",
@@ -221229,25 +219927,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "neurology"
   },
-  {
-    "rel_doi": "10.1101/2022.08.10.22278638",
-    "rel_title": "Assessment of COVID-19 Effect on the Health of Families in South-West, Nigeria",
-    "rel_date": "2022-08-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.10.22278638",
-    "rel_abs": "AimThis study was to assess the effect of the coronavirus disease and its associated lockdown on the physical, spiritual, emotional, and socio-economic health of families living in South-West, Nigeria.\n\nBackgroundThe outbreak of the COVID-19 pandemic create a universal health crisis that has a major effect on our day-to-day activities and these global concerns have shifted from the diseases to the physical, emotional, spiritual, and socioeconomic effects of the situation on the people.\n\nMethodThis is a descriptive study with five hundred and thirty-six (536) respondents; a convenient sampling technique was used to select samples through online Google form.\n\nResultThe majority of the respondents ages ranged between 20 and 30years (53.0%). COVID 19 pandemic affected 17.2% of the respondents physical health. The lockdown improved bonding among family members (74.6%), also the lockdown favourable affected 56.0% of the respondents emotional health. The spirituality of the respondents was negatively affected (79.9%) by the lockdown, family expenses were increased (82.6%), there was an increased in the prices of goods (92.9%), and in general COVID 19 pandemic unfavorably affected (77.2%) the respondents socio-economic health.\n\nConclusionThis study reveals that COVID-19 and the lockdown produced an adverse effect on the physical, emotional, spiritual, and socio-economic wellbeing of the families in southwest Nigeria.\n\nImplications for nursing and health policynurses working in COVID-19 unit need to give total care to the affected patient; therefore, they have obligation to include physical, emotional, spiritual and mental intervention in their care. The government needs to plan and strategize properly in the method for distribution of the palliatives, and if possible identify the vulnerable and less privileged in each state for easy distribution.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "olaolorunpo olorunfemi",
-        "author_inst": "Federal University Oye Ekiti, Ekiti State"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "nursing"
-  },
   {
     "rel_doi": "10.1101/2022.08.10.503531",
     "rel_title": "Development of highly potent non-covalent inhibitors of SARS-CoV-2 3CLpro",
@@ -221762,6 +220441,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "allergy and immunology"
   },
+  {
+    "rel_doi": "10.1101/2022.08.09.22274874",
+    "rel_title": "Procalcitonin and High APACHE Scores are Associated with the Development of Acute Kidney Injury in Patients with SARS-CoV-2",
+    "rel_date": "2022-08-10",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.09.22274874",
+    "rel_abs": "BackgroundAcute kidney injury (AKI) is associated with poor outcomes in patients infected with SARS-CoV-2. Sepsis, direct injury to kidney cells by the virus, and severe systemic inflammation are mechanisms implicated in its development. We investigated the association between inflammatory markers (C-reactive protein, procalcitonin, D-dimer, lactate dehydrogenase, and ferritin) in patients infected with SARS-CoV-2 and the development of AKI.\n\nMethodsA prospective cohort study performed at the Civil Hospital (Dr. Juan I. Menchaca) Guadalajara, Mexico, included patients aged >18 years with a diagnosis of SARS-CoV-2 pneumonia confirmed by RT-PCR and who did or did not present with AKI (KDIGO) while hospitalized. Biomarkers of inflammation were recorded, and kidney function was estimated using the CKD-EPI formula.\n\nResults291 patients were included (68% men; mean age, 57 years). The incidence of AKI was 40.5% (118 patients); 21% developed stage 1 AKI, 6% developed stage 2 AKI, and 14% developed stage 3 AKI. The development of AKI was associated with phosphate higher (p = 0.002) (RR 1.39, CI 95% 1.13 - 1.72), high procalcitonin levels at hospital admission (p = 0.005) (RR 2.09, CI 95% 1.26-3.50), and high APACHE scores (p = 0.011) (RR 2.0, CI 95% 1.17-3.40). The survival analysis free of AKI according to procalcitonin levels and APACHE scores demonstrated a lower survival in patients with procalcitonin >0.5 ng/ml (p= 0.001) and APACHE >15 points (p = 0.004).\n\nConclusionsphosphate, high procalcitonin levels, and APACHE scores >15 were predictors of AKI development in patients hospitalized with COVID-19.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Jorge Andrade-Sierra",
+        "author_inst": "University of Guadalajara"
+      },
+      {
+        "author_name": "Claudia Delgado Astorga",
+        "author_inst": "Civil  Hospital. Guadalajara, Mexico."
+      },
+      {
+        "author_name": "Miriam Gabriela Nava Vargas",
+        "author_inst": "Civil Hospital, Guadalajara Mexico"
+      },
+      {
+        "author_name": "Enrique Rojas Campos",
+        "author_inst": "Mexican Institute of Social Security. Jalisco, Mexico"
+      },
+      {
+        "author_name": "Karla Hernandez Morales",
+        "author_inst": "Civil Hospital, Guadalajara Mexico."
+      },
+      {
+        "author_name": "Carlos A Andrade Castellanos",
+        "author_inst": "Civil Hospital, Guadalajara Mexico"
+      },
+      {
+        "author_name": "Kevin Javier Arellano Arteaga",
+        "author_inst": "Civil Hospital. Guadalajara Mexico."
+      },
+      {
+        "author_name": "Antonio de Jesus Andrade-Ortega Sr.",
+        "author_inst": "Universidad de Guadalajara"
+      },
+      {
+        "author_name": "Luis Gerardo Gonzalez-Correa",
+        "author_inst": "Mexican Institute of Social Security. Guadalajara, Jalisco, Mexico"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "nephrology"
+  },
   {
     "rel_doi": "10.1101/2022.08.09.22278592",
     "rel_title": "Distinguishing features of Long COVID identified through immune profiling",
@@ -223611,53 +222341,6 @@
     "type": "new results",
     "category": "evolutionary biology"
   },
-  {
-    "rel_doi": "10.1101/2022.08.08.22278547",
-    "rel_title": "Infectiousness of SARS-CoV-2 breakthrough infections and reinfections during the Omicron wave",
-    "rel_date": "2022-08-09",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.08.22278547",
-    "rel_abs": "SARS-CoV-2 breakthrough infections in vaccinated individuals and reinfections among previously infected individuals have become increasingly common. Such infections highlight a broader need to understand the contribution of vaccination, including booster doses, and natural immunity to the infectiousness of persons with SARS-CoV-2 infections, especially in high-risk populations with intense transmission such as prisons. Here, we show that both vaccine-derived and naturally acquired immunity independently reduce the infectiousness of persons with Omicron variant SARS-CoV-2 infections in a prison setting. Analyzing SARS-CoV-2 surveillance data from December 2021 to May 2022 across 35 California state prisons with a predominately male population, we estimate that unvaccinated Omicron cases had a 36% (95% confidence interval (CI): 31-42%) risk of transmitting infection to close contacts, as compared to 28% (25-31%) risk among vaccinated cases. In adjusted analyses, we estimated that any vaccination, prior infection alone, and both vaccination and prior infection reduced an index cases risk of transmitting infection by 22% (6-36%), 23% (3-39%) and 40% (20-55%), respectively. Receipt of booster doses and more recent vaccination further reduced infectiousness among vaccinated cases. These findings suggest that although vaccinated and/or previously infected individuals remain highly infectious upon SARS-CoV-2 infection in this prison setting, their infectiousness is reduced compared to individuals without any history of vaccination or infection, underscoring some benefit of vaccination to reduce but not eliminate transmission.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Sophia T Tan",
-        "author_inst": "University of California, San Francisco"
-      },
-      {
-        "author_name": "Ada T Kwan",
-        "author_inst": "University of California, San Francisco"
-      },
-      {
-        "author_name": "Isabel Rodriguez-Barraquer",
-        "author_inst": "University of California, San Francisco"
-      },
-      {
-        "author_name": "Benjamin J Singer",
-        "author_inst": "University of California, San Francisco"
-      },
-      {
-        "author_name": "Hailey J Park",
-        "author_inst": "University of California, San Francisco"
-      },
-      {
-        "author_name": "Joseph A Lewnard",
-        "author_inst": "University of California, Berkeley"
-      },
-      {
-        "author_name": "David Sears",
-        "author_inst": "University of California, San Francisco"
-      },
-      {
-        "author_name": "Nathan C Lo",
-        "author_inst": "University of California, San Francisco"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.08.08.22278536",
     "rel_title": "A study to assess the impact of cobas Liat point-of-care PCR assays (SARS-CoV-2 and Influenza A/B) on patient clinical management in the emergency department of the University of California at Davis Medical Center",
@@ -223928,6 +222611,109 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "cardiovascular medicine"
   },
+  {
+    "rel_doi": "10.1101/2022.08.07.22278510",
+    "rel_title": "Metabolomic and gut microbiome profiles across the spectrum of community-based COVID and non-COVID disease: A COVID-19 Biobank study.",
+    "rel_date": "2022-08-09",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.07.22278510",
+    "rel_abs": "Whilst many with SARS-CoV-2 infection have mild disease, managed in the community, individuals with cardiovascular risk factors experienced often more severe acute disease, requiring hospitalisation. Increasing concern has also developed over long symptom duration in many individuals, including the majority who managed acutely in the community. Risk factors for long symptom duration, including biological variables, are still poorly defined.\n\nWe examine post-illness metabolomic and gut-microbiome profiles, in community-dwelling participants with SARS-CoV-2, ranging from asymptomatic illness to Post-COVID Syndrome, and participants with prolonged non-COVID-19 illnesses. We also assess a pre-established metabolomic biomarker score for its association with illness duration.\n\nWe found an atherogenic-dyslipidaemic metabolic profile, and greater biomarker scores, associated with longer illness, both in individuals with and without SARS-CoV-2 infection. We found no association between illness duration and gut microbiome in convalescence.\n\nFindings highlight the potential role of cardiometabolic dysfunction to the experience of long illness duration, including after COVID-19.",
+    "rel_num_authors": 22,
+    "rel_authors": [
+      {
+        "author_name": "Marc F \u00d6sterdahl",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Ronan Whiston",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Carole H Sudre",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Francesco Asnicar",
+        "author_inst": "University of Trento"
+      },
+      {
+        "author_name": "Nathan J Cheetham",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Aitor Blanco Miguez",
+        "author_inst": "University of Trento"
+      },
+      {
+        "author_name": "Vicky Bowyer",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Michela Antonelli",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Olivia Snell",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Liane dos Santos Canas",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Christina Hu",
+        "author_inst": "ZOE Global Ltd."
+      },
+      {
+        "author_name": "Jonathan Wolf",
+        "author_inst": "ZOE Global Ltd."
+      },
+      {
+        "author_name": "Cristina Menni",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Michael Malim",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Deborah Hart",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Tim Spector",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Sarah Berry",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Nicola Segata",
+        "author_inst": "University of Trento"
+      },
+      {
+        "author_name": "Katie Doores",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Sebastien Ourselin",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Emma L Duncan",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Claire J Steves",
+        "author_inst": "King's College London"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2022.08.08.22278528",
     "rel_title": "Quantifying the impact of delaying the second COVID-19 vaccine dose in England: a mathematical modelling study",
@@ -225533,57 +224319,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.08.05.22278489",
-    "rel_title": "Heterologous vaccination as a strategy to minimize inequity in COVID-19 vaccine access: A modeling study in Thailand",
-    "rel_date": "2022-08-07",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.05.22278489",
-    "rel_abs": "BackgroundVaccinations are the best hope to control the COVID-19 pandemic and save lives. Due to the high demand and failure to share vaccines equitably, there were not enough vaccine supplies to cover the majority of people in low- and middle-income countries during the early stage of vaccination. To cope with this problem, Thailand, an upper-middle-income country, decided to employ a heterologous vaccination strategy as the primary COVID-19 vaccination regimen in the country. The CoronaVac (CV) vaccine was administered as the first dose, followed by the ChAdOx1 nCoV-19 (AZ) vaccine as the second dose. However, there is no study to assess the effectiveness of the heterologous vaccination employed in Thailand compared to the standard homologous vaccination.\n\nMethodsWe delineated the course and timeline of COVID-19 vaccination in Thailand. An age-structured compartmental model for COVID-19 transmission and vaccination was constructed and employed to assess the effectiveness of the heterologous vaccination strategy. The impact of the vaccine prioritization strategies on COVID-19 mortality and infections was also investigated.\n\nResultsWe found that the CV+AZ heterologous vaccination strategy outperforms the separate CV and AZ homologous vaccinations in reducing cumulative cases and deaths when combined with other non-pharmaceutical interventions. Furthermore, the results suggested that prioritizing vaccines for the elderly could be optimal in reducing COVID-19 mortality for a wide range of vaccination rates and disease transmission dynamics.\n\nConclusionsOur modeling results suggested that to minimize the impacts of inequity in early COVID-19 vaccine access in low- and middle-income countries, those countries may use early accessible but maybe lower-efficacy vaccines as the first dose of heterologous vaccination in combination with higher-efficacy vaccines as the second dose when they are available.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Suparinthon Anupong",
-        "author_inst": "Mahidol University"
-      },
-      {
-        "author_name": "Tanakorn Chantanasaro",
-        "author_inst": "Mahidol University"
-      },
-      {
-        "author_name": "Chaiwat Wilasang",
-        "author_inst": "Mahidol University"
-      },
-      {
-        "author_name": "Natcha C. Jitsuk",
-        "author_inst": "Mahidol University"
-      },
-      {
-        "author_name": "Chayanin Sararat",
-        "author_inst": "Mahidol University"
-      },
-      {
-        "author_name": "Kan Sornbundit",
-        "author_inst": "KMUTT"
-      },
-      {
-        "author_name": "Busara Pattanasiri",
-        "author_inst": "Kasetsart University Kamphaeng Saen Campus"
-      },
-      {
-        "author_name": "Sudarat Chadsuthi",
-        "author_inst": "Naresuan University"
-      },
-      {
-        "author_name": "Charin Modchang",
-        "author_inst": "Mahidol University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.08.05.22278481",
     "rel_title": "Two years of COVID-19 Pandemic: Framework of Health Interventions in a Brazilian City",
@@ -225878,6 +224613,193 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
+  {
+    "rel_doi": "10.1101/2022.08.05.22278466",
+    "rel_title": "Performance of Screening for SARS-CoV-2 using Rapid Antigen Tests to Detect Incidence of Symptomatic and Asymptomatic SARS-CoV-2 Infection: findings from the Test Us at Home prospective cohort study",
+    "rel_date": "2022-08-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.05.22278466",
+    "rel_abs": "BackgroundPerformance of rapid antigen tests for SARS-CoV-2 (Ag-RDT) varies over the course of an infection, and their performance in screening for SARS-CoV-2 is not well established. We aimed to evaluate performance of Ag-RDT for detection of SARS-CoV-2 for symptomatic and asymptomatic participants.\n\nMethodsParticipants >2 years old across the United States enrolled in the study between October 2021 and February 2022. Participants completed Ag-RDT and molecular testing (RT-PCR) for SARS-CoV-2 every 48 hours for 15 days. This analysis was limited to participants who were asymptomatic and tested negative on their first day of study participation. Onset of infection was defined as the day of first positive RT-PCR result. Sensitivity of Ag-RDT was measured based on testing once, twice (after 48-hours), and thrice (after 96 hours). Analysis was repeated for different Days Post Index PCR Positivity (DPIPP) and stratified based on symptom-status.\n\nResultsIn total, 5,609 of 7,361 participants were eligible for this analysis. Among 154 participants who tested positive for SARS-CoV-2, 97 were asymptomatic and 57 had symptoms at infection onset. Serial testing with Ag-RDT twice 48-hours apart resulted in an aggregated sensitivity of 93.4% (95% CI: 89.1-96.1%) among symptomatic participants on DPIPP 0-6. Excluding singleton positives, aggregated sensitivity on DPIPP 0-6 for two-time serial-testing among asymptomatic participants was lower at 62.7% (54.7-70.0%) but improved to 79.0% (71.0-85.3%) with testing three times at 48-hour intervals.\n\nDiscussionPerformance of Ag-RDT was optimized when asymptomatic participants tested three-times at 48-hour intervals and when symptomatic participants tested two-times separated by 48-hours.",
+    "rel_num_authors": 43,
+    "rel_authors": [
+      {
+        "author_name": "Apurv Soni",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Carly Herbert",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Honghuang Lin",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Yi Yan",
+        "author_inst": "US Food and Drug Administration"
+      },
+      {
+        "author_name": "Caitlin Pretz",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Pamela Stamegna",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Biqi Wang",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Taylor Orwig",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Colton Wright",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Seanan Tarrant",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Stephanie Behar",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Thejas Suvarna",
+        "author_inst": "CareEvolution, LLC"
+      },
+      {
+        "author_name": "Summer Schrader",
+        "author_inst": "CareEvolution, LLC"
+      },
+      {
+        "author_name": "Emma Harman",
+        "author_inst": "CareEvolution, LLC"
+      },
+      {
+        "author_name": "Chris Nowak",
+        "author_inst": "CareEvolution, LLC"
+      },
+      {
+        "author_name": "Vik Kheterpal",
+        "author_inst": "CareEvolution, LLC"
+      },
+      {
+        "author_name": "Lokinendi V Rao",
+        "author_inst": "Quest Diagnostics"
+      },
+      {
+        "author_name": "Lisa Cashman",
+        "author_inst": "Quest Diagnostics"
+      },
+      {
+        "author_name": "Elizabeth Orvek",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Didem Ayturk",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Laura Gibson",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Adrian Zai",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Steven Wong",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Peter Lazar",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Ziyue Wang",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Andreas Filippaios",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Bruce Barton",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Chad Achenbach",
+        "author_inst": "Northwestern University"
+      },
+      {
+        "author_name": "Robert Murphy",
+        "author_inst": "Northwestern University"
+      },
+      {
+        "author_name": "Matthew Robinson",
+        "author_inst": "Johns Hopkins University School of Medicine"
+      },
+      {
+        "author_name": "Yuka Manabe",
+        "author_inst": "Johns Hopkins University School of Medicine"
+      },
+      {
+        "author_name": "Shishir Pandey",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Andres Colubri",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Stephenie Lemon",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Nisha Fahey",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Katherine L Luzuriaga",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Nathaniel Hafer",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "Kristian Roth",
+        "author_inst": "Food and Drug administration"
+      },
+      {
+        "author_name": "Toby Lowe",
+        "author_inst": "Food and Drug administration"
+      },
+      {
+        "author_name": "Timothy Stenzel",
+        "author_inst": "Food and Drug administration"
+      },
+      {
+        "author_name": "Bill Heetderks",
+        "author_inst": "National Institute of Biomedical Imaging and Bioengineering"
+      },
+      {
+        "author_name": "John Broach",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      },
+      {
+        "author_name": "David D McManus",
+        "author_inst": "University of Massachusetts Chan Medical School"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.08.04.22278446",
     "rel_title": "Differential Impacts of Perceived Social Support on Alcohol and Cannabis Use in Young Adults: Lessons from the COVID-19 Pandemic",
@@ -227755,37 +226677,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.08.04.22278204",
-    "rel_title": "\"I don't know what to do or where to go\". experiences of accessing healthcare support from the perspectives of people living with Long Covid and healthcare professionals: A qualitative study in Bradford, UK.",
-    "rel_date": "2022-08-04",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.04.22278204",
-    "rel_abs": "BackgroundIn July 2022 it was estimated 2 million people in the UK have self-reported Long Covid (LC).1 Many people have reported not receiving adequate healthcare support. There is a lack of research which provides an in-depth exploration of the barriers faced by people with LC in accessing healthcare support. It is important to understand these barriers to provide better support, care and advice for those experiencing LC.\n\nObjectiveTo understand the barriers faced in accessing primary, secondary and specialist healthcare support for people with LC.\n\nDesign and participation40 interviews were conducted with people with LC alongside 12 interviews with healthcare professionals (HCPs) providing LC support in Bradford, as part of a UK wide qualitative longitudinal study.\n\nResultsPeople living with LC had a large degree of difficulty in accessing healthcare services for LC support. We categorised the healthcare access experiences of participants into five main types: 1) being unable to access primary care 2) accessing primary care but receiving (perceived) inadequate support 3) extreme persistence 4) alternatives to mainstream healthcare 5) positive experiences. There was a severe lack of access to specialist LC services. Ethnic minority participants faced a further barrier of mistrust and fear of services deterring them from accessing support. HCPs discussed systemic barriers to delivering services. Experiences were embedded in macro structural issues further exacerbated by the pandemic.\n\nConclusionTo better support people with LC the barriers faced in accessing healthcare support must be addressed. Of significance, improvements to GP access are required; especially as GPs are the first line of support for people living with LC.\n\nPatient and public involvementA PPI group is engaged at regular intervals in the project.\n\nO_TEXTBOXBox 1Patient and Public Contribution\n\nDesigning an interview schedule for people with LC: The wider CONVALSCENCE research project has a PPI group involved in various work packages. The PPI group is hosted by researchers at University of West of England who have expertise in patient and public involvement. Members of the PPI group all have or had LC. After an extensive literature review4, a draft of the interview schedule was presented to the group via a workshop. It was then revised after incorporating their feedback and piloted by the research team for further refinement.\n\nData interpretation workshop: Following advice of the UWE researchers, the PPI group were presented ahead of time with 4 interview transcripts from the dataset and provided their interpretation of the interviews via a workshop. The theme of barriers to accessing healthcare was also highlighted by attendees, for example they discussed patients being disbelieved (particularly young people) and fragmented services as some points of interest within the transcripts.\n\nC_TEXTBOX",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Sarah Akhtar Baz",
-        "author_inst": "University of York"
-      },
-      {
-        "author_name": "Chao Fang",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "JD Carpentieri",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Laura Sheard",
-        "author_inst": "University of York"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2022.08.03.502703",
     "rel_title": "Double-dose mRNA vaccination to SARS-CoV-2 progressively increases recognition of variants-of-concern by Spike RBD-specific memory B cells",
@@ -228096,6 +226987,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2022.08.03.22278359",
+    "rel_title": "COVID-19 convalescent plasma for the treatment of immunocompromised patients: a systematic review.",
+    "rel_date": "2022-08-03",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.03.22278359",
+    "rel_abs": "Immunosuppressed patients have increased risk for morbidity and mortality from COVID-19 because they less frequently mount antibody responses to vaccines and often cannot tolerate small-molecule antivirals. The Omicron variant of concern of SARS-CoV-2 has progressively defeated anti-Spike mAbs authorized so far, paving the way to a return to COVID-19 convalescent plasma (CCP) therapy. In this systematic review we performed a metanalysis of 9 controlled studies (totaling 535 treated patients and 1365 controls and including 4 randomized controlled trials), an individual patient data analysis of 125 case reports/series (totaling 265 patients), and a descriptive analysis of 13 uncontrolled large case series without individual patient data available (totaling 358 patients). The metanalysis of controlled studies showed a risk ratio for mortality of 0.65 (risk difference -0.11) in treatment with CCP versus standard of care for immunosuppressed COVID-19 patients. On the basis of this evidence, we encourage initiation of high-titer CCP from vaccinees( hybrid plasma) in immunocompromised patients.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Jonathon Senefeld",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Massimo Franchini",
+        "author_inst": "Carlo Poma Hospital, Mantua, Italy"
+      },
+      {
+        "author_name": "Carlo Mengoli",
+        "author_inst": "Carlo Poma Hospital, Mantua, Italy"
+      },
+      {
+        "author_name": "Mario Cruciani",
+        "author_inst": "Carlo Poma Hospital, Mantua, Italy"
+      },
+      {
+        "author_name": "Matteo Zani",
+        "author_inst": "Carlo Poma Hospital, Mantua, Italy"
+      },
+      {
+        "author_name": "Ellen K Gorman",
+        "author_inst": "Mayo Clinic, Rochester, USA"
+      },
+      {
+        "author_name": "Daniele Focosi",
+        "author_inst": "Pisa University Hospital"
+      },
+      {
+        "author_name": "Arturo Casadevall",
+        "author_inst": "Johns Hopkins School of Public Health"
+      },
+      {
+        "author_name": "Michael J Joyner",
+        "author_inst": "Mayo Clinic, Rochester, USA"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.08.02.22278342",
     "rel_title": "Cellular and humoral immunity towards parental SARS-CoV-2 and variants of concern after two doses of the NVX-CoV2373-vaccine in comparison to homologous BNT162b and mRNA1273 regimens",
@@ -229493,85 +228435,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2022.08.02.502427",
-    "rel_title": "UVC-based air disinfection system for rapid inactivation of SARS-CoV-2 present in the air",
-    "rel_date": "2022-08-02",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.02.502427",
-    "rel_abs": "The novel coronavirus disease 2019 (COVID-19) infections have rapidly spread throughout the world, and the virus has acquired an ability to spread via aerosols even at long distances. Hand washing, face-masking, and social distancing are the primary preventive measures against infections. With mounting scientific evidence, World Health Organisation (WHO) declared COVID-19 an air-borne disease. This ensued the need to disinfect air to reduce the transmission. Ultraviolet C (UVC) comprising the light radiation of 200-280 nm range is a commonly used method for inactivation of pathogens. The heating, ventilation, and air conditioning (HVAC) systems are not beneficial in closed spaces due to poor or no ability to damage circulating viruses. Therefore, standard infection-prevention practices coupled with a strategy to reduce infectious viral load in air substantially might be helpful in reducing virus transmissibility. In this study, we implemented UV light-based strategies to combat COVID-19 and future pandemics. We tested various disinfection protocols by using UVC-based air purification systems and currently installed such a system in workspaces, rushed out places, hospitals and healthcare facilities for surface, air, and water disinfection. In this study, we designed a prototype device to test the dose of UVC required to inactivate SARS-CoV-2 in aerosols and demonstrate that the radiation rapidly destroys the virus in aerosols. The UVC treatment renders the virus non-infectious due to chemical modification of nucleic acid. We also demonstrate that UVC treatment alters the Spike protein conformation that may further affect the infectivity of the virus. We show by using a mathematical model based on the experimental data that UVC-based air disinfection strategy can substantially reduce the risk of virus transmission. The systematic treatment by UVC of air in the closed spaces via ventilation systems could be helpful in reducing the active viral load in the air.",
-    "rel_num_authors": 16,
-    "rel_authors": [
-      {
-        "author_name": "Harry Garg",
-        "author_inst": "CSIR-Central Scientific Instruments Organisation"
-      },
-      {
-        "author_name": "Rajesh P Ringe",
-        "author_inst": "CSIR-Institute of Microbial technology"
-      },
-      {
-        "author_name": "Supankar Das",
-        "author_inst": "CSIR-Central Scientific Instruments Organisation"
-      },
-      {
-        "author_name": "Suraj Parkash",
-        "author_inst": "CSIR-Central Scientific Instruments Organisation"
-      },
-      {
-        "author_name": "Bhuwaneshwar Thakur",
-        "author_inst": "CSIR-Institute of Microbial Technology"
-      },
-      {
-        "author_name": "Rathina Delipan",
-        "author_inst": "CSIR-Institute of Microbial Technology"
-      },
-      {
-        "author_name": "Ajay Kumar",
-        "author_inst": "CSIR-Central Scientific Instruments Organisation"
-      },
-      {
-        "author_name": "Kishor S Kulkarni",
-        "author_inst": "CSIR-Central Scientific Instruments Organisation"
-      },
-      {
-        "author_name": "Kanika Bansal",
-        "author_inst": "CSIR-Institute of Microbial Technology"
-      },
-      {
-        "author_name": "Prabhu B Patil",
-        "author_inst": "CSIR-Institute of Microbial Technology"
-      },
-      {
-        "author_name": "Tabish Alam",
-        "author_inst": "CSIR-Central Building Research Institute"
-      },
-      {
-        "author_name": "Nagesh Babu Balam",
-        "author_inst": "CSIR-Central Building Research Institute"
-      },
-      {
-        "author_name": "Chandan Swaroop Meena",
-        "author_inst": "CSIR-Central Building Research Institute"
-      },
-      {
-        "author_name": "Krishan Gopal Thakur",
-        "author_inst": "CSIR-Institute of Microbial Technology"
-      },
-      {
-        "author_name": "Ashok Kumar",
-        "author_inst": "CSIR-Central Building Research Institute"
-      },
-      {
-        "author_name": "Ashwani Kumar",
-        "author_inst": "CSIR-Institute of Microbial Technology"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2022.08.02.502186",
     "rel_title": "DNA Origami Presenting the Receptor Binding Domain of SARS-CoV-2 Elicit Robust Protective Immune Response",
@@ -229866,6 +228729,65 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2022.07.29.502014",
+    "rel_title": "Coronaviruses using different strategies to antagonize antiviral responses and pyroptosis",
+    "rel_date": "2022-08-01",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.29.502014",
+    "rel_abs": "Viral infection triggers inflammasome-mediated caspase-1 activation. However, less is known about how viruses use the active caspase-1 to evade host immune response. Here, we use porcine epidemic diarrhea virus (PEDV) as a model of coronaviruses (CoVs) to illustrate the sophisticated regulation of CoVs to counteract IFN-I signaling and pyroptosis. We show that PEDV infection stabilizes caspase-1 expression via papain-like protease PLP2s deubiquitinase activity and the enhanced stabilization of caspase-1 disrupts IFN-I signaling by cleaving RIG-I at D189 residue. Meanwhile, PLP2 can degrade GSDMD-p30 by removing its K27-linked ubiquitin chain at K275 to restrain pyroptosis. Papain-like proteases from other genera of CoVs (PDCoV and SARS-CoV-2) have the similar activity to degrade GSDMD-p30. We further demonstrate that SARS-CoV-2 N protein induced NLRP3 inflammasome activation also uses the active caspase-1 to counter IFN-I signaling by cleaving RIG-I. Therefore, our work unravels a novel antagonistic mechanism employed by CoVs to evade host antiviral response.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Xinyu Fu",
+        "author_inst": "Zhejiang University"
+      },
+      {
+        "author_name": "Yang Yang",
+        "author_inst": "Zhejiang A&F University"
+      },
+      {
+        "author_name": "Weilv Xu",
+        "author_inst": "Zhejiang University"
+      },
+      {
+        "author_name": "Danyue Li",
+        "author_inst": "Zhejiang University"
+      },
+      {
+        "author_name": "Xinyue Li",
+        "author_inst": "Zhejiang University"
+      },
+      {
+        "author_name": "Nan Chen",
+        "author_inst": "Zhejiang University"
+      },
+      {
+        "author_name": "Qian Lv",
+        "author_inst": "Zhejiang University"
+      },
+      {
+        "author_name": "Yuhua Shi",
+        "author_inst": "Zhejiang University"
+      },
+      {
+        "author_name": "Xiaoliang Li",
+        "author_inst": "Zhejiang University"
+      },
+      {
+        "author_name": "Jidong Xu",
+        "author_inst": "Zhejiang University"
+      },
+      {
+        "author_name": "Fushan Shi",
+        "author_inst": "Zhejiang University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2022.08.01.502275",
     "rel_title": "SARS-CoV-2 ORF8 is a viral cytokine regulating immune responses",
@@ -231251,29 +230173,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2022.07.27.22278107",
-    "rel_title": "Psychological impacts of COVID-19 outbreak in Ethiopia: a systematic review and meta-analysis",
-    "rel_date": "2022-07-29",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.27.22278107",
-    "rel_abs": "BackgroundThe novel coronavirus disease has led individuals in several medical, psychosocial and economic impacts among the majority of the society such as psychological distress, anxiety, depression, denial, panic, and fear. This pandemic is a disastrous health crisis and becoming a current public health emergency and affects several nations across the world. The widespread of COVID-19 has brought not only the risk of death but also major psychological pressure.\n\nThe COVID-19 pandemic led individuals to unavoidable psychological distress, anxiety, depression, denial, panic, and fear. The COVID-19 pandemic is a global public health emergency concern, which is severely affected the community and influences the day-to-day life of individuals in Ethiopia. This systematic review used to investigate the pooled estimate on the psychological impact of COVID-19 in Ethiopia.\n\nObjectiveThe main aim of this systematic review and meta-analysis were to provide comprehensive evidence on the psychological impact of COVID-19 in Ethiopia.\n\nMethodsThis systematic review and meta-analysis searched through Pub Med, Cochrane Library, Google, Google Scholar, and web of sciences. Data extracted by Microsoft Excel then statistical analyses done using STATA Version 14 software with a random-effects model. The funnel plot checked. The heterogeneity of the studies checked. Subgroup analysis done in relation to the study area and authors names.\n\nResultsA total of 10 studies with 4,215 participants were included in this systematic review and the overall estimated psychological impact of coronavirus disease in Ethiopia was 42.50% (95% CI (31.18%, 53.81%). According to subgroup analysis, the highest estimated status of the psychological impact of coronavirus disease in Ethiopia are 66.40% and 16.20% in Addis Ababa and Amhara regions respectively.\n\nConclusionThis systematic review revealed that the psychological impact of coronavirus disease in Ethiopia is 42.50%. Multiple education and training and adequate personal protective equipment supplies focusing on the psychological impact of COVID-19 should be avail properly for the community in Ethiopia.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Tadele Lankrew",
-        "author_inst": "Wolaita Sodo University"
-      },
-      {
-        "author_name": "Belete Gelaw",
-        "author_inst": "Wolaita Sodo University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "psychiatry and clinical psychology"
-  },
   {
     "rel_doi": "10.1101/2022.07.29.502029",
     "rel_title": "A multispecific antibody confers pan-reactive SARS-CoV-2 neutralization and prevents immune escape",
@@ -231640,6 +230539,69 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.07.24.22277784",
+    "rel_title": "Efficacy of a patient isolation hood in reducing exposure to airborne infectious virus in a simulated healthcare setting",
+    "rel_date": "2022-07-29",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.24.22277784",
+    "rel_abs": "BackgroundHealthcare workers treating patients with SARS-CoV-2 are at risk of infection from patient-emitted virus-laden aerosols. We quantified the reduction of airborne infectious virus in a simulated hospital room when a ventilated patient isolation (McMonty) hood was in use.\n\nMethodsWe nebulised 109 plaque forming units (PFU) of bacteriophage PhiX174 virus into a 35.1m3 room with a hood active or inactive. The airborne concentration of infectious virus was measured by BioSpot-VIVAS and settle plates using plaque assay quantification on the bacterial host Escherichia coli C. The particle number concentration (PNC) was monitored continuously using an optical particle sizer.\n\nResultsMedian airborne viral concentration in the room reached 1.41 x 105 PFU.m-3 with the hood inactive. Using the active hood as source containment reduced infectious virus concentration by 374-fold in air samples. This was associated with a 109-fold reduction in total airborne particle number escape rate. The deposition of infectious virus on the surface of settle plates was reduced by 87-fold.\n\nConclusionsThe isolation hood significantly reduced airborne infectious virus exposure in a simulated hospital room. Our findings support the use of the hood to limit exposure of healthcare workers to airborne virus in clinical environments.\n\nLay summaryCOVID-19 patients exhale aerosol particles which can potentially carry infectious viruses into the hospital environment, putting healthcare workers at risk of infection. This risk can be reduced by proper use of personal protective equipment (PPE) to protect workers from virus exposure. More effective strategies, however, aim to provide source control, reducing the amount of virus-contaminated air that is exhaled into the hospital room.\n\nThe McMonty isolation hood has been developed to trap and decontaminate the air around an infected patient. We tested the efficacy of the hood using a live virus model to mimic a COVID-19 patient in a hospital room. Using the McMonty hood reduced the amount of exhaled air particles in the room by over 109-times. In our tests, people working in the room were exposed to 374-times less infectious virus in the air, and room surfaces were 87-times less contaminated. Our study supports using devices like the McMonty hood in combination with PPE to keep healthcare workers safe from virus exposure at work.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Leo Yi Yang Lee",
+        "author_inst": "The University of Melbourne"
+      },
+      {
+        "author_name": "Shane A Landry",
+        "author_inst": "Monash University"
+      },
+      {
+        "author_name": "Milan Jamriska",
+        "author_inst": "Defence Science and Technology Group"
+      },
+      {
+        "author_name": "Dinesh Subedi",
+        "author_inst": "Monash University"
+      },
+      {
+        "author_name": "Simon A Joosten",
+        "author_inst": "Monash University"
+      },
+      {
+        "author_name": "Jeremy J Barr",
+        "author_inst": "Monash University"
+      },
+      {
+        "author_name": "Reece Brown",
+        "author_inst": "Defence Science and Technology Group"
+      },
+      {
+        "author_name": "Kevin Kevin",
+        "author_inst": "The University of Melbourne"
+      },
+      {
+        "author_name": "Robyn Schofield",
+        "author_inst": "The University of Melbourne"
+      },
+      {
+        "author_name": "Jason Monty",
+        "author_inst": "The University of Melbourne"
+      },
+      {
+        "author_name": "Kanta Subbarao",
+        "author_inst": "WHO Collaborating Centre for Reference and Research on Influenza"
+      },
+      {
+        "author_name": "Forbes McGain",
+        "author_inst": "Western Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.07.27.22278117",
     "rel_title": "Projecting COVID-19 Cases and Subsequent Hospital Burden in Ohio",
@@ -233245,37 +232207,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2022.07.28.501901",
-    "rel_title": "Effect of Delta and Omicron mutations on the RBD-SD1 do-main of the Spike protein in SARS-CoV-2 and the Omicron mutations on RBD-ACE2 interface complex",
-    "rel_date": "2022-07-28",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.28.501901",
-    "rel_abs": "The receptor-binding domain (RBD) is the essential part in the Spike-protein (S-protein) of SARS-CoV-2 virus that directly binds to the human ACE2 receptor, making it a key target for many vaccines and therapies. Therefore, any mutations at this domain could affect the efficacy of these treatments as well as the viral-cell entry mechanism. We introduce ab initio DFT-based computational study that mainly focuses on two parts: (1) Mutations effects of both Delta and Omicron variants in the RBD-SD1 domain. (2) Impact of Omicron RBD mutations on the structure and properties of the RBD-ACE2 interface system. The in-depth analysis is based on the novel concept of amino acid-amino acid bond pair units (AABPU) that reveal the differences between the Delta and/or Omicron mutations and its corresponding wild-type strain in terms of the role played by non-local amino acid interactions, their 3D shapes and sizes, as well as contribution to hydrogen bonding and partial charge distributions. Our results also show that the interaction of Omicron RBD with ACE2 significantly increased its bonding between amino acids at the interface providing information on the implications of penetration of S-protein into ACE2, and thus offering a possible explanation for its high infectivity. Our findings enable us to present in more conspicuous atomic level detail the effect of specific mutations that may help in predicting and/or mitigating the next variant of concern.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Wai-Yim Ching",
-        "author_inst": "University of Missouri-Kansas City"
-      },
-      {
-        "author_name": "Puja Adhikari",
-        "author_inst": "University of Missouri-Kanas City"
-      },
-      {
-        "author_name": "Bahaa Jawad",
-        "author_inst": "University of Missouri-Kansas City"
-      },
-      {
-        "author_name": "Rudolf Podgornik",
-        "author_inst": "University of Chinese Academy of Sciences"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "biochemistry"
-  },
   {
     "rel_doi": "10.1101/2022.07.27.22277642",
     "rel_title": "Large-scale web scraping for problem gambling research: a case study of COVID-19 lockdown effects in Germany",
@@ -233514,6 +232445,121 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "geriatric medicine"
   },
+  {
+    "rel_doi": "10.1101/2022.07.26.22278045",
+    "rel_title": "Effectiveness of the BNT162b2 vaccine against SARS-CoV-2 infection among children and adolescents in Qatar",
+    "rel_date": "2022-07-26",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.26.22278045",
+    "rel_abs": "BackgroundThe BNT162b2 COVID-19 vaccine is authorized for children 5-11 years of age and adolescents 12-17 years of age, but in different dose sizes. We assessed BNT162b2 real-world effectiveness against SARS-CoV-2 infection among children and adolescents in Qatar.\n\nMethodsThree matched, retrospective, target-trial, cohort studies were conducted to compare incidence of SARS-CoV-2 infection in the national cohort of vaccinated individuals to incidence in the national cohort of unvaccinated individuals. Associations were estimated using Cox proportional-hazards regression models.\n\nResultsEffectiveness of the 10 {micro}g dose for children against Omicron infection was 25.7% (95% CI: 10.0-38.6%). It was highest at 49.6% (95% CI: 28.5-64.5%) right after the second dose, but waned rapidly thereafter and was negligible after 3 months. Effectiveness was 46.3% (95% CI: 21.5-63.3%) among those aged 5-7 years and 16.6% (-4.2-33.2%) among those aged 8-11 years. Effectiveness of the 30 {micro}g dose for adolescents against Omicron infection was 30.6% (95% CI: 26.9-34.1%), but many adolescents were vaccinated months earlier. Effectiveness waned with time after the second dose. Effectiveness was 35.6% (95% CI: 31.2-39.6%) among those aged 12-14 years and 20.9% (13.8-27.4%) among those aged 15-17 years. Effectiveness of the 30 {micro}g dose for adolescents against pre-Omicron infection was 87.6% (95% CI: 84.0-90.4%) and waned relatively slowly after the second dose.\n\nConclusionsPediatric vaccination is associated with modest and rapidly waning protection against Omicron infection. Adolescent vaccination is associated with stronger and more durable protection, perhaps because of the larger dose size. Age at such young age appears to play a role in determining vaccine protection, with greater protection observed in younger than older children or adolescents.",
+    "rel_num_authors": 25,
+    "rel_authors": [
+      {
+        "author_name": "Hiam Chemaitelly",
+        "author_inst": "Weill Cornell Medicine-Qatar"
+      },
+      {
+        "author_name": "Sawsan AlMukdad",
+        "author_inst": "Weill Cornell Medicine-Qatar"
+      },
+      {
+        "author_name": "Houssein Ayoub",
+        "author_inst": "Qatar University"
+      },
+      {
+        "author_name": "Heba N. Altarawneh",
+        "author_inst": "Weill Cornell Medicine-Qatar"
+      },
+      {
+        "author_name": "Peter Coyle",
+        "author_inst": "Hamad Medical Corporation"
+      },
+      {
+        "author_name": "Patrick Tang",
+        "author_inst": "Sidra Medicine"
+      },
+      {
+        "author_name": "HADI M. YASSINE",
+        "author_inst": "Qatar University"
+      },
+      {
+        "author_name": "Hebah A. Al-Khatib",
+        "author_inst": "Qatar University"
+      },
+      {
+        "author_name": "Maria K. Smatti",
+        "author_inst": "Qatar University"
+      },
+      {
+        "author_name": "Mohammad R. Hasan",
+        "author_inst": "Sidra Medicine"
+      },
+      {
+        "author_name": "Zaina Al-Kanaani",
+        "author_inst": "Hamad Medical Corporation"
+      },
+      {
+        "author_name": "Einas Al-Kuwari",
+        "author_inst": "Hamad Medical Corporation"
+      },
+      {
+        "author_name": "Andrew Jeremijenko",
+        "author_inst": "Hamad Medical Corporation"
+      },
+      {
+        "author_name": "Anvar Hassan Kaleeckal",
+        "author_inst": "Hamad Medical Corporation"
+      },
+      {
+        "author_name": "Ali Nizar Latif",
+        "author_inst": "Hamad Medical Corporation"
+      },
+      {
+        "author_name": "Riyazuddin Mohammad Shaik",
+        "author_inst": "Hamad Medical Corporation"
+      },
+      {
+        "author_name": "Hanan F. Abdul-Rahim",
+        "author_inst": "Qatar University"
+      },
+      {
+        "author_name": "Gheyath Nasrallah",
+        "author_inst": "Qatar University"
+      },
+      {
+        "author_name": "Mohamed Ghaith Al-Kuwari",
+        "author_inst": "Primary Health Care Corporation"
+      },
+      {
+        "author_name": "Hamad  E. Al-Romaihi",
+        "author_inst": "MoPH: Ministry of Public Health Qatar"
+      },
+      {
+        "author_name": "Adeel A Butt",
+        "author_inst": "Hamad Medical Corporation"
+      },
+      {
+        "author_name": "Mohamed H. Al-Thani",
+        "author_inst": "MoPH: Ministry of Public Health Qatar"
+      },
+      {
+        "author_name": "Abdullatif Al-Khal",
+        "author_inst": "Hamad Medical Corporation"
+      },
+      {
+        "author_name": "Roberto Bertollini",
+        "author_inst": "Ministry of Public Health"
+      },
+      {
+        "author_name": "Laith J Abu-Raddad",
+        "author_inst": "Weill Cornell Medicine-Qatar"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2022.07.26.501570",
     "rel_title": "Primary Omicron infection elicits weak antibody response but robust cellularimmunity in children",
@@ -234803,45 +233849,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2022.07.25.501370",
-    "rel_title": "Poor sensitivity of iPSC-derived neural progenitors and glutamatergic neurons to SARS-CoV-2",
-    "rel_date": "2022-07-25",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.25.501370",
-    "rel_abs": "COVID-19 is a respiratory disease affecting multiple organs including the central nervous system (CNS), with a characteristic loss of smell and taste. Although frequently reported, the neurological symptoms remain enigmatic. There is no consensus on the extent of CNS infection. Here, we derived human induced pluripotent stem cells (hiPSC) into neural progenitor cells (NPCs) and cortical excitatory neurons to study their permissiveness to SARS-CoV-2 infection. Flow cytometry and western blot analysis indicated that NPCs and neurons do not express detectable levels of the SARS-CoV-2 receptor ACE2. We thus generated cells expressing ACE2 by lentiviral transduction to analyze in a controlled manner the properties of SARS-CoV-2 infection relative to ACE2 expression. Sensitivity of parental and ACE2 expressing cells was assessed with GFP- or luciferase-carrying pseudoviruses and with authentic SARS-CoV-2 Wuhan, D614G, Alpha or Delta variants. SARS-CoV-2 replication was assessed by microscopy, RT-qPCR and infectivity assays. Pseudoviruses infected only cells overexpressing ACE2. Neurons and NPCs were unable to efficiently replicate SARS-CoV-2, whereas ACE2 overexpressing neurons were highly sensitive to productive infection. Altogether, our results indicate that primary NPCs and cortical neurons remain poorly permissive to SARS-CoV-2 across the variants spectrum, in the absence of ACE2 expression.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Marija Zivaljic",
-        "author_inst": "Institut Pasteur"
-      },
-      {
-        "author_name": "Mathieu Hubert",
-        "author_inst": "Pasteur Institute"
-      },
-      {
-        "author_name": "Ludivine Grzelak",
-        "author_inst": "Institut Pasteur"
-      },
-      {
-        "author_name": "Giulia Sansone",
-        "author_inst": "Pasteur Institute"
-      },
-      {
-        "author_name": "Uwe Maskos",
-        "author_inst": "Institut Pasteur"
-      },
-      {
-        "author_name": "Olivier Schwartz",
-        "author_inst": "Institut Pasteur"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "neuroscience"
-  },
   {
     "rel_doi": "10.1101/2022.07.22.501163",
     "rel_title": "Waning and boosting of functional humoral immunity to SARS-CoV-2",
@@ -235264,6 +234271,129 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2022.07.22.22277947",
+    "rel_title": "High titre neutralizing antibodies in response to SARS-CoV-2 infection require RBD-specific CD4 T cells that include proliferative memory cells.",
+    "rel_date": "2022-07-24",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.22.22277947",
+    "rel_abs": "Long-term immunity to SARS-CoV-2 infection, including neutralizing antibodies and T cell-mediated immunity, is required in a very large majority of the population in order to reduce ongoing disease burden. We have investigated the association between memory CD4 and CD8 T cells and levels of neutralizing antibodies in convalescent COVID-19 subjects. Higher titres of convalescent neutralizing antibodies were associated with significantly higher levels of RBD-specific CD4 T cells, including specific memory cells that proliferated vigorously in vitro. Conversely, up to half of convalescent individuals had low neutralizing antibody titres together with a lack of receptor binding domain (RBD)- specific memory CD4 T cells. These low antibody subjects had other, non-RBD, spike-specific CD4 T cells, but with more of an inhibitory Foxp3+ and CTLA-4+ cell phenotype, rather than the effector T- bet+, cytotoxic granzymes+ and perforin+ cells seen in high antibody subjects. Single cell transcriptomics of antigen-specific CD4+ T cells from high antibody subjects revealed heterogenous RBD-specific CD4+ T cells that comprised central memory, transitional memory and Tregs, as well as cytotoxic clusters containing diverse TCR repertoires, that were absent in individuals with low antibody levels. However, vaccination in low antibody convalescent individuals led to a slight but significant improvement in RBD-specific memory CD4 T cells and increased neutralizing antibody titres. Our results suggest that targeting CD4 T cell epitopes proximal to and within the RBD- region should be prioritized in booster vaccines.\n\nOne Sentence SummaryIndividuals with low neutralising antibody titres may be at risk of SARS-CoV-2 re-infection due to a failure to generate a high quality CD4 T cell response specific for receptor binding domain (RBD), including memory CD4 T cells that proliferate in vitro in response to RBD, and which are also therefore an important target for vaccine design.",
+    "rel_num_authors": 27,
+    "rel_authors": [
+      {
+        "author_name": "Chansavath Phetsouphanh",
+        "author_inst": "The Kirby Institute, University of New South Wales"
+      },
+      {
+        "author_name": "Weng Hua Khoo",
+        "author_inst": "Garvan Institute of Medical Research"
+      },
+      {
+        "author_name": "Katherine Jackson",
+        "author_inst": "Garvan Institute of Medical Research"
+      },
+      {
+        "author_name": "Vera Klemm",
+        "author_inst": "Kirby Institute, UNSW"
+      },
+      {
+        "author_name": "Annett Howe",
+        "author_inst": "Kirby Institute, UNSW"
+      },
+      {
+        "author_name": "Anupriya Aggarwal",
+        "author_inst": "Kirby Institute, UNSW"
+      },
+      {
+        "author_name": "Anouschka Akerman",
+        "author_inst": "Kirby Institute, UNSW"
+      },
+      {
+        "author_name": "Vanessa Milogiannakis",
+        "author_inst": "Kirby Institute, UNSW"
+      },
+      {
+        "author_name": "Alberto Ospina Stella",
+        "author_inst": "Kirby Institute, UNSW"
+      },
+      {
+        "author_name": "Romain Rouet",
+        "author_inst": "Garvan Institute of Medical Research"
+      },
+      {
+        "author_name": "Peter Schofield",
+        "author_inst": "Garvan Institute of Medical Research"
+      },
+      {
+        "author_name": "Megan L. Faulks",
+        "author_inst": "Garvan Institute of Medical Research"
+      },
+      {
+        "author_name": "Hannah Law",
+        "author_inst": "Kirby Institute, UNSW"
+      },
+      {
+        "author_name": "Thidarat Danwilai",
+        "author_inst": "NSW State Reference Laboratory for HIV St Vincents Centre for Applied Medical Research"
+      },
+      {
+        "author_name": "Mitchell Starr",
+        "author_inst": "NSW State Reference Laboratory for HIV St Vincents Centre for Applied Medical Research"
+      },
+      {
+        "author_name": "C.Mee Ling Munier",
+        "author_inst": "Kirby Institute, UNSW"
+      },
+      {
+        "author_name": "Daniel Christ",
+        "author_inst": "Garvan Institute of Medical Research"
+      },
+      {
+        "author_name": "Mandeep Singh",
+        "author_inst": "Garvan Institute of Medical Research"
+      },
+      {
+        "author_name": "Peter I Croucher",
+        "author_inst": "Garvan Institute of Medical Research"
+      },
+      {
+        "author_name": "Fabienne Brilot-Turville",
+        "author_inst": "Sydney Institute for Infectious Diseases The University of Sydney"
+      },
+      {
+        "author_name": "Stuart Turville",
+        "author_inst": "Kirby Institute, UNSW"
+      },
+      {
+        "author_name": "Tri Giang Phan",
+        "author_inst": "Garvan Institute of Medical Research"
+      },
+      {
+        "author_name": "Gregory J Dore",
+        "author_inst": "Kirby Institute, UNSW"
+      },
+      {
+        "author_name": "Philip Cunningham",
+        "author_inst": "NSW State Reference Laboratory for HIV, St Vincents Centre for Applied Medical Research"
+      },
+      {
+        "author_name": "Gail V Matthews",
+        "author_inst": "Kirby Institute, UNSW"
+      },
+      {
+        "author_name": "Anthony D Kelleher",
+        "author_inst": "Kirby Institute, UNSW"
+      },
+      {
+        "author_name": "John J Zaunders",
+        "author_inst": "St Vincent's Hospital"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.07.19.22277806",
     "rel_title": "Cervical cancer screening improvements with self- sampling during the COVID-19 pandemic",
@@ -236469,37 +235599,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2022.07.21.500931",
-    "rel_title": "Decoding the Effects of Spike Receptor Binding Domain Mutations on Antibody Escape Abilities of Omicron Variants",
-    "rel_date": "2022-07-22",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.21.500931",
-    "rel_abs": "Recent times witnessed an upsurge in the number of COVID cases which is primarily attributed to the emergence of several omicron variants, although there is substantial population vaccination coverage across the globe. Currently, many therapeutic antibodies have been approved for emergency usage. The present study critically evaluates the effect of mutations observed in several omicron variants on the binding affinities of different classes of RBD-specific antibodies using a combined approach of immunoinformatics and binding free energy calculations. Our binding affinity data clearly show that omicron variants achieve antibody escape abilities by incorporating mutations at the immunogenic hotspot residues for each specific class of antibody. K417N and Y505H point mutations are primarily accountable for the loss of class I antibody binding affinities. The K417N/Q493R/Q498R/Y505H combined mutant significantly reduces binding affinities for all the class I antibodies. E484A single mutation, on the other hand, drastically reduces binding affinities for most of the class II antibodies. E484A and E484A/Q493R double mutations cause a 33-38% reduction in binding affinity for the approved therapeutic monoclonal antibodies, Bamlanivimab (LY-CoV555). The Q498R RBD mutation observed across all the omicron variants can reduce ~12% binding affinity for REGN10987, a class III therapeutic antibody, and the L452R/Q498R double mutation causes a ~6% decrease in binding affinities for another class III therapeutic antibody, LY-CoV1404. Our data suggest that achieving the immune evasion abilities appears to be the selection pressure behind the emergence of omicron variants.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Aditi Saha",
-        "author_inst": "Amity University, Kolkata"
-      },
-      {
-        "author_name": "Chiranjeet Saha",
-        "author_inst": "Amity University, Kolkata"
-      },
-      {
-        "author_name": "Sanjana Ghosh",
-        "author_inst": "Amity University, Kolkata"
-      },
-      {
-        "author_name": "Trisha Mondal",
-        "author_inst": "Amity University, Kolkata"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "bioinformatics"
-  },
   {
     "rel_doi": "10.1101/2022.07.21.22277831",
     "rel_title": "COVID-19 vaccine effectiveness against mortality and risk of death from other causes after COVID-19 vaccination, the Netherlands, January 2021- January 2022",
@@ -236874,6 +235973,85 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.07.20.22277838",
+    "rel_title": "National and regional prevalence of SARS-CoV-2 antibodies in primary and secondary school children in England: the School Infection Survey, a national open cohort study, November 2021",
+    "rel_date": "2022-07-21",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.20.22277838",
+    "rel_abs": "BackgroundRisk factors for infection and, therefore, antibody positivity rates will be different in children compared to adults. We aim to estimate national and regional prevalence of SARS-CoV-2 antibodies in primary (4-11-year-olds) and secondary (11-15-year-olds) school children between 10 November and 10 December 2021.\n\nMethodsCross-sectional surveillance in England using two stage sampling, firstly stratifying into regions and selecting local authorities, then selecting schools according to a stratified sample within selected local authorities. Participants were sampled using a novel oral fluid validated assay for SARS-CoV-2 spike and nucleocapsid IgG antibodies.\n\nResults4,980 students from 117 state-funded schools (2,706 from 83 primary schools, 2,274 from 34 secondary schools) provided a valid sample. After weighting for age, sex and ethnicity, and adjusting for assay accuracy, the national prevalence of SARS-CoV-2 antibodies in primary school students, who were all unvaccinated, was 40.1% (95%CI; 37.3-43.0). Antibody prevalence increased with age (p<0.001) and were higher in urban than rural schools (p=0.01). In secondary school students, the adjusted, weighted national prevalence of SARS-CoV-2 antibodies was 82.4% (95%CI; 79.5-85.1); including 57.5% (95%CI; 53.9-61.1) in unvaccinated and 97.5% (95%CI; 96.1-98.5) in vaccinated students. Antibody prevalence increased with age (p<0.001), and was not significantly different in urban versus rural students (p=0.1).\n\nConclusionsUsing a validated oral fluid assay, we estimated national and regional seroprevalence of SARS-CoV-2 antibodies in primary and secondary school students. In November 2021, 40% of primary school students and nearly all secondary school students in England had SARS-CoV2 antibodies through a combination of natural infection and vaccination.",
+    "rel_num_authors": 16,
+    "rel_authors": [
+      {
+        "author_name": "Annabel A Powell",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Georgina Ireland",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Rebecca Leeson",
+        "author_inst": "Office for National Statistics"
+      },
+      {
+        "author_name": "Andrea Lacey",
+        "author_inst": "Office for National Statistics"
+      },
+      {
+        "author_name": "Ben Ford",
+        "author_inst": "Office for National Statistics"
+      },
+      {
+        "author_name": "John Poh",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Samreen Ijaz",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Justin Shute",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Peter Cherepanov",
+        "author_inst": "Imperial College London"
+      },
+      {
+        "author_name": "Richard Tedder",
+        "author_inst": "Francis Crick Institute"
+      },
+      {
+        "author_name": "Christian Bottomley",
+        "author_inst": "London School of Hygiene & Tropical Medicine"
+      },
+      {
+        "author_name": "Fiona Dawe",
+        "author_inst": "Office for National Statistics"
+      },
+      {
+        "author_name": "Punam Mangtani",
+        "author_inst": "London School of Hygiene & Tropical Medicine"
+      },
+      {
+        "author_name": "Peter Jones",
+        "author_inst": "Office for National Statistics"
+      },
+      {
+        "author_name": "Patrick Nguipdop-Djomo",
+        "author_inst": "London School of Hygiene & Tropical Medicine"
+      },
+      {
+        "author_name": "Shamez Ladhani",
+        "author_inst": "UK Health Security Agency"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2022.07.20.22277872",
     "rel_title": "Geographic and Temporal Patterns in Covid-19 Mortality by Race and Ethnicity in the United States from March 2020 to February 2022",
@@ -238219,137 +237397,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2022.07.18.500332",
-    "rel_title": "Neutralizing antibody evasion and receptor binding features of SARS-CoV-2 Omicron BA.2.75",
-    "rel_date": "2022-07-19",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.18.500332",
-    "rel_abs": "Recently emerged SARS-CoV-2 Omicron subvariant, BA.2.75, displayed a local growth advantage over BA.2.38, BA.2.76 and BA.5 in India. The underlying mechanism of BA.2.75s enhanced infectivity, especially compared to BA.5, remains unclear. Here, we show that BA.2.75 exhibits substantially higher ACE2-binding affinity than BA.5. Also, BA.2.75 spike shows decreased thermostability and increased \"up\" RBD conformation in acidic conditions, suggesting enhanced low-pH-endosomal cell-entry pathway utilization. BA.2.75 is less humoral immune evasive than BA.4/BA.5 in BA.1/BA.2 breakthrough-infection convalescents; however, BA.2.75 shows heavier neutralization evasion in Delta breakthrough-infection convalescents. Importantly, plasma from BA.5 breakthrough infection exhibit significantly weaker neutralization against BA.2.75 than BA.5, mainly due to BA.2.75s distinct RBD and NTD-targeting antibody escaping pattern from BA.4/BA.5. Additionally, Evusheld and Bebtelovimab remain effective against BA.2.75, and Sotrovimab recovered RBD-binding affinity. Together, our results suggest BA.2.75 may prevail after the global BA.4/BA.5 wave, and its increased receptor-binding capability could allow further incorporation of immune-evasive mutations.",
-    "rel_num_authors": 29,
-    "rel_authors": [
-      {
-        "author_name": "Yunlong Cao",
-        "author_inst": "Peking University"
-      },
-      {
-        "author_name": "Weiliang Song",
-        "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University"
-      },
-      {
-        "author_name": "Lei Wang",
-        "author_inst": "Chinese Academy of Sciences"
-      },
-      {
-        "author_name": "Pan Liu",
-        "author_inst": "Chinese Academy of Sciences"
-      },
-      {
-        "author_name": "Can Yue",
-        "author_inst": "University of Chinese Academy of Science"
-      },
-      {
-        "author_name": "Fanchong Jian",
-        "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University"
-      },
-      {
-        "author_name": "Yuanling Yu",
-        "author_inst": "Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC)"
-      },
-      {
-        "author_name": "Ayijiang Yisimayi",
-        "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University"
-      },
-      {
-        "author_name": "Peng Wang",
-        "author_inst": "Changping Laboratory, Beijing, P.R. China."
-      },
-      {
-        "author_name": "Yao Wang",
-        "author_inst": "Changping Laboratory, Beijing, P.R. China."
-      },
-      {
-        "author_name": "Qianhui Zhu",
-        "author_inst": "Chinese Academy of Sciences"
-      },
-      {
-        "author_name": "Jie Deng",
-        "author_inst": "Chinese Academy of Sciences"
-      },
-      {
-        "author_name": "Wangjun Fu",
-        "author_inst": "Chinese Academy of Sciences"
-      },
-      {
-        "author_name": "Lingling Yu",
-        "author_inst": "Changping Laboratory, Beijing, P.R. China."
-      },
-      {
-        "author_name": "Na Zhang",
-        "author_inst": "Changping Laboratory, Beijing, P.R. China."
-      },
-      {
-        "author_name": "Jing Wang",
-        "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University"
-      },
-      {
-        "author_name": "Tianhe Xiao",
-        "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P."
-      },
-      {
-        "author_name": "Ran An",
-        "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China."
-      },
-      {
-        "author_name": "Jing Wang",
-        "author_inst": "Changping Laboratory, Beijing, P.R. China."
-      },
-      {
-        "author_name": "Lu Liu",
-        "author_inst": "Changping Laboratory, Beijing, P.R. China."
-      },
-      {
-        "author_name": "Sijie Yang",
-        "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China."
-      },
-      {
-        "author_name": "Xiao Niu",
-        "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China."
-      },
-      {
-        "author_name": "Qingqing Gu",
-        "author_inst": "Changping Laboratory, Beijing, P.R. China."
-      },
-      {
-        "author_name": "Fei Shao",
-        "author_inst": "Changping Laboratory, Beijing, P.R. China."
-      },
-      {
-        "author_name": "Xiaohua Hao",
-        "author_inst": "Beijing Ditan Hospital, Capital Medical University, Beijing, P.R. China."
-      },
-      {
-        "author_name": "Ronghua Jin",
-        "author_inst": "Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China"
-      },
-      {
-        "author_name": "Youchun Wang",
-        "author_inst": "Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO"
-      },
-      {
-        "author_name": "Xiaoliang Sunney Xie",
-        "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University"
-      },
-      {
-        "author_name": "Xiangxi Wang",
-        "author_inst": "CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, P.R. China."
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2022.07.19.500662",
     "rel_title": "Persistence of SARS-CoV-2 neutralizing antibodies longer than 13 months in naturally-infected, captive white-tailed deer (Odocoileus virginianus), Texas",
@@ -238604,6 +237651,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2022.07.16.22277716",
+    "rel_title": "The association of typical and atypical symptoms on in-hospital mortality of older adults with COVID-19: a multicentre cohort study",
+    "rel_date": "2022-07-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.16.22277716",
+    "rel_abs": "Atypical disease presentations are common in older adults with COVID-19. The objective of this study was to determine the prevalence of atypical and typical symptoms in older adults with COVID-19 through progressive pandemic waves and the association of these symptoms with in-hospital mortality. This retrospective cohort study included consecutive adults aged over 65 years with confirmed COVID-19 infection who were admitted to seven hospitals in Toronto, Canada from March 1, 2020 to June 30, 2021. The median age for the 1786 patients was 78.0 years and 847 (47.5%) were female. Atypical symptoms (as defined by geriatric syndromes) occurred in 1187 patients (66.5%), but rarely occurred in the absence of other symptoms (n=106, 6.2%). The most common atypical symptoms were anorexia (n=598, 33.5%), weakness (n=519, 23.9%), and delirium (n=449, 25.1%). Dyspnea (adjusted odds ratio [aOR] 2.05, 95% confidence interval [CI] 1.62-2.62), tachycardia (aOR 1.87, 95% CI 1.14-3.04), and delirium (aOR 1.52, 95% CI 1.18-1.96) were independently associated with in-hospital mortality. In a cohort of older adults hospitalized with COVID-19 infection, atypical presentations frequently overlapped with typical symptoms. Further research should be directed at understanding the cause and clinical significance of atypical presentations in older adults.",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Eric Kai-Chung Wong",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Jennifer Watt",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Hanyan Zou",
+        "author_inst": "Sinai Health and University Health Network"
+      },
+      {
+        "author_name": "Arthana Chandraraj",
+        "author_inst": "Li Ka Shing Knowledge Institute"
+      },
+      {
+        "author_name": "Alissa Wenyue Zhang",
+        "author_inst": "Sunnybrook Health Sciences Centre"
+      },
+      {
+        "author_name": "Jahnel Brookes",
+        "author_inst": "Baycrest Health Sciences Centre"
+      },
+      {
+        "author_name": "Ashley Verduyn",
+        "author_inst": "Providence Healthcare and Houses of Providence"
+      },
+      {
+        "author_name": "Anna Berall",
+        "author_inst": "Baycrest Health Sciences Centre"
+      },
+      {
+        "author_name": "Richard Norman",
+        "author_inst": "Sinai Health and University Health Network"
+      },
+      {
+        "author_name": "Katrina Lynn Piggott",
+        "author_inst": "Sunnybrook Health Sciences Centre"
+      },
+      {
+        "author_name": "Terumi Izukawa",
+        "author_inst": "Baycrest Health Sciences Centre"
+      },
+      {
+        "author_name": "Sharon E Straus",
+        "author_inst": "Unity Health Toronto"
+      },
+      {
+        "author_name": "Barbara Liu",
+        "author_inst": "Sunnybrook Health Sciences Centre"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "geriatric medicine"
+  },
   {
     "rel_doi": "10.1101/2022.07.18.22277744",
     "rel_title": "A pilot surveillance report of SARS-CoV-2 rapid antigen test results among volunteers in Germany, 1st week of July 2022",
@@ -239953,129 +239067,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2022.07.15.22277665",
-    "rel_title": "Differential symptoms among COVID-19 outpatients before and during periods of SARS-CoV-2 Omicron variant dominance in Blantyre, Malawi: a prospective observational study",
-    "rel_date": "2022-07-17",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.15.22277665",
-    "rel_abs": "BackgroundIt is widely reported that the SARS-CoV-2 Omicron variant has resulted in high number of cases, but relatively low incidence of severe disease and deaths, compared to the pre-Omicron variants of concern. We aim to assess the differences in symptom prevalence between Omicron and pre-Omicron infections in a sub-Saharan African population.\n\nMethodsIn this cross-sectional observational study, we collected data from children and adult outpatients presenting at two primary healthcare facilities in Blantyre, Malawi. Eligible participants were aged >1month old, with signs suggestive of COVID-19, and those not suspected of COVID-19. Nasopharyngeal swabs were collected for SARS-CoV-2 PCR testing and positive samples whole genome sequenced to identify the infecting variant. The primary outcome was the likelihood of presenting with a given symptom in individuals testing positive during the period in which Omicron-dominated (December 2021 to March 2022) with those infected during the pre-Omicron period (August 2021 to November 2021).\n\nFindingsAmong 5176 study participants, the median age was 28 years (IQR 21-38), of which 6.4% were under 5, 9.2% were 6 to 17 years, 77% were 18 to 50 years, and 7.1% were above 50 years old. Prevalence of SARS-CoV-2 infection was 23% (1187/5188), varying over time, with peaks in January 2021, July 2021 and December 2021, driven by the Beta (B.1.351), Delta (B.1.617.2) and Omicron (BA.1/2) variants, respectively. Headache (OR 0.47[CI 0.29 - 0.79]), cough (OR 0.37[CI 0.22 - 0.61]), fatigue (OR 0.20[CI 0.08 - 0.48]) and abdominal pain (OR 0.38[CI 0.18 - 0.78]) were less common in participants infected during the Omicron-dominant period than during pre-Omicron period. Fever was more common in participants infected during the Omicron-dominated period than during pre-Omicron period (OR 2.46[CI 1.29 - 4.97]). COVID-19 vaccination, accounting for number of doses and days since last dose, was not associated with a reduced risk of PCR-confirmed SARS-CoV-2 infection (1 dose, OR 1.10[CI 0.39 - 2.66]; 2 doses, OR 1.11[CI 0.40 - 2.57]; all p=0.8).\n\nInterpretationIn this Malawian population, the prevalence of clinical symptoms associated with Omicron infection differ from those of pre-Omicron infections and may be harder to identify clinically with current symptom guidelines. To maintain robust surveillance for COVID-19 and emerging variants, case definitions and testing policies will need to be regularly reviewed to ensure case ascertainment.",
-    "rel_num_authors": 27,
-    "rel_authors": [
-      {
-        "author_name": "Marah Grace Chibwana",
-        "author_inst": "Malawi-Liverpool-Wellcome Programme"
-      },
-      {
-        "author_name": "Herbert W Thole",
-        "author_inst": "Malawi-Liverpool-Wellcome Programme"
-      },
-      {
-        "author_name": "Cat Anscombe",
-        "author_inst": "Malawi-Liverpool-Wellcome Programme"
-      },
-      {
-        "author_name": "Phillip M Ashton",
-        "author_inst": "Malawi-Liverpool-Wellcome Programme"
-      },
-      {
-        "author_name": "Edward Green",
-        "author_inst": "Liverpool School of Tropical Medicine"
-      },
-      {
-        "author_name": "Kayla G Barnes",
-        "author_inst": "Malawi-Liverpool-Wellcome Programme"
-      },
-      {
-        "author_name": "Jen Cornick",
-        "author_inst": "Malawi-Liverpool-Wellcome Programme"
-      },
-      {
-        "author_name": "Ann Turner",
-        "author_inst": "University of Liverpool"
-      },
-      {
-        "author_name": "Desiree Witte",
-        "author_inst": "Malawi-Liverpool-Wellcome Programme"
-      },
-      {
-        "author_name": "Sharon Nthala",
-        "author_inst": "Malawi-Liverpool-Wellcome Programme"
-      },
-      {
-        "author_name": "Chikondi Thom",
-        "author_inst": "Malawi-Liverpool-Wellcome Programme"
-      },
-      {
-        "author_name": "Felistas Kanyandula",
-        "author_inst": "Malawi-Liverpool-Wellcome Programme"
-      },
-      {
-        "author_name": "Anna Ainani",
-        "author_inst": "Malawi-Liverpool-Wellcome Programme"
-      },
-      {
-        "author_name": "Natasha Mtike",
-        "author_inst": "Malawi-Liverpool-Wellcome Programme"
-      },
-      {
-        "author_name": "Hope Tambala",
-        "author_inst": "Blantyre District Health Office"
-      },
-      {
-        "author_name": "Veronica N'goma",
-        "author_inst": "Blantyre District Health Office"
-      },
-      {
-        "author_name": "Dorah Mwafulirwa",
-        "author_inst": "Blantyre District Health Office"
-      },
-      {
-        "author_name": "Erick Asima",
-        "author_inst": "Blantyre District Health Office"
-      },
-      {
-        "author_name": "Ben Morton",
-        "author_inst": "Liverpool School of Tropical Medicine"
-      },
-      {
-        "author_name": "Markus Gmeiner",
-        "author_inst": "Malawi-Liverpool-Wellcome Programme"
-      },
-      {
-        "author_name": "Zaziwe Gundah",
-        "author_inst": "Blantyre District Health Office"
-      },
-      {
-        "author_name": "Gift Kawalazira",
-        "author_inst": "Blantyre District Health Office"
-      },
-      {
-        "author_name": "Neil French",
-        "author_inst": "University of Liverpool"
-      },
-      {
-        "author_name": "Nicholas Feasey",
-        "author_inst": "Malawi-Liverpool-Wellcome Programme"
-      },
-      {
-        "author_name": "Robert S Heyderman",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Todd D Swarthout",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Kondwani Charles Jambo",
-        "author_inst": "Malawi-Liverpool-Wellcome Programme"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.07.17.500346",
     "rel_title": "Identification of novel antiviral drug candidates using an optimized SARS-CoV-2 phenotypic screening platform",
@@ -240562,6 +239553,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.07.12.22277518",
+    "rel_title": "Tracing the international arrivals of SARS-CoV-2 Omicron variants after Aotearoa New Zealand reopened its border",
+    "rel_date": "2022-07-15",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.12.22277518",
+    "rel_abs": "Recently there has been a surge in emergent SARS-CoV-2 lineages that are able to evade both vaccine induced immunity as well as prior infection from the founding Omicron BA.1 and BA.2 lineages. These highly transmissible and evasive lineages are on the rise and include Omicron variants BA.2.12.1, BA.4, and BA.5. Aotearoa New Zealand recently reopened its borders to many travellers, without their need to enter quarantine. By generating 10,403 complete SARS-CoV-2 genomes classified as Omicron, we show that New Zealand is observing an influx of these immune-evasive variants through the border. Specifically, there has been a recent surge of BA.5 and BA.2.12.1 introductions into the community and these can be explained by the gradual return to pre-pandemic levels of international traveller arrival rates. We estimate there is one Omicron transmission event from the border to the community for every [~]5,000 passenger arrivals into the country, or around one introduction event per day at the current levels of travel. Given the waning levels of population immunity, this rate of importation presents the risk of a large wave in New Zealand during the second half of 2022. Genomic surveillance, coupled with modelling the rate at which new variants cross the border into the community, provides a lens on the rate at which new variants might gain a foothold and trigger new waves of infection.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Jordan Douglas",
+        "author_inst": "University of Auckland"
+      },
+      {
+        "author_name": "David Winter",
+        "author_inst": "Institute of Environmental Science and Research"
+      },
+      {
+        "author_name": "Xiaoyun Ren",
+        "author_inst": "Institute of Environmental Science and Research"
+      },
+      {
+        "author_name": "Andrea McNeill",
+        "author_inst": "Institute of Environmental Science and Research"
+      },
+      {
+        "author_name": "Michael Bunce",
+        "author_inst": "Institute of Environmental Science and Research"
+      },
+      {
+        "author_name": "Nigel French",
+        "author_inst": "Massey University"
+      },
+      {
+        "author_name": "James Hadfield",
+        "author_inst": "Fred Hutchinson Cancer Research Centre"
+      },
+      {
+        "author_name": "Joep de Ligt",
+        "author_inst": "Institute of Environmental Science and Research"
+      },
+      {
+        "author_name": "David Welch",
+        "author_inst": "University of Auckland"
+      },
+      {
+        "author_name": "Jemma L Geoghegan",
+        "author_inst": "University of Otago"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2022.07.14.22277617",
     "rel_title": "An Evaluation of the Safety and Immunogenicity of MVC-COV1901: Results of an interim analysis of a phase III, parallel group, randomized, double-blind, active-controlled study",
@@ -242163,33 +241209,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2022.07.13.22277613",
-    "rel_title": "Assessing Risk Exposure of COVID-19 in Indonesian Government-owned Public Health Center Physicians",
-    "rel_date": "2022-07-15",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.13.22277613",
-    "rel_abs": "In 2020, the death of physicians due to COVID-19 in Indonesia raises questions about the condition that caused the incident. What was the situation at the early stage of the pandemic, the use of WHOs Risk Assessment questionnaire, and what lesson was learned about it? A Cross-sectional survey, using blast mail surveys targeting the Government-owned Public Health Center Physicians WhatsApp application across Indonesia had held. A Self-administered questionnaire, using WHOs \"Risk assessment and management of exposure of health care workers in the context of Covid-19\" which has been translated into Bahasa Indonesia. As result, there were 2.099 responses eligible for this study. At the early stage of the pandemic, 99,29% of Government-owned Public Health Center Physicians were at high risk of COVID-19 exposure. Its because on average 64,23% of the respondent not use PPE correctly, 15,53% of respondents still performing actions that produced aerosols in health centers, or 22,73% of respondents got biological accidents. At the early stage of the pandemic in Indonesia marked by the scarcity of PPE, the lack of awareness from the physicians and or the government make a double burden on the physicians. As for the use of questionnaires, there were challenging issues in conducting the study, such as respondents feeling redundant in answering the questionnaire. It is recommended that the Central and Regional Governments, health centers, and hospitals increase their commitment to protecting physicians from possible exposure to Covid-19, among others, through meeting standard APD needs, maintaining the cleanliness of health care facilities, updating the skill and knowledge about pandemics on physicians, and providing adequate incentives. The physician is also expected to adapt in many ways.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Anton Suryatma",
-        "author_inst": "National Research and Innovation Agency, Indonesia"
-      },
-      {
-        "author_name": "Telly Purnamasari",
-        "author_inst": "National Research and Innovation Agency, Indonesia"
-      },
-      {
-        "author_name": "Harimat Hendarwan",
-        "author_inst": "National Research and Innovation Agency, Indonesia"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2022.07.13.22277610",
     "rel_title": "Bayesian Shrinkage Priors in Zero-Inflated and Negative Binomial Regression models with Real World Data Applications of COVID-19 Vaccine, and RNA-Seq",
@@ -242532,6 +241551,77 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2022.07.14.500068",
+    "rel_title": "Ending transmission of SARS-CoV-2: sterilizing immunity using an intranasal subunit vaccine",
+    "rel_date": "2022-07-15",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.14.500068",
+    "rel_abs": "Immunization programs against SARS-CoV-2 with commercial intramuscular (IM) vaccines prevent disease but not infections. The continued evolution of variants of concern (VOC) like Delta and Omicron has increased infections even in countries with high vaccination coverage. This is due to commercial vaccines being unable to prevent viral infection in the upper airways and exclusively targeting the spike (S) protein that is subject to continuous evolution facilitating immune escape. Here we report a multi-antigen, intranasal vaccine, NanoSTING-NS that yields sterilizing immunity and leads to the rapid and complete elimination of viral loads in both the lungs and the nostrils upon viral challenge with SARS-CoV-2 VOC. We formulated vaccines with the S and nucleocapsid (N) proteins individually to demonstrate that immune responses against S are sufficient to prevent disease whereas combination immune responses against both proteins prevents viral replication in the nasal compartment. Studies with the highly infectious Omicron VOC showed that even in vaccine-naive animals, a single dose of NanoSTING-NS significantly reduced transmission. These observations have two implications: (1) mucosal multi-antigen vaccines present a pathway to preventing transmission and ending the pandemic, and (2) an explanation for why hybrid immunity in humans is superior to vaccine-mediated immunity by current IM vaccines.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Ankita Leekha",
+        "author_inst": "Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA"
+      },
+      {
+        "author_name": "Arash Saeedi",
+        "author_inst": "Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA"
+      },
+      {
+        "author_name": "Samiur Rahman Sefat",
+        "author_inst": "Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA"
+      },
+      {
+        "author_name": "Monish Kumar",
+        "author_inst": "Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA"
+      },
+      {
+        "author_name": "Melisa Martinez Paniagua",
+        "author_inst": "Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA"
+      },
+      {
+        "author_name": "Adrian Damian",
+        "author_inst": "Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA"
+      },
+      {
+        "author_name": "Rohan Kulkarni",
+        "author_inst": "Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA"
+      },
+      {
+        "author_name": "Ali Rezvan",
+        "author_inst": "Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA"
+      },
+      {
+        "author_name": "Shalaleh Mosoumi",
+        "author_inst": "Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA"
+      },
+      {
+        "author_name": "Xinli Liu",
+        "author_inst": "Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, USA"
+      },
+      {
+        "author_name": "Laurence J.N. Cooper",
+        "author_inst": "AuraVax Therapeutics, Houston, TX, USA"
+      },
+      {
+        "author_name": "Manu Sebastian",
+        "author_inst": "AuraVax Therapeutics, Houston, TX, USA"
+      },
+      {
+        "author_name": "Brett L. Hurst",
+        "author_inst": "Institute for Antiviral Research, Utah State University, Logan, UT, USA"
+      },
+      {
+        "author_name": "Navin Varadarajan",
+        "author_inst": "Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2022.07.14.500031",
     "rel_title": "A zebrafish model of COVID-19-associated cytokine storm syndrome reveals that the Spike protein signals via TLR2",
@@ -243857,69 +242947,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2022.07.11.22277504",
-    "rel_title": "Estimation of disease burden and clinical severity of COVID-19 caused by Omicron BA.2 in Shanghai, February-June 2022",
-    "rel_date": "2022-07-12",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.11.22277504",
-    "rel_abs": "BackgroundAn outbreak of COVID-19 caused by the SARS-CoV-2 Omicron BA.2 sublineage occurred in Shanghai, China from February to June 2022. The government organized multiple rounds of molecular test screenings for the entire population, providing a unique opportunity to capture the majority of subclinical infections and better characterize disease burden and the full spectrum of Omicron BA.2 clinical severity.\n\nMethodsUsing daily reports from the websites of the Shanghai Municipal Health Commission, we estimated the incidence of infections, severe/critical infections, and deaths to assess the disease burden. By adjusting for right censoring and Reverse Transcription-Polymerase Chain Reaction (RT{square}PCR) sensitivity, we provide estimates of clinical severity, including the infection fatality risk, symptomatic case fatality risk, and risk of developing severe/critical disease upon infection.\n\nFindingsFrom February 26 to June 30, 2022, the overall infection rate, severe/critical infection rate, and mortality rate were 2.74 (95% CI: 2.73-2.74) per 100 individuals, 6.34 (95% CI: 6.02-6.66) per 100,000 individuals and 2.42 (95% CI: 2.23-2.62) per 100,000 individuals, respectively. The severe/critical infection rate and mortality rate increased with age with the highest rates of 125.29 (95% CI: 117.05-133.44) per 100,000 and 57.17 (95% CI: 51.63-62.71) per 100,000 individuals, respectively, noted in individuals aged 80 years or older. The overall fatality risk and risk of developing severe/critical disease upon infection were 0.09% (95% CI: 0.08-0.10%) and 0.23% (95% CI: 0.20-0.25%), respectively. Having received at least one vaccine dose led to a 10-fold reduction in the risk of death for infected individuals aged 80 years or older.\n\nInterpretationUnder the repeated population-based screenings and strict intervention policies implemented in Shanghai, our results found a lower disease burden and mortality of the outbreak compared to other settings and countries, showing the impact of the successful outbreak containment in Shanghai. The estimated low clinical severity of this Omicron BA.2 epidemic in Shanghai highlight the key contribution of vaccination and availability of hospital beds to reduce the risk of death.\n\nFundingKey Program of the National Natural Science Foundation of China (82130093).\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed and Europe PMC for manuscripts published or posted on preprint servers after January 1, 2022 using the following query: (\"SARS-CoV-2 Omicron\") AND (\"burden\" OR \"severity\"). No studies that characterized the whole profile of disease burden and clinical severity during the Shanghai Omicron outbreak were found. One study estimated confirmed case fatality risk between different COVID-19 waves in Hong Kong; other outcomes, such as fatality risk and risk of developing severe/critical illness upon infection, were not estimated. One study based on 21 hospitals across the United States focused on Omicron-specific in-hospital mortality based on a limited sample of inpatients (565). In southern California, United States, a study recruited more than 200 thousand Omicron-infected individuals and estimated the 30-day risk of hospital admission, intensive care unit admission, mechanical ventilation, and death. None of these studies estimated infection and mortality rates or other indictors associated with disease burden. Overall, the disease burden and clinical severity of the Omicron BA.2 variant have not been fully characterized, especially in populations predominantly immunized with inactivated vaccines.\n\nAdded value of this studyThe large-scale and multiround molecular test screenings conducted on the entire population during the Omicron BA.2 outbreak in Shanghai, leading to a high infection ascertainment ratio, provide a unique opportunity to capture the majority of subclinical infections. As such, our study provides a comprehensive assessment of both the disease burden and clinical severity of the SARS-CoV-2 Omicron BA.2 sublineage, which are especially lacking for populations predominantly immunized with inactivated vaccines.\n\nImplications of all the available evidenceWe estimated the disease burden and clinical severity of the Omicron BA.2 outbreak in Shanghai in February-June 2022. These estimates are key to properly interpreting field evidence and assessing the actual spread of Omicron in other settings. Our results also provide support for the importance of strategies to prevent overwhelming the health care system and increasing vaccine coverage to reduce mortality.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Xinhua Chen",
-        "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China"
-      },
-      {
-        "author_name": "Xuemei Yan",
-        "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China"
-      },
-      {
-        "author_name": "Kaiyuan Sun",
-        "author_inst": "Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA"
-      },
-      {
-        "author_name": "Nan Zheng",
-        "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China"
-      },
-      {
-        "author_name": "Ruijia Sun",
-        "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China"
-      },
-      {
-        "author_name": "Jiaxin Zhou",
-        "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China"
-      },
-      {
-        "author_name": "Xiaowei Deng",
-        "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China"
-      },
-      {
-        "author_name": "Tingyu Zhuang",
-        "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China"
-      },
-      {
-        "author_name": "Jun Cai",
-        "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China"
-      },
-      {
-        "author_name": "Juanjuan Zhang",
-        "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China"
-      },
-      {
-        "author_name": "Marco Ajelli",
-        "author_inst": "Laboratory for Computational Epidemiology and Public Health, Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomingt"
-      },
-      {
-        "author_name": "Hongjie Yu",
-        "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.07.11.22277475",
     "rel_title": "Type 1 and type 2 diabetes mellitus: Clinical outcomes due to COVID-19. Protocol of a systematic literature review",
@@ -244266,6 +243293,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.07.12.22277538",
+    "rel_title": "Dengue seroprevalence study during COVID-19 pandemic in Bali",
+    "rel_date": "2022-07-12",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.12.22277538",
+    "rel_abs": "IntroductionDengue infection poses significant public health problems in tropical and subtropical regions all over the world. The clinical manifestation of dengue varies from asymptomatic cases to severe dengue manifestation. The detection of clinical cases enables us to measure the incidence of dengue infection, whereas serological surveys give insights into the prevalence of infection. This study aimed to determine the dengue prevalence among healthy adult patients in Bali.\n\nMethodCross-sectional seroprevalence surveys were performed from July 2020 to June 2021 among healthy and adult patients in Denpasar Bali. Blood samples were collected from 539 randomly selected samples from urban sites in Denpasar. IgG antibodies against DENV were detected in serum using a commercial enzyme-linked immunosorbent assay (ELISA) kit.\n\nResultsOverall, the positive dengue seroprevalence rate among 539 clinically healthy adult patients was high (85.5%). The subjects median age was 34.1 (range between 18-86.1) years old. Most participants in the study were younger than 40 years old (61.2%). The gender is dominated by males (54.5%). The study found a significant association of dengue seropositivity among people age more than 40 years old with healthy status (p=0.005 and p<0.001, respectively). Another seroprevalence study reported a lower rate of dengue infection in children in Indonesia (69.4%). The difference may be associated with less probability of Aedes bites among the children. The study reflected the proportion of asymptomatic dengue that needs better assessment with a serological test.\n\nConclusionThe current study highlighted a high prevalence of dengue seropositive with a relatively dominant proportion of asymptomatic cases. The study guides the physicians o to beware of every dengue infection in tropical countries and prevents the spread of the disease.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Sri Masyeni",
+        "author_inst": "University of Warmadewa: Universitas Warmadewa"
+      },
+      {
+        "author_name": "Rois  Muqsith Fatawy",
+        "author_inst": "Universitas Indonesia Fakultas Kedokteran"
+      },
+      {
+        "author_name": "AAAL Paramasatiari",
+        "author_inst": "University of Warmadewa Faculty of Health and Medicine: Universitas Warmadewa Fakultas Kedokteran dan Ilmu Kesehatan"
+      },
+      {
+        "author_name": "Ananda Maheraditya",
+        "author_inst": "University of Warmadewa Faculty of Health and Medicine: Universitas Warmadewa Fakultas Kedokteran dan Ilmu Kesehatan"
+      },
+      {
+        "author_name": "Ratna  Kartika Dewi",
+        "author_inst": "University of Warmadewa Faculty of Health and Medicine: Universitas Warmadewa Fakultas Kedokteran dan Ilmu Kesehatan"
+      },
+      {
+        "author_name": "NW Winianti",
+        "author_inst": "University of Warmadewa Faculty of Health and Medicine: Universitas Warmadewa Fakultas Kedokteran dan Ilmu Kesehatan"
+      },
+      {
+        "author_name": "Agus Santosa",
+        "author_inst": "University of Warmadewa Faculty of Health and Medicine: Universitas Warmadewa Fakultas Kedokteran dan Ilmu Kesehatan"
+      },
+      {
+        "author_name": "Marta Setiabudy",
+        "author_inst": "University of Warmadewa Faculty of Health and Medicine: Universitas Warmadewa Fakultas Kedokteran dan Ilmu Kesehatan"
+      },
+      {
+        "author_name": "Nyoman  Trisna Sumadewi",
+        "author_inst": "Udayana University Faculty of Medicine: Universitas Udayana Fakultas Kedokteran"
+      },
+      {
+        "author_name": "Sianny Herawati",
+        "author_inst": "Udayana University Faculty of Medicine: Universitas Udayana Fakultas Kedokteran"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.07.12.22277549",
     "rel_title": "Delayed generation of functional virus-specific circulating T follicular helper cells correlates with severe COVID-19",
@@ -246031,169 +245113,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "obstetrics and gynecology"
   },
-  {
-    "rel_doi": "10.1101/2022.07.09.22277457",
-    "rel_title": "Human Epidemiology and RespOnse to SARS-CoV-2 (HEROS): Objectives, Design and Enrollment Results of a 12-City Remote Observational Surveillance Study of Households with Children using Direct-to-Participant Methods",
-    "rel_date": "2022-07-10",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.09.22277457",
-    "rel_abs": "The Human Epidemiology and Response to SARS-CoV-2 (HEROS) is a prospective multi-city 6-month incidence study which was conducted from May 2020-February 2021. The objectives were to identify risk factors for SARS-CoV-2 infection and household transmission among children and people with asthma and allergic diseases, and to use the host nasal transcriptome sampled longitudinally to understand infection risk and sequelae at the molecular level. To overcome challenges of clinical study implementation due to the coronavirus pandemic, this surveillance study used direct-to-participant methods to remotely enroll and prospectively follow eligible children who are participants in other NIH-funded pediatric research studies and their household members. Households participated in weekly surveys and biweekly nasal sampling regardless of symptoms. The aim of this report is to widely share the methods and study instruments and to describe the rationale, design, execution, logistics and characteristics of a large, observational, household-based, remote cohort study of SARS-CoV-2 infection and transmission in households with children. The study enrolled a total of 5,598 individuals, including 1,913 principal participants (children), 1,913 primary caregivers, 729 secondary caregivers and 1,043 other household children. This study was successfully implemented without necessitating any in-person research visits and provides an approach for rapid execution of clinical research.",
-    "rel_num_authors": 37,
-    "rel_authors": [
-      {
-        "author_name": "Patricia Fulkerson",
-        "author_inst": "NIAID"
-      },
-      {
-        "author_name": "Stephanie Lussier",
-        "author_inst": "Rho"
-      },
-      {
-        "author_name": "Casper Bendixsen",
-        "author_inst": "Marshfield"
-      },
-      {
-        "author_name": "Sharon Castina",
-        "author_inst": "Rho"
-      },
-      {
-        "author_name": "Tebeb Gebretsadik",
-        "author_inst": "Vanderbilt University Medical Center"
-      },
-      {
-        "author_name": "Jessica Marlin",
-        "author_inst": "Vanderbilt University Medical Center"
-      },
-      {
-        "author_name": "Patty Russell",
-        "author_inst": "Vanderbilt University Medical Center"
-      },
-      {
-        "author_name": "Max Seibold",
-        "author_inst": "National Jewish Health"
-      },
-      {
-        "author_name": "Jamie Everman",
-        "author_inst": "National Jewish Health"
-      },
-      {
-        "author_name": "Camille Moore",
-        "author_inst": "National Jewish Health"
-      },
-      {
-        "author_name": "Britney Snyder",
-        "author_inst": "Vanderbilt University Medical Center"
-      },
-      {
-        "author_name": "Kathy Thompson",
-        "author_inst": "NIAID"
-      },
-      {
-        "author_name": "George Tregoning",
-        "author_inst": "Vanderbilt University Medical Center"
-      },
-      {
-        "author_name": "Stephanie Wellford",
-        "author_inst": "Rho"
-      },
-      {
-        "author_name": "Samuel Arbes",
-        "author_inst": "Rho"
-      },
-      {
-        "author_name": "Leonard Bacharier",
-        "author_inst": "Vanderbilt University Medical Center"
-      },
-      {
-        "author_name": "Augustin Calatroni",
-        "author_inst": "Rho"
-      },
-      {
-        "author_name": "Carlos Camrgo Jr.",
-        "author_inst": "Massachusetts General Hospital"
-      },
-      {
-        "author_name": "William Dupont",
-        "author_inst": "Vanderbilt University Medical Center"
-      },
-      {
-        "author_name": "Glenn Furuta",
-        "author_inst": "Children's Hospital Colorado"
-      },
-      {
-        "author_name": "Rebecca Gruchalla",
-        "author_inst": "University of Texas Southwestern Medical Center"
-      },
-      {
-        "author_name": "Ruchi Gupta",
-        "author_inst": "Northwestern University Feinberg School of Medicine"
-      },
-      {
-        "author_name": "Gurjit Khurana Hershey",
-        "author_inst": "Cincinnati Childrens Hospital Medical Center"
-      },
-      {
-        "author_name": "Daniel J Jackson",
-        "author_inst": "University of Wisconsin School of Medicine and Public Health"
-      },
-      {
-        "author_name": "Christine C Johnson",
-        "author_inst": "Henry Ford Health System"
-      },
-      {
-        "author_name": "Meyer Kattan",
-        "author_inst": "Columbia University Medical Center"
-      },
-      {
-        "author_name": "Andrew H Liu",
-        "author_inst": "Childrens Hospital Colorado"
-      },
-      {
-        "author_name": "Liza Murrison",
-        "author_inst": "Cincinnati Childrens Hospital Medical Center"
-      },
-      {
-        "author_name": "George T O'Connor",
-        "author_inst": "Boston University School of Medicine"
-      },
-      {
-        "author_name": "Wanda Phipatanakul",
-        "author_inst": "Boston Childrens Hospital"
-      },
-      {
-        "author_name": "Katherine Rivera-Spoljaric",
-        "author_inst": "Washington University School of Medicine"
-      },
-      {
-        "author_name": "Marc E Rothenberg",
-        "author_inst": "Cincinnati Childrens Hospital Medical Center"
-      },
-      {
-        "author_name": "Christine Seroogy",
-        "author_inst": "University of Wisconsin School of Medicine and Public Health"
-      },
-      {
-        "author_name": "Stephen Teach",
-        "author_inst": "Childrens National Hospital"
-      },
-      {
-        "author_name": "Edward Zoratti",
-        "author_inst": "Henry Ford Health System"
-      },
-      {
-        "author_name": "Alkis Togias",
-        "author_inst": "NIAID"
-      },
-      {
-        "author_name": "Tina Hartert",
-        "author_inst": "Vanderbilt University School of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc0",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.07.09.22277456",
     "rel_title": "Examining the Impact of Increasing Vaccine Coverage and Nonpharmaceutical Interventions against Coronavirus Disease 2019 In Ghana using Mathematical Modeling",
@@ -246540,6 +245459,89 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.07.08.22276768",
+    "rel_title": "Healthcare utilization following SARS-CoV-2 infection in children and adolescents with chronic conditions: An EHR-based Cohort Study from the RECOVER Program",
+    "rel_date": "2022-07-09",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.08.22276768",
+    "rel_abs": "BackgroundChronic medical conditions are a risk factor for moderate or severe COVID-19 in children, but little is known about post-acute sequelae of SARS-CoV-2 infection (PASC) in children with chronic medical conditions (CMCs). To understand whether SARS-CoV-2 infection led to potential exacerbation of underlying chronic disease in children, we explored whether children with CMCs had increased healthcare utilization in the post-acute (28 days after infection) period compared to children with CMCs without SARS-CoV-2 infection.\n\nMethodsWe conducted a retrospective, matched-cohort study using electronic health record data collected from 8 pediatric health care systems participating in the PEDSnet network. We included children <21 years of age with a wide array of chronic conditions, defined by the presence of diagnostic codes, who were diagnosed with COVID-19 between March 1, 2020 and February 28, 2022. Cohort entry was defined by presence of a positive SARS-CoV-2 PCR test (polymerase chain reaction or antigen) or diagnostic codes for COVID-19, PASC or MIS-C. A comparison cohort of patients testing negative or without these conditions was matched using a stratified propensity score model and exact matching on age group, race/ethnicity, institution, test location, and month of cohort entry. A negative binomial model was used to examine our primary outcome: composite and setting-specific (inpatient, outpatient, ED) utilization rate ratios between the positive and comparison cohorts. Secondary outcomes included time to first utilization in the post-acute period, and utilization stratified by severity at cohort entry.\n\nResultsWe identified 748,692 patients with at least one chronic condition, 78,744 of whom met inclusion criteria for the COVID-19 cohort. 96% of patients from the positive cohort were matched. Cohorts were well-balanced for chronic condition clusters, total number of conditions, time since first diagnosis, baseline utilization, cohort entry period, age, sex, race/ethnicity and test location. We found that among children with chronic medical conditions, those with COVID-19 had higher healthcare utilization than those with no recorded COVID-19 diagnosis or positive test, with utilization rate ratio of 1.21 (95% CI: 1.18-1.24). The utilization was highest for inpatient care with utilization rate ratio of 2.03 (95% CI: 1.85-2.23) but the utilization was increased across all settings. Hazard ratios estimated in time-to-first-utilization analysis mirrored these results. Patients with severe or moderate acute COVID-19 illness had greater increases in utilization in all settings than those with mild or asymptomatic disease.\n\nConclusionsWe found that care utilization in all settings was increased following COVID-19 in children with chronic medical conditions in the post-acute period, particularly in the inpatient setting. Increased utilization was correlated with more severe COVID-19. Additional research is needed to better understand the reasons for higher care utilization by studying condition-specific outcomes in children with chronic disease.",
+    "rel_num_authors": 17,
+    "rel_authors": [
+      {
+        "author_name": "Nathan M Pajor",
+        "author_inst": "Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine"
+      },
+      {
+        "author_name": "Vitaly Lorman",
+        "author_inst": "Applied Clinical Research Center, Children's Hospital of Philadelphia"
+      },
+      {
+        "author_name": "Hanieh Razzaghi",
+        "author_inst": "Applied Clinical Research Center, Children's Hospital of Philadelphia"
+      },
+      {
+        "author_name": "Abigail Case",
+        "author_inst": "Division of Physical Medicine & Rehabilitation, The Children's Hospital of Philadelphia"
+      },
+      {
+        "author_name": "Priya Prahalad",
+        "author_inst": "Department of Pediatrics, Division of Endocrinology, Stanford University"
+      },
+      {
+        "author_name": "Seuli Bose-Brill",
+        "author_inst": "Internal Medicine and Pediatrics Section, Division of General Internal Medicine, Department of Internal Medicine, Ohio State University College of Medicine and "
+      },
+      {
+        "author_name": "Qiong Wu",
+        "author_inst": "Department of Biostatistics, Epidemiology and Informatics, the University of Pennsylvania"
+      },
+      {
+        "author_name": "Yong Chen",
+        "author_inst": "Department of Biostatistics, Epidemiology and Informatics, the University of Pennsylvania"
+      },
+      {
+        "author_name": "Jason P Block",
+        "author_inst": "Harvard Pilgrim Health Care Institute/Harvard Medical School"
+      },
+      {
+        "author_name": "Payal B Patel",
+        "author_inst": "Department of Neurology, University of Washington"
+      },
+      {
+        "author_name": "Suchitra Rao",
+        "author_inst": "Department of Pediatrics, University of Colorado School of Medicine and Children's Hospital of Colorado"
+      },
+      {
+        "author_name": "Asuncion Mejias",
+        "author_inst": "Division of Infectious Diseases, Department of Pediatrics, Nationwide Children's Hospital and The Ohio State University"
+      },
+      {
+        "author_name": "Deepika Thacker",
+        "author_inst": "Nemours Cardiac Center, Nemours Childrens Health"
+      },
+      {
+        "author_name": "Ravi Jhaveri",
+        "author_inst": "Division of Infectious Diseases, Ann & Robert H. Lurie Children's Hospital of Chicago"
+      },
+      {
+        "author_name": "L Charles Bailey",
+        "author_inst": "Applied Clinical Research Center, Children's Hospital of Philadelphia"
+      },
+      {
+        "author_name": "Christopher B Forrest",
+        "author_inst": "Applied Clinical Research Center, Children's Hospital of Philadelphia"
+      },
+      {
+        "author_name": "Grace M Lee",
+        "author_inst": "Division of Infectious Diseases, Department of Pediatrics, Stanford University School of Medicine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "pediatrics"
+  },
   {
     "rel_doi": "10.1101/2022.07.07.22277395",
     "rel_title": "Analysing COVID treatment outcomes in dedicated wards at a large university hospital in northern Poland. A result-based observational study.",
@@ -248093,77 +247095,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.07.04.22277223",
-    "rel_title": "Strong neutralizing antibody responses to SARS-CoV-2 variants following a single vaccine dose in subjects with previous SARS-CoV-2 infection",
-    "rel_date": "2022-07-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.04.22277223",
-    "rel_abs": "BackgroundPrevious SARS-CoV-2 infection primes the immune system and thus individuals who recovered from infection have enhanced immune responses to subsequent vaccination (hybrid immunity). However, it remains unclear how well hybrid immunity induced by severe or mild infection can cross-neutralize emerging variants. We aimed to compare the strength and breadth of antibody responses in vaccinated recovered and uninfected subjects.\n\nMethodsWe measured spike-specific IgG and neutralizing antibodies (NAbs) from vaccinated subjects including 320 with hybrid immunity and 20 without previous infection. From 29 subjects with a previous severe or mild infection, we also measured NAb responses against Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2) and Omicron (B.1.1.529/BA.1) variants following vaccination.\n\nResultsA single vaccine dose induced 2-fold higher anti-spike IgG concentrations and 3-fold higher neutralizing potency of antibodies in previously infected compared to uninfected fully vaccinated subjects. We found similar IgG concentrations in previously infected subjects after one or two vaccine doses. NAb titers were higher in subjects with severe compared to those with mild infection. This difference remained after vaccination with sequentially decreasing titers against Alpha, Beta, Delta, and Omicron variants.\n\nConclusionsHybrid immunity induced strong IgG responses, particularly after severe infection. However, the NAb titers were low against heterologous variants, especially against Omicron.",
-    "rel_num_authors": 14,
-    "rel_authors": [
-      {
-        "author_name": "Nina Ekstrom",
-        "author_inst": "Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland"
-      },
-      {
-        "author_name": "Anu Haveri",
-        "author_inst": "Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland"
-      },
-      {
-        "author_name": "Anna Solastie",
-        "author_inst": "Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland"
-      },
-      {
-        "author_name": "Camilla Virta",
-        "author_inst": "Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland"
-      },
-      {
-        "author_name": "Pamela Osterlund",
-        "author_inst": "Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland"
-      },
-      {
-        "author_name": "Hanna Nohynek",
-        "author_inst": "Department of Health Security,, Finnish Institute for Health and Welfare, Helsinki, Finland"
-      },
-      {
-        "author_name": "Tuomo Nieminen",
-        "author_inst": "Department of Knowledge Brokers, Finnish Institute for Health and Welfare, Helsinki, Finland"
-      },
-      {
-        "author_name": "Lauri Ivaska",
-        "author_inst": "Department of Pediatrics and Adolescent Medicine, Turku University Hospital, Turku, Finland"
-      },
-      {
-        "author_name": "Paula A Tahtinen",
-        "author_inst": "Department of Pediatrics and Adolescent Medicine, Turku University Hospital, Turku, Finland"
-      },
-      {
-        "author_name": "Johanna Lempainen",
-        "author_inst": "Department of Pediatrics and Adolescent Medicine/Clinical Microbiology, Turku University Hospital /Immunogenetics laboratory, Institute of Biomedicine, Universi"
-      },
-      {
-        "author_name": "Pinja Jalkanen",
-        "author_inst": "Infection and Immunity, Institute of Biomedicine, University of Turku, Turku, Finland"
-      },
-      {
-        "author_name": "Ilkka Julkunen",
-        "author_inst": "Clinical Microbiology, Turku University Hospital/Infection and Immunity, Institute of Biomedicine, University of Turku, Turku, Finland"
-      },
-      {
-        "author_name": "Arto A Palmu",
-        "author_inst": "Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Tampere, Finland"
-      },
-      {
-        "author_name": "Merit Melin",
-        "author_inst": "Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.07.04.22277230",
     "rel_title": "SARS-CoV-2 seroprevalence among public school staff in Metro Vancouver after the first Omicron wave in British Columbia, Canada",
@@ -248518,6 +247449,69 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "respiratory medicine"
   },
+  {
+    "rel_doi": "10.1101/2022.07.04.22277193",
+    "rel_title": "Reductions in stillbirths and preterm birth in COVID-19 vaccinated women: a multi-center cohort study of vaccination uptake and perinatal outcomes",
+    "rel_date": "2022-07-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.04.22277193",
+    "rel_abs": "BackgroundCOVID-19 infection in pregnancy is associated with a higher risk of progression to severe disease, but vaccine uptake by pregnant women is hindered by persistent safety concerns. COVID-19 vaccination in pregnancy has been shown to reduce stillbirth, but its relationship with preterm birth is uncertain.\n\nObjectiveThe aim of this study was to investigate the sociodemographic characteristics associated with vaccine uptake in Melbourne, Australia, and to compare perinatal outcomes by vaccination status.\n\nStudy designRetrospective multicenter cohort study in Melbourne following the national recommendations for mRNA COVID-19 vaccination during pregnancy in June 2021. Routinely collected data from all 12 public maternity hospitals in Melbourne were extracted on births [&ge;] 20 weeks gestation from 1st July 2021 to 31 March 2022. Maternal sociodemographic characteristics were analyzed from the total birth cohort. Perinatal outcomes were compared between vaccinated and unvaccinated women for whom weeks 20-43 of gestation fell entirely within the 9-month data collection period. The primary outcome was the rate of congenital anomaly in singleton infants [&ge;] 20 weeks gestation among women vaccinated during pregnancy. Secondary perinatal outcomes including stillbirth, preterm birth (spontaneous and iatrogenic), birthweight [&le;] 3rd centile, and newborn intensive care unit admissions were examined for singleton infants [&ge;] 24 weeks gestation without congenital anomalies. We calculated the adjusted odds ratio of congenital anomalies and perinatal outcomes among vaccinated versus unvaccinated women using inverse propensity score weighting regression adjustment with multiple covariates; p< 0.05 was considered statistically significant.\n\nResultsBirths from 32,536 women were analyzed: 17,365 (53.4%) were vaccinated and 15,171 (47.6%) were unvaccinated. Vaccinated women were significantly more likely to be older, nulliparous, non-smoking, not requiring an interpreter, of higher socioeconomic status, and vaccinated against pertussis and influenza. Vaccination status also varied by region of birth: compared with women born in Australia, women born in South and Eastern Europe, the Middle East, Africa and Oceania had lower adjusted odds of vaccination. There was no significant increase in the rate of congenital anomalies or birth weight [&le;] 3rd centile in vaccinated women. Vaccinated women were significantly less like to have an infant with a major congenital anomaly compared with the unvaccinated group (2.4% vs 3.0%, aOR 0.72, 95%CI 0.56-0.94, p=0.02). This finding remained significant even when the analysis was restricted to women vaccinated before 20 weeks gestation. Vaccinated women had a significantly lower rate of stillbirth (0.2% vs 0.8%, aOR 0.18, 95%CI 0.09-0.37, P < 0.001. Vaccination was associated with a significant reduction in total preterm births < 37 weeks (5.1% vs 9.2%, aOR 0.60, 95% CI 0.51-0.71, p< 0.001), spontaneous preterm birth (2.4% vs 4.0%, aOR 0.73 95% CI 0.56-0.96, p=0.02) and iatrogenic preterm birth (2.7% vs 5.2%, aOR 0.52, 95%CI 0.41-0.65, p< 0.001).\n\nConclusionsCOVID-19 Vaccine coverage was significantly influenced by known social determinants of health, which is likely to influence the strong association between COVID-19 vaccination and lower risks of stillbirth and preterm birth. We did not observe any adverse impacts of vaccination on fetal growth or development.\n\nAT A GLANCEO_ST_ABSWhy was this study conducted?C_ST_ABS COVID-19 infection in pregnancy is associated with a higher risk of progression to severe disease, but vaccine uptake by pregnant women is hindered by persistent safety concerns. COVID-19 vaccination in pregnancy has been shown to reduce stillbirth, but its relationship with preterm birth is uncertain.\n Most of the published literature on COVID-19 vaccination in pregnancy have methodological limitations including fixed cohort bias and time-varying exposure.\n We conducted this multicenter study to provide robust evidence on mRNA COVID-19 vaccination and perinatal outcomes including congenital anomalies, stillbirth, and preterm birth.\n\n\nWhat are the key findings? The adjusted odds of stillbirth, preterm birth, and neonatal intensive care admission were significantly reduced among infants born to COVID-19 vaccinated women compared with unvaccinated women. COVID-19 vaccination during pregnancy was not associated with an increase in congenital anomalies.\n Our results conclusively demonstrate a significant reduction in both spontaneous and iatrogenic preterm birth for vaccinated women\n Vaccinated women were significantly more likely to be older, nulliparous, non-smoking, not requiring an interpreter, residing in a higher socioeconomic postcode, and vaccinated against pertussis and influenza. There were also significant differences in vaccination rates by region of birth.\n\n\nWhat does this study add to what is already known? Our analysis confirmed a strong relationship between the COVID-19 mRNA vaccine and lower preterm births and stillbirths\n In addition to its impact on reducing severe COVID-19 illness, vaccination may be a proxy for other biological and social determinants of health among our pregnant population.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Lisa Hui",
+        "author_inst": "University of Melbourne"
+      },
+      {
+        "author_name": "Melvin B Marzan",
+        "author_inst": "University of Melbourne"
+      },
+      {
+        "author_name": "Daniel L Rolnik",
+        "author_inst": "Monash University"
+      },
+      {
+        "author_name": "Stephanie Potenza",
+        "author_inst": "Mercy Hospital for Women"
+      },
+      {
+        "author_name": "Natasha Pritchard",
+        "author_inst": "University of Melbourne"
+      },
+      {
+        "author_name": "Joanne M Said",
+        "author_inst": "University of Melbourne"
+      },
+      {
+        "author_name": "Kirsten R Palmer",
+        "author_inst": "Monash University"
+      },
+      {
+        "author_name": "Clare L Whitehead",
+        "author_inst": "University of Melbourne"
+      },
+      {
+        "author_name": "Penelope M Sheehan",
+        "author_inst": "Monash University"
+      },
+      {
+        "author_name": "Jolyon Ford",
+        "author_inst": "Peninsula Health"
+      },
+      {
+        "author_name": "Ben W. Mol",
+        "author_inst": "Monash University"
+      },
+      {
+        "author_name": "Susan P Walker",
+        "author_inst": "University of Melbourne"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "obstetrics and gynecology"
+  },
   {
     "rel_doi": "10.1101/2022.07.05.22277281",
     "rel_title": "Efficacy and longevity of immune response to 3rd COVID-19 vaccine and effectiveness of a 4th dose in severely immunocompromised patients with cancer",
@@ -251127,245 +250121,6 @@
     "type": "new results",
     "category": "evolutionary biology"
   },
-  {
-    "rel_doi": "10.1101/2022.07.05.22277210",
-    "rel_title": "Safety and immunogenicity of the protein-based PHH-IV compared to BNT162b2 as a heterologous SARS-CoV-2 booster vaccine in adults vaccinated against COVID-19: a multicentre, randomised, double-blind, non-inferiority phase IIb trial.",
-    "rel_date": "2022-07-05",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.05.22277210",
-    "rel_abs": "BackgroundA SARS-CoV-2 protein-based heterodimer vaccine, PHH-1V, has been shown to be safe and welltolerated in healthy young adults in a first-in-human, Phase I/IIa study dose-escalation trial. Here, we report the interim results of the Phase IIb HH-2, where the immunogenicity and safety of a heterologous booster with PHH-1V is assessed versus a homologous booster with BNT162b2 at 14, 28 and 98 days after vaccine administration.\n\nMethodsThe HH-2 study is an ongoing multicentre, randomised, active-controlled, double-blind, non-inferiority Phase IIb trial, where participants 18 years or older who had received two doses of BNT162b2 were randomly assigned in a 2:1 ratio to receive a booster dose of vaccine --either heterologous (PHH-1V group) or homologous (BNT162b2 group)-- in 10 centres in Spain. Eligible subjects were allocated to treatment stratified by age group (18-64 versus [&ge;]65 years) with approximately 10% of the sample enrolled in the older age group. The primary endpoints were humoral immunogenicity measured by changes in levels of neutralizing antibodies (PBNA) against the ancestral Wuhan-Hu-1 strain after the PHH-1V or the BNT162b2 boost, and the safety and tolerability of PHH-1V as a boost. The secondary endpoints were to compare changes in levels of neutralizing antibodies against different variants of SARS-CoV-2 and the T-cell responses towards the SARS-CoV-2 spike glycoprotein peptides. The exploratory endpoint was to assess the number of subjects with SARS-CoV-2 infections [&ge;]14 days after PHH-1V booster. This study is ongoing and is registered with ClinicalTrials.gov, NCT05142553.\n\nFindingsFrom 15 November 2021, 782 adults were randomly assigned to PHH-1V (n=522) or BNT162b2 (n=260) boost vaccine groups. The geometric mean titre (GMT) ratio of neutralizing antibodies on days 14, 28 and 98, shown as BNT162b2 active control versus PHH-1V, was, respectively, 1{middle dot}68 (p<0{middle dot}0001), 1{middle dot}31 (p=0{middle dot}0007) and 0{middle dot}86 (p=0{middle dot}40) for the ancestral Wuhan-Hu-1 strain; 0{middle dot}62 (p<0{middle dot}0001), 0{middle dot}65 (p<0{middle dot}0001) and 0{middle dot}56 (p=0{middle dot}003) for the Beta variant; 1{middle dot}01 (p=0{middle dot}92), 0{middle dot}88 (p=0{middle dot}11) and 0{middle dot}52 (p=0{middle dot}0003) for the Delta variant; and 0{middle dot}59 (p=<0{middle dot}0001), 0{middle dot}66 (p<0{middle dot}0001) and 0{middle dot}57 (p=0{middle dot}0028) for the Omicron BA.1 variant. Additionally, PHH-1V as a booster dose induced a significant increase of CD4+ and CD8+ T-cells expressing IFN-{gamma} on day 14. There were 458 participants who experienced at least one adverse event (89{middle dot}3%) in the PHH-1V and 238 (94{middle dot}4%) in the BNT162b2 group. The most frequent adverse events were injection site pain (79{middle dot}7% and 89{middle dot}3%), fatigue (27{middle dot}5% and 42{middle dot}1%) and headache (31{middle dot}2 and 40{middle dot}1%) for the PHH-1V and the BNT162b2 groups, respectively. A total of 52 COVID-19 cases occurred from day 14 post-vaccination (10{middle dot}14%) for the PHH-1V group and 30 (11{middle dot}90%) for the BNT162b2 group (p=0{middle dot}45), and none of the subjects developed severe COVID-19.\n\nInterpretationOur interim results from the Phase IIb HH-2 trial show that PHH-1V as a heterologous booster vaccine, when compared to BNT162b2, although it does not reach a non-inferior neutralizing antibody response against the Wuhan-Hu-1 strain at days 14 and 28 after vaccination, it does so at day 98. PHH-1V as a heterologous booster elicits a superior neutralizing antibody response against the previous circulating Beta and the currently circulating Omicron BA.1 SARS-CoV-2 variants in all time points assessed, and for the Delta variant on day 98 as well. Moreover, the PHH-1V boost also induces a strong and balanced T-cell response. Concerning the safety profile, subjects in the PHH-1V group report significantly fewer adverse events than those in the BNT162b2 group, most of mild intensity, and both vaccine groups present comparable COVID-19 breakthrough cases, none of them severe.\n\nFundingHIPRA SCIENTIFIC, S.L.U.",
-    "rel_num_authors": 56,
-    "rel_authors": [
-      {
-        "author_name": "Julia Corominas",
-        "author_inst": "HIPRA SCIENTIFIC S.L.U."
-      },
-      {
-        "author_name": "Carme Garriga",
-        "author_inst": "HIPRA SCIENTIFIC, S.L.U"
-      },
-      {
-        "author_name": "Antoni Prenafeta",
-        "author_inst": "HIPRA SCIENTIFIC, S.L.U"
-      },
-      {
-        "author_name": "Alexandra Moros",
-        "author_inst": "HIPRA SCIENTIFIC, S.L.U"
-      },
-      {
-        "author_name": "Manuel Canete",
-        "author_inst": "HIPRA SCIENTIFIC, S.L.U"
-      },
-      {
-        "author_name": "Antonio Barrero",
-        "author_inst": "HIPRA SCIENTIFIC, S.L.U"
-      },
-      {
-        "author_name": "Luis Gonzalez-Gonzalez",
-        "author_inst": "HIPRA SCIENTIFIC, S.L.U"
-      },
-      {
-        "author_name": "Laia Madrenas",
-        "author_inst": "HIPRA SCIENTIFIC, S.L.U"
-      },
-      {
-        "author_name": "Irina Guell",
-        "author_inst": "HIPRA SCIENTIFIC, S.L.U"
-      },
-      {
-        "author_name": "Bonaventura Clotet",
-        "author_inst": "IrsiCaixa AIDS Research Institute, Badalona, Spain"
-      },
-      {
-        "author_name": "Nuria Izaquierdo-Useros",
-        "author_inst": "IrsiCaixa AIDS Research Institute, Badalona, Spain"
-      },
-      {
-        "author_name": "Dalia Raich-Regue",
-        "author_inst": "IrsiCaixa AIDS Research Institute, Badalona, Spain"
-      },
-      {
-        "author_name": "Marcal Gallemi",
-        "author_inst": "IrsiCaixa AIDS Research Institute, Badalona, Spain"
-      },
-      {
-        "author_name": "Julia Blanco",
-        "author_inst": "IrsiCaixa AIDS Research Institute, Badalona, Spain"
-      },
-      {
-        "author_name": "Edwards Pradenas",
-        "author_inst": "IrsiCaixa AIDS Research Institute, Badalona, Spain"
-      },
-      {
-        "author_name": "Benjamin Trinite",
-        "author_inst": "IrsiCaixa AIDS Research Institute, Badalona, Spain"
-      },
-      {
-        "author_name": "Julia G Prado",
-        "author_inst": "IrsiCaixa AIDS Research Institute, Badalona, Spain"
-      },
-      {
-        "author_name": "Oscar Blanch-Lombarte",
-        "author_inst": "IrsiCaixa AIDS Research Institute, Badalona, Spain"
-      },
-      {
-        "author_name": "Raul Perez-Caballero",
-        "author_inst": "IrsiCaixa AIDS Research Institute, Badalona, Spain"
-      },
-      {
-        "author_name": "Montserrat Plana",
-        "author_inst": "AIDS Research Group, Institut de Investigacions Biomediques August Pi and Sunyer, IDIBAPS, Barcelona, Spain"
-      },
-      {
-        "author_name": "Ignasi Esteban",
-        "author_inst": "AIDS Research Group, Institut de Investigacions Biomediques August Pi and Sunyer, IDIBAPS, Barcelona, Spain"
-      },
-      {
-        "author_name": "Carmen Pastor-Quinones",
-        "author_inst": "AIDS Research Group, Institut de Investigacions Biomediques August Pi and Sunyer, IDIBAPS, Barcelona, Spain"
-      },
-      {
-        "author_name": "Xavier Nunez-Costa",
-        "author_inst": "Veristat, LLC. Barcelona, Spain, Toronto, Canada, Pickmere, UK"
-      },
-      {
-        "author_name": "Rachel Abu Taleb",
-        "author_inst": "Veristat, LLC. Barcelona, Spain, Toronto, Canada, Pickmere, UK"
-      },
-      {
-        "author_name": "Paula McSkimming",
-        "author_inst": "Veristat, LLC. Barcelona, Spain, Toronto, Canada, Pickmere, UK"
-      },
-      {
-        "author_name": "Alex Soriano",
-        "author_inst": "Hospital Clinic of Barcelona"
-      },
-      {
-        "author_name": "Jocelyn Planol",
-        "author_inst": "Hospital Clinic of Barcelona"
-      },
-      {
-        "author_name": "Jesse Omar Anagua",
-        "author_inst": "Hospital Clinic of Barcelona"
-      },
-      {
-        "author_name": "Rafael Ramos",
-        "author_inst": "Biomedical Research Institute, Girona, IdIBGi, Catalan Institute of Health"
-      },
-      {
-        "author_name": "Ruth Marti Lluch",
-        "author_inst": "Biomedical Research Institute, Girona, IdIBGi, Catalan Institute of Health"
-      },
-      {
-        "author_name": "Aida Corpes Comes",
-        "author_inst": "Biomedical Research Institute, Girona, IdIBGi, Catalan Institute of Health"
-      },
-      {
-        "author_name": "Susana Otero Romero",
-        "author_inst": "Hospital Universitari Vall de Hebron"
-      },
-      {
-        "author_name": "Xavier Martinez Gomez",
-        "author_inst": "Hospital Universitari Vall de Hebron"
-      },
-      {
-        "author_name": "Carla Sans-Pola",
-        "author_inst": "Hospital Universitari Vall de Hebron"
-      },
-      {
-        "author_name": "Jose Molto",
-        "author_inst": "Infectious Diseases Department, Hospital Universitari Germans Trias and Pujol, Badalona, Spain"
-      },
-      {
-        "author_name": "Susana Benet",
-        "author_inst": "Infectious Diseases Department, Hospital Universitari Germans Trias and Pujol, Badalona, Spain"
-      },
-      {
-        "author_name": "Lucia Bailon",
-        "author_inst": "Infectious Diseases Department, Hospital Universitari Germans Trias and Pujol, Badalona, Spain"
-      },
-      {
-        "author_name": "Jose Arribas",
-        "author_inst": "Infectious Diseases Unit. Internal Medicine Department, La Paz University Hospital, IdiPAZ, Madrid"
-      },
-      {
-        "author_name": "Alberto M Borobia",
-        "author_inst": "Infectious Diseases Unit. Internal Medicine Department, La Paz University Hospital, IdiPAZ, Madrid"
-      },
-      {
-        "author_name": "Javier Queiruga Parada",
-        "author_inst": "Infectious Diseases Unit. Internal Medicine Department, La Paz University Hospital, IdiPAZ, Madrid"
-      },
-      {
-        "author_name": "Jorge Navarro-Perez",
-        "author_inst": "Hospital Clinico Universitario Valencia"
-      },
-      {
-        "author_name": "Maria Jose Forner Giner",
-        "author_inst": "Hospital Clinico Universitario Valencia"
-      },
-      {
-        "author_name": "Rafael Orti Lucas",
-        "author_inst": "Hospital Clinico Universitario Valencia"
-      },
-      {
-        "author_name": "Maria del Mar Vazquez Jimenez",
-        "author_inst": "Hospital Regional Universitario de Malaga"
-      },
-      {
-        "author_name": "Salvador Ona Compan",
-        "author_inst": "Hospital Regional Universitario de Malaga"
-      },
-      {
-        "author_name": "Melchor Alvarez-Mon",
-        "author_inst": "Hospital Universitario Principe de Asturias, Madrid"
-      },
-      {
-        "author_name": "Daniel Troncoso",
-        "author_inst": "Hospital Universitario Principe de Asturias, Madrid"
-      },
-      {
-        "author_name": "Eunate Arana-Arri",
-        "author_inst": "Scientific Coordination, Biocruces Bizkaia HRI, Osakidetza, Barakaldo, Spain"
-      },
-      {
-        "author_name": "Susana Meijide",
-        "author_inst": "Scientific Coordination, Biocruces Bizkaia HRI, Osakidetza, Barakaldo, Spain"
-      },
-      {
-        "author_name": "Natale Imaz-Ayo",
-        "author_inst": "Scientific Coordination, Biocruces Bizkaia HRI, Osakidetza, Barakaldo, Spain"
-      },
-      {
-        "author_name": "Patricia Munoz Garcia",
-        "author_inst": "Instituto de Investigacion Sanitaria Hospital Gregorio Maranon, Madrid, Spain"
-      },
-      {
-        "author_name": "Sofia de la Villa Martinez",
-        "author_inst": "Instituto de Investigacion Sanitaria Hospital Gregorio Maranon, Madrid, Spain"
-      },
-      {
-        "author_name": "Sara Rodriguez Fernandez",
-        "author_inst": "Instituto de Investigacion Sanitaria Hospital Gregorio Maranon, Madrid, Spain"
-      },
-      {
-        "author_name": "Teresa Prat",
-        "author_inst": "HIPRA SCIENTIFIC, S.L.U"
-      },
-      {
-        "author_name": "Elia Torroella",
-        "author_inst": "HIPRA SCIENTIFIC S.L.U."
-      },
-      {
-        "author_name": "Laura Ferrer",
-        "author_inst": "HIPRA SCIENTIFIC S.L.U."
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.07.04.498661",
     "rel_title": "Proteome dynamics of COVID-19 severity learnt by a graph convolutional network of multi-scale topology",
@@ -251828,6 +250583,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.07.02.495455",
+    "rel_title": "SARS-CoV-2 3CLpro mutations confer resistance to Paxlovid (nirmatrelvir/ritonavir) in a VSV-based, non-gain-of-function system",
+    "rel_date": "2022-07-04",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.02.495455",
+    "rel_abs": "Protease inhibitors are among the most powerful antiviral drugs. A first protease inhibitor against the SARS-CoV-2 protease 3CLpro, Paxlovid (nirmatrelvir / ritonavir), has recently been authorized by the U.S. FDA for emergency use (EUA 105 Pfizer Paxlovid). To find resistant mutants against the protease-inhibitor-component of Paxlovid, nirmatrelvir, we engineered a chimeric Vesicular Stomatitis Virus (VSV). By replacing an intergenic region, which is essential for separate gene transcription, with 3CLpro, this chimeric VSV became dependent on the protease to process two of its genes. We then applied selective pressure with nirmatrelvir to induce mutations. The effect of those mutants was confirmed by re-introduction in the 3CLpro and testing with a recently developed cellular assay. Furthermore, we found that mutations predicted by our method already exist in SARS-CoV-2 sequence depositions in NCBI and GISAID data bases. These may represent emerging resistant virus variants or a natural heterogeneity in the susceptibility to nirmatrelvir.\n\nOne-Sentence SummaryMutations of the main protease of SARS-CoV-2 result in resistance against licensed drugs such as Paxlovid (nirmatrelvir / ritonavir).\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=144 SRC=\"FIGDIR/small/495455v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (32K):\norg.highwire.dtl.DTLVardef@1d539d3org.highwire.dtl.DTLVardef@1c76534org.highwire.dtl.DTLVardef@1c54c4corg.highwire.dtl.DTLVardef@14355d_HPS_FORMAT_FIGEXP  M_FIG C_FIG",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Emmanuel Heilmann",
+        "author_inst": "Medical University of Innsbruck"
+      },
+      {
+        "author_name": "Francesco Costacurta",
+        "author_inst": "Medical University of Innsbruck"
+      },
+      {
+        "author_name": "Andre Volland",
+        "author_inst": "Medical University of Innsbruck"
+      },
+      {
+        "author_name": "Dorothee von Laer",
+        "author_inst": "Medical University of Innsbruck"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2022.06.28.22276997",
     "rel_title": "Role of Error Catastrophe in Transmission Ability of Virus",
@@ -253101,49 +251887,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2022.06.29.22277073",
-    "rel_title": "Association of Right Ventricular Dilation and Dysfunction on Echocardiogram with In-Hospital Mortality Among Patients Hospitalized with COVID-19 Compared with Other Acute Respiratory Illness",
-    "rel_date": "2022-06-30",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.29.22277073",
-    "rel_abs": "BackgroundAlthough right ventricular (RV) dysfunction is associated with mortality in acute COVID-19, the role of RV dilation is uncertain. The prognostic significance of RV dilation and dysfunction among hospitalized patients with acute COVID-19 compared to other respiratory illnesses.\n\nMethodsWe conducted a retrospective cohort study to examine 225 consecutive adults admitted for acute COVID-19 and 6,150 control adults admitted for influenza, pneumonia or ARDS who had a clinical echocardiogram performed. We used logistic regression models to assess associations between RV parameters and in-hospital mortality adjusted for confounders.\n\nResultsAmong those with COVID-19, 48/225 (21.3%) died during the index hospitalization compared to 727/6150 (11.8%) with other respiratory illness (p=0.001). Independent of COVID-19, mild and moderate to severe RV dilation were associated with 1.4 and 2.0 times higher risk of inpatient mortality, respectively (95%CI 1.17 to 1.69; p=0.0003; 95%CI 1.62 to 2.47; p<0.0001, respectively). Similarly, mild and moderate RV dysfunction were associated with 1.4 and 1.7 times higher risk of inpatient mortality (95%CI 1.10 to 1.77; p=0.007; 95%CI 1.17 to 2.42; p=0.005, respectively). Relative to normal RV size and non-COVID-19 acute respiratory illness, mild and moderate RV dilation were associated with 1.4 times and 2.0 times higher risk among those without COVID-19 and 1.9 times higher and 3.0 times higher risk among those with COVID-19, with similar findings for RV dysfunction. Having both RV dilation and dysfunction or RV dilation alone were associated with 1.7 times higher risk while RV dysfunction alone was associated with 1.4 times higher risk compared to normal RV size and function.\n\nConclusionsRV dilation and dysfunction are associated with increased risk of inpatient mortality among those with COVID-19 and other respiratory illnesses. Abnormal RV findings may identify those at higher risk of short-term mortality from acute respiratory illness including COVID-19 beyond other risk markers.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Kaiwen Sun",
-        "author_inst": "University of California, San Francisco"
-      },
-      {
-        "author_name": "Emily R Cedarbaum",
-        "author_inst": "University of California, San Francisco"
-      },
-      {
-        "author_name": "Christopher Hill",
-        "author_inst": "University of California, San Francisco"
-      },
-      {
-        "author_name": "Sithu Win",
-        "author_inst": "University of California, San Francisco"
-      },
-      {
-        "author_name": "Nisha I Parikh",
-        "author_inst": "University of California, San Francisco"
-      },
-      {
-        "author_name": "Priscilla Y Hsue",
-        "author_inst": "University of California, San Francisco"
-      },
-      {
-        "author_name": "Matthew S Durstenfeld",
-        "author_inst": "University of California, San Francisco & Zuckerberg San Francisco General Hospital"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "cardiovascular medicine"
-  },
   {
     "rel_doi": "10.1101/2022.06.29.22277065",
     "rel_title": "Missing Americans: Early Death in the United States, 1933-2021",
@@ -253494,6 +252237,57 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2022.06.29.498191",
+    "rel_title": "Inhibitory effects of GT0918 on acute lung injury and the molecular mechanisms of anti-inflammatory response",
+    "rel_date": "2022-06-30",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.29.498191",
+    "rel_abs": "Coronavirus disease 2019 (COVID-19) has caused the public health crisis in the whole world. Anti-androgens block severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry and protect against severe clinical COVID-19 outcomes. GT0918, a novel androgen receptor antagonist, accelerated viral clearance and increased recovery rate in outpatients by blocking SARS-CoV-2 infection though down-regulating ACE2 and TMPRSS2 expression. Further clinical study showed that GT0918 reduced mortality rate and shortened hospital stay in hospitalized COVID-19 patients. GT0918 also exhibits protective efficacy in severe COVID-19 patient in critical care. However, the mechanism of GT0918 treatment for severe COVID-19 disease is unknown. Here, we found GT0918 decreased the expression and secretion of proinflammatory cytokines through NF-{kappa}B signaling pathway. The acute lung injury induced by LPS or Poly(I:C) was also attenuated in GT0918-treated mice, compared with vehicle control group. Moreover, GT0918 elevated the NRF2 protein level but not mRNA transcription activity. GT0918 induced proinflammatory cytokines downregulation was partially dependent on NRF2. In conclusion, our data demonstrate that GT0918 reduced cytokine release and suppressed inflammatory responses through inhibiting NF-{kappa}B signaling and activating NRF2. GT0918 is not only effective for treatment of mild to moderate COVID-19 patients, but also a potential therapeutic drug for severe COVID-19 patients by reducing the risk of cytokine storm and acute respiratory distress syndrome.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Xiaodan Hou",
+        "author_inst": "Kintor Pharmaceutical Limited"
+      },
+      {
+        "author_name": "Honghua Yan",
+        "author_inst": "Kintor Pharmaceutical Limited"
+      },
+      {
+        "author_name": "Ao Wang",
+        "author_inst": "Kintor Pharmaceutical Limited"
+      },
+      {
+        "author_name": "Cong Liu",
+        "author_inst": "Kintor Pharmaceutical Limited"
+      },
+      {
+        "author_name": "Qianxiang Zhou",
+        "author_inst": "Kintor Pharmaceutical Limited"
+      },
+      {
+        "author_name": "Liandong Ma",
+        "author_inst": "Kintor Pharmaceutical Limited"
+      },
+      {
+        "author_name": "Jie Chen",
+        "author_inst": "Kintor Pharmaceutical Limited"
+      },
+      {
+        "author_name": "Zhihua Ren",
+        "author_inst": "Kintor Pharmaceutical Limited"
+      },
+      {
+        "author_name": "Youzhi Tong",
+        "author_inst": "Kintor Pharmaceutical Limited"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "cell biology"
+  },
   {
     "rel_doi": "10.1101/2022.06.29.22277044",
     "rel_title": "Severity of Omicron (B.1.1.529) and Delta (B.1.1.617.2) SARS-CoV-2 infection among hospitalised adults: a prospective cohort study",
@@ -254803,113 +253597,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2022.06.28.22276989",
-    "rel_title": "Hybrid and vaccine-induced immunity against SARS-CoV-2 in MS patients on different disease-modifying therapies",
-    "rel_date": "2022-06-28",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.28.22276989",
-    "rel_abs": "ObjectiveTo compare  hybrid immunity (prior COVID-19 infection plus vaccination) and post-vaccination immunity to SARS CoV-2 in MS patients on different disease-modifying therapies (DMTs) and to assess the impact of vaccine product and race/ethnicity on post-vaccination immune responses.\n\nMethodsConsecutive MS patients from NYU MS Care Center (New York, NY), aged 18-60, who completed COVID-19 vaccination series [&ge;]6 weeks previously were evaluated for SARS CoV-2-specific antibody responses with electro-chemiluminescence and multiepitope bead-based immunoassays and, in a subset, live virus immunofluorescence-based microneutralization assay. SARS CoV-2-specific cellular responses were assessed with cellular stimulation TruCulture IFN{gamma} and IL-2 assay and, in a subset, with IFN{gamma} and IL-2 ELISpot assays. Multivariate analyses examined associations between immunologic responses and prior COVID-19 infection while controlling for age, sex, DMT at vaccination, time-to-vaccine, and vaccine product.\n\nResultsBetween 6/01/2021-11/11/2021, 370 MS patients were recruited (mean age 40.6 years; 76% female; 53% non-White; 22% with prior infection; common DMT classes: ocrelizumab 40%; natalizumab 15%, sphingosine-1-phosphate receptor modulators 13%; and no DMT 8%). Vaccine-to-collection time was 18.7 ({+/-}7.7) weeks and 95% of patients received mRNA vaccines. In multivariate analyses, patients with laboratory-confirmed prior COVID-19 infection had significantly increased antibody and cellular post-vaccination responses compared to those without prior infection. Vaccine product and DMT class were independent predictors of antibody and cellular responses, while race/ethnicity was not.\n\nInterpretationPrior COVID-19 infection is associated with enhanced antibody and cellular post-vaccine responses independent of DMT class and vaccine type. There were no differences in immune responses across race/ethnic groups.",
-    "rel_num_authors": 23,
-    "rel_authors": [
-      {
-        "author_name": "Ilya Kister",
-        "author_inst": "NYU Multiple Sclerosis Comprehensive Care Center, Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA"
-      },
-      {
-        "author_name": "Ryan Curtin",
-        "author_inst": "Laura and Isaac Perlmutter Cancer Center and Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA"
-      },
-      {
-        "author_name": "Jinglan Pei",
-        "author_inst": "Genentech, Inc., South San Francisco, CA, USA"
-      },
-      {
-        "author_name": "Katherine Perdomo",
-        "author_inst": "NYU Multiple Sclerosis Comprehensive Care Center, Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA"
-      },
-      {
-        "author_name": "Tamar E. Bacon",
-        "author_inst": "NYU Multiple Sclerosis Comprehensive Care Center, Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA"
-      },
-      {
-        "author_name": "Iryna Voloshyna",
-        "author_inst": "Laura and Isaac Perlmutter Cancer Center and Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA"
-      },
-      {
-        "author_name": "Joseph Kim",
-        "author_inst": "Laura and Isaac Perlmutter Cancer Center and Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA"
-      },
-      {
-        "author_name": "Ethan Tardio",
-        "author_inst": "Laura and Isaac Perlmutter Cancer Center and Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA"
-      },
-      {
-        "author_name": "Yogambigai Velmurugu",
-        "author_inst": "Laura and Isaac Perlmutter Cancer Center and Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA"
-      },
-      {
-        "author_name": "Samantha Nyovanie",
-        "author_inst": "Laura and Isaac Perlmutter Cancer Center and Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA"
-      },
-      {
-        "author_name": "Andrea Valeria Calderon",
-        "author_inst": "Laura and Isaac Perlmutter Cancer Center and Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA"
-      },
-      {
-        "author_name": "Fatoumatta Dibba",
-        "author_inst": "Laura and Isaac Perlmutter Cancer Center and Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA"
-      },
-      {
-        "author_name": "Stanzin Idga",
-        "author_inst": "Laura and Isaac Perlmutter Cancer Center and Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA"
-      },
-      {
-        "author_name": "Marie Samanovic",
-        "author_inst": "NYU Langone Vaccine Center, Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA"
-      },
-      {
-        "author_name": "Pranil Raut",
-        "author_inst": "Genentech, Inc., South San Francisco, CA, USA"
-      },
-      {
-        "author_name": "Catarina Raposo",
-        "author_inst": "F. Hoffmann-La Roche Ltd, Basel, Switzerland"
-      },
-      {
-        "author_name": "Jessica Priest",
-        "author_inst": "Genentech, Inc., South San Francisco, CA, USA"
-      },
-      {
-        "author_name": "Mark Cabatingan",
-        "author_inst": "Genentech, Inc., South San Francisco, CA, USA"
-      },
-      {
-        "author_name": "Ryan C. Winger",
-        "author_inst": "Genentech, Inc., South San Francisco, CA, USA"
-      },
-      {
-        "author_name": "Mark J. Mulligan",
-        "author_inst": "NYU Langone Vaccine Center, Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA"
-      },
-      {
-        "author_name": "Yury Patskovsky",
-        "author_inst": "Laura and Isaac Perlmutter Cancer Center and Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA"
-      },
-      {
-        "author_name": "Gregg J. Silverman",
-        "author_inst": "Division of Rheumatology, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA"
-      },
-      {
-        "author_name": "Michelle Krogsgaard",
-        "author_inst": "Laura and Isaac Perlmutter Cancer Center and Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "neurology"
-  },
   {
     "rel_doi": "10.1101/2022.06.27.22276976",
     "rel_title": "Hand Dermatitis among Health Care Workers during the COVID-19 Pandemic: Prevalence, and Risk Factors",
@@ -255244,6 +253931,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.06.28.22276851",
+    "rel_title": "The COVID-19 pandemic sparked off a large-scale outbreak of carbapenem-resistant Acinetobacter baumannii from the endemic strains of an Italian hospital",
+    "rel_date": "2022-06-28",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.28.22276851",
+    "rel_abs": "Acinetobacter baumannii is a nosocomial pathogen that poses a serious threat due to the rise of incidence of multidrug resistant (MDR) strains. During the COVID-19 pandemic, MDR A.baumannii clones have caused several outbreaks worldwide. Here we describe a detailed investigation of an MDR A. baumannii outbreak that occurred at Fondazione IRCCS Policlinico San Matteo (Pavia, Italy). A total of 96 A. baumannii strains, isolated between January and July 2020 from 41 inpatients (both SARS-CoV-2 positive and negative) in different wards, were characterized by phenotypic and genomic analyses combining Illumina and Nanopore sequencing. Antibiotic susceptibility testing revealed that all isolates were resistant to carbapenems and the sequence analysis attributed this to the carbapenemase gene blaOXA-23. Screening of virulence factors unveiled that all strains carried determinants for biofilm formation, while plasmid analysis revealed the presence of two plasmids, one of which was a 100kbp long and encoded a phage sequence.\n\nA core genome-based phylogeny was inferred to integrate outbreak strain genomes with background genomes from public databases and from the local surveillance program. All strains belonged to the globally disseminated ST2 clone and were mainly divided into two clades. Isolates from the outbreak clustered with surveillance isolates from 2019, suggesting that the outbreak was caused by two strains that were already circulating in the hospital before the start of the pandemic. The intensive spread of A. baumannii in the hospital was enhanced by the extreme emergency situation of the first COVID-19 pandemic wave that resulted in minor attention to infection prevention and control practices.\n\nImportanceThe COVID-19 pandemic, especially during the first wave, posed a great challenge to the hospital management and generally promoted nosocomial pathogen dissemination. Multidrug resistant (MDR) A. baumannii can easily spread and persist for a long time on surfaces, causing outbreaks in healthcare settings. Infection prevention and control practices, epidemiological surveillance and microbiological screening are fundamental in order to control such outbreaks.\n\nHere, we sequenced the genomes of 96 isolates from an outbreak of MDR A. baumannii strains using both short- and long-read technology in order to reconstruct the outbreak events in fine detail. The sequence data demonstrated that two endemic clones of MDR A. baumannii were the source of this large hospital outbreak during the first COVID-19 pandemic wave, confirming the effect of COVID-19 emergency disrupting the protection provided by the use of the standard prevention procedures.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Greta Petazzoni",
+        "author_inst": "Fondazione IRCCS Policlinico San Matteo"
+      },
+      {
+        "author_name": "Greta Bellinzona",
+        "author_inst": "Universit\u00e0 degli Studi di Pavia"
+      },
+      {
+        "author_name": "Cristina Merla",
+        "author_inst": "Fondazione IRCCS Policlinico San Matteo"
+      },
+      {
+        "author_name": "Marta Corbella",
+        "author_inst": "Fondazione IRCCS Policlinico San Matteo"
+      },
+      {
+        "author_name": "\u00d8rjan Samuelsen",
+        "author_inst": "University Hospital of North Norway"
+      },
+      {
+        "author_name": "Jukka Corander",
+        "author_inst": "University of Oslo"
+      },
+      {
+        "author_name": "Davide Sassera",
+        "author_inst": "Universit\u00e0 degli Studi di Pavia"
+      },
+      {
+        "author_name": "Stefano Gaiarsa",
+        "author_inst": "Fondazione IRCCS Policlinico San Matteo"
+      },
+      {
+        "author_name": "Patrizia Cambieri",
+        "author_inst": "Fondazione IRCCS Policlinico San Matteo"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.06.28.22276983",
     "rel_title": "Outcomes of laboratory-confirmed SARS-CoV-2 infection during resurgence driven by Omicron lineages BA.4 and BA.5 compared with previous waves in the Western Cape Province, South Africa",
@@ -256629,45 +255367,6 @@
     "type": "new results",
     "category": "synthetic biology"
   },
-  {
-    "rel_doi": "10.1101/2022.06.26.22276906",
-    "rel_title": "Non-Adherence of PLWHA in taking Antiretroviral during the COVID-19 pandemic in West Sumatra, Indonesia: Qualitative analysis",
-    "rel_date": "2022-06-27",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.26.22276906",
-    "rel_abs": "IntroductionCOVID-19 pandemic condition affects the adherence of PLWHA in taking antiretroviral drugs. People with Lost to Follow-up (LTFU) were an average of 26 %, The feared impact is the high mortality rate and decreased productivity, visits of PLWHA patients to M Jamil Hospital come from all regions in West Sumatra to the southern provinces of Jambi and Bengkulu. This study aimed to determine factors that influence patient non-Adherence during the COVID-19 pandemic.\n\nMethodThis study was conducted by exploring the experiences of patients and health workers by observing adherence to taking antiretroviral, 34 informant: 25 patients, 5 NGOs, and 4 health workers, The data were collected from September 6th to October 9th 2021, Analysis data using N VIVO 12.\n\nResultsPatients in taking medication during the COVID-19 pandemic were feeling bored, most of the patient lived was so far, so patients often asked for help from NGOs to take medication. Forgetfulness, busyness, and fear of being exposed to COVID-19. Then, the economic factor, due to the large number of layoffs, and the absence of BPJS insurance affects compliance, while the factors of stigma, stress, feeling well are slightly expressed by patients. It turns out that the Covid-19 condition affects patients to come for treatment to the hospital. In addition to drug side effects, dizziness, nausea, and vomiting also affect medication adherence. The role of NGOs in providing information and education as well as motivating and taking medication during the COVID-19 condition is very important.\n\nConclusionThe most common causes of non-compliance from loss to follow-up during the COVID-19 pandemic are; bored, far from home, forgetful, and economic factors for fear of covid-19. Most of the side effects of drugs are dizziness, and nausea and vomiting so that the role of NGOs is important in helping patients take medication.\n\nO_TEXTBOXStrength and limitation of this study\n\n[tpltrtarr]This qualitative research is about medication adherence during the covid-19\n[tpltrtarr]The factors that influence patient adherence to taking ART are different during this covid-19 pandemic, namely the distance from which they live has an effect on patients wanting to take medication, so the role of NGOs in sending drugs is very important, according to the doctors approval, after the next 3 months the patient is required to come, this is never happened before the Covid-19 condition, Patients adherence are very dependent on the patients self-awareness to live in the long term, the convenience has been provided by M Jamil Hospital by making it easy to send drugs to the patients own address.\n[tpltrtarr]This qualitative analysis using N vivo 12, which has now developed into N vivo 14\n[tpltrtarr]Patient recruitment is divided into two, namely obedient and non-compliant patients, but the patients answers are almost the same.\n\n\nC_TEXTBOX",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Adriani suwito",
-        "author_inst": "fort de kock, Bukittinggi-West Sumatra"
-      },
-      {
-        "author_name": "Ikhwana ikhwana",
-        "author_inst": "Andalas university wes Sumatra"
-      },
-      {
-        "author_name": "Elly usman",
-        "author_inst": "Andalas University West Sumatra"
-      },
-      {
-        "author_name": "Arina widya murni",
-        "author_inst": "Andalas Univesity west Sumatra Indonesia"
-      },
-      {
-        "author_name": "Evi Hasnita",
-        "author_inst": "Fort de Kock Univesity,Bukittinggi,West Sumatra,Indonesia"
-      },
-      {
-        "author_name": "Rianingsih Indra",
-        "author_inst": "Andalas university, VCT Departemen, Padang,West Sumatra, Indonesia"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "hiv aids"
-  },
   {
     "rel_doi": "10.1101/2022.06.27.22276938",
     "rel_title": "Capturing the SARS-CoV-2 infection pyramid within the municipality of Rotterdam using longitudinal sewage surveillance",
@@ -256938,6 +255637,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "respiratory medicine"
   },
+  {
+    "rel_doi": "10.1101/2022.06.27.22276736",
+    "rel_title": "An Economic Evaluation of a virtual Covid Ward in Leicester, Leicestershire, and Rutland",
+    "rel_date": "2022-06-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.27.22276736",
+    "rel_abs": "ObjectiveThe objective of this study was to demonstrate the impact of a virtual Covid--19 ward on NHS resource use.\n\nMethodsDifferent methods were used to derive comparators for the observational data on acute length of stay versus the actual lengths of stay of 310 patients on acute wards and differences estimated. The resource use associated with delivering care in the virtual ward were collected on an ongoing basis.\n\nResultsThe virtual ward delivered estimated health care system savings of 1,103 bed days, {pound}529,719 in net financial savings across two key groups of patients; those who had been on oxygen and required weaning off it while within the virtual ward and those not requiring oxygen therapy with less severe acute Covid disease. The costs of the intervention were 9.7% of the estimated gross savings and the mean net saving per patient was {pound}1,709 in the base case without including the savings associated with a likely reduction in re-admissions. The 30-day re-admission rate was 2.9%, which was substantially beneath alternative comparative data. The mean cost of the intervention was {pound}184.38 per patient.\n\nConclusionThe virtual ward delivered significant financial savings in both groups of patients, did so with a high degree of confidence, whilst doing so at a very low absolute and relative cost.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Jim Swift",
+        "author_inst": "Spirit Health Group"
+      },
+      {
+        "author_name": "Noel O'Kelly",
+        "author_inst": "Spirit Health"
+      },
+      {
+        "author_name": "Chris Barker",
+        "author_inst": "Spirit Health"
+      },
+      {
+        "author_name": "Alex Woodward",
+        "author_inst": "Leicestershire Partnership Trust"
+      },
+      {
+        "author_name": "Sudip Ghosh",
+        "author_inst": "De Montford University & Leicestershire Partnership Trust"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health economics"
+  },
   {
     "rel_doi": "10.1101/2022.06.27.22276960",
     "rel_title": "Telemedicine Use Among People with HIV in 2021: The Hybrid-Care Environment",
@@ -258299,37 +257033,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2022.06.23.497326",
-    "rel_title": "DESIGN OF A CHIMERIC ACE-2/Fc-SILENT FUSION PROTEIN WITH ULTRAHIGH AFFINITY AND NEUTRALIZING CAPACITY FOR SARS-CoV-2 VARIANTS",
-    "rel_date": "2022-06-24",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.23.497326",
-    "rel_abs": "As the coronavirus SARS-CoV-2 continues to mutate into Variants of Concern (VOC), there is a growing and urgent need to develop effective antivirals to combat the newly emerged infectious disease COVID-19. Recent data indicate that monoclonal antibodies developed early in the pandemic are no longer capable of effectively neutralizing currently active VOCs. This report describes the design of a class of variant-agnostic chimeric molecules consisting of an Angiotensin Converting Enzyme-2 (ACE-2) domain mutated to retain ultrahigh affinity binding to a wide variety of SARS-CoV-2 variants, coupled to an Fc-silent immunoglobulin domain that eliminates antibody-dependent enhancement (ADE) and simultaneously extends biological half-life compared to existing mABs. Molecular modeling revealed that ACE-2 mutations L27, V34 and E90 resulted in ultrahigh affinity binding of the LVE-ACE-2 domain to the widest variety of VOCs, with KDs of 93 pM, 507 pM and 73 pM for binding to the Alpha B1.1.7, Delta B.1.617.2 and Omicron B.1.1.529 variants, and notably, 78fM affinity to the Omicron BA.2 variant, respectively. Surrogate viral neutralization assays (sVNT) revealed titers of[&ge;] 4.9ng/ml, for neutralization of recombinant viral proteins corresponding to the Alpha, Delta and Omicron variants. The values above were obtained with LVE-ACE-2/mAB chimeras containing the Y-T-E sequence that enhances binding to the FcRn receptor, which in turn is expected to extend biological half-life 3-4-fold. It is proposed that this new class of chimeric ACE-2/mABs will constitute variant-agnostic and cost-effective prophylactics against SARS-CoV-2, particularly when administered by nasal delivery systems.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Bruce Uhal",
-        "author_inst": "Michigan State University"
-      },
-      {
-        "author_name": "Neil M Bodie",
-        "author_inst": "Paradigm Immunotherapeutics LTD"
-      },
-      {
-        "author_name": "David Connolly",
-        "author_inst": "Michigan State University"
-      },
-      {
-        "author_name": "Jennifer Chu",
-        "author_inst": "ACROBiosystems"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2022.06.24.497526",
     "rel_title": "In Vitro Evaluation and Mitigation of Niclosamide Liabilities as a COVID-19 Treatment.",
@@ -258688,6 +257391,181 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.06.22.22276362",
+    "rel_title": "Immune Correlates Analysis of the PREVENT-19 COVID-19 Vaccine Efficacy Clinical Trial",
+    "rel_date": "2022-06-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.22.22276362",
+    "rel_abs": "In the randomized, placebo-controlled PREVENT-19 phase 3 trial conducted in the U.S. and Mexico of the NVX-CoV2373 adjuvanted, recombinant spike protein nanoparticle vaccine, anti-spike binding IgG concentration (spike IgG) and pseudovirus 50% neutralizing antibody titer (nAb ID50) measured two weeks after two doses were assessed as correlates of risk and as correlates of protection against PCR-confirmed symptomatic SARS-CoV-2 infection (COVID- 19). These immune correlates analyses were conducted in the U.S. cohort of baseline SARS- CoV-2 negative per-protocol participants using a case-cohort design that measured the antibody markers from all 12 vaccine recipient breakthrough COVID-19 cases starting 7 days post antibody measurement and from 639 vaccine recipient non-cases (Mexico was excluded due to zero breakthrough cases with the efficacy data cut-off date April 19, 2021). In vaccine recipients, the baseline risk factor-adjusted hazard ratio of COVID-19 was 0.36 (95% CI: 0.20, 0.63), p<0.001 (adjusted p-0.005) per 10-fold increase in IgG spike concentration and 0.39 (0.19, 0.82), p=0.013 (adjusted p=0.030) per 10-fold increase in nAb ID50 titer. At spike IgG concentration 100, 1000, and 6934 binding antibody units/ml (100 is the 3rd percentile, 6934 is the 97.5th percentile), vaccine efficacy to reduce the probability of acquiring COVID-19 at 59 days post marker measurement was 65.5% (95% CI: 23.0%, 90.8%), 87.7% (77.7%, 94.4%), and 94.8% (88.0%, 97.9%), respectively. At nAb ID50 titers of 50, 100, 1000, and 7230 IU50/ml (50 is the 5th percentile, 7230 the 97.5th percentile), these estimates were 75.7% (49.8%, 93.2%), 81.7% (66.3%, 93.2%), 92.8% (85.1%, 97.4%) and 96.8% (88.3%, 99.3%). The same two antibody markers were assessed as immune correlates via the same study design and statistical analysis in the mRNA-1273 phase 3 COVE trial (except in COVE the markers were measured four weeks post dose two). Spike IgG levels were slightly lower and nAb ID50 titers slightly higher after NVX-CoV2373 than after mRNA-1273 vaccination. The strength of the nAb ID50 correlate was similar between the trials, whereas the spike IgG antibodies appeared to correlate more strongly with NVX-CoV2373 in PREVENT-19, as quantified by the hazard ratio and the degree of change in vaccine efficacy across antibody levels. However, the relatively few breakthrough cases in PREVENT-19 limited the ability to infer a stronger correlate. The conclusion is that both markers were consistent correlates of protection for the two vaccines, supporting potential cross-vaccine platform applications of these markers for guiding decisions about vaccine approval and use.",
+    "rel_num_authors": 40,
+    "rel_authors": [
+      {
+        "author_name": "Youyi Fong",
+        "author_inst": "Fred Hutchinson Cancer Center"
+      },
+      {
+        "author_name": "Yunda Huang",
+        "author_inst": "Fred Hutchinson Cancer Center"
+      },
+      {
+        "author_name": "David Benkeser",
+        "author_inst": "Emory"
+      },
+      {
+        "author_name": "Lindsay N. Carpp",
+        "author_inst": "Fred Hutchinson Cancer Center"
+      },
+      {
+        "author_name": "Germ\u00e1n \u00c1\u00f1ez",
+        "author_inst": "Novavax, Inc."
+      },
+      {
+        "author_name": "Wayne Woo",
+        "author_inst": "Novavax, Inc."
+      },
+      {
+        "author_name": "Alice McGarry",
+        "author_inst": "Novavax, Inc."
+      },
+      {
+        "author_name": "Lisa M. Dunkle",
+        "author_inst": "Novavax, Inc."
+      },
+      {
+        "author_name": "Iksung Cho",
+        "author_inst": "Novavax, Inc."
+      },
+      {
+        "author_name": "Christopher R. Houchens",
+        "author_inst": "Biomedical Advanced Research and Development Authority"
+      },
+      {
+        "author_name": "Karen Martins",
+        "author_inst": "Biomedical Advanced Research and Development Authority"
+      },
+      {
+        "author_name": "Lakshmi Jayashankar",
+        "author_inst": "Biomedical Advanced Research and Development Authority"
+      },
+      {
+        "author_name": "Flora Castellino",
+        "author_inst": "Biomedical Advanced Research and Development Authority"
+      },
+      {
+        "author_name": "Christos Petropoulos",
+        "author_inst": "Monogram Biosciences"
+      },
+      {
+        "author_name": "Andrew Leith",
+        "author_inst": "Nexelis"
+      },
+      {
+        "author_name": "Deanne Haugaard",
+        "author_inst": "Nexelis"
+      },
+      {
+        "author_name": "Bill Webb",
+        "author_inst": "Nexelis"
+      },
+      {
+        "author_name": "Yiwen Lu",
+        "author_inst": "Fred Hutchinson Cancer Center"
+      },
+      {
+        "author_name": "Chenchen Yu",
+        "author_inst": "Fred Hutchinson Cancer Center"
+      },
+      {
+        "author_name": "Bhavesh Borate",
+        "author_inst": "Fred Hutchinson Cancer Center"
+      },
+      {
+        "author_name": "Lars W. P. van der Laan",
+        "author_inst": "Fred Hutchinson Cancer Center"
+      },
+      {
+        "author_name": "Nima S. Hejazi",
+        "author_inst": "Fred Hutchinson Cancer Center"
+      },
+      {
+        "author_name": "April Kaur Randhawa",
+        "author_inst": "Fred Hutchinson Cancer Center"
+      },
+      {
+        "author_name": "Michele P. Andrasik",
+        "author_inst": "Fred Hutchinson Cancer Center"
+      },
+      {
+        "author_name": "James G. Kublin",
+        "author_inst": "Fred Hutchinson Cancer Center"
+      },
+      {
+        "author_name": "Julia Hutter",
+        "author_inst": "Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases"
+      },
+      {
+        "author_name": "Maryam Keshtkar-Jahromi",
+        "author_inst": "Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases"
+      },
+      {
+        "author_name": "Tatiana H. Beresnev",
+        "author_inst": "Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases"
+      },
+      {
+        "author_name": "Lawrence Corey",
+        "author_inst": "Fred Hutchinson Cancer Center"
+      },
+      {
+        "author_name": "Kathleen M. Neuzil",
+        "author_inst": "Center for Vaccine Development and Global Health, University of Maryland School of Medicine"
+      },
+      {
+        "author_name": "Dean Follmann",
+        "author_inst": "Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
+      },
+      {
+        "author_name": "Julie A. Ake",
+        "author_inst": "U.S. Military HIV Research Program, Walter Reed Army Institute of Research"
+      },
+      {
+        "author_name": "Cynthia L. Gay",
+        "author_inst": "University of North Carolina School of Medicine"
+      },
+      {
+        "author_name": "Karen L. Kotloff",
+        "author_inst": "Center for Vaccine Development and Global Health, University of Maryland School of Medicine"
+      },
+      {
+        "author_name": "Richard A. Koup",
+        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
+      },
+      {
+        "author_name": "Ruben O. Donis",
+        "author_inst": "Biomedical Advanced Research and Development Authority"
+      },
+      {
+        "author_name": "Peter B. Gilbert",
+        "author_inst": "Fred Hutchinson Cancer Center"
+      },
+      {
+        "author_name": "- Immune Assays Team",
+        "author_inst": "Immune Assays Team"
+      },
+      {
+        "author_name": "- Coronavirus Vaccine Prevention Network (CoVPN)/2019nCoV-301 Principal Investigators and Study Team",
+        "author_inst": ""
+      },
+      {
+        "author_name": "- United States Government (USG)/CoVPN Biostatistics Team",
+        "author_inst": ""
+      }
+    ],
+    "version": "1",
+    "license": "cc0",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.06.22.22276755",
     "rel_title": "New, fast, and precise method of COVID-19 detection in nasopharyngeal and tracheal aspirate samples combining optical spectroscopy and machine learning",
@@ -259997,69 +258875,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "allergy and immunology"
   },
-  {
-    "rel_doi": "10.1101/2022.06.20.22276636",
-    "rel_title": "Effectiveness of Subcutaneous Casirivimab and Imdevimab Relative to no COVID-19 Antibody Treatment Among Patients Diagnosed With COVID-19 in the Ambulatory Setting",
-    "rel_date": "2022-06-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.20.22276636",
-    "rel_abs": "ImportanceData on real-world effectiveness of subcutaneous (SC) administration of casirivimab and imdevimab (CAS+IMD) for treatment of COVID-19 are limited.\n\nObjectiveTo assess effectiveness of SC CAS+IMD vs no COVID-19 antibody treatment among patients diagnosed with COVID-19 in ambulatory settings during the Delta-dominant period prior to Omicron emergence.\n\nDesignRetrospective cohort study.\n\nSettingEncrypted linked data between Komodo Health closed claims database and CDR Maguire Health & Medical database.\n\nParticipantsPatients with COVID-19 in ambulatory settings between August 1, 2021 and October 30, 2021 treated with SC CAS+IMD were exact- and propensity score-matched to up to 5 untreated patients who were treatment-eligible under the Emergency Use Authorization (EUA)\n\nExposureSubcutaneous CAS+IMD.\n\nMain Outcomes and MeasuresComposite endpoint of 30-day all-cause mortality or COVID- 19-related hospitalization. Kaplan-Meier estimators were used to calculate composite risk overall and across subgroups including age, COVID-19 vaccination status, immunocompromised, and elevated risk defined as age [&ge;] 65 years or 55-64 years with body mass index [&ge;] 35 kg/m2, type 2 diabetes, chronic obstructive pulmonary disease, or chronic kidney disease. Cox proportional- hazards models were used to estimate adjusted hazard ratios (aHR) and 95% confidence intervals (CI).\n\nResultsAmong 13 522 patients treated with SC CAS+IMD, 12 972 (95.9%) were matched to 41 848 EUA-eligible untreated patients; patients were 57-58% female, with mean age between 50 and 52 years. The 30-day composite outcome risk was 1.9% (95% CI, 1.7-2.2; 247 events) and 4.4% (95% CI, 4.2-4.6; 1822 events) in the CAS+IMD-treated and untreated cohorts, respectively; CAS+IMD treatment was associated with a 49% lower risk (aHR 0.51; 95% CI, 0.46-0.58). Treatment was also associated with a 67% lower 30-day risk of all-cause mortality (aHR 0.33, 95% CI, 0.18-0.60). Treatment effectiveness was consistent regardless of vaccination status and across subgroups, including those at elevated risk (aHR 0.51, 95% CI 0.42-0.60) or immunocompromised (aHR 0.34, 95% CI 0.17-0.66).\n\nConclusions and RelevanceSubcutaneous treatment with CAS+IMD is effective for reducing all-cause mortality or COVID-19-related hospitalization in patients diagnosed with COVID-19 and managed in real-world outpatient settings during the Delta-dominant period. Effectiveness is maintained among immunocompromised, vaccinated, and elevated risk patients.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Jessica J Jalbert",
-        "author_inst": "Regeneron Pharmaceuticals, Inc."
-      },
-      {
-        "author_name": "Mohamed Hussein",
-        "author_inst": "Regeneron Pharmaceuticals, Inc., Tarrytown, NY"
-      },
-      {
-        "author_name": "Vera Mastey",
-        "author_inst": "Regeneron Pharmaceuticals, Inc., Tarrytown, NY"
-      },
-      {
-        "author_name": "Robert J. Sanchez",
-        "author_inst": "Regeneron Pharmaceuticals, Inc., Tarrytown, NY"
-      },
-      {
-        "author_name": "Degang Wang",
-        "author_inst": "Regeneron Pharmaceuticals, Inc., Tarrytown, NY"
-      },
-      {
-        "author_name": "Dana Murdock",
-        "author_inst": "Regeneron Pharmaceuticals, Inc., Tarrytown, NY"
-      },
-      {
-        "author_name": "Laura Farinas",
-        "author_inst": "CDR Maguire, Tallahassee, FL"
-      },
-      {
-        "author_name": "Jonathan Bussey",
-        "author_inst": "CDR Maguire, Tallahassee, FL"
-      },
-      {
-        "author_name": "Carlos Duart",
-        "author_inst": "CDR Maguire, Tallahassee, FL"
-      },
-      {
-        "author_name": "Boaz Hirshberg",
-        "author_inst": "Regeneron Pharmaceuticals, Inc., Tarrytown, NY"
-      },
-      {
-        "author_name": "David M. Weinreich",
-        "author_inst": "Regeneron Pharmaceuticals, Inc., Tarrytown, NY"
-      },
-      {
-        "author_name": "Wenhui Wei",
-        "author_inst": "Regeneron Pharmaceuticals, Inc., Tarrytown, NY"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.06.21.22276717",
     "rel_title": "VirPool: Model-Based Estimation of SARS-CoV-2 Variant Proportions in Wastewater Samples",
@@ -260546,6 +259361,85 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2022.06.21.497047",
+    "rel_title": "Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection",
+    "rel_date": "2022-06-22",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.21.497047",
+    "rel_abs": "The global evolution of SARS-CoV-2 depends in part upon the evolutionary dynamics within individual hosts with varying immune histories. To characterize the within-host evolution of acute SARS-CoV-2 infection, we deep sequenced saliva and nasal samples collected daily from immune and unvaccinated individuals early during infection. We show that longitudinal sampling facilitates high-confidence genetic variant detection and reveals evolutionary dynamics missed by less-frequent sampling strategies. Within-host dynamics in both naive and immune individuals appeared largely stochastic; however, we identified clear mutational hotspots within the viral genome, consistent with selection and differing between naive and immune individuals. In rare cases, minor genetic variants emerged to frequencies sufficient for forward transmission. Finally, we detected significant genetic compartmentalization of virus between saliva and nasal swab sample sites in many individuals. Altogether, these data provide a high-resolution profile of within-host SARS-CoV-2 evolutionary dynamics.",
+    "rel_num_authors": 16,
+    "rel_authors": [
+      {
+        "author_name": "Mireille Farjo",
+        "author_inst": "University of Illinois at Urbana-Champaign"
+      },
+      {
+        "author_name": "Katia Koelle",
+        "author_inst": "Emory University"
+      },
+      {
+        "author_name": "Michael A. Martin",
+        "author_inst": "Emory University"
+      },
+      {
+        "author_name": "Laura L Gibson",
+        "author_inst": "University of Massachusetts Medical School"
+      },
+      {
+        "author_name": "Kimberly KO Walden",
+        "author_inst": "University of Illinois at Urbana-Champaign"
+      },
+      {
+        "author_name": "Gloria Rendon",
+        "author_inst": "University of Illinois at Urbana Champaign"
+      },
+      {
+        "author_name": "Christopher J. Fields",
+        "author_inst": "University of Illinois at Urbana Champaign"
+      },
+      {
+        "author_name": "Fadi Alnaji",
+        "author_inst": "University of Illinois at Urbana Champaign"
+      },
+      {
+        "author_name": "Nicholas Gallagher",
+        "author_inst": "Johns Hopkins University School of Medicine"
+      },
+      {
+        "author_name": "Chun Huai Luo",
+        "author_inst": "Johns Hopkins University School of Medicine"
+      },
+      {
+        "author_name": "Heba H. Mostafa",
+        "author_inst": "Johns Hopkins University School of Medicine"
+      },
+      {
+        "author_name": "Yukari C Manabe",
+        "author_inst": "Johns Hopkins University School of Medicine"
+      },
+      {
+        "author_name": "Andrew Pekosz",
+        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
+      },
+      {
+        "author_name": "Rebecca Lee Smith",
+        "author_inst": "University of Illinois at Urbana-Champaign"
+      },
+      {
+        "author_name": "David D McManus",
+        "author_inst": "University of Massachusetts Medical School"
+      },
+      {
+        "author_name": "Christopher B Brooke",
+        "author_inst": "University of Illinois at Urbana-Champaign"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2022.06.21.22276712",
     "rel_title": "U.S. state-level COVID-19 transmission insights from a mechanistic mobility-incidence model",
@@ -261999,49 +260893,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
-  {
-    "rel_doi": "10.1101/2022.06.20.22276460",
-    "rel_title": "Responses to COVID-19 Threats: An Evolutionary Psychological Analysis",
-    "rel_date": "2022-06-21",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.20.22276460",
-    "rel_abs": "Responses to COVID-19 public health interventions have been lukewarm. For example, only 64% of the US population has received at least two vaccinations. Because most public health interventions require people to behave in ways that are evolutionarily novel and mismatched with evolved human perceptual and decision-making mechanisms, it is imperative that we gain a better understanding of how people respond to public health information, including how they respond under different pandemic conditions and how specific groups may differ in their responses. We conducted two studies, using data from primarily public sources. We found that state-level COVID-19 threats (e.g., infection and mortality rates) had no relationships with mental health symptoms, suggesting that people were not attending to threat information. This result is consistent with the evolutionary psychological explanation that COVID-19 threat information is insufficient to activate the human behavioral immune system. Furthermore, individual differences affected how people responded to COVID-19 threats, supporting a niche picking explanation. Finally, aggregate state IQ levels correlated positively with aggregate vaccination rates, suggesting that intelligence can partially counteract the evolutionary novelty of abstract threat information, supporting the savanna-IQ interaction hypothesis. We conclude with policy implications for improving interventions and promoting greater compliance.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Stephen M Colarelli",
-        "author_inst": "Central Michigan University"
-      },
-      {
-        "author_name": "Tyler J Mirando",
-        "author_inst": "Central Michigan University"
-      },
-      {
-        "author_name": "Kyunghee Han",
-        "author_inst": "Central Michigan University"
-      },
-      {
-        "author_name": "Norman P. Li",
-        "author_inst": "Singapore Management University"
-      },
-      {
-        "author_name": "Carter Vespi",
-        "author_inst": "Central Michigan University"
-      },
-      {
-        "author_name": "Katherine A. Klein",
-        "author_inst": "Central Michigan University"
-      },
-      {
-        "author_name": "Charles P. Fales",
-        "author_inst": "Central Michigan University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2022.06.20.22276647",
     "rel_title": "Natural and hybrid immunity following four COVID-19 waves in a South African cohort",
@@ -262428,6 +261279,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.06.17.22276229",
+    "rel_title": "Low level of knowledge about COVID-19 among a sample of Deaf persons in Ghana.",
+    "rel_date": "2022-06-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.17.22276229",
+    "rel_abs": "Global observations have shown that the success or failure in preventing and controlling the spread of COVID-19 largely relies on human behaviours. Human behaviours in preventing and controlling the spread of the disease principally, is dependent on the level of knowledge of the disease, the attitudes adopted by persons due to the level of knowledge of the disease and the decision to adhere to the preventive practices (KAP) of the disease. Since the beginning of this pandemic, numerous studies have been conducted to investigate the KAP on the novel COVID-19 among diverse demographic groups. However, no reported studies have been found on the KAP of the COVID-19 pandemic among the deaf in various populations around the world. This study sought to assess the KAP of COVID-19 among deaf persons in the Greater Accra region of Ghana.\n\nThe design of this study utilized the knowledge, attitude and practice (KAP) survey. Good attitude and adherence to the preventive practices of COVID-19 was observed among the deaf persons. However, knowledge about the science of the disease was lacking. Educational campaigns about COVID-19 should also emphasize the teaching and understanding of the science of the virus and the disease to its audience.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Reginald Arthur-Mensah Jr.",
+        "author_inst": "Pentecost University College"
+      },
+      {
+        "author_name": "Jacob  Nartey Quao",
+        "author_inst": "Ghana Health Service"
+      },
+      {
+        "author_name": "Louisa Yeboah",
+        "author_inst": "Ga North Municipal Hospital"
+      },
+      {
+        "author_name": "Zanu Dassah",
+        "author_inst": "Ghana Health Service"
+      },
+      {
+        "author_name": "Abigail  Agartha Kyei",
+        "author_inst": "Pentecost University College"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2022.06.18.22276437",
     "rel_title": "A patient-centric characterization of systemic recovery from SARS-CoV-2 infection",
@@ -263981,33 +262867,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.06.16.496458",
-    "rel_title": "Electrostatic features for the Receptor binding domain of SARS-COV-2 wildtype and its variants. Compass to the severity of the future variants with the charge rule.",
-    "rel_date": "2022-06-17",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.16.496458",
-    "rel_abs": "Electrostatic intermolecular interactions are important in many aspects of biology. We have studied the main electrostatic features involved in the interaction of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein with the human receptor Angiotensin-converting enzyme 2 (ACE2). As the principal computational tool, we have used the FORTE approach, capable to model proton fluctuations and computing free energies for a very large number of protein-protein systems under different physical-chemical conditions, here focusing on the RBD-ACE2 interactions. Both the wild-type and all critical variants are included in this study. From our large ensemble of extensive simulations, we obtain, as a function of pH, the binding affinities, charges of the proteins, their charge regulation capacities, and their dipole moments. In addition, we have calculated the pKas for all ionizable residues and mapped the electrostatic coupling between them. We are able to present a simple predictor for the RBD-ACE2 binding based on the data obtained for Alpha, Beta, Gamma, Delta, and Omicron variants, as a linear correlation between the total charge of the RBD and the corresponding binding affinity. This \"RBD charge rule\" should work as a quick test of the degree of severity of the coming SARS-CoV-2 variants in the future.\n\nCategories and Subject Descriptors:",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Fernando Luis Barroso da Silva",
-        "author_inst": "University of Sao Paulo"
-      },
-      {
-        "author_name": "Carolina Correa Giron",
-        "author_inst": "Universidade Federal do Triangulo Mineiro"
-      },
-      {
-        "author_name": "Aatto Laaksonen",
-        "author_inst": "Stockholm University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "biophysics"
-  },
   {
     "rel_doi": "10.1101/2022.06.17.496544",
     "rel_title": "COVFlow: virus phylodynamics analyses from selected SARS-CoV-2 sequences",
@@ -264350,6 +263209,69 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.06.15.22276466",
+    "rel_title": "Effectiveness of mRNA COVID-19 vaccine boosters against infection, hospitalization and death: a target trial emulation in the omicron (B.1.1.529) variant era",
+    "rel_date": "2022-06-16",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.15.22276466",
+    "rel_abs": "AbstractO_ST_ABSBackgroundC_ST_ABSThe effectiveness of a 3rd mRNA COVID-19 vaccine (\"booster\") dose against the omicron (B.1.1.529) variant is uncertain especially in older, high-risk populations.\n\nObjectiveTo determine mRNA booster vaccine effectiveness (VE) against SARS-CoV-2 infection, hospitalization and death in the omicron era by type of booster, type of primary vaccine, time since primary vaccine, age and comorbidity burden.\n\nDesignTarget trial emulation study comparing booster vaccination versus no booster.\n\nSettingU.S. Department of Veterans Affairs (VA) healthcare system\n\nParticipants and InterventionAmong persons who had received two mRNA COVID-19 vaccine doses at least 5 months earlier, we designed this retrospective matched cohort study to emulate a target trial of booster mRNA vaccination (BNT162b2 or mRNA-1273) versus no booster, conducted from 12/01/2021 to 03/31/2022.\n\nMeasurementsBooster VE.\n\nResultsEach group included 490,838 well-matched persons, predominantly male (88%), mean age 63.0{+/-}14.0 years, followed for up to 121 days (mean 79.8 days). Booster VE >10 days after booster was 42.3% (95% CI 40.6-43.9) against SARS-CoV-2 infection, 53.3% (48.1-58.0) against SARS-CoV-2-related hospitalization and 79.1% (71.2-84.9) against SARS-CoV-2-related death. Booster VE was similar for different booster types (BNT162b2 or mRNA-1273), age groups or primary vaccination regimens, but was significantly higher with longer time since primary vaccination and with higher comorbidity burden.\n\nLimitationsPredominantly male population.\n\nConclusionsBooster mRNA vaccination was highly effective in preventing death and moderately effective in preventing infection and hospitalization for up to 4 months after administration in the omicron era. Increased uptake of booster vaccination, which is currently suboptimal, should be pursued to limit the morbidity and mortality of SARS-CoV-2 infection, especially in persons with high comorbidity burden.\n\nPrimary Funding Source: Department of Veterans Affairs",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "George N. Ioannou",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Amy S.B. Bohnert",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Ann M. O'Hare",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Edward J. Boyko",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Valerie A. Smith",
+        "author_inst": "Duke University"
+      },
+      {
+        "author_name": "Matthew L. Maciejewski",
+        "author_inst": "Duke University"
+      },
+      {
+        "author_name": "C. Barrett Bowling",
+        "author_inst": "Duke University"
+      },
+      {
+        "author_name": "Elizabeth Viglianti",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Theodore J. Iwashyna",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Denise M. Hynes",
+        "author_inst": "Veterans Affairs Portland Healthcare System"
+      },
+      {
+        "author_name": "Kristin Berry",
+        "author_inst": "Veterans Affairs Puget Sound Healthcare System"
+      },
+      {
+        "author_name": "- COVID-19 Observational Research Collaboratory (CORC)",
+        "author_inst": ""
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.06.12.22276048",
     "rel_title": "Prevalence of COVID-19 and Long COVID in Collegiate Student Athletes from Spring 2020 to Fall 2021: A Retrospective Survey",
@@ -265735,53 +264657,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2022.06.15.22276090",
-    "rel_title": "Two-Step Machine Learning to Diagnose and Predict Involvement of Lungs in COVID-19 and Pneumonia using CT Radiomics",
-    "rel_date": "2022-06-16",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.15.22276090",
-    "rel_abs": "ObjectiveWe aimed to develop a two-step machine learning (ML) based model to diagnose and predict involvement of lungs in COVID-19 and non COVID-19 pneumonia patients using CT chest radiomic features.\n\nMethodsThree hundred CT scans (3-classes: 100 COVID-19, 100 pneumonia, and 100 healthy subjects) were enrolled in this study. Diagnostic task included 3-class classification. For severity prediction, two radiologists scored involvement of lungs in COVID-19 and pneumonia scans based on percentage of involvement in all 5 lobes. Datasets were classified into mild (0-25%), moderate (26-50%), and severe (>50%). Whole lungs were segmented utilizing deep learning-based segmentation method. Altogether, 107 features including shape, first-order histogram, second and high order texture features were extracted. For both tasks, datasets were randomly divided into 90% training sets (70% and 30% for training and validation, respectively) and 10% test sets. Pearson correlation coefficient (PCC[&ge;]90%) was performed to exclude highly correlated features. Subsequently, different feature selection algorithms (Correlation attribute evaluation, Information gain attribute, Wrapper Subset selection algorithm, Relief method, and Correlation-based feature selection) were assessed. The most pertinent features were finally selected using voting method based on the evaluation of all algorithms. Several ML-based supervised algorithms were utilized, namely Naive Bays, Support Vector Machine, Bagging, Random Forest, K-nearest neighbors, Decision Tree and Ensemble Meta voting. The synthetic minority oversampling technique (SMOTE) was used to balance the three classes in training sets. The optimal model was first selected based on precision, recall and area-under-curve (AUC) by randomizing the training/validation sets 20 times, followed by testing using the test set. To ensure the repeatability of the results, the entire process was repeated 50 times.\n\nResultsNine pertinent features (2 shape, 1 first-order, and 6 second-order features) were obtained after feature selection for both phases. In diagnostic task, the performance of 3-class classification using Random Forest was 0.909{+/-}0.026, 0.907{+/-}0.056, 0.902{+/-}0.044, 0.939{+/-}0.031, and 0.982{+/-}0.010 for precision, recall, F1-score, accuracy, and AUC, respectively. The severity prediction task using Random Forest achieved 0.868{+/-}0.123 precision, 0.865{+/-}0.121 recall, 0.853{+/-}0.139 F1-score, 0.934{+/-}0.024 accuracy, and 0.969{+/-}0.022 AUC.\n\nConclusionThe two-phase ML-based model accurately classified COVID-19 and pneumonia patients using CT radiomics, and adequately predicted severity of lungs involvement. This 2-steps model showed great potential in assessing COVID-19 CT images towards improved management of patients.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Pegah Moradi Khaniabadi",
-        "author_inst": "Sultan Qaboos University"
-      },
-      {
-        "author_name": "Yassine Bouchareb",
-        "author_inst": "Sultan  Qaboos University"
-      },
-      {
-        "author_name": "Humoud Al-Dhuhli",
-        "author_inst": "Sultab Qaboos University"
-      },
-      {
-        "author_name": "Isaac Shiri",
-        "author_inst": "Geneva University Hospital"
-      },
-      {
-        "author_name": "Faiza Al-Kindi",
-        "author_inst": "Royal Hospital"
-      },
-      {
-        "author_name": "Bita Moradi Khaniabadi",
-        "author_inst": "Isfahan University of Medical Sciences"
-      },
-      {
-        "author_name": "Habib Zaidi",
-        "author_inst": "Geneva University Hospital, Geneva University, University Medical Center Groningen, University of Southern Denmark"
-      },
-      {
-        "author_name": "Arman Rahmim",
-        "author_inst": "University of British Columbia,BC Cancer Research Institute"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "radiology and imaging"
-  },
   {
     "rel_doi": "10.1101/2022.06.14.22276391",
     "rel_title": "Factors associated with COVID-19 vaccine uptake in people with kidney disease: an OpenSAFELY cohort study",
@@ -266656,6 +265531,69 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2022.06.14.22276393",
+    "rel_title": "Nirmatrelvir plus ritonavir for early COVID-19 and hospitalization in a large US health system",
+    "rel_date": "2022-06-16",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.14.22276393",
+    "rel_abs": "BackgroundIn the EPIC-HR trial, nirmatrelvir plus ritonavir led to an 88% reduction in hospitalization or death among unvaccinated outpatients with early COVID-19. Clinical impact of nirmatrelvir plus ritonavir among vaccinated populations is uncertain.\n\nObjectiveTo assess whether nirmatrelvir plus ritonavir reduces risk of hospitalization among outpatients with early COVID-19 in the setting of prevalent SARS-CoV-2 immunity and immune evasive SARS-CoV-2 lineages.\n\nDesignPopulation-based cohort study analyzed to emulate a clinical trial utilizing two-stage, inverse-probability weighted models to account for anticipated bias in testing and treatment.\n\nSettingA large healthcare system providing care for 1.5 million patients in Massachusetts and New Hampshire during Omicron wave (January 1 to May 15, 2022) with staged access and capacity to prescribe nirmatrelvir plus ritonavir.\n\nPatients30,322 non-hospitalized adults (87.2% vaccinated) aged 50 and older with COVID-19 and without contraindications to nirmatrelvir plus ritonavir.\n\nMeasurementPrimary outcome was hospitalization within 14 days of COVID-19 diagnosis.\n\nResultsDuring the study period, 6036 (19.9%) patients were prescribed nirmatrelvir plus ritonavir and 24,286 (80.1%) patients were not. Patients prescribed nirmatrelvir were more likely to be older, have more comorbidities, and be unvaccinated. Hospitalization occurred in 40 (0.66%) and 232 (0.96%) patients prescribed and not prescribed nirmatrelvir plus ritonavir, respectively. The adjusted risk ratio was 0.55 (95% confidence interval 0.38 to 0.80, p = 0.002). Observed risk reduction was greater among unvaccinated patients and obese patients.\n\nLimitationsPotential for residual confounding due to differential access and uptake of COVID-19 vaccines, diagnostics, and treatment.\n\nConclusionsThe overall risk of hospitalization was already low (<1%) following an outpatient diagnosis of COVID-19, but this risk was 45% lower among patients prescribed nirmatrelvir plus ritonavir.\n\nFundingNational Institutes of Health (P30 AI060354 and R01 CA236546).",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Scott Dryden-Peterson",
+        "author_inst": "Brigham and Women's Hospital, Boston, Massachusetts"
+      },
+      {
+        "author_name": "Andy Kim",
+        "author_inst": "Brigham and Women's Hospital, Boston, Massachusetts"
+      },
+      {
+        "author_name": "Arthur Y Kim",
+        "author_inst": "Massachusetts General Hospital, Boston, Massachusetts"
+      },
+      {
+        "author_name": "Ellen C Caniglia",
+        "author_inst": "Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania"
+      },
+      {
+        "author_name": "Inga Lennes",
+        "author_inst": "Massachusetts General Hospital, Boston, Massachusetts"
+      },
+      {
+        "author_name": "Rajesh Patel",
+        "author_inst": "Beth Israel Lahey Health, Cambridge, Massachusetts"
+      },
+      {
+        "author_name": "Lindsay Gainer",
+        "author_inst": "Mass General Brigham Integrated Care"
+      },
+      {
+        "author_name": "Lisa Dutton",
+        "author_inst": "Brigham and Women's Hospital, Boston, Massachusetts"
+      },
+      {
+        "author_name": "Elizabeth Donahue",
+        "author_inst": "Brigham and Women's Hospital, Boston, Massachusetts"
+      },
+      {
+        "author_name": "Rajesh T Gandhi",
+        "author_inst": "Massachusetts General Hospital, Boston, Massachusetts"
+      },
+      {
+        "author_name": "Lindsey R Baden",
+        "author_inst": "Brigham and Women's Hospital, Boston, Massachusetts"
+      },
+      {
+        "author_name": "Ann E Woolley",
+        "author_inst": "Brigham and Women's Hospital, Boston, Massachusetts"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.06.15.496220",
     "rel_title": "The Omicron variant BA.1.1 presents a lower pathogenicity than B.1 D614G and Delta variants in a feline model of SARS-CoV-2 infection",
@@ -267917,189 +266855,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.06.09.22276196",
-    "rel_title": "Accelerated waning of the humoral response to SARS-CoV-2 vaccines in obesity",
-    "rel_date": "2022-06-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.09.22276196",
-    "rel_abs": "Obesity is associated with an increased risk of severe Covid-19. However, the effectiveness of SARS-CoV-2 vaccines in people with obesity is unknown. Here we studied the relationship between body mass index (BMI), hospitalization and mortality due to Covid-19 amongst 3.5 million people in Scotland. Vaccinated people with severe obesity (BMI>40 kg/m2) were significantly more likely to experience hospitalization or death from Covid-19. Excess risk increased with time since vaccination. To investigate the underlying mechanisms, we conducted a prospective longitudinal study of the immune response in a clinical cohort of vaccinated people with severe obesity. Compared with normal weight people, six months after their second vaccine dose, significantly more people with severe obesity had unquantifiable titres of neutralizing antibody against authentic SARS-CoV-2 virus, reduced frequencies of antigen-experienced SARS-CoV-2 Spike-binding B cells, and a dissociation between anti-Spike antibody levels and neutralizing capacity. Neutralizing capacity was restored by a third dose of vaccine, but again declined more rapidly in people with severe obesity. We demonstrate that waning of SARS-CoV-2 vaccine-induced humoral immunity is accelerated in people with severe obesity and associated with increased hospitalization and mortality from breakthrough infections. Given the prevalence of obesity, our findings have significant implications for global public health.",
-    "rel_num_authors": 42,
-    "rel_authors": [
-      {
-        "author_name": "Agatha A. van der Klaauw MD, PhD",
-        "author_inst": "University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Meta"
-      },
-      {
-        "author_name": "Emily C. Horner BSc",
-        "author_inst": "Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR"
-      },
-      {
-        "author_name": "Pehuen Pereyra-Gerber PhD",
-        "author_inst": "Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, UK; Department of Medi"
-      },
-      {
-        "author_name": "Utkarsh Agrawal PhD",
-        "author_inst": "School of Medicine, University of St. Andrews"
-      },
-      {
-        "author_name": "William S. Foster BSc, MRes,",
-        "author_inst": "Immunology, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT"
-      },
-      {
-        "author_name": "Sarah Spencer MD, BSc",
-        "author_inst": "Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR"
-      },
-      {
-        "author_name": "Bensi Vergese BSc Hons.",
-        "author_inst": "University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Meta"
-      },
-      {
-        "author_name": "Miriam E. Smith BSc PhD",
-        "author_inst": "University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Meta"
-      },
-      {
-        "author_name": "Elana Henning B.Soc.Sc",
-        "author_inst": "University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Meta"
-      },
-      {
-        "author_name": "Isobel D. Ramsay MA BM BCh",
-        "author_inst": "1. Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, UK 2. Department of"
-      },
-      {
-        "author_name": "Jack A. Smith BSc MBiol",
-        "author_inst": "1. Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, UK 2. Department of"
-      },
-      {
-        "author_name": "Stephane M. Guillaume BSc",
-        "author_inst": "Immunology, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT"
-      },
-      {
-        "author_name": "Hayley J. Sharpe BSc, PhD",
-        "author_inst": "Signalling, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT"
-      },
-      {
-        "author_name": "Iain M. Hay BSc, PhD",
-        "author_inst": "Signalling, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT; Cambridge Institute for Medical Research, Cambridge UK."
-      },
-      {
-        "author_name": "Sam Thompson BSc",
-        "author_inst": "Flow cytometry core, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT"
-      },
-      {
-        "author_name": "Silvia Innocentin BSc., Ph.D",
-        "author_inst": "Babraham Institute, Babraham Research Campus, Cambridge"
-      },
-      {
-        "author_name": "Lucy H Booth BSc",
-        "author_inst": "Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR"
-      },
-      {
-        "author_name": "Chris Robertson Ph.D.",
-        "author_inst": "Department of Mathematics and Statistics, University of Strathclyde"
-      },
-      {
-        "author_name": "Colin McCowan Ph.D.",
-        "author_inst": "School of Medicine, University of St. Andrews"
-      },
-      {
-        "author_name": "Thomas E Mulroney PhD",
-        "author_inst": "Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR"
-      },
-      {
-        "author_name": "Martin J O'Reilly",
-        "author_inst": "Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR"
-      },
-      {
-        "author_name": "Thevinya P Guragama",
-        "author_inst": "Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR"
-      },
-      {
-        "author_name": "Lihinya P Guragama",
-        "author_inst": "Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR"
-      },
-      {
-        "author_name": "Maria A Rust BSc",
-        "author_inst": "Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR"
-      },
-      {
-        "author_name": "Alex Ferreira",
-        "author_inst": "Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR"
-      },
-      {
-        "author_name": "Soraya Ebrahimi MSc",
-        "author_inst": "NIHR Cambridge Clinical Research Facility, Departments of Immunology and Clinical Biochemistry"
-      },
-      {
-        "author_name": "Lourdes Ceron-Gutierrez MSc.",
-        "author_inst": "NIHR Cambridge Clinical Research Facility, Departments of Immunology and Clinical Biochemistry"
-      },
-      {
-        "author_name": "Jacopo Scotucci MD",
-        "author_inst": "University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Meta"
-      },
-      {
-        "author_name": "Barbara Kronsteiner Ph.D.",
-        "author_inst": "Nuffield Department of Clinical Medicine, University of Oxford"
-      },
-      {
-        "author_name": "Susanna J. Dunachie MD., Ph.D.",
-        "author_inst": "Nuffield Department of Clinical Medicine, University of Oxford"
-      },
-      {
-        "author_name": "Paul Klenerman MD., Ph.D.",
-        "author_inst": "Nuffield Department of Clinical Medicine, University of Oxford"
-      },
-      {
-        "author_name": "- PITCH Consortium",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Adrian J. Park MD PhD",
-        "author_inst": "Cambridge University Hospitals NHS Foundation Trust, Department of Clinical Biochemistry, Cambridge, United Kingdom"
-      },
-      {
-        "author_name": "Francesco Rubino MD.,",
-        "author_inst": "Kings College London, Department of Diabetes, School of Life Course Science, London"
-      },
-      {
-        "author_name": "Hannah Stark BSc",
-        "author_inst": "NIHR BioResource"
-      },
-      {
-        "author_name": "Nathalie Kingson PhD",
-        "author_inst": "NIHR BioResource"
-      },
-      {
-        "author_name": "Rainer Doffinger PhD",
-        "author_inst": "NIHR Cambridge Clinical Research Facility, Departments of Immunology, Clinical Biochemistry"
-      },
-      {
-        "author_name": "Michelle A. Linterman BBmedSc (H",
-        "author_inst": "Immunology, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT"
-      },
-      {
-        "author_name": "Nicholas J. Matheson MA BM BCh",
-        "author_inst": "1. Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, UK 2. Department of"
-      },
-      {
-        "author_name": "Aziz Sheikh MD",
-        "author_inst": "Usher Institute, University of Edinburgh"
-      },
-      {
-        "author_name": "I. Sadaf Farooqi MD, PhD",
-        "author_inst": "University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Meta"
-      },
-      {
-        "author_name": "James E. Thaventhiran MD, PhD",
-        "author_inst": "Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.06.13.22276244",
     "rel_title": "Association of Lung Fibrotic Changes and Cardiological Dysfunction with Hypertension in Long COVID-19 cohort",
@@ -268486,6 +267241,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "obstetrics and gynecology"
   },
+  {
+    "rel_doi": "10.1101/2022.06.08.22276134",
+    "rel_title": "Implementation of a digital early warning score (NEWS2) in a cardiac specialist and general hospital settings in the COVID-19 pandemic: A qualitative study.",
+    "rel_date": "2022-06-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.08.22276134",
+    "rel_abs": "ObjectivesTo evaluate implementation of EHR-integrated NEWS2 in a cardiac care setting and a general hospital setting in the COVID-19 pandemic.\n\nDesignThematic analysis of qualitative semi-structured interviews with purposefully sampled nurses and managers, as well as online surveys.\n\nSettingsSpecialist cardiac hospital (St Bartholomews Hospital) and General teaching hospital (University College London Hospital).\n\nParticipantsEleven nurses and managers from cardiology, cardiac surgery, oncology, and intensive care wards (St Bartholomews) and medical, haematology and intensive care wards (UCLH) were interviewed and sixty-seven were surveyed online.\n\nResultsThree main themes emerged: (i) Implementing NEWS2 challenges and supports; (ii) Value of NEWS2 to alarm, escalate, particularly during the pandemic; and (iii) Digitalisation: EHR integration and automation. The value of NEWS2 was partly positive in escalation, yet there were concerns by nurses who undervalued NEWS2 particularly in cardiac care. Challenges, like clinicians behaviours, lack of resources and training and the perception of NEWS2 value, limit the success of this implementation. Changes in guidelines in the pandemic have led to overlooking NEWS2. EHR integration and automated monitoring are improvement solutions that are not fully employed yet.\n\nConclusionWhether in specialist or general medical settings, the health professionals implementing EWS in healthcare face cultural and systems related challenges to adopting NEWS2 and digital solutions. The validity of NEWS2 in specialised settings and complex conditions is not yet apparent and requires comprehensive validation. EHRs integration and automation are powerful tools to facilitate NEWS2 if its principles are reviewed and rectified, and resources and training are accessible. Further examination of implementation from the cultural and automation domains are needed.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Baneen Alhmoud",
+        "author_inst": "University College London, University College London Hospital, Barts Health Trust."
+      },
+      {
+        "author_name": "Timothy Bonicci",
+        "author_inst": "University College London, University College London Hospital"
+      },
+      {
+        "author_name": "Riyaz Patel",
+        "author_inst": "University College London, University College London Hospital."
+      },
+      {
+        "author_name": "Daniel Melley",
+        "author_inst": "Barts Health Trust"
+      },
+      {
+        "author_name": "Louise Hicks",
+        "author_inst": "Barts Health Trust"
+      },
+      {
+        "author_name": "Amitava Banerjee",
+        "author_inst": "University College London, University College London Hospital, Barts Health Trust."
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health informatics"
+  },
   {
     "rel_doi": "10.1101/2022.06.10.22276247",
     "rel_title": "Using routinely collected hospital data to investigate healthcare worker mobility and patient contacts within a UK hospital during the COVID-19 pandemic",
@@ -269895,25 +268689,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2022.06.13.495895",
-    "rel_title": "Dynamics of SARS-CoV-2 genetic mutations and their information entropy",
-    "rel_date": "2022-06-13",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.13.495895",
-    "rel_abs": "We report an investigation of the mutations dynamics of the SARS-CoV-2 virus using Shannons information theory. Our study includes seventeen RNA genetic sequences collected at different geographic locations and timeframes ranging from Dec. 2019 to Oct. 2021. The data shows a previously unobserved relationship between the information entropy of genomes and their mutation dynamics. The information entropy of the mutated variants decreases linearly with the number of genetic mutations with a negative slope of 1.52 x 10-5 bits / mutations, pointing to a possible deterministic approach to the dynamics of genetic mutations. The method proposed here could be used to develop a predictive algorithm of genetic mutations.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Melvin M Vopson",
-        "author_inst": "University of Portsmouth"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "bioinformatics"
-  },
   {
     "rel_doi": "10.1101/2022.06.12.495841",
     "rel_title": "Structure of SARS-CoV-2 M protein in lipid nanodiscs",
@@ -270268,6 +269043,25 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2022.06.10.22276252",
+    "rel_title": "Ivermectin for Treatment of Mild-to-Moderate COVID-19 in the Outpatient Setting: A Decentralized, Placebo-controlled, Randomized, Platform Clinical Trial",
+    "rel_date": "2022-06-12",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.10.22276252",
+    "rel_abs": "BackgroundThe effectiveness of ivermectin to shorten symptom duration or prevent hospitalization among outpatients in the United States with mild-to-moderate symptomatic coronavirus disease 2019 (COVID-19) is unknown.\n\nObjectiveWe evaluated the efficacy of ivermectin 400 {micro}g/kg daily for 3 days compared with placebo for the treatment of early mild-to-moderate COVID-19.\n\nMethodsACTIV-6 is an ongoing, decentralized, double-blind, randomized, placebo-controlled platform trial to evaluate repurposed therapies in outpatients with mild-to-moderate COVID-19. Non-hospitalized adults age [&ge;]30 years with confirmed COVID-19, experiencing [&ge;]2 symptoms of acute infection for [&le;]7 days were randomized to receive ivermectin 400 {micro}g/kg daily for 3 days or placebo. The main outcome measure was time to sustained recovery, defined as achieving at least 3 consecutive days without symptoms. Secondary outcomes included a composite of hospitalization or death by day 28.\n\nResultsOf the 3457 participants who consented to be evaluated for inclusion in the ivermectin arm, 1591 were eligible for this study arm, randomized to receive ivermectin 400 {micro}g/kg (n=817) or placebo (n=774), and received study drug. Of those enrolled, 47% reported receiving at least 2 doses of SARS-CoV-2 vaccination. The posterior probability for any improvement in time to recovery was 0.91 (hazard ratio 1.07, 95% credible interval 0.96-1.17). The posterior probability of this benefit exceeding 24 hours was less than 0.01, as measured by the difference in mean time unwell. Hospitalizations or deaths were uncommon (ivermectin [n=10]; placebo [n=9]). Ivermectin at 400 {micro}g/kg was safe and without serious adverse events as compared with placebo (ivermectin [n=10]; placebo [n=9]).\n\nConclusionsIvermectin dosed at 400 {micro}g/kg daily for 3 days resulted in less than one day of shortening of symptoms and did not lower incidence of hospitalization or death among outpatients with COVID-19 in the United States during the delta and omicron variant time periods.\n\nTrial registrationClinicalTrials.gov Identifier: NCT04885530.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Susanna Naggie",
+        "author_inst": "Duke Clinical Research Institute, Duke University School of Medicine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.06.11.495733",
     "rel_title": "Evolutionary trajectory of the physicochemical mechanism of interaction of SARS-CoV-2 spike protein with ACE2",
@@ -271613,53 +270407,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2022.06.07.22276108",
-    "rel_title": "Long-term prognosis of adults with moderate-severe SARS-CoV-2 lower respiratory tract infection managed in primary care: prospective cohort study",
-    "rel_date": "2022-06-08",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.07.22276108",
-    "rel_abs": "ObjectivesTo determine differences in health-related quality of life (HRQoL) and presence and duration of symptoms between adults with and without established SARS-CoV-2 moderately severe lower respiratory tract infection (LRTI) in the 12 months following their primary care visit.\n\nDesignProspective cohort study\n\nSetting35 general practices in the provinces Noord-Brabant and Utrecht, the Netherlands.\n\nParticipantsIndividuals aged [&ge;]18 years who presented to their general practitioner (GP) with a moderately severe LRTI during the first COVID-19 waive in The Netherlands (March-June 2021) underwent serology testing (participants, GPs and study personnel remained blinded for serology outcomes during study conduct) and completed baseline and follow-up questionnaires. Of the 315 participants who gave consent, 277 (88%) were suitable for inclusion in the analyses. Complete follow-up date was available in 97% of participants.\n\nMain outcome measures1) Scores of SF-36; physical component summary (PCS), mental component summary (MCS) and subscales. 2) Risk of any and individual persisting symptoms (of cough, dyspnea, chest pain, fatigue, brain fog, headache, and anosmia/ageusia) over time.\n\nResultsThe change in SF-36 PSC (p=0.13), MCS (p=0.30), as well as subscale scores, over time did not differ between SARS-CoV-2 serology positive and negative participants after adjusting for sex, age, BMI, diabetes and chronic pulmonary conditions. The risk of any persisting symptom over time did not significantly differ between the groups (aHR 0.61, 95% CI 0.33-1.15), nor did the risk of individual symptoms.\n\nConclusionsIn the 12 months following their moderately severe LRTI, primary care patients with and without confirmed SARS-CoV-2 infection had a comparable HRQoL profile. Albeit a considerable proportion of patients reported persistent symptoms, there was no evidence of a difference in the course of symptoms over time between patients with and without confirmed SARS-CoV-2 infection.\n\nTrial registrationDutch Trial Register (NTR) number NL8729",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Tamara Platteel",
-        "author_inst": "University Medical Center Utrecht"
-      },
-      {
-        "author_name": "Johannes Koelmans",
-        "author_inst": "University Medical Center Utrecht"
-      },
-      {
-        "author_name": "Daniela Cianci",
-        "author_inst": "University Medical Center Utrecht"
-      },
-      {
-        "author_name": "Natascha Broers",
-        "author_inst": "Maastricht University"
-      },
-      {
-        "author_name": "Eefje de Bont",
-        "author_inst": "Maastricht University"
-      },
-      {
-        "author_name": "Jochen Cals",
-        "author_inst": "Maastricht University"
-      },
-      {
-        "author_name": "Roderick Venekamp",
-        "author_inst": "University Medical Center Utrecht"
-      },
-      {
-        "author_name": "Theo Verheij",
-        "author_inst": "University Medical Center Utrecht"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.06.07.22276117",
     "rel_title": "Safety of the fourth COVID-19 BNT162b2 mRNA (second booster) vaccine",
@@ -271906,6 +270653,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.06.07.22275493",
+    "rel_title": "Precarious employment and associations with health during COVID-19: a nationally representative survey in Wales, UK",
+    "rel_date": "2022-06-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.07.22275493",
+    "rel_abs": "BackgroundThe COVID-19 pandemic had an early impact on employment, with the United States (US) and the United Kingdom (UK) experiencing more severe immediate labour market impacts than other Western countries. Emerging evidence from the initial phase of the pandemic highlighted that job losses were experienced more by those holding atypical contracts. Furthermore, it is predicted that this associated unemployment will increase precarious employment arrangements during the COVID-19 pandemic.\n\nIn this paper we seek to answer the following research questions:\n\nO_LIWhat is the prevalence of precarious employment in Wales and are there differences in employment precariousness by socio-demographic characteristics and self-reported health status?\nC_LIO_LIWhich domains are the main contributing factors of precarious employment in Wales?\nC_LIO_LIWhich domains of precarious employment are associated with poorer health?\nC_LIO_LIHaves there been changes in job quality (as reflected by precarious employment domains) during the COVID pandemic (between February 2020 and Winter 2020/2021)?\nC_LI\n\nMethodsData was collected from a national household survey carried out in May/June 2020, with a sample of 1,032 residents in Wales and follow-up responses from 429 individuals collected between November 2020 and January 2021. To examine the associations between experiencing precarious employment or the separate domains of employment precariousness and socio-demographics and health, chi-squared analyses and logistic regression models (multinomial and binary) were used. To determine longitudinal changes in precarious employment experienced by socio-demographic groups and furlough status, McNemars test was used. The data is presented as proportion of respondents or adjusted odds ratios (aOR) and 95% confidence intervals following logistic regression.\n\nResultsOverall, pre-pandemic, one in four respondents were determined to be in precarious employment (26.5%). A higher proportion of females (28.3%) and those aged 18-29 years (41.0%) were in precarious employment in February 2020. In addition, a greater percentage of individuals who reported poorer health across all self-reported measures were in precarious employment compared to those reporting better health. Worse perceived treatment at work was twice as likely in those who reported a pre-existing condition (aOR 2.45 95% CI [1.33-4.49]), poorer general health (aOR 2.33 95% CI [1.22-4.47]) or low mental wellbeing (aOR 2.81 95% CI [1.34-5.88]) when compared to their healthier counterparts. Those calculated to have high wage precariousness were three times more likely to report low mental wellbeing (aOR 3.12 95% CI [1.54-6.32]). In the subsample, there was an observed increase in the prevalence of precarious employment, with this being attributable to lower affordability of wages and a perceived increase in vulnerability at work. The subgroups that were most impacted by this decrease in job quality were females and the 30-39 years age group.\n\nImplicationsImproving the vulnerability and wages domains, through the creation and provision of secure, adequately paid job opportunities has the potential to reduce the prevalence of precarious employment in Wales. In turn, these changes would improve the health and wellbeing of the working age population, some of which are already adversely impacted by the COVID-19 pandemic.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Benjamin J Gray",
+        "author_inst": "Research and Evaluation Division, Public Health Wales"
+      },
+      {
+        "author_name": "Richard G Kyle",
+        "author_inst": "Academy of Nursing, University of Exeter"
+      },
+      {
+        "author_name": "Kate R Isherwood",
+        "author_inst": "School of Sport and Health Sciences, Cardiff Metropolitan University"
+      },
+      {
+        "author_name": "Ciar\u00e1n Humphreys",
+        "author_inst": "Wider Determinants of Health Unit, Public Health Wales"
+      },
+      {
+        "author_name": "Melda Lois Griffiths",
+        "author_inst": "Research and Evaluation Division, Public Health Wales; National Centre for Population Health and Wellbeing Research, Swansea University"
+      },
+      {
+        "author_name": "Alisha R Davies",
+        "author_inst": "Research and Evaluation Division, Public Health Wales; National Centre for Population Health and Wellbeing Research, Swansea University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2022.06.07.22276080",
     "rel_title": "Non-pharmacological therapies for post-viral syndromes, including Long COVID: A systematic review",
@@ -273615,41 +272401,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "transplantation"
   },
-  {
-    "rel_doi": "10.1101/2022.06.02.494567",
-    "rel_title": "Origins and Evolution of Seasonal Human Coronaviruses",
-    "rel_date": "2022-06-06",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.02.494567",
-    "rel_abs": "Four seasonal human coronaviruses (sHCoVs) are endemic globally (229E, NL63, OC43, and HKU1), accounting for 5-30% of human respiratory infections. However, the epidemiology and evolution of these CoVs remain understudied due to their association with mild symptomatology. Using a multigene and complete genomes analysis approach, we find the evolutionary histories of sHCoVs to be more complex than previously recognized, owing to frequent recombination of CoVs, including within and between sHCoVs. Within sHCoV recombination rate was highest for 229E and OC43, and within genus highest for betaCoVs, whereas substitutions per recombination event inversely highest in NL63 and HKU1, and the alphaCoVs. Depending on the gene studied, OC43 may have ungulate, canine, or rabbit CoV ancestors, while 229E may have origins in a bat, camel or an unsampled intermediate host. HKU1 had the earliest most recent common ancestor (MRCA: 1809-1899), comprised two genetically divergent genotypes (A and B) possibly representing two independent transmission events from murine CoVs, and genotype B was genetically more diverse than all the other sHCoVs. Finally, we found shared amino acid substitutions in multiple proteins along the non-human to sHCoV host-jump branches. The complex evolution of CoVs and their frequent host switches could benefit from continued surveillance of CoVs across non-human hosts.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "James R. Otieno",
-        "author_inst": "Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, United States"
-      },
-      {
-        "author_name": "Joshua L. Cherry",
-        "author_inst": "National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA"
-      },
-      {
-        "author_name": "David J. Spiro",
-        "author_inst": "Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, United States"
-      },
-      {
-        "author_name": "Martha I. Nelson",
-        "author_inst": "Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, United States"
-      },
-      {
-        "author_name": "N\u00eddia S. Trov\u00e3o",
-        "author_inst": "Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, United States"
-      }
-    ],
-    "version": "1",
-    "license": "cc0",
-    "type": "new results",
-    "category": "evolutionary biology"
-  },
   {
     "rel_doi": "10.1101/2022.06.02.494559",
     "rel_title": "Zooanthroponotic transmission of SARS-CoV-2 and host-specific viral mutations revealed by genome-wide phylogenetic analysis",
@@ -274048,6 +272799,33 @@
     "type": "new results",
     "category": "biophysics"
   },
+  {
+    "rel_doi": "10.1101/2022.06.06.22276040",
+    "rel_title": "Transcriptomics Meta-Analysis Predicts Two Robust Human Biomarkers for Severe Infection with SARS-CoV-2",
+    "rel_date": "2022-06-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.06.22276040",
+    "rel_abs": "Defining the human factors associated with severe vs mild SARS-CoV-2 infection has become of increasing interest. Mining large numbers of public gene expression datasets is an effective way to identify genes that contribute to a given phenotype. Combining RNA-sequencing data with the associated clinical metadata describing disease severity can enable earlier identification of patients who are at higher risk of developing severe COVID-19 disease. We consequently identified 358 public RNA-seq human transcriptome samples from the Gene Expression Omnibus database that had disease severity metadata. We then subjected these samples to a robust RNA-seq data processing workflow to quantify gene expression in each patient. This process involved using Salmon to map the reads to the reference transcriptomes, edgeR to calculate significant differential expression levels, and gene ontology enrichment using Camera. We then applied a machine learning algorithm to the read counts data to identify features that best differentiated samples based on COVID-19 severity phenotype. Ultimately, we produced a ranked list of genes based on their Gini importance values that includes GIMAP7 and S1PR2, which are associated with immunity and inflammation (respectively). Our results show that these two genes can potentially predict people with severe COVID-19 at up to [~]90% accuracy. We expect that our findings can help contribute to the development of improved prognostics for severe COVID-19.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Jeffrey Clancy",
+        "author_inst": "Brigham Young University-Provo: Brigham Young University"
+      },
+      {
+        "author_name": "Curtis  S Hoffmann",
+        "author_inst": "Brigham Young University-Provo: Brigham Young University"
+      },
+      {
+        "author_name": "Brett  E Pickett",
+        "author_inst": "Brigham Young University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.06.06.22276025",
     "rel_title": "The impact of surgical mask-wearing, contact tracing program, and vaccination on COVID-19 transmission in Taiwan 2020-2022: a modelling study",
@@ -275433,65 +274211,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.06.02.22275934",
-    "rel_title": "Increase of scabies infestations during the COVID-19 pandemic in Catalonia",
-    "rel_date": "2022-06-03",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.02.22275934",
-    "rel_abs": "During the COVID-19 pandemic, several clinicians in Spain reported an increase in scabies diagnoses. We performed a time-series analysis with data from 2014 to 2022 to quantify this increase. We found an increasing trend during late 2020 and 2021, peaking in March 2022 with an almost 4.5-fold incidence than expected, especially in those aged between 16 and 30 years. Although scabies is more frequent in most socioeconomic deprived areas, the observed rise occurs in all the areas. We recommend increasing surveillance among other countries to detect unexpected increases in scabies outbreaks.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Manuel Medina",
-        "author_inst": "Institut Catal\u00e0 de la Salut"
-      },
-      {
-        "author_name": "Nuria Mora",
-        "author_inst": "Institut Catal\u00e0 de la Salut"
-      },
-      {
-        "author_name": "Francisca Ramos",
-        "author_inst": "Institut Catal\u00e0 de la Salut"
-      },
-      {
-        "author_name": "Leonardo Mendez-Boo",
-        "author_inst": "Institut Catal\u00e0 de la Salut"
-      },
-      {
-        "author_name": "Carolina Guiriguet",
-        "author_inst": "Institut Catal\u00e0 de la Salut"
-      },
-      {
-        "author_name": "Eduardo Hermosilla",
-        "author_inst": "Idiap Jordi Gol"
-      },
-      {
-        "author_name": "Mireia Fabregas",
-        "author_inst": "Institut Catal\u00e0 de la Salut"
-      },
-      {
-        "author_name": "Ariadna Mas",
-        "author_inst": "Institut Catal\u00e0 de la Salut"
-      },
-      {
-        "author_name": "Sara Rodoreda",
-        "author_inst": "Institut Catal\u00e0 de la Salut"
-      },
-      {
-        "author_name": "Ermengol Coma",
-        "author_inst": "Institut Catal\u00e0 de la Salut"
-      },
-      {
-        "author_name": "Francesc Fina",
-        "author_inst": "Institut Catal\u00e0 de la Salut"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.06.02.494552",
     "rel_title": "Age exacerbates SARS-CoV-2-induced blood-brain barrier leakage and neuropsychiatric dysfunction",
@@ -275862,6 +274581,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.05.31.22275835",
+    "rel_title": "One Million and Counting: Estimates of Deaths in the United States from Ancestral SARS-CoV-2 and Variants",
+    "rel_date": "2022-06-02",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.31.22275835",
+    "rel_abs": "BackgroundOver one million COVID-19 deaths have been recorded in the United States. Sustained global SARS-CoV-2 transmission has led to the emergence of new variants with increased transmissibility, virulence, and/or immune evasion. The specific burden of mortality from each variant over the course of the U.S. COVID-19 epidemic remains unclear.\n\nMethodsWe constructed an epidemiologic model using data reported by the CDC on COVID-19 mortality and circulating variant proportions to estimate the number of recorded COVID-19 deaths attributable to each SARS-CoV-2 variant in the U.S. We conducted sensitivity analysis to account for parameter uncertainty.\n\nFindingsOf the 1,003,419 COVID-19 deaths recorded as of May 12, 2022, we estimate that 460,124 (46%) were attributable to WHO-designated variants. By U.S. Census Region, the South recorded the most variant deaths per capita (median estimate 158 per 100,000), while the Northeast recorded the fewest (111 per 100,000). Over 40 percent of national COVID-19 deaths were estimated to be caused by the combination of Alpha (median estimate 39,548 deaths), Delta (273,801), and Omicron (117,560).\n\nInterpretationSARS-CoV-2 variants that have emerged around the world have imposed a significant mortality burden in the U.S. In addition to national public health strategies, greater efforts are needed to lower the risk of new variants emerging, including through global COVID-19 vaccination, treatment, and outbreak mitigation.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Jo Walker",
+        "author_inst": "Yale School of Public Health"
+      },
+      {
+        "author_name": "Nathan D. Grubaugh",
+        "author_inst": "Yale School of Public Health"
+      },
+      {
+        "author_name": "Gregg Gonsalves",
+        "author_inst": "Yale School of Public Health"
+      },
+      {
+        "author_name": "Virginia E. Pitzer",
+        "author_inst": "Yale School of Public Health"
+      },
+      {
+        "author_name": "Zain Rizvi",
+        "author_inst": "Public Citizen"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2022.06.01.494393",
     "rel_title": "OxoScan-MS: Oxonium ion scanning mass spectrometry facilitates plasma glycoproteomics in large scale",
@@ -277255,45 +276009,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2022.06.01.22275878",
-    "rel_title": "COVID-19 is not an Independent Cause of Death",
-    "rel_date": "2022-06-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.01.22275878",
-    "rel_abs": "The COVID-19 pandemic has had overwhelming global impacts with deleterious social, economic, and health consequences. To assess the COVID-19 death toll researchers have estimated declines in 2020 life expectancy at birth. Because data are often available only for COVID-19 deaths, the risks of dying from COVID-19 are assumed to be independent of those from other causes. We explore the soundness of this assumption based on data from the US and Brazil, the countries with the largest number of reported COVID-19 deaths. We use three methods. One estimates the difference between 2019 and 2020 life tables and therefore does not require the assumption of independence. The other two assume independence to simulate scenarios in which COVID-19 mortality is added to 2019 death rates or is eliminated from 2020 rates. Our results reveal that COVID-19 is not independent of other causes of death. The assumption of independence can lead to either an overestimate (Brazil) or an underestimate (US) of the decline in e0, depending on how the number of other reported causes of death changed in 2020.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Marcia C. Castro",
-        "author_inst": "Harvard TH Chan School of Public Health"
-      },
-      {
-        "author_name": "Susie Gurzenda",
-        "author_inst": "The University of North Carolina at Chapel Hill"
-      },
-      {
-        "author_name": "Cassio M Turra",
-        "author_inst": "Universidade Federal de Minas Gerais"
-      },
-      {
-        "author_name": "Sun Kim",
-        "author_inst": "Harvard T.H. Chan School of Public Health"
-      },
-      {
-        "author_name": "Theresa Andrasfay",
-        "author_inst": "University of Southern California"
-      },
-      {
-        "author_name": "Noreen Goldman",
-        "author_inst": "Princeton University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2022.06.01.22275872",
     "rel_title": "Artificial intelligence tool for the study of COVID-19 microdroplet spread across the human diameter and airborne space",
@@ -277656,6 +276371,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "genetic and genomic medicine"
   },
+  {
+    "rel_doi": "10.1101/2022.05.31.22275814",
+    "rel_title": "Heterogeneous evolution of SARS-CoV-2 seroprevalence in school-age children: Results from the Ciao Corona study in November-December 2021 in the canton of Zurich",
+    "rel_date": "2022-05-31",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.31.22275814",
+    "rel_abs": "BackgroundMuch remains unknown regarding the evolution of SARS-CoV-2 seroprevalence and variability in seropositive children in districts, schools, and classes as only a few school-based co-hort studies exist. Vaccination of children, initiated at different times for different age groups, adds additional complexity to understand how seroprevalence developed in the school aged population.\n\nAimWe investigated the evolution of SARS-CoV-2 seroprevalence in children and its variability in districts, schools, and classes in Switzerland from June/July 2020 to November/December 2021.\n\nMethodsIn this school-based cohort study, SARS-CoV-2 antibodies were measured in primary and secondary school children from randomly selected schools in the canton of Zurich in October/November 2020, March/April 2021, and November/December 2021. Seroprevalence was estimated using Bayesian logistic regression to adjust for test sensitivity and specificity. Variability of seroprevalence between school classes was expressed as maximum minus minimum sero-prevalence in a class and summarized as median (interquartile range).\n\nResults1875 children from 287 classes in 43 schools were tested, with median age 12 (range 6-17), 51% 12+ vaccinated. Seroprevalence increased from 5.6% (95% CrI: 3.5-7.6%) to 31.1% (27.0-36.1%) in unvaccinated children, and 46.4% (42.6-50.9%) in all children (including vaccinated). Earlier in the pandemic, seropositivity rates in primary schools were similar to or slightly higher (<5%) than those in secondary schools, but by late 2021, primary schools had 12.3% (44.3%) lower seroprevalence for unvaccinated (all) subjects. Variability in seroprevalence among districts and schools increased more than twofold over time, and in classes from 11% (7-17%) to 40% (22-49%).\n\nConclusionSeroprevalence in children increased greatly, especially in 2021 following introduction of vaccines. Variability in seroprevalence was high and increased substantially over time, suggesting complex transmission chains.\n\nTrial Registration: ClinicalTrials.gov NCT04448717",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Sarah R Haile",
+        "author_inst": "University of Zurich, Epidemiology, Biostatistics and Prevention Institute (EBPI)"
+      },
+      {
+        "author_name": "Alessia Raineri",
+        "author_inst": "University of Zurich, Epidemiology, Biostatistics and Prevention Institute (EBPI)"
+      },
+      {
+        "author_name": "Sonja Rueegg",
+        "author_inst": "University of Zurich, Epidemiology, Biostatistics and Prevention Institute (EBPI)"
+      },
+      {
+        "author_name": "Thomas Radtke",
+        "author_inst": "University of Zurich, Epidemiology, Biostatistics and Prevention Institute (EBPI)"
+      },
+      {
+        "author_name": "Agne Ulyte",
+        "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI)"
+      },
+      {
+        "author_name": "Milo  A. Puhan",
+        "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI)"
+      },
+      {
+        "author_name": "Susi Kriemler",
+        "author_inst": "Epidemiology, Biostatistics and Prevention Institute (EBPI)"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.05.31.494170",
     "rel_title": "Accurate Prediction of Virus-Host Protein-Protein Interactions via a Siamese Neural Network Using Deep Protein Sequence Embeddings",
@@ -278889,77 +277647,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2022.05.29.493850",
-    "rel_title": "The SARS-CoV-2 accessory factor ORF7a downregulates MHC class I surface expression",
-    "rel_date": "2022-05-30",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.29.493850",
-    "rel_abs": "The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in over 500 million infections and more than six million deaths worldwide. Although the viral genomes of SARS-CoV-1 and SARS-CoV-2 share high sequence homology, the clinical and pathological features of COVID-19 differ profoundly from those of SARS. It is apparent that changes in viral genes contribute to the increased transmissibility of SARS-CoV-2 and pathology of COVID-19.\n\nCytotoxic T lymphocytes play a key role in the elimination of virus-infected cells, mediated by recognition of virus-derived peptides that are presented on MHC class I molecules. Here, we show that SARS-CoV-2 can interfere with antigen presentation thereby evading immune surveillance. SARS-CoV-2 infection of monkey and human cell lines resulted in reduced cell-surface expression of MHC class I molecules. We identified a single viral gene product, the accessory factor open reading frame 7a (ORF7a), that mediates this effect. ORF7a interacts with HLA class I molecules in the ER, resulting in ER retention or impaired HLA heavy chain (HC) trafficking to the Golgi. Ultimately, these actions result in reduced HLA class I surface expression on infected cells. Whereas ORF7a from SARS-CoV-2 reduces surface HLA class I levels, the homologous ORF7a from the 2002 pandemic SARS-CoV-1 did not, suggesting that SARS-CoV-2 ORF7a acquired the ability to downregulate HLA-I during evolution of the virus. We identified a single amino acid in the SARS-CoV-1 ORF7a luminal domain that, upon mutating to the corresponding SARS-CoV-2 ORF7a sequence, induced a gain-of-function in HLA surface downregulation. By abrogating HLA class I antigen presentation via ORF7a, SARS-CoV-2 may evade host immune responses by inhibiting anti-viral cytotoxic T cell activity, thereby contributing to the pathology of COVID-19.",
-    "rel_num_authors": 14,
-    "rel_authors": [
-      {
-        "author_name": "Shuxuan Zheng",
-        "author_inst": "University Medical Center Utrecht"
-      },
-      {
-        "author_name": "Hendrik de Buhr",
-        "author_inst": "University Medical Center Utrecht"
-      },
-      {
-        "author_name": "Patrique Praest",
-        "author_inst": "University Medical Center Utrecht"
-      },
-      {
-        "author_name": "Anouk Evers",
-        "author_inst": "University Medical Center Utrecht"
-      },
-      {
-        "author_name": "Ingrid Brak Boer",
-        "author_inst": "University Medical Center Utrecht"
-      },
-      {
-        "author_name": "Marielle van Grinsven",
-        "author_inst": "University Medical Center Utrecht"
-      },
-      {
-        "author_name": "Ylenia Longo",
-        "author_inst": "Heinrich Heine University Duesseldorf"
-      },
-      {
-        "author_name": "Wilco Nijenhuis",
-        "author_inst": "Utrecht University"
-      },
-      {
-        "author_name": "Lukas C. Kapitein",
-        "author_inst": "Utrecht University"
-      },
-      {
-        "author_name": "Jeffrey M. Beekman",
-        "author_inst": "University Medical Center Utrecht"
-      },
-      {
-        "author_name": "Monique Nijhuis",
-        "author_inst": "University Medical Center Utrecht"
-      },
-      {
-        "author_name": "Ingo Drexler",
-        "author_inst": "Heinrich Heine University Duesseldorf"
-      },
-      {
-        "author_name": "Emmanuel JHJ Wiertz",
-        "author_inst": "University Medical Center Utrecht"
-      },
-      {
-        "author_name": "Robert Jan Lebbink",
-        "author_inst": "University Medical Center Utrecht"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2022.05.29.493871",
     "rel_title": "Genome similarities between human-derived and mink-derived SARS-CoV-2 make mink a potential reservoir of the virus",
@@ -279226,6 +277913,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.05.27.22275708",
+    "rel_title": "Identifying COVID-19 phenotypes using cluster analysis and assessing their clinical outcomes",
+    "rel_date": "2022-05-29",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.27.22275708",
+    "rel_abs": "Multiple clinical phenotypes have been proposed for COVID-19, but few have stemmed from data-driven methods. We aimed to identify distinct phenotypes in patients admitted with COVID-19 using cluster analysis, and compare their respective characteristics and clinical outcomes.\n\nWe analyzed the data from 547 patients hospitalized with COVID-19 in a Canadian academic hospital from January 1, 2020, to January 30, 2021. We compared four clustering algorithms: K-means, PAM (partition around medoids), divisive and agglomerative hierarchical clustering. We used imaging data and 34 clinical variables collected within the first 24 hours of admission to train our algorithm. We then conducted survival analysis to compare clinical outcomes across phenotypes and trained a classification and regression tree (CART) to facilitate phenotype interpretation and phenotype assignment.\n\nWe identified three clinical phenotypes, with 61 patients (17%) in Cluster 1, 221 patients (40%) in Cluster 2 and 235 (43%) in Cluster 3. Cluster 2 and Cluster 3 were both characterized by a low-risk respiratory and inflammatory profile, but differed in terms of demographics. Compared with Cluster 3, Cluster 2 comprised older patients with more comorbidities. Cluster 1 represented the group with the most severe clinical presentation, as inferred by the highest rate of hypoxemia and the highest radiological burden. Mortality, mechanical ventilation and ICU admission risk were all significantly different across phenotypes.\n\nWe conducted a phenotypic analysis of adult inpatients with COVID-19 and identified three distinct phenotypes associated with different clinical outcomes. Further research is needed to determine how to properly incorporate those phenotypes in the management of patients with COVID-19.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Eric Yamga",
+        "author_inst": "CHUM: Centre Hospitalier de L'Universite de Montreal"
+      },
+      {
+        "author_name": "Louis Mullie",
+        "author_inst": "CHUM: Centre Hospitalier de L'Universite de Montreal"
+      },
+      {
+        "author_name": "Madeleine Durand",
+        "author_inst": "CHUM: Centre Hospitalier de L'Universite de Montreal"
+      },
+      {
+        "author_name": "Alexandre Cadrin-Chenevert",
+        "author_inst": "Centre hospitalier de Lanaudi\u00e8re: Centre hospitalier de Lanaudiere"
+      },
+      {
+        "author_name": "An Tang",
+        "author_inst": "CHUM: Centre Hospitalier de L'Universite de Montreal"
+      },
+      {
+        "author_name": "Emmanuel Montagnon",
+        "author_inst": "CHUM Research Centre: Centre Hospitalier de l'Universite de Montreal Centre de Recherche"
+      },
+      {
+        "author_name": "Carl Chartrand-Lefebvre",
+        "author_inst": "CHUM: Centre Hospitalier de L'Universite de Montreal"
+      },
+      {
+        "author_name": "Micha\u00ebl Chass\u00e9",
+        "author_inst": "Centre Hospitalier de l'Universite de Montreal Centre de Recherche"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health informatics"
+  },
   {
     "rel_doi": "10.1101/2022.05.28.22275707",
     "rel_title": "Comparison of the burnout among medical residents before and during the pandemic: not more exhausted but less accomplished",
@@ -280703,45 +279437,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2022.05.26.22275624",
-    "rel_title": "SHIVIR - An Agent-Based Model to assess the transmission of COVID-19 in India",
-    "rel_date": "2022-05-27",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.26.22275624",
-    "rel_abs": "BackgroundCOVID-19 has tormented the global health and economy like no other event in the recent past. Researchers and policymakers have been working strenuously to end the pandemic completely.\n\nMethodology/Principal FindingsInfectious disease dynamics could be well-explained at an individual level with established contact networks and disease models that represent the behaviour of the infection. Hence, an Agent-Based Model, SHIVIR (Susceptible, Infected, Admitted, ICU, Ventilator, Recovered, Immune) that can assess the transmission dynamics of COVID-19 and the effects of Non-Pharmaceutical Interventions (NPI) was developed. Two models were developed using to test the synthetic populations of Rangareddy, a district in Telangana state, and the state itself respectively. NPI such as lockdowns, masks, and social distancing along with the effect of post-recovery immunity were tested across scenarios.\n\nThe actual and forecast curves were plotted till the unlock phase began in India. The Mean Absolute Percentage Error of scenario MD100I180 was 6.41 percent while those of 3 other scenarios were around 10 percent each. Since the model anticipated lifting of lockdowns that would increase the contact rate proportionately, the forecasts exceeded the actual estimates. Some possible reasons for the difference are discussed.\n\nConclusionsModels like SHIVIR that employ a bottom-up Agent-Based Modelling are more suitable to investigate various aspects of infectious diseases owing to their ability to hold details of each individual in the population. Also, the scalability and reproducibility of the model allow modifications to variables, disease model, agent attributes, etc. to provide localized estimates across different places.\n\nAuthor SummaryThe world has witnessed several infectious disease outbreaks from time to time. COVID-19 is one such event that tormented the life of mankind. Healthcare practitioners, policymakers, and governments struggled enormously to handle the influx of infections and devise suitable interventions. Agent-Based Models that use the population data could cater to these requirements better. Hence, we developed a disease model that represents various states acquired by COVID-19 infected individuals. The contact network among the individuals in the population was defined based on which the simulation progresses. The effect of various Non-Pharmaceutical Interventions such as lockdowns, the use of masks and social distancing along with post-recovery immunity were enacted considering two case studies viz. population of Rangareddy district and Telangana state. The capability of these models to adapt to different input data fields and types make them handy to be tailored based on available inputs and desired outputs. Simulating them using local population data would fetch useful estimates for policymakers.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Narassima M.S.",
-        "author_inst": "Great Lakes Institute of Management"
-      },
-      {
-        "author_name": "Denny John",
-        "author_inst": "Ramaiah University of Applied Sciences"
-      },
-      {
-        "author_name": "Anbuudayasankar S.P.",
-        "author_inst": "Amrita Vishwa Vidyapeetham"
-      },
-      {
-        "author_name": "Guru Rajesh Jammy",
-        "author_inst": "World Bank Group"
-      },
-      {
-        "author_name": "Rashmi Pant",
-        "author_inst": "Society for Health Allied Research and Education India"
-      },
-      {
-        "author_name": "Lincoln Choudhury",
-        "author_inst": "Krashapana Consultancy Private Limited"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.05.26.22275639",
     "rel_title": "Protection against Omicron conferred by mRNA primary vaccine series, boosters, and prior infection",
@@ -281200,6 +279895,53 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2022.05.24.22275478",
+    "rel_title": "Effective antiviral regimens to reduce COVID-19 hospitalizations: a systematic comparison of randomized controlled trials",
+    "rel_date": "2022-05-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.24.22275478",
+    "rel_abs": "BackgroundDuring pandemics, early outpatient treatments reduce the health system burden. Randomized controlled trials (RCTs) in COVID-19 outpatients have tested therapeutic agents, but no RCT or systematic review has been conducted comparing the efficacy of the main outpatient treatment classes to each other. We aimed in this systematic review of outpatient RCTs in COVID-19 to compare hospitalisation rate reductions with four classes of treatment: convalescent plasma, monoclonal antibodies, small molecule antivirals and repurposed drugs.\n\nMethodsWe conducted a systematic review and meta-analysis of all COVID-19 outpatient RCTs that included the endpoint of progression to hospitalisation. We assembled, from multiple published and preprint databases, participant characteristics, hospitalisations, resolution of symptoms and mortality from January 2020 to May 21, 2023. The risk of bias from COVID-NMA was incorporated into the Grading of Recommendations Assessment, Development and Evaluation (GRADE) system. We measured heterogeneity with I2. Meta-analysis by a random or fixed effect model dependent on significant heterogeneity (I2 >50%) was performed. The protocol was registered in PROSPERO, CRD42022369181.\n\nFindingsThe search identified 281 studies of which 54 RCTs for 30 diverse interventions were included in the final analysis. These trials, performed largely in unvaccinated cohorts during pre-Omicron waves, focused on populations with at least one COVID-19 hospitalisation risk factor. Grouping by class, monoclonal antibodies (OR=0.31 [95% CI=0.24-0.40]) had highest efficacy, followed by COVID-19 convalescent plasma (CCP) (OR=0.69 [95% CI=0.53 to 0.90]) and small molecule antivirals (OR=0.78 [95% CI=0.48-1.33]) for hospital reduction. Repurposed drugs (OR=0.82 [95% CI-0.72-0.93]) had lower efficacy.\n\nInterpretationInasmuch as omicron sublineages (XBB and BQ.1.1) are now resistant to monoclonal antibodies, oral antivirals are the preferred treatment in outpatients where available, but intravenous interventions from convalescent plasma to remdesivir are also effective and necessary in constrained medical resource settings or for acute and chronic COVID-19 in the immunocompromised.\n\nFundingUS Department of Defense and National Institute of Health\n\nResearch in context Evidence before this studyWe systematically searched the published and preprint data bases for outpatient randomized clinical trials of treatment of COVID-19 disease with hospitalisation as an endpoint. Previous systematic reviews and meta-analyses have confined the reviews to specific classes such as convalescent plasma, monoclonal antibodies, small molecule antivirals or repurposed drugs. Few comparisons have been made between these therapeutic classes. The trials took place both in the pre-vaccination and the vaccination era, spanning periods with dominance of different COVID variants. We sought to compare efficacy between the four classes of treatments listed above when used in outpatient COVID-19 patients as shown in randomized, placebo-controlled trials.\n\nAdded value of this studyThis systematic review and meta-analysis brings together trials that assessed hospitalisation rates in diverse COVID-19 outpatient populations varying in age and comorbidities, permitting us to assess the efficacy of interventions both within and across therapeutic classes. While heterogeneity exists within and between these intervention classes, the meta-analysis can be placed in context of trial diverse populations over variant time periods of the pandemic. At present most of the world population has either had COVID-19 or been vaccinated with a high seropositivity rate, indicating that future placebo-controlled trials will be limited because of the sample sizes required to document hospitalisation outcomes.\n\nImplications of all the available evidenceNumerous diverse therapeutic tools need to be ready for a resilient response to changing SARS-CoV-2 variants in both immunocompetent and immunocompromised COVID-19 outpatient populations. To date few head-to-head randomized controlled trials (RCTs) has compared treatment options for COVID-19 outpatients, making comparisons and treatment choices difficult. This systematic review compares outcomes among RCTs of outpatient therapy for COVID-19, taking into account time between onset of symptoms and treatment administration. We found that small-chemical antivirals, convalescent plasma and monoclonal antibodies had comparable efficacy between classes and amongst interventions within the four classes. Monoclonals have lost efficacy with viral mutation, and chemical antivirals have contraindications and adverse events, while intravenous interventions like convalescent plasma or remdesivir remain resilient options for the immunocompromised, and, in the case of CCP, in resource constrained settings with limited availability of oral drugs.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "David J Sullivan",
+        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
+      },
+      {
+        "author_name": "Daniele Focosi",
+        "author_inst": "Pisa University Hospital"
+      },
+      {
+        "author_name": "Daniel F Hanley",
+        "author_inst": "Johns Hopkins University"
+      },
+      {
+        "author_name": "Mario Cruciani",
+        "author_inst": "Division of Hematology, Carlo Poma Hospital"
+      },
+      {
+        "author_name": "Massimo Franchini",
+        "author_inst": "Pisa University Hospital"
+      },
+      {
+        "author_name": "Jiangda Ou",
+        "author_inst": "Johns Hopkins University"
+      },
+      {
+        "author_name": "Arturo Casadevall",
+        "author_inst": "Johns Hopkins School of Public Health"
+      },
+      {
+        "author_name": "Nigel Paneth",
+        "author_inst": "Michigan State University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.05.25.22275533",
     "rel_title": "Intrahost evolution and forward transmission of a novel SARS-CoV-2 Omicron BA.1 subvariant",
@@ -283033,81 +281775,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.05.24.22275544",
-    "rel_title": "Clinical features and burden of post-acute sequelae of SARS-CoV-2 infection in children and adolescents: an exploratory EHR-based cohort study from the RECOVER program",
-    "rel_date": "2022-05-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.24.22275544",
-    "rel_abs": "ImportanceThe post-acute sequelae of SARS-CoV-2 (PASC) has emerged as a long-term complication in adults, but current understanding of the clinical presentation of PASC in children is limited.\n\nObjectiveTo identify diagnosed symptoms, diagnosed health conditions and medications associated with PASC in children.\n\nDesign, Setting and ParticipantsRetrospective cohort study using electronic health records from 9 US childrens hospitals for individuals <21 years-old who underwent reverse transcriptase polymerase chain reaction (RT-PCR) testing for SARS-CoV-2 between March 1, 2020 - October 31, 2021 and had at least 1 encounter in the 3 years before testing.\n\nExposureSARS-CoV-2 PCR positivity.\n\nMain Outcomes and MeasuresWe identified syndromic (symptoms), systemic (conditions), and medication PASC features in the 28-179 days following the initial test date. Adjusted hazard ratios (aHRs) were obtained for 151 clinically predicted PASC features by contrasting PCR-positive with PCR-negative groups using proportional hazards models, adjusting for site, age, sex, testing location, race/ethnicity, and time-period of cohort entrance. We estimated the incidence proportion for any syndromic, systemic or medication PASC feature in the two groups to obtain a burden of PASC estimate.\n\nResultsAmong 659,286 children in the study sample, 59,893 (9.1%) tested positive by PCR for SARS-CoV-2. Most were tested in outpatient testing facility (50.3%) or office (24.6%) settings. The most common syndromic, systemic, and medication features were loss of taste or smell (aHR 1.96 [95% CI 1.16-3.32), myocarditis (aHR 3.10 [95% CI 1.94-4.96]), and cough and cold preparations (aHR 1.52 [95% CI 1.18-1.96]). The incidence of at least one systemic/syndromic/medication feature of PASC was 41.9% among PCR-positive children versus 38.2% among PCR-negative children, with an incidence proportion difference of 3.7% (95% CI 3.2-4.2%). A higher strength of association for PASC was identified in those cared for in the ICU during the acute illness phase, children less than 5 years-old, and individuals with complex chronic conditions.\n\nConclusions and RelevanceIn this large-scale, exploratory study, the burden of pediatric PASC that presented to health systems was low. Myocarditis was the most commonly diagnosed PASC-associated condition. Acute illness severity, young age, and comorbid complex chronic disease increased the risk of PASC.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhat are the incidence and clinical features of post-acute sequelae of SARS-CoV-2 infection (PASC) in children?\n\nFindingsIn this retrospective cohort study of 659,286 children tested for SARS-CoV-2 by polymerase chain reaction (PCR), the symptom, condition and medication with the strongest associations with SARS-CoV-2 infection were loss of taste/smell, myocarditis, and cough and cold preparations. The incidence proportion of non-MIS-C related PASC in the PCR-positive group exceeded the PCR-negative group by 3.7% (95% CI 3.2-4.2), with increased rates associated with acute illness severity, young age, and medical complexity.\n\nMeaningPASC in children appears to be uncommon, with features that differ from adults.",
-    "rel_num_authors": 15,
-    "rel_authors": [
-      {
-        "author_name": "Suchitra Rao",
-        "author_inst": "University of Colorado School of Medicine"
-      },
-      {
-        "author_name": "Grace M Lee",
-        "author_inst": "Stanford University School of Medicine"
-      },
-      {
-        "author_name": "Hanieh Razzaghi",
-        "author_inst": "Applied Clinical Research Center, Childrens Hospital of Philadelphia"
-      },
-      {
-        "author_name": "Vitaly Lorman",
-        "author_inst": "Applied Clinical Research Center, Childrens Hospital of Philadelphia"
-      },
-      {
-        "author_name": "Asuncion Mejias",
-        "author_inst": "Department of Pediatrics, Nationwide Childrens Hospital and The Ohio State University"
-      },
-      {
-        "author_name": "Nathan M Pajor",
-        "author_inst": "Cincinnati Childrens Hospital Medical Center and University of Cincinnati College of Medicine"
-      },
-      {
-        "author_name": "Deepika Thacker",
-        "author_inst": "Nemours Childrens Health"
-      },
-      {
-        "author_name": "Ryan Webb",
-        "author_inst": "Applied Clinical Research Center, Childrens Hospital of Philadelphia"
-      },
-      {
-        "author_name": "Kimberley Dickinson",
-        "author_inst": "Applied Clinical Research Center, Childrens Hospital of Philadelphia"
-      },
-      {
-        "author_name": "Charles Bailey",
-        "author_inst": "Applied Clinical Research Center, Childrens Hospital of Philadelphia"
-      },
-      {
-        "author_name": "Ravi Jhaveri",
-        "author_inst": "Ann & Robert H. Lurie Childrens Hospital of Chicago"
-      },
-      {
-        "author_name": "Dimitri A Christakis",
-        "author_inst": "Center for Child Health, Behavior and Development, Seattle Childrens Hospital"
-      },
-      {
-        "author_name": "Tellen D Bennett",
-        "author_inst": "University of Colorado School of Medicine"
-      },
-      {
-        "author_name": "Yong Chen",
-        "author_inst": "Perelman School of Medicine, University of Pennsylvania"
-      },
-      {
-        "author_name": "Christopher B Forrest",
-        "author_inst": "Applied Clinical Research Center, Childrens Hospital of Philadelphia"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.05.22.22275422",
     "rel_title": "SARS-CoV-2 NSP3, NSP4 and NSP6 mutations and Epistasis during the pandemic in the world: Evolutionary Trends and Natural Selections in Six Continents",
@@ -283546,6 +282213,33 @@
     "type": "new results",
     "category": "pharmacology and toxicology"
   },
+  {
+    "rel_doi": "10.1101/2022.05.24.22275529",
+    "rel_title": "Depressive and anxiety symptoms during the COVID-19 pandemic: A two-year follow-up",
+    "rel_date": "2022-05-25",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.24.22275529",
+    "rel_abs": "BackgroundThere has been much research into the mental health impact of the COVID-19 pandemic and how it is related to time-invariant individual characteristics (e.g. age and gender). However, there is still a lack of research showing long-term trajectories of mental health across different stages of the pandemic. And little is known regarding the longitudinal association of time-varying contextual and individual factors (e.g. COVID-19 policy response and pandemic intensity) with mental health outcomes. This study aimed to provide a longitudinal profile of how depressive and anxiety symptoms changed by month between March 2020 and April 2022, and to examine their longitudinal associations with time-varying contextual and individual level factors.\n\nMethods and findingsDrawing data from a large panel study of over 58,000 adults living in England, we showed that mental health changes were largely in line with changes in COVID-19 policy response and pandemic intensity. Further, data were analysed using fixed-effects, with models fitted separately across three stages of the COVID-19 pandemic. We found that more stringent policy response was associated with increased mental health symptoms, in particular during lockdown periods. Higher COVID-19 deaths were also associated with poorer mental health, but this association weakened over time. Finally, there was also evidence for the longitudinal association of mental health with individual level factors, including confidence in government/healthcare/essentials, COVID-19 knowledge, COVID-19 stress, COVID-19 infection and social support.\n\nConclusionsOur results provided empirical evidence on how changes in contextual and individual level factors were related to depressive and anxiety symptoms. While some factors clearly acted as consistent predictors of mental health during a pandemic, other factors were dependent on the specific situations occurring within society. This could provide important implications for policy making and for a better understanding of mental health of the general public during a national or global health crisis.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Feifei Bu",
+        "author_inst": "UCL"
+      },
+      {
+        "author_name": "Andrew Steptoe",
+        "author_inst": "UCL"
+      },
+      {
+        "author_name": "Daisy Fancourt",
+        "author_inst": "University College London"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2022.05.23.22275444",
     "rel_title": "Evaluation of triage checklist for mild COVID-19 outpatients in predicting subsequent emergency department visits and hospitalization during isolation period",
@@ -285027,97 +283721,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2022.05.21.22275412",
-    "rel_title": "Machine Learning for Identifying Data-Driven Subphenotypes of Incident Post-Acute SARS-CoV-2 Infection Conditions with Large Scale Electronic Health Records: Findings from the RECOVER Initiative",
-    "rel_date": "2022-05-23",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.21.22275412",
-    "rel_abs": "The post-acute sequelae of SARS-CoV-2 infection (PASC) refers to a broad spectrum of symptoms and signs that are persistent, exacerbated, or newly incident in the post-acute SARS-CoV-2 infection period of COVID-19 patients. Most studies have examined these conditions individually without providing concluding evidence on co-occurring conditions. To answer this question, this study leveraged electronic health records (EHRs) from two large clinical research networks from the national Patient-Centered Clinical Research Network (PCORnet) and investigated patients newly incident diagnoses that appeared within 30 to 180 days after a documented SARS-CoV-2 infection. Through machine learning, we identified four reproducible subphenotypes of PASC dominated by blood and circulatory system, respiratory, musculoskeletal and nervous system, and digestive system problems, respectively. We also demonstrated that these subphenotypes were associated with distinct patterns of patient demographics, underlying conditions present prior to SARS-CoV-2 infection, acute infection phase severity, and use of new medications in the post-acute period. Our study provides novel insights into the heterogeneity of PASC and can inform stratified decision-making in the treatment of COVID-19 patients with PASC conditions.",
-    "rel_num_authors": 19,
-    "rel_authors": [
-      {
-        "author_name": "Hao Zhang",
-        "author_inst": "Weill Cornell Medicine, Cornell University"
-      },
-      {
-        "author_name": "CHENGXI ZANG",
-        "author_inst": "Weill Cornell Medicine"
-      },
-      {
-        "author_name": "Zhenxing Xu",
-        "author_inst": "Weill Cornell Medical College"
-      },
-      {
-        "author_name": "Yongkang Zhang",
-        "author_inst": "Weill Cornell Medicine"
-      },
-      {
-        "author_name": "Jie Xu",
-        "author_inst": "University of Florida"
-      },
-      {
-        "author_name": "Jiang Bian",
-        "author_inst": "University of Florida"
-      },
-      {
-        "author_name": "Dmitry Morozyuk",
-        "author_inst": "Weill Cornell Medicine"
-      },
-      {
-        "author_name": "Dhruv Khullar",
-        "author_inst": "Weill Cornell Medicine"
-      },
-      {
-        "author_name": "Yiye Zhang",
-        "author_inst": "Weill Cornell Medicine"
-      },
-      {
-        "author_name": "Anna Starikovsky Nordvig",
-        "author_inst": "Weill Cornell Medicine"
-      },
-      {
-        "author_name": "Edward J. Schenck",
-        "author_inst": "Weill Cornell Medicine"
-      },
-      {
-        "author_name": "Elizabeth Ann Shenkman",
-        "author_inst": "University of Florida"
-      },
-      {
-        "author_name": "Russel L. Rothman",
-        "author_inst": "Vanderbilt University Medical Center"
-      },
-      {
-        "author_name": "Jason P Block",
-        "author_inst": "Harvard Pilgrim Health Care Institute/Harvard Medical School"
-      },
-      {
-        "author_name": "Kristin Lyman",
-        "author_inst": "Louisiana Public Health Institute"
-      },
-      {
-        "author_name": "Mark Weiner",
-        "author_inst": "Weill Cornell Medicine"
-      },
-      {
-        "author_name": "Thomas W. Carton",
-        "author_inst": "Louisiana Public Health Institute"
-      },
-      {
-        "author_name": "Fei Wang",
-        "author_inst": "Weill Cornell Medical College"
-      },
-      {
-        "author_name": "Rainu Kaushal",
-        "author_inst": "Weill Cornell Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2022.05.20.22275319",
     "rel_title": "Low testing rates limit the ability of genomic surveillance programs to monitor SARS-CoV-2 variants: a mathematical modelling study",
@@ -285460,6 +284063,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.05.21.492928",
+    "rel_title": "Modeling suggests that multiple immunizations or infections will reveal the benefits of updating SARS-CoV-2 vaccines",
+    "rel_date": "2022-05-23",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.21.492928",
+    "rel_abs": "When should vaccines to evolving pathogens such as SARS-CoV-2 be updated? Our computational models address this focusing on updating SARS-CoV-2 vaccines to the currently circulating Omicron variant. Current studies typically compare the antibody titers to the new variant following a single dose of the original-vaccine versus the updated-vaccine in previously immunized individuals. These studies find that the updated-vaccine does not induce higher titers to the vaccine-variant compared with the original-vaccine, suggesting that updating may not be needed. Our models recapitulate this observation but suggest that vaccination with the updated-vaccine generates qualitatively different humoral immunity, a small fraction of which is specific for unique epitopes to the new variant. Our simulations suggest that these new variant-specific responses could dominate following subsequent vaccination or infection with either the currently circulating or future variants. We suggest a two-dose strategy for determining if the vaccine needs updating and for vaccinating high-risk individuals.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Rajat Desikan",
+        "author_inst": "GSK"
+      },
+      {
+        "author_name": "Susanne L Linderman",
+        "author_inst": "Emory University"
+      },
+      {
+        "author_name": "Carl W. Davis",
+        "author_inst": "Emory University School of Medicine"
+      },
+      {
+        "author_name": "Veronika I Zarnitsyna",
+        "author_inst": "Emory University School of Medicine"
+      },
+      {
+        "author_name": "Hasan R Ahmed",
+        "author_inst": "Emory University"
+      },
+      {
+        "author_name": "Rustom Antia",
+        "author_inst": "Emory University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2022.05.21.492903",
     "rel_title": "Reduced Neutralization of SARS-CoV-2 Omicron Variant in Sera from SARS-CoV-1 Survivors after 3-dose of Vaccination",
@@ -287093,129 +285735,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pediatrics"
   },
-  {
-    "rel_doi": "10.1101/2022.05.18.22275274",
-    "rel_title": "Levels and determinants of COVID-19 vaccine hesitancy among sub-Saharan African adolescents",
-    "rel_date": "2022-05-21",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.18.22275274",
-    "rel_abs": "COVID-19 vaccine hesitancy among adolescents poses a challenge to the global effort to control the pandemic. This multi-country survey aimed to assess the levels and determinants of COVID-19 vaccine hesitancy among adolescents in sub-Saharan Africa between July and December 2021. The survey was conducted using computer-assisted telephone interviewing among adolescents in five sub-Saharan African countries, Burkina Faso, Ethiopia, Ghana, Nigeria, and Tanzania. A rural area and an urban area were included in each country (except Ghana, which only had a rural area), with approximately 300 adolescents in each area and 2803 in total. Sociodemographic characteristics and perceptions and attitudes on COVID-19 vaccines were measured. Vaccine hesitancy was defined as definitely not getting vaccinated or being undecided on whether to get vaccinated if a COVID-19 vaccine were available. Log-binomial models were used to calculate the adjusted prevalence ratios (aPRs) and 95% confidence intervals (CIs) for associations between potential determinants and COVID-19 vaccine hesitancy. The percentage of COVID-19 vaccine hesitancy was 15% in rural Kersa, 24% in rural Ibadan, 31% in rural Nouna, 33% in urban Ouagadougou, 37% in urban Addis Ababa, 48% in rural Kintampo, 64% in urban Lagos, 76% in urban Dar es Salaam, and 88% in rural Dodoma. Perceived low necessity, concerns about vaccine safety, and concerns about vaccine effectiveness were the leading reasons for hesitancy. Healthcare workers, parents or family members, and schoolteachers had the greatest impacts on vaccine willingness. Perceived lack of safety (aPR: 3.61; 95% CI: 3.10, 4.22) and lack of effectiveness (aPR: 3.59; 95% CI: 3.09, 4.18) were associated with greater vaccine hesitancy. The levels of COVID-19 vaccine hesitancy among adolescents are alarmingly high across the five sub-Saharan African countries, especially in Tanzania. COVID-19 vaccination campaigns among sub-Saharan African adolescents should address their concerns and misconceptions about vaccine safety and effectiveness.",
-    "rel_num_authors": 27,
-    "rel_authors": [
-      {
-        "author_name": "Dongqing Wang",
-        "author_inst": "Harvard University T H Chan School of Public Health"
-      },
-      {
-        "author_name": "Angela Chukwu",
-        "author_inst": "University of Ibadan"
-      },
-      {
-        "author_name": "Mary Mwanyika-Sando",
-        "author_inst": "Africa Academy for Public Health"
-      },
-      {
-        "author_name": "Sulemana  Watara Abubakari",
-        "author_inst": "Kintampo Health Research Centre"
-      },
-      {
-        "author_name": "Nega Assefa",
-        "author_inst": "Haramaya University College of Health Sciences: Haramaya University College of Health and Medical Sciences"
-      },
-      {
-        "author_name": "Isabel Madzorera",
-        "author_inst": "Harvard University T H Chan School of Public Health"
-      },
-      {
-        "author_name": "Elena  C Hemler",
-        "author_inst": "Harvard University T H Chan School of Public Health"
-      },
-      {
-        "author_name": "Abbas Ismail",
-        "author_inst": "The University of Dodoma"
-      },
-      {
-        "author_name": "Bruno Lankoande",
-        "author_inst": "University of Ouagadougou"
-      },
-      {
-        "author_name": "Frank Mapendo",
-        "author_inst": "Africa Academy for Public Health"
-      },
-      {
-        "author_name": "Ourohir\u00e9 Millogo",
-        "author_inst": "Nouna Health Research Center: Centre de Recherche en Sante de Nouna"
-      },
-      {
-        "author_name": "Firehiwot Workneh",
-        "author_inst": "Addis Continental Institute of Public Health"
-      },
-      {
-        "author_name": "Temesgen Azemraw",
-        "author_inst": "Addis Continental Institute of Public Health"
-      },
-      {
-        "author_name": "Lawrence  G Febir",
-        "author_inst": "Kintampo Health Research Centre"
-      },
-      {
-        "author_name": "Christabel James",
-        "author_inst": "University of Ibadan"
-      },
-      {
-        "author_name": "Amani Tinkasimile",
-        "author_inst": "Africa Academy for Public Health"
-      },
-      {
-        "author_name": "Kwaku  Poku Asante",
-        "author_inst": "Kintampo Health Research Centre"
-      },
-      {
-        "author_name": "Till Baernighausen",
-        "author_inst": "University of Heidelberg"
-      },
-      {
-        "author_name": "Yemane Berhane",
-        "author_inst": "Addis Continental Institute of Public Health"
-      },
-      {
-        "author_name": "Japhet Killewo",
-        "author_inst": "Muhimbili University College of Health Sciences: Muhimbili University of Health and Allied Sciences"
-      },
-      {
-        "author_name": "Ayoade  MJ Oduola",
-        "author_inst": "University of Ibadan"
-      },
-      {
-        "author_name": "Ali Sie",
-        "author_inst": "Nouna Health Research Center: Centre de Recherche en Sante de Nouna"
-      },
-      {
-        "author_name": "Emily  R Smith",
-        "author_inst": "The George Washington University Milken Institute of Public Health"
-      },
-      {
-        "author_name": "Abdramane  Bassiahi Soura",
-        "author_inst": "University of Ouagadougou"
-      },
-      {
-        "author_name": "Raji Tajudeen",
-        "author_inst": "Africa Centres for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Said Vuai",
-        "author_inst": "The University of Dodoma"
-      },
-      {
-        "author_name": "Wafaie  W Fawzi",
-        "author_inst": "Harvard University T H Chan School of Public Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2022.05.20.22275397",
     "rel_title": "Comorbidities and sociodemographic factors on COVID-19 fatalities",
@@ -287526,6 +286045,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.05.20.492819",
+    "rel_title": "Revealing druggable cryptic pockets in the Nsp-1 of SARS-CoV-2 and other \u03b2-coronaviruses by simulations and crystallography",
+    "rel_date": "2022-05-20",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.20.492819",
+    "rel_abs": "Non-structural protein 1 (Nsp1) is a main pathogenicity factor of - and {beta}-coronaviruses. Nsp1 of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) suppresses the host gene expression by sterically blocking 40S host ribosomal subunits and promoting host mRNA degradation. This mechanism leads to the downregulation of the translation-mediated innate immune response in host cells, ultimately mediating the observed immune evasion capabilities of SARS-CoV-2. Here, by combining extensive Molecular Dynamics simulations, fragment screening and crystallography, we reveal druggable pockets in Nsp1. Structural and computational solvent mapping analyses indicate the partial crypticity of these newly discovered and druggable binding sites. The results of fragment-based screening via X-ray crystallography confirm the druggability of the major pocket of Nsp1. Finally, we show how the targeting of this pocket could disrupt the Nsp1-mRNA complex and open a novel avenue to design new inhibitors for other Nsp1s present in homologous {beta}-coronaviruses.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Alberto Borsatto",
+        "author_inst": "University of Geneva"
+      },
+      {
+        "author_name": "Obaeda Akkad",
+        "author_inst": "University of Geneva"
+      },
+      {
+        "author_name": "Ioannis Galdadas",
+        "author_inst": "University of Geneva"
+      },
+      {
+        "author_name": "Shumeng Ma",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Shymaa Damfo",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Shozeb Haider",
+        "author_inst": "University College London School of Pharmacy"
+      },
+      {
+        "author_name": "Frank Kozielski",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Carolina Estarellas",
+        "author_inst": "University of Barcelona"
+      },
+      {
+        "author_name": "Francesco Luigi Gervasio",
+        "author_inst": "University of Geneva"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "biophysics"
+  },
   {
     "rel_doi": "10.1101/2022.05.20.492834",
     "rel_title": "SARS-CoV-2 Infects Peripheral and Central Neurons of Mice Before Viremia, Facilitated by Neuropilin-1",
@@ -289015,65 +287585,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
-  {
-    "rel_doi": "10.1101/2022.05.16.22275151",
-    "rel_title": "Neutralization Escape by the SARS-CoV-2 Omicron Variants BA.2.12.1 and BA.4/BA.5",
-    "rel_date": "2022-05-19",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.16.22275151",
-    "rel_abs": "Multiple lineages of the SARS-CoV-2 Omicron variant (B.1.1.529) have emerged, and BA.1 and BA.2 have demonstrated substantial escape from neutralizing antibodies (NAbs). BA.2.12.1 has now become dominant in the United States, and BA.4 and BA.5 have become dominant in South Africa. Our data show that BA.2.12.1 and BA.4/BA.5 substantially escape NAbs induced by both vaccination and infection. Moreover, BA.4/BA.5 NAb titers, and to lesser extent BA.2.12.1 NAb titers, were lower than BA.1 and BA.2 NAb titers, suggesting that the SARS-CoV-2 Omicron variant has continued to evolve with increasing neutralization escape. These findings have important public health implications and provide immunologic context for the current surges with BA.2.12.1 and BA.4/BA.5 in populations with high rates of vaccination and BA.1/BA.2 infection.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Nicole Hachmann",
-        "author_inst": "Beth Israel Deaconess Medical Center"
-      },
-      {
-        "author_name": "Jessica Miller",
-        "author_inst": "Beth Israel Deaconess Medical Center"
-      },
-      {
-        "author_name": "Ai-ris Collier",
-        "author_inst": "Beth Israel Deaconess Medical Center"
-      },
-      {
-        "author_name": "John Ventura",
-        "author_inst": "Beth Israel Deaconess Medical Center"
-      },
-      {
-        "author_name": "Jingyou Yu",
-        "author_inst": "Beth Israel Deaconess Medical Center"
-      },
-      {
-        "author_name": "Marjorie Rowe",
-        "author_inst": "Beth Israel Deaconess Medical Center"
-      },
-      {
-        "author_name": "Esther Bondzie",
-        "author_inst": "Beth Israel Deaconess Medical Center"
-      },
-      {
-        "author_name": "Olivia Powers",
-        "author_inst": "Beth Israel Deaconess Medical Center"
-      },
-      {
-        "author_name": "Nehalee Surve",
-        "author_inst": "Beth Israel Deaconess Medical Center"
-      },
-      {
-        "author_name": "Kevin Hall",
-        "author_inst": "Beth Israel Deaconess Medical Center"
-      },
-      {
-        "author_name": "Dan H. Barouch",
-        "author_inst": "Beth Israel Deaconess Medical Center"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.05.16.22274315",
     "rel_title": "Clinical validation of 3D-printed nasopharyngeal and oropharyngeal swabs for SARS-CoV-2 RT-PCR",
@@ -289476,6 +287987,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2022.05.19.22275055",
+    "rel_title": "How Should COVID-19 Vaccines be Distributed between the Global North and South? A Discrete Choice Experiment in Six European Countries",
+    "rel_date": "2022-05-19",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.19.22275055",
+    "rel_abs": "BackgroundThe global distribution of COVID-19 vaccinations remains highly unequal. We examine public preferences in six European countries regarding the allocation of COVID-19 vaccines between the Global South and Global North.\n\nMethodsWe conducted online discrete choice experiments with adult participants in France (n=766), Germany (n=1964), Italy (n=767), Poland (n=670), Spain (n=925), and Sweden (n=938). Respondents were asked to decide which one of two candidates, who varied along four attributes: age, mortality risk, employment, and living in a low- or high-income country, should receive the vaccine first. We analysed the relevance of each attribute in allocation decisions using a conditional logit regression.\n\nResultsAcross countries, respondents selected candidates with a high mortality and infection risk, irrespective of whether the candidate lived in their own country. All else equal, respondents in Italy, France, Spain, and Sweden gave priority to a candidate from a low-income country, whereas German respondents were significantly more likely to choose the candidate from their own country. Female, younger, and more educated respondents were more favourable of an equitable vaccine distribution.\n\nConclusionsGiven these preferences for global solidarity, European governments should promote vaccine transfers to poorer world regions.\n\nFundingFunding was provided by the European Unions Horizon H2020 research and innovation programme under grant agreement 101016233 (PERISCOPE).",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Janina Isabel Steinert",
+        "author_inst": "Technical University of Munich"
+      },
+      {
+        "author_name": "Henrike Sternberg",
+        "author_inst": "Technical University of Munich"
+      },
+      {
+        "author_name": "Giuseppe Alessandro Veltri",
+        "author_inst": "University of Trento"
+      },
+      {
+        "author_name": "Tim Buethe",
+        "author_inst": "Technical University of Munich"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2022.05.18.492441",
     "rel_title": "Comprehensive analysis of pathways in Coronavirus 2019 (COVID-19) using an unsupervised machine learning method",
@@ -290685,61 +289227,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.05.16.22275074",
-    "rel_title": "Jinhua Qinggan Granules for Nonhospitalized COVID-19 Patients: a Double-Blind, Placebo-Controlled, Randomized Controlled Trial",
-    "rel_date": "2022-05-17",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.16.22275074",
-    "rel_abs": "BackgroundKey findings from the World Health Organization Expert Meeting on Evaluation of Traditional Chinese Medicine in treating COVID-19 reported that TCMs are beneficial, particularly for mild-to-moderate cases. The efficacy of Jinhua Qinggan Granules (JHQG) in COVID-19 patients with mild symptoms has yet to be clearly defined.\n\nMethodsWe conducted a phase 2/3, double-blind, randomized, placebo-controlled trial to evaluate the efficacy and safety of treatment with JHQG in mild, nonhospitalized, laboratory-confirmed COVID-19 patients. Participants were randomly assigned to receive 5g/sacket of JHQG or placebo granules orally thrice daily for 10 days. The primary outcomes were the improvement in clinical symptoms and proportion tested negative on viral PCR after treatment. Secondary outcomes were the time to recovery from clinical symptoms and changes in white blood cells (WBC) and acute phase reactants (C-reactive protein (CRP) and ferritin) 10-15 days after treatment.\n\nResultsA total of 300 patients were randomly assigned to receive JHQG (150 patients) and placebo (150 patients). Baseline characteristics were similar in the two groups. In the modified intention-to-treat analysis, JHQG showed greater clinical efficacy (82.67%) after 10 days of treatment compared with the placebo group (10.74%) (rate difference: 71.93%; 95% CI 64.09 - 79.76). The proportion of patients with a negative PCR after treatment were comparable (rate difference: -4.67%; 95% CI -15.76 - 6.42). While all changes in WBC, ferritin, and CRP levels showed a statistically significant decline in JHQG (P[&le;]0.044) after treatment, but not the latter in placebo (P=0.077). The median time to recovery of COVID-19 related symptoms including cough, sputum, sore throat, dyspnea, headache, nasal obstruction, fatigue, and myalgia were shorter in the JHQG group compared to the placebo group (P<0.001 for all). 3 patients experienced mild to moderate adverse events during the treatment period in the JHQG group. Findings were similar between the modified intention-to-treat and the per-protocol analysis that included only patients who reported 100% adherence to the assigned regimen.\n\nConclusionsJHQG is a safe and effective TCM for the treatment of mild COVID-19 patients.\n\nClinical Trial RegistrationThe Trial was prospectively registered on www.clinicaltrials.gov with registration number: NCT04723524.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Muhammad R. Shah",
-        "author_inst": "Center for Bioequivalence Studies and Clinical Research (CBSCR), International Center for Chemical and Biological Sciences, University of Karachi, Pakistan"
-      },
-      {
-        "author_name": "Samreen Fatima",
-        "author_inst": "Center for Bioequivalence Studies and Clinical Research (CBSCR), Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and"
-      },
-      {
-        "author_name": "Sehrosh N. Khan",
-        "author_inst": "Center for Bioequivalence Studies and Clinical Research (CBSCR), Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and"
-      },
-      {
-        "author_name": "Shafi Ullah",
-        "author_inst": "Center for Bioequivalence Studies and Clinical Research (CBSCR), Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and"
-      },
-      {
-        "author_name": "Gulshan Himani",
-        "author_inst": "The Indus Hospital Karachi, Plot C-76, Sector 31/5, Opposite Korangi Crossing, Darussalam Society Sector 39, Pakistan"
-      },
-      {
-        "author_name": "Kelvin H. Wan",
-        "author_inst": "Hong Kong Alliance of Integrated Medicine Against Covid, Hong Kong"
-      },
-      {
-        "author_name": "Timothy P.H. Lin",
-        "author_inst": "Hong Kong Alliance of Integrated Medicine Against Covid, Hong Kong"
-      },
-      {
-        "author_name": "Johnson Y. Lau",
-        "author_inst": "School of Chinese Medicine, Hong Kong Baptist University, China"
-      },
-      {
-        "author_name": "Qingquan Liu",
-        "author_inst": "Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, China"
-      },
-      {
-        "author_name": "Dennis S.C. Lam",
-        "author_inst": "Hong Kong Alliance of Integrated Medicine Against Covid, Hong Kong"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.05.17.22275205",
     "rel_title": "A hybrid approach to predict COVID-19 cases using neural networks and inverse problem",
@@ -290998,6 +289485,89 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2022.05.15.22275086",
+    "rel_title": "Clinical Performance of Direct RT-PCR Testing of Raw Saliva for Detection of SARS-CoV-2 in Symptomatic and Asymptomatic Individuals",
+    "rel_date": "2022-05-16",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.15.22275086",
+    "rel_abs": "RT-qPCR tests based on RNA extraction from nasopharyngeal swab samples are promoted as the \"gold standard\" for SARS-CoV-2 detection. However, self-collected saliva samples offer a non-invasive alternative more suited to high-throughput testing. This study evaluated the performance of TaqPath COVID-19 Fast PCR Combo Kit 2.0 assay for detection of SARS-CoV-2 in raw saliva relative to a lab-developed direct RT-qPCR test (SalivaDirect-based PCR) and a RT-qPCR test based on RNA extraction from NPS samples. Both samples were collected from symptomatic and asymptomatic individuals (N=615). Saliva samples were tested for SARS-CoV-2 using the TaqPath COVID-19 Fast PCR Combo Kit 2.0 and the SalivaDirect-based PCR, while RNA extracts from NPS samples were tested by RT-qPCR according to the Irish national testing system. The TaqPath COVID-19 Fast PCR detected SARS-CoV-2 in 52 saliva samples, of which 51 were also positive with the SalivaDirect-based PCR. 49 samples displayed concordant results with the NPS extraction-based method, while three samples were positive on raw saliva. Among the negative samples, 10 discordant cases were found with the TaqPath COVID-19 Fast PCR (PPA-85.7%; NPA-99.5%), when compared to the RNA extraction-based NPS method, performing similarly to the SalivaDirect-based PCR (PPA-87.5%; NPA-99.5%). The direct RT-qPCR testing of saliva samples shows high concordance with NPS extraction-based method for SARS-CoV-2 detection, providing a cost-effective and highly-scalable system for high-throughput COVID-19 rapid-testing.",
+    "rel_num_authors": 17,
+    "rel_authors": [
+      {
+        "author_name": "Rosa Castillo-Bravo",
+        "author_inst": "National University of Ireland Galway"
+      },
+      {
+        "author_name": "Noel Lucca",
+        "author_inst": "National University of Ireland Galway"
+      },
+      {
+        "author_name": "Linyi Lai",
+        "author_inst": "National University of Ireland Galway"
+      },
+      {
+        "author_name": "Killian Marlborough",
+        "author_inst": "National University of Ireland Galway"
+      },
+      {
+        "author_name": "Galina Brychkova",
+        "author_inst": "National University of Ireland Galway"
+      },
+      {
+        "author_name": "Charlie Lonergan",
+        "author_inst": "National University of Ireland Galway"
+      },
+      {
+        "author_name": "Justin O'Grady",
+        "author_inst": "Quadram Institute Bioscience"
+      },
+      {
+        "author_name": "Nabil-Fareed Alikhan",
+        "author_inst": "Quadram Institute Bioscience"
+      },
+      {
+        "author_name": "Alexander Trotter",
+        "author_inst": "Quadram Institute Bioscience"
+      },
+      {
+        "author_name": "Andrew Page",
+        "author_inst": "Quadram Institute Bioscience"
+      },
+      {
+        "author_name": "Breda Smyth",
+        "author_inst": "National University of Ireland Galway"
+      },
+      {
+        "author_name": "Peter C. McKeown",
+        "author_inst": "National University of Ireland Galway"
+      },
+      {
+        "author_name": "Jelena Feenstra",
+        "author_inst": "Thermo Fisher Scientific"
+      },
+      {
+        "author_name": "Camilla Ulekleiv",
+        "author_inst": "Thermo Fisher Scientific"
+      },
+      {
+        "author_name": "Oceane Sorel",
+        "author_inst": "Thermo Fisher Scientific"
+      },
+      {
+        "author_name": "Manoj Gandhi",
+        "author_inst": "Thermo Fisher Scientific"
+      },
+      {
+        "author_name": "Charles Spillane",
+        "author_inst": "National University of Ireland Galway"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.05.12.22274993",
     "rel_title": "Applying machine-learning to rapidly analyse large qualitative text datasets to inform the COVID-19 pandemic response: Comparing human and machine-assisted topic analysis techniques",
@@ -292339,33 +290909,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2022.05.16.22275130",
-    "rel_title": "Modelling long-term COVID-19 hospital admission dynamics using immune protection waning data",
-    "rel_date": "2022-05-16",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.16.22275130",
-    "rel_abs": "Immune waning is key to the timely anticipation of COVID-19 long-term dynamics. We assess the impact of periodic vaccination campaigns using a compartmental epidemiological model with embedded multiple age structures and empiric time-dependent vaccine protection kinetics. Despite the uncertainty inherent to such scenarios, we show that vaccination campaigns decreases the yearly number of COVID-19 admissions. However, especially if restricted to individuals over 60 years old, vaccination on its own seems insufficient to prevent thousands of hospital admissions and it suffers the comparison with non-pharmaceutical interventions aimed at decreasing infection transmission. The combination of such interventions and vaccination campaigns appear to provide the greatest reduction in hospital admissions.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Bastien Reyn\u00e9",
-        "author_inst": "University of Montpellier"
-      },
-      {
-        "author_name": "Mircea T. Sofonea",
-        "author_inst": "Univ. Montpellier"
-      },
-      {
-        "author_name": "Samuel Alizon",
-        "author_inst": "CNRS"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.05.16.22275128",
     "rel_title": "School Reopening Simulations with COVID-19 Agent-based Model for the Philippine Regions",
@@ -292608,6 +291151,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.05.15.22273842",
+    "rel_title": "Summaries, Analysis and Simulations of Recent COVID-19 Epidemic in Shanghai",
+    "rel_date": "2022-05-16",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.15.22273842",
+    "rel_abs": "BackgroundAfter successfully preventing the spread of five wave COVID-19 epidemics in Shanghai, Omicron and Delta variants have been causing a surge COVID-19 infection in this city recently. Summaries, analysis and simulations for this wave epidemic are important issues.\n\nMethodsUsing differential equations and real word data, this study modelings and simulates the recent COVID-19 epidemic in Shanghai, estimates transmission rates, recovery rates, and blocking rates to symptomatic and asymptomatic infections, and symptomatic (infected) individuals death rates. Visual simulations predict the outcomes of this wave Shanghai epidemic. It compares parallely with the recent mainland China COVID-19 epidemics (RMCE).\n\nResultsThe simulation results were in good agreement with the real word data at the end points of 11 investigated time-intervals. Visual simulation results showed that on the day 90, the number of the current symptomatic (infected) individuals may be between 852 and 7314, the number of the current asymptomatic (infected) individuals charged in the observations may be between 10066 and 50292, the number of the current cumulative recovered symptomatic infected individuals may be between 52070 and 74687, the number of the current cumulative asymptomatic individuals discharged from the medical observations may be between 63509 and 5164535. The number of the died symptomatic individuals may be between 801 and 1226.\n\nO_LIThe transmission rate of the symptomatic infections caused by the symptomatic individuals was much lower than the corresponding average transmission rate of the RMCE.\nC_LIO_LIThe transmission rate of the asymptomatic infections caused by the symptomatic individuals was much higher than the first 90 days average transmission rate of RMCE.\nC_LIO_LIThe transmission rate of the symptomatic infections caused by the asymptomatic individuals was much lower than the first 60 days average transmission rate of RMCE, and was much higher than the last 60 days average transmission rate of RMCE.\nC_LIO_LIThe transmission rate to the asymptomatic infections caused by the asymptomatic individuals was much higher than the corresponding average transmission rate of RMCE.\nC_LIO_LIThe last 30 days average blocking rate to the symptomatic infections were lower than the last 30 days average blocking rates of RMCE\nC_LIO_LIThe last 30 days average blocking rate to the asymptomatic infections were much higher than the last 30 days average blocking rate of RMCE. However the first 30 days average blocking rate to the asymptomatic infections were much lower than the first 30 days average blocking rate of RMCE.\nC_LIO_LIThe first 37 days recovery rates of the symptomatic individuals were much lower than the corresponding first 70 days recovery rates of the symptomatic individuals of RMCE. The recovery rates between 38- and 52-days of the symptomatic individuals were much lower than the corresponding the recovery rates between 91- and 115-days of the symptomatic individuals of RMCE. The last weeks recovery rate was similar to the last weeks recovery rate of RMCE.\nC_LIO_LIThe first 30 days average recovery rate recovery rate to the symptomatic individuals were much lower than the first 30 days average recovery rate recovery rate of RMCE. The last 30 days average recovery rate recovery rate of the symptomatic individuals were still much lower than the last 30 days average recovery rate of RMCE.\nC_LI\n\nConclusionsThe last 30 days low blocking rates to the symptomatic infections, the first 30 days low blocking rates to the symptomatic infections to asymptomatic infections, the low recovery rates of the symptomatic and asymptomatic individuals, and the high transmission rate of the asymptomatic infections may be the reasons to cause the rapid spread of the recent Shanghai epidemic. It needs to implement more strict prevention and control strategies, rise the recovery rates of symptomatic and asymptomatic infections, and reduce the death rates for preventing the spread of this wave COVID-19 epidemic in Shanghai.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Lequan Min",
+        "author_inst": "University of Science and Technology Beijing"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2022.05.16.492138",
     "rel_title": "A live attenuated vaccine confers superior mucosal and systemic immunity to SARS-CoV-2 variants",
@@ -293953,33 +292515,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "occupational and environmental health"
   },
-  {
-    "rel_doi": "10.1101/2022.05.09.22274840",
-    "rel_title": "The impact of side effect framing on COVID-19 booster vaccine intentions in an Australian sample",
-    "rel_date": "2022-05-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.09.22274840",
-    "rel_abs": "ObjectiveTo evaluate the effect of presenting positively attribute-framed side effect information on COVID-19 booster vaccine intention relative to standard negatively-framed wording and a no-intervention control.\n\nDesign setting and participantsA representative sample of Australian adults (N=1,204) were randomised to one of six conditions within a factorial design: Framing (Positive; Negative; Control) * Vaccine (Familiar (Pfizer); Unfamiliar (Moderna)).\n\nInterventionNegative Framing involved presenting the likelihood of experiencing side effects (e.g., heart inflammation is very rare, 1 in every 80,000 will be affected), whereas Positive Framing involved presenting the same information but as the likelihood of not experiencing side effects (e.g., 79,999 in every 80,000 will not be affected).\n\nPrimary OutcomeBooster vaccine intention measured pre- and post-intervention.\n\nResultsPositive Framing (M=75.7, SE=0.9, 95% CI[73.9, 77.4]) increased vaccine intention relative to Negative Framing (M=70.7, SE=0.9, 95% CI[68.9, 72.4]) overall (F(1, 1192)=4.68, p=.031,{eta} p2=.004). Framing interacted with Vaccine and Baseline Intention (F(2, 1192)=6.18, p=.002,{eta} p2=.01). Positive Framing was superior, or at least equal, to Negative Framing and Control at increasing Booster Intention, irrespective of the participants pre-intervention level of intent. Side effect worry and perceived severity mediated the effect of Positive vs. Negative Framing across vaccines.\n\nConclusionPositive framing of side effect information appears superior for increasing vaccine intent relative to the standard negative wording currently used.\n\nPre-registrationSee: aspredicted.org/LDX_2ZL",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Kirsten Barnes",
-        "author_inst": "University of Sydney"
-      },
-      {
-        "author_name": "Kate Faasse",
-        "author_inst": "University of New South Wales"
-      },
-      {
-        "author_name": "Ben Colagiuri",
-        "author_inst": "University of Sydney"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2022.05.09.491227",
     "rel_title": "Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern",
@@ -294374,6 +292909,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2022.05.09.22274776",
+    "rel_title": "Early detection of fraudulent COVID-19 products from Twitter chatter",
+    "rel_date": "2022-05-11",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.09.22274776",
+    "rel_abs": "Social media have served as lucrative platforms for misinformation and for promoting fraudulent products for the treatment, testing and prevention of COVID-19. This has resulted in the issuance of many warning letters by the United States Food and Drug Administration (FDA). While social media continue to serve as the primary platform for the promotion of such fraudulent products, they also present the opportunity to identify these products early by employing effective social media mining methods. In this study, we employ natural language processing and time series anomaly detection methods for automatically detecting fraudulent COVID-19 products early from Twitter. Our approach is based on the intuition that increases in the popularity of fraudulent products lead to corresponding anomalous increases in the volume of chatter regarding them. We utilized an anomaly detection method on streaming COVID-19-related Twitter data to detect potentially anomalous increases in mentions of fraudulent products. Our unsupervised approach detected 34/44 (77.3%) signals about fraudulent products earlier than the FDA letter issuance dates, and an additional 6/44 (13.6%) within a week following the corresponding FDA letters. Our proposed method is simple, effective and easy to deploy, and do not require high performance computing machinery unlike deep neural network-based methods.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Abeed Sarker",
+        "author_inst": "Emory University"
+      },
+      {
+        "author_name": "Sahithi Lakamana",
+        "author_inst": "Emory University"
+      },
+      {
+        "author_name": "Ruqi Liao",
+        "author_inst": "Emory University"
+      },
+      {
+        "author_name": "Aamir Abbas",
+        "author_inst": "Carnegie Mellon University"
+      },
+      {
+        "author_name": "Yuan-Chi Yang",
+        "author_inst": "Emory University"
+      },
+      {
+        "author_name": "Mohammed Al-Garadi",
+        "author_inst": "Emory University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2022.05.09.491196",
     "rel_title": "Persistent serum protein signatures define an inflammatory subset of long COVID",
@@ -296079,77 +294653,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2022.05.09.22274846",
-    "rel_title": "Assessing the impacts of timing on the health benefits, cost-effectiveness and relative affordability of COVID-19 vaccination programmes in 27 African Countries",
-    "rel_date": "2022-05-10",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.09.22274846",
-    "rel_abs": "BackgroundThe COVID-19 vaccine supply shortage in 2021 constrained rollout efforts in Africa while populations experienced waves of epidemics. As supply picks up, a key question becomes if vaccination remains an impactful and cost-effective strategy given changes in the timing of implementation.\n\nMethodsWe assessed the impact of timing using an epidemiological and economic model. We fitted our mathematical epidemiological model to reported COVID-19 deaths in 27 African countries to estimate the existing immunity (resulting from infection) before substantial vaccine rollout. We then projected health outcomes for different programme start dates (2021-01-01 to 2021-12-01, n = 12) and roll-out rates (slow, medium, fast; 275, 826, and 2066 doses/ million population-day, respectively) for viral vector and mRNA vaccines. Rollout rates used were derived from observed uptake trajectories. We collected data on vaccine delivery costs by country income group. Lastly, we calculated incremental cost-effectiveness ratios and relative affordability.\n\nFindingsVaccination programmes with early start dates incur the most health benefits and are most cost-effective. While incurring the most health benefits, fast vaccine roll-outs are not always the most cost-effective. At a willingness-to-pay threshold of 0.5xGDP per capita, vaccine programmes starting in August 2021 using mRNA and viral vector vaccines were cost-effective in 6-10 and 17-18 of 27 countries, respectively.\n\nInterpretationAfrican countries with large proportions of their populations unvaccinated by late 2021 may find vaccination programmes less cost-effective than they could have been earlier in 2021. Lower vaccine purchasing costs and/or the emergence of new variants may improve cost-effectiveness.\n\nFundingBill and Melinda Gates Foundation, World Health Organization, National Institute of Health Research (UK), Health Data Research (UK)",
-    "rel_num_authors": 14,
-    "rel_authors": [
-      {
-        "author_name": "Yang Liu",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Carl AB Pearson",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Andres Madriz Montero",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Sergio Torres-Rueda",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Elias Asfaw",
-        "author_inst": "Africa Centres for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Benjamin Uzochukwu",
-        "author_inst": "University of Nigeria Nsukka"
-      },
-      {
-        "author_name": "Tom Drake",
-        "author_inst": "Centre for Global Development"
-      },
-      {
-        "author_name": "Eleanor Bergren",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Rosalind M Eggo",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Francis Ruiz",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Nicaise Ndembi",
-        "author_inst": "Institute of Human Virology Nigeria"
-      },
-      {
-        "author_name": "Justice Nonvignon",
-        "author_inst": "Africa Centres for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Mark Jit",
-        "author_inst": "London School of Hygiene & Tropical Medicine"
-      },
-      {
-        "author_name": "Anna Vassall",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health economics"
-  },
   {
     "rel_doi": "10.1101/2022.05.09.22274863",
     "rel_title": "Comparison of pandemic excess mortality in 2020-2021 across different empirical calculations",
@@ -296436,6 +294939,121 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.05.09.491201",
+    "rel_title": "COVID-19 mRNA third dose induces a unique hybrid immunity-like antibody response",
+    "rel_date": "2022-05-10",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.09.491201",
+    "rel_abs": "The continuous evolution of SARS-CoV-2 generated highly mutated variants, like omicron BA.1 and BA.2, able to escape natural and vaccine-induced primary immunity1,2. The administration of a third dose of mRNA vaccines induces a secondary response with increased protection. We investigated, at single-cell level, the longitudinal evolution of the neutralizing antibody response in four donors after three mRNA doses3. A total of 4,100 spike protein specific memory B cells were single cell sorted and 350 neutralizing antibodies were identified. The third dose increased the antibody neutralization potency and breadth against all SARS-CoV-2 variants of concern as previously observed with hybrid immunity3. However, the B cell repertoire that stands behind the response is dramatically different. The increased neutralizing response was largely due to the expansion of B cell germlines poorly represented after two doses, and the reduction of germlines predominant after primary immunization such as IGHV3-53;IGHJ6-1 and IGHV3-66;IGHJ4-1. Divergently to hybrid immunity, cross-protection after a third dose was mainly guided by Class 1/2 antibodies encoded by IGHV1-58;IGHJ3-1 and IGHV1-69;IGHJ4-1 germlines. The IGHV2-5;IGHJ3-1 germline, which induced broadly cross-reactive Class 3 antibodies after infection or viral vector vaccination, was not induced by a third mRNA dose. Our data show that while neutralizing breadth and potency can be improved by different immunization regimens, each of them has a unique molecular signature which should be considered while designing novel vaccines and immunization strategies.",
+    "rel_num_authors": 25,
+    "rel_authors": [
+      {
+        "author_name": "Emanuele Andreano",
+        "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy"
+      },
+      {
+        "author_name": "Ida Paciello",
+        "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy"
+      },
+      {
+        "author_name": "Giulio Pierleoni",
+        "author_inst": "VisMederi Research S.r.l., Siena, Italy"
+      },
+      {
+        "author_name": "Giulia Piccini",
+        "author_inst": "VisMederi S.r.l, Siena, Italy"
+      },
+      {
+        "author_name": "Valentina Abbiento",
+        "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy"
+      },
+      {
+        "author_name": "Giada Antonelli",
+        "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy"
+      },
+      {
+        "author_name": "Piero Pileri",
+        "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy"
+      },
+      {
+        "author_name": "Noemi Manganaro",
+        "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy"
+      },
+      {
+        "author_name": "Elisa Pantano",
+        "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy"
+      },
+      {
+        "author_name": "Giuseppe Maccari",
+        "author_inst": "Data Science for Health (DaScH) Lab, Fondazione Toscana Life Sciences, Siena, Italy"
+      },
+      {
+        "author_name": "Silvia Marchese",
+        "author_inst": "Department of Pharmacological and Biomolecular Sciences DiSFeB, University of Milan, Milan, Italy"
+      },
+      {
+        "author_name": "Lorena Donnici",
+        "author_inst": "INGM, Istituto Nazionale Genetica Molecolare \"Romeo ed Enrica Invernizzi\", Milan, Italy"
+      },
+      {
+        "author_name": "Linda Benincasa",
+        "author_inst": "VisMederi Research S.r.l., Siena, Italy"
+      },
+      {
+        "author_name": "Ginevra Giglioli",
+        "author_inst": "VisMederi Research S.r.l., Siena, Italy"
+      },
+      {
+        "author_name": "Margherita Leonardi",
+        "author_inst": "VisMederi Research S.r.l., Siena, Italy; VisMederi S.r.l, Siena, Italy"
+      },
+      {
+        "author_name": "Concetta De Santi",
+        "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy"
+      },
+      {
+        "author_name": "Massimiliano Fabbiani",
+        "author_inst": "Department of Medical Sciences, Infectious and Tropical Diseases Unit, Siena University Hospital, Siena, Italy"
+      },
+      {
+        "author_name": "Ilaria Rancan",
+        "author_inst": "Department of Medical Sciences, Infectious and Tropical Diseases Unit, Siena University Hospital, Siena, Italy"
+      },
+      {
+        "author_name": "Mario Tumbarello",
+        "author_inst": "Department of Medical Sciences, Infectious and Tropical Diseases Unit, Siena University Hospital, Siena, Italy; Department of Medical Biotechnologies, Universit"
+      },
+      {
+        "author_name": "Francesca Montagnani",
+        "author_inst": "Department of Medical Sciences, Infectious and Tropical Diseases Unit, Siena University Hospital, Siena, Italy; Department of Medical Biotechnologies, Universit"
+      },
+      {
+        "author_name": "Claudia Sala",
+        "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy"
+      },
+      {
+        "author_name": "Duccio Medini",
+        "author_inst": "Data Science for Health (DaScH) Lab, Fondazione Toscana Life Sciences, Siena, Italy"
+      },
+      {
+        "author_name": "Raffaele De Francesco",
+        "author_inst": "Department of Pharmacological and Biomolecular Sciences DiSFeB, University of Milan, Milan, Italy; INGM, Istituto Nazionale Genetica Molecolare \"Romeo ed Enrica"
+      },
+      {
+        "author_name": "Emanuele Montomoli",
+        "author_inst": "VisMederi Research S.r.l., Siena, Italy; VisMederi S.r.l, Siena, Italy; Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy"
+      },
+      {
+        "author_name": "Rino Rappuoli",
+        "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2022.05.10.491266",
     "rel_title": "Activated interstitial macrophages are a predominant target of viral takeover and focus of inflammation in COVID-19 initiation in human lung",
@@ -297813,49 +296431,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
-  {
-    "rel_doi": "10.1101/2022.05.05.22274702",
-    "rel_title": "Managing COVID-19 in an Australian designated isolation facility: Implications for current and future healthcare crises",
-    "rel_date": "2022-05-07",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.05.22274702",
-    "rel_abs": "Health care workers (HCWs) lived experiences and perceptions of the pandemic can prove to be a valuable resource in the face of a seemingly persistent Novel coronavirus disease 2019 (COVID-19) - to inform ongoing efforts, as well as identify components essential to a crisis preparedness plan and the issues pertinent to supporting relevant, immediate change. We employed a phenomenological approach and, using purposive sampling, conducted 39 semi-structured interviews with senior healthcare professionals who were employed at a designated COVID-19 facility in New South Wales (NSW), Australia during the height of the pandemic in 2020. Participants comprised administrators, heads of department and senior clinicians. We obtained these HCWs (i) perspectives of their lived experience on what was done well and what could have been done differently and (ii) recommendations on actions for current and future crisis response. Four themes encapsulated respondents insights that should inform our capacity to meet current needs, direct meaningful and in situ change, and prepare us for future crises. Respondents observations and recommendations are informative for decision-makers tasked with mobilising an efficacious approach to the next health crisis and, in the interim, would aid the governance of a more robust workforce to effect high quality patient care in a safe environment.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Helen M Achat",
-        "author_inst": "Western Sydney Local Health District"
-      },
-      {
-        "author_name": "Rakhi Mittal",
-        "author_inst": "Western Sydney Local Health District"
-      },
-      {
-        "author_name": "Joanne M Stubbs",
-        "author_inst": "Western Sydney Local Health District"
-      },
-      {
-        "author_name": "Nicky Gilroy",
-        "author_inst": "Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney"
-      },
-      {
-        "author_name": "Suzanne K Schindeler",
-        "author_inst": "Western Sydney Local Health District"
-      },
-      {
-        "author_name": "Ramon Z Shaban",
-        "author_inst": "Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney"
-      },
-      {
-        "author_name": "Thomas Solano",
-        "author_inst": "Westmead Hospital, Western Sydney Local Health District"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health systems and quality improvement"
-  },
   {
     "rel_doi": "10.1101/2022.05.05.22274731",
     "rel_title": "Deep learning identified genetic variants associated with COVID-19 related mortality",
@@ -298158,6 +296733,121 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.05.06.22274701",
+    "rel_title": "COVID-19 vaccine effectiveness during a prison outbreak when the Omicron was the dominant circulating variant, Zambia, December 2021",
+    "rel_date": "2022-05-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.06.22274701",
+    "rel_abs": "During a COVID-19 outbreak in a prison in Zambia from 14th to 19th December 2021, a case control study was done to measure vaccine effectiveness (VE) against infection and symptomatic infection, when the Omicron variant was the dominant circulating variant. Among 382 participants, 74.1% were fully vaccinated and the median time since full vaccination was 54 days. There were no hospitalizations or deaths. COVID-19 VE against any SARS-CoV-2 infection was 64.8% and VE against symptomatic SARS-CoV-2 infection was 72.9%. COVID-19 vaccination helped protect incarcerated persons against SARS-CoV-2 infection during an outbreak while Omicron was the dominant variant in Zambia.",
+    "rel_num_authors": 25,
+    "rel_authors": [
+      {
+        "author_name": "John Simwanza",
+        "author_inst": "Zambia Field Epidemiology Training Program"
+      },
+      {
+        "author_name": "Jonas Z. Hines",
+        "author_inst": "U.S. Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Danny Sinyange",
+        "author_inst": "Zambia Field Epidemiology Training Program"
+      },
+      {
+        "author_name": "Nyambe Sinyange",
+        "author_inst": "Zambia National Public Health Institute"
+      },
+      {
+        "author_name": "Chilufya Mulenga",
+        "author_inst": "Zambia Field Epidemiology Training Program"
+      },
+      {
+        "author_name": "Sarah Hanyinza",
+        "author_inst": "Zambia National Public Health Institute"
+      },
+      {
+        "author_name": "Patrick Sakubita",
+        "author_inst": "Zambia National Public Health Institute"
+      },
+      {
+        "author_name": "Nelia Langa",
+        "author_inst": "Zambia National Public Health Institute"
+      },
+      {
+        "author_name": "Haggai Nowa",
+        "author_inst": "Zambia Prison Services"
+      },
+      {
+        "author_name": "Priscilla Gardner",
+        "author_inst": "Lusaka District Health Office"
+      },
+      {
+        "author_name": "Ngonda Saasa",
+        "author_inst": "University of Zambia Veterinary Medicine Laboratory School"
+      },
+      {
+        "author_name": "Gabriel Chipeta",
+        "author_inst": "Lusaka District Health Office"
+      },
+      {
+        "author_name": "James Simpungwe",
+        "author_inst": "U.S. Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Warren Malambo",
+        "author_inst": "U.S. Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Busiku Hamainza",
+        "author_inst": "National Malaria Elimination Centre"
+      },
+      {
+        "author_name": "Nathan Kapata",
+        "author_inst": "Zambia National Public Health Institute"
+      },
+      {
+        "author_name": "Muzala Kapina",
+        "author_inst": "Zambia National Public Health Institute"
+      },
+      {
+        "author_name": "Kunda Musonda",
+        "author_inst": "Zambia National Public Health Institute"
+      },
+      {
+        "author_name": "Mazyanga Liwewe",
+        "author_inst": "Zambia National Public Health Institute"
+      },
+      {
+        "author_name": "Consity Mwale",
+        "author_inst": "Lusaka Province Health Office"
+      },
+      {
+        "author_name": "Sombo Fwoloshi",
+        "author_inst": "Zambia Ministry of Health"
+      },
+      {
+        "author_name": "Lloyd B. Mulenga",
+        "author_inst": "Zambia Ministry of Health"
+      },
+      {
+        "author_name": "Simon Agolory",
+        "author_inst": "U.S. Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Victor Mukonka",
+        "author_inst": "Zambia National Public Health Institute"
+      },
+      {
+        "author_name": "Roma Chilengi",
+        "author_inst": "Zambia National Public Health Institute"
+      }
+    ],
+    "version": "1",
+    "license": "cc0",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2022.05.04.22274665",
     "rel_title": "School immunization coverage during the COVID-19 pandemic: A retrospective cohort study",
@@ -299375,129 +298065,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.05.04.22274668",
-    "rel_title": "Antibody responses to AZD1222 vaccination in West Africa",
-    "rel_date": "2022-05-05",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.04.22274668",
-    "rel_abs": "BackgroundThere are no real world data on vaccine elicited neutralising antibody responses for the worlds most widely used vaccine, AZD1222, in African populations following scale up. Here, we measured i) baseline SARS-CoV-2 seroprevalence and levels of protective neutralizing antibodies prior to vaccination rollout using both flow cytometric based analysis of binding antibodies to nucleocapsid (N), coupled with virus neutralisation approaches and ii) neutralizing antibody responses to VOC prior to vaccination (January 2021) and after two-doses of AZD1222 vaccine administered with a 12 week interval in Lagos, Nigeria - a period when the Delta variant was circulating.\n\nMethodsHealth workers at multiple sites in Lagos were recruited to the study. For binding antibody measurement, IgG antibodies against SARS-COV-2 Wuhan-1 receptor-binding domain (RBD), trimeric spike protein (S), nucleocapsid protein (N) and Omicron S1 were measured using the Luminex-based SARS-CoV-2-IgG assay by flow cytometry. For plasma neutralising antibody measurement, SARS-CoV-2 lentiviral pseudovirus (PV) were prepared by transfecting 293T cells with Wuhan-614G wild type (WT), B.1.617.2 (Delta) and BA.1 (Omicron) plasmids in conjunction with HIV-1 expression vectors and luciferase encoding genome flanked by LTRs. We performed serial plasma dilutions from each time point and mixed plasma with PV before infecting HeLa-ACE2 cell lines, reading out luminescence and calculating ID50 (reciprocal dilution of sera required to inhibit 50% of PV infection).\n\nResultsOur underlying study population receiving at least one dose of vaccine comprised 140 participants with a median age of 40 (interquartile range: 33, 48). 62/140 (44%) participants were anti-N IgG positive prior to administration of first vaccine dose. 49 had plasma samples available at baseline prior to vaccination and at two follow-up timepoints post two dose vaccination for neutralization assays. Half of the participants, 25/49 (51%) were IgG anti-N positive at baseline. Of the 24 individuals anti-N Ab negative at baseline, 12/24 had ID50 above the cut-off of 20. In these individuals, binding antibodies to S were also detectable, and neutralisation correlated with IgG anti-S, suggesting waning of N antibody after infection. Overall, neutralizing Ab titres to WT 1 month after second dose were 2579 and at 3 months post second-dose were 1695. As expected, lower levels of neutralization were observed against the Delta GMT 549 and Omicron variants 269 at 1 month. Positive anti-N IgG Ab status at baseline was associated with significantly higher titres of neutralizing antibodies following vaccination across all tested VOC. Those with anti-N Abs present at baseline did not experience waning of responses between months 1 and 3 post second dose. When data were analysed for negative anti-N IgG status at any timepoint, there was a significant decline in neutralization and binding antibodies between 1 month and 3 months post second-dose. The GMT in these individuals for Delta and Omicron was approximately 100, nearly a log lower in comparison to WT. We tested anti-N IgG in subjects who were anti-N IgG negative at baseline (n=78) and became positive between 1- and 3-months post second dose and found 7/49 (14%) with de-novo infection, with one additional participant demonstrating both reinfection and breakthrough infection to yield a total breakthrough rate of 8/49 (16%). Neutralising and binding Ab titres 1 month post vaccine, prior to breakthrough, were not associated with breakthrough infection. Neutralizing titres were higher at the last time point in individuals who had experienced vaccine breakthrough infection (with no evidence of infection prior to vaccine), indicating a boosting effect of infection in addition to vaccine. However, neutralisation and binding S antibodies against Omicron were low in those with either prior exposure or infection following two dose AZD1222.\n\nConclusionsAZD1222 is immunogenic in this real world west African cohort with significant background seroprevalence and incidence of breakthrough infection over a short time period. Prior infection and breakthrough infection induced higher anti-SARS-CoV-2 Ab responses at 3 months post vaccine against all widely circulating VOC. However, responses to Omicron BA.1 were low at three months regardless of hybrid immunity from prior exposure or breakthrough infection. Booster doses after AZD1222 should be considered in the African setting, even after natural infection, as future variants may be more pathogenic as well as immune evasive in the context of waning immunity.",
-    "rel_num_authors": 27,
-    "rel_authors": [
-      {
-        "author_name": "Adam Abdullahi",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "David Oladele",
-        "author_inst": "NIMR"
-      },
-      {
-        "author_name": "Steven Kemp",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "James Ayorinde",
-        "author_inst": "NIMR"
-      },
-      {
-        "author_name": "Abideen Salako",
-        "author_inst": "NIMR"
-      },
-      {
-        "author_name": "Fehintola Ige",
-        "author_inst": "NIMR"
-      },
-      {
-        "author_name": "Douglas Fink",
-        "author_inst": "UCL, London"
-      },
-      {
-        "author_name": "Chika Onwuamah",
-        "author_inst": "NIMR"
-      },
-      {
-        "author_name": "Qosim Osuolale",
-        "author_inst": "NIMR"
-      },
-      {
-        "author_name": "Rufai Abubakar",
-        "author_inst": "NIMR"
-      },
-      {
-        "author_name": "Azuka Okuruawe",
-        "author_inst": "NIMR"
-      },
-      {
-        "author_name": "Gideon Liboro",
-        "author_inst": "NIMR"
-      },
-      {
-        "author_name": "Oluwatosin Odubela",
-        "author_inst": "NIMR"
-      },
-      {
-        "author_name": "Gregory Ohihoin",
-        "author_inst": "NIMR"
-      },
-      {
-        "author_name": "Oliver Ezechi",
-        "author_inst": "NIMR"
-      },
-      {
-        "author_name": "Olagoke Usman",
-        "author_inst": "Federal Medical Centre, Ebutte Metta, Lagos"
-      },
-      {
-        "author_name": "Sunfay Mogaji",
-        "author_inst": "Federal Medical Centre, Ebutte Metta, Lagos"
-      },
-      {
-        "author_name": "Adedamola Dada",
-        "author_inst": "Federal Medical Centre, Ebutte Metta, Lagos"
-      },
-      {
-        "author_name": "Soraya Ebrahimi",
-        "author_inst": "NIMR"
-      },
-      {
-        "author_name": "Lourdes Ceron Gutierrez",
-        "author_inst": "Cambridge University NHS Trust"
-      },
-      {
-        "author_name": "Sani H Aliyu",
-        "author_inst": "Cambridge University NHS Trust"
-      },
-      {
-        "author_name": "Rainer Doffinger",
-        "author_inst": "Cambridge University NHS Trust"
-      },
-      {
-        "author_name": "Rosemary Audu",
-        "author_inst": "NIMR"
-      },
-      {
-        "author_name": "Richard Adegbola",
-        "author_inst": "NIMR"
-      },
-      {
-        "author_name": "Petra Mlcochova",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Babatunde Lawal Salako",
-        "author_inst": "NIMR"
-      },
-      {
-        "author_name": "Ravindra K Gupta",
-        "author_inst": "University of Cambridge"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.05.03.22274622",
     "rel_title": "SARS-CoV-2 neutralizing antibodies in Chile after a vaccination campaign with five different schemes",
@@ -300028,6 +298595,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2022.05.04.490614",
+    "rel_title": "SARS-CoV-2 variants do not evolve to promote further escape from MHC-I recognition",
+    "rel_date": "2022-05-04",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.04.490614",
+    "rel_abs": "SARS-CoV-2 variants of concern (VOCs) possess mutations that confer resistance to neutralizing antibodies within the Spike protein and are associated with breakthrough infection and reinfection. By contrast, less is known about the escape from CD8+ T cell-mediated immunity by VOC. Here, we demonstrated that all SARS-CoV-2 VOCs possess the ability to suppress MHC I expression. We identified several viral genes that contribute to the suppression of MHC I expression. Notably, MHC-I upregulation was strongly inhibited after SARS-CoV-2 infection in vivo. While earlier VOCs possess similar capacity as the ancestral strain to suppress MHC I, Omicron subvariants exhibit a greater ability to suppress surface MHC-I expressions. Collectively, our data suggest that, in addition to escape from neutralizing antibodies, the success of Omicron subvariants to cause breakthrough infection and reinfection may in part be due to its optimized evasion from T cell recognition.\n\nSignificanceNumerous pathogenic viruses have developed strategies to evade host CD8+ T cell-mediated clearance. Here, we demonstrated that SARS-CoV-2 encodes multiple viral factors that can modulate MHC-I expression in the host cells. We found that MHC-I upregulation was strongly suppressed during SARS-CoV-2 infection in vivo. Notably, the Omicron subvariants showed an enhanced ability to suppress MHC-I compared to the original strain and the earlier SARS-CoV-2 variants of concern (VOCs). Our results point to the inherently strong ability of SARS-CoV-2 to hinder MHC-I expression and demonstrated that Omicron subvariants have evolved an even more optimized capacity to evade CD8 T cell recognition.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Miyu Moriyama",
+        "author_inst": "Yale University School of Medicine"
+      },
+      {
+        "author_name": "Carolina Lucas",
+        "author_inst": "Yale University School of Medicine"
+      },
+      {
+        "author_name": "Valter Silva Monteiro",
+        "author_inst": "Yale University School of Medicine"
+      },
+      {
+        "author_name": "- Yale SARS-CoV-2 Genomic Surveillance Initiative",
+        "author_inst": "-"
+      },
+      {
+        "author_name": "Akiko Iwasaki",
+        "author_inst": "Yale University School of Medicine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2022.05.04.490631",
     "rel_title": "Adsorption of Pulmonary and Exogeneous Surfactants on SARS-CoV-2 Spike Protein",
@@ -301685,45 +300287,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2022.05.02.490272",
-    "rel_title": "Nsp1 proteins of human coronaviruses HCoV-OC43 and SARS-CoV2 inhibit stress granule formation",
-    "rel_date": "2022-05-02",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.02.490272",
-    "rel_abs": "Stress granules (SGs) are cytoplasmic condensates that often form as part of the cellular antiviral response. Despite the growing interest in understanding the interplay between SGs and other biological condensates and viral replication, the role of SG formation during coronavirus infection remains poorly understood. Several proteins from different coronaviruses have been shown to suppress SG formation upon overexpression, but there are only a handful of studies analyzing SG formation in coronavirus- infected cells. To better understand SG inhibition by coronaviruses, we analyzed SG formation during infection with the human common cold coronavirus OC43 (HCoV-OC43) and the highly pathogenic SARS-CoV2. We did not observe SG induction in infected cells and both viruses inhibited eukaryotic translation initiation factor 2 (eIF2) phosphorylation and SG formation induced by exogenous stress (e.g. sodium arsenite treatment). Furthermore, in SARS-CoV2 infected cells we observed a sharp decrease in the levels of SG-nucleating protein G3BP1. Ectopic overexpression of nucleocapsid (N) and non-structural protein 1 (Nsp1) from both HCoV-OC43 and SARS-CoV-2 inhibited SG formation. The Nsp1 proteins of both viruses inhibited arsenite-induced eIF2 phosphorylation, and the Nsp1 of SARS- CoV2 alone was sufficient to cause decrease in G3BP1 levels. This phenotype was dependent on the depletion of cytoplasmic mRNA mediated by Nsp1 and associated with nuclear retention of the SG- nucleating protein TIAR. To test the role of G3BP1 in coronavirus replication, we infected cells overexpressing EGFP-tagged G3BP1 with HCoV-OC43 and observed a significant decrease in infection compared to control cells expressing EGFP. The antiviral role of G3BP1 and the existence of multiple SG suppression mechanisms that are conserved between HCoV-OC43 and SARS-CoV2 suggest that SG formation may represent an important antiviral host defense that coronaviruses target to ensure efficient replication.\n\nAuthor SummaryHost cells possess many mechanisms that can detect viral infections and trigger defense programs to suppress viral replication and spread. One of such antiviral mechanisms is the formation of stress granules - large aggregates of RNA and proteins that sequester viral components and cellular factors needed by the virus to replicate. Because of this threat, viruses evolved specific mechanisms that prevent stress granule formation. Understanding these mechanisms can reveal potential targets for therapies that would disable viral inhibition of stress granules and render cells resistant to infection. In this study we analyzed inhibition of stress granules by two human coronaviruses: the common cold coronavirus OC43 and the pandemic SARS-CoV2. We have demonstrated that these viruses employ at least two proteins - nucleocapsid protein (N) and the non-structural protein 1 (Nsp1) to suppress stress granules. These proteins act through distinct complementary mechanisms to ensure successful virus replication. Because both OC43 and SARS-CoV2 each dedicate more than one gene product to inhibit stress granule formation, our work suggests that viral disarming of stress granule responses is central for a productive infection.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Stacia  M Dolliver",
-        "author_inst": "Dalhousie Medical School: Dalhousie University Faculty of Medicine"
-      },
-      {
-        "author_name": "Mariel Kleer",
-        "author_inst": "University of Calgary"
-      },
-      {
-        "author_name": "Maxwell  P Bui-Marinos",
-        "author_inst": "University of Calgary"
-      },
-      {
-        "author_name": "Shan Ying",
-        "author_inst": "Dalhousie University Faculty of Medicine"
-      },
-      {
-        "author_name": "Jennifer  A Corcoran",
-        "author_inst": "University of Calgary"
-      },
-      {
-        "author_name": "Denys Khaperskyy",
-        "author_inst": "Dalhousie University Faculty of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2022.05.02.22274436",
     "rel_title": "Omicron infection induces low-level, narrow-range SARS-CoV-2 neutralizing activity",
@@ -302246,6 +300809,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.04.29.22274485",
+    "rel_title": "Human behaviour, NPI and mobility reduction effects on COVID-19 transmission in different countries of the world",
+    "rel_date": "2022-05-01",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.29.22274485",
+    "rel_abs": "BackgroundThe outbreak of Coronavirus disease, which originated in Wuhan, China in 2019, has affected the lives of billions of people globally. Throughout 2020, the reproduction number of COVID-19 was widely used by decision-makers to explain their strategies to control the pandemic.\n\nMethodsIn this work, we deduce and analyze both initial and effective reproduction numbers for 12 diverse world regions between February and December of 2020. We consider mobility reductions, mask wearing and compliance with masks, mask efficacy values alongside other non-pharmaceutical interventions (NPIs) in each region to get further insights in how each of the above factored into each regions SARS-COV-2 transmission dynamic.\n\nResultsWe quantify in each region the following reductions in the observed effective reproduction numbers of the pandemic: i) reduction due to decrease in mobility (as captured in Google mobility reports); ii) reduction due to mask wearing and mask compliance; iii) reduction due to other NPIs, over and above the ones identified in i) and ii).\n\nConclusionIn most cases mobility reduction coming from nationwide lockdown measures has helped stave off the initial wave in countries who took these types of measures. Beyond the first waves, mask mandates and compliance, together with social-distancing measures (which we refer to as other NPIs) have allowed some control of subsequent disease spread. The methodology we propose here is novel and can be applied to other respiratory diseases such as influenza or RSV.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Zahra Mohammadi",
+        "author_inst": "University of Guelph"
+      },
+      {
+        "author_name": "Monica Gabriela Cojocaru",
+        "author_inst": "University of Guelph"
+      },
+      {
+        "author_name": "Edward Wolfgang Thommes",
+        "author_inst": "Sanofi Pasteur Global, Toronto, Canada"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2022.04.28.22274446",
     "rel_title": "Vaccine Stockpile Sharing For Selfish Objectives",
@@ -303587,85 +302177,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.04.26.22274329",
-    "rel_title": "Mobile Primary Healthcare for post-COVID Patients in Rural Areas: a Proof-of-Concept Study",
-    "rel_date": "2022-04-28",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.26.22274329",
-    "rel_abs": "IntroductionPost-COVID syndrome is increasingly recognized as a new clinical entity after SARS-CoV-2 infection. Patients living in rural areas may have to travel long with subjectively great effort to be examined using all necessary interdisciplinary tools. This problem could be addressed with mobile outpatient clinics.\n\nMethodsIn this prospective observational study, we investigated physical fitness, fatigue, depression, cognitive dysfunction and dyspnea in patients with post-COVID syndrome in a mobile interdisciplinary post-COVID outpatient clinic. Upon referral from their primary care physician, patients were offered an appointment at a mobile post-COVID outpatient clinic close to their home.\n\nResultsWe studied 125 patients (female, n=79; 63.2%) in our mobile unit. All patients reported symptoms lasting for more than 12 weeks after acute infection. 88.3% and 64.1% of patients reported significant impairment in physical and mental quality of life. Patients reported a median of three symptoms. The most frequently reported symptoms were fatigue (86.4%), cognitive dysfunction (85.6%), and dyspnea (37.6%). 56.0% of patients performed at <2.5th percentile at the 1 min sit-to-stand test compared to age and sex-matched healthy controls and 25 patients (20.0%) exhibited a drop in oxygen saturation. A questionnaire given to each patient regarding the mobile unit revealed a very high level of patient satisfaction.\n\nConclusionThere is an increasing need for high-quality and locally available care for patients with post-COVID syndrome. A mobile post-COVID outpatient clinic is a new concept that may be particularly suitable for use in rural regions. Patients satisfaction following visits in such units is very high.",
-    "rel_num_authors": 16,
-    "rel_authors": [
-      {
-        "author_name": "Andreas Stallmach",
-        "author_inst": "Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital/Friedrich-Schiller-University Jena, Jena, G"
-      },
-      {
-        "author_name": "Katrin Katzer",
-        "author_inst": "Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital/Friedrich-Schiller-University Jena, Jena, G"
-      },
-      {
-        "author_name": "Bianca Besteher",
-        "author_inst": "Department of Psychiatry, Jena University Hospital/Friedrich-Schiller-University Jena, Jena, Germany"
-      },
-      {
-        "author_name": "Kathrin Finke",
-        "author_inst": "Department of Neurology, Jena University Hospital/Friedrich-Schiller-University Jena, Jena, Germany"
-      },
-      {
-        "author_name": "Benjamin Giszas",
-        "author_inst": "Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital/Friedrich-Schiller-University Jena, Jena, G"
-      },
-      {
-        "author_name": "Yvonne Gremme",
-        "author_inst": "Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital/Friedrich-Schiller-University Jena, Jena, G"
-      },
-      {
-        "author_name": "Rami Abou-Hamdan",
-        "author_inst": "Department of Sports Medicine and Health Promotion, Friedrich-Schiller-University Jena, Jena, Germany"
-      },
-      {
-        "author_name": "Katja Lehmann-Pohl",
-        "author_inst": "Center for Sepsis Control and Care (CSCC), Jena University Hospital/Friedrich-Schiller-University Jena, Jena, Germany"
-      },
-      {
-        "author_name": "Maximilian Legen",
-        "author_inst": "Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital/Friedrich-Schiller-University Jena, Jena, G"
-      },
-      {
-        "author_name": "Jan C Lewejohann",
-        "author_inst": "Department of Emergency Medicine, Friedrich-Schiller-University, Jena University Hospital, Jena, Germany"
-      },
-      {
-        "author_name": "Marlene Machnik",
-        "author_inst": "Department of Psychiatry, Jena University Hospital/Friedrich-Schiller-University Jena, Jena, Germany"
-      },
-      {
-        "author_name": "Majd Moshmosh Alsabbagh",
-        "author_inst": "Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital/Friedrich-Schiller-University Jena, Jena, G"
-      },
-      {
-        "author_name": "Luisa Nardini",
-        "author_inst": "Department of Sports Medicine and Health Promotion, Friedrich-Schiller-University Jena, Jena, Germany"
-      },
-      {
-        "author_name": "Christian Puta",
-        "author_inst": "Department of Sports Medicine and Health Promotion, Friedrich-Schiller-University Jena, Jena, Germany"
-      },
-      {
-        "author_name": "Zoe Stallmach",
-        "author_inst": "Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital/Friedrich-Schiller-University Jena, Jena, G"
-      },
-      {
-        "author_name": "Philipp Reuken",
-        "author_inst": "Department of Internal Medicine IV (Gastroenterology, Hepatology, and Infectious Diseases), Jena University Hospital/Friedrich-Schiller-University Jena, Jena, G"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.04.25.22274276",
     "rel_title": "Exploring U.S. food system workers' intentions to work while ill during the early COVID-19 pandemic: a national survey analysis",
@@ -304016,6 +302527,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.04.26.22274301",
+    "rel_title": "Trends in non-COVID-19 hospitalizations prior to and during the COVID-19 pandemic period, United States, 2017-2021",
+    "rel_date": "2022-04-28",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.26.22274301",
+    "rel_abs": "COVID-19 pandemic-related shifts in healthcare utilization, in combination with trends in non-COVID-19 disease transmission and NPI use, had clear impacts on infectious and chronic disease hospitalization rates. Using a national healthcare billing database (C19RDB), we estimated the monthly incidence rate ratio of hospitalizations between March 2020 and June 2021 according to 19 ICD-10 diagnostic chapters and 189 subchapters. The majority of hospitalization causes showed an immediate decline in incidence during March 2020. Hospitalizations for diagnoses such as reproductive neoplasms, hypertension, and diabetes returned to pre-pandemic norms in incidence during late 2020 and early 2021, while others, like those for infectious respiratory disease, never returned to pre-pandemic norms. These results are crucial for contextualizing future research, particularly time series analyses, utilizing surveillance and hospitalization data for non-COVID-19 disease. Our assessment of subchapter level primary hospitalization codes offers new insight into trends among less frequent causes of hospitalization during the COVID-19 pandemic.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Kelsie Cassell",
+        "author_inst": "Yale School of Public Health"
+      },
+      {
+        "author_name": "Casey M Zipfel",
+        "author_inst": "Georgetown University"
+      },
+      {
+        "author_name": "Shweta Bansal",
+        "author_inst": "Georgetown University"
+      },
+      {
+        "author_name": "Daniel Weinberger",
+        "author_inst": "Yale School of Public Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2022.04.25.22274300",
     "rel_title": "Characterization of Autonomic Symptom Burden in Long COVID: A Global Survey of 2,314 Adults",
@@ -305745,33 +304287,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2022.04.26.22274235",
-    "rel_title": "CLINICAL MANIFESTATIONS AND DIAGNOSIS OF CO-INFECTION OF COVID-19, TUBERCULOSIS AND OPPORTUNISTIC PULMONARY INFECTIONS IN LATE-STAGE HIV PATIENTS WITH IMMUNODEFICIENCY",
-    "rel_date": "2022-04-28",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.26.22274235",
-    "rel_abs": "ObjectiveThe purpose of the study was to investigate the specific features of clinical manifestations and diagnosis of co-infection of COVID-19, tuberculosis and opportunistic pulmonary infections in late-stage HIV patients.\n\nDesign27 patients with co-infection of COVID-19, tuberculosis, opportunistic pulmonary infections and late-stage HIV infection with immunodeficiency without antiretroviral therapy (group 1) and 27 patients with equivalent parameters but without COVID-19 (group 2) were examined.\n\nResultsThe patients of the group 1 and group 2 are the persons with social maladjustment and substance addiction. All of them have concomitant viral hepatitis B/C, COPD, opportunistic pulmonary infections and similar clinical and radiological manifestations, which can only be differentiated with microbiological and molecular genetic studies. The patients with co-infection of COVID-19, tuberculosis and HIV pose a high risk of transmission of infection to healthy persons in view of non-adherence to examination and treatment.\n\nConclusionTo prevent the spread of infection among the healthy population, it is necessary to arrange in a mandatory manner an active and regular COVID-19 testing of all patients with tuberculosis/HIV co-infection, especially of late-stage HIV patients without antiretroviral therapy, in the tuberculosis care unit for HIV-infected persons at the tuberculosis dispensary.\n\nSettingThere are few data on the specific features of clinical manifestations of co-infection of COVID-19, tuberculosis (TB) and opportunistic pulmonary infections (OPI) in late-stage HIV patients with immunodeficiency.\n\nObjectiveStudy purpose is to investigate the specific features of clinical manifestations and diagnosis of co-infection of COVID-19, TB and OPI in late-stage HIV patients with immunodeficiency.\n\nDesignFifty-four (54) patients admitted for inpatient treatment at the TB Clinical Hospital N 3 named after Zakharyin were enrolled in this prospective study. The participants were assigned to two groups: group 1 (main) and group 2 (comparison group). Group 1 consisted of twenty-seven (27) aged 28-52 patients (18 men (66.7 {+/-} 9.1%) and 9 women (33.3 {+/-} 9.1%)) with known co-infection of COVID-19, sputum smear-positive for M. tuberculosis (MBT) pulmonary tuberculosis (PTB) and with late-stage HIV infection in progression phase without antiretroviral therapy (ART). Group 2 included 27 patients who were selected using the \"copy-pair\" method and were completely identical to the patients of the main group (with virtually the same age, sex, social parameters and clinical and laboratory indicators), but without diagnosis of COVID-19.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Anastasiya V. Mishina",
-        "author_inst": "FSBEI HE The A.I. Yevdokimov Moscow State University of Medicine and Dentistry of the Ministry of Health of Russia, Moscow, Russia"
-      },
-      {
-        "author_name": "Vladimir Y. Mishin",
-        "author_inst": "FSBEI HE The A.I. Yevdokimov Moscow State University of Medicine and Dentistry of the Ministry of Health of Russia, Moscow, Russia"
-      },
-      {
-        "author_name": "Ivan V. Shashenkov",
-        "author_inst": "FSBEI HE The A.I. Yevdokimov Moscow State University of Medicine and Dentistry of the Ministry of Health of Russia, Moscow, Russia"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "hiv aids"
-  },
   {
     "rel_doi": "10.1101/2022.04.28.489618",
     "rel_title": "A Pan-Coronavirus Vaccine Candidate: Nine Amino Acid Substitutions in the ORF1ab Gene Attenuate 99% of 365 Unique Coronaviruses: A Comparative Effectiveness Research Study",
@@ -306110,6 +304625,89 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2022.04.25.22273197",
+    "rel_title": "Clinical characteristics and outcome of immunocompromised patients with COVID-19 caused by the Omicron variant: a prospective observational study",
+    "rel_date": "2022-04-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.25.22273197",
+    "rel_abs": "BackgroundIn the general population, illness after infection with the SARS-CoV-2 Omicron variant is less severe compared with previous variants. Data on the disease burden of Omicron in immunocompromised patients are lacking. We investigated the clinical characteristics and outcome of a cohort of immunocompromised patients with COVID-19 caused by Omicron.\n\nMethodsSolid organ transplant recipients, patients on anti-CD20 therapy, and allogenic hematopoietic stem cell transplantation recipients on immunosuppressive therapy infected with the Omicron variant, were included. Patients were contacted regularly until symptom resolution. Clinical characteristics of consenting patients were collected through their electronic patient files. To identify possible risk factors for hospitalization, a univariate logistic analysis was performed.\n\nResultsA total of 114 consecutive immunocompromised patients were enrolled. Eighty-nine percent had previously received three mRNA vaccinations. While only one patient died, 23 (20%) required hospital admission for a median of 11 days. A low SARS-CoV-2 IgG antibody response (<300 BAU/mL) at diagnosis, higher age, being a lung transplant recipient, more comorbidities and a higher frailty were associated with hospital admission (all p<0.01). At the end of follow-up, 25% had still not fully recovered. Of the 23 hospitalized patients, 70% had a negative and 92% a low IgG (<300 BAU/mL) antibody response at admission. Sotrovimab was administered to 17 of them, of which one died.\n\nConclusionsWhile the mortality in immunocompromised patients infected with Omicron was low, hospital admission was frequent and the duration of symptoms often prolonged. Besides vaccination, other interventions are needed to limit the morbidity from COVID-19 in immunocompromised patients.\n\nSummaryCOVID-19-associated morbidity and mortality in immunocompromised patients is unknown for the SARS-CoV-2 Omicron variant. This prospective registry, demonstrated low COVID-19-associated mortality in these vulnerable patients. However, morbidity remained substantial. Other interventions to abate COVID-19 severity are needed.",
+    "rel_num_authors": 17,
+    "rel_authors": [
+      {
+        "author_name": "S. Reshwan K. Malahe",
+        "author_inst": "Department of Internal Medicine, Erasmus, University Medical Center, Rotterdam,"
+      },
+      {
+        "author_name": "Rogier A.S. Hoek",
+        "author_inst": "Department of Pulmonary Medicine, Erasmus, University Medical Center, Rotterdam, The Netherlands"
+      },
+      {
+        "author_name": "Virgil A.S.H. Dalm",
+        "author_inst": "Department of Internal Medicine, division of Allergy and Clinical Immunology; Department of  Immunology, Erasmus, University Medical Center, Rotterdam, The Neth"
+      },
+      {
+        "author_name": "Annoek E.C. Broers",
+        "author_inst": "Department of Hematology, Erasmus, Cancer Institute, Rotterdam, The Netherlands"
+      },
+      {
+        "author_name": "Caroline M. den Hoed",
+        "author_inst": "Department of Gastroenterology and Hepatology, Erasmus, University Medical Center, Rotterdam, The Netherlands"
+      },
+      {
+        "author_name": "Olivier C. Manintveld",
+        "author_inst": "Department of Cardiology, Erasmus, University Medical Center, Rotterdam, The Netherlands"
+      },
+      {
+        "author_name": "Carla C. Baan",
+        "author_inst": "Erasmus MC Transplant Institute, Erasmus, University Medical Center, Rotterdam, The Netherlands"
+      },
+      {
+        "author_name": "Charlotte M. van Deuzen",
+        "author_inst": "Department of Internal Medicine, Section of Infectious Diseases and Department of Medical Microbiology and Infectious Diseases, Erasmus, University Medical Cent"
+      },
+      {
+        "author_name": "Grigorios Papageorgiou",
+        "author_inst": "Department of Biostatistics and department of Epidemiology, Erasmus, University Medical Center, Rotterdam, the Netherlands"
+      },
+      {
+        "author_name": "Hannelore I. Bax",
+        "author_inst": "Department of Internal Medicine, Section of Infectious Diseases and Department of Medical Microbiology and Infectious Diseases, Erasmus, University Medical Cent"
+      },
+      {
+        "author_name": "Jeroen J. van Kampen",
+        "author_inst": "Department of Viroscience, Erasmus, University Medical Center, Rotterdam, The Netherlands"
+      },
+      {
+        "author_name": "Merel E. Hellemons",
+        "author_inst": "Department of Pulmonary Medicine, Erasmus, University Medical Center, Rotterdam, The Netherlands"
+      },
+      {
+        "author_name": "Marcia M.L. Kho",
+        "author_inst": "Department of Internal Medicine, Erasmus, University Medical Center, Rotterdam, The Netherlands"
+      },
+      {
+        "author_name": "Rory D. de Vries",
+        "author_inst": "Department of Viroscience, Erasmus, University Medical Center, Rotterdam, The Netherlands"
+      },
+      {
+        "author_name": "Richard Molenkamp",
+        "author_inst": "Department of Viroscience, Erasmus, University Medical Center, Rotterdam, The Netherlands"
+      },
+      {
+        "author_name": "Marlies E.J. Reinders",
+        "author_inst": "Department of Internal Medicine, Erasmus, University Medical Center, Rotterdam, The Netherlands"
+      },
+      {
+        "author_name": "Bart J.A. Rijnders",
+        "author_inst": "Department of Internal Medicine, Section of Infectious Diseases and Department of Medical Microbiology and Infectious Diseases, Erasmus, University Medical Cent"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.04.26.22271727",
     "rel_title": "Risk of COVID-19 breakthrough infection and hospitalization in individuals with comorbidities",
@@ -307251,129 +305849,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
-  {
-    "rel_doi": "10.1101/2022.04.26.489529",
-    "rel_title": "A cocktail containing two synergetic antibodies broadly neutralizes SARS-CoV-2 and its variants including Omicron BA.1 and BA.2",
-    "rel_date": "2022-04-26",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.26.489529",
-    "rel_abs": "Neutralizing antibodies (NAbs) can prevent and treat infections caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, continuously emerging variants, such as Omicron, have significantly reduced the potency of most known NAbs. The selection of NAbs with broad neutralizing activities and the identification of conserved critical epitopes are still urgently needed. Here, we identified an extremely potent antibody (55A8) by single B-cell sorting from convalescent SARS-CoV-2-infected patients that recognized the receptor-binding domain (RBD) in the SARS-CoV-2 spike (S) protein. 55A8 could bind to wild-type SARS-CoV-2, Omicron BA.1 and Omicron BA.2 simultaneously with 58G6, a NAb previously identified by our group. Importantly, an antibody cocktail containing 55A8 and 58G6 (2-cocktail) showed synergetic neutralizing activity with a half-maximal inhibitory concentration (IC50) in the picomolar range in vitro and prophylactic efficacy in hamsters challenged with Omicron (BA.1) through intranasal delivery at an extraordinarily low dosage (25 g of each antibody daily) at 3 days post-infection. Structural analysis by cryo-electron microscopy (cryo-EM) revealed that 55A8 is a Class III NAb that recognizes a highly conserved epitope. It could block angiotensin-converting enzyme 2 (ACE2) binding to the RBD in the S protein trimer via steric hindrance. The epitopes in the RBD recognized by 55A8 and 58G6 were found to be different and complementary, which could explain the synergetic mechanism of these two NAbs. Our findings not only provide a potential antibody cocktail for clinical use against infection with current SARS-CoV-2 strains and future variants but also identify critical epitope information for the development of better antiviral agents.",
-    "rel_num_authors": 27,
-    "rel_authors": [
-      {
-        "author_name": "Xinghai Zhang",
-        "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences"
-      },
-      {
-        "author_name": "Feiyang Luo",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Huajun Zhang",
-        "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences"
-      },
-      {
-        "author_name": "Hangtian Guo",
-        "author_inst": "Nanjing University; ShanghaiTech University"
-      },
-      {
-        "author_name": "Junhui Zhou",
-        "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences; University of Chinese Academy of Sciences"
-      },
-      {
-        "author_name": "Tingting Li",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Shaohong Chen",
-        "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences; University of Chinese Academy of Sciences"
-      },
-      {
-        "author_name": "Shuyi Song",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Meiying Shen",
-        "author_inst": "The First Affiliated Hospital of Chongqing Medical University"
-      },
-      {
-        "author_name": "Yan Wu",
-        "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences"
-      },
-      {
-        "author_name": "Yan Gao",
-        "author_inst": "ShanghaiTech University; Shanghai Clinical Research and Trial Center"
-      },
-      {
-        "author_name": "Xiaojian Han",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Yingming Wang",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Chao Hu",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Yuchi Lu",
-        "author_inst": "ShanghaiTech University"
-      },
-      {
-        "author_name": "Wei Wang",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Kai Wang",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Ni Tang",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Tengchuan Jin",
-        "author_inst": "University of Science and Technology of China"
-      },
-      {
-        "author_name": "Chengyong Yang",
-        "author_inst": "Mindao Haoyue Co., Ltd."
-      },
-      {
-        "author_name": "Guofeng Cheng",
-        "author_inst": "Mindao Haoyue Co., Ltd."
-      },
-      {
-        "author_name": "Haitao Yang",
-        "author_inst": "ShanghaiTech University"
-      },
-      {
-        "author_name": "Aishun Jin",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Xiaoyun Ji",
-        "author_inst": "Nanjing University; Chongqing Medical University; Engineering Research Center of Protein and Peptide Medicine, Ministry of Education"
-      },
-      {
-        "author_name": "Rui Gong",
-        "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences"
-      },
-      {
-        "author_name": "Sandra Chiu",
-        "author_inst": "University of Science and Technology of China"
-      },
-      {
-        "author_name": "Ailong Huang",
-        "author_inst": "Chongqing Medical University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2022.04.24.489298",
     "rel_title": "Anti-SARS-Cov-2 S-RBD IgG formed after BNT162b2 vaccination can bind C1q and activate complement",
@@ -307660,6 +306135,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.04.19.22274030",
+    "rel_title": "Estimating the distribution of COVID-19-susceptible, -recovered, and -vaccinated individuals in Germany up to April 2022",
+    "rel_date": "2022-04-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.19.22274030",
+    "rel_abs": "After having affected the population for two years, the COVID-19 pandemic has reached a phase where a considerable number of people in Germany have been either infected with a SARS-CoV-2 variant, vaccinated, or both. Yet the full extent to which the population has been in contact with either virus or vaccine remains elusive, particularly on a regional level, because (a) infection counts suffer from under-reporting, and (b) the overlap between the vaccinated and recovered subpopulations is unknown. Since previous infection, vaccination, or especially a combination of both reduce the risk of severe disease, a high share of individuals with SARS-CoV-2 immunity lowers the probability of severe outbreaks that could potentially overburden the public health system once again, given that emerging variants do not escape this reduction in susceptibility. Here, we estimate the share of immunologically naive individuals by age group for each of the 16 German federal states by integrating an infectious disease model based on weekly incidences of SARS-CoV-2 infections in the national surveillance system and vaccine uptake, as well as assumptions regarding under-ascertainment. We estimate a median share of 7.0% of individuals in the German population have neither been in contact with vaccine nor any variant as of March 31, 2022 (quartile range [3.6%- 9.8%]). For the adult population at higher risk of severe disease, this figure is reduced to 3.5% [1.3%-5.5%] for ages 18-59 and 4.3% [2.7%-5.8%] for ages 60 and above. However, estimates vary between German states mostly due to heterogeneous vaccine uptake. Excluding Omicron infections from the analysis, 16.1% [14.0%-17.8%] of the population in Germany, across all ages, are estimated to be immunologically naive, highlighting the large impact the Omicron wave had until the beginning of spring in 2022.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Benjamin F Maier",
+        "author_inst": "Robert Koch Institute"
+      },
+      {
+        "author_name": "Annika H Rose",
+        "author_inst": "Robert Koch Institute"
+      },
+      {
+        "author_name": "Angelique Burdinski",
+        "author_inst": "Robert Koch Institute"
+      },
+      {
+        "author_name": "Pascal Klamser",
+        "author_inst": "Robert Koch Institute"
+      },
+      {
+        "author_name": "Hannelore Neuhauser",
+        "author_inst": "Robert Koch Institute"
+      },
+      {
+        "author_name": "Ole Wichmann",
+        "author_inst": "Robert Koch Institute"
+      },
+      {
+        "author_name": "Lars Schaade",
+        "author_inst": "Robert Koch Institute"
+      },
+      {
+        "author_name": "Lothar H Wieler",
+        "author_inst": "Robert Koch Institute"
+      },
+      {
+        "author_name": "Dirk Brockmann",
+        "author_inst": "Robert Koch Institute"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2022.04.19.22273864",
     "rel_title": "Immune and pathophysiologic profiling of antenatal COVID-19 in the GIFT cohort: A Singaporean case-control study.",
@@ -309061,45 +307587,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.04.22.22274160",
-    "rel_title": "Regional replacement of SARS-CoV-2 variant BA.1 with BA.2 as observed through wastewater surveillance",
-    "rel_date": "2022-04-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.22.22274160",
-    "rel_abs": "An understanding of circulating SARS-CoV-2 variants can inform pandemic response, vaccine development, disease epidemiology, and use of monoclonal antibody treatments. We developed custom assays targeting characteristic mutations in SARS-CoV-2 variants Omicron BA.1 and BA.2 and confirmed their sensitivity and specificity in silico and in vitro. We then applied these assays to daily wastewater solids samples from eight publicly owned treatment works in the greater Bay Area of California, USA, over four months to obtain a spatially and temporally intensive data set. We documented regional replacement of BA.1 with BA.2 in agreement with, and ahead of, clinical sequencing data. This study highlights the utility of wastewater surveillance for real time tracking of SARS-CoV-2 variant circulation.\n\nSynopsisWastewater surveillance was used to document regional emergence of SARS-CoV-2 variant Omicron BA.2 ahead of clinical surveillance.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC=\"FIGDIR/small/22274160v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (31K):\norg.highwire.dtl.DTLVardef@10e4406org.highwire.dtl.DTLVardef@1941dd9org.highwire.dtl.DTLVardef@133b438org.highwire.dtl.DTLVardef@17ce1c4_HPS_FORMAT_FIGEXP  M_FIG C_FIG",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Alexandria Boehm",
-        "author_inst": "Stanford University"
-      },
-      {
-        "author_name": "Bridgette Hughes",
-        "author_inst": "Verily Life Sciences"
-      },
-      {
-        "author_name": "Marlene K Wolfe",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Bradley White",
-        "author_inst": "Verily Life Sciences"
-      },
-      {
-        "author_name": "Dorothea Duong",
-        "author_inst": "Verily Life Sciences"
-      },
-      {
-        "author_name": "Vikram Chan-Herur",
-        "author_inst": "Verily Life Sciences"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.04.21.22274140",
     "rel_title": "Snotwatch COVID-Toes: An ecological study of chilblains and COVID-19 diagnoses in Victoria, Australia",
@@ -309518,6 +308005,69 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "cardiovascular medicine"
   },
+  {
+    "rel_doi": "10.1101/2022.04.19.22274026",
+    "rel_title": "A Platform for Data-centric, Continuous Epidemiological Analyses",
+    "rel_date": "2022-04-21",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.19.22274026",
+    "rel_abs": "Guaranteeing durability, provenance, accessibility, and trust in open datasets can be challenging for researchers and organizations that rely on public repositories of data critical to epidemiology and other health analytics. Not only are the required repositories sometimes difficult to locate, and nearly always require conversion into a compatible format, they may move or change unpredictably. Any single change of the rules in one repository can hinder updating of a public dashboard reliant on pulling data from external sources. These concerns are particularly challenging at the international level, because systems aimed at harmonizing health and related data are typically dictated by national governments to serve their individual needs. In this paper, we introduce a comprehensive public health data platform, the EpiGraphHub, that aims to provide a single interoperable repository for open health and related data, curated by the international research community, which allows secure local integration of sensitive databases whilst facilitating the development of data-driven applications and reports for decision-makers. The platform development is co-funded by the World Health Organization and is fully open-source to maximize its value for large-scale public health studies.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Fl\u00e1vio Code\u00e7o Coelho",
+        "author_inst": "Funda\u00e7\u00e3o Getulio Vargas"
+      },
+      {
+        "author_name": "Daniel C P C\u00e2mara",
+        "author_inst": "Fundacao Oswaldo Cruz"
+      },
+      {
+        "author_name": "Eduardo Correa Araujo",
+        "author_inst": "Universidade Tecnologica Federal do Parana"
+      },
+      {
+        "author_name": "Lucas Bianchi",
+        "author_inst": "Fundacao Oswaldo Cruz"
+      },
+      {
+        "author_name": "Ivan Ogasawara",
+        "author_inst": "The Graph Network"
+      },
+      {
+        "author_name": "Jyoti Dalal",
+        "author_inst": "The Graph Network"
+      },
+      {
+        "author_name": "Ananthu James",
+        "author_inst": "Indian Institute of Science, Bangalore"
+      },
+      {
+        "author_name": "Jessica Lee Abbate",
+        "author_inst": "Geomatys"
+      },
+      {
+        "author_name": "Aziza Merzouki",
+        "author_inst": "University of Geneva"
+      },
+      {
+        "author_name": "Izabel Reis",
+        "author_inst": "World Health Organization"
+      },
+      {
+        "author_name": "Kenechukwu David Nwosu",
+        "author_inst": "Institute of Global Health - University of Geneva"
+      },
+      {
+        "author_name": "Olivia Keiser",
+        "author_inst": "Institute of Global Health - University of Geneva"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2022.04.19.22274036",
     "rel_title": "A Statistical Argument Against Vaccine Injury",
@@ -312471,113 +311021,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2022.04.12.22273675",
-    "rel_title": "SARS-CoV-2 evolution and immune escape in immunocompromised patients treated with exogenous antibodies",
-    "rel_date": "2022-04-19",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.12.22273675",
-    "rel_abs": "BackgroundSARS-CoV-2 mutations conferring escape from neutralizing antibodies can arise in immunocompromised patients with prolonged infection, but the conditions that facilitate immune escape are still not fully understood.\n\nMethodsWe characterized endogenous immune responses, within-host SARS-CoV-2 evolution, and autologous neutralization of the viral variants that arose in five immunocompromised patients with prolonged infection and B cell deficiencies.\n\nResultsIn two patients treated with the monoclonal antibody bamlanivimab, viral resistance to autologous serum arose early and persisted for several months, accompanied by ongoing evolution in the spike protein. These patients exhibited deficiencies in both T and B cell arms, and one patient succumbed to disease. In contrast, we did not observe spike mutations in immunologically important regions in patients who did not receive exogenous antibodies or who received convalescent plasma and had intact T cell responses to SARS-CoV-2.\n\nConclusionsOur results underscore the potential importance of multiple factors - the absence of an effective endogenous immune response, persistent virus replication, and selective pressure such as single-agent bamlanivimab - in promoting the emergence of SARS-CoV-2 mutations associated with immune evasion. These findings highlight the need for larger clinical studies in immunocompromised populations to better understand the ramifications of different therapies. Our results also confirm that patients with B cell deficiencies can elicit effector T cells and may suggest an important role for T cells in controlling infection, which is relevant to vaccines and therapeutics.",
-    "rel_num_authors": 23,
-    "rel_authors": [
-      {
-        "author_name": "Erin Scherer",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Ahmed Babiker",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Max W. Adelman",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Brent Allman",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Autum Key",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Jennifer M Kleinhenz",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Rose M Langsjoen",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Phuong-Vi Nguyen",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Ivy Onyechi",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Jacob D Sherman",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Trevor W. Simon",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Hannah Soloff",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Jessica Tarabay",
-        "author_inst": "Emory Healthcare"
-      },
-      {
-        "author_name": "Jay Varkey",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Andrew S Webster",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Daniela Weiskopf",
-        "author_inst": "La Jolla Institute For Allergy & Immunology"
-      },
-      {
-        "author_name": "Daniel B Weissman",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Yongxian Xu",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Jesse J Waggoner",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Katia Koelle",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Nadine Rouphael",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Stephanie M Pouch",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Anne Piantadosi",
-        "author_inst": "Emory University School of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "intensive care and critical care medicine"
-  },
   {
     "rel_doi": "10.1101/2022.04.13.22272869",
     "rel_title": "Estimating the risk of hospitalisation and death in England's remaining unvaccinated population",
@@ -312892,6 +311335,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.04.18.22271936",
+    "rel_title": "Anti-nucleocapsid antibodies following SARS-CoV-2 infection in the blinded phase of the mRNA-1273 Covid-19 vaccine efficacy clinical trial",
+    "rel_date": "2022-04-19",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.18.22271936",
+    "rel_abs": "ImportanceThe performance of immunoassays for determining past SARS-CoV-2 infection, which were developed in unvaccinated individuals, has not been assessed in vaccinated individuals.\n\nObjectiveTo evaluate anti-nucleocapsid antibody (anti-N Ab) seropositivity in mRNA-1273 vaccine efficacy trial participants after SARS-CoV-2 infection during the trials blinded phase.\n\nDesignNested analysis in a Phase 3 randomized, placebo-controlled vaccine efficacy trial. Nasopharyngeal swabs for SARS-CoV-2 PCR testing were taken from all participants on Day 1 and Day 29 (vaccination days), and during symptom-prompted illness visits. Serum samples from Days 1, 29, 57, and the Participant Decision Visit (PDV, when participants were informed of treatment assignment, median day 149) were tested for anti-N Abs.\n\nSettingMulticenter, randomized, double-blind, placebo-controlled trial at 99 sites in the US.\n\nParticipantsTrial participants were [&ge;] 18 years old with no known history of SARS-CoV-2 infection and at appreciable risk of SARS-CoV-2 infection and/or high risk of severe Covid-19. Nested sub-study consists of participants with SARS-CoV-2 infection during the blinded phase of the trial.\n\nInterventionTwo mRNA-1273 (Moderna) or Placebo injections, 28 days apart.\n\nMain Outcome and MeasureDetection of serum anti-N Abs by the Elecsys (Roche) immunoassay in samples taken at the PDV from participants with SARS-CoV-2 infection during the blinded phase. The hypothesis tested was that mRNA-1273 recipients have different anti-N Ab seroconversion and/or seroreversion profiles after SARS-CoV-2 infection, compared to placebo recipients. The hypothesis was formed during data collection; all main analyses were pre-specified before being conducted.\n\nResultsWe analyzed data from 1,789 participants (1,298 placebo recipients and 491 vaccine recipients) with SARS-CoV-2 infection during the blinded phase (through March 2021). Among participants with PCR-confirmed Covid-19 illness, seroconversion to anti-N Abs at a median follow up of 53 days post diagnosis occurred in 21/52 (40%) of the mRNA-1273 vaccine recipients vs. 605/648 (93%) of the placebo recipients (p < 0.001). Higher SARS-CoV-2 viral copies at diagnosis was associated with a higher likelihood of anti-N Ab seropositivity (odds ratio 1.90 per 1-log increase; 95% confidence interval 1.59, 2.28).\n\nConclusions and RelevanceAs a marker of recent infection, anti-N Abs may have lower sensitivity in mRNA-1273-vaccinated persons who become infected. Vaccination status should be considered when interpreting seroprevalence and seropositivity data based solely on anti-N Ab testing\n\nTrial RegistrationClinicalTrials.gov NCT04470427\n\nKey PointsO_ST_ABSQuestionC_ST_ABSDoes prior mRNA-1273 vaccination influence anti-nucleocapsid antibody seroconversion and/or seroreversion after SARS-CoV-2 infection?\n\nFindingsAmong participants in the mRNA-1273 vaccine efficacy trial with PCR-confirmed Covid-19, anti-nucleocapsid antibody seroconversion at the time of study unblinding (median 53 days post diagnosis and 149 days post enrollment) occurred in 40% of the mRNA-1273 vaccine recipients vs. 93% of the placebo recipients, a significant difference. Higher SARS-CoV-2 viral copy number upon diagnosis was associated with a greater chance of anti-nucleocapsid antibody seropositivity (odds ratio 1.90 per 1-log increase; 95% confidence interval 1.59, 2.28). All infections analyzed occurred prior to the circulation of delta and omicron viral variants.\n\nMeaningConclusions about the prevalence and incidence of SARS-CoV-2 infection in vaccinated persons based on anti-nucleocapsid antibody assays need to be weighed in the context of these results.",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Dean Follmann",
+        "author_inst": "National Institute of Allergy and Infectious Diseases"
+      },
+      {
+        "author_name": "Holly E. Janes",
+        "author_inst": "Fred Hutchinson Cancer Center"
+      },
+      {
+        "author_name": "Olive D. Buhule",
+        "author_inst": "National Institute of Allergy and Infectious Diseases"
+      },
+      {
+        "author_name": "Honghong Zhou",
+        "author_inst": "Moderna, Inc."
+      },
+      {
+        "author_name": "Bethany Girard",
+        "author_inst": "Moderna, Inc."
+      },
+      {
+        "author_name": "Kristen Marks",
+        "author_inst": "Weill Cornell Medicine"
+      },
+      {
+        "author_name": "Karen Kotloff",
+        "author_inst": "University of Maryland School of Medicine"
+      },
+      {
+        "author_name": "Micha\u00ebl Desjardins",
+        "author_inst": "Harvard Medical School"
+      },
+      {
+        "author_name": "Lawrence Corey",
+        "author_inst": "Fred Hutchinson Cancer Center"
+      },
+      {
+        "author_name": "Kathleen M. Neuzil",
+        "author_inst": "University of Maryland School of Medicine"
+      },
+      {
+        "author_name": "Jacqueline M. Miller",
+        "author_inst": "Moderna, Inc."
+      },
+      {
+        "author_name": "Hana M. El Sahly",
+        "author_inst": "Baylor College of Medicine"
+      },
+      {
+        "author_name": "Lindsey R. Baden",
+        "author_inst": "Harvard Medical School"
+      }
+    ],
+    "version": "1",
+    "license": "cc0",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.04.18.22273989",
     "rel_title": "Validation of Reduced S-gene Target Performance and Failure for Rapid Surveillance of SARS-CoV-2 Variants",
@@ -314109,101 +312619,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.04.14.22273898",
-    "rel_title": "Effectiveness and waning of protection with different SARS-CoV-2 primary and booster vaccines during the Delta pandemic wave in 2021 in Hungary (HUN-VE 3 study)",
-    "rel_date": "2022-04-18",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.14.22273898",
-    "rel_abs": "BackgroundIn late 2021, the pandemic wave was dominated by the Delta SARS-CoV-2 variant in Hungary. Booster vaccines were offered starting from August 2021.\n\nMethodsThe nationwide HUN-VE 3 study examined the effectiveness and durability of primary immunization and single booster vaccinations on SARS-CoV-2-related infection, hospitalization and mortality during the Delta wave.\n\nResultsThe study population included 8,087,988 individuals aged 18-100 years at the beginning of the pandemic. During the Delta wave, after adjusting for age, sex, calendar day, and chronic diseases, vaccine effectiveness (VE) of primary vaccination against registered SARS-CoV-2 infection was between 11% to 77% and 18% to 79% 14-120 days after primary immunization in the 16-64 and 65-100 years age cohort respectively, while it decreased to close to zero in the younger age group and around 40% or somewhat less in the elderly after 6 months for almost all vaccine types. In the population aged 65-100 years, we found high, 88.1%-92.5% adjusted effectiveness against Covid-19 infection after the Pfizer-BioNTech, and 92.2%-95.6% after the Moderna booster dose, while Sinopharm and Janssen booster doses provided 26.5%-75.3% and 72.9%-100.0% adjusted VE, respectively. Adjusted VE against Covid-19 related hospitalization was high within 14-120 days for Pfizer-BioNTech: 76.6%, Moderna: 83.8%, Sputnik-V: 78.3%, AstraZeneca: 73.8%, while modest for Sinopharm: 45.7% and Janssen: 26.4%. The waning of protection against Covid-19 related hospitalization was modest and booster vaccination with mRNA vaccines or the Janssen vaccine increased adjusted VE up to almost 100%, while the Sinopharm booster dose proved to be less effective. VE against Covid-19 related death after primary immunization was high or moderate: for Pfizer-BioNTech: 81.5%, Moderna: 93.2%, Sputnik-V: 100.0%, AstraZeneca: 84.8%, Sinopharm: 58.6%, Janssen: 53.3%). VE against this outcome also showed moderate decline over time, while booster vaccines restored effectiveness up to almost 100%, except for the Sinopharm booster.\n\nConclusionsThe HUN-VE 3 study demonstrated waning VE with all vaccine types for all examined outcomes during the Delta wave and confirmed the outstanding benefit of booster vaccination with the mRNA or Janssen vaccines. This is the first study to provide comparable effectiveness results for six different booster types during the Delta pandemic wave.",
-    "rel_num_authors": 20,
-    "rel_authors": [
-      {
-        "author_name": "Zoltan Voko",
-        "author_inst": "Center for Health Technology Assessment Semmelweis University and Syreon Research Institute, Budapest, Hungary"
-      },
-      {
-        "author_name": "Zoltan Kiss",
-        "author_inst": "Second Department of Medicine and Nephrology-Diabetes Center, University of Pecs Medical School, Pecs, Hungary"
-      },
-      {
-        "author_name": "Gyorgy Surjan",
-        "author_inst": "Ministry of Human Resources, Budapest, Hungary and Institute of Digital Health Sciences, Semmelweis University, Budapest"
-      },
-      {
-        "author_name": "Orsolya Surjan",
-        "author_inst": "Department of Deputy Chief Medical Officer II., National Public Health Center, Budapest, Hungary"
-      },
-      {
-        "author_name": "Zsofia Barcza",
-        "author_inst": "Syntesia Medical Communications Ltd., Budapest, Hungary"
-      },
-      {
-        "author_name": "Istvan Wittmann",
-        "author_inst": "Second Department of Medicine and Nephrology-Diabetes Center, University of Pecs Medical School, Pecs, Hungary"
-      },
-      {
-        "author_name": "Gergo A. Molnar",
-        "author_inst": "Second Department of Medicine and Nephrology-Diabetes Center, University of Pecs Medical School, Pecs, Hungary"
-      },
-      {
-        "author_name": "David Nagy",
-        "author_inst": "Center for Health Technology Assessment, Semmelweis University, Budapest and Syreon Research Institute, Budapest, Hungary"
-      },
-      {
-        "author_name": "Veronika Muller",
-        "author_inst": "Department of Pulmonology, Semmelweis University, Budapest, Hungary"
-      },
-      {
-        "author_name": "Krisztina Bogos",
-        "author_inst": "Department of Pulmonology, National Koranyi Institute of Pulmonology, Budapest, Hungary"
-      },
-      {
-        "author_name": "Peter Nagy",
-        "author_inst": "National Institute of Oncology, Budapest, Hungary and Institute of Oncochemistry, University of Debrecen, Debrecen, Hungary"
-      },
-      {
-        "author_name": "Istvan Kenessey",
-        "author_inst": "National Institute of Oncology, Budapest, Hungary and Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Budapest, Hungary"
-      },
-      {
-        "author_name": "Andras Weber",
-        "author_inst": "National Institute of Oncology, Budapest, Hungary and Cancer Surveillance Branch, International Agency for Research on Cancer, Lyon, France"
-      },
-      {
-        "author_name": "Lorinc Polivka",
-        "author_inst": "Department of Pulmonology, Semmelweis University, Budapest, Hungary"
-      },
-      {
-        "author_name": "Mihaly Palosi",
-        "author_inst": "National Health Insurance Fund, Budapest, Hungary"
-      },
-      {
-        "author_name": "Janos Szlavik",
-        "author_inst": "South-Pest Hospital Centre - National Institute for Infectology and Haematology, Budapest, Hungary"
-      },
-      {
-        "author_name": "Gyorgy Rokszin",
-        "author_inst": "Second Department of Medicine and Nephrology-Diabetes Center, University of Pecs Medical School, Pecs, Hungary and RxTarget Ltd., Szolnok, Hungary"
-      },
-      {
-        "author_name": "Cecilia Muller",
-        "author_inst": "Department of Chief Medical Officer, National Public Health Center, Budapest, Hungary"
-      },
-      {
-        "author_name": "Zoltan Szekanecz",
-        "author_inst": "Department of Rheumatology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary"
-      },
-      {
-        "author_name": "Miklos Kasler",
-        "author_inst": "Ministry of Human Resources, Budapest, Hungary"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.04.18.488660",
     "rel_title": "Modeling COVID-19 disease biology to identify drug treatment candidates",
@@ -314466,6 +312881,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.04.18.22273961",
+    "rel_title": "Clonal diversity determines persistence of SARS-CoV-2 epitope-specific T cell response",
+    "rel_date": "2022-04-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.18.22273961",
+    "rel_abs": "T cells play a pivotal role in reducing disease severity during SARS-CoV-2 infection and formation of long-term immune memory. We studied 50 COVID-19 convalescent patients and found that T cell response was induced more frequently and persisted longer than circulating antibodies. To identify epitopes that give rise to long-lived T cell memory, we performed ex vivo T cell expansion, MHC-tetramer cell-sorting, and high-throughput sequencing. We identified 756 clonotypes specific to nine known CD8+ T cell receptor (TCR) epitopes. Some epitopes were recognized by highly similar public clonotypes with restricted variable and joining segment usage. Receptors for other epitopes were extremely diverse, suggesting alternative modes of recognition. We also tracked persistence of epitope-specific response and individual clonotypes for a median of eight months after infection. The number of recognized epitopes per patient and quantity of epitope-specific clonotypes decreased over time, but the studied epitopes were characterized by uneven decline in the number of specific T cells. Epitopes with more clonally diverse TCR repertoires induced more pronounced and durable responses. In contrast, the abundance of specific clonotypes in peripheral circulation had no influence on their persistence. Our study demonstrates the durability of SARS-CoV-2-specific CD8+ memory, and offers important implications for vaccine design.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Ksenia V Zornikova",
+        "author_inst": "National Medical Research Center for Hematology, Moscow, Russia"
+      },
+      {
+        "author_name": "Alexandra Khmelevskaya",
+        "author_inst": "National Medical Research Center for Hematology, Moscow, Russia"
+      },
+      {
+        "author_name": "Savely A Sheetikov",
+        "author_inst": "National Medical Research Center for Hematology, Moscow, Russia"
+      },
+      {
+        "author_name": "Dmitry O Kiryukhin",
+        "author_inst": "National Medical Research Center for Hematology, Moscow, Russia"
+      },
+      {
+        "author_name": "Olga V Shcherbakova",
+        "author_inst": "National Medical Research Center for Hematology, Moscow, Russia"
+      },
+      {
+        "author_name": "Aleksei Titov",
+        "author_inst": "National Medical Research Center for Hematology, Moscow, Russia"
+      },
+      {
+        "author_name": "Ivan V Zvyagin",
+        "author_inst": "Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia"
+      },
+      {
+        "author_name": "Grigory Efimov",
+        "author_inst": "National Medical Research Center for Hematology, Moscow, Russia"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "allergy and immunology"
+  },
   {
     "rel_doi": "10.1101/2022.04.13.22273830",
     "rel_title": "Why were Twitter Users Obsessed with Vitamin D during the first year of the pandemic?",
@@ -315767,185 +314229,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2022.04.11.22273690",
-    "rel_title": "Evaluation of isotype specific salivary antibody assays for detecting previous SARS-CoV-2 infection in children and adults",
-    "rel_date": "2022-04-17",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.11.22273690",
-    "rel_abs": "Saliva is easily obtainable non-invasively and potentially suitable for detecting both current and previous SARS-CoV-2 infection. We established 6 standardised enzyme linked immunosorbent assays (ELISA) capable of detecting IgA and IgG antibodies to whole SARS-CoV-2 spike protein, to its receptor binding domain region and to nucleocapsid protein in saliva. In test accuracy (n=320), we found that spike IgG performed best (ROC AUC: 95.0%, 92.8-97.3%), followed by spike IgA (ROC AUC: 89.9%, 86.5-93.2%) for discriminating between pre-pandemic and post COVID-19 saliva samples. Using machine learning, diagnostic performance was improved when a combination of tests was used. As expected, salivary IgA was poorly correlated with serum, indicating an oral mucosal response whereas salivary IgG responses were predictive of those in serum. When deployed to 20 household outbreaks undergoing Delta and Omicron infection, antibody responses were heterogeneous but remained a reliable indicator of recent infection. Intriguingly, unvaccinated children showed evidence of exposure almost exclusively through specific IgA responses in the absence of evidence of viral infection. We have provided robust standardisation, evaluation, and field-testing of salivary antibody assays as tools for monitoring SARS-CoV-2 immune responses. Future work should focus on investigating salivary antibody responses following infection and vaccination to understand patterns of SARS-CoV-2 transmission and inform ongoing vaccination strategies.",
-    "rel_num_authors": 41,
-    "rel_authors": [
-      {
-        "author_name": "Amy C Thomas",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Elizabeth Oliver",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Holly Baum",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Kapil Gupter",
-        "author_inst": "University of Bristol and Imophoron Ltd."
-      },
-      {
-        "author_name": "Kathryn Shelley",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Anna Long",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Hayley Jones",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Joyce Smith",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Benjamin Hitchings",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Natalie di Bartolo",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Kate Vasileiou",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Fruzsina Rabi",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Hanin Alamir",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Malak Eghleilib",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Ore Francis",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Jennifer Oliver",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Begonia Morales-Aza",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Ulrike Obst",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Debbie Shattock",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Rachael Barr",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Lucy Collingwood",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Kaltun Duale",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Niall Grace",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Guillaume Gonnage Livera",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Lindsay Bishop",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Harriet Downing",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Fernanda Rodrigues",
-        "author_inst": "Universidade de Coimbra"
-      },
-      {
-        "author_name": "Nicholas J Timpson",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Caroline J Relton",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Ashley Mark Toye",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Derek N Woolfson",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Imre Berger",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Anu Goenka",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Andrew  D. Mark Davidson",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Kathleen M Gillespie",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Alistair JK Williams",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Mick Bailey",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Ellen Brooks-Pollock",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Adam Finn",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Alice Halliday",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "- CoMMinS Study Team",
-        "author_inst": "-"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.04.07.22273558",
     "rel_title": "Safety and effectiveness of RBD-specific polyclonal equine F(ab')2 fragments for the treatment of hospitalized patients with severe Covid-19 disease: a retrospective cohort study.",
@@ -316348,6 +314631,69 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.04.08.22273532",
+    "rel_title": "Heterologous Gam-COVID-Vac (Sputnik V) / mRNA-1273 (Moderna) vaccination induces a stronger humoral response than homologous Sputnik V in a real-world data analysis",
+    "rel_date": "2022-04-16",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.08.22273532",
+    "rel_abs": "IntroductionGrowing data are demonstrating safety and immunogenicity of heterologous vaccination schemes against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. This strategy opens up the possibility of a shorter path towards the end of the pandemic.\n\nObjectiveTo compare the homologous prime-boost vaccination scheme of Gam-COVID-Vac (Sputnik V, SpV) to its heterologous combination with mRNA-1273 (Moderna, Mod) vaccine.\n\nMethodsSARS-CoV-2 anti-spike (S)-receptor binding domain (RBD) IgG concentration was assessed three to seven weeks after complete vaccination. Reactogenicity was evaluated by declared side events and medical assistance required until day 7 post-boost.\n\nResultsOf 190 participants enrolled, 105 received homologous SpV/SpV and the remaining heterologous SpV/Mod vaccination scheme, respectively. Median (interquartile range, IQR) age was 54 (37-63) years, 132 (69.5%) were female and 46 (24.2%) individuals had a prior confirmed COVID-19. Anti-S-RBD IgG median (IQR) titers were significantly higher for SpV/Mod [2511 (1476-3992) BAU/mL] than for SpV/SpV [582 (209-1609) BAU/mL, p<0.001] vaccination scheme. In a linear model adjusted for age, gender, time to the serological assay and time between doses, SpV/Mod [4.154 (6.585-615.554), p<0.001] and prior COVID [3.732 (8.641-202.010), p<0.001] were independently associated with higher anti-S-RBD IgG values. A higher frequency of mild-moderate adverse effects was associated with the heterologous scheme, although it was well tolerated by all individuals and no medical assistance was required.\n\nConclusionThe heterologous SpV/Mod combination against SARS-CoV-2 is well tolerated and significantly increases humoral immune response as compared to the homologous SpV/SpV immunization.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Matias Javier Pereson",
+        "author_inst": "Universidad de Buenos Aires. Facultad de Farmacia y Bioquimica. Instituto de Investigaciones en Bacteriologia y Virologia Molecular (IBaViM). Buenos Aires, Arge"
+      },
+      {
+        "author_name": "Lucas Amaya",
+        "author_inst": "Virology Section, Centro de Educacion Medica e Investigaciones Clinicas Norberto Quirno \"CEMIC\". Buenos Aires, Argentina."
+      },
+      {
+        "author_name": "Karin Neukam",
+        "author_inst": "Servicio de Enfermedades Infecciosas, UCEIMP. Hospital Universitario Virgen del Rocio. Seville, Spain."
+      },
+      {
+        "author_name": "Patricia Bare",
+        "author_inst": "Academia Nacional de Medicina"
+      },
+      {
+        "author_name": "Natalia Echegoyen",
+        "author_inst": "Virology Section, Centro de Educacion Medica e Investigaciones Clinicas Norberto Quirno \"CEMIC\". Buenos Aires, Argentina."
+      },
+      {
+        "author_name": "Maria Noel Badano",
+        "author_inst": "Instituto de Medicina Experimental (IMEX), Academia Nacional de Medicina, Ciudad Autonoma de Buenos Aires, Argentina."
+      },
+      {
+        "author_name": "Alicia Lucero",
+        "author_inst": "Virology Section, Centro de Educacion Medica e Investigaciones Clinicas Norberto Quirno \"CEMIC\". Buenos Aires, Argentina."
+      },
+      {
+        "author_name": "Antonella Martelli",
+        "author_inst": "Virology Section, Centro de Educacion Medica e Investigaciones Clinicas Norberto Quirno \"CEMIC\". Buenos Aires, Argentina."
+      },
+      {
+        "author_name": "Gabriel Garcia",
+        "author_inst": "Universidad de Buenos Aires. Facultad de Farmacia y Bioquimica. Instituto de Investigaciones en Bacteriologia y Virologia Molecular (IBaViM). Buenos Aires, Arge"
+      },
+      {
+        "author_name": "Cristina Videla",
+        "author_inst": "Virology Section, Centro de Educacion Medica e Investigaciones Clinicas Norberto Quirno \"CEMIC\". Buenos Aires, Argentina."
+      },
+      {
+        "author_name": "Alfredo Martinez",
+        "author_inst": "Virology Section, Centro de Educacion Medica e Investigaciones Clinicas Norberto Quirno \"CEMIC\". Buenos Aires, Argentina."
+      },
+      {
+        "author_name": "Federico Alejandro Di Lello Sr.",
+        "author_inst": "Universidad de Buenos Aires. Facultad de Farmacia y Bioquimica. Instituto de Investigaciones en Bacteriologia y Virologia Molecular (IBaViM). Buenos Aires, Arge"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.04.07.22273591",
     "rel_title": "Monitoring real-time transmission heterogeneity from Incidence data",
@@ -317373,73 +315719,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2022.04.15.22273909",
-    "rel_title": "Introduction and Establishment of SARS-CoV-2 Gamma Variant in New York City in Early 2021",
-    "rel_date": "2022-04-16",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.15.22273909",
-    "rel_abs": "BackgroundMonitoring the emergence and spread of SARS-CoV-2 variants is an important public health objective. Travel restrictions, aimed to prevent viral spread, have major economic consequences and unclear effectiveness despite considerable research. We investigated the introduction and establishment of the Gamma variant in New York City (NYC) in 2021.\n\nMethodsWe performed phylogeographic analysis on 15,967 Gamma sequences available on GISAID and sampled between March 10th through May 1st, 2021, to identify geographic sources of Gamma lineages introduced into NYC. We identified locally circulating Gamma transmission clusters and inferred the timing of their establishment in NYC.\n\nFindingsWe identified 16 phylogenetically-distinct Gamma clusters established in NYC (cluster sizes ranged 2-108 genomes). Most of the NYC clusters were introduced from Florida and Illinois; only one was introduced from outside the United States (US). By the time the first Gamma case was reported by genomic surveillance in NYC on March 10th, the majority (57%) of circulating Gamma lineages had already been established in the city for at least two weeks.\n\nInterpretationDespite the expansion of SARS-CoV-2 genomic surveillance in NYC, there was a substantial gap between Gamma variant introduction and establishment in January/February 2021, and its identification by genomic surveillance in March 2021. Although travel from Brazil to the US was restricted from May 2020 through the end of the study period, this restriction did not prevent Gamma from becoming established in NYC as most introductions occurred from domestic locations.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Tetyana I Vasylyeva",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Courtney E. Fang",
-        "author_inst": "New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA"
-      },
-      {
-        "author_name": "Michelle Su",
-        "author_inst": "New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA"
-      },
-      {
-        "author_name": "Jennifer L. Havens",
-        "author_inst": "Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, US"
-      },
-      {
-        "author_name": "Edyth Parker",
-        "author_inst": "Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, US"
-      },
-      {
-        "author_name": "Jade C. Wang",
-        "author_inst": "New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA"
-      },
-      {
-        "author_name": "Mark Zeller",
-        "author_inst": "Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, US"
-      },
-      {
-        "author_name": "Anna Yakovleva",
-        "author_inst": "Medical Sciences Division, University of Oxford, Oxford, UK"
-      },
-      {
-        "author_name": "Gabriel W. Hassler",
-        "author_inst": "Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, USA"
-      },
-      {
-        "author_name": "Moinuddin A. Chowdhury",
-        "author_inst": "New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA"
-      },
-      {
-        "author_name": "Kristian G. Andersen",
-        "author_inst": "Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, US"
-      },
-      {
-        "author_name": "Scott Hughes",
-        "author_inst": "New York City Public Health Laboratory, New York City Department of Health and Mental Hygiene, New York, NY, USA"
-      },
-      {
-        "author_name": "Joel O. Wertheim",
-        "author_inst": "Department of Medicine, University of California San Diego, La Jolla, CA, USA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.04.15.22273881",
     "rel_title": "Can We Really Trust the Findings of the COVID-19 Research? Quality Assessment of Randomized Controlled Trials Published on COVID-19",
@@ -317882,6 +316161,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.04.13.22273835",
+    "rel_title": "Evaluation of machine learning for predicting COVID-19 outcomes from a national electronic medical records database",
+    "rel_date": "2022-04-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.13.22273835",
+    "rel_abs": "ObjectiveWhen novel diseases such as COVID-19 emerge, predictors of clinical outcomes might be unknown. Using data from electronic medical records (EMR) allows evaluation of potential predictors without selecting specific features a priori for a model. We evaluated different machine learning models for predicting outcomes among COVID-19 inpatients using raw EMR data.\n\nMaterials and MethodsIn Premier Healthcare Data Special Release: COVID-19 Edition (PHD-SR COVID-19, release date March, 24 2021), we included patients admitted with COVID-19 during February 2020 through April 2021 and built time-ordered medical histories. Setting the prediction horizon at 24 hours into the first COVID-19 inpatient visit, we aimed to predict intensive care unit (ICU) admission, hyperinflammatory syndrome (HS), and death. We evaluated the following models: L2-penalized logistic regression, random forest, gradient boosting classifier, deep averaging network, and recurrent neural network with a long short-term memory cell.\n\nResultsThere were 57,355 COVID-19 patients identified in PHD-SR COVID-19. ICU admission was the easiest outcome to predict (best AUC=79%), and HS was the hardest to predict (best AUC=70%). Models performed similarly within each outcome.\n\nDiscussionAlthough the models learned to attend to meaningful clinical information, they performed similarly, suggesting performance limitations are inherent to the data.\n\nConclusionPredictive models using raw EMR data are promising because they can use many observations and encompass a large feature space; however, traditional and deep learning models may perform similarly when few features are available at the individual patient level.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Scott Lee",
+        "author_inst": "CDC: Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Sean Browning",
+        "author_inst": "US Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Ermias Belay",
+        "author_inst": "US Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Jennifer DeCuir",
+        "author_inst": "US Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Shana Godfred Cato",
+        "author_inst": "US Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Pragna Patel",
+        "author_inst": "US Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Noah Schwartz",
+        "author_inst": "US Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Karen Wong",
+        "author_inst": "US Centers for Disease Control and Prevention"
+      }
+    ],
+    "version": "1",
+    "license": "cc0",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.04.12.22273466",
     "rel_title": "Level and duration of IgG and neutralizing antibodies to SARS-CoV-2 in children with symptomatic or asymptomatic SARS-CoV-2 infection",
@@ -319006,101 +317332,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2022.04.12.488087",
-    "rel_title": "Broadly neutralizing and protective nanobodies against diverse sarbecoviruses",
-    "rel_date": "2022-04-13",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.12.488087",
-    "rel_abs": "As SARS-CoV-2 Omicron and other variants of concern continue spreading around the world, development of antibodies and vaccines to confer broad and protective activity is a global priority. Here, we report on the identification of a special group of nanobodies from immunized alpaca with exceptional breadth and potency against diverse sarbecoviruses including SARS-CoV-1, Omicron BA.1, and BA.2. Crystal structure analysis of one representative nanobody, 3-2A2-4, revealed a highly conserved epitope between the cryptic and the outer face of the receptor binding domain (RBD). The epitope is readily accessible regardless of RBD in \"up\" or \"down\" conformation and distinctive from the receptor ACE2 binding site. Passive delivery of 3-2A2-4 protected K18-hACE2 mice from infection of authentic SARS-CoV-2 Delta and Omicron. This group of nanobodies and the epitope identified should provide invaluable reference for the development of next generation antibody therapies and vaccines against wide varieties of SARS-CoV-2 infection and beyond.",
-    "rel_num_authors": 20,
-    "rel_authors": [
-      {
-        "author_name": "Mingxi Li",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Yifei Ren",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Zhen Qin Aw",
-        "author_inst": "National University of Singapore"
-      },
-      {
-        "author_name": "Bo Chen",
-        "author_inst": "NB BIOLAB Co. Ltd, Chengdu, China"
-      },
-      {
-        "author_name": "Ziqing Yang",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Yuqing Lei",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Qingtai Liang",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Junxian Hong",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Yiling Yang",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Jing Chen",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Yi Hao Wong",
-        "author_inst": "National University of Singapore"
-      },
-      {
-        "author_name": "Sisi Shan",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Senyan Zhang",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Jiwan Ge",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Ruoke Wang",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Xuanling Shi",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Qi Zhang",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Justin Jang Hann Chu",
-        "author_inst": "National University of Singapore"
-      },
-      {
-        "author_name": "Xinquan Wang",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Linqi Zhang",
-        "author_inst": "Tsinghua University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2022.04.12.488092",
     "rel_title": "SARS-CoV-2 Delta breakthrough infections in vaccinated patients",
@@ -319507,6 +317738,85 @@
     "type": "new results",
     "category": "pathology"
   },
+  {
+    "rel_doi": "10.1101/2022.04.12.487988",
+    "rel_title": "An ACAT inhibitor regulates SARS-CoV-2 replication and antiviral T cell activity",
+    "rel_date": "2022-04-12",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.12.487988",
+    "rel_abs": "The severity of disease following infection with SARS-CoV-2 is determined by viral replication kinetics and host immunity, with early T cell responses and/or suppression of viraemia driving a favourable outcome. Recent studies have uncovered a role for cholesterol metabolism in the SARS-CoV-2 life cycle and in T cell function. Here we show that blockade of the enzyme Acyl-CoA:cholesterol acyltransferase (ACAT) with Avasimibe inhibits SARS-CoV-2 entry and fusion independent of transmembrane protease serine 2 expression in multiple cell types. We also demonstrate a role for ACAT in regulating SARS-CoV-2 RNA replication in primary bronchial epithelial cells. Furthermore, Avasimibe boosts the expansion of functional SARS-CoV-2-specific T cells from the blood of patients sampled in the acute phase of infection. Thus, re-purposing of available ACAT inhibitors provides a compelling therapeutic strategy for the treatment of COVID-19 to achieve both antiviral and immunomodulatory effects.",
+    "rel_num_authors": 16,
+    "rel_authors": [
+      {
+        "author_name": "Nathalie M Schmidt",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Peter AC Wing",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Rory Peters",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Rachel Brown",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Hao Wang",
+        "author_inst": "Scripps Research Institute"
+      },
+      {
+        "author_name": "Leo Swadling",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Joseph Newman",
+        "author_inst": "The Pirbright Institute"
+      },
+      {
+        "author_name": "Nazia Thakur",
+        "author_inst": "The Pirbright Institute"
+      },
+      {
+        "author_name": "Kaho Shionoya",
+        "author_inst": "National Institute of Infectious Diseases, Tokyo"
+      },
+      {
+        "author_name": "Sophie B Morgan",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Timothy SC Hinks",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Koichi Watashi",
+        "author_inst": "National Institute of Infectious Diseases"
+      },
+      {
+        "author_name": "Dalan Bailey",
+        "author_inst": "The Pirbright Institute"
+      },
+      {
+        "author_name": "Scott B Hansen",
+        "author_inst": "The Scripps Research Institute"
+      },
+      {
+        "author_name": "Mala K Maini",
+        "author_inst": "UCL"
+      },
+      {
+        "author_name": "Jane A. McKeating",
+        "author_inst": "University of Oxford"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2022.04.11.487660",
     "rel_title": "A high potent synthetic nanobody with broad-spectrum activity neutralizes SARS-Cov-2 virus and Omicron variant through a unique binding mode",
@@ -320717,65 +319027,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "occupational and environmental health"
   },
-  {
-    "rel_doi": "10.1101/2022.04.08.22273571",
-    "rel_title": "Risk and severity of SARS-CoV-2 reinfections during 2020-2022 in Vojvodina, Serbia: a population-level study",
-    "rel_date": "2022-04-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.08.22273571",
-    "rel_abs": "BackgroundData on the rate and severity of SARS-CoV-2 reinfections in real-world settings are scarce and the effects of vaccine boosters on reinfection risk are unknown.\n\nMethodsIn a retrospective cohort study, registered SARS-CoV-2 laboratory-confirmed Vojvodina residents, between March 6, 2020 and October 31, 2021, were followed for reinfection [&ge;]90 days after primary infection. Data were censored at the end of follow-up (January 31, 2022) or death. The reinfection risk was visualized with Kaplan-Meier plots. To examine the protective effect of vaccination, the subset of individuals with primary infection in 2020 (March 6-December 31) were matched (1:2) with controls without reinfection.\n\nFindingsUntil January 31, 2022, 13,792 reinfections were recorded among 251,104 COVID-19 primary infections (5.49%). Most reinfections (86.8%) were recorded in January 2022. Reinfections were mostly mild (99.2%). Hospitalizations were uncommon (1.8% vs. 3.70% in primary infection) and COVID-19 deaths were very rare (n=20, case fatality rate 0.15%). The overall incidence rate of reinfections was 5.99 (95% CI 5.89-6.09) per 1,000 person-months. The reinfection risk was estimated as 0.76% at six months, 1.36% at nine months, 4.96% at 12 months, 16.7% at 15 months, and 18.9% at 18 months. Unvaccinated (OR=1.23; 95%CI=1.14-1.33), incompletely (OR=1.33; 95%CI=1.08-1.64) or completely vaccinated (OR=1.50; 95%CI=1.37-1.63), were modestly more likely to be reinfected compared with recipients of a third (booster) vaccine dose.\n\nInterpretationSARS-CoV-2 reinfections were uncommon until the end of 2021 but became common with the advent of Omicron. Very few reinfections were severe. Boosters may modestly reduce reinfection risk.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Snezana Medic",
-        "author_inst": "Institute of Public Health of Vojvodina"
-      },
-      {
-        "author_name": "Cleo Anastassopoulou",
-        "author_inst": "Medical School, National and Kapodistrian University of Athens"
-      },
-      {
-        "author_name": "Zagorka Lozanov-Crvenkovic",
-        "author_inst": "University of Novi Sad"
-      },
-      {
-        "author_name": "Vladimir Vukovic",
-        "author_inst": "Institute of Public Health of Vojvodina"
-      },
-      {
-        "author_name": "Natasa Dragnic",
-        "author_inst": "Institute of Public Health of Vojvodina"
-      },
-      {
-        "author_name": "Vladimir Petrovic",
-        "author_inst": "Institute of Public Health of Vojvodina"
-      },
-      {
-        "author_name": "Mioljub Ristic",
-        "author_inst": "Institute of Public Health of Vojvodina"
-      },
-      {
-        "author_name": "Tatjana Pustahija",
-        "author_inst": "Center for Disease Control and Prevention, Institute of Public Health of Vojvodina, Novi Sad, Serbia"
-      },
-      {
-        "author_name": "Zoran Gojkovic",
-        "author_inst": "University of Novi Sad"
-      },
-      {
-        "author_name": "Athanasios Tsakris",
-        "author_inst": "Medical School, National and Kapodistrian University of Athens"
-      },
-      {
-        "author_name": "John Ioannidis",
-        "author_inst": "Stanford University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.04.11.487924",
     "rel_title": "Independent acquisition of short insertions at the RIR1 site in the spike N-terminal domain of the SARS-CoV-2 BA.2 lineage",
@@ -320998,6 +319249,33 @@
     "type": "new results",
     "category": "molecular biology"
   },
+  {
+    "rel_doi": "10.1101/2022.04.11.487882",
+    "rel_title": "Receptor binding domain of SARS-CoV-2 is a functional \u03b1v-integrin agonist",
+    "rel_date": "2022-04-11",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.11.487882",
+    "rel_abs": "Among the novel mutations distinguishing SARS-CoV-2 from similar respiratory coronaviruses is a K403R substitution in the receptor-binding domain (RBD) of the viral spike (S) protein within its S1 region. This amino acid substitution occurs near the angiotensin-converting enzyme 2 (ACE2)-binding interface and gives rise to a canonical RGD adhesion motif that is often found in native extracellular matrix proteins, including fibronectin. In the present study, the ability of recombinant S1-RBD to bind to cell surface integrins and trigger downstream signaling pathways was assessed and compared to RGD-containing, integrin-binding fragments of fibronectin. S1-RBD supported adhesion of both fibronectin-null mouse embryonic fibroblasts as well as primary human small airway epithelial cells. Cell adhesion to S1-RBD was cation- and RGD-dependent, and was inhibited by blocking antibodies against v and {beta}3, but not 5 or {beta}1, integrins. Similarly, direct binding of S1-RBD to recombinant human v{beta}3 and v{beta}6 integrins, but not 5{beta}1 integrins, was observed by surface plasmon resonance. Adhesion to S1-RBD initiated cell spreading, focal adhesion formation, and actin stress fiber organization to a similar extent as fibronectin. Moreover, S1-RBD stimulated tyrosine phosphorylation of the adhesion mediators FAK, Src, and paxillin, Akt activation, and supported cell proliferation. Together, these data demonstrate that the RGD sequence within S1-RBD can function as an v-selective integrin agonist. This study provides evidence that cell surface v-containing integrins can respond functionally to spike protein and raise the possibility that S1-mediated dysregulation of ECM dynamics may contribute to the pathogenesis and/or post-acute sequelae of SARS-CoV-2 infection.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Emma G Norris",
+        "author_inst": "University of Rochester Medical Center"
+      },
+      {
+        "author_name": "Xuan Sabrina Pan",
+        "author_inst": "University of Rochester"
+      },
+      {
+        "author_name": "Denise C Hocking",
+        "author_inst": "University of Rochester Medical Center"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "new results",
+    "category": "cell biology"
+  },
   {
     "rel_doi": "10.1101/2022.04.09.22273420",
     "rel_title": "Characteristics and outcomes of COVID-19 patients during B.1.1.529 (Omicron) dominance compared to B.1.617.2 (Delta) in 89 German hospitals",
@@ -322395,69 +320673,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2022.04.07.487556",
-    "rel_title": "SARS-CoV-2 and its variants, but not Omicron, induces thymic atrophy and impaired T cell development",
-    "rel_date": "2022-04-08",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.07.487556",
-    "rel_abs": "Pathogenic infections cause thymic atrophy, perturb thymic-T cell development and alter immunological response. Previous studies reported dysregulated T cell function and lymphopenia in coronavirus disease-19 (COVID-19) patients. However, immune-pathological changes, in the thymus, post severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection have not been elucidated. Here, we report SARS-CoV-2 infects thymocytes, depletes CD4+CD8+ (double positive; DP) T cell population associated with an increased apoptosis of thymocytes, which leads to severe thymic atrophy in K18-hACE2-Tg mice. CD44+CD25-T cells were found to be enriched in infected thymus, indicating an early arrest in the T cell developmental pathway. Further, Interferon gamma (IFN-{gamma}) was crucial for thymic atrophy, as anti-IFN-{gamma} antibody neutralization rescued the loss of thymic involution. Therapeutic use of remdesivir (prototype anti-viral drug) was also able to rescue thymic atrophy. While Omicron variant of SARS-CoV2 caused marginal thymic atrophy, delta variant of SARS-CoV-2 exhibited most profound thymic atrophy characterized by severely depleted DP T cells. Recently characterized broadly SARS-CoV-2 neutralizing monoclonal antibody P4A2 was able to rescue thymic atrophy and restore thymic developmental pathway of T cells. Together, we provide the first report of SARS-CoV-2 associated thymic atrophy resulting from impaired T cell developmental pathway and also explains dysregulated T cell function in COVID-19.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Zaigham Abbas Rizvi",
-        "author_inst": "Translational Health Science and Technology Institute"
-      },
-      {
-        "author_name": "Srikanth Sadhu",
-        "author_inst": "Translational Health Science and Technology Institute"
-      },
-      {
-        "author_name": "Jyotsna Dandotiya",
-        "author_inst": "Translational Health Science and Technology Institute"
-      },
-      {
-        "author_name": "Akshay Binayke",
-        "author_inst": "Translational Health Science and Technology Institute"
-      },
-      {
-        "author_name": "Puja Sharma",
-        "author_inst": "Regional Centre Biotechnology"
-      },
-      {
-        "author_name": "Virendra Singh",
-        "author_inst": "Translational Health Science and Technology Institute"
-      },
-      {
-        "author_name": "Vinayaka Das",
-        "author_inst": "Translational Health Science and Technology Institute"
-      },
-      {
-        "author_name": "Ritika Khatri",
-        "author_inst": "Translational Health Science and Technology Institute"
-      },
-      {
-        "author_name": "Rajesh Kumar",
-        "author_inst": "Translational Health Science and Technology Institute"
-      },
-      {
-        "author_name": "Sweety Samal",
-        "author_inst": "Translational Health Science and Technology Institute"
-      },
-      {
-        "author_name": "Manjula Kalia",
-        "author_inst": "Regional Centre for Biotechnology"
-      },
-      {
-        "author_name": "Amit Awasthi",
-        "author_inst": "Translational Health Science and Technology Institute"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2022.04.08.487674",
     "rel_title": "NVX-CoV2373 vaccination induces functional SARS-CoV-2-specific CD4+ and CD8+ T cell responses",
@@ -322864,6 +321079,85 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2022.04.07.487489",
+    "rel_title": "Antibody Resistance of SARS-CoV-2 Omicron BA.1, BA.1.1, BA.2 and BA.3 Sub-lineages",
+    "rel_date": "2022-04-07",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.07.487489",
+    "rel_abs": "The SARS-CoV-2 Omicron variant has been partitioned into four sub-lineages designated BA.1, BA.1.1, BA.2 and BA.3, with BA.2 becoming dominant worldwide recently by outcompeting BA.1 and BA.1.1. We and others have reported the striking antibody evasion of BA.1 and BA.2, but side-by-side comparison of susceptibility of all the major Omicron sub-lineages to vaccine-elicited or monoclonal antibody (mAb)-mediated neutralization are urgently needed. Using VSV-based pseudovirus, we found that sera from individuals vaccinated by two doses of inactivated whole-virion vaccines (BBIBP-CorV) showed very weak to no neutralization activity, while a homologous inactivated vaccine booster or a heterologous booster with protein subunit vaccine (ZF2001) markedly improved the neutralization titers against all Omicron variants. The comparison between sub-lineages indicated that BA.1.1, BA.2 and BA.3 had comparable or even greater antibody resistance than BA.1. We further evaluated the neutralization profile of a panel of 20 mAbs, including 10 already authorized or approved, against these Omicron sub-lineages as well as viruses with different Omicron spike single or combined mutations. Most mAbs lost their neutralizing activity completely or substantially, while some demonstrated distinct neutralization patterns among Omicron sub-lineages, reflecting their antigenic difference. Taken together, our results suggest all four Omicron sub-lineages threaten the efficacies of current vaccines and antibody therapeutics, highlighting the importance of vaccine boosters to combat the emerging SARS-CoV-2 variants.",
+    "rel_num_authors": 16,
+    "rel_authors": [
+      {
+        "author_name": "Jingwen Ai",
+        "author_inst": "Fudan University"
+      },
+      {
+        "author_name": "Xun Wang",
+        "author_inst": "Fudan University"
+      },
+      {
+        "author_name": "Xinyi He",
+        "author_inst": "Fudan University"
+      },
+      {
+        "author_name": "Xiaoyu Zhao",
+        "author_inst": "Fudan University"
+      },
+      {
+        "author_name": "Yi Zhang",
+        "author_inst": "Fudan University"
+      },
+      {
+        "author_name": "Yuchao Jiang",
+        "author_inst": "Pigentech Lab Limited"
+      },
+      {
+        "author_name": "Minghui Li",
+        "author_inst": "Fudan University"
+      },
+      {
+        "author_name": "Yuchen Cui",
+        "author_inst": "Fudan University"
+      },
+      {
+        "author_name": "Yanjia Chen",
+        "author_inst": "Fudan University"
+      },
+      {
+        "author_name": "Rui Qiao",
+        "author_inst": "Fudan University"
+      },
+      {
+        "author_name": "Lin Li",
+        "author_inst": "Fudan University"
+      },
+      {
+        "author_name": "Lulu Yang",
+        "author_inst": "Fudan University"
+      },
+      {
+        "author_name": "Yi Li",
+        "author_inst": "Fudan University"
+      },
+      {
+        "author_name": "Zixin Hu",
+        "author_inst": "Fudan University"
+      },
+      {
+        "author_name": "Wenhong Zhang",
+        "author_inst": "Huashan Hospital, Fudan University"
+      },
+      {
+        "author_name": "Pengfei Wang",
+        "author_inst": "Fudan University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2022.04.07.487460",
     "rel_title": "Distinct evolutionary trajectories of SARS-CoV-2 interacting proteins in bats and primates identify important host determinants of COVID-19",
@@ -324325,41 +322619,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "genetic and genomic medicine"
   },
-  {
-    "rel_doi": "10.1101/2022.04.06.22273503",
-    "rel_title": "High incidence of sotrovimab resistance and viral persistence after treatment of immunocompromised patients infected with the SARS-CoV-2 Omicron variant",
-    "rel_date": "2022-04-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.06.22273503",
-    "rel_abs": "BackgroundSotrovimab is a monoclonal antibody that neutralizes SARS-CoV-2 by binding to a highly conserved epitope in the receptor binding domain. It retains activity against the Omicron BA.1 variant and is used to treat immunocompromised patients as they are at increased risk for a severe outcome of COVID-19.\n\nMethodsWe studied viral evolution in 47 immunocompromised patients infected with Omicron BA.1 or 2 and treated with sotrovimab. SARS-CoV-2 PCR was performed at baseline and weekly thereafter until Ct-value was [&ge;] 30. All RNA samples were sequenced to determine the variant and occurrence of mutations, in particular in the Spike protein, after treatment.\n\nResultsTwenty-four (51%) of the 47 patients were male and their median age was 63 years. Thirty-one (66%) had undergone a solid organ transplantation and 13 (28%) had received prior B-cell depleting therapy. Despite a history of vaccination, 24 of 30 patients with available data on anti-SARS-CoV-2 IgG Spike antibodies prior to treatment with sotrovimab had very low or no antibodies. Median time to viral clearance (Ct-value [&ge;] 30) after treatment was 15 days (IQR 7-22). However, viral RNA with low Ct-values was continuously detected for at least 28 days after treatment in four patients infected with BA.1. Mutations in the Spike protein at position 337 or 340 were observed in all four patients. Similar mutations were also found after treatment of two patients with a BA.2 infection but both cleared the virus within two weeks. Thus following treatment with sotrovimab, spike mutations associated with reduced in vitro susceptibility were detected in 6 of 47 (13%) patients.\n\nConclusionViral evolution towards resistance against sotrovimab can explain treatment failure in most immunocompromised patients and these patients can remain infectious after treatment. Therefore, documenting viral clearance after treatment is recommended to avoid that these patients unintentionally become a source of new, sotrovimab resistant, variants. Research on direct acting antivirals and possibly combination therapy for the treatment of COVID-19 in immunocompromised patients is needed.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Sammy Huygens",
-        "author_inst": "Erasmus Medical Center"
-      },
-      {
-        "author_name": "Bas Oude Munnink",
-        "author_inst": "Erasmus Medical Center"
-      },
-      {
-        "author_name": "Arvind Gharbharan",
-        "author_inst": "Erasmus Medical Center"
-      },
-      {
-        "author_name": "Marion Koopmans",
-        "author_inst": "Erasmus Medical Center"
-      },
-      {
-        "author_name": "Bart Rijnders",
-        "author_inst": "Erasmus Medical Center"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.04.03.22273345",
     "rel_title": "Racial/Ethnic, Biomedical, and Sociodemographic Risk Factors for COVID-19 Positivity and Hospitalization in the San Francisco Bay Area",
@@ -324642,6 +322901,45 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2022.04.06.487306",
+    "rel_title": "An Ultralong Bovine CDRH3 that Targets a Conserved, Cryptic Epitope on SARS-CoV and SARS-CoV-2",
+    "rel_date": "2022-04-06",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.06.487306",
+    "rel_abs": "The ability of broadly neutralising antibodies to target conserved epitopes gives them huge potential as antibody-based therapeutics, particularly in the face of constant viral antigen evolution. Certain bovine antibodies are highly adept at binding conserved, glycosylated epitopes, courtesy of their ultralong complementarity determining region (CDR)H3. Here, we used a SARS-naive, bovine ultralong CDRH3 library and mammalian cell display, to isolate a bovine paratope that engages the SARS-CoV and SARS-CoV-2 receptor-binding domain (RBD). This neutralises viruses pseudo-typed with SARS-CoV Spike protein but not by competition with RBD binding to ACE2. Instead, using differential hydrogen-deuterium exchange mass spectrometry and site-directed mutagenesis, we demonstrate that this ultralong CDRH3 recognises a rarely identified, conserved, cryptic epitope that overlaps the target of pan-sarbecovirus antibodies (7D6/6D6). The epitope is glycan-shielded and becomes accessible only transiently via inter-domain movements. This represents the first bovine anti-sarbecovirus paratope and highlights the power of this approach in identifying novel tools to combat emerging pathogens.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Matthew J Burke",
+        "author_inst": "University of Leeds"
+      },
+      {
+        "author_name": "James NF Scott",
+        "author_inst": "University of Leeds"
+      },
+      {
+        "author_name": "Thomas Minshull",
+        "author_inst": "University of Leeds"
+      },
+      {
+        "author_name": "Peter G Stockley",
+        "author_inst": "University of Leeds"
+      },
+      {
+        "author_name": "Antonio N Calabrese",
+        "author_inst": "University of Leeds"
+      },
+      {
+        "author_name": "Joan Boyes",
+        "author_inst": "University of Leeds"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "molecular biology"
+  },
   {
     "rel_doi": "10.1101/2022.04.03.22273360",
     "rel_title": "Real-World Evidence of the Neutralizing Monoclonal Antibody Sotrovimab for Preventing Hospitalization and Mortality in COVID-19 Outpatients",
@@ -325987,65 +324285,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2022.04.04.22273427",
-    "rel_title": "Sustained patient use and improved outcomes with digital transformation of a COPD service: RECEIVER trial and DYNAMIC-SCOT COVID-19 scale-up response.",
-    "rel_date": "2022-04-05",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.04.22273427",
-    "rel_abs": "IntroductionLenusCOPD has been co-designed to enable digital transformation of COPD services for proactive preventative care. Patient-facing progressive web application, clinician dashboard and support website integrate patient-reported outcomes (PROs), self-management resources, structured clinical summary, wearable and home NIV data with asynchronous patient-clinician messaging. We commenced the implementation-effectiveness observational cohort RECEIVER trial in September 2019, with the primary endpoint of sustained patient usage and secondary endpoints including admissions, mortality, exacerbations, service workload and quality of life. We paused recruitment in March 2021 and provided LenusCOPD as routine care in the \"DYNAMIC-SCOT\" COVID-19 response service scale-up.\n\nMethods83 RECEIVER trial participants and 142 DYNAMIC-SCOT participants had completed minimum 1 year follow-up when we censored data on 31st August 2021. We established a control cohort with 5 patients matched per RECEIVER participant from de-identified contemporary routine clinical data.\n\nResultsSustained patient app utilisation was noted in both cohorts. Median time to admission or death was 43 days in control, 338 days in RECEIVER and 400 days in DYNAMIC-SCOT participants who had had a respiratory-related admission in the preceding year. The 12-month risk of admission or death was 74% in control patients, 53% in RECEIVER and 47% in the DYNAMIC-SCOT sub-cohort participants. There was a median of 2.5 COPD exacerbations per patient per year with stable quality of life across follow up and a manageable workload for clinical users.\n\nConclusionsA high proportion of people continued to use the co-designed LenusCOPD application during extended follow-up. Outcome data supports scale-up of this digital service transformation.\n\nKey messages\n\nWhat is the key question?Can sustained patient interaction and improved patient outcomes be achieved with digital transformation of a COPD service?\n\nWhat is the bottom line?Participants continue to use the LenusCOPD patient app, with an average of 3-3.5 interactions per person per week sustained >1-year post-onboarding. COPD- related hospital admissions and occupied bed days were reduced following LenusCOPD onboarding in participants with a history of a severe exacerbation in the previous year, with a median time to readmission of 380 days compared with 50 days in a contemporary matched control patient cohort.\n\nWhy read on?Feasibility and utility results support scale-up adoption of these digital tools, to support optimised co-management of COPD and other long-term conditions within a continuous implementation-evaluation framework. This will establish a test-bed infrastructure for additional innovations including artificial intelligence-insights for MDT decision support.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Anna Taylor",
-        "author_inst": "Queen Elizabeth University Hospital, Glasgow"
-      },
-      {
-        "author_name": "Andrew Cushing",
-        "author_inst": "LenusHealth, Edinburgh"
-      },
-      {
-        "author_name": "Morgan Dow",
-        "author_inst": "LenusHealth, Edinburgh"
-      },
-      {
-        "author_name": "Jacqueline Anderson",
-        "author_inst": "Queen Elizabeth University Hospital, Glasgow"
-      },
-      {
-        "author_name": "Grace McDowell",
-        "author_inst": "Queen Elizabeth University Hospital, Glasgow"
-      },
-      {
-        "author_name": "Maureen Manthe",
-        "author_inst": "Queen Elizabeth University Hospital, Glasgow"
-      },
-      {
-        "author_name": "Sandosh Padmanabhan",
-        "author_inst": "Institute of Cardiovascular and Medical Sciences, University of Glasgow"
-      },
-      {
-        "author_name": "Shane Burns",
-        "author_inst": "LenusHealth, Edinburgh"
-      },
-      {
-        "author_name": "Paul McGineess",
-        "author_inst": "LenusHealth, Edinburgh"
-      },
-      {
-        "author_name": "David J Lowe",
-        "author_inst": "Queen Elizabeth University Hospital, Glasgow"
-      },
-      {
-        "author_name": "Christopher M Carlin",
-        "author_inst": "Queen Elizabeth University Hospital, Glasgow"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "respiratory medicine"
-  },
   {
     "rel_doi": "10.1101/2022.03.29.22272960",
     "rel_title": "Nonutility of procalcitonin for diagnosing bacterial pneumonia in COVID-19",
@@ -326408,6 +324647,89 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.04.03.22272610",
+    "rel_title": "Cardiac impairment in Long Covid 1-year post-SARS-CoV-2 infection",
+    "rel_date": "2022-04-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.03.22272610",
+    "rel_abs": "BackgroundLong Covid is associated with multiple symptoms and impairment in multiple organs. Cardiac impairment has been reported to varying degrees by varying methodologies in cross-sectional studies. Using cardiac magnetic resonance (CMR), we investigated the 12-month trajectory of cardiac impairment in individuals with Long Covid.\n\nMethods534 individuals with Long Covid underwent baseline CMR (T1 and T2 mapping, cardiac mass, volumes, function, and strain) and multi-organ MRI at 6 months (IQR 4.3,7.3) since first post-COVID-19 symptoms and 330 were rescanned at 12.6 (IQR 11.4, 14.2) months if abnormal findings were reported at baseline. Symptoms, standardised questionnaires, and blood samples were collected at both timepoints. Cardiac impairment was defined as one or more of: low left or right ventricular ejection fraction (LVEF and RVEF), high left or right ventricular end diastolic volume (LVEDV and RVEDV), low 3D left ventricular global longitudinal strain (GLS), or elevated native T1 in [&ge;]3 cardiac segments. A significant change over time was reported by comparison with 92 healthy controls.\n\nResultsThe technical success of this multiorgan assessment in non-acute settings was 99.1% at baseline, and 98.3% at follow up, with 99.6% and 98.8% for CMR respectively. Of individuals with Long Covid, 102/534 [19%] had cardiac impairment at baseline; 71/102 had complete paired data at 12 months. Of those, 58% presented with ongoing cardiac impairment at 12 months. High sensitivity cardiac troponin I and B-type natriuretic peptide were not predictive of CMR findings, symptoms, or clinical outcomes. At baseline, low LVEF, high RVEDV and low GLS were associated with cardiac impairment. Low LVEF at baseline was associated with persistent cardiac impairment at 12 months.\n\nConclusionCardiac impairment, other than myocarditis, is present in 1 in 5 individuals with Long Covid at 6 months, persisting in over half of those at 12 months. Cardiac-related blood biomarkers are unable to identify cardiac impairment in Long COVID. Subtypes of disease (based on symptoms, examination, and investigations) and predictive biomarkers are yet to be established. Interventional trials with pre-specified subgroup analyses are required to inform therapeutic options.",
+    "rel_num_authors": 17,
+    "rel_authors": [
+      {
+        "author_name": "Adriana Roca-Fernandez",
+        "author_inst": "Perspectum Diagnostics"
+      },
+      {
+        "author_name": "Malgorzata Wamil",
+        "author_inst": "Great Western Hospital Foundation NHS Trust, Swindon, UK"
+      },
+      {
+        "author_name": "Alison Telford",
+        "author_inst": "Perspectum Ltd"
+      },
+      {
+        "author_name": "Valentina Carapella",
+        "author_inst": "Perspectum Ltd"
+      },
+      {
+        "author_name": "Alessandra Borlotti",
+        "author_inst": "Perspectum Ltd"
+      },
+      {
+        "author_name": "David Monteiro",
+        "author_inst": "Perspectum Ltd"
+      },
+      {
+        "author_name": "Helena Thomaides-Brears",
+        "author_inst": "Perspectum Ltd"
+      },
+      {
+        "author_name": "Matthew D Kelly",
+        "author_inst": "Perspectum Ltd"
+      },
+      {
+        "author_name": "Andrea Dennis",
+        "author_inst": "Perspectum Ltd"
+      },
+      {
+        "author_name": "Rajarshi Banerjee",
+        "author_inst": "Perspectum Ltd"
+      },
+      {
+        "author_name": "Matthew Robson",
+        "author_inst": "Perspectum Ltd"
+      },
+      {
+        "author_name": "Michael Brady",
+        "author_inst": "Perspectum Ltd"
+      },
+      {
+        "author_name": "Gregory Lip",
+        "author_inst": "University of Liverpool"
+      },
+      {
+        "author_name": "Sacha Bull",
+        "author_inst": "Royal Berkshire Hospital, Reading"
+      },
+      {
+        "author_name": "Melissa J Heightman",
+        "author_inst": "UCLH"
+      },
+      {
+        "author_name": "Ntobeko Ntusi",
+        "author_inst": "University of Cape Town, Cape Town, South Africa"
+      },
+      {
+        "author_name": "Amitava Banerjee",
+        "author_inst": "University College London"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "cardiovascular medicine"
+  },
   {
     "rel_doi": "10.1101/2022.04.04.22272731",
     "rel_title": "Estimating the number of breakthrough COVID-19 deaths in the United States",
@@ -328005,29 +326327,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.04.03.22273353",
-    "rel_title": "Does Metformin Decrease Mortality in Patients with Type 2 Diabetes Mellitus Hospitalized for COVID-19? A Multivariable and Propensity Score-adjusted Meta-analysis",
-    "rel_date": "2022-04-03",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.03.22273353",
-    "rel_abs": "AimsCoronavirus disease 2019 (COVID-19) is a new pandemic that the entire world is facing since December of 2019. Increasing evidence has shown that metformin is linked to favorable outcomes in patients with COVID-19. The aim of this study was to address whether outpatient or inpatient metformin therapy offers low in-hospital mortality in patients with type 2 diabetes mellitus hospitalized for COVID-19.\n\nMethodsWe searched studies published in PubMed, Embase, Google Scholar and Cochrane Library up to October 1, 2021. Raw event data extracted from individual study were pooled using the Mantel-Haenszel approach. Odds ratio (OR) or hazard ratio (HR) adjusted for covariates that potentially confound the association using multivariable regression or propensity score matching was pooled by the inverse-variance method. Random effect models were applied for meta-analysis due to variation among studies.\n\nResultsNineteen retrospective observational studies were selected. The pooled unadjusted OR for outpatient metformin therapy and in-hospital mortality was 0.54 (95% CI, 0.42-0.68), whereas the pooled OR adjusted with multivariable regression or propensity score matching was 0.72 (95% CI, 0.47-1.12). The pooled unadjusted OR for inpatient metformin therapy and in-hospital mortality was 0.19 (95% CI, 0.10-0.36), whereas the pooled adjusted HR was 1.10 (95% CI, 0.38-3.15).\n\nConclusionsOur results suggest that there is a significant reduction of in-hospital mortality with metformin therapy in patients with type 2 diabetes mellitus hospitalized for COVID-19 in the unadjusted analysis, but this mortality benefit does not retain after adjustments for confounding bias.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Zhiyuan Ma",
-        "author_inst": "St Luke's University Health Network-Easton campus"
-      },
-      {
-        "author_name": "Mahesh Krishnamurthy",
-        "author_inst": "St Luke's University Health Network-Easton campus"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "endocrinology"
-  },
   {
     "rel_doi": "10.1101/2022.04.02.22273341",
     "rel_title": "Variation in National COVID-19 Mortality Rates Across Asian Subgroups in the United States, 2020",
@@ -328362,6 +326661,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.03.27.22271628",
+    "rel_title": "Spatial prediction of COVID-19 pandemic dynamics in the United States",
+    "rel_date": "2022-04-02",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.27.22271628",
+    "rel_abs": "BackgroundThe impact of COVID-19 across the United States has been heterogeneous, with some areas demonstrating more rapid spread and greater mortality than others. We used geographically-linked data to test the hypothesis that the risk for COVID-19 is spatially defined and sought to define which features are most closely associated with elevated COVID-19 spread and mortality.\n\nMethodsLeveraging geographically-restricted social, economic, political, and demographic information from U.S. counties, we developed a computational framework using structured Gaussian processing to predict county-level case and death counts during both the initial and the nationwide phases of the pandemic. After identifying the most predictive spatial features, we applied an unsupervised clustering algorithm, topic modelling, to identify groups of features that are most closely associated with COVID-19 spread.\n\nFindingsWe found that the inclusion of spatial features modeled case counts very well, with overall Pearsons correlation coefficient (PCC) and R2of 0.96 and 0.84 during the initial phase and 0.95 and 0.87, respectively, during the nationwide phase. The most frequently selected features were associated with urbanicity and 2020 presidential vote margins. When trained using death counts, models revealed similar performance metrics, with the addition of aging metrics to those most frequently selected. Topic modeling showed that counties with similar socioeconomic and demographic features tended to group together, and some feature sets were associated with COVID-19 dynamics. Unsupervised clustering of counties based on these topics revealed groups of counties that experienced markedly different COVID-19 spread.\n\nInterpretationSpatial features explained most of the variability in COVID-19 dynamics between counties. Topic modeling can be used to group collinear features and identify counties with similar features in epidemiologic research.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Cigdem Ak",
+        "author_inst": "Oregon Health & Science University"
+      },
+      {
+        "author_name": "Alex D Chitsazan",
+        "author_inst": "Oregon Health & Science University"
+      },
+      {
+        "author_name": "Mehmet Gonen",
+        "author_inst": "Koc University"
+      },
+      {
+        "author_name": "Ruth Etzioni",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      },
+      {
+        "author_name": "Aaron Grossberg",
+        "author_inst": "Oregon Health and Science University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health informatics"
+  },
   {
     "rel_doi": "10.1101/2022.03.28.22273020",
     "rel_title": "Detection of a BA.1/BA.2 recombinant in travelers arriving in Hong Kong, February 2022",
@@ -329723,89 +328057,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.03.30.22273193",
-    "rel_title": "Effectiveness of an Inactivated Covid-19 Vaccine with Homologous and Heterologous Boosters against the Omicron (B.1.1.529) Variant",
-    "rel_date": "2022-04-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.30.22273193",
-    "rel_abs": "The effectiveness of inactivated vaccines (VE) against symptomatic and severe COVID-19 caused by omicron is unknown. We conducted a nationwide, test-negative, case-control study to estimate VE for homologous and heterologous (BNT162b2) booster doses in adults who received two doses of CoronaVac in Brazil in the Omicron context. Analyzing 1,386,544 matched-pairs, VE against symptomatic disease was 8.6% (95% CI, 5.6-11.5) and 56.8% (95% CI, 56.3-57.3) in the period 8-59 days after receiving a homologous and heterologous booster, respectively. During the same interval, VE against severe Covid-19 was 73.6% (95% CI, 63.9-80.7) and 86.0% (95% CI, 84.5-87.4) after receiving a homologous and heterologous booster, respectively. Waning against severe Covid-19 after 120 days was only observed after a homologous booster. Heterologous booster might be preferable to individuals with completed primary series inactivated vaccine.",
-    "rel_num_authors": 17,
-    "rel_authors": [
-      {
-        "author_name": "Otavio T. Ranzani",
-        "author_inst": "Barcelona Institute for Global Health, ISGlobal, UPF, CIBERESP, Spain / Pulmonary Division, University of Sao Paulo"
-      },
-      {
-        "author_name": "Matt Hitchings",
-        "author_inst": "Department of Biostatistics, College of Public Health & Health Professions, University of Florida, Gainesville, FL, USA"
-      },
-      {
-        "author_name": "Rosana Leite de Melo",
-        "author_inst": "Secretaria Extraordinaria de Enfrentamento a Covid-19, Ministerio da Saude, Brasilia, DF, Brazil"
-      },
-      {
-        "author_name": "Giovanny V. A. de Fran\u00e7a",
-        "author_inst": "Secretaria de Vigilancia em Saude, Ministerio da Saude, Brasilia, DF, Brazil"
-      },
-      {
-        "author_name": "C\u00e1ssia de F\u00e1tima R. Fernandes",
-        "author_inst": "Secretaria de Vigilancia em Saude, Ministerio da Saude, Brasilia, DF, Brasil"
-      },
-      {
-        "author_name": "Margaret Lind",
-        "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA"
-      },
-      {
-        "author_name": "Mario Sergio Scaramuzzini Torres",
-        "author_inst": "Municipal Health Secretary of Manaus, AM, Brazil"
-      },
-      {
-        "author_name": "Daniel Henrique Tsuha",
-        "author_inst": "Fiocruz Mato Grosso do Sul, Fundacao Oswaldo Cruz, Campo Grande, MS, Brazil"
-      },
-      {
-        "author_name": "Leticia C. S. David",
-        "author_inst": "Pan American Health Organization, Brasilia, DF, Brazil"
-      },
-      {
-        "author_name": "Rodrigo F. C. Said",
-        "author_inst": "Pan American Health Organization, Brasilia, DF, Brazil"
-      },
-      {
-        "author_name": "Maria Almiron",
-        "author_inst": "Pan American Health Organization, Brasilia, DF, Brazil"
-      },
-      {
-        "author_name": "Roberto D. de Oliveira",
-        "author_inst": "Fiocruz Mato Grosso do Sul, Fundacao Oswaldo Cruz, Campo Grande, MS, Brazil / State University of Mato Grosso do Sul, Dourados, MS, Brazil"
-      },
-      {
-        "author_name": "Derek A.T. Cummings",
-        "author_inst": "Department of Biology, University of Florida, Gainesville, FL, USA / Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA"
-      },
-      {
-        "author_name": "Natalie E. Dean",
-        "author_inst": "Department of Biostatistics & Bioinformatics, Rollins School of Public Health, Emory University"
-      },
-      {
-        "author_name": "Jason R. Andrews",
-        "author_inst": "Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA"
-      },
-      {
-        "author_name": "Albert I. Ko",
-        "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA / Instituto Goncalo Moniz, Fundacao Oswaldo Cruz, Salvador, B"
-      },
-      {
-        "author_name": "Julio Croda",
-        "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA / Fiocruz Mato Grosso do Sul, Fundacao Oswaldo Cruz, Campo Gr"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.04.01.22273305",
     "rel_title": "Long-term psychological consequences of long Covid: a propensity score matching analysis comparing trajectories of depression and anxiety symptoms before and after contracting long Covid vs short Covid",
@@ -330224,6 +328475,53 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2022.03.30.486345",
+    "rel_title": "Ancestral origins are associated with SARS-CoV-2 susceptibility and protection in a Florida patient population",
+    "rel_date": "2022-03-31",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.30.486345",
+    "rel_abs": "COVID-19 is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The severity of COVID-19 is highly variable and related to known (e.g., age, obesity, immune deficiency) and unknown risk factors. The widespread clinical symptoms encompass a large group of asymptomatic COVID-19 patients, raising a crucial question regarding genetic susceptibility, e.g., whether individual differences in immunity play a role in patient symptomatology and how much human leukocyte antigen (HLA) contributes to this. To reveal genetic determinants of susceptibility to COVID-19 severity in the population and further explore potential immune-related factors, we performed a genome-wide association study on 284 confirmed COVID-19 patients (cases) and 95 healthy individuals (controls). We compared cases and controls of European (EUR) ancestry and African American (AFR) ancestry separately. We identified two loci on chromosomes 5q32 and 11p12, which reach the significance threshold of suggestive association (p<1x10-5 threshold adjusted for multiple trait testing) and are associated with the COVID-19 susceptibility in the European ancestry (index rs17448496: odds ratio [OR] = 0.173; 95% confidence interval [CI], 0.08-0.36 for G allele; p=5.15x 10-5 and index rs768632395: OR = 0.166; 95% CI, 0.07-0.35 for A allele; p= 4.25x10-6, respectively), which were associated with two genes, PPP2R2B at 5q32, and LRRC4C at 11p12, respectively. To explore the linkage between HLA and COVID-19 severity, we applied fine-mapping analysis to dissect the HLA association with mild and severe cases. Using In-silico binding predictions to map the binding of risk/protective HLA to the viral structural proteins, we found the differential presentation of viral peptides in both ancestries. Lastly, extrapolation of the identified HLA from the cohort to the worldwide population revealed notable correlations. The study uncovers possible differences in susceptibility to COVID-19 in different ancestral origins in the genetic background, which may provide new insights into the pathogenesis and clinical treatment of the disease.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Yiran Shen",
+        "author_inst": "University of Florida College of Veterinary Medicine"
+      },
+      {
+        "author_name": "Bhuwan Khatri",
+        "author_inst": "Oklahoma Medical Research Foundation"
+      },
+      {
+        "author_name": "Santosh Rananaware",
+        "author_inst": "University of Florida College of Engineering: University of Florida Herbert Wertheim College of Engineering"
+      },
+      {
+        "author_name": "Danmeng Li",
+        "author_inst": "University of Florida College of Veterinary Medicine"
+      },
+      {
+        "author_name": "David Ostrov",
+        "author_inst": "University of Florida College of Medicine"
+      },
+      {
+        "author_name": "Piyush Jain",
+        "author_inst": "University of Florida College of Medicine"
+      },
+      {
+        "author_name": "Christopher Lessard",
+        "author_inst": "Oklahoma Medical Research Foundation"
+      },
+      {
+        "author_name": "Cuong Nguyen",
+        "author_inst": "University of Florida"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "new results",
+    "category": "genetics"
+  },
   {
     "rel_doi": "10.1101/2022.03.30.486418",
     "rel_title": "Contributions of the N-terminal intrinsically disordered region of the SARS-CoV-2 nucleocapsid protein to RNA-induced phase separation",
@@ -331861,145 +330159,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2022.03.30.486377",
-    "rel_title": "ACE2 engagement exposes the fusion peptide to pan-coronavirus neutralizing antibodies",
-    "rel_date": "2022-03-30",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.30.486377",
-    "rel_abs": "Coronaviruses use diverse Spike (S) glycoproteins to attach to host receptors and fuse with target cells. Using a broad screening approach, we isolated from SARS-CoV-2 immune donors seven monoclonal antibodies (mAbs) that bind to all human alpha and beta coronavirus S proteins. These mAbs recognize the fusion peptide and acquire high affinity and breadth through somatic mutations. Despite targeting a conserved motif, only some mAbs show broad neutralizing activity in vitro against alpha and beta coronaviruses, including Omicron BA.1 variant and bat WIV-1, and reduce viral titers and pathology in vivo. Structural and functional analyses show that the fusion peptide-specific mAbs bind with different modalities to a cryptic epitope which is concealed by prefusion-stabilizing  2P mutations and becomes exposed upon binding of ACE2 or ACE2-mimicking mAbs. This study identifies a new class of pan-coronavirus neutralizing mAbs and reveals a receptor-induced conformational change in the S protein that exposes the fusion peptide region.",
-    "rel_num_authors": 31,
-    "rel_authors": [
-      {
-        "author_name": "Jun Siong Low",
-        "author_inst": "Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland"
-      },
-      {
-        "author_name": "Josipa Jerak",
-        "author_inst": "Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland"
-      },
-      {
-        "author_name": "M. Alejandra Tortorici",
-        "author_inst": "Department of Biochemistry, University of Washington, Seattle WA, 98195, USA"
-      },
-      {
-        "author_name": "Matthew McCallum",
-        "author_inst": "Department of Biochemistry, University of Washington, Seattle WA, 98195, USA"
-      },
-      {
-        "author_name": "Dora Pinto",
-        "author_inst": "Humabs BioMed SA, subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland"
-      },
-      {
-        "author_name": "Antonino Cassotta",
-        "author_inst": "Institute for Research in Biomedicine, Universita della Svizzera italiana, 6500 Bellinzona, Switzerland"
-      },
-      {
-        "author_name": "Mathilde Foglierini",
-        "author_inst": "Institute for Research in Biomedicine, Universita della Svizzera italiana, 6500 Bellinzona, Switzerland"
-      },
-      {
-        "author_name": "Federico Mele",
-        "author_inst": "Institute for Research in Biomedicine, Universita della Svizzera italiana, 6500 Bellinzona, Switzerland"
-      },
-      {
-        "author_name": "Rana Abdelnabi",
-        "author_inst": "KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuve"
-      },
-      {
-        "author_name": "Birgit Weynand",
-        "author_inst": "KU Leuven Department of Imaging and Pathology, Translational Cell and Tissue Research, B-18 3000"
-      },
-      {
-        "author_name": "Julia Noack",
-        "author_inst": "Humabs BioMed SA, subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland"
-      },
-      {
-        "author_name": "Martin Montiel-Ruiz",
-        "author_inst": "Humabs BioMed SA, subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland"
-      },
-      {
-        "author_name": "Siro Bianchi",
-        "author_inst": "Humabs BioMed SA, subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland"
-      },
-      {
-        "author_name": "Fabio Benigni",
-        "author_inst": "Humabs BioMed SA, subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland"
-      },
-      {
-        "author_name": "Nicole Sprugasci",
-        "author_inst": "Humabs BioMed SA, subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland"
-      },
-      {
-        "author_name": "Anshu Joshi",
-        "author_inst": "Department of Biochemistry, University of Washington, Seattle WA, 98195, USA"
-      },
-      {
-        "author_name": "John E Bowen",
-        "author_inst": "Department of Biochemistry, University of Washington, Seattle WA, 98195, USA"
-      },
-      {
-        "author_name": "Alexandra C. Walls",
-        "author_inst": "Department of Biochemistry, University of Washington, Seattle WA, 98195, USA"
-      },
-      {
-        "author_name": "David Jarrossay",
-        "author_inst": "Institute for Research in Biomedicine, Universita della Svizzera italiana, 6500 Bellinzona, Switzerland"
-      },
-      {
-        "author_name": "Diego Morone",
-        "author_inst": "Institute for Research in Biomedicine, Universita della Svizzera italiana, 6500 Bellinzona, Switzerland"
-      },
-      {
-        "author_name": "Philipp Paparoditis",
-        "author_inst": "Institute for Research in Biomedicine, Universita della Svizzera italiana, 6500 Bellinzona, Switzerland"
-      },
-      {
-        "author_name": "Christian Garzoni",
-        "author_inst": "Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, 6900 Lugano, 22 Switzerland"
-      },
-      {
-        "author_name": "Paolo Ferrari",
-        "author_inst": "Faculty of Biomedical Sciences, Universita della Svizzera italiana, 6900 Lugano, Switzerland"
-      },
-      {
-        "author_name": "Alessandro Ceschi",
-        "author_inst": "Faculty of Biomedical Sciences, Universita della Svizzera italiana, 6900 Lugano, Switzerland"
-      },
-      {
-        "author_name": "Johan Neyts",
-        "author_inst": "KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuve"
-      },
-      {
-        "author_name": "Lisa A. Purcell",
-        "author_inst": "Humabs BioMed SA, subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland"
-      },
-      {
-        "author_name": "Gyorgy Snell",
-        "author_inst": "Humabs BioMed SA, subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland"
-      },
-      {
-        "author_name": "Davide Corti",
-        "author_inst": "Humabs BioMed SA, subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland"
-      },
-      {
-        "author_name": "Antonio Lanzavecchia",
-        "author_inst": "National Institute of Molecular Genetics, 20122 Milano, Italy"
-      },
-      {
-        "author_name": "David Veesler",
-        "author_inst": "Department of Biochemistry, University of Washington, Seattle WA, 98195, USA"
-      },
-      {
-        "author_name": "Federica Sallusto",
-        "author_inst": "Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2022.03.30.486403",
     "rel_title": "SARS-CoV-2 accessory protein ORF8 decreases antibody-dependent cellular cytotoxicity",
@@ -332266,6 +330425,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "sexual and reproductive health"
   },
+  {
+    "rel_doi": "10.1101/2022.03.29.486331",
+    "rel_title": "Genetic surveillance of SARS-CoV-2 Mpro reveals high sequence and structural conservation prior to the introduction of protease inhibitor Paxlovid",
+    "rel_date": "2022-03-30",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.29.486331",
+    "rel_abs": "SARS-CoV-2 continues to represent a global health emergency as a highly transmissible, airborne virus. An important coronaviral drug target for treatment of COVID-19 is the conserved main protease (Mpro). Nirmatrelvir is a potent Mpro inhibitor and the antiviral component of Paxlovid. The significant viral sequencing effort during the ongoing COVID-19 pandemic represented a unique opportunity to assess potential nirmatrelvir escape mutations from emerging variants of SARS-CoV-2. To establish the baseline mutational landscape of Mpro prior to the introduction of Mpro inhibitors, Mpro sequences and its cleavage junction regions were retrieved from [~]4,892,000 high-quality SARS-CoV-2 genomes in GISAID. Any mutations identified from comparison to the reference sequence (Wuhan-hu-1) were cataloged and analyzed. Mutations at sites key to nirmatrelvir binding and protease functionality (e.g., dimerization sites) were still rare. Structural comparison of Mpro also showed conservation of key nirmatrelvir contact residues across the extended Coronaviridae family (alpha-, beta-, and gamma-coronaviruses). Additionally, we showed that over time the SARS-CoV-2 Mpro enzyme remained under purifying selection and was highly conserved relative to the spike protein. Now, with the EUA approval of Paxlovid and its expected widespread use across the globe, it is essential to continue large-scale genomic surveillance of SARS-CoV-2 Mpro evolution. This study establishes a robust analysis framework for monitoring emergent mutations in millions of virus isolates, with the goal of identifying potential resistance to present and future SARS-CoV-2 antivirals.\n\nImportanceThe recent authorization of oral SARS-CoV-2 antivirals, such as Paxlovid, has ushered in a new era of the COVID-19 pandemic. Emergence of new variants, as well as selective pressure imposed by antiviral drugs themselves, raise concern for potential escape mutations in key drug binding motifs. To determine the potential emergence of antiviral resistance in globally circulating isolates and its implications for the clinical response to the COVID-19 pandemic, sequencing of SARS-CoV-2 viral isolates before, during, and after the introduction of new antiviral treatments is critical. The infrastructure built herein for active genetic surveillance of Mpro evolution and emergent mutations will play an important role in assessing potential antiviral resistance as the pandemic progresses and Mpro inhibitors are introduced. We anticipate our framework to be the starting point in a larger effort for global monitoring of the SARS-CoV-2 Mpro mutational landscape.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Jonathan T Lee",
+        "author_inst": "Pfizer, Inc"
+      },
+      {
+        "author_name": "Qingyi Yang",
+        "author_inst": "Pfizer Inc."
+      },
+      {
+        "author_name": "Alexey Gribenko",
+        "author_inst": "Pfizer"
+      },
+      {
+        "author_name": "B Scott Perrin Jr.",
+        "author_inst": "Pfizer Inc."
+      },
+      {
+        "author_name": "Yuao Zhu",
+        "author_inst": "Pfizer Inc."
+      },
+      {
+        "author_name": "Rhonda Cardin",
+        "author_inst": "Pfizer Inc."
+      },
+      {
+        "author_name": "Paul A Liberator",
+        "author_inst": "Pfizer, Inc."
+      },
+      {
+        "author_name": "Annaliesa S Anderson",
+        "author_inst": "Pfizer (United States)"
+      },
+      {
+        "author_name": "Li Hao",
+        "author_inst": "Pfizer, Inc"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "genomics"
+  },
   {
     "rel_doi": "10.1101/2022.03.28.22273033",
     "rel_title": "Key topics in pandemic health risk communication: A qualitative study of expert opinions and knowledge",
@@ -334403,221 +332613,6 @@
     "type": "new results",
     "category": "cell biology"
   },
-  {
-    "rel_doi": "10.1101/2022.03.28.486152",
-    "rel_title": "Convergent epitope specificities, V gene usage and public clones elicited by primary exposure to SARS-CoV-2 variants",
-    "rel_date": "2022-03-29",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.28.486152",
-    "rel_abs": "An important consequence of infection with a SARS-CoV-2 variant is protective humoral immunity against other variants. The basis for such cross-protection at the molecular level is incompletely understood. Here we characterized the repertoire and epitope specificity of antibodies elicited by Beta, Gamma and ancestral variant infection and assessed their cross-reactivity to these and the more recent Delta and Omicron variants. We developed a high-throughput approach to obtain immunoglobulin sequences and produce monoclonal antibodies for functional assessment from single B cells. Infection with any variant elicited similar cross-binding antibody responses exhibiting a remarkably conserved hierarchy of epitope immunodominance. Furthermore, convergent V gene usage and similar public B cell clones were elicited regardless of infecting variant. These convergent responses despite antigenic variation may represent a general immunological principle that accounts for the continued efficacy of vaccines based on a single ancestral variant.",
-    "rel_num_authors": 50,
-    "rel_authors": [
-      {
-        "author_name": "Noemia S Lima",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Maryam Musayev",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Timothy S Johnston",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Danielle A Wagner",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Amy R Henry",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Lingshu Wang",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Eun Sung Yang",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Yi Zhang",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Kevina Birungi",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Walker P Black",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Stephen D Schmidt",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Cynthia G Lorang",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Bingchun Zhao",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Man Chen",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Kristin L. Boswell",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Jesmine Roberts-Torres",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Rachel L Davis",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Lowrey Peyton",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Sandeep R Narpala",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Jennifer Wang",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Chloe Adrienna Talana",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Kwanyee Leung",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Wei Shi",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Rawan Khashab",
-        "author_inst": "Sheba Medical Center"
-      },
-      {
-        "author_name": "Asaf Biber",
-        "author_inst": "Sheba Medical Center & Tel Aviv University"
-      },
-      {
-        "author_name": "Tal Zilberman",
-        "author_inst": "Sheba Medical Center & Tel Aviv University"
-      },
-      {
-        "author_name": "Joshua Rhein",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Sara Vetter",
-        "author_inst": "Minnesota Department of Health"
-      },
-      {
-        "author_name": "Afeefa Ahmed",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Laura Novik",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Alicia Widge",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Ingelise Gordon",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Mercy Guech",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "I-Ting Teng",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Emily Phung",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Tracy J. Ruckwardt",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Amarendra Pegu",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "John Misasi",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Nicole A Doria-Rose",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Martin Gaudinski",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Richard A Koup",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Peter D Kwong",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Adrian B McDermott",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Sharon Amit",
-        "author_inst": "Sheba Medical Center"
-      },
-      {
-        "author_name": "Timothy W Schacker",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Itzchak Levy",
-        "author_inst": "Sheba Medical Center & Tel Aviv University"
-      },
-      {
-        "author_name": "John R Mascola",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Nancy J Sullivan",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Chaim A Schramm",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Daniel C Douek",
-        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2022.03.29.486282",
     "rel_title": "Repeated ethanol exposure and withdrawal alters ACE2 expression in discrete brain regions: Implications for SARS-CoV-2 infection",
@@ -335072,6 +333067,197 @@
     "type": "new results",
     "category": "bioinformatics"
   },
+  {
+    "rel_doi": "10.1101/2022.03.25.485832",
+    "rel_title": "A SARS-CoV-2 Spike Ferritin Nanoparticle Vaccine is Protective and Promotes a Strong Immunological Response in the Cynomolgus Macaque Coronavirus Disease 2019 (COVID-19) Model",
+    "rel_date": "2022-03-28",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.25.485832",
+    "rel_abs": "The COVID-19 pandemic has had a staggering impact on social, economic, and public health systems worldwide. Vaccine development and mobilization against SARS-CoV-2 (the etiologic agent of COVID-19) has been rapid. However, novel strategies are still necessary to slow the pandemic, and this includes new approaches to vaccine development and/or delivery, which improve vaccination compliance and demonstrate efficacy against emerging variants. Here we report on the immunogenicity and efficacy of a SARS-CoV-2 vaccine comprised of stabilized, pre-fusion Spike protein trimers displayed on a ferritin nanoparticle (SpFN) adjuvanted with either conventional aluminum hydroxide or the Army Liposomal Formulation QS-21 (ALFQ) in a cynomolgus macaque COVID-19 model. Vaccination resulted in robust cell-mediated and humoral responses and a significant reduction of lung lesions following SARS-CoV-2 infection. The strength of the immune response suggests that dose sparing through reduced or single dosing in primates may be possible with this vaccine. Overall, the data support further evaluation of SpFN as a SARS-CoV-2 protein-based vaccine candidate with attention to fractional dosing and schedule optimization.",
+    "rel_num_authors": 44,
+    "rel_authors": [
+      {
+        "author_name": "Sara C Johnston",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "Keersten M Ricks",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "Ines Lakhal-Naouar",
+        "author_inst": "Walter Reed Army Institute of Research"
+      },
+      {
+        "author_name": "Alexandra Jay",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "Caroline Subra",
+        "author_inst": "Walter Reed Army Institute for Research"
+      },
+      {
+        "author_name": "Jo Lynne Raymond",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "Hannah A D King",
+        "author_inst": "NIH"
+      },
+      {
+        "author_name": "Franco Rossi",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "Tamara L Clements",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "David Fetterer",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "Samantha Tostenson",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "Camila Macedo Cincotta",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Holly R Hack",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Caitlin Kuklis",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Sandrine Soman",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Jocelyn King",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Kristina K Peachman",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Dohoon Kim",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Wei-Hung Chen",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Rajeshwer S Sankhala",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Elizabeth J Martinez",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Agnes Hajduczki",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "William C Chang",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Misook Choe",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Paul V Thomas",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Caroline E Peterson",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Alexander Anderson",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Isabella Swafford",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Jeffrey R Currier",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Dominic Paquin-Proulx",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Linda L Jagodzinski",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Gary R Matyas",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Mangala Rao",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Gregory D Gromowski",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Sheila A Peel",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Lauren White",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "Jeffrey M Smith",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "Jay W Hooper",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "Nelson L L Michael",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Kayvon Modjarrad",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "M. Gordon Joyce",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Aysegul Nalca",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "Diane L Bolton",
+        "author_inst": "WRAIR"
+      },
+      {
+        "author_name": "Margaret LM Pitt",
+        "author_inst": "USAMRIID"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2022.03.28.486075",
     "rel_title": "An engineered ACE2 decoy receptor can be administered by inhalation and potently targets the BA.1 and BA.2 omicron variants of SARS-CoV-2",
@@ -336797,37 +334983,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2022.03.24.22271703",
-    "rel_title": "International Travel-Related Control Measures to contain The Covid-19 Pandemic: An update to a Cochrane Rapid Review",
-    "rel_date": "2022-03-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.24.22271703",
-    "rel_abs": "BackgroundCOVID-19 has proven to be more difficult to manage for many reasons including its high infectivity rate. One of the potential ways to limit its spread is by controlling international travel. The objective of this systematic review is to identify, critically-appraise and summarize evidence on international travel-related control measures.\n\nMethodsThis review is based on the Cochrane review: International travel-related control measures to contain the COVID-19 pandemic and followed the same methods. In brief, we searched for clinical and modelling studies in general health and COVID-19-specific bibliographic databases. The primary outcome categories were (i) cases avoided, (ii) a shift in epidemic development and, (iii) cases detected. Secondary outcomes were other infectious disease transmission outcomes, healthcare utilisation, resource requirements and adverse effects if identified in studies assessing at least one primary outcome.\n\nResultsWe assessed 66 full-text articles that met with our inclusion criteria. Seventeen new studies (modelling = 9, observational = 8) were identified in the updated search. Most studies were of critical to moderate risk of bias. The added studies did not change the main conclusions of the Cochrane review nor the quality of the evidence (very low to low certainty). However, it did add to the evidence base for most outcomes.\n\nConclusionsWeak evidence supports the use of international travel-related control measures to limit the spread of COVID-19 via air travel. Real-world studies are required to support these conclusions.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Ameer Hohlfeld",
-        "author_inst": "SA Medical Research Centre"
-      },
-      {
-        "author_name": "leila abdullahi",
-        "author_inst": "Save the Children International"
-      },
-      {
-        "author_name": "Ahmed M Abou-Setta",
-        "author_inst": "University of Manitoba"
-      },
-      {
-        "author_name": "Mark E Engel",
-        "author_inst": "University of Cape Town"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.03.23.22272819",
     "rel_title": "Vaccine Adverse Event Reporting System (VAERS): Evaluation of 31 Years of Reports and Pandemics' Impact",
@@ -337082,6 +335237,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.03.24.22272854",
+    "rel_title": "Vaccine effectiveness with BNT162b2 (Comirnaty, Pfizer-BioNTech) vaccine against reported SARS-CoV-2 Delta and Omicron infection among adolescents, Norway, August 2021 to January 2022",
+    "rel_date": "2022-03-25",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.24.22272854",
+    "rel_abs": "BackgroundCOVID-19 vaccination was recommended for adolescents in Norway since August 2021. In this population-based cohort study, we estimated the BNT162b2 vaccine effectiveness against any PCR-confirmed (symptomatic or not) SARS-CoV-2 infections caused by the Delta and Omicron variant among adolescents (12-17-years-old) in Norway from August 2021 to January 2022.\n\nMethodsUsing Cox proportional hazard models, we estimated the BNT162b2 vaccine effectiveness against any Delta and Omicron infections. Vaccine status was included as a time-varying covariate and models were adjusted for age, sex, comorbidities, county of residence, country of birth, and living conditions. Data were obtained from the National Preparedness registry for COVID-19, which contains individual-level data from national health and administrative registries.\n\nFindingsVaccine effectiveness against Delta infection peaked at 68% (95%CI: 64-71%) and 62% (95%CI: 57- 66%) in days 21-48 after the first dose among 12-15-year-olds and 16-17-year-olds respectively. Among 16-17-year-olds that received two doses, vaccine effectiveness peaked at 93% (95%CI: 90-95%) in days 35-62 and declined to 84% (95%CI: 76-89%) in 63 days or more after the second dose. For both age-groups, we found no protection against Omicron infection after receiving one dose. Among 16-17-year-olds, vaccine effectiveness against Omicron infection peaked at 53% (95%CI: 43-62%) in 7-34 days after the second dose and decreased to 23% (95%CI: 3-40%) in 63 days or more after vaccination. Vaccine effectiveness decreased with time since vaccination for both variants, but waning was observed to occur faster for Omicron.\n\nInterpretationOur results suggest reduced protection from BNT162b2 vaccination against any SARS-CoV-2 infection caused by the Omicron variant compared to the Delta. In addition, waning immunity was observed to occur faster for Omicron. The impact of vaccination among adolescents on reducing infection and thus transmission is limited during omicron dominance.\n\nFundingNo funding was received.\n\nResearch in context\n\nEvidence before this studyBNT162b2 (Comirnaty, Pfizer-BioNTech) and mRNA-1273 (Spikevax, Moderna) vaccines have been approved for use in adolescents, based on results from randomized placebo-controlled trials demonstrating comparable immunogenicity and safety profile as in young adults. In addition, observational studies from Israel, the USA and England have reported high protection of BNT162b2 vaccines against SARS-CoV-2 Delta infection among adolescents. These studies also reported decrease in effectiveness with time since last vaccine dose. Evidence on the effect of an extended interval between doses, longer time since vaccination and the effect against different variants is limited. When we first planned this study in early February 2022, no data were available regarding vaccine effectiveness against SARS-CoV-2 Omicron infection among adolescents. To our knowledge when we completed this study and before submitting this article, only one study from England reported results in a preprint on vaccine effectiveness against symptomatic SARS-CoV-2 Omicron infection among adolescents. We searched for studies that evaluated vaccine efficacy or effectiveness after vaccination of adolescents during 2021-2022 in PubMed, medRxiv, bioRxiv, SSRN. We searched for studies with several variations of the primary key search terms \"COVID-19\", \"SARS-CoV-2\", and \"vaccine\" (including names of specific vaccines, as BNT162b2), \"vaccine effectiveness\", \"adolescents\", \"children\".\n\nAdded value of this studyThe rapid increase in the incidence of SARS-CoV-2 infection caused by the Omicron variant in highly vaccinated populations has raised concerns about the effectiveness of current vaccines in adults but also adolescents. In this population-based cohort study, we showed that the vaccine effectiveness against Omicron is lower than against Delta infections among adolescents, including symptomatic and asymptomatic infections. We should note that evidence suggests higher rates of asymptomatic carriage for Omicron than other variants of concern. Vaccine effectiveness that includes asymptomatic cases, as in the study from England, is expected to be lower than when including symptomatic cases only. We found that one and two doses of BNT162b2 among adolescents protected well against Delta. Vaccination provided high protection against Delta infections (>91%) among Norwegian 16-17-year-olds 7-62 days after the second dose. We found no protection against Omicron SARS-CoV-2 infection after one vaccine dose, and moderate effectiveness after two doses (peaked at 53%) among the 16-17-year-olds. Moreover, waning immunity was observed to occur faster for Omicron.\n\nImplications of all the available evidenceBased on the available evidence, the vaccine effectiveness among adolescents is similar to that reported among adults, also with an extended period of 8-12 weeks between doses which was used in Norway. Protection is significantly lower against Omicron than Delta infections and immunity wanes faster against Omicron. The impact of vaccination among adolescents on reducing infection and thus transmission is limited during omicron dominance. Policies should take into account the impact of vaccination campaigns among adolescents and their primary objective. Vaccine effectiveness should be re-evaluated when other variants appear as they might have different outcomes as shown between Delta and Omicron infections.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Lamprini Veneti",
+        "author_inst": "Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway"
+      },
+      {
+        "author_name": "Jacob Dag Berild",
+        "author_inst": "Department of Infection Control and Vaccines, Norwegian Institute of Public Health, Oslo, Norway"
+      },
+      {
+        "author_name": "Sara Viksmoen Watle",
+        "author_inst": "Department of Infection Control and Vaccines, Norwegian Institute of Public Health, Oslo, Norway"
+      },
+      {
+        "author_name": "Jostein Starrfelt",
+        "author_inst": "Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway"
+      },
+      {
+        "author_name": "Margrethe Greve-Isdahl",
+        "author_inst": "Department of Infection Control and Vaccines, Norwegian Institute of Public Health, Oslo, Norway"
+      },
+      {
+        "author_name": "Petter Langlete",
+        "author_inst": "Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway"
+      },
+      {
+        "author_name": "Hakon Boas",
+        "author_inst": "Department of Infection Control and Vaccines, Norwegian Institute of Public Health, Oslo, Norway"
+      },
+      {
+        "author_name": "Karoline Bragstad",
+        "author_inst": "Department of Virology, Norwegian Institute of Public Health, Oslo, Norway"
+      },
+      {
+        "author_name": "Olav Hungnes",
+        "author_inst": "Department of Virology, Norwegian Institute of Public Health, Oslo, Norway"
+      },
+      {
+        "author_name": "Hinta Meijerink",
+        "author_inst": "Department of Infection Control and Vaccines, Norwegian Institute of Public Health, Oslo, Norway"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2022.03.25.22272950",
     "rel_title": "THE IMPACT OF ROUTINES ON EMOTIONAL AND BEHAVIOURAL DIFFICULTIES IN CHILDREN AND ON PARENTAL ANXIETY DURING COVID-19",
@@ -338223,85 +336433,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "oncology"
   },
-  {
-    "rel_doi": "10.1101/2022.03.23.22272828",
-    "rel_title": "Neutrophils in severe COVID-19 are characterized by a hyperactive immature state and maintained CXCR2 expression",
-    "rel_date": "2022-03-24",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.23.22272828",
-    "rel_abs": "Neutrophils are vital in defence against pathogens but excessive neutrophil activity can lead to tissue damage and promote acute respiratory distress syndrome (ARDS). COVID-19 is associated with systemic expansion of immature neutrophils but the functional consequences of this shift to immaturity are not understood. We used flow cytometry to investigate activity and phenotypic diversity of circulating neutrophils in acute and convalescent COVID-19 patients. First, we demonstrate hyperactivation of immature CD10- subpopulations in severe disease, with elevated markers of secondary granule release. Partially activated immature neutrophils were detectable three months post symptom onset, indication long term myeloid dysregulation in convalescent COVID-19 patients. Second, we demonstrate that neutrophils from moderately ill patients downregulate the chemokine receptor CXCR2, while neutrophils from severely ill individuals failed to do so, suggesting altered ability for organ trafficking and a potential mechanism for induction of disease tolerance. CD10-and CXCR2hi neutrophil subpopulations were enriched in severe disease and may represent prognostic biomarkers for identification of individuals at high risk of progressing to severe COVID-19.",
-    "rel_num_authors": 16,
-    "rel_authors": [
-      {
-        "author_name": "Christopher M Rice",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Philip Lewis",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Fernando M Ponce-Garcia",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Willem Gibbs",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Drinalda Cela",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Fergus Hamilton",
-        "author_inst": "North Bristol NHS Trust and University of Bristol"
-      },
-      {
-        "author_name": "David Arnold",
-        "author_inst": "North Bristol NHS Trust"
-      },
-      {
-        "author_name": "Catherine Hyams",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Elizabeth Oliver",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Rachael Barr",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Anu Goenka",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Andrew Davidson",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Linda Wooldridge",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Adam Finn",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Laura Rivino",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Borko Amulic",
-        "author_inst": "University of Bristol"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "allergy and immunology"
-  },
   {
     "rel_doi": "10.1101/2022.03.24.485618",
     "rel_title": "Improved And Optimized Drug Repurposing For The SARS-CoV-2 Pandemic",
@@ -338616,6 +336747,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.03.21.22272673",
+    "rel_title": "Sequential appearance and isolation of a SARS-CoV-2 recombinant between two major SARS-CoV-2 variants in a chronically infected immunocompromised patient",
+    "rel_date": "2022-03-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.21.22272673",
+    "rel_abs": "Genetic recombination is a major evolutionary mechanism among RNA viruses, and it is common in coronaviruses, including those infecting humans. A few SARS-CoV-2 recombinants have been reported to date whose genome harbored combinations of mutations from different mutants or variants, but a single patients sample was analyzed, and the virus was not isolated. Here, we re-port the gradual creation of a hybrid genome of B.1.160 and Alpha variants in a lymphoma patient chronically infected for 14 months, and we isolated the recombinant virus. The hybrid genome was obtained by next-generation sequencing, and recombination sites were confirmed by PCR. This consisted of a parental B.1.160 backbone interspersed with two fragments, including the spike gene, from an Alpha variant. Analysis of seven sequential samples from the patient decoded the recombination steps, including the initial infection with a B.1.160 variant, then a concurrent infec-tion with this variant and an Alpha variant, the generation of hybrid genomes, and eventually the emergence of a predominant recombinant virus isolated at the end of the patients follow-up. This case exemplifies the recombination process of SARS-CoV-2 in real life, and it calls for intensifying genomic surveillance in patients coinfected with different SARS-CoV-2 variants, and more gener-ally with several RNA viruses, as this may lead to the creation of new viruses.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Emilie Burel",
+        "author_inst": "IHU Mediterranee Infection"
+      },
+      {
+        "author_name": "Philippe Colson",
+        "author_inst": "Aix-Marseille university"
+      },
+      {
+        "author_name": "Jean-Christophe Lagier",
+        "author_inst": "IHU Mediterranee Infection"
+      },
+      {
+        "author_name": "Anthony LEVASSEUR",
+        "author_inst": "Aix-Marseille University"
+      },
+      {
+        "author_name": "Marielle Bedotto",
+        "author_inst": "IHU Mediterranee Infection"
+      },
+      {
+        "author_name": "Philippe Lavrard",
+        "author_inst": "IHU Mediterranee Infection"
+      },
+      {
+        "author_name": "Pierre-Edouard Fournier",
+        "author_inst": "IHU Mediterranee Infection"
+      },
+      {
+        "author_name": "Bernard LA SCOLA",
+        "author_inst": "Aix Marseille University"
+      },
+      {
+        "author_name": "Didier Raoult",
+        "author_inst": "Aix-Marseille Universite IHU Mediterranee Infection"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.03.22.484725",
     "rel_title": "Jupytope: Computational extraction of structural properties of viral epitopes",
@@ -340257,73 +338439,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.03.21.22272611",
-    "rel_title": "Regional importation and asymmetric within-country spread of SARS-CoV-2 variants of concern in the Netherlands",
-    "rel_date": "2022-03-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.21.22272611",
-    "rel_abs": "Variants of concern (VOCs) of SARS-CoV-2 have caused resurging waves of infections worldwide. In the Netherlands, Alpha, Beta, Gamma and Delta variants circulated widely between September 2020 and August 2021. To understand how various control measures had impacted the spread of these VOCs, we analyzed 39,844 SARS-CoV-2 genomes collected under the Dutch national surveillance program. We found that all four VOCs were introduced before targeted flight restrictions were imposed on countries where the VOCs first emerged. Importantly, foreign introductions, predominantly from other European countries, continued during these restrictions. Our findings show that flight restrictions had limited effectiveness in deterring VOC introductions due to the strength of regional land travel importation risks. We also found that the Alpha and Delta variants largely circulated more populous regions with international connections after their respective introduction before asymmetric bidirectional transmissions occurred with the rest of the country and the variant dominated infections in the Netherlands. As countries consider scaling down SARS-CoV-2 surveillance efforts in the post-crisis phase of the pandemic, our results highlight that robust surveillance in regions of early spread is important for providing timely information for variant detection and outbreak control.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Alvin X. Han",
-        "author_inst": "Amsterdam University Medical Center"
-      },
-      {
-        "author_name": "Eva Kozanli",
-        "author_inst": "Amsterdam University Medical Center"
-      },
-      {
-        "author_name": "Jelle Koopsen",
-        "author_inst": "Amsterdam University Medical Center"
-      },
-      {
-        "author_name": "Harry Vennema",
-        "author_inst": "National Institute for Public Health and the Environment"
-      },
-      {
-        "author_name": "- RIVM COVID-19 molecular epidemiology group",
-        "author_inst": "National Institute for Public Health and the Environment"
-      },
-      {
-        "author_name": "Karim Hajji",
-        "author_inst": "National Institute for Public Health and the Environment"
-      },
-      {
-        "author_name": "Annelies Kroneman",
-        "author_inst": "National Institute for Public Health and the Environment"
-      },
-      {
-        "author_name": "Ivo van Walle",
-        "author_inst": "National Institute for Public Health and the Environment"
-      },
-      {
-        "author_name": "Don Klinkenberg",
-        "author_inst": "National Institute for Public Health and the Environment"
-      },
-      {
-        "author_name": "Jacco Wallinga",
-        "author_inst": "National Institute for Public Health and the Environment"
-      },
-      {
-        "author_name": "Colin A. Russell",
-        "author_inst": "Amsterdam University Medical Center"
-      },
-      {
-        "author_name": "Dirk Eggink",
-        "author_inst": "National Institute for Public Health and the Environment"
-      },
-      {
-        "author_name": "Chantal B.E.M. Reusken",
-        "author_inst": "National Institute for Public Health and the Environment"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.03.21.22272490",
     "rel_title": "Early detection of SARS-CoV-2 variants using traveler-based genomic surveillance at four US airports, September 2021- January 2022",
@@ -340694,6 +338809,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.03.21.22272722",
+    "rel_title": "The dramatic surge of excess mortality in the United States between 2017 and 2021",
+    "rel_date": "2022-03-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.21.22272722",
+    "rel_abs": "A mortality gap between the United States and other high-income nations emerged before the pandemic. International comparisons of Covid-19 mortality suggest this gap might have increased during the pandemic.\n\nApplying average mortality rates of the five largest West European countries to the US population shows that the number of \"excess deaths\" attributable to this mortality gap continues to increase year after year in the United States. The annual number of such excess deaths has doubled between 2017 and 2021, with most of the increase occurring during the pandemic (+89.1% between 2019 and 2021). In 2021, excess mortality in the United States relative to its European peers contributed 892,491 excess deaths, amounting to 25.8% of all US deaths that year, up from 15.7% in 2017.\n\nOf the 450,224 excess deaths added between 2017 and 2021, 42,317 are attributable to population change (9.4%), 230,672 to differential rates of Covid-19 mortality (51.2%), and the remaining 177,235 to differential rates of mortality from other causes (39.4%, possibly including misclassified deaths due to Covid-19). The contribution of Covid-19 mortality to excess mortality in the United States (relative to its European peers) grew between 2020 and 2021 due to diverging trends in Covid-19 mortality, especially towards the end of 2021 as US vaccination rates plateaued at lower levels than in European countries. While this contribution might be transient, divergent trends in mortality from other causes persistently separates the United States from West European countries. Excess mortality is particularly high between ages 15 and 64. In 2021, nearly half of all US deaths in this age range are excess deaths (48.0%).",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Patrick Heuveline",
+        "author_inst": "UCLA"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2022.03.20.22271891",
     "rel_title": "Immunogenic superiority and safety of Biological E CORBEVAX vaccine compared to COVISHIELD (ChAdOx1 nCoV-19) vaccine studied in a phase III, single blind, multicenter, randomized clinical trial",
@@ -342087,141 +340221,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
-  {
-    "rel_doi": "10.1101/2022.03.18.22272631",
-    "rel_title": "Modifications to student quarantine policies in K-12 schools implementing multiple COVID-19 prevention strategies restores in-person education without increasing SARS-CoV-2 transmission risk, January-March 2021",
-    "rel_date": "2022-03-21",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.18.22272631",
-    "rel_abs": "ObjectiveTo determine whether modified K-12 student quarantine policies that allow some students to continue in-person education during their quarantine period increase schoolwide SARS-CoV-2 transmission risk following the increase in cases in winter 2020-2021.\n\nMethodsWe conducted a prospective cohort study of COVID-19 cases and exposures among students and staff (n=65,621) in 103 Missouri public schools. Participants were offered free, saliva-based RT-PCR testing. An adjusted Cox regression model compared hazard rates of school-based SARS-CoV-2 infections between schools with a modified versus standard quarantine policy.\n\nResultsFrom January-March 2021, a projected 23 (1%) school-based transmission events occurred among 1,636 school close contacts. There was no difference in the adjusted hazard rates of school-based SARS-CoV-2 infections between schools with a modified versus standard quarantine policy (hazard ratio=1.00; 95% confidence interval: 0.97-1.03).\n\nDiscussionSchool-based SARS-CoV-2 transmission was rare in 103 K-12 schools implementing multiple COVID-19 prevention strategies. Modified student quarantine policies were not associated with increased school incidence of COVID-19. Modifications to student quarantine policies may be a useful strategy for K-12 schools to safely reduce disruptions to in-person education during times of increased COVID-19 community incidence.",
-    "rel_num_authors": 30,
-    "rel_authors": [
-      {
-        "author_name": "Patrick Dawson",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Mary Claire Worrell",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Sara Malone",
-        "author_inst": "Washington University in St Louis"
-      },
-      {
-        "author_name": "Stephanie  A Fritz",
-        "author_inst": "Washington University in St Louis"
-      },
-      {
-        "author_name": "Heather  P McLaughlin",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Brock  K Montgomery",
-        "author_inst": "Washington University in St Louis"
-      },
-      {
-        "author_name": "Mary Boyle",
-        "author_inst": "Washington University in St Louis"
-      },
-      {
-        "author_name": "Ashley Gomel",
-        "author_inst": "Saint Louis University"
-      },
-      {
-        "author_name": "Samantha Hayes",
-        "author_inst": "Saint Louis University"
-      },
-      {
-        "author_name": "Brett Maricque",
-        "author_inst": "Washington University in St Louis"
-      },
-      {
-        "author_name": "Albert  M. Lai",
-        "author_inst": "Washington University in St Louis"
-      },
-      {
-        "author_name": "Julie  A Neidich",
-        "author_inst": "Washington University in St Louis"
-      },
-      {
-        "author_name": "Sarah  C Tinker",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Justin  S Lee",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Rachel  C. Orscheln",
-        "author_inst": "Washington University in St Louis"
-      },
-      {
-        "author_name": "Suxiang Tong",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Rachel Charney",
-        "author_inst": "Saint Louis University"
-      },
-      {
-        "author_name": "Terri Rebmann",
-        "author_inst": "Saint Louis University"
-      },
-      {
-        "author_name": "Jon Mooney",
-        "author_inst": "Springfield-Greene County Health Department"
-      },
-      {
-        "author_name": "Catherine Rains",
-        "author_inst": "Springfield-Greene County Health Department"
-      },
-      {
-        "author_name": "Nancy Yoon",
-        "author_inst": "Springfield-Greene County Health Department"
-      },
-      {
-        "author_name": "Machelle Petit",
-        "author_inst": "Springfield-Greene County Health Department"
-      },
-      {
-        "author_name": "Katie Towns",
-        "author_inst": "Springfield-Greene County Health Department"
-      },
-      {
-        "author_name": "Clay Goddard",
-        "author_inst": "Springfield-Greene County Health Department"
-      },
-      {
-        "author_name": "Spring Schmidt",
-        "author_inst": "Saint Louis County Department of Public Health"
-      },
-      {
-        "author_name": "Lisa  C Barrios",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "John  C Neatherlin",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Johanna  S Salzer",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Jason  G Newland",
-        "author_inst": "Washington University in St Louis"
-      },
-      {
-        "author_name": "COVID-19 Response Fieldwork and Laboratory Teams AND Missouri School District Data and Coordination",
-        "author_inst": ""
-      }
-    ],
-    "version": "1",
-    "license": "cc0",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2022.03.18.22272605",
     "rel_title": "Medical students' crisis-induced stress and the association with social support",
@@ -342664,6 +340663,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "cardiovascular medicine"
   },
+  {
+    "rel_doi": "10.1101/2022.03.19.22272644",
+    "rel_title": "More severe pneumonitis in children predicts the need for admission and elevation of some but not all markers of severe Covid-19.",
+    "rel_date": "2022-03-21",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.19.22272644",
+    "rel_abs": "Unlike most other viral pneumonitis, SARS-CoV-2 often causes hyperferritinemia, elevations in D-dimer, lactate dehydrogenase (LDH), transaminases, troponin, CRP, and other inflammatory markers. We questioned (1) if the severity of pneumonitis observed on lung ultrasound was associated with hospitalization and (2) could lung ultrasound be used to stratify which children needed blood tests?\n\nMethodsWe did a retrospective cross-sectional review of children aged between 14 days and 21 years of age being evaluated for Covid-19 in our pediatric emergency department from 30/November/2019 to 14/August/2021 who had had a point-of-care lung ultrasound. Lung ultrasounds were categorized using a 6-point ordinal scale. We used logistic regression to estimate the adjusted effect of lung ultrasound on hospital admission. We performed ordinary least square regression for the association between lung ultrasound severity and laboratory abnormalities. We adjusted these using propensity score derived inverse probability weighting to account for the non-random decision to obtain laboratory investigations.\n\nResultsWe identified 500 point-of-care lung ultrasounds of which 427 could be assigned a severity category. Increasing lung ultrasound severity was associated with increased hospital admission OR 1.36(95% CI 1.08, 1.72.) Ferritin, LDH, transaminases, and D-dimer, but not CRP or troponin were significantly associated with more than moderately severe lung ultrasounds. D-Dimer, CRP, and troponin were sometimes elevated even when lung ultrasound was normal.\n\nConclusionSeverity of pneumonitis was associated with hospital admission. Ferritin, LDH, transaminases, and D-dimer were increased in more than moderately severe pneumonitis but lung ultrasound did not predict elevation of other markers.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Paul Walsh",
+        "author_inst": "Sutter Medical Center Sacramento"
+      },
+      {
+        "author_name": "Andrea Hankins",
+        "author_inst": "Sutter Institute for Medical Research"
+      },
+      {
+        "author_name": "Heejung Bang",
+        "author_inst": "University of California Davis"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "emergency medicine"
+  },
   {
     "rel_doi": "10.1101/2022.03.19.484981",
     "rel_title": "Identification of a Novel SARS-CoV-2 Delta-Omicron Recombinant Virus in the United States",
@@ -344305,25 +342331,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.03.17.484837",
-    "rel_title": "Cytokine and chemokine profile in patients hospitalized with COVID-19: A comparative study",
-    "rel_date": "2022-03-18",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.17.484837",
-    "rel_abs": "Abnormal cytokine and chemokine concentrations during SARS-CoV-2 infection may represent disease severity. We aimed to assess plasma cytokine and chemokine concentrations in patients with SARS-CoV-2 in Addis Ababa, Ethiopia. In this study, 260 adults: 126 hospitalized patients with confirmed COVID-19 sorted into severity groups: severe (n=68) and mild or moderate (n=58), and 134 healthy controls were enrolled. We quantified 39 plasma cytokines and chemokines using multiplex ELISA. Spearman rank correlation and Mann-Whitney U test were used to identify mechanistically coupled cytokines/chemokines and compare disease severity. Compared to healthy controls, patients with COVID-19 had significantly higher levels of interleukins 1, 2, 6, 7, 8, 10 and 15, C-reactive protein (CRP), serum amyloid A (SAA), intercellular adhesion molecule 1 (ICAM-1), vascular cell adhesion protein 1 (VCAM-1), IFN-{gamma}-inducible protein-10 (IP-10), macrophage inflammatory protein-1 alpha (MIP-1), eotaxin-3, interferon-gamma (IFN-{Upsilon}), tumor necrosis factor- (TNF-), basic fibroblast growth factor (bFGF), placental growth factor (PlGF), and fms-like tyrosine kinase 1 (Flt-1). Patients with severe COVID-19 had higher IL-10 and lower macrophage-derived chemokine (MDC) compared to the mild or moderate group (P<0.05). In the receiver operating characteristic curve, SAA, IL-6 and CRP showed strong sensitivity and specificity predicting the severity and prognosis of COVID-19. Greater age and higher CRP had a significant association with disease severity (P<0.05). Our findings reveal that CRP, SAA, VCAM-1, IP-10, MDC and IL-10 levels are promising biomarkers for COVID-19 disease severity, suggesting that plasma cytokines/chemokines could be used as warning indicators of COVID-19 severity, aid in COVID-19 prognosis and treatment.\n\nIMPORTANCESARS-CoV-2 triggers inflammatory reaction resulting in respiratory discomfort and in critical case may result in death. Cytokines and chemokines are inflammatory biomarkers that regulate and determine the nature of immune responses. Measuring cytokine and chemokine levels is useful in stratification, management and treatment of COVID-19 patients as well as guide resource allocations and therapeutic options. Here, we examined ctytokine and chemokine profiles in COVID-19 patients. Understanding how distinct cytokines and chemokines change over time as COVID-19 disease progresses might aid clinicians in detecting severe illness earlier and thereby improve patient prognosis.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Abdisa Tufa Bedada",
-        "author_inst": "Addis Ababa University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "biochemistry"
-  },
   {
     "rel_doi": "10.1101/2022.03.17.484817",
     "rel_title": "Potent and specific human monoclonal antibodies against SARS-CoV-2 Omicron variant by rapid mRNA immunization of humanized mice",
@@ -344766,6 +342773,81 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.03.16.22271100",
+    "rel_title": "Effectiveness of whole virus COVID-19 vaccine at protecting health care personnel against SARS-CoV-2 infections in Lima, Peru",
+    "rel_date": "2022-03-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.16.22271100",
+    "rel_abs": "In February 2021, Peru launched a vaccination campaign among healthcare personnel using BBIBP-CorV inactivated whole virus (BBIBP-CorV) COVID-19 vaccine. Two doses of BBIBP-CorV vaccine are recommended, 21 days apart. Data on BBIBP-CorV vaccine effectiveness will inform the use and acceptance of vaccination with BBIBP-CorV vaccine.\n\nWe evaluated BBIBP-CorV vaccine effectiveness among an existing multi-year influenza cohort at two hospitals in Lima. We analyzed data on 290 participants followed between February and May 2021. Participants completed a baseline questionnaire and provided weekly self-collected anterior nasal swabs tested for SARS-CoV-2 by rRT-PCR for sixteen weeks. We performed multivariable logistic regression models adjusting for pre-selected characteristics (age, sex, exposure to COVID-19 patients, work in intensive care unit or emergency department, BMI, and exposure time in days). BBIBP-CorV vaccine effectiveness was calculated after the two-week post-vaccination period as (1-Odds Ratio for testing SARS-CoV-2 positive)x100%.\n\nSARS-CoV-2 was detected by rRT-PCR among 25 (9%) participants during follow-up (February-May 2021). Follow-up period ranged 1-11 weeks (median: 2 weeks). Among cohort participants who were fully vaccinated the adjusted vaccine effectiveness against SARS-CoV-2 infection was estimated as 95% (95% CI: 70%, 99%) and 100% (95% CI: 88%, 100%) for those partially vaccinated.\n\nDuring the study period, vaccination of healthcare personnel with BBIBP-CorV vaccine was effective at reducing SARS-CoV-2 infections in the weeks immediately following vaccination. This information can be used to support vaccination efforts in the region, especially among those who could be concerned about their effectiveness.",
+    "rel_num_authors": 15,
+    "rel_authors": [
+      {
+        "author_name": "Carmen Arriola",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Giselle Soto",
+        "author_inst": "Naval Medical Research Unit No 6 (NAMRU-6)"
+      },
+      {
+        "author_name": "Matthew Westercamp",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Susan Bollinger",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Angelica Espinoza",
+        "author_inst": "Naval Medical Research Unit No 6 (NAMRU-6)"
+      },
+      {
+        "author_name": "Max Grogl",
+        "author_inst": "Naval Medical Research Unit No 6 (NAMRU-6)"
+      },
+      {
+        "author_name": "Alejandro Llanos-Cuentas",
+        "author_inst": "Cayetano Heredia Hospital"
+      },
+      {
+        "author_name": "Eduardo Matos",
+        "author_inst": "Arzobispo Loayza National Hospital"
+      },
+      {
+        "author_name": "Candice Romero",
+        "author_inst": "Naval Medical Research Unit No 6 (NAMRU-6)"
+      },
+      {
+        "author_name": "Maria Silva",
+        "author_inst": "Naval Medical Research Unit No 6 (NAMRU-6)"
+      },
+      {
+        "author_name": "Rachel Smith",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Natalie Olson",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Michael Prouty",
+        "author_inst": "Naval Medical Research Unit No 6 (NAMRU-6)"
+      },
+      {
+        "author_name": "Eduardo Azziz-Baumgartner",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Fernanda Lessa",
+        "author_inst": "Centers for Disease Control and Prevention"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2022.03.17.22272479",
     "rel_title": "Characteristics of mental health stability during COVID-19: An online survey with people residing in the Liverpool City Region",
@@ -346187,53 +344269,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.03.15.22271255",
-    "rel_title": "Conditions of Confinement in U.S. Carceral Facilities during COVID-19: Individuals Speak: Incarcerated during the COVID-19 Epidemic (INSIDE)",
-    "rel_date": "2022-03-17",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.15.22271255",
-    "rel_abs": "ObjectivesWe aimed to describe conditions of confinement among people incarcerated in the United States during the coronavirus disease 2019 (COVID-19) pandemic and assess the feasibility of a community-science data collection approach.\n\nMethodsWe developed a web-based survey with community partners to collect information on confinement conditions (COVID-19 safety, basic needs, support). Formerly incarcerated adults released after March 1, 2020, or non-incarcerated adults in communication with an incarcerated person (proxy) were recruited through social media from July 25, 2020, through March 27, 2021. Descriptive statistics were estimated in aggregate and separately by proxy or formerly incarcerated status. Additionally, we compared responses between proxy and formerly incarcerated respondents using chi-square or Fishers exact tests as appropriate based on alpha=0.05.\n\nResultsOf 378 responses, 94% were by proxy, and 76% reflected state prison conditions. Participants reported inability to physically distance ([&ge;]6ft at all times) (92%), inadequate access to soap (89%), water (46%), toilet paper (49%) and showers (68%). Among people who received mental healthcare before the pandemic, 75% reported reduced care. We found that responses were consistent between formerly incarcerated people and proxy-respondents.\n\nConclusionsOur findings suggest that a community-science approach to data collection is feasible. Based on these findings, COVID-19 safety and basic needs were not sufficiently addressed within some carceral settings. Thus, we recommend the lived experiences of incarcerated individuals should be included to make informed and equitable policy decisions.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Nicole Cassarino",
-        "author_inst": "Division of Women's Health, Brigham and Women's Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Harika Dabbara",
-        "author_inst": "Division of Women's Health, Brigham and Women's Hospital, Boston, MA, USA & Boston University School of Medicine,"
-      },
-      {
-        "author_name": "Carla B. Monteiro",
-        "author_inst": "Brigham Health Bridge Clinic, Boston, MA, USA & Cape Verdean Social Workers Association, Boston, MA, USA"
-      },
-      {
-        "author_name": "Arthur Bembury",
-        "author_inst": "Partakers Organization - College Behind Bars, Auburndale, MA, USA"
-      },
-      {
-        "author_name": "Leslie Credle",
-        "author_inst": "National Council for Incarcerated and Formerly Incarcerated Women and Girls & Justice 4 Housing, Boston, MA & Families for Justice as Healing, Boston, MA"
-      },
-      {
-        "author_name": "Uma Grandhi",
-        "author_inst": "University of California Santa Cruz, Santa Cruz, CA, USA"
-      },
-      {
-        "author_name": "Samantha White",
-        "author_inst": "Harvard University, Cambridge, MA, USA"
-      },
-      {
-        "author_name": "Monik C. Jimenez",
-        "author_inst": "Division of Women's Health, Brigham and Women's Hospital, Boston, MA, USA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.03.17.484640",
     "rel_title": "Long-term T cell perturbations and waning antibody levels in individuals needing hospitalization for COVID-19",
@@ -346560,6 +344595,85 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2022.03.15.484467",
+    "rel_title": "A conserved immune trajectory of recovery in hospitalized COVID-19 patients",
+    "rel_date": "2022-03-16",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.15.484467",
+    "rel_abs": "Many studies have provided insights into the immune response to COVID-19; however, little is known about the immunological changes and immune signaling occurring during COVID-19 resolution. Individual heterogeneity and variable disease resolution timelines obscure unifying immune characteristics. Here, we collected and profiled >200 longitudinal peripheral blood samples from patients hospitalized with COVID-19, with other respiratory infections, and healthy individuals, using mass cytometry to measure immune cells and signaling states at single cell resolution. COVID-19 patients showed a unique immune composition and an early, coordinated and elevated immune cell signaling profile, which correlated with early hospital discharge. Intra-patient time course analysis tied to clinically relevant events of recovery revealed a conserved set of immunological processes that accompany, and are unique to, disease resolution and discharge. This immunological process, together with additional changes in CD4 regulatory T cells and basophils, accompanies recovery from respiratory failure and is associated with better clinical outcomes at the time of admission. Our work elucidates the biological timeline of immune recovery from COVID-19 and provides insights into the fundamental processes of COVID-19 resolution in hospitalized patients.",
+    "rel_num_authors": 16,
+    "rel_authors": [
+      {
+        "author_name": "Trine Line Hauge Okholm",
+        "author_inst": "University of California San Francisco"
+      },
+      {
+        "author_name": "Cassandra E Burnett",
+        "author_inst": "University of California San Francisco"
+      },
+      {
+        "author_name": "Iliana Tenvooren",
+        "author_inst": "University of California San Francisco"
+      },
+      {
+        "author_name": "Diana M Marquez",
+        "author_inst": "University of California San Francisco"
+      },
+      {
+        "author_name": "Stanley Tamaki",
+        "author_inst": "University of California San Francisco"
+      },
+      {
+        "author_name": "Priscila Munoz Sandoval",
+        "author_inst": "University of California San Francisco"
+      },
+      {
+        "author_name": "- The UCSF COMET Consortium",
+        "author_inst": "-"
+      },
+      {
+        "author_name": "Carolyn S Calfee",
+        "author_inst": "University of California San Francisco"
+      },
+      {
+        "author_name": "Carolyn M Hendrickson",
+        "author_inst": "University of California San Francisco"
+      },
+      {
+        "author_name": "Kirsten N Kangelaris",
+        "author_inst": "University of California San Francisco"
+      },
+      {
+        "author_name": "Charles R Langelier",
+        "author_inst": "University of California San Francisco"
+      },
+      {
+        "author_name": "Matthew F Krummel",
+        "author_inst": "University of California San Francisco"
+      },
+      {
+        "author_name": "Prescott G Woodruff",
+        "author_inst": "University of California San Francisco"
+      },
+      {
+        "author_name": "David J Erle",
+        "author_inst": "UCSF"
+      },
+      {
+        "author_name": "Karl Mark Ansel",
+        "author_inst": "UCSF"
+      },
+      {
+        "author_name": "Matthew H. Spitzer",
+        "author_inst": "University of California, San Francisco"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2022.03.16.22271983",
     "rel_title": "Minimal SARS-CoV-2 classroom transmission at a large urban university experiencing repeated into campus introduction",
@@ -347849,61 +345963,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2022.03.14.22272325",
-    "rel_title": "Safety and immunogenicity of SARS-CoV-2 vaccine MVC-COV1901 in adolescents in Taiwan: A double-blind, randomized, placebo-controlled phase 2 trial",
-    "rel_date": "2022-03-15",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.14.22272325",
-    "rel_abs": "BackgroundMVC-COV1901 is a subunit SARS-CoV-2 vaccine based on the prefusion spike protein S-2P and adjuvanted with CpG 1018 and aluminum hydroxide. Although MVC-COV1901 has been licensed for emergency use for adults in Taiwan, the safety and immunogenicity of MVC-COV1901 in adolescents remained unknown. As young people play an important role in SARS-CoV-2 transmission and epidemiology, a vaccine approved for adolescents and eventually, children, will be important in mitigating the COVID-19 pandemic.\n\nMethodsThis study is a prospective, double-blind, multi-center phase 2 trial evaluating the safety, tolerability and immunogenicity of two doses of the SARS-CoV-2 vaccine MVC-COV1901 in adolescents. Healthy adolescents from age of 12 to 17 years were recruited and randomly assigned (6:1) to receive two intramuscular doses of either MVC-COV1901 or placebo at 28 days apart. The primary outcomes were safety and immunogenicity from the day of first vaccination (Day 1) to 28 days after the second vaccination (Day 57), and immunogenicity of MVC COV1901 in adolescents as compared to young adult vaccinees in terms of neutralizing antibody titers and seroconversion rate. The secondary outcomes were safety and immunogenicity of MVC-COV1901 as compared to placebo in adolescents in terms of immunoglobulin titers and neutralizing antibody titers over the study period.\n\nResultsBetween July 21, 2021 and December 22, 2021, a total of 399 adolescent participants were included for safety evaluation after enrollment to receive at least one dose of either MVC-COV1901 (N=341) or placebo (N=58). Of these, 334 and 46 participants went on to receive two doses of either MVC-COV1901 or placebo, respectively, and were included in the per protocol set (PPS) for immunogenicity analysis. Adverse events were mostly mild and were similar in MVC-COV1901 and placebo groups. The most commonly reported adverse events were pain/tenderness and malaise/fatigue. All immunogenicity endpoints in the adolescent group were non-inferior to the endpoints seen in the young adult and placebo groups.\n\nConclusionsThe safety and immunogenicity data presented here showed that MVC-COV1901 has similar safety profile and non-inferior immunogenicity in adolescents compared to young adults.\n\nClinicalTrials.gov registrationNCT04951388.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Luke Tzu Chi Liu",
-        "author_inst": "Medigen Vaccine Biologics Corp"
-      },
-      {
-        "author_name": "Cheng-Hsun Chiu",
-        "author_inst": "Department of Pediatrics, Chang Gung Childrens Hospital, Chang Gung University College of Medicine, Taoyuan City, Taiwan"
-      },
-      {
-        "author_name": "Nan-Chang Chiu",
-        "author_inst": "Department of Pediatrics, MacKay Childrens Hospital, Taipei City, Taiwan"
-      },
-      {
-        "author_name": "Boon-Fatt Tan",
-        "author_inst": "Department of Pediatrics, National Taiwan University Hospital Hsinchu Branch, Hsinchu County, Taiwan"
-      },
-      {
-        "author_name": "Chien-Yu Lin",
-        "author_inst": "Department of Pediatrics, Hsinchu MacKay Memorial Hospital, Hsinchu City, Taiwan"
-      },
-      {
-        "author_name": "Hao-Yuan Cheng",
-        "author_inst": "Medigen Vaccine Biologics Corp"
-      },
-      {
-        "author_name": "Meei-Yun Lin",
-        "author_inst": "Medigen Vaccine Biologics Corp"
-      },
-      {
-        "author_name": "Chia En Lien",
-        "author_inst": "Medigen Vaccine Biologics Corp"
-      },
-      {
-        "author_name": "Charles Chen",
-        "author_inst": "Medigen Vaccine Biologics Corp"
-      },
-      {
-        "author_name": "Li-Min Huang",
-        "author_inst": "Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.03.15.22272371",
     "rel_title": "Neutralizing responses in fully vaccinated with BNT162b2, CoronaVac, ChAdOx1, and Ad26.COV2.S against SARS-CoV-2 lineages in Colombia, 2020-2021",
@@ -348338,6 +346397,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "dentistry and oral medicine"
   },
+  {
+    "rel_doi": "10.1101/2022.03.10.22272193",
+    "rel_title": "Presence of Mediastinal Lymphadenopathy in Hospitalized Covid-19 Patients in a Tertiary Care Hospital in Pakistan - A cross-sectional study",
+    "rel_date": "2022-03-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.10.22272193",
+    "rel_abs": "BackgroundThe aim of this study was to investigate the presence of mediastinal lymphadenopathy in hospitalized Covid-19 patients in a tertiary care hospital in the metropolitan city of Lahore, Pakistan from September 2020 till July 2021.\n\nMethodsWe retrospectively collected data of Covid-19 patients hospitalized from September 2020 till July 2021. Only those patients who tested PCR positive through a nasopharyngeal swab, were enrolled in the study. Patients whose data were missing were excluded from this study. Our exclusion criteria included patients who tested negative on Covid-19 PCR, patients with comorbidities that may cause enlarged mediastinal lymphadenopathies such as haemophagocytic lymphohistiocytosis, neoplasia, tuberculosis, sarcoidosis or a systemic disease. The extent of lung involvement in Covid-19 patients was quantified by using a 25-point visual quantitative assessment called the Chest Computed Tomography Score. This score was then correlated with the presence of mediastinal lymphadenopathy.\n\nFindingsOf the 210 hospitalized patients included in the study, 131 (62.4%) had mediastinal lymphadenopathy. The mean and median Severity Score of Covid-19 patients with mediastinal lymphadenopathy (mean: 17.1, SD:5.7; median: 17, IQR: 13-23) were higher as compared to those without mediastinal lymphadenopathy (mean: 12.3, SD:5.4; median: 12, IQR:9-16)\n\nInterpretationOur study documents a high prevalence of mediastinal lymphadenopathy in hospitalized patients with Covid-19 with the severity score being higher in its presence representing a more severe course of disease.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Amyn  Abdul Malik",
+        "author_inst": "Yale University School of Medicine"
+      },
+      {
+        "author_name": "Faryal  S. Bhatti",
+        "author_inst": "Royal Devon and Exeter NHS Foundation Trust"
+      },
+      {
+        "author_name": "Adeel  A. Malik",
+        "author_inst": "Doctors Hospital & Medical Centre"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.03.11.483867",
     "rel_title": "Accelerating PERx Reaction Enables Covalent Nanobodies for Potent Neutralization of SARS-Cov-2 and Variants",
@@ -349643,25 +347729,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "emergency medicine"
   },
-  {
-    "rel_doi": "10.1101/2022.03.10.22272221",
-    "rel_title": "Spatial patterns of excess mortality in the first year of the COVID-19 pandemic in Germany",
-    "rel_date": "2022-03-13",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.10.22272221",
-    "rel_abs": "In order to quantify the impact of the SARS-CoV-2/COVID-19 pandemic, several studies have estimated excess mortality rather than infections or COVID-19-related deaths. The current study investigates excess mortality in Germany in 2020 at a small-scale spatial level (400 counties) and under consideration of demographic changes. Mortality is operationalized using standardized mortality ratios (SMRs), visualized on maps, and analyzed descriptively. Regional mortality and COVID-19-related morbidity are tested for spatial dependence by the Morans I index. It is, furthermore, tested whether all-cause mortality is associated with COVID-19-related morbidity by correlation coefficients. Excess mortality only occurrs in a minority of counties. There are large regional disparities of all-cause mortality and COVID-19-related morbidity. In older age groups, both indicators show spatial dependence. (Excess) mortality in older age groups is impacted by COVID-19, but this association is not found for young and middle age groups.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Thomas Wieland",
-        "author_inst": "Karlsruhe Institute of Technology"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.03.10.22272196",
     "rel_title": "Milder disease trajectory among COVID-19 patients hospitalised with the SARS-CoV-2 Omicron variant compared with the Delta variant in Norway",
@@ -350088,6 +348155,97 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "dentistry and oral medicine"
   },
+  {
+    "rel_doi": "10.1101/2022.03.11.22271912",
+    "rel_title": "External validation of risk scores to predict in-hospital mortality in patients hospitalized due to coronavirus disease 2019.",
+    "rel_date": "2022-03-13",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.11.22271912",
+    "rel_abs": "BackgroundThe coronavirus disease 2019 (COVID-19) presents an urgent threat to global health. Prediction models that accurately estimate mortality risk in hospitalized patients could assist medical staff in treatment and allocating limited resources.\n\nAimsTo externally validate two promising previously published risk scores that predict in-hospital mortality among hospitalized COVID-19 patients.\n\nMethodsTwo cohorts were available; a cohort of 1028 patients admitted to one of nine hospitals in Lombardy, Italy (the Lombardy cohort) and a cohort of 432 patients admitted to a hospital in Leiden, the Netherlands (the Leiden cohort). The primary endpoint was in-hospital mortality. All patients were adult and tested COVID-19 PCR-positive. Model discrimination and calibration were assessed.\n\nResultsThe C-statistic of the 4C mortality score was good in the Lombardy cohort (0.85, 95CI: 0.82-0.89) and in the Leiden cohort (0.87, 95CI: 0.80-0.94). Model calibration was acceptable in the Lombardy cohort but poor in the Leiden cohort due to the model systematically overpredicting the mortality risk for all patients. The C-statistic of the CURB-65 score was good in the Lombardy cohort (0.80, 95CI: 0.75-0.85) and in the Leiden cohort (0.82, 95CI: 0.76-0.88). The mortality rate in the CURB-65 development cohort was much lower than the mortality rate in the Lombardy cohort. A similar but less pronounced trend was found for patients in the Leiden cohort.\n\nConclusionAlthough performances did not differ greatly, the 4C mortality score showed the best performance. However, because of quickly changing circumstances, model recalibration may be necessary before using the 4C mortality score.",
+    "rel_num_authors": 19,
+    "rel_authors": [
+      {
+        "author_name": "Shermarke Hassan",
+        "author_inst": "University of Milan, Department of Pathophysiology and Transplantation. Leiden University Medical Center, Department of Clinical Epidemiology."
+      },
+      {
+        "author_name": "Chava L. Ramspek",
+        "author_inst": "Leiden University Medical Center, Department of Clinical Epidemiology."
+      },
+      {
+        "author_name": "Barbara Ferrari",
+        "author_inst": "Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, U.O.C. Medicina Generale Emostasi e Trombosi."
+      },
+      {
+        "author_name": "Merel van Diepen",
+        "author_inst": "Leiden University Medical Center, Department of Clinical Epidemiology."
+      },
+      {
+        "author_name": "Raffaella Rossio",
+        "author_inst": "Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, U.O.C. Medicina Generale Emostasi e Trombosi."
+      },
+      {
+        "author_name": "Rachel Knevel",
+        "author_inst": "Leiden University Medical Center, Department of Rheumatology."
+      },
+      {
+        "author_name": "Vincenzo la Mura",
+        "author_inst": "University of Milan, Department of Pathophysiology and Transplantation. Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, U.O.C. Medicina Generale Emos"
+      },
+      {
+        "author_name": "Andrea Artoni",
+        "author_inst": "Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Angelo Bianchi Bonomi Hemophilia and Thrombosis Centre."
+      },
+      {
+        "author_name": "Ida Martinelli",
+        "author_inst": "Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Angelo Bianchi Bonomi Hemophilia and Thrombosis Centre."
+      },
+      {
+        "author_name": "Alessandra Bandera",
+        "author_inst": "University of Milan, Department of Pathophysiology and Transplantation. Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Infectious Disease Unit."
+      },
+      {
+        "author_name": "Alessandro Nobili",
+        "author_inst": "Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Department of Health Policy."
+      },
+      {
+        "author_name": "Andrea Gori",
+        "author_inst": "University of Milan, Department of Pathophysiology and Transplantation. Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Infectious Disease Unit."
+      },
+      {
+        "author_name": "Francesco Blasi",
+        "author_inst": "University of Milan, Department of Pathophysiology and Transplantation. Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Respiratory Unit and Cystic F"
+      },
+      {
+        "author_name": "Ciro Canetta",
+        "author_inst": "Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Department of Medicine, High Care Internal Medicine Unit."
+      },
+      {
+        "author_name": "Nicola Montano",
+        "author_inst": "Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Medicina Generale Immunologia e Allergologia."
+      },
+      {
+        "author_name": "Frits R. Rosendaal",
+        "author_inst": "Leiden University Medical Center, Department of Clinical Epidemiology."
+      },
+      {
+        "author_name": "Flora Peyvandi",
+        "author_inst": "University of Milan, Department of Pathophysiology and Transplantation. Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, U.O.C. Medicina Generale Emos"
+      },
+      {
+        "author_name": "- LUMC COVID-19 Research Group",
+        "author_inst": ""
+      },
+      {
+        "author_name": "- COVID-19 Network working group",
+        "author_inst": ""
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "emergency medicine"
+  },
   {
     "rel_doi": "10.1101/2022.03.11.22272264",
     "rel_title": "Daily Rapid Antigen Testing in a University Setting to Inform COVID-19 Isolation Duration Policy",
@@ -351637,53 +349795,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.03.10.22271815",
-    "rel_title": "Current epidemiological situation of COVID-19 in the Republic of Belarus: characteristics of the epidemic process, sanitary and anti-epidemic measures",
-    "rel_date": "2022-03-12",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.10.22271815",
-    "rel_abs": "This is an analysis of the features of the COVID-19 pandemic the population of the Republic of Belarus from February 2020 to January 2022, the characteristics of sanitary and anti-epidemic measures carried out in the country, assessment of study the safety (tolerance) of the vaccines used the epidemiological efficacy of the vaccination.\n\nA retrospective analysis of COVID-19 cases in the Republic of Belarus from the beginning of registration (February 28, 2020) to January, 3, 2022 was performed. Vaccine safety (tolerance) and efficacy were assessed in an observational study. Safety (tolerance) was assessed by presence/absence of adverse reactions: general (fever, malaise, headache, muscle pain, runny nose, nausea, vomiting, sore throat, etc) and local ones (redness, swelling, soreness at the injection place).\n\nThe COVID-19 pandemic in the Republic of Belarus is characterized by successive development stages: from no cases in early 2020 to detected cases where most individuals had no history of contact with COVID-19 patients; periods of rising and falling incidence\n\nVaccines against COVID-19 (Gam-COVID-Vac (Russia), inactivated vaccine against SARS-CoV-2 (Vero Cell) Sinopharm / BIBP (China) demonstrated a high safety profile in mass vaccination of the population of the Republic of Belarus.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Ala M Dashkevich",
-        "author_inst": "Republican Centre of Hygiene, Epidemiology and Public Health"
-      },
-      {
-        "author_name": "Natalia D Kolomiets",
-        "author_inst": "Belarusian Medical Academy of Postgraduate Education"
-      },
-      {
-        "author_name": "Veronika S Vysotskaya",
-        "author_inst": "Republican Center of Hygiene, Epidemiology and Public Health"
-      },
-      {
-        "author_name": "Iryna N Hlinskaya",
-        "author_inst": "Republican Center of Hygiene, Epidemiology and Public Health"
-      },
-      {
-        "author_name": "Anzhela L Skuranovich",
-        "author_inst": "Republican Center of Hygiene, Epidemiology and Public Health"
-      },
-      {
-        "author_name": "Aliaksandr A Tarasenka",
-        "author_inst": "Ministry of Health of the Republic of Belarus"
-      },
-      {
-        "author_name": "Inna A Karaban",
-        "author_inst": "Ministry of Health of the Republic of Belarus"
-      },
-      {
-        "author_name": "Elena L Gasich",
-        "author_inst": "Republican Research and Practical Center for Epidemiology and Microbiology"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.03.10.22271805",
     "rel_title": "SARS-CoV-2 seroconversion in response to infection and vaccination: A time series local study in Brazil",
@@ -352058,6 +350169,337 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2022.03.10.22272081",
+    "rel_title": "Interstitial lung damage following COVID-19 hospitalisation: an interim analysis of the UKILD Post-COVID study.",
+    "rel_date": "2022-03-12",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.10.22272081",
+    "rel_abs": "IntroductionShared characteristics between COVID-19 and pulmonary fibrosis, including symptoms, genetic architecture, and circulating biomarkers, suggests interstitial lung disease (ILD) development may be associated with SARS-CoV-2 infection.\n\nMethodsThe UKILD Post-COVID study planned interim analysis was designed to stratify risk groups and estimate the prevalence of Post-COVID Interstitial Lung Damage (ILDam) using the Post-HOSPitalisation COVID-19 (PHOSP-COVID) Study. Demographics, radiological patterns and missing data were assessed descriptively. Bayes binomial regression was used to estimate the risk ratio of persistent lung damage >10% involvement in linked, clinically indicated CT scans. Indexing thresholds of percent predicted DLco, chest X-ray findings and severity of admission were used to generate risk strata. Number of cases within strata were used to estimate the amount of suspected Post-COVID ILDam.\n\nResultsA total 3702 people were included in the UKILD interim cohort, 2406 completed an early follow-up research visit within 240 days of discharge and 1296 had follow-up through routine clinical review. We linked the cohort to 87 clinically indicated CTs with visually scored radiological patterns (median 119 days from discharge; interquartile range 83 to 155, max 240), of which 74 people had ILDam. ILDam was associated with abnormal chest X-ray (RR 1.21 95%CrI 1.05; 1.40), percent predicted DLco<80% (RR 1.25 95%CrI 1.00; 1.56) and severe admission (RR 1.27 95%CrI 1.07; 1.55). A risk index based on these features suggested 6.9% of the interim cohort had moderate to very-high risk of Post-COVID ILDam. Comparable radiological patterns were observed in repeat scans >90 days in a subset of participants.\n\nConclusionThese interim data highlight that ILDam was not uncommon in clinically indicated thoracic CT up to 8 months following SARS-CoV-2 hospitalisation. Whether the ILDam will progress to ILD is currently unknown, however health services should radiologically and physiologically monitor individuals who have Post-COVID ILDam risk factors.",
+    "rel_num_authors": 79,
+    "rel_authors": [
+      {
+        "author_name": "I Stewart",
+        "author_inst": "National Heart & Lung Institute, Imperial College London"
+      },
+      {
+        "author_name": "J Jacob",
+        "author_inst": "Respiratory Medicine, University College London"
+      },
+      {
+        "author_name": "PM George",
+        "author_inst": "Royal Brompton and Harefield NHS Foundation Trust"
+      },
+      {
+        "author_name": "PL Molyneaux",
+        "author_inst": "National Heart & Lung Institute, Imperial College London"
+      },
+      {
+        "author_name": "JC Porter",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "RJ Allen",
+        "author_inst": "University of Leicester"
+      },
+      {
+        "author_name": "JK Baillie",
+        "author_inst": "University of Edinburgh"
+      },
+      {
+        "author_name": "SL Barratt",
+        "author_inst": "North Bristol NHS Trust"
+      },
+      {
+        "author_name": "P Beirne",
+        "author_inst": "Leeds Teaching Hospitals & University of Leeds"
+      },
+      {
+        "author_name": "SM Bianchi",
+        "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "JF Blaikley",
+        "author_inst": "University of Manchester"
+      },
+      {
+        "author_name": "J Chalmers",
+        "author_inst": "University of Dundee"
+      },
+      {
+        "author_name": "RC Chambers",
+        "author_inst": "Respiratory Medicine, University College London"
+      },
+      {
+        "author_name": "N Chadhuri",
+        "author_inst": "University of Manchester"
+      },
+      {
+        "author_name": "C Coleman",
+        "author_inst": "University of Nottingham"
+      },
+      {
+        "author_name": "G Collier",
+        "author_inst": "University of Sheffield"
+      },
+      {
+        "author_name": "EK Denneny",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "A Docherty",
+        "author_inst": "University of Edinburgh"
+      },
+      {
+        "author_name": "O Elneima",
+        "author_inst": "University Hospitals of Leicester NHS Trust"
+      },
+      {
+        "author_name": "RA Evans",
+        "author_inst": "University Hospitals of Leicester NHS Trust"
+      },
+      {
+        "author_name": "L Fabbri",
+        "author_inst": "National Heart & Lung Institute, Imperial College London"
+      },
+      {
+        "author_name": "MA Gibbons",
+        "author_inst": "Royal Devon and Exeter NHS Foundation Trust"
+      },
+      {
+        "author_name": "FV Gleeson",
+        "author_inst": "Oxford University Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "B Gooptu",
+        "author_inst": "University of Leicester"
+      },
+      {
+        "author_name": "NJ Greening",
+        "author_inst": "University of Leicester"
+      },
+      {
+        "author_name": "B Guillen Guio",
+        "author_inst": "University of Leicester"
+      },
+      {
+        "author_name": "IP Hall",
+        "author_inst": "University of Nottingham"
+      },
+      {
+        "author_name": "NA Hanley",
+        "author_inst": "University of Manchester"
+      },
+      {
+        "author_name": "V Harris",
+        "author_inst": "University Hospitals of Leicester NHS Trust"
+      },
+      {
+        "author_name": "E Harrison",
+        "author_inst": "University of Edinburgh"
+      },
+      {
+        "author_name": "M Heightman",
+        "author_inst": "University College London Hospital"
+      },
+      {
+        "author_name": "TE Hillman",
+        "author_inst": "University College London Hospital"
+      },
+      {
+        "author_name": "A Horsley",
+        "author_inst": "University of Manchester"
+      },
+      {
+        "author_name": "L Houchen-Wolloff",
+        "author_inst": "University Hospitals of Leicester NHS Trust"
+      },
+      {
+        "author_name": "I Jarrold",
+        "author_inst": "Asthma UK British Lung Foundation"
+      },
+      {
+        "author_name": "SR Johnson",
+        "author_inst": "University of Nottingham"
+      },
+      {
+        "author_name": "MG Jones",
+        "author_inst": "Faculty of Medicine, University of Southampton"
+      },
+      {
+        "author_name": "F Khan",
+        "author_inst": "University of Nottingham"
+      },
+      {
+        "author_name": "R Lawson",
+        "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "OC Leavy",
+        "author_inst": "University of Leicester"
+      },
+      {
+        "author_name": "N Lone",
+        "author_inst": "Usher Institute, University of Edinburgh"
+      },
+      {
+        "author_name": "M Marks",
+        "author_inst": "University College London Hospital"
+      },
+      {
+        "author_name": "H McAuley",
+        "author_inst": "University of Leicester"
+      },
+      {
+        "author_name": "P Mehta",
+        "author_inst": "University College London Hospital"
+      },
+      {
+        "author_name": "E Omer",
+        "author_inst": "University of Leicester"
+      },
+      {
+        "author_name": "D Parekh",
+        "author_inst": "University of Birmingham"
+      },
+      {
+        "author_name": "K Piper Hanley",
+        "author_inst": "University of Manchester"
+      },
+      {
+        "author_name": "M Plate",
+        "author_inst": "University College London Hospital"
+      },
+      {
+        "author_name": "J Pearl",
+        "author_inst": "University of Leicester"
+      },
+      {
+        "author_name": "K Poinasamy",
+        "author_inst": "British Lung Foundation"
+      },
+      {
+        "author_name": "JK Quint",
+        "author_inst": "National Heart & Lung Institute, Imperial College London"
+      },
+      {
+        "author_name": "B Raman",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "M Richardson",
+        "author_inst": "University of Leicester"
+      },
+      {
+        "author_name": "P Rivera-Ortega",
+        "author_inst": "University of Manchester"
+      },
+      {
+        "author_name": "L Saunders",
+        "author_inst": "University of Sheffield"
+      },
+      {
+        "author_name": "R Saunders",
+        "author_inst": "University of Leicester"
+      },
+      {
+        "author_name": "MG Semple",
+        "author_inst": "Liverpool University"
+      },
+      {
+        "author_name": "M Sereno",
+        "author_inst": "University of Leicester"
+      },
+      {
+        "author_name": "A Shikotra",
+        "author_inst": "University Hospitals of Leicester NHS Trust"
+      },
+      {
+        "author_name": "AJ Simpson",
+        "author_inst": "Newcastle University"
+      },
+      {
+        "author_name": "A Singapuri",
+        "author_inst": "University of Leicester"
+      },
+      {
+        "author_name": "DJF Smith",
+        "author_inst": "Royal Brompton and Harefield NHS Foundation Trust"
+      },
+      {
+        "author_name": "M Spears",
+        "author_inst": "Perth Royal Infirmary, NHS Tayside"
+      },
+      {
+        "author_name": "LG Spencer",
+        "author_inst": "Liverpool University Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "S Stanel",
+        "author_inst": "University of Manchester"
+      },
+      {
+        "author_name": "D Thickett",
+        "author_inst": "University of Birmingham"
+      },
+      {
+        "author_name": "AAR Thompson",
+        "author_inst": "University of Sheffield"
+      },
+      {
+        "author_name": "M Thorpe",
+        "author_inst": "University of Edinburgh"
+      },
+      {
+        "author_name": "R Thwaites",
+        "author_inst": "National Heart & Lung Institute, Imperial College London"
+      },
+      {
+        "author_name": "SLF Walsh",
+        "author_inst": "National Heart & Lung Institute, Imperial College London"
+      },
+      {
+        "author_name": "S Walker",
+        "author_inst": "Sheffield Teaching NHS Foundation Trust"
+      },
+      {
+        "author_name": "ND Weatherley",
+        "author_inst": "Sheffield Teaching NHS Foundation Trust"
+      },
+      {
+        "author_name": "M Weeks",
+        "author_inst": "National Heart & Lung Institute, Imperial College London"
+      },
+      {
+        "author_name": "JM Wild",
+        "author_inst": "Sheffield Teaching NHS Foundation Trust"
+      },
+      {
+        "author_name": "DG Wootton",
+        "author_inst": "University of Liverpool"
+      },
+      {
+        "author_name": "CE Brightling",
+        "author_inst": "University Hospitals of Leicester NHS Trust"
+      },
+      {
+        "author_name": "LP Ho",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "LV Wain",
+        "author_inst": "University of Leicester"
+      },
+      {
+        "author_name": "RG Jenkins",
+        "author_inst": "National Heart & Lung Institute, Imperial College London"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "respiratory medicine"
+  },
   {
     "rel_doi": "10.1101/2022.03.09.22272170",
     "rel_title": "SARS-CoV-2 Omicron disease burden in Australia following border reopening: a modelling analysis",
@@ -353455,57 +351897,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2022.03.09.22271896",
-    "rel_title": "Quantifying the vaccine-induced humoral immune response to spike-receptor binding domain as a surrogate for neutralization testing following mRNA-1273 (Spikevax) vaccination against COVID-19",
-    "rel_date": "2022-03-10",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.09.22271896",
-    "rel_abs": "BackgroundThere is a need for automated, high throughput assays to quantify immune response after vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This study assessed the combined utility of the Roche assays, Elecsys(R) Anti-SARS-CoV-2 S (ACOV2S) and Elecsys Anti-SARS-CoV-2 (ACOV2N) using samples from the 2019-nCoV vaccine (mRNA-1273, Spikevax) phase 2 trial (NCT04405076).\n\nMethodsSamples from 593 healthy participants in two age cohorts (18-54 years and [&ge;]55 years), who received two injections with either placebo (n=198) or mRNA-1273 at a dose of either 50 g (n=197) or 100 g (n=198), were collected at Days 1 (first vaccination), 15, 29 (second vaccination), 43 and 57. ACOV2S results were used to assess the humoral response to vaccination in different clinical trial subgroups and were compared to a live virus microneutralization assay. Sample panels from patients with evidence of previous or concomitant infection (as identified using ACOV2N) or with an inconsistent antibody response pattern were analyzed separately.\n\nResultsReceptor-binding domain (RBD)-specific antibodies were readily detectable by ACOV2S for the vast majority of participants (174/189 [50 g dose group] and 178/192 [100 g]) at the first time point of assessment, with non-converters predominantly older in age. Complete seroconversion for all participants was observed at the subsequent timepoint (Day 29) and before administration of the second dose of vaccine. Two weeks after the first vaccine dose (Day 15), geometric mean concentration (GMC) of antibody levels were 1.37-fold higher in the 100 g compared with the 50 g dose group; this difference reduced to 1.09-fold two weeks after the second dose (Day 43). In both the 50 g and 100 g dose groups, a more pronounced response was observed in the younger versus the older age group on Day 15 (2.49-fold and 3.94-fold higher GMC, respectively) and Day 43 (1.35-fold and 1.50-fold higher GMC). Few subjects had a previous or concomitant natural SARS-CoV-2-infection (n=8). Vaccination of pre-infected individuals boosted the immune response to very high ACOV2S results compared to infection-naive vaccine recipients. ACOV2S measurements were strongly correlated with those from the live microneutralization assay (Pearsons r=0.779; p<0.0001) and good qualitative agreement was achieved (100% positive and 91.8% negative percentage agreement; 90.0% positive and 100% negative predictive value).\n\nConclusionThe results from this study confirmed that ACOV2S is a highly valuable assay for the tracking of vaccine-related immune responses. Combined application with ACOV2N enables serologic monitoring for breakthrough infection or stratification of previous natively-infected individuals. The adaptive measuring range and high resolution of ACOV2S allows for the early identification of seroconversion as well as for resolution of very high titers and detection of longitudinal differences between age and dose groups. Additionally, good correlation of ACOV2S with live virus microneutralization indicates the utility of ACOV2S as a reliable estimate of neutralization capacity in routine diagnostic settings.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Imke Kirste",
-        "author_inst": "Clinical Development & Medical Affairs, Roche Diagnostics Operations, Indianapolis, USA"
-      },
-      {
-        "author_name": "Sayuri Hortsch",
-        "author_inst": "Biostatistics and Data Science, Roche Diagnostics GmbH, Penzberg, Germany"
-      },
-      {
-        "author_name": "Veit Peter Grunert",
-        "author_inst": "Biostatistics and Data Science, Roche Diagnostics GmbH, Penzberg, Germany"
-      },
-      {
-        "author_name": "Holly Legault",
-        "author_inst": "Clinical Biomarkers, Moderna, Cambridge, MA, USA"
-      },
-      {
-        "author_name": "Maha Maglinao",
-        "author_inst": "Clinical Biomarkers, Moderna, Cambridge, MA, USA"
-      },
-      {
-        "author_name": "Udo Eichenlaub",
-        "author_inst": "Clinical Development & Medical Affairs, Roche Diagnostics Operations, Indianapolis, USA"
-      },
-      {
-        "author_name": "Basel Kashlan",
-        "author_inst": "Lab Operations, PPD, part of Thermo Fisher Scientific, Highland Heights, KY, USA"
-      },
-      {
-        "author_name": "Rolando Pajon",
-        "author_inst": "Clinical Biomarkers, Moderna, Cambridge, MA, USA"
-      },
-      {
-        "author_name": "Simon Jochum",
-        "author_inst": "Research and Development Immunoassays, Roche Diagnostics GmbH, Penzberg, Germany"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.03.08.22272057",
     "rel_title": "Physical, psychological and cognitive profile of post-COVID condition in healthcare workers, Quebec, Canada",
@@ -354124,6 +352515,201 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
+  {
+    "rel_doi": "10.1101/2022.03.09.22271788",
+    "rel_title": "Comparison of influenza and COVID-19-associated hospitalizations among children < 18 years old in the United States - FluSurv-NET (October-April 2017-2021) and COVID-NET (October 2020-September 2021)",
+    "rel_date": "2022-03-10",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.09.22271788",
+    "rel_abs": "BackgroundInfluenza virus and SARS-CoV-2 are significant causes of respiratory illness in children.\n\nMethodsInfluenza and COVID-19-associated hospitalizations among children <18 years old were analyzed from FluSurv-NET and COVID-NET, two population-based surveillance systems with similar catchment areas and methodology. The annual COVID-19-associated hospitalization rate per 100 000 during the ongoing COVID-19 pandemic (October 1, 2020-September 30, 2021) was compared to influenza-associated hospitalization rates during the 2017-18 through 2019-20 influenza seasons. In-hospital outcomes, including intensive care unit (ICU) admission and death, were compared.\n\nResultsAmong children <18 years old, the COVID-19-associated hospitalization rate (48.2) was higher than influenza-associated hospitalization rates: 2017-18 (33.5), 2018-19 (33.8), and 2019-20 (41.7). The COVID-19-associated hospitalization rate was higher among adolescents 12-17 years old (COVID-19: 59.9; influenza range: 12.2-14.1), but similar or lower among children 5-11 (COVID-19: 25.0; influenza range: 24.3-31.7) and 0-4 (COVID-19: 66.8; influenza range: 70.9-91.5) years old. Among children <18 years old, a higher proportion with COVID-19 required ICU admission compared with influenza (26.4% vs 21.6%; p<0.01). Pediatric deaths were uncommon during both COVID-19- and influenza-associated hospitalizations (0.7% vs 0.5%; p=0.28).\n\nConclusionsIn the setting of extensive mitigation measures during the COVID-19 pandemic, the annual COVID-19-associated hospitalization rate during 2020-2021 was higher among adolescents and similar or lower among children <12 years old compared with influenza during the three seasons before the COVID-19 pandemic. COVID-19 adds substantially to the existing burden of pediatric hospitalizations and severe outcomes caused by influenza and other respiratory viruses.\n\nSummaryAnnual hospitalization rates and proportions of hospitalized children experiencing severe outcomes were as high or higher for COVID-19 during October 2020-September 2021 compared with influenza during the three seasons before the COVID-19 pandemic, based on U.S. population-based surveillance data.",
+    "rel_num_authors": 45,
+    "rel_authors": [
+      {
+        "author_name": "Miranda Delahoy",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Dawud Ujamaa",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Christopher A. Taylor",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Charisse Cummings",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Onika Anglin",
+        "author_inst": "CDC"
+      },
+      {
+        "author_name": "Rachel A Holstein",
+        "author_inst": "Centers for Disease Control and Prevention (CDC)"
+      },
+      {
+        "author_name": "Jennifer Milucky",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Alissa O'Halloran",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Kadam Patel",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Huong Pham",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Michael Whitaker",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Arthur Reingold",
+        "author_inst": "University of California Berkeley"
+      },
+      {
+        "author_name": "Shua J. Chai",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Nisha B. Alden",
+        "author_inst": "Colorado Department of Public Health and Environment"
+      },
+      {
+        "author_name": "Breanna Kawasaki",
+        "author_inst": "Colorado Department of Public Health and Environment"
+      },
+      {
+        "author_name": "James Meek",
+        "author_inst": "Connecticut Emerging Infections Program, Yale School of Public Health"
+      },
+      {
+        "author_name": "Kimberly Yousey-Hindes",
+        "author_inst": "Connecticut Emerging Infections Program, Yale School of Public Health"
+      },
+      {
+        "author_name": "Evan J. Anderson",
+        "author_inst": "Emory University School of Medicine Emerging Infections Program, Georgia Department of Health Veterans Affairs Medical Center"
+      },
+      {
+        "author_name": "Kyle P. Openo",
+        "author_inst": "Georgia EIP"
+      },
+      {
+        "author_name": "Andy Weigel",
+        "author_inst": "Iowa Department of Public Health"
+      },
+      {
+        "author_name": "Kenzie Teno",
+        "author_inst": "Iowa Department of Public Health"
+      },
+      {
+        "author_name": "Libby Reeg",
+        "author_inst": "Michigan Department of Health and Human Services"
+      },
+      {
+        "author_name": "Lauren Leegwater",
+        "author_inst": "Michigan Department of Health and Human Services"
+      },
+      {
+        "author_name": "Ruth Lynfield",
+        "author_inst": "Minnesota Department of Health"
+      },
+      {
+        "author_name": "Melissa McMahon",
+        "author_inst": "Minnesota Department of Health"
+      },
+      {
+        "author_name": "Susan Ropp",
+        "author_inst": "New Mexico Department of Health"
+      },
+      {
+        "author_name": "Dominic Rudin",
+        "author_inst": "University of New Mexico Health Sciences Center"
+      },
+      {
+        "author_name": "Alison Muse",
+        "author_inst": "New York State Department of Health"
+      },
+      {
+        "author_name": "Nancy Spina",
+        "author_inst": "New York State Department of Health"
+      },
+      {
+        "author_name": "Nancy M. Bennett",
+        "author_inst": "University of Rochester School of Medicine and Dentistry"
+      },
+      {
+        "author_name": "Kevin Popham",
+        "author_inst": "University of Rochester School of Medicine and Dentistry"
+      },
+      {
+        "author_name": "Laurie M. Billing",
+        "author_inst": "Ohio Department of Health"
+      },
+      {
+        "author_name": "Eli Shiltz",
+        "author_inst": "Ohio Department of Health"
+      },
+      {
+        "author_name": "Melissa Sutton",
+        "author_inst": "Oregon Health Authority"
+      },
+      {
+        "author_name": "Ann Thomas",
+        "author_inst": "Public Health Division, Oregon Health Authority"
+      },
+      {
+        "author_name": "William Schaffner",
+        "author_inst": "Vanderbilt University of Medicine"
+      },
+      {
+        "author_name": "H. Keipp Talbot",
+        "author_inst": "Vanderbilt University of Medicine"
+      },
+      {
+        "author_name": "Melanie T. Crossland",
+        "author_inst": "Salt Lake County Health Department"
+      },
+      {
+        "author_name": "Keegan McCaffrey",
+        "author_inst": "Utah Department of Health"
+      },
+      {
+        "author_name": "Aron J. Hall",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Erin Burns",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Meredith McMorrow",
+        "author_inst": "U.S. Public Health Services"
+      },
+      {
+        "author_name": "Carrie Reed",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Fiona P. Havers",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Shikha Garg",
+        "author_inst": "Centers for Disease Control and Prevention"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.03.08.22272041",
     "rel_title": "Impacts of COVID-19 on glycemia and risk of diabetic ketoacidosis",
@@ -355461,117 +354047,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "cardiovascular medicine"
   },
-  {
-    "rel_doi": "10.1101/2022.03.06.21267462",
-    "rel_title": "Risk of myocarditis and pericarditis following COVID-19 vaccination in England and Wales",
-    "rel_date": "2022-03-08",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.06.21267462",
-    "rel_abs": "We describe our analyses of data from over 49.7 million people in England, representing near-complete coverage of the relevant population, to assess the risk of myocarditis and pericarditis following BNT162b2 and ChAdOx1 COVID-19 vaccination. A self-controlled case series (SCCS) design has previously reported increased risk of myocarditis after first ChAdOx1, BNT162b2, and mRNA-1273 dose and after second doses of mRNA COVID-19 vaccines in England. Here, we use a cohort design to estimate hazard ratios for hospitalised or fatal myocarditis/pericarditis after first and second doses of BNT162b2 and ChAdOx1 vaccinations. SCCS and cohort designs are subject to different assumptions and biases and therefore provide the opportunity for triangulation of evidence. In contrast to the findings from the SCCS approach previously reported for England, we found evidence for lower incidence of hospitalised or fatal myocarditis/pericarditis after first ChAdOx1 and BNT162b2 vaccination, as well as little evidence to suggest higher incidence of these events after second dose of either vaccination.",
-    "rel_num_authors": 24,
-    "rel_authors": [
-      {
-        "author_name": "Samanatha Ip",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Fatemeh Torabi",
-        "author_inst": "Swansea University"
-      },
-      {
-        "author_name": "Spiros Denaxas",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Ashley Akbari",
-        "author_inst": "Swansea University"
-      },
-      {
-        "author_name": "Hoda Abbasizanjani",
-        "author_inst": "Swansea University"
-      },
-      {
-        "author_name": "Rochelle Knight",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Jennifer Anne Cooper",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Rachel Denholm",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Spencer Keene",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Thomas Bolton",
-        "author_inst": "Health Data Research UK"
-      },
-      {
-        "author_name": "Sam Hollings",
-        "author_inst": "NHS Digital"
-      },
-      {
-        "author_name": "Efosa Omigi",
-        "author_inst": "NHS Digital"
-      },
-      {
-        "author_name": "Teri-Louise North",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Arun Karthikeyan Suseeladevi",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Emanuele Di Angelantonio",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Kamlesh Khunti",
-        "author_inst": "University of Leicester"
-      },
-      {
-        "author_name": "Jonathan A C Sterne",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Cathie Sudlow",
-        "author_inst": "Health Data Research UK"
-      },
-      {
-        "author_name": "William Whiteley",
-        "author_inst": "University of Edinburgh"
-      },
-      {
-        "author_name": "Angela Wood",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Venexia Walker",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "- British Heart Foundation Data Science Centre (HDR UK) CVD-COVID-UK/COVID-IMPACT Consortium",
-        "author_inst": ""
-      },
-      {
-        "author_name": "- UK Covid-19 Longitudinal Health and Wellbeing National Core Study",
-        "author_inst": ""
-      },
-      {
-        "author_name": "- UK Covid-19 Data and Connectivity National Core Study",
-        "author_inst": ""
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.03.06.22270594",
     "rel_title": "Post COVID-19 Condition in South Africa: 3-month follow-up after hospitalisation with SARS-CoV-2",
@@ -355902,6 +354377,105 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "respiratory medicine"
   },
+  {
+    "rel_doi": "10.1101/2022.03.06.22271809",
+    "rel_title": "Defining factors that influence vaccine-induced, cross-variant neutralizing antibodies for SARS-CoV-2 in Asians",
+    "rel_date": "2022-03-08",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.06.22271809",
+    "rel_abs": "The scale and duration of neutralizing antibody responses targeting SARS-CoV-2 viral variants represents a critically important serological parameter that predicts protective immunity for COVID-19. In this study, we present longitudinal data illustrating the impact of age, sex and comorbidities on the kinetics and strength of vaccine-induced neutralizing antibody responses for key variants in an Asian volunteer cohort. We demonstrate a reduction in neutralizing antibody titres across all groups six months post-vaccination and show a marked reduction in the serological binding and neutralizing response targeting Omicron compared to other viral variants. We also highlight the increase in cross-protective neutralizing antibody responses against Omicron induced by a third dose (booster) of vaccine. These data illustrate how key virological factors such as immune escape mutation combined with host factors such as age and sex of the vaccinated individuals influence the strength and duration of cross-protective serological immunity for COVID-19.",
+    "rel_num_authors": 21,
+    "rel_authors": [
+      {
+        "author_name": "Yue Gu",
+        "author_inst": "National University of Singapore"
+      },
+      {
+        "author_name": "Bhuvaneshwari D/O Shunmuganathan",
+        "author_inst": "National University of Singapore"
+      },
+      {
+        "author_name": "Xinlei Qian",
+        "author_inst": "National University of Singapore"
+      },
+      {
+        "author_name": "Rashi Gupta",
+        "author_inst": "National University of Singapore"
+      },
+      {
+        "author_name": "Rebecca S.W. Tan",
+        "author_inst": "National University of Singapore"
+      },
+      {
+        "author_name": "Mary Kozma",
+        "author_inst": "National University of Singapore"
+      },
+      {
+        "author_name": "Kiren Purushotorman",
+        "author_inst": "National University of Singapore"
+      },
+      {
+        "author_name": "Tanusya M. Murali",
+        "author_inst": "National University of Singapore"
+      },
+      {
+        "author_name": "Nikki Y.J. Tan",
+        "author_inst": "National University of Singapore"
+      },
+      {
+        "author_name": "Peter R. Preiser",
+        "author_inst": "Nanyang Technological University"
+      },
+      {
+        "author_name": "Julien Lescar",
+        "author_inst": "Nanyang Technological University"
+      },
+      {
+        "author_name": "Haziq Nasir",
+        "author_inst": "National University Hospital"
+      },
+      {
+        "author_name": "Jyoti Somani",
+        "author_inst": "National University Hospital"
+      },
+      {
+        "author_name": "Paul A. Tambyah",
+        "author_inst": "National University Hospital"
+      },
+      {
+        "author_name": "- SCOPE Cohort Study Group",
+        "author_inst": "-"
+      },
+      {
+        "author_name": "Kenneth G.C. Smith",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Laurent Renia",
+        "author_inst": "Agency for Science, Technology and Research (A*STAR), Singapore"
+      },
+      {
+        "author_name": "Lisa F.P. Ng",
+        "author_inst": "Agency for Science, Technology and Research (A*STAR), Singapore"
+      },
+      {
+        "author_name": "David C. Lye",
+        "author_inst": "National Centre of Infectious Diseases"
+      },
+      {
+        "author_name": "Barnaby E. Young",
+        "author_inst": "National Centre for Infectious Diseases"
+      },
+      {
+        "author_name": "Paul A. MacAry",
+        "author_inst": "National University of Singapore"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "allergy and immunology"
+  },
   {
     "rel_doi": "10.1101/2022.03.08.483381",
     "rel_title": "Hetero-bivalent Nanobodies Provide Broad-spectrum Protection against SARS-CoV-2 Variants of Concern including Omicron",
@@ -357411,33 +355985,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2022.03.04.22271940",
-    "rel_title": "A new compartment model of COVID-19 transmission: The broken-link model",
-    "rel_date": "2022-03-07",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.04.22271940",
-    "rel_abs": "We propose a new compartment model of COVID-19 spread, the broken-link model, which includes the effect from unconnected infectious links of the transmission. The traditional SIR-type epidemic models are widely used to analyze the spread status, and the models show the exponential growth of the number of infected people. However, even in the early stage of the spread, it is proven by the actual data that the exponential growth did not occur all over the world. We consider this is caused by the suppression of secondary and higher transmissions of COVID-19. We find that the proposed broken-link model quantitatively describes the mechanism of this suppression and is consistent with the actual data.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Yoichi Ikeda",
-        "author_inst": "Kyushu Univ."
-      },
-      {
-        "author_name": "Kenji Sasaki",
-        "author_inst": "Osaka Univ."
-      },
-      {
-        "author_name": "Takashi Nakano",
-        "author_inst": "Osaka University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2022.03.05.22271947",
     "rel_title": "Efficacy and safety of intensified versus standard prophylactic anticoagulation therapy in patients with Covid-19: a systematic review and meta-analysis",
@@ -357708,6 +356255,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2022.03.04.22271706",
+    "rel_title": "Remdesivir for the treatment of patients hospitalized with COVID-19 receiving supplemental oxygen: a targeted literature review and meta-analysis",
+    "rel_date": "2022-03-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.04.22271706",
+    "rel_abs": "This network meta-analysis (NMA) assessed the efficacy of remdesivir in hospitalized patients with COVID-19 requiring supplemental oxygen. Randomized controlled trials of hospitalized patients with COVID-19, where patients were receiving supplemental oxygen at baseline and at least one arm received treatment with remdesivir, were identified. Outcomes included mortality, recovery, and no longer requiring supplemental oxygen. NMAs were performed for low-flow oxygen (LFO2); high-flow oxygen (HFO2), including NIV; or oxygen at any flow (AnyO2) at early (day 14/15) and late (day 28/29) time points. Six studies were included (N=5,245 patients) in the NMA. Remdesivir lowered early and late mortality among AnyO2 patients (risk ratio (RR) 0.52, 95% credible interval (CrI) 0.34-0.79; RR 0.81, 95%CrI 0.69-0.95) and LFO2 patients (RR 0.21, 95%CI 0.09-0.46; RR 0.24, 95%CI 0.11-0.48); no improvement was observed among HFO2 patients. Improved early and late recovery was observed among LFO2 patients (RR 1.22, 95%CrI 1.09-1.38; RR 1.17, 95%CrI 1.09-1.28). Remdesivir also lowered the requirement for oxygen support among all patient subgroups. Among hospitalized patients with COVID-19 requiring supplemental oxygen at baseline, use of remdesivir compared to best supportive care is likely to improve the risk of mortality, recovery and need for oxygen support in AnyO2 and LFO2 patients.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Rachel Beckerman",
+        "author_inst": "Maple Health Group"
+      },
+      {
+        "author_name": "Andrea Gori",
+        "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano"
+      },
+      {
+        "author_name": "Sushanth Jeyakumar",
+        "author_inst": "Maple Health Group"
+      },
+      {
+        "author_name": "Jakob J. Malin",
+        "author_inst": "Department I of Internal Medicine, Division of Infectious Diseases, Medical Faculty and University Hospital Cologne, University of Cologne"
+      },
+      {
+        "author_name": "Roger Paredes",
+        "author_inst": "Infectious Diseases Department & irsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain"
+      },
+      {
+        "author_name": "Pedro Povoa",
+        "author_inst": "Nova Medical School, CHRC, New University of Lisbon, Lisbon, Portugal"
+      },
+      {
+        "author_name": "Nathaniel J. Smith",
+        "author_inst": "Maple Health Group"
+      },
+      {
+        "author_name": "Armando Teixeira-Pinto",
+        "author_inst": "School of Public Health, Faculty of Medicine and Health, University of Sydney, Sydney, Australia"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.03.07.22271833",
     "rel_title": "GWAS and meta-analysis identifies multiple new genetic mechanisms underlying severe Covid-19.",
@@ -359117,69 +357711,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2022.02.22.22271222",
-    "rel_title": "NOVEL RT-qPCR ASSAYS ENABLE RAPID DETECTION AND DIFFERENTIATION BETWEEN SARS-COV-2 OMICRON (BA.1) AND BA.2 VARIANTS",
-    "rel_date": "2022-03-04",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.22.22271222",
-    "rel_abs": "In this report, we describe the development and initial validation of novel SARS-COV-2 Omicron-specific reactions that enable the identification of Omicron (BA.1) and BA.2 variants. Mutations that are either shared by both BA.1 and BA.2, or are exclusive for BA.1 or for BA.2 were identified by bioinformatic analysis, and corresponding probe-based quantitative PCR reactions were developed to identify them. We show that multiplex combinations of these reactions provide a single-reaction identification of the sample as BA.1, BA.2, or as non-Omicron SARS-COV-2. All four reactions described herein have a sensitivity of less than ten copies per reaction, and are amendable for multiplexing. The results of this study suggest that the new assays may be useful for testing both clinical and environmental samples to differentiate between these two variants.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "ORAN ERSTER",
-        "author_inst": "Israel Central Virology laboratory"
-      },
-      {
-        "author_name": "Areej Kabat",
-        "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel"
-      },
-      {
-        "author_name": "Hadar Asraf",
-        "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel"
-      },
-      {
-        "author_name": "Virginia Levy",
-        "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel"
-      },
-      {
-        "author_name": "Batya Mannasse",
-        "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel"
-      },
-      {
-        "author_name": "Roberto Azar",
-        "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel"
-      },
-      {
-        "author_name": "Ital Nemet",
-        "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel"
-      },
-      {
-        "author_name": "Limor Kliker",
-        "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel"
-      },
-      {
-        "author_name": "Shay Fleishon",
-        "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel"
-      },
-      {
-        "author_name": "Michal Mandelboim",
-        "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel, School of Public Health, Sackler Faculty"
-      },
-      {
-        "author_name": "Ella Mendelson",
-        "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel, School of Public Health, Sackler Faculty"
-      },
-      {
-        "author_name": "Neta S Zuckerman",
-        "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.03.02.22271710",
     "rel_title": "Daily tenofovir disoproxil fumarate/emtricitabine and hydroxychloroquine for pre-exposure prophylaxis of COVID-19: a double-blind placebo controlled randomized trial in healthcare workers",
@@ -359410,6 +357941,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2022.03.01.22271611",
+    "rel_title": "Predicting missed health care visits during the COVID-19 pandemic using machine learning methods: Evidence from 55,500 individuals from 28 European Countries",
+    "rel_date": "2022-03-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.01.22271611",
+    "rel_abs": "BackgroundThe COVID-19 pandemic has led many individuals to miss essential care. Machine-learning models that predict which patients are at greatest risk of missing care visits can help health administrators prioritize retentions efforts towards patients with the most need. Such approaches may be especially useful for efficiently targeting interventions for health systems overburdened by the COVID-19 pandemic.\n\nMethodsWe compare the performance of four machine learning algorithms to predict missed health care visits based on common patient characteristics available to most health care providers. We use data from 55,500 respondents of the Survey of Health, Ageing and Retirement in Europe (SHARE) COVID-19 survey (June - September 2020) in conjunction with longitudinal data from waves 1-8 (April 2004 - March 2020). We use stepwise selection, group lasso, random forest and neural network algorithms and employ 5-fold cross-validation to test the prediction accuracy, sensitivity, and specificity of the selected models.\n\nFindingsWithin our sample, 15.5% of the respondents reported any missed essential health care visit due to the COVID-19 pandemic. All four machine learning methods perform similarly in their predictive power. When classifying all individuals with a predicted probability for missed care above 17% as at risk of a missed visit, they correctly identify between 41% and 53% of the respondents at risk, while correctly identifying between 74% and 64% of the individuals not at risk. We find that the sensitivity and specificity of the models are strongly related to the risk threshold used to classify individuals; thus, the models can be calibrated depending on users resource constraints and targeting approach. All models had an area under the curve around 0.62, indicating that they outperform random prediction.\n\nInterpretationPandemics such as COVID-19 require rapid and efficient responses to reduce disruptions in health care. Based on characteristics available to health insurance providers, machine learning algorithms can be used to efficiently target efforts to reduce missed essential care.\n\nFundingResearch in this article is a part of the European Unions H2020 SHARE-COVID19 project (Grant Agreement No. 101015924).",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Anna Reuter",
+        "author_inst": "Heidelberg Institute of Global Health, Heidelberg University"
+      },
+      {
+        "author_name": "\u0160ime Smoli\u0107",
+        "author_inst": "Department of Macroeconomics and Economic Development, University of Zagreb"
+      },
+      {
+        "author_name": "Till B\u00e4rnighausen",
+        "author_inst": "Heidelberg Institute of Global Health, Heidelberg University"
+      },
+      {
+        "author_name": "Nikkil Sudharsanan",
+        "author_inst": "Technical University of Munich"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2022.03.02.22271734",
     "rel_title": "An observational study of the association between COVID-19 vaccination rates and participation in a vaccine lottery",
@@ -361035,73 +359597,6 @@
     "type": "new results",
     "category": "cell biology"
   },
-  {
-    "rel_doi": "10.1101/2022.03.02.22271610",
-    "rel_title": "Optimal vaccination with time-varying based on immunity barrier in Hunan Province, China",
-    "rel_date": "2022-03-03",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.02.22271610",
-    "rel_abs": "The current outbreak of novel coronavirus disease 2019 (COVID-19) is already causing a serious disease burden worldwide, this paper analyzed data of a delta variant Covid-19 outbreak in Hunan, China, and proposed an optimal dose-wise dynamical vaccinating process based on local contact pattern and vaccine coverage that minimize the accumulative cases in a certain future time interval. The optimized result requires an immediate vaccination to that none vaccinated at age group 30 to 39, which is coherent to the prevailing strategies. The dose-wise optimal vaccinating process can be directive for countries or regions where vaccines are not abundant. We recommend that vaccination should be further intensified to increase the coverage of booster shots, thus effectively reducing the spread of COVID-19.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Xiaohao Guo",
-        "author_inst": "Xiamen University"
-      },
-      {
-        "author_name": "Ziyan Liu",
-        "author_inst": "Hunan Provincial Center for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Shiting Yang",
-        "author_inst": "Xiamen University"
-      },
-      {
-        "author_name": "Zeyu Zhao",
-        "author_inst": "Xiamen University"
-      },
-      {
-        "author_name": "Yichao Guo",
-        "author_inst": "Xiamen University"
-      },
-      {
-        "author_name": "Guzainuer Abudurusuli",
-        "author_inst": "Xiamen University"
-      },
-      {
-        "author_name": "Jia Rui",
-        "author_inst": "Xiamen University"
-      },
-      {
-        "author_name": "Yao Wang",
-        "author_inst": "Xiamen University"
-      },
-      {
-        "author_name": "Shanlu Zhao",
-        "author_inst": "Hunan Provincial Center for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Ge Zeng",
-        "author_inst": "Hunan Provincial Center for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Shixiong Hu",
-        "author_inst": "Hunan Provincial Center for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Kaiwei Luo",
-        "author_inst": "Hunan Provincial Center for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Tianmu Chen",
-        "author_inst": "Xiamen University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2022.03.02.22271552",
     "rel_title": "A predictive model for hospitalization and survival to COVID-19 in a retrospective population-based study",
@@ -361508,6 +360003,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "hematology"
   },
+  {
+    "rel_doi": "10.1101/2022.02.28.22271591",
+    "rel_title": "Ammonium Sulfate Addition Reduces the Need for Guanidinium Isothiocyanate in the Denaturing Transport Medium Used for SARS-COV-2 RNA Detection",
+    "rel_date": "2022-03-02",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.28.22271591",
+    "rel_abs": "Rapid identification of SARS-CoV-2 infected individuals through viral RNA detection followed by effective personal isolation remains the most effective way to prevent the spread of this virus. Large-scale RNA detection involves mass specimen collection and transportation. For biosafety reasons, denaturing viral transport medium has been extensively used during the pandemic. But the high concentrations of guanidinium isothiocyanate (GITC) in such media have raised issues around sufficient GITC supply and laboratory safety. Here, we tested whether supplementing media containing low concentrations of GITC with ammonium sulfate (AS) would affect the throat-swab detection of SARS-CoV-2 pseudovirus or a viral inactivation assay targeting both enveloped and non-enveloped viruses. Adding AS to the denaturing transport media reduced the need for high levels of GITC and improved SARS-COV-2 RNA detection without compromising virus inactivation.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Ge Liu",
+        "author_inst": "Shenzhen Technology University"
+      },
+      {
+        "author_name": "Jiaoyan Jia",
+        "author_inst": "Shenzhen University"
+      },
+      {
+        "author_name": "Jianfeng Zhong",
+        "author_inst": "Shenzhen University"
+      },
+      {
+        "author_name": "Hanfang Jiang",
+        "author_inst": "Shenzhen Children's Hospital"
+      },
+      {
+        "author_name": "Yongqi Yang",
+        "author_inst": "Shenzhen University"
+      },
+      {
+        "author_name": "Xiujing Lu",
+        "author_inst": "GBCBIO Technologies Inc."
+      },
+      {
+        "author_name": "Zhendan He",
+        "author_inst": "Shenzhen Technology University"
+      },
+      {
+        "author_name": "Qinchang Zhu",
+        "author_inst": "Shenzhen Technology University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.03.01.22271576",
     "rel_title": "Transcriptomic clustering of critically ill COVID-19 patients",
@@ -362977,53 +361519,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2022.03.01.22271496",
-    "rel_title": "Development of a vocal biomarker for fatigue monitoring in people with COVID-19",
-    "rel_date": "2022-03-02",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.01.22271496",
-    "rel_abs": "ObjectiveTo develop a vocal biomarker for fatigue monitoring in people with COVID-19.\n\nDesignProspective cohort study.\n\nSettingPredi-COVID data between May 2020 and May 2021.\n\nParticipantsA total of 1772 voice recordings was used to train an AI-based algorithm to predict fatigue, stratified by gender and smartphones operating system (Android/iOS). The recordings were collected from 296 participants tracked for two weeks following SARS-CoV-2 infection.\n\nprimary and secondary outcome measuresFour machine learning algorithms (Logistic regression, k-nearest neighbors, support vector machine, and soft voting classifier) were used to train and derive the fatigue vocal biomarker. A t-test was used to evaluate the distribution of the vocal biomarker between the two classes (Fatigue and No fatigue).\n\nResultsThe final study population included 56% of women and had a mean ({+/-}SD) age of 40 ({+/-}13) years. Women were more likely to report fatigue (P<.001). We developed four models for Android female, Android male, iOS female, and iOS male users with a weighted AUC of 79%, 85%, 86%, 82%, and a mean Brier Score of 0.15, 0.12, 0.17, 0.12, respectively. The vocal biomarker derived from the prediction models successfully discriminated COVID-19 participants with and without fatigue (t-test P<.001).\n\nConclusionsThis study demonstrates the feasibility of identifying and remotely monitoring fatigue thanks to voice. Vocal biomarkers, digitally integrated into telemedicine technologies, are expected to improve the monitoring of people with COVID-19 or Long-COVID.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Abir Elbeji",
-        "author_inst": "Luxembourg Institute of Health"
-      },
-      {
-        "author_name": "Lu Zhang",
-        "author_inst": "Luxembourg Institute of Health"
-      },
-      {
-        "author_name": "Eduardo Higa",
-        "author_inst": "Luxembourg Institute of Health"
-      },
-      {
-        "author_name": "Aur\u00e9lie Fischer",
-        "author_inst": "Luxembourg Institute of Health"
-      },
-      {
-        "author_name": "Vladimir Despotovic",
-        "author_inst": "Luxembourg Institute of Health"
-      },
-      {
-        "author_name": "Petr V. Nazarov",
-        "author_inst": "Luxembourg Institute of Health"
-      },
-      {
-        "author_name": "Gloria A. Aguayo",
-        "author_inst": "Luxembourg Institute of Health"
-      },
-      {
-        "author_name": "Guy Fagherazzi",
-        "author_inst": "Luxembourg Institute of Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2022.03.02.22271697",
     "rel_title": "Recurrent SARS-CoV-2 Mutations in Immunodeficient Patients",
@@ -363686,6 +362181,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.02.27.22271579",
+    "rel_title": "Vaccine hesitancy strongly correlates with COVID-19 deaths underreporting",
+    "rel_date": "2022-03-01",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.27.22271579",
+    "rel_abs": "Vaccine acceptance is a key factor in achieving high immunization coverage and reducing the death toll of COVID-19 pandemic. Analyzing data from Europe and Americas we demonstrated that vaccine hesitancy strongly correlates with underreporting of COVID-19 deaths and cases. This correlation cannot be explained by the differences in economic indexes: GDP and Gini coefficient (measure of income inequalities). There is no correlation of vaccination percentage and Gini coefficient and the correlation with GDP is decreasing in time. The most striking is the comparison of Eastern European and South American countries; the latter group of countries shows significantly higher vaccination percentage while having a lower or comparable GDP and higher Gini coefficient. The analysis suggests that timely and reliable information about the COVID-19 cases and the associated deaths plays a key role in achieving population-wide vaccine acceptance.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Adam Sobieszek",
+        "author_inst": "Faculty of Psychology, University of Warsaw"
+      },
+      {
+        "author_name": "Miriam Lipniacka",
+        "author_inst": "Inter-Faculty Individual Studies in Mathematics and Natural Sciences, The MISMaP College, University of Warsaw"
+      },
+      {
+        "author_name": "Tomasz Lipniacki",
+        "author_inst": "Institute of Fundamental Technological Research, Polish Academy of Sciences"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2022.02.21.22270847",
     "rel_title": "COVID-19 testing: disparity between national and institution-based case detection",
@@ -364891,81 +363413,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2022.02.27.482176",
-    "rel_title": "Design, Synthesis and Evaluation of Inhibitors of the SARS-CoV-2 nsp3 Macrodomain",
-    "rel_date": "2022-02-28",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.27.482176",
-    "rel_abs": "A series of amino acid based 7H-pyrrolo[2,3-d]pyrimidines were designed and synthesized to discern the structure activity relationships against the SARS-CoV-2 nsp3 macrodomain (Mac1), an ADP-ribosylhydrolase that is critical for coronavirus replication and pathogenesis. Structure activity studies identified compound 15c as a low-micromolar inhibitor of Mac1 in two ADP-ribose binding assays. This compound also demonstrated inhibition in an enzymatic assay of Mac1 and displayed a thermal shift comparable to ADPr in the melting temperature of Mac1 supporting binding to the target protein. A structural model reproducibly predicted a binding mode where the pyrrolo pyrimidine forms a hydrogen bonding network with Asp22 and the amide backbone NH of Ile23 in the adenosine binding pocket and the carboxylate forms hydrogen bonds to the amide backbone of Phe157 and Asp156, part of the oxyanion subsite of Mac1. Compound 15c also demonstrated notable selectivity for coronavirus macrodomains when tested against a panel of ADP-ribose binding proteins. Together, this study identified several low MW, low M Mac1 inhibitors to use as small molecule chemical probes for this potential anti-viral target and offers starting points for further optimization.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC=\"FIGDIR/small/482176v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (16K):\norg.highwire.dtl.DTLVardef@167aceorg.highwire.dtl.DTLVardef@1d88c47org.highwire.dtl.DTLVardef@1e1b34borg.highwire.dtl.DTLVardef@c2321a_HPS_FORMAT_FIGEXP  M_FIG C_FIG",
-    "rel_num_authors": 15,
-    "rel_authors": [
-      {
-        "author_name": "Lavinia M Sherrill",
-        "author_inst": "McDaniel College"
-      },
-      {
-        "author_name": "Elva E Joya",
-        "author_inst": "McDaniel College"
-      },
-      {
-        "author_name": "AnnMarie Walker",
-        "author_inst": "McDaniel College"
-      },
-      {
-        "author_name": "Anuradha Roy",
-        "author_inst": "University of Kansas"
-      },
-      {
-        "author_name": "Yousef M Alhammad",
-        "author_inst": "University of Kansas"
-      },
-      {
-        "author_name": "Moriama Atobatele",
-        "author_inst": "University of Kansas"
-      },
-      {
-        "author_name": "Sarah Wazir",
-        "author_inst": "Oulu University"
-      },
-      {
-        "author_name": "George Abbas",
-        "author_inst": "McDaniel College"
-      },
-      {
-        "author_name": "Patrick Keane",
-        "author_inst": "McDaniel College"
-      },
-      {
-        "author_name": "Junlin Zhuo",
-        "author_inst": "Johns Hopkins University"
-      },
-      {
-        "author_name": "Anthony Leung",
-        "author_inst": "Johns Hopkins University"
-      },
-      {
-        "author_name": "David K Johnson",
-        "author_inst": "University of Kansas"
-      },
-      {
-        "author_name": "Lari Lehtio",
-        "author_inst": "University of Oulu"
-      },
-      {
-        "author_name": "Anthony Fehr",
-        "author_inst": "University of Kansas"
-      },
-      {
-        "author_name": "Dana V Ferraris",
-        "author_inst": "McDaniel College"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "biochemistry"
-  },
   {
     "rel_doi": "10.1101/2022.02.27.22271090",
     "rel_title": "Comparison of Rapid Antigen Tests' Performance between Delta (B.1.61.7; AY.X) and Omicron (B.1.1.529; BA1) Variants of SARS-CoV-2: Secondary Analysis from a Serial Home Self-Testing Study",
@@ -365440,6 +363887,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.02.25.22271529",
+    "rel_title": "Study on the usefulness of Direct Saliva sample Collection (DiSC) by polyester swab",
+    "rel_date": "2022-02-28",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.25.22271529",
+    "rel_abs": "Saliva sample can be self-collected and used in testing of SARS-CoV-2 nucleic acid amplification tests (NAATs) test in Japan. However, this may have difficulty collecting a proper specimen when collecting for the first time. We compared 2 collection methods, conventional methods and Direct Saliva Sample Collection method (DiSC) from 44 asymptomatic or symptomatic individuals who were in quarantine in Toho university hospital. RT-PCR by DiSC method showed about 70 % positive percent agreement compared to RT-PCR by conventional methods. In addition, comparing RT-PCR and TMA by DiSC method, TMA showed about 90 % positive percent agreement compared to RT-PCR. DiSC method is easy to perform by every person, does not have complicated restrictions/instructions and can be used in RT-PCR and TMA. This method allows for ease of saliva collection in certain patient populations.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Kotaro Aoki",
+        "author_inst": "Toho University"
+      },
+      {
+        "author_name": "Mami Nagashima",
+        "author_inst": "Tokyo Metropolitan Institute of Public Health"
+      },
+      {
+        "author_name": "Katsuhito Kashiwagi",
+        "author_inst": "Toho University Omori Medical Center"
+      },
+      {
+        "author_name": "Takashi Chiba",
+        "author_inst": "Tokyo Metropolitan Institute of Public Health"
+      },
+      {
+        "author_name": "Kenji Sadamasu",
+        "author_inst": "Tokyo Metropolitan Institute of Public Health"
+      },
+      {
+        "author_name": "Yoshikazu Ishii",
+        "author_inst": "Toho University"
+      },
+      {
+        "author_name": "Kazuhiro Tateda",
+        "author_inst": "Toho University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.02.27.22271593",
     "rel_title": "Vaccination and Variants: retrospective model for the evolution of Covid-19 in Italy",
@@ -366741,73 +365231,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health systems and quality improvement"
   },
-  {
-    "rel_doi": "10.1101/2022.02.25.22271515",
-    "rel_title": "Duration of Protection Against SARS-CoV-2 Reinfection and Associated Risk of Reinfection Assessed with Real-World Data",
-    "rel_date": "2022-02-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.25.22271515",
-    "rel_abs": "ImportanceBetter understanding of the protective duration of prior SARS-CoV-2 infection against reinfection is needed.\n\nObjectivePrimary: To assess the durability of immunity to SARS-CoV-2 reinfection among initially unvaccinated individuals with previous SARS-CoV-2 infection. Secondary: Evaluate the crude SARS-CoV-2 reinfection rate and associated characteristics.\n\nDesign and SettingRetrospective observational study of HealthVerity data among 144,678,382 individuals, during the pandemic era through April 2021.\n\nParticipantsIndividuals studied had SARS-CoV-2 molecular diagnostic or antibody index test results from February 29 through December 9, 2020, with [&ge;]365 days of pre-index continuous closed medical enrollment, claims, or electronic health record activity.\n\nMain Outcome(s) and Measure(s)Rates of reinfection among index-positive individuals were compared to rates of infection among index-negative individuals. Factors associated with reinfection were evaluated using multivariable logistic regression. For both objectives, the outcome was a subsequent positive molecular diagnostic test result.\n\nResultsAmong 22,786,982 individuals with index SARS-CoV-2 laboratory test data (2,023,341 index positive), the crude rate of reinfection during follow-up was significantly lower (9.89/1,000-person years) than that of primary infection (78.39/1,000 person years). Consistent with prior findings, the risk of reinfection among index-positive individuals was 87% lower than the risk of infection among index-negative individuals (hazard ratio, 0.13; 95% CI, 0.13, 0.13). The cumulative incidence of reinfection among index-positive individuals and infection among index-negative individuals was 0.85% (95% CI: 0.82%, 0.88%) and 6.2% (95% CI: 6.1%, 6.3%), respectively, over follow-up of 375 days. The duration of protection against reinfection was stable over the median 5 months and up to 1-year follow-up interval. Factors associated with an increased reinfection risk included older age, comorbid immunologic conditions, and living in congregate care settings; healthcare workers had a decreased reinfection risk.\n\nConclusions and RelevanceThis large US population-based study demonstrates that SARS-CoV-2 reinfection is uncommon among individuals with laboratory evidence of a previous infection. Protection from SARS-CoV-2 reinfection is stable up to one year. Reinfection risk was primarily associated with age 85+ years, comorbid immunologic conditions and living in congregate care settings; healthcare workers demonstrated a decreased reinfection risk. These findings suggest that infection induced immunity is durable for variants circulating prior to Delta.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSHow long does prior SARS-CoV-2 infection provide protection against SARS-CoV-2 reinfection?\n\nFindingAmong >22 million individuals tested February 2020 through April 2021, the relative risk of reinfection among those with prior infection was 87% lower than the risk of infection among individuals without prior infection. This protection was durable for up to a year. Factors associated with increased likelihood of reinfection included older age (85+ years), comorbid immunologic conditions, and living in congregate care settings; healthcare workers had lower risk.\n\nMeaningPrior SARS-CoV-2 infection provides a durable, high relative degree of protection against reinfection.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Shannon L Reynolds",
-        "author_inst": "Aetion, Inc."
-      },
-      {
-        "author_name": "Harvey W Kaufman",
-        "author_inst": "Quest Diagnostics"
-      },
-      {
-        "author_name": "William A Meyer III",
-        "author_inst": "Quest Diagnostics"
-      },
-      {
-        "author_name": "Christopher Bush",
-        "author_inst": "Aetion, Inc."
-      },
-      {
-        "author_name": "Oren Cohen",
-        "author_inst": "Labcorp Drug Development"
-      },
-      {
-        "author_name": "Kathy Cronin",
-        "author_inst": "National Cancer Institute"
-      },
-      {
-        "author_name": "Carly Kabelac",
-        "author_inst": "Aetion, Inc."
-      },
-      {
-        "author_name": "Sandy Leonard",
-        "author_inst": "HealthVerity"
-      },
-      {
-        "author_name": "Steve Anderson",
-        "author_inst": "Labcorp Drug Development"
-      },
-      {
-        "author_name": "Valentia Petkov",
-        "author_inst": "National Cancer Institute"
-      },
-      {
-        "author_name": "Douglas Lowy",
-        "author_inst": "National Cancer Institute"
-      },
-      {
-        "author_name": "Norman Sharpless",
-        "author_inst": "National Cancer Institute"
-      },
-      {
-        "author_name": "Lynne Penberthy",
-        "author_inst": "National Cancer Institute"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.02.25.22271499",
     "rel_title": "Reassessment of persistent symptoms, self-reported COVID-19 infection and SARS-CoV-2 serology in the SAPRIS-SERO cohort: identifying possible sub-syndromes of Long Covid.",
@@ -367090,6 +365513,49 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2022.02.25.481997",
+    "rel_title": "Adenosine A2A Receptor (A2AR) agonists improve survival in K28-hACE2 mice following SARS CoV-2 infection",
+    "rel_date": "2022-02-26",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.25.481997",
+    "rel_abs": "Effective and available therapies for the treatment of COVID-19 disease are limited. Apadenoson is a highly potent selective anti-inflammatory adenosine A2A receptor (A2AR) agonist and potential treatment option for COVID-19 patients. Apadenoson, when administered after infection with SARS CoV-2, was found to decrease weight loss, improve clinical symptoms, reduce levels of a several proinflammatory cytokines and chemokines in bronchial lavage (BAL) fluid, and promote increased survival in K18hACE2 transgenic mice. Of note, administering apadenoson after, but not prior to Covid-19 infection, caused a rapid decrease in lung viral burden. The work presented provides the foundation for further examination of these drugs as a therapy option for COVID-19.\n\nSummaryApadenoson therapy improves COVID-19 outcome",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Barbara J Mann",
+        "author_inst": "University of Virginia"
+      },
+      {
+        "author_name": "Preeti Chhabra",
+        "author_inst": "University of Virginia"
+      },
+      {
+        "author_name": "Mingyang Ma",
+        "author_inst": "University of Virginia"
+      },
+      {
+        "author_name": "Savannah G Brovero",
+        "author_inst": "University of Virginia"
+      },
+      {
+        "author_name": "Marieka K Jones",
+        "author_inst": "University of Virginia"
+      },
+      {
+        "author_name": "Joel M Linden",
+        "author_inst": "University of Virginia"
+      },
+      {
+        "author_name": "Kenneth L Brayman",
+        "author_inst": "University of Virginia"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2022.02.24.481848",
     "rel_title": "Discovery of a novel coronavirus in Swedish bank voles (Myodes glareolus)",
@@ -368551,129 +367017,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2022.02.21.481223",
-    "rel_title": "Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions",
-    "rel_date": "2022-02-24",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.21.481223",
-    "rel_abs": "The COVID-19 pandemic is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The betacoronvirus has a positive sense RNA genome which encodes for several RNA binding proteins. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral and host RNAs in authentic virus-infected cells. SARS-CoV-2 proteins, NSP8, NSP12, and nucleocapsid display distinct preferences to specific regions in the RNA viral genome, providing evidence for their shared and separate roles in replication, transcription, and viral packaging. SARS-CoV-2 proteins expressed in human lung epithelial cells bind to 4773 unique host coding RNAs. Nine SARS-CoV-2 proteins upregulate target gene expression, including NSP12 and ORF9c, whose RNA substrates are associated with pathways in protein N-linked glycosylation ER processing and mitochondrial processes. Furthermore, siRNA knockdown of host genes targeted by viral proteins in human lung organoid cells identify potential antiviral host targets across different SARS-CoV-2 variants. Conversely, NSP9 inhibits host gene expression by blocking mRNA export and dampens cytokine productions, including interleukin-1/{beta}. Our viral protein-RNA interactome provides a catalog of potential therapeutic targets and offers insight into the etiology of COVID-19 as a safeguard against future pandemics.",
-    "rel_num_authors": 27,
-    "rel_authors": [
-      {
-        "author_name": "Joy S Xiang",
-        "author_inst": "Agency for Science, Technology and Research (A*STAR)"
-      },
-      {
-        "author_name": "Jasmine R Mueller",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "En-Ching Luo",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Brian A Yee",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Danielle Schafer",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Jonathan C Schmok",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Frederick E Tan",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Katherine Rothamel",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Rachael N McVicar",
-        "author_inst": "Sanford Burnham Prebys Medical Discovery Institute"
-      },
-      {
-        "author_name": "Elizabeth M Kwong",
-        "author_inst": "Sanford Burnham Prebys Medical Discovery Institute"
-      },
-      {
-        "author_name": "Krysten L Jones",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Hsuan-Lin Her",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Chun-Yuan Chen",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Anthony Q Vu",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Wenhao Jin",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Samuel S Park",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Phuong Le",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Kristopher W Brannan",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Eric R Kofman",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Yanhua Li",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "Alexandra T Tankka",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Kevin D Dong",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Yan Song",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Aaron F Carlin",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Eric L Van Nostrand",
-        "author_inst": "Baylor College of Medicine"
-      },
-      {
-        "author_name": "Sandra L Leibel",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Gene W Yeo",
-        "author_inst": "University of California San Diego"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "molecular biology"
-  },
   {
     "rel_doi": "10.1101/2022.02.18.481096",
     "rel_title": "Omicron and Alpha P680H block SARS-CoV2 spike protein from accessing cholinergic inflammatory pathway via \u03b19-nAChR mitigating the risk of MIS-C",
@@ -368940,6 +367283,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health systems and quality improvement"
   },
+  {
+    "rel_doi": "10.1101/2022.02.22.22270091",
+    "rel_title": "Abdominal Imaging Associates Body Composition with COVID-19 Severity",
+    "rel_date": "2022-02-24",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.22.22270091",
+    "rel_abs": "The main drivers of COVID-19 disease severity and the impact of COVID-19 on long-term health after recovery are yet to be fully understood. Medical imaging studies investigating COVID-19 to date have mostly been limited to small datasets and post-hoc analyses of severe cases. The UK Biobank recruited recovered SARS-CoV-2 positive individuals (n=967) and matched controls (n=913) who were extensively imaged prior to the pandemic and underwent follow-up scanning. In this study, we investigated longitudinal changes in body composition, as well as the associations of pre-pandemic image-derived phenotypes with COVID-19 severity. Our longitudinal analysis, in a population of mostly mild cases, associated a decrease in lung volume with SARS-CoV-2 positivity. We also observed that increased visceral adipose tissue and liver fat, and reduced muscle volume, prior to COVID-19, were associated with COVID-19 disease severity. Finally, we trained a machine classifier with demographic, anthropometric and imaging traits, and showed that visceral fat, liver fat and muscle volume have prognostic value for COVID-19 disease severity beyond the standard demographic and anthropometric measurements. This combination of image-derived phenotypes from abdominal MRI scans and ensemble learning to predict risk may have future clinical utility in identifying populations at-risk for a severe COVID-19 outcome.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Nicolas Basty",
+        "author_inst": "Research Centre for Optimal Health, School of Life Sciences, University of Westminster, London, UK"
+      },
+      {
+        "author_name": "Elena P Sorokin",
+        "author_inst": "Calico Life Sciences LLC, South San Francisco, California, USA"
+      },
+      {
+        "author_name": "Marjola Thanaj",
+        "author_inst": "Research Centre for Optimal Health, School of Life Sciences, University of Westminster, London, UK"
+      },
+      {
+        "author_name": "Ramprakash Srinivasan",
+        "author_inst": "Calico Life Sciences LLC, South San Francisco, California, USA"
+      },
+      {
+        "author_name": "Brandon Whitcher",
+        "author_inst": "Research Centre for Optimal Health, School of Life Sciences, University of Westminster, London, UK"
+      },
+      {
+        "author_name": "Jimmy D Bell",
+        "author_inst": "Research Centre for Optimal Health, School of Life Sciences, University of Westminster, London, UK"
+      },
+      {
+        "author_name": "Madeleine Cule",
+        "author_inst": "Calico Life Sciences LLC, South San Francisco, California, USA"
+      },
+      {
+        "author_name": "E. Louise Thomas",
+        "author_inst": "Research Centre for Optimal Health, School of Life Sciences, University of Westminster, London, UK"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.02.18.22271189",
     "rel_title": "Avoiding false positive SARS-CoV-2 rapid antigen test results with point-of-care molecular testing on residual test buffer",
@@ -370105,29 +368495,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2022.02.23.22271390",
-    "rel_title": "Challenges and Opportunities Experienced by Performing Artists during COVID-19 Lockdown: Scoping Review",
-    "rel_date": "2022-02-24",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.23.22271390",
-    "rel_abs": "This scoping review synthesises published literature on the experiences of professional and amateur performing artists during COVID-19 and their perceptions of the challenges and opportunities faced. Six electronic databases were searched for published English-language articles containing primary data on this topic; twenty-one studies were reviewed. Themes included loss of work, financial impact, concerns about the future, psychological wellbeing, social connections, continuing creative pursuits, and inequalities. Participants reported both detrimental psychological effects of lockdown such as anxiety and sleep problems and positive effects including reduced stress and enjoyment of having more free time. Most continued creative pursuits throughout lockdown, most commonly shifting to online platforms. However, many barriers to creative pursuits were reported, including lack of technological expertise or equipment. Concerns were raised about inequality, in particular racial disparities in the financial impact of the pandemic and additional pressures faced by performers with disabilities; with insufficient funds to afford the equipment needed to shift to remote performing; and with additional caring responsibilities. It is important that performing artists have access to peer support; that education on digital technologies is incorporated into future performing arts education; and that inequities are addressed to ensure the needs of diverse communities are met.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Samantha K Brooks",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Sonny S Patel",
-        "author_inst": "Department of Global Health and Population, Harvard T.H. Chan School of Public Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "occupational and environmental health"
-  },
   {
     "rel_doi": "10.1101/2022.02.23.22271409",
     "rel_title": "Olfactory loss is an early and reliable marker for COVID-19",
@@ -370530,6 +368897,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "gastroenterology"
   },
+  {
+    "rel_doi": "10.1101/2022.02.21.22271127",
+    "rel_title": "Favourable vaccine-induced SARS-CoV-2 specific T cell response profile in patients undergoing immune-modifying therapies",
+    "rel_date": "2022-02-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.21.22271127",
+    "rel_abs": "Patients undergoing immune-modifying therapies demonstrate a reduced humoral response after COVID-19 vaccination, but we lack a proper evaluation of the impact of such therapies on vaccine-induced T cell responses. Here, we longitudinally characterised humoral and Spike-specific T cell responses in inflammatory bowel disease (IBD) patients who are on antimetabolite therapy (azathioprine or methotrexate), TNF inhibitors and/or other biologic treatment (anti-integrin or anti-p40) after mRNA vaccination up to 3 months after completing two vaccine doses. We demonstrated that a Spike-specific T cell response is not only induced in treated IBD patients at levels similar to healthy individuals, but also sustained at higher magnitude, particularly in those treated with TNF inhibitor therapy. Furthermore, the Spike-specific T cell response in these patients is mainly preserved against mutations present in SARS-CoV-2 B.1.1.529 (Omicron) and characterized by a Th1/IL-10 cytokine profile. Thus, despite the humoral response defects, the favourable profile of vaccine-induced T cell responses might still provide a layer of COVID-19 protection to patients under immune-modifying therapies.",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Martin QI",
+        "author_inst": "Programme in Emerging Infectious Diseases, Duke-NUS Medical School; Singapore"
+      },
+      {
+        "author_name": "Nina Le Bert",
+        "author_inst": "Programme in Emerging Infectious Diseases, Duke-NUS Medical School; Singapore."
+      },
+      {
+        "author_name": "Webber Chan",
+        "author_inst": "Department of Gastroenterology and Hepatology, Singapore General Hospital; Singapore"
+      },
+      {
+        "author_name": "Malcom Tan",
+        "author_inst": "Department of Gastroenterology and Hepatology, Singapore General Hospital; Singapore"
+      },
+      {
+        "author_name": "Shou Kit Hang",
+        "author_inst": "Programme in Emerging Infectious Diseases, Duke-NUS Medical School; Singapore"
+      },
+      {
+        "author_name": "Smrithi Hariharaputran",
+        "author_inst": "Programme in Emerging Infectious Diseases, Duke-NUS Medical School; Singapore"
+      },
+      {
+        "author_name": "Jean Xiang Ying Sim",
+        "author_inst": "Department of Infectious Disease, Singapore General Hospital; Singapore"
+      },
+      {
+        "author_name": "Jenny Low",
+        "author_inst": "Department of Infectious Disease, Singapore General Hospital; Singapore"
+      },
+      {
+        "author_name": "Wei Ling Ng",
+        "author_inst": "Department of Microbiology, Singapore General Hospital; Singapore"
+      },
+      {
+        "author_name": "Wei Yee Wan",
+        "author_inst": "Department of Microbiology, Singapore General Hospital; Singapore"
+      },
+      {
+        "author_name": "Tiing Leong Ang",
+        "author_inst": "Department of Gastroenterology and Hepatology, Changi General Hospital; Singapore"
+      },
+      {
+        "author_name": "Antonio Bertoletti",
+        "author_inst": "Duke-Nus Medical School"
+      },
+      {
+        "author_name": "Ennaliza Salazar",
+        "author_inst": "Department of Gastroenterology and Hepatology, Singapore General Hospital; Singapore"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.02.21.22271234",
     "rel_title": "Cell-Mediated Immune Response after COVID 19 Vaccination in Patients with Inflammatory Bowel Disease",
@@ -372074,49 +370508,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2022.02.21.481267",
-    "rel_title": "Edible formulations of chicken egg derived IgY antibodies neutralize SarsCoV2 Omicron RBD binding to human ACE2",
-    "rel_date": "2022-02-22",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.21.481267",
-    "rel_abs": "SarsCoV2 virus driven pandemic continues to surge propelled by new mutations such as seen in Omicron strain. Omicron is now rapidly becoming the dominant strain globally with more than 30 mutations in the spike protein. The mutations have resulted in Omicron strain escaping most of the neutralizing antibodies generated by the current set of approved vaccines and diluting the protection offered by the vaccines and therapeutic monoclonal antibodies.\n\nThis has necessitated the need for newer strategies to prevent this strain from spreading. Towards this unmet need we have developed chicken egg derived anti-RBD IgY antibodies that neutralize the binding of Omicron RBD to human ACE2. Furthermore, we have formulated the edible IgY as flavored beverages to allow for use as oral rinse and prevent the entry of Omicron in the oropharyngeal passage, a major access and accumulation point for this strain in humans.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Kranti Meher",
-        "author_inst": "Reagene Biosciences Pvt Ltd"
-      },
-      {
-        "author_name": "S Sivakumar",
-        "author_inst": "Kyntox Bio Pvt Ltd"
-      },
-      {
-        "author_name": "Gopi Kadiyala",
-        "author_inst": "Kyntox Bio Pvt Ltd"
-      },
-      {
-        "author_name": "Subramanian Iyer",
-        "author_inst": "Prodigy Inc USA"
-      },
-      {
-        "author_name": "Subrahmanyam Vangala",
-        "author_inst": "Reagene Biosciences Pvt Ltd"
-      },
-      {
-        "author_name": "Satish Chandran",
-        "author_inst": "Prodigy Bio Inc USA"
-      },
-      {
-        "author_name": "Uday Saxena",
-        "author_inst": "Reagene Biosciences Pvt Ltd"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2022.02.21.22271300",
     "rel_title": "COVID infection rates, clinical outcomes, and racial/ethnic and gender disparities before and after Omicron emerged in the US",
@@ -372419,6 +370810,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.02.21.22271298",
+    "rel_title": "Effectiveness of Covid-19 vaccines against symptomatic and asymptomatic SARS-CoV-2 infections in an urgent care setting",
+    "rel_date": "2022-02-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.21.22271298",
+    "rel_abs": "BackgroundIt is critical to monitor changes in vaccine effectiveness against COVID-19 outcomes for various vaccine products in different population subgroups.\n\nMethodsWe conducted a retrospective study in patients [&ge;]12 years who underwent testing for the SARS-CoV-2 virus from April 1 - October 25, 2021 at urgent care centers in the New York City metropolitan area. Patients self-reported vaccination status at the time of testing. We used a test-negative design to estimate vaccine effectiveness (VE) by comparing odds of a positive test for SARS-CoV-2 infection among vaccinated (n=484,468), partially vaccinated (n=107,573), and unvaccinated (n=466,452) patients, adjusted for demographic factors and calendar time.\n\nResultsVE against symptomatic infection after 2 doses of mRNA vaccines was 96% (95% Confidence Interval [CI]: 95%, 97%) in the pre-delta period and reduced to 79% (95% CI: 77%, 81%) in the delta period. In the delta period, VE for 12-15-year-olds (85%; [95% CI: 81%, 89%]) was higher compared to older age groups (<65% for all other age groups). VE estimates did not differ by sex, race/ethnicity, and comorbidity. VE against symptomatic infection was the highest for individuals with a prior infection followed by full vaccination. VE against symptomatic infection after the mRNA-1273 vaccine (83% [95% CI: 81%, 84%]) was higher compared to the BNT162b2 vaccine (76% [95% CI: 74%, 78%]) in the delta period. VE after the single-dose Ad26.COV2.S vaccine was the lowest compared to other vaccines (29% [95% CI: 26%, 32%]) in the delta period.\n\nConclusionsVE against infection after two doses of the mRNA vaccine was high initially, but significantly reduced against the delta variant for all three FDA-approved vaccines.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Madhura S. Rane",
+        "author_inst": "Institute for Implementation Science in Population Health, City University of New York. New York, NY USA"
+      },
+      {
+        "author_name": "McKaylee Robertson",
+        "author_inst": "Institute for Implementation Science in Population Health, City University of New York. New York, NY USA"
+      },
+      {
+        "author_name": "Sarah Kulkarni",
+        "author_inst": "Institute for Implementation Science in Population Health, City University of New York. New York, NY USA"
+      },
+      {
+        "author_name": "Daniel Frogel",
+        "author_inst": "CityMD/Summit Medical Group, New York, NY, USA"
+      },
+      {
+        "author_name": "Chris Gainus",
+        "author_inst": "CityMD/Summit Medical Group, New York, NY, USA"
+      },
+      {
+        "author_name": "Denis Nash",
+        "author_inst": "CUNY Graduate School of Public Health; Institute for Implementation Science in Population Health, City University of New York. New York, NY USA"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.02.19.22271230",
     "rel_title": "A role for Nucleocapsid-specific antibody function in Covid-19 Convalescent plasma therapy",
@@ -374104,121 +372534,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.02.17.22269742",
-    "rel_title": "Genomically informed clinical comparison of three epidemic waves of COVID-19 in Malawi",
-    "rel_date": "2022-02-19",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.17.22269742",
-    "rel_abs": "BackgroundCompared to the abundance of clinical and genomic information available on patients hospitalised with COVID-19 disease from high-income countries, there is a paucity of data from low-income countries. Our aim was to explore the relationship between viral lineage and patient outcome.\n\nMethodsWe enrolled a prospective observational cohort of adult patients hospitalised with PCR-confirmed COVID-19 disease between July 2020 and March 2022 from Blantyre, Malawi, covering four waves of SARS-CoV-2 infections. Clinical and diagnostic data were collected using an adapted ISARIC clinical characterization protocol for COVID-19. SARS-CoV-2 isolates were sequenced using the MinION in Blantyre.\n\nResultsWe enrolled 314 patients, good quality sequencing data was available for 55 patients. The sequencing data showed that 8 of 11 participants recruited in wave one had B.1 infections, 6/6 in wave two had Beta, 25/26 in wave three had Delta and 11/12 in wave four had Omicron. Patients infected during the Delta and Omicron waves reported fewer underlying chronic conditions and a shorter time to presentation. Significantly fewer patients required oxygen (22.7% [17/75] vs. 58.6% [140/239], p<0.001) and steroids (38.7% [29/75] vs. 70.3% [167/239], p<0.001) in the Omicron wave compared with the other waves. Multivariable logistic-regression demonstrated a trend toward increased mortality in the Delta wave (OR 4.99 [95% CI 1.0-25.0 p=0.05) compared to the first wave of infection.\n\nConclusionsOur data show that each wave of patients hospitalised with SARS-CoV-2 was infected with a distinct viral variant. The clinical data suggests that patients with severe COVID-19 disease were more likely to die during the Delta wave.\n\nSummaryWe used genome sequencing to identify the variants of SARS-CoV-2 causing disease in Malawi, and found that each of the four waves was caused by a distinct variant. Clinical investigation suggested that the Delta wave had the highest mortality.",
-    "rel_num_authors": 25,
-    "rel_authors": [
-      {
-        "author_name": "Catherine Anscombe",
-        "author_inst": "Malawi-Liverpool-Wellcome Clinical Research Programme"
-      },
-      {
-        "author_name": "Samantha Lissauer",
-        "author_inst": "Malawi-Liverpool-Wellcome Clinical Research Programme"
-      },
-      {
-        "author_name": "Herbert Thole",
-        "author_inst": "Malawi-Liverpool-Wellcome Clinical Research Programme"
-      },
-      {
-        "author_name": "Jamie Rylance",
-        "author_inst": "Malawi-Liverpool-Wellcome Clinical Research Programme"
-      },
-      {
-        "author_name": "Dingase Dula",
-        "author_inst": "Malawi-Liverpool-Wellcome Clinical Research Programme"
-      },
-      {
-        "author_name": "Mavis Menyere",
-        "author_inst": "Malawi-Liverpool-Wellcome Clinical Research Programme"
-      },
-      {
-        "author_name": "Belson Kutambe",
-        "author_inst": "Malawi-Liverpool-Wellcome Clinical Research Programme"
-      },
-      {
-        "author_name": "Charlotte van der Veer",
-        "author_inst": "Malawi-Liverpool-Wellcome Clinical Research Programme"
-      },
-      {
-        "author_name": "Tamara Phiri",
-        "author_inst": "Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi"
-      },
-      {
-        "author_name": "Ndaziona P. Banda",
-        "author_inst": "Kamuzu University of Health Sciences (formerly University of Malawi-College of Medicine) Blantyre, Malawi"
-      },
-      {
-        "author_name": "Kwazizira S. Mndolo",
-        "author_inst": "Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi"
-      },
-      {
-        "author_name": "Kelvin Mponda",
-        "author_inst": "Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi"
-      },
-      {
-        "author_name": "Chimota Phiri",
-        "author_inst": "Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi"
-      },
-      {
-        "author_name": "Jane Mallewa",
-        "author_inst": "Kamuzu University of Health Sciences (formerly University of Malawi-College of Medicine) Blantyre, Malawi"
-      },
-      {
-        "author_name": "Mulinda Nyirenda",
-        "author_inst": "Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi"
-      },
-      {
-        "author_name": "Grace Katha",
-        "author_inst": "Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi"
-      },
-      {
-        "author_name": "Jennifer Cornick",
-        "author_inst": "Malawi-Liverpool-Wellcome Clinical Research Programme"
-      },
-      {
-        "author_name": "Henry Mwandumba",
-        "author_inst": "Malawi-Liverpool-Wellcome Clinical Research Programme"
-      },
-      {
-        "author_name": "Stephen B. Gordon",
-        "author_inst": "Malawi-Liverpool-Wellcome Clinical Research Programme"
-      },
-      {
-        "author_name": "Kondwani C. Jambo",
-        "author_inst": "Malawi-Liverpool-Wellcome Clinical Research Programme"
-      },
-      {
-        "author_name": "Nicholas Feasey",
-        "author_inst": "Malawi-Liverpool-Wellcome Clinical Research Programme"
-      },
-      {
-        "author_name": "Kayla G. Barnes",
-        "author_inst": "Malawi-Liverpool-Wellcome Clinical Research Programme"
-      },
-      {
-        "author_name": "Ben Morton",
-        "author_inst": "Malawi-Liverpool-Wellcome Clinical Research Programme"
-      },
-      {
-        "author_name": "Philip M. Ashton",
-        "author_inst": "Malawi-Liverpool-Wellcome Clinical Research Programme"
-      },
-      {
-        "author_name": "- Blantyre COVID-Consortium",
-        "author_inst": ""
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.02.17.22271030",
     "rel_title": "Clinical severity of Omicron sub-lineage BA.2 compared to BA.1 in South Africa",
@@ -374605,6 +372920,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.02.19.22271221",
+    "rel_title": "Risk of SARS-CoV-2 reinfection 18 months after primary infection: population-level observational study.",
+    "rel_date": "2022-02-19",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.19.22271221",
+    "rel_abs": "Current data suggest that SARS-CoV-2 reinfections are rare, but uncertainties remain on the duration of the natural immunity, its protection against Omicron variant, finally the impact of vaccination to reduce reinfection rates. In this retrospective cohort analysis of the entire population of an Italian Region, we followed 1,293,941 subjects from the beginning of the pandemic to the current scenario of Omicron predominance (up to mid-January 2022). After an average of 334 days, we recorded 260 reinfections among 84,907 previously infected subjects (overall rate: 0.31%), two hospitalizations (2.4 x100,000), and one death. Importantly, the incidence of reinfection did not vary substantially over time: after 18-22 months from the primary infection, the reinfection rate was still 0.32%, suggesting that protection conferred by natural immunity may last beyond 12 months. The risk of reinfection was significantly higher among the unvaccinated subjects, and during the Omicron wave.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Maria Elena Flacco",
+        "author_inst": "University of Ferrara"
+      },
+      {
+        "author_name": "Graziella Soldato",
+        "author_inst": "Local Health Unit of Pescara"
+      },
+      {
+        "author_name": "Cecilia Acuti Martellucci",
+        "author_inst": "University of Ferrara"
+      },
+      {
+        "author_name": "Giuseppe Di Martino",
+        "author_inst": "Local Health Unit of Pescara"
+      },
+      {
+        "author_name": "Roberto Carota",
+        "author_inst": "Local Health Unit of Pescara"
+      },
+      {
+        "author_name": "Antonio Caponetti",
+        "author_inst": "Local Health Unit of Pescara"
+      },
+      {
+        "author_name": "Lamberto Manzoli",
+        "author_inst": "University of Bologna"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.02.15.22271010",
     "rel_title": "The level of liver and renal function biomarker abnormalities among hospitalized COVID-19 patients in Ethiopia",
@@ -376046,57 +374404,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2022.02.17.22271122",
-    "rel_title": "Effectiveness and durability of the mRNA vaccine-induced SARS-CoV-2-specific humoral and cellular immunity in severe asthma patients on biological therapy",
-    "rel_date": "2022-02-17",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.17.22271122",
-    "rel_abs": "The COVID-19 vaccines effectively elicit humoral and cellular immunity against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a healthy population. This immunity decreases several months after the vaccination. However, the efficacy of the vaccine-induced immunity and its durability in patients with severe asthma on biological therapy is unknown. In this study, we evaluated the effectiveness and durability of the mRNA vaccine-induced SARS-CoV-2-specific humoral and cellular immunity in severe asthma patients on biological therapy. The study included 37 patients with severe asthma treated with anti-IgE (omalizumab, n=18), anti-IL5 (mepolizumab, n=14; reslizumab, n=4), or anti-IL5R (benralizumab, n=1) biological therapy. All patients were vaccinated with two doses of BNT162b2 mRNA vaccine (Comirnaty) at a 6-week period between the doses. We found that the COVID-19 vaccination elicited SARS-CoV-2-specific humoral and cellular immunity, which significantly declined 6 months after the second dose of the vaccine. The type of biological treatment did not affect the vaccine-elicited immunity. However, the patients age negatively impacted the vaccine-induced humoral response. On the other hand, no such age-related impact was observed on the vaccine-elicited cellular immunity. Our findings showed that biological therapy of patients with severe asthma does not compromise the effectiveness and durability of the COVID-19 vaccine-induced immunity.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Michal Podrazil",
-        "author_inst": "Department of Immunology, Second Faculty of Medicine, Charles University, and Motol University Hospital, Prague, Czech Republic"
-      },
-      {
-        "author_name": "Pavla Taborska",
-        "author_inst": "Department of Immunology, Second Faculty of Medicine, Charles University, and Motol University Hospital, Prague, Czech Republic"
-      },
-      {
-        "author_name": "Dmitry Stakheev",
-        "author_inst": "Department of Immunology, Second Faculty of Medicine, Charles University, and Motol University Hospital, Prague, Czech Republic"
-      },
-      {
-        "author_name": "Michal Rataj",
-        "author_inst": "Department of Immunology, Second Faculty of Medicine, Charles University, and Motol University Hospital, Prague, Czech Republic"
-      },
-      {
-        "author_name": "Jan Lastovicka",
-        "author_inst": "Department of Immunology, Second Faculty of Medicine, Charles University, and Motol University Hospital, Prague, Czech Republic"
-      },
-      {
-        "author_name": "Alena Vlachova",
-        "author_inst": "Department of Pneumology, Second Faculty of Medicine, Charles University, and Motol University Hospital, Prague, Czech Republic"
-      },
-      {
-        "author_name": "Petr Pohunek",
-        "author_inst": "Department of Pediatrics, Second Faculty of Medicine, Charles University, and Motol University Hospital, Prague, Czech Republic"
-      },
-      {
-        "author_name": "Jirina Bartunkova",
-        "author_inst": "Department of Immunology, Second Faculty of Medicine, Charles University, and Motol University Hospital, Prague, Czech Republic"
-      },
-      {
-        "author_name": "Daniel Smrz",
-        "author_inst": "Department of Immunology, Second Faculty of Medicine, Charles University, and Motol University Hospital, Prague, Czech Republic"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "allergy and immunology"
-  },
   {
     "rel_doi": "10.1101/2022.02.15.22271016",
     "rel_title": "Relative Virulence of SARS-CoV-2 Among Vaccinated and Unvaccinated Individuals Hospitalized with SARS-CoV-2",
@@ -376463,6 +374770,141 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.02.15.22270954",
+    "rel_title": "Validation of the RT-LAMP assay in a large cohort of nasopharyngeal swab samples shows that it is a useful screening method for detecting SARS-CoV-2 and its VOC variants",
+    "rel_date": "2022-02-17",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.15.22270954",
+    "rel_abs": "The COVID-19 pandemic is challenging the global supply chain and equipment needed for mass testing with RT-qPCR, the gold standard for SARS-CoV-2 diagnosis. Here, we propose the RT-LAMP assay as an additional strategy for rapid virus diagnosis. However, its validation as a diagnostic method remains uncertain. In this work, we validated the RT-LAMP assay in 1,266 nasopharyngeal swab samples with confirmed diagnosis by CDC 2019-nCoV RT-qPCR. Our cohort was divided, the first (n=984) was used to evaluate two sets of oligonucleotides (S1 and S3) and the second (n=281) to determine whether RT-LAMP could detect samples with several types of variants. This assay can identify positive samples by color change or fluorescence within 40 minutes and shows high concordance with RT-qPCR in samples with CT [&le;]35. Also, S1 and S3 are able to detect SARS-CoV-2 with a sensitivity of 68.4% and 65.8%, and a specificity of 98.9% and 97.1%, respectively. Furthermore, RT-LAMP assay identified 279 sequenced samples as positive (99.3% sensitivity) corresponding to the Alpha, Beta, Gamma, Delta, Epsilon, Iota, Kappa, Lambda, Mu and Omicron variants. In conclusion, RT-LAMP is able to identify SARS-CoV-2 with good sensitivity and excellent specificity, including all VOC, VOI, VUM and FMV variants.",
+    "rel_num_authors": 30,
+    "rel_authors": [
+      {
+        "author_name": "Mireya Cisneros-Villanueva",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Sugela S Blancas",
+        "author_inst": "Catedras CONACYT-Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Alberto Cedro-Tanda",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Magdalena Rios-Romero",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Eduardo Hurtado-Cordova",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Oscar Almaraz-Rojas",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Diana R Ortiz-Soriano",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Victor Alvarez-Hernandez",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Ivonne E Arriaga-Guzman",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Laura Tolentino-Garcia",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Antonia Sanchez-Vizcarra",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Laura F Lozada-Rodriguez",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Irlanda Peralta-Arrieta",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Jose E Perez-Aquino",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Marco A Andonegui-Elguera",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Mariana Cendejas-Orozco",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Alfredo Mendoza-Vargas",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Juan P Reyes-Grajeda",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Abraham Campos-Romero",
+        "author_inst": "Innovation and Research Department, Salud Digna"
+      },
+      {
+        "author_name": "Jonathan Alcantar-Fernandez",
+        "author_inst": "Innovation and Research Department, Salud Digna"
+      },
+      {
+        "author_name": "Jose L Moreno-Camacho",
+        "author_inst": "Clinical Laboratory Division, Salud Digna,"
+      },
+      {
+        "author_name": "Jorge Gallegos-Rodriguez",
+        "author_inst": "Clinical Laboratory Division, Salud Digna,"
+      },
+      {
+        "author_name": "Marco Esparza-Luna-Ruiz",
+        "author_inst": "Clinical Laboratory Division, Salud Digna,"
+      },
+      {
+        "author_name": "Jesus Ortiz-Ramirez",
+        "author_inst": "Hospital General Ajusco Medio"
+      },
+      {
+        "author_name": "Mariana Benitez-Gonzalez",
+        "author_inst": "Hospital General Ajusco Medio"
+      },
+      {
+        "author_name": "Laura Uribe-Figueroa",
+        "author_inst": "Laboratorio Arion Genetica"
+      },
+      {
+        "author_name": "Ofelia Angulo",
+        "author_inst": "Secretaria de Educacion, Ciencia, Tecnologia e Innovacion de la Ciudad de Mexico"
+      },
+      {
+        "author_name": "Rosaura Ruiz",
+        "author_inst": "Secretaria de Educacion, Ciencia, Tecnologia e Innovacion de la Ciudad de Mexico"
+      },
+      {
+        "author_name": "Luis A Herrera",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Alfredo Hidalgo-Miranda",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "intensive care and critical care medicine"
+  },
   {
     "rel_doi": "10.1101/2022.02.17.479764",
     "rel_title": "Biomechanical dependence of SARS-CoV-2 infections",
@@ -377808,49 +376250,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.02.12.22270893",
-    "rel_title": "Demographic Characteristics and Clinical Features of COVID-19 Patients Admitted in a Combined Military Hospital of Bangladesh",
-    "rel_date": "2022-02-15",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.12.22270893",
-    "rel_abs": "BackgroundCOVID-19, one of the worst pandemics in humankinds history on December 2019. Clinical presentations of COVID-19 patients are varied and being closely similar to those of seasonal flu, its difficult to differentiate it on first presentation as COVID. Clinical scenario and demographic characteristics provide important guideline in the management of COVID.\n\nMaterials and MethodsThe objective of this cross-sectional study was to explore the demographic characteristics and clinical features of COVID-19 patients admitted in a Combined Military Hospital of Bangladesh. Data were collected from treatment records of patients of the CMH Bogura during the period of June 2020 to August 2020. Total 219 RT-PCR positive admitted patients were included as study population.\n\nResultAmong 219 patients, 78.6% were male and 21.5% female. Mean age of patients was 34.3 {+/-} 12.2. Highest percentages (67.2%) of patients were from age group 21-40 years. 85.4% of the patients had no comorbidities, and hypertension (10.1%) was the most common comorbidity. Most (83.1%) of the admitted patients were diagnosed as mild cases. 96.4% cases were symptomatic and fever (84.5%) was the most common symptoms of COVID, followed by dry cough (46.6%), sore throat (19.6%), headache (18.3%), bodyache (17.8%), loss of appetite (15.5%), tiredness (15.5%) and anorexia (14.2%).\n\nConclusionThis single center study revealed younger age, male predominance, less presence of comorbidites, mild cases, high proportion of symptomatic patients, and fever and cough as the most common presenting features among the admitted COVID-19 patients in CMH Bogura.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Sabiha Mahboob",
-        "author_inst": "CMH Bogura, Bangladesh"
-      },
-      {
-        "author_name": "Fatema Johora",
-        "author_inst": "Army Medical College Bogura"
-      },
-      {
-        "author_name": "Asma Akter Abbasy",
-        "author_inst": "Brahmanbaria Medical College"
-      },
-      {
-        "author_name": "Fatiha Tasmin Jeenia",
-        "author_inst": "Chattogram International Medical College"
-      },
-      {
-        "author_name": "Mohammad Ali",
-        "author_inst": "Asgar Ali Hospital Ltd, Dhaka, Bangladesh"
-      },
-      {
-        "author_name": "Noor E Naharin",
-        "author_inst": "Army Medical College Bogura"
-      },
-      {
-        "author_name": "Jannatul Ferdoush",
-        "author_inst": "BGC Trust Medical College, Chattogram"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.02.11.22270844",
     "rel_title": "Source terms for benchmarking models of SARS-CoV-2 transmission via aerosols and droplets",
@@ -378161,6 +376560,117 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.02.13.22270755",
+    "rel_title": "Co-infection with SARS-COV-2 Omicron and Delta Variants Revealed by Genomic Surveillance",
+    "rel_date": "2022-02-15",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.13.22270755",
+    "rel_abs": "We identified the co-infection of the SARS-CoV-2 Omicron and Delta variants in two epidemiologically unrelated patients with chronic kidney disease requiring haemodialysis. Both SARS-CoV-2 variants were co-circulating locally at the time of detection. Amplicon- and probe-based sequencing using short- and long-read technologies identified and quantified Omicron and Delta subpopulations in respiratory samples from the two patients. These findings highlight the importance of genomic surveillance in vulnerable populations.",
+    "rel_num_authors": 24,
+    "rel_authors": [
+      {
+        "author_name": "Rebecca J Rockett",
+        "author_inst": "Sydney Institute for Infectious Diseases, University of Sydney, Sydney, New South Wales, Australia"
+      },
+      {
+        "author_name": "Jenny Draper",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology Wes"
+      },
+      {
+        "author_name": "Mailie Gall",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology Wes"
+      },
+      {
+        "author_name": "Eby M Sim",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology Wes"
+      },
+      {
+        "author_name": "Alicia Arnott",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology Wes"
+      },
+      {
+        "author_name": "Jessica E Agius",
+        "author_inst": "Sydney Institute for Infectious Diseases, University of Sydney, Sydney, New South Wales, Australia"
+      },
+      {
+        "author_name": "Jessica Johnson-Mackinnon",
+        "author_inst": "Sydney Institute for Infectious Diseases, University of Sydney, Sydney, New South Wales, Australia"
+      },
+      {
+        "author_name": "Elena Martinez",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology Wes"
+      },
+      {
+        "author_name": "Alexander P Drew",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology Wes"
+      },
+      {
+        "author_name": "Clement Lee",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology Wes"
+      },
+      {
+        "author_name": "Christine Ngo",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology Wes"
+      },
+      {
+        "author_name": "Marc Ramsperger",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology Wes"
+      },
+      {
+        "author_name": "Andrew N Ginn",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology Wes"
+      },
+      {
+        "author_name": "Qinning Wang",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology Wes"
+      },
+      {
+        "author_name": "Michael Fennell",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology Wes"
+      },
+      {
+        "author_name": "Danny Ko",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology Wes"
+      },
+      {
+        "author_name": "Linda Huston",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology Wes"
+      },
+      {
+        "author_name": "Lukas Kairaitis",
+        "author_inst": "Renal Services, Blacktown Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia"
+      },
+      {
+        "author_name": "Edward C Holmes",
+        "author_inst": "School of Life & Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia"
+      },
+      {
+        "author_name": "Matthew N O'Sullivan",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology Wes"
+      },
+      {
+        "author_name": "Sharon C-A Chen",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology Wes"
+      },
+      {
+        "author_name": "Jen Kok",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology Wes"
+      },
+      {
+        "author_name": "Dominic E Dwyer",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, Institute for Clinical Pathology and Medical Research, New South Wales Health Pathology Wes"
+      },
+      {
+        "author_name": "Vitali Sintchenko",
+        "author_inst": "Sydney Institute for Infectious Diseases, University of Sydney, Sydney, New South Wales, Australia"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.02.07.22270630",
     "rel_title": "COVID-19 onset reduced the sex ratio at birth in South Africa",
@@ -380022,29 +378532,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.02.11.22270784",
-    "rel_title": "An extended SIR model with vaccine dynamics for SARS-CoV-2 adaptation rate",
-    "rel_date": "2022-02-15",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.11.22270784",
-    "rel_abs": "The COVID-19 pandemic is caused by infection with a SARS-CoV-2 virus, a RNA virus characterized by high mutation and replication rates. From epidemiological perspective, the trajectory in time of viral adaptation is determined by two opposite forces: (a) proportion of the population who has acquired immunity, exerting thereby a selective pressure on the virus and (b) proportion of infected people in the population, measuring the net viral load in the population. We calculate both the number of advantageous mutations in the population that have accumulated by time t and the amount of viral adaptation transmitted to a susceptible compartment, the latter being called the Evolutionary Infectivity Profile (EIP). To this end we employ first a simple compartmental SIR model with a single parameter describing reduction in transmission due to vaccination. Then we switch to a model which actuates the full vaccine dynamics, including vaccination rate and short duration of immunity. In our models we have never come across a situation where vaccination plays a dominant role in driving new SARS-CoV-2 variants. Nevertheless if the vaccination rate is not high enough, the EIP would continuously grow with time, pointing to a fruitful field for proliferation of genetically variable SARS-CoV-2 viruses.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Tihomir Suric",
-        "author_inst": "Rudjer Boskovic Institute"
-      },
-      {
-        "author_name": "Raul Horvat",
-        "author_inst": "Rudjer Boskovic Institute"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.02.13.22270900",
     "rel_title": "Required COVID-19 Vaccination Certification to Attend Certain U.S. Professional Football Games in Fall 2021: A Natural Experiment",
@@ -380327,6 +378814,97 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.02.14.22270845",
+    "rel_title": "Quantitative, multiplexed, targeted proteomics for ascertaining variant specific SARS-CoV-2 antibody response",
+    "rel_date": "2022-02-15",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.14.22270845",
+    "rel_abs": "Determining the protection an individual has to SARS-CoV-2 variants of concern (VoC) will be crucial for future immune surveillance and understanding the changing immune response. As further variants emerge, current serology tests are becoming less effective in reflecting neutralising capability of the immune system. A better measure of an evolving antigen-antibody immune response is needed. We describe a multiplexed, baited, targeted-proteomic assay for direct detection of multiple proteins in the SARS-CoV-2 anti-spike antibody immunocomplex. This enables a more sophisticated and informative characterisation of the antibody response to vaccination and infection against VoC. Using this assay, we detail different and specific responses to each variant by measuring several antibody classes, isotypes and associated complement binding. Furthermore, we describe how these proteins change using serum from individuals collected after infection, first and second dose vaccination. We show complete IgG1 test concordance with gold standard ELISA (r>0.8) and live virus neutralisation against Wuhan Hu-1, Alpha B.1.1.7, Beta B.1.351, and Delta B.1.617.1 variants (r>0.79). We also describe a wide degree of heterogeneity in the immunocomplex of individuals and a greater IgA response in those patients who had a previous infection. Significantly, our test points to an important role the complement system may play particularly against VoC. Where we observe altered Complement C1q association to the Delta VoC response and a stronger overall association with neutralising antibodies than IgG1. A detailed understanding of an individuals antibody response could benefit public health immunosurveillance, vaccine design and inform vaccination dosing using a personalised medicine approach.",
+    "rel_num_authors": 19,
+    "rel_authors": [
+      {
+        "author_name": "Ivan Doykov",
+        "author_inst": "UCL Institute of Child Health, London"
+      },
+      {
+        "author_name": "Justyna Spiewak",
+        "author_inst": "UCL Institute of Child Health, London"
+      },
+      {
+        "author_name": "Kimberly C Gilmour",
+        "author_inst": "Great Ormond Street Children's Hospital NHS Foundation Trust, Great Ormond Street, London; WC1N 3JH, UK"
+      },
+      {
+        "author_name": "Joseph M Gibbons",
+        "author_inst": "Barts and The London School of Medicine and Dentistry Blizard Institute"
+      },
+      {
+        "author_name": "Corinna Pade",
+        "author_inst": "Barts and The London School of Medicine and Dentistry Blizard Institute"
+      },
+      {
+        "author_name": "Aine McKnight",
+        "author_inst": "Barts and The London School of Medicine and Dentistry Blizard Institute"
+      },
+      {
+        "author_name": "Mahdad Noursadeghi",
+        "author_inst": "Division of Infection and Immunity, University College London, London, UK"
+      },
+      {
+        "author_name": "Mala Maini",
+        "author_inst": "Division of Infection and Immunity, University College London, London, UK"
+      },
+      {
+        "author_name": "Charlotte Manisty",
+        "author_inst": "University College London and Barts Heart Centre"
+      },
+      {
+        "author_name": "Thomas A Treibel",
+        "author_inst": "University College London and Barts Heart Centre"
+      },
+      {
+        "author_name": "Gabriella Captur",
+        "author_inst": "Institute of Cardiovascular Science, University College London, London, UK"
+      },
+      {
+        "author_name": "Marianna Fontana",
+        "author_inst": "Institute of Cardiovascular Science, University College London, London, UK"
+      },
+      {
+        "author_name": "Rosemary Boyton",
+        "author_inst": "Imperial College London"
+      },
+      {
+        "author_name": "Daniel M Altmann",
+        "author_inst": "Imperial College"
+      },
+      {
+        "author_name": "Tim Brooks",
+        "author_inst": "UK Health Security Agency; Porton Down, UK"
+      },
+      {
+        "author_name": "Amanda Semper",
+        "author_inst": "UK Health Security Agency; Porton Down, UK"
+      },
+      {
+        "author_name": "James Moon",
+        "author_inst": "University College London and Barts Heart Centre"
+      },
+      {
+        "author_name": "Kevin Mills",
+        "author_inst": "UCL Institute of Child Health, London"
+      },
+      {
+        "author_name": "Wendy E Heywood",
+        "author_inst": "UCL Institute of Child Health, London"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.02.14.22270934",
     "rel_title": "SARS-CoV-2 infection in Africa: A systematic review and meta-analysis of standardised seroprevalence studies, from January 2020 to December 2021",
@@ -381844,53 +380422,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "nutrition"
   },
-  {
-    "rel_doi": "10.1101/2022.02.10.22270732",
-    "rel_title": "Neonatal and Maternal Outcome of COVID-19 positive women in Sri Lanka: Secondary Analysis using National COVID-19 Positive Pregnant Women Surveillance",
-    "rel_date": "2022-02-13",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.10.22270732",
-    "rel_abs": "ObjectivesThis study aims to describe the population level data on neonatal and maternal outcomes of COVID-19 positive pregnant women of Sri Lanka by secondary analysis using National COVID-19 Positive Pregnant Women Surveillance.\n\nDesignSecondary analysis of surveillance data from the National COVID-19 positive pregnant women surveillance, Sri Lanka. Data of all pregnant women whose maternal and neonatal outcomes were reported in National Surveillance from 1st March 2020 to 31st October 2021 were included in the study. Associated factors for maternal and neonatal outcomes, namely POA at delivery, mode of delivery, birthweight, immediate place of newborn care, congenital abnormalities, and condition of neonate at completion of one month were calculated using univariate and multivariate Odds ratios.\n\nResultsMaternal COVID-19 infection reported preterm birth rate of 11.9%, LSCS rate of 54.5%, low birthweight rate16.5% and 8.3% of the newborns requiring intensive care. Neonatal mortality rate was 9 per 1000 live births. Pre-pregnancy overweight and obesity increased the risk of preterm delivery compared to pregnant women with normal BMI by 46.7% (AOR=1.467, CI=1.111-1.938, P=0.007). In contrast, the risk of preterm delivery reduced by 82.4% (AOR=0.176, CI=0.097-0.317, p<0.001) and presence of any type of congenital abnormalities in newborns by 72.4% among the COVID-19 positive women who required only inward treatment in comparison to women with severe COVID-19 infection requiring intensive care (AOR=0.276, CI=0.112-0.683, p=0.005).\n\nConclusionIncreased severity of maternal COVID-19 infection and pre-pregnancy overweight/ obesity were associated with many adverse pregnancy and neonatal outcomes. Therefore, close observation and aggressive management of COVID-19 among the pregnant women should be considered to reduce the risk of progressing to severe illness.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Malith Kumarasinghe",
-        "author_inst": "Family Health Bureau"
-      },
-      {
-        "author_name": "Kaushalya Kasturiaratchi",
-        "author_inst": "Family Health Bureau"
-      },
-      {
-        "author_name": "Hemali Jayakody",
-        "author_inst": "Family Health Bureau"
-      },
-      {
-        "author_name": "Shakira Irfaan",
-        "author_inst": "Family Health Bureau"
-      },
-      {
-        "author_name": "Wasana Samarasinghe",
-        "author_inst": "Family Health Bureau"
-      },
-      {
-        "author_name": "Harendra Dassanayake",
-        "author_inst": "Family Health Bureau"
-      },
-      {
-        "author_name": "Sanjeeva Godakandage",
-        "author_inst": "Family Health Bureau"
-      },
-      {
-        "author_name": "Chithramalee de Silva",
-        "author_inst": "Family Health Bureau"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "obstetrics and gynecology"
-  },
   {
     "rel_doi": "10.1101/2022.02.11.22270873",
     "rel_title": "Evaluation of the specificity and accuracy of SARS-CoV-2 rapid antigen self-tests compared to RT-PCR from 1015 asymptomatic volunteers",
@@ -382337,6 +380868,105 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.02.11.22270854",
+    "rel_title": "Persistence of SARS-CoV-2 immunity, Omicron's footprints, and projections of epidemic resurgences in South African population cohorts.",
+    "rel_date": "2022-02-13",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.11.22270854",
+    "rel_abs": "Understanding the build-up of immunity with successive SARS-CoV-2 variants and the epidemiological conditions that favor rapidly expanding epidemics will facilitate future pandemic control. High-resolution infection and serology data from longitudinal household cohorts in South Africa reveal high cumulative infection rates and durable cross-protective immunity conferred by prior infection in the pre-Omicron era. Building on the cohorts history of past exposures to different SARS-CoV-2 variants and vaccination, we use mathematical models to explore the fitness advantage of the Omicron variant and its epidemic trajectory. Modelling suggests the Omicron wave infected a large fraction of the population, leaving a complex landscape of population immunity primed and boosted with antigenically distinct variants. Future SARS-CoV-2 resurgences are likely under a range of scenarios of viral characteristics, population contacts, and residual cross-protection.\n\nOne Sentence SummaryClosely monitored population in South Africa reveal high cumulative infection rates and durable protection by prior infection against pre-Omicron variants. Modelling indicates that a large fraction of the population has been infected with Omicron; yet epidemic resurgences are plausible under a wide range of epidemiologic scenarios.",
+    "rel_num_authors": 21,
+    "rel_authors": [
+      {
+        "author_name": "Kaiyuan Sun",
+        "author_inst": "Division of International Epidemiology and Population Studies, Fogarty International Center, NIH"
+      },
+      {
+        "author_name": "Stefano Tempia",
+        "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri"
+      },
+      {
+        "author_name": "Jackie Kleynhans",
+        "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri"
+      },
+      {
+        "author_name": "Anne von Gottberg",
+        "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri"
+      },
+      {
+        "author_name": "Meredith L McMorrow",
+        "author_inst": "Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America."
+      },
+      {
+        "author_name": "Nicole Wolter",
+        "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri"
+      },
+      {
+        "author_name": "Jinal N. Bhiman",
+        "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri"
+      },
+      {
+        "author_name": "Jocelyn Moyes",
+        "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri"
+      },
+      {
+        "author_name": "Mignon du Plessis",
+        "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri"
+      },
+      {
+        "author_name": "Maimuna Carrim",
+        "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri"
+      },
+      {
+        "author_name": "Amelia Buys",
+        "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri"
+      },
+      {
+        "author_name": "Neil A Martinson",
+        "author_inst": "Perinatal HIV Research Unit, University of the Witwatersrand, South Africa."
+      },
+      {
+        "author_name": "Kathleen Kahn",
+        "author_inst": "MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersr"
+      },
+      {
+        "author_name": "Stephen Tollman",
+        "author_inst": "MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersr"
+      },
+      {
+        "author_name": "Limakatso Lebina",
+        "author_inst": "Perinatal HIV Research Unit, University of the Witwatersrand, South Africa."
+      },
+      {
+        "author_name": "Floidy Wafawanaka",
+        "author_inst": "MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersr"
+      },
+      {
+        "author_name": "Jacques du Toit",
+        "author_inst": "MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersr"
+      },
+      {
+        "author_name": "Francesc Xavier G\u00f3mez-Oliv\u00e9",
+        "author_inst": "MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersr"
+      },
+      {
+        "author_name": "Thulisa Mkhencele",
+        "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri"
+      },
+      {
+        "author_name": "C\u00e9cile Viboud",
+        "author_inst": "Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of"
+      },
+      {
+        "author_name": "Cheryl Cohen",
+        "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2022.02.11.22269594",
     "rel_title": "Syndromic surveillance for severe acute respiratory infections (SARI) enables valid estimation of COVID-19 hospitalization incidence and reveals underreporting of hospitalizations during pandemic peaks of three COVID-19 waves in Germany, 2020-2021",
@@ -383549,29 +382179,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
-  {
-    "rel_doi": "10.1101/2022.02.09.22270272",
-    "rel_title": "The COVID-19 Community Research Partnership: Objectives, Study Design, Baseline Recruitment, and Retention",
-    "rel_date": "2022-02-10",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.09.22270272",
-    "rel_abs": "The COVID-19 Community Research Partnership (CCRP) is a multisite surveillance platform designed to characterize the epidemiology of the SARS-CoV-2 pandemic. This manuscript describes the CCRP study design and methodology. The CCRP includes two prospective cohorts, one with six health systems in the mid-Atlantic and southern United States, and the other with six health systems in North Carolina. With enrollment beginning April 2020, sites invited persons within their healthcare systems as well as community members to participate in daily surveillance for symptoms of COVID-like illnesses, testing and risk behaviors. Participants with electronic health records were also asked to volunteer data access. Subsets of participants, representative of the general population and including oversampling of populations of interest, were selected for repeated at home serology testing. By October 2021, 65,739 participants (62,261 adult and 3,478 pediatric) were enrolled with 89% providing syndromic data, 74% providing EHR data, and 70% participating in one of two serology sub-studies. An average of 62% of participants completed a daily survey at least once a week, and 55% of serology kits were returned. The CCRP provides rich regional epidemiologic data and opportunities to more fully characterize the risks and sequelae of SARS-CoV-2 infection.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "- The COVID-19 Community Research Partnership Study Group",
-        "author_inst": "Wake Forest School of Medicine"
-      },
-      {
-        "author_name": "John Sanders",
-        "author_inst": "Wake Forest School of Medicine, Winston Salem, North Carolina, USA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.02.09.22270547",
     "rel_title": "Cov2MS: an automated matrix-independent assay for mass spectrometric detection and measurement of SARS-CoV-2 nucleocapsid protein in infectious patients",
@@ -383914,6 +382521,133 @@
     "type": "new results",
     "category": "bioinformatics"
   },
+  {
+    "rel_doi": "10.1101/2022.02.10.479867",
+    "rel_title": "Lyophilized mRNA-lipid nanoparticles vaccine with long-term stability and high antigenicity against SARS-CoV-2",
+    "rel_date": "2022-02-10",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.10.479867",
+    "rel_abs": "Advanced mRNA vaccines play vital roles against SARS-CoV-2. However, due to their poor stability, most current mRNA delivery platforms need to be stored at -20{degrees}C or -70{degrees}C, which severely limits their distribution. Herein, we present lyophilized SARS-CoV-2 mRNA-lipid nanoparticle vaccines, which can be stored at room temperature with long-term thermostability. In the in vivo Delta virus challenge experiment, lyophilized Delta variant mRNA vaccine successfully protected mice from infection and cleared the virus. Lyophilized omicron mRNA vaccine enabled to elicit both potent humoral and cellular immunity. In booster immunization experiments in mice and old monkeys, lyophilized omicron mRNA vaccine could effectively increase the titers of neutralizing antibodies against wild-type coronavirus and omicron variants. In humans, lyophilized omicron mRNA vaccine as a booster shot could also engender excellent immunity and had less severe adverse events. This lyophilization platform overcomes the instability of mRNA vaccines without affecting their bioactivity, and significantly improved their accessibility, particularly in remote regions.",
+    "rel_num_authors": 28,
+    "rel_authors": [
+      {
+        "author_name": "Liangxia Ai",
+        "author_inst": "Shenzhen Rhegen Biotechnology Co. Ltd"
+      },
+      {
+        "author_name": "Yafei Li",
+        "author_inst": "Shenzhen Rhegen Biotechnology Co. Ltd"
+      },
+      {
+        "author_name": "Li Zhou",
+        "author_inst": "Animal Biosafety Level 3 Laboratory, Wuhan University"
+      },
+      {
+        "author_name": "Hao Zhang",
+        "author_inst": "Shenzhen Rhegen Biotechnology Co. Ltd"
+      },
+      {
+        "author_name": "Wenrong Yao",
+        "author_inst": "Jiangsu Rec-biotechnology Co. Ltd"
+      },
+      {
+        "author_name": "Jinyu Han",
+        "author_inst": "Shenzhen Rhegen Biotechnology Co. Ltd"
+      },
+      {
+        "author_name": "Junmiao Wu",
+        "author_inst": "Shenzhen Rhegen Biotechnology Co. Ltd"
+      },
+      {
+        "author_name": "Ruiyue Wang",
+        "author_inst": "Shenzhen Rhegen Biotechnology Co. Ltd"
+      },
+      {
+        "author_name": "Weijie Wang",
+        "author_inst": "Shenzhen Rhegen Biotechnology Co. Ltd"
+      },
+      {
+        "author_name": "Pan Xu",
+        "author_inst": "Shenzhen Rhegen Biotechnology Co. Ltd"
+      },
+      {
+        "author_name": "Zhouwang Li",
+        "author_inst": "Shenzhen Rhegen Biotechnology Co. Ltd"
+      },
+      {
+        "author_name": "Chengliang Wei",
+        "author_inst": "Shenzhen Rhegen Biotechnology Co. Ltd"
+      },
+      {
+        "author_name": "Haobo Chen",
+        "author_inst": "Shenzhen Rhegen Biotechnology Co. Ltd"
+      },
+      {
+        "author_name": "Jianqun Liang",
+        "author_inst": "Shenzhen Rhegen Biotechnology Co. Ltd"
+      },
+      {
+        "author_name": "Ming Guo",
+        "author_inst": "State Key Laboratory of Virology College of Life Sciences, Wuhan University"
+      },
+      {
+        "author_name": "Zhixiang Huang",
+        "author_inst": "Animal Biosafety Level 3 Laboratory, Wuhan University"
+      },
+      {
+        "author_name": "Xin Wang",
+        "author_inst": "State Key Laboratory of Virology College of Life Sciences, Wuhan University"
+      },
+      {
+        "author_name": "Zhen Zhang",
+        "author_inst": "State Key Laboratory of Virology College of Life Sciences, Wuhan University"
+      },
+      {
+        "author_name": "Wenjie Xiang",
+        "author_inst": "State Key Laboratory of Virology College of Life Sciences, Wuhan University"
+      },
+      {
+        "author_name": "Bin Lv",
+        "author_inst": "Shenzhen Rhegen Biotechnology Co. Ltd"
+      },
+      {
+        "author_name": "Peiqi Peng",
+        "author_inst": "Shenzhen Rhegen Biotechnology Co. Ltd"
+      },
+      {
+        "author_name": "Shangfeng Zhang",
+        "author_inst": "Shenzhen Rhegen Biotechnology Co. Ltd"
+      },
+      {
+        "author_name": "Xuhao Ji",
+        "author_inst": "Shenzhen Rhegen Biotechnology Co. Ltd"
+      },
+      {
+        "author_name": "Zhangyi Li",
+        "author_inst": "Shenzhen Rhegen Biotechnology Co. Ltd"
+      },
+      {
+        "author_name": "Huiyi Luo",
+        "author_inst": "Shenzhen Rhegen Biotechnology Co. Ltd"
+      },
+      {
+        "author_name": "Jianping Chen",
+        "author_inst": "Jiangsu Rec-biotechnology Co. Ltd, Wuhan Recogen Biotechnology Co. Ltd"
+      },
+      {
+        "author_name": "Ke Lan",
+        "author_inst": "State Key Laboratory of Virology College of Life Sciences, Animal Biosafety Level 3 Laboratory, Wuhan University"
+      },
+      {
+        "author_name": "Yong Hu",
+        "author_inst": "Shenzhen Rhegen Biotechnology Co. Ltd, Wuhan Recogen Biotechnology Co. Ltd"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2022.02.09.479588",
     "rel_title": "Epigenetic Memory of COVID-19 in Innate Immune Cells and Their Progenitors",
@@ -385403,57 +384137,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2022.02.08.479556",
-    "rel_title": "Plasticity in structure and assembly of SARS-CoV-2 nucleocapsid protein",
-    "rel_date": "2022-02-09",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.08.479556",
-    "rel_abs": "Worldwide SARS-CoV-2 sequencing efforts track emerging mutations in its spike protein, as well as characteristic mutations in other viral proteins. Besides their epidemiological importance, the observed SARS-CoV-2 sequences present an ensemble of viable protein variants, and thereby a source of information on viral protein structure and function. Charting the mutational landscape of the nucleocapsid (N) protein that facilitates viral assembly, we observe variability exceeding that of the spike protein, with more than 86% of residues that can be substituted, on average by 3-4 different amino acids. However, mutations exhibit an uneven distribution that tracks known structural features but also reveals highly protected stretches of unknown function. One of these conserved regions is in the central disordered linker proximal to the N-G215C mutation that has become dominant in the Delta variant, outcompeting G215 variants without further spike or N-protein substitutions. Structural models suggest that the G215C mutation stabilizes conserved transient helices in the disordered linker serving as protein-protein interaction interfaces. Comparing Delta variant N-protein to its ancestral version in biophysical experiments, we find a significantly more compact and less disordered structure. N-G215C exhibits substantially stronger self-association, shifting the unliganded protein from a dimeric to a tetrameric oligomeric state, which leads to enhanced co-assembly with nucleic acids. This suggests that the sequence variability of N-protein is mirrored by high plasticity of N-protein biophysical properties, which we hypothesize can be exploited by SARS-CoV-2 to achieve greater efficiency of viral assembly, and thereby enhanced infectivity.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Huaying Zhao",
-        "author_inst": "National Institutes of Health"
-      },
-      {
-        "author_name": "Ai Nguyen",
-        "author_inst": "National Institutes of Health"
-      },
-      {
-        "author_name": "Di Wu",
-        "author_inst": "National Institutes of Health"
-      },
-      {
-        "author_name": "Yan Li",
-        "author_inst": "National Institutes of Health"
-      },
-      {
-        "author_name": "Sergio A Hassan",
-        "author_inst": "National Institutes of Heath"
-      },
-      {
-        "author_name": "Jiji Chen",
-        "author_inst": "National Institutes of Health"
-      },
-      {
-        "author_name": "Hari Shroff",
-        "author_inst": "National Institutes of Health"
-      },
-      {
-        "author_name": "Grzegorz Piszczek",
-        "author_inst": "National Heart, Lung, and Blood Institute"
-      },
-      {
-        "author_name": "Peter Schuck",
-        "author_inst": "National Institutes of Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc0",
-    "type": "new results",
-    "category": "biophysics"
-  },
   {
     "rel_doi": "10.1101/2022.02.07.479443",
     "rel_title": "Olverembatinib inhibits SARS-CoV-2-Omicron variant-mediated cytokine release",
@@ -385840,6 +384523,97 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2022.02.08.479661",
+    "rel_title": "N-acylethanolamine acid amide hydrolase is a novel target for drugs against SARS-CoV-2 and Zika virus",
+    "rel_date": "2022-02-09",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.08.479661",
+    "rel_abs": "Several compounds have been tested against SARS-CoV-2; at present, COVID-19 treatments decrease the deleterious inflammatory response and acute lung injury. However, the best therapeutic response would be expected by combining anti-inflammatory properties, while concomitantly blocking viral replication. These combined effects should drastically reduce both infection rate and severe complications induced by novel SARS-CoV-2 variants. Therefore, we explored the antiviral potency of a class of anti-inflammatory compounds that inhibit the N-Acylethanolamine acid amidase (NAAA). This enzyme catalyzes the hydrolysis of palmitoylethanolamide (PEA), a bioactive lipid that mediates anti-inflammatory and analgesic activity through the activation of peroxisome proliferator receptor- (PPAR-). Similarly, this pathway is likely to be a significant target to impede viral replication since PPAR- activation leads to dismantling of lipid droplets, where viral replication of Flaviviruses and Coronaviruses occurs.\n\nHere, we show that either genetic or pharmacological inhibition of the NAAA enzyme leads to five-fold reduction in the replication of both SARS-CoV-2 and ZIKV in various cell lines. Once NAAA enzyme is blocked, both ZIKV and SARS CoV-2 replication decrease, which parallels a sudden five-fold decrease in virion release. These effects induced by NAAA inhibition occurs concomitantly with stimulation of autophagy during infection. Remarkably, parallel antiviral and anti-inflammatory effects of NAAA antagonism were confirmed in ex-vivo experiments, within SARS-CoV-2 infected human PBMC cells, in which both viral genomes and TNF- production drop by ~60%. It is known that macrophages contribute to viral spread, excessive inflammation and macrophage activation syndrome that NAAA inhibitors might prevent, reducing the macrophage-induced acute respiratory distress syndrome and subsequent death of COVID-19 patients.",
+    "rel_num_authors": 19,
+    "rel_authors": [
+      {
+        "author_name": "Michele Lai",
+        "author_inst": "University of Pisa School of Medicine and Surgery: Universita degli Studi di Pisa"
+      },
+      {
+        "author_name": "Veronica La Rocca",
+        "author_inst": "University of Pisa School of Medicine and Surgery: Universita degli Studi di Pisa"
+      },
+      {
+        "author_name": "Rachele Amato",
+        "author_inst": "University of Pisa School of Medicine and Surgery: Universita degli Studi di Pisa"
+      },
+      {
+        "author_name": "Elena Iacono",
+        "author_inst": "University of Pisa School of Medicine and Surgery: Universita degli Studi di Pisa"
+      },
+      {
+        "author_name": "carolina filipponi",
+        "author_inst": "University of Pisa School of Medicine and Surgery: Universita degli Studi di Pisa"
+      },
+      {
+        "author_name": "Elisa Catelli",
+        "author_inst": "University of Pisa School of Medicine and Surgery: Universita degli Studi di Pisa"
+      },
+      {
+        "author_name": "Lucia Bogani",
+        "author_inst": "University of Pisa School of Medicine and Surgery: Universita degli Studi di Pisa"
+      },
+      {
+        "author_name": "Rossella Fonnesu",
+        "author_inst": "University of Pisa School of Medicine and Surgery: Universita degli Studi di Pisa"
+      },
+      {
+        "author_name": "giulia lottini",
+        "author_inst": "University of Pisa School of Medicine and Surgery: Universita degli Studi di Pisa"
+      },
+      {
+        "author_name": "Alessandro De Carli",
+        "author_inst": "University of Pisa School of Medicine and Surgery: Universita degli Studi di Pisa"
+      },
+      {
+        "author_name": "Alessandro Mengozzi",
+        "author_inst": "University of Pisa School of Medicine and Surgery: Universita degli Studi di Pisa"
+      },
+      {
+        "author_name": "Stefano Masi",
+        "author_inst": "University of Pisa School of Medicine and Surgery: Universita degli Studi di Pisa"
+      },
+      {
+        "author_name": "Paola Quaranta",
+        "author_inst": "University of Pisa School of Medicine and Surgery: Universita degli Studi di Pisa"
+      },
+      {
+        "author_name": "Pietro  Giorgio Spezia",
+        "author_inst": "University of Pisa School of Medicine and Surgery: Universita degli Studi di Pisa"
+      },
+      {
+        "author_name": "Giulia Freer",
+        "author_inst": "University of Pisa School of Medicine and Surgery: Universita degli Studi di Pisa"
+      },
+      {
+        "author_name": "Paola Lenzi",
+        "author_inst": "University of Pisa School of Medicine and Surgery: Universita degli Studi di Pisa"
+      },
+      {
+        "author_name": "Francesco Fornai",
+        "author_inst": "University of Pisa School of Medicine and Surgery: Universita degli Studi di Pisa"
+      },
+      {
+        "author_name": "Daniele Piomelli",
+        "author_inst": "University of California Irvine"
+      },
+      {
+        "author_name": "Mauro Pistello",
+        "author_inst": "University of Pisa School of Medicine and Surgery: Universita degli Studi di Pisa"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2022.02.08.22270506",
     "rel_title": "Symptoms and severity in vaccinated and unvaccinated patients hospitalised with SARS-CoV-2 delta (B.1.617.2) variant infection",
@@ -387477,45 +386251,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2022.02.07.22270588",
-    "rel_title": "Inequalities in mental and social wellbeing during the COVID-19 pandemic: prospective longitudinal observational study of five UK cohorts",
-    "rel_date": "2022-02-08",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.07.22270588",
-    "rel_abs": "BackgroundResearch suggests that there have been inequalities in the impact of the COVID-19 pandemic and related non-pharmaceutical interventions on population mental health. We explored these inequalities during the first year of the pandemic using nationally representative cohorts from the UK.\n\nMethodsWe analysed data from 26,772 participants from five longitudinal cohorts representing generations born between 1946 and 2000, collected in May 2020, September-October 2020, and February-March 2021 across all five cohorts. We used a multilevel growth curve modelling approach to explore sociodemographic and socioeconomic differences in levels of anxiety and depressive symptomatology, loneliness, and life satisfaction over time.\n\nResultsYounger generations had worse levels of mental and social wellbeing throughout the first year of the pandemic. Whereas these generational inequalities narrowed between the first and last observation periods for life satisfaction (-0.33 [95% CI: -0.51, -0.15]), they became larger for anxiety (0.22 [0.10, 0.33]). Pre-existing generational inequalities in depression and loneliness did not change, but initial depression levels of the youngest cohort were worse than expected if the generational inequalities had not accelerated. Women and those experiencing financial difficulties had worse initial mental and social wellbeing levels than men and those financially living comfortably, respectively, and these gaps did not substantially differ between the first and last observation periods. Inequalities by additional factors are reported.\n\nConclusionsBy March 2021, mental and social wellbeing inequalities persisted in the UK adult population. Pre-existing generational inequalities may have been exacerbated with the pandemic onset. Policies aimed at protecting vulnerable groups are needed.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Dario Moreno-Agostino",
-        "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London; ESRC Centre for Society and Mental Health, King's College London"
-      },
-      {
-        "author_name": "Helen L. Fisher",
-        "author_inst": "ESRC Centre for Society and Mental Health, King's College London; King's College London, Social, Genetic & Developmental Psychiatry Centre, Institute of Psychia"
-      },
-      {
-        "author_name": "Stephani L. Hatch",
-        "author_inst": "ESRC Centre for Society and Mental Health, King's College London; King's College London, Department of Psychological Medicine, Institute of Psychiatry, Psycholo"
-      },
-      {
-        "author_name": "Craig Morgan",
-        "author_inst": "ESRC Centre for Society and Mental Health, King's College London; King's College London, Health Service and Population Research Department, Institute of Psychia"
-      },
-      {
-        "author_name": "George B. Ploubidis",
-        "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London; ESRC Centre for Society and Mental Health, King's College London"
-      },
-      {
-        "author_name": "Jayati Das-Munshi",
-        "author_inst": "ESRC Centre for Society and Mental Health, King's College London; King's College London, Department of Psychological Medicine, Institute of Psychiatry, Psycholo"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.02.07.22270593",
     "rel_title": "Factors associated with higher levels of grief and support needs among people bereaved during the pandemic: Results from a national online survey",
@@ -388050,6 +386785,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.02.07.22270596",
+    "rel_title": "Role of Covid vaccine in determining ICU admission and death due to Covid -19 in Tamil Nadu",
+    "rel_date": "2022-02-08",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.07.22270596",
+    "rel_abs": "COVID-19 pandemic threatened the world in terms of its rapid spread, strain on health infrastructure and many people lost their lives due to COVID. Mass Vaccination of public against Covid-19 were done with the notion that it protects against the severe form of the disease and death due to Covid-19. Covid vaccination was rolled out in Tamil Nadu from 16th January 2021 in a phased manner. This study was done using secondary data to assess the role of COVID vaccination in preventing ICU admission and death due to Covid-19 in Tamil Nadu for the period of August - December 2021. Unvaccinated individuals contributed to a higher proportion of hospitalization (60.9%) and ICU admission (65.5%) among Covid-19 infected during this period. Similarly, among patients who died due to Covid-19, 75.5% were unvaccinated. Odds of ICU admission and death among unvaccinated was 2.01 and 3.19 - times higher compared to fully vaccinated individuals infected with Covid-19. Unvaccinated Covid-19 patients had 2.73- and 1.46- times increased odds of dying and ICU admission respectively, compared to partially vaccinated. Population Attributable Risk showed that receiving at least one dose of vaccine could have reduced the mortality among Covid patients by 54% and ICU admission by 23.3%. This article emphasizes the need for vaccination against Covid-19 to reduce ICU admission and death among those infected with Covid-19.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Selvavinayagam T.S",
+        "author_inst": "Directorate of Public Health and Preventive Medicine, Teynampet, Anna Salai, Chennai-06"
+      },
+      {
+        "author_name": "Parthipan Kumarasamy",
+        "author_inst": "Directorate of Public Health and Preventive Medicine, Teynampet, Chennai-06"
+      },
+      {
+        "author_name": "sudharshini subramaniam",
+        "author_inst": "Madras Medical College"
+      },
+      {
+        "author_name": "Somasundaram A",
+        "author_inst": "Institute of Community Medicine, Madras Medical College"
+      },
+      {
+        "author_name": "Sampath P",
+        "author_inst": "Directorate of Public Health and Preventive Medicine, Teynampet, Chennai-06"
+      },
+      {
+        "author_name": "Vinay Kumar Krishnamurthy",
+        "author_inst": "Directorate of Public Health and Preventive Medicine, Teynampet, Chennai -06"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2022.02.07.22270557",
     "rel_title": "History of SARS-CoV-2 infection, anti-spike IgG antibody kinetics and neutralization capacities following the second and third dose of BNT162b2 vaccine in nursing home residents",
@@ -389547,65 +388321,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2022.02.07.478848",
-    "rel_title": "Preclinical Pharmacokinetics and In Vitro Properties of GS-441524, A Potential Oral Drug Candidate for COVID-19 Treatment",
-    "rel_date": "2022-02-07",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.07.478848",
-    "rel_abs": "Preclinical pharmacokinetics (PK) and in vitro ADME properties of GS-441524, a potential oral agent for the treatment of Covid-19, were studied. GS-441524 was stable in vitro in liver microsomes, cytosols, and hepatocytes of mice, rats, monkeys, dogs, and humans. The plasma free fractions of GS-441524 were 62-78% across all studied species. The in vitro transporter study results showed that GS-441524 was a substrate of MDR1, BCRP, CNT3, ENT1, and ENT2; but not a substrate of CNT1, CNT2, and ENT4. GS-441524 had a low to moderate plasma clearance (CLp), ranging from 4.1 mL/min/kg in dogs to 26 mL/min/kg in mice; the steady state volume distribution (Vdss) ranged from 0.9 L/kg in dogs to 2.2 L/kg in mice after IV administration. Urinary excretion appeared to be the major elimination process for GS-441524. Following oral administration, the oral bioavailability was 8.3% in monkeys, 33% in rats, 39% in mice, and 85% in dogs. The PK and ADME properties of GS-441524 support its further development as an oral drug candidate.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Amy Q Wang",
-        "author_inst": "National Institutes of Health"
-      },
-      {
-        "author_name": "Natalie R Hagen",
-        "author_inst": "National Institutes of Health"
-      },
-      {
-        "author_name": "Elias C Padilha",
-        "author_inst": "National Institutes of Health"
-      },
-      {
-        "author_name": "Mengbi Yang",
-        "author_inst": "National Institutes of Health"
-      },
-      {
-        "author_name": "Pranav Shah",
-        "author_inst": "National Institutes of Health"
-      },
-      {
-        "author_name": "Catherine Z Chen",
-        "author_inst": "National Institutes of Health"
-      },
-      {
-        "author_name": "Wenwei Huang",
-        "author_inst": "National Institutes of Health"
-      },
-      {
-        "author_name": "Pramod Terse",
-        "author_inst": "National Institutes of Health"
-      },
-      {
-        "author_name": "Philip Sanderson",
-        "author_inst": "National Institutes of Health"
-      },
-      {
-        "author_name": "Wei Zheng",
-        "author_inst": "National Institutes of Health"
-      },
-      {
-        "author_name": "Xin Xu",
-        "author_inst": "National Institutes of Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc0",
-    "type": "new results",
-    "category": "pharmacology and toxicology"
-  },
   {
     "rel_doi": "10.1101/2022.02.07.479349",
     "rel_title": "Comprehensive Epitope Mapping of Broad Sarbecovirus Neutralizing Antibodies",
@@ -390096,6 +388811,113 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health systems and quality improvement"
   },
+  {
+    "rel_doi": "10.1101/2022.02.06.22270482",
+    "rel_title": "Early genomic, epidemiological, and clinical description of the SARS-CoV-2 Omicron variant in Mexico City",
+    "rel_date": "2022-02-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.06.22270482",
+    "rel_abs": "BackgroundOmicron is the most mutated SARS-CoV-2 variant that has emerged, resulting in viral phenotype alterations, which can affect transmissibility, disease severity, and immune evasiveness. Genomic surveillance of a highly transmissible variant is important in cities with millions of inhabitants and an economic center such as Mexico City. In this work, we describe the early effects of the Omicron variant in Mexico City, exploring its genomic profile and clinical description.\n\nMethodologyWe sequenced SARS-CoV-2-positive samples in November and December 2021 and we using the public database GISAID. Haplotype and phylogenetic analyses were performed to genomically characterize Omicron. We used the Mexican federal database toexplore the association with clinical information such as symptoms and vaccination status.\n\nFindingsThe first case of Omicron was detected on November 16, 2022, and until December 31, 2021, we observed an increase from 88% in sequenced samples. Nineteen nonsynonymous mutations were found in the Omicron RBD, and we further explored the R346K substitution, which was prevalent in 42% of the samples and associated with immune escape by monoclonal antibodies. In the phylogenetic analysis, we found that there were several independent exchanges between Mexico and the world, and there was an event followed by local transmission that gave rise to most of the Omicron diversity in Mexico City. The haplotype analysis allowed us to observe that there was no association between haplotype and vaccination status. Of the patients with clinical data, 66% were vaccinated, none of the reported comorbidities were associated with Omicron, the presence of odynophagia and absence of dysgeusia were significant predictor symptoms for Omicron, and the Ct value on RT-qPCR was lower in Omicron.\n\nConclusionsGenomic surveillance in highly populated and fast-moving urban regions such as Mexico City is key to detecting the emergence and spread of SARS-CoV-2 variants in a timely manner, even weeks before the onset of an infection wave, to detect patterns that can inform public health decisions. It is also necessary to continue sequencing to detect the spread of any mutation that may affect the therapeutic efficacy or guide it.",
+    "rel_num_authors": 23,
+    "rel_authors": [
+      {
+        "author_name": "Alberto Cedro-Tanda",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Laura Gomez-Romero",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Guillermo de Anda-Jauregui",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Dora Garnica-Lopez",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Yair Alfaro-Mora",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Sonia Sanchez-Xochipa",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Eulices F Garcia-Garcia",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Alfredo Mendoza-Vargas",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Emmanuel J Frias-Jimenez",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Bernardo Moreno-Quiroga",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Abraham Campos-Romero",
+        "author_inst": "Innovation and Research Department, Salud Digna"
+      },
+      {
+        "author_name": "Jose L Moreno-Camacho",
+        "author_inst": "Clinical Laboratory Division, Salud Digna,"
+      },
+      {
+        "author_name": "Jonathan Alcantar-Fernandez",
+        "author_inst": "Innovation and Research Department, Salud Digna"
+      },
+      {
+        "author_name": "Jesus Ortiz-Ramirez",
+        "author_inst": "Hospital General Ajusco Medio"
+      },
+      {
+        "author_name": "Mariana Benitez Gonzalez",
+        "author_inst": "Hospital General Ajusco Medio"
+      },
+      {
+        "author_name": "Roxana Trejo-Gonzalez",
+        "author_inst": "Centro Medico ABC"
+      },
+      {
+        "author_name": "Daniel Aguirre-Chavarria",
+        "author_inst": "Centro Medico ABC"
+      },
+      {
+        "author_name": "Marcela E Nunez-Martinez",
+        "author_inst": "Centro Medico ABC"
+      },
+      {
+        "author_name": "Laura Uribe-Figueroa",
+        "author_inst": "Laboratorio Arion Genetica"
+      },
+      {
+        "author_name": "Ofelia Angulo",
+        "author_inst": "Secretaria de Educacion, Ciencia, Tecnologia e Innovacion de la Ciudad de Mexico"
+      },
+      {
+        "author_name": "Rosaura Ruiz",
+        "author_inst": "Secretaria de Educacion, Ciencia, Tecnologia e Innovacion de la Ciudad de Mexico"
+      },
+      {
+        "author_name": "Alfredo Hidalgo-Miranda",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      },
+      {
+        "author_name": "Luis A Herrera",
+        "author_inst": "Instituto Nacional de Medicina Genomica"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.02.06.22270533",
     "rel_title": "Comparable Neutralization of the SARS-CoV-2 Omicron BA.1 and BA.2 Variants",
@@ -392041,113 +390863,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.02.05.22270494",
-    "rel_title": "Impacts of the COVID-19 pandemic on future seasonal influenza epidemic",
-    "rel_date": "2022-02-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.05.22270494",
-    "rel_abs": "BackgroundDuring the first two years of the COVID-19 pandemic, the circulation of seasonal influenza viruses was unprecedentedly low. This led to concerns that the lack of immune stimulation to influenza viruses combined with waning antibody titres could lead to increased susceptibility to influenza in subsequent seasons, resulting in larger and more severe epidemics.\n\nMethodsWe analyzed historical influenza virus epidemiological data from 2003-2019 to assess the historical frequency of near-absence of seasonal influenza virus circulation and its impact on the size and severity of subsequent epidemics. Additionally, we measured haemagglutination inhibition-based antibody titres against seasonal influenza viruses using longitudinal serum samples from 165 healthy adults, collected before and during the COVID-19 pandemic, and estimated how antibody titres against seasonal influenza waned during the first two years of the pandemic.\n\nFindingsLow country-level prevalence of influenza virus (sub)types over one or more years occurred frequently before the COVID-19 pandemic and had relatively small impacts on subsequent epidemic size and severity. Additionally, antibody titres against seasonal influenza viruses waned negligibly during the first two years of the pandemic.\n\nInterpretationThe commonly held notion that lulls in influenza virus circulation, as observed during the COVID-19 pandemic, will lead to larger and/or more severe subsequent epidemics might not be fully warranted, and it is likely that post-lull seasons will be similar in size and severity to pre-lull seasons.\n\nFundingEuropean Research Council, Netherlands Organization for Scientific Research, Royal Dutch Academy of Sciences, Public Health Service of Amsterdam.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSDuring the first years of the COVID-19 pandemic, the incidence of seasonal influenza was unusually low, leading to widespread concerns of exceptionally large and/or severe influenza epidemics in the coming years. We searched PubMed and Google Scholar using a combination of search terms (i.e., \"seasonal influenza\", \"SARS-CoV-2\", \"COVID-19\", \"low incidence\", \"waning rates\", \"immune protection\") and critically considered published articles and preprints that studied or reviewed the low incidence of seasonal influenza viruses since the start of the COVID-19 pandemic and its potential impact on future seasonal influenza epidemics. We found a substantial body of work describing how influenza virus circulation was reduced during the COVID-19 pandemic, and a number of studies projecting the size of future epidemics, each positing that post-pandemic epidemics are likely to be larger than those observed pre-pandemic. However, it remains unclear to what extent the assumed relationship between accumulated susceptibility and subsequent epidemic size holds, and it remains unknown to what extent antibody levels have waned during the COVID-19 pandemic. Both are potentially crucial for accurate prediction of post-pandemic epidemic sizes.\n\nAdded value of this studyWe find that the relationship between epidemic size and severity and the magnitude of circulation in the preceding season(s) is decidedly more complex than assumed, with the magnitude of influenza circulation in preceding seasons having only limited effects on subsequent epidemic size and severity. Rather, epidemic size and severity are dominated by season-specific effects unrelated to the magnitude of circulation in the preceding season(s). Similarly, we find that antibody levels waned only modestly during the COVID-19 pandemic.\n\nImplications of all the available evidenceThe lack of changes observed in the patterns of measured antibody titres against seasonal influenza viruses in adults and nearly two decades of epidemiological data suggest that post-pandemic epidemic sizes will likely be similar to those observed pre-pandemic, and challenge the commonly held notion that the widespread concern that the near-absence of seasonal influenza virus circulation during the COVID-19 pandemic, or potential future lulls, are likely to result in larger influenza epidemics in subsequent years.",
-    "rel_num_authors": 23,
-    "rel_authors": [
-      {
-        "author_name": "Simon P.J. de Jong",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Zandra C. Felix Garza",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Joseph Gibson",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Alvin X. Han",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Sarah van Leeuwen",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Robert P. de Vries",
-        "author_inst": "Utrecht University"
-      },
-      {
-        "author_name": "Geert-Jan Boons",
-        "author_inst": "Utrecht University"
-      },
-      {
-        "author_name": "Marliek van Hoesel",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Karen de Haan",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Laura van Groeningen",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Katina D Hulme",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Hugo D.G. van Willigen",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Elke Wynberg",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Godelieve J. C. de Bree",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Amy Matser",
-        "author_inst": "GGD Amsterdam"
-      },
-      {
-        "author_name": "Margreet Bakker",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Lia van der Hoek",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Maria Prins",
-        "author_inst": "GGD Amsterdam"
-      },
-      {
-        "author_name": "Neeltje A. Kootstra",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Dirk Eggink",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Brooke E Nichols",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Menno D de  Jong",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Colin A Russell",
-        "author_inst": "Amsterdam UMC"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.02.04.22270480",
     "rel_title": "SARS-CoV-2 Omicron symptomatic infections in previously infected or vaccinated South African healthcare workers",
@@ -392390,6 +391105,101 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.02.05.22269021",
+    "rel_title": "Wastewater Surveillance of U.S. Coast Guard Installations and Seagoing Military Vessels to Mitigate the Risk of COVID-19 Outbreaks",
+    "rel_date": "2022-02-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.05.22269021",
+    "rel_abs": "Military training centers may be high risk environments for the spread of disease such as COVID-19. Individuals arrive after traveling from many parts of the country, live in communal settings, and undergo high-interaction training. A pilot study of wastewater testing was initiated in February, 2021 to determine its feasibility as a sentinel surveillance tool in the U.S. Coast Guard for SARS-CoV-2. Wastewater was analyzed for the presence of two viral genes, N and E, and quantified relative to levels of a fecal indicator virus, Pepper Mild Mottle Virus (PMMoV). A stability control, Bovine Syncytial Respiratory Virus vaccine, was added to samples to assess sample stability and degradation. Wastewater data was validated by comparison with concomitant screening and surveillance programs that identified asymptomatic individuals infected with SARS-CoV-2 by diagnostic testing at on site medical clinics using PCR. Elevated levels of SARS-CoV-2 in wastewater were frequently associated with diagnosed cases, and in several instances, led to screenings of asymptomatic individuals that identified infected personnel, mitigating the risk of spread of disease. Wastewater screening also successfully indicated the presence of breakthrough cases in vaccinated individuals. A method for assessing blackwater from Coast Guard vessels was also developed, allowing detection of SARS-CoV-2 virus in shipboard populations. In one instance, virus was detected in the blackwater four weeks following the diagnosis of a single person on a Coast Guard cutter. These data show that wastewater testing is an effective tool for measuring the presence and prevalence of SARS-CoV-2 in military populations so that mitigation can occur and suggest other diseases may be assessed similarly. As a result, the Coast Guard has established three laboratories with wastewater testing capability at strategic locations and is actively continuing its wastewater testing program.",
+    "rel_num_authors": 20,
+    "rel_authors": [
+      {
+        "author_name": "Gregory J Hall",
+        "author_inst": "U.S. Coast Guard Academy"
+      },
+      {
+        "author_name": "Eric J Page",
+        "author_inst": "U.S. Coast Guard Academy"
+      },
+      {
+        "author_name": "Min Rhee",
+        "author_inst": "U.S. Coast Guard Academy"
+      },
+      {
+        "author_name": "Clara M Hay",
+        "author_inst": "U.S. Coast Guard Academy"
+      },
+      {
+        "author_name": "Amelia Krause",
+        "author_inst": "U.S. Coast Guard Academy"
+      },
+      {
+        "author_name": "Emma Langenbacher",
+        "author_inst": "U.S. Coast Guard Academy"
+      },
+      {
+        "author_name": "Allison Ruth",
+        "author_inst": "U.S. Coast Guard Academy"
+      },
+      {
+        "author_name": "Stephen Grenier",
+        "author_inst": "U.S. Coast Guard Academy"
+      },
+      {
+        "author_name": "Alexander P Duran",
+        "author_inst": "U.S. Coast Guard Academy"
+      },
+      {
+        "author_name": "Ibrahim Kamara",
+        "author_inst": "U.S. Coast Guard"
+      },
+      {
+        "author_name": "John K Iskander",
+        "author_inst": "U.S. Coast Guard"
+      },
+      {
+        "author_name": "Dana L Thomas",
+        "author_inst": "U.S. Coast Guard"
+      },
+      {
+        "author_name": "Edward Bock",
+        "author_inst": "U.S. Coast Guard"
+      },
+      {
+        "author_name": "Nicholas Porta",
+        "author_inst": "U.S. Coast Guard"
+      },
+      {
+        "author_name": "Jessica Pharo",
+        "author_inst": "U.S. Coast Guard"
+      },
+      {
+        "author_name": "Beth A. Osterink",
+        "author_inst": "U.S. Coast Guard"
+      },
+      {
+        "author_name": "Sharon Zelmanowitz",
+        "author_inst": "U.S. Coast Guard Academy"
+      },
+      {
+        "author_name": "Corinna Fleischmann",
+        "author_inst": "U.S. Coast Guard Academy"
+      },
+      {
+        "author_name": "Dilhara Liyanage",
+        "author_inst": "U.S. Coast Guard Academy"
+      },
+      {
+        "author_name": "Joshua P Gray",
+        "author_inst": "U.S. Coast Guard Academy"
+      }
+    ],
+    "version": "1",
+    "license": "cc0",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2022.02.04.22270479",
     "rel_title": "Comparative effectiveness of different primary vaccination courses on mRNA based booster vaccines against SARs-COV-2 infections: A time-varying cohort analysis using trial emulation in the Virus Watch community cohort",
@@ -394023,69 +392833,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2022.02.02.22270351",
-    "rel_title": "Effectiveness of the inactivated COVID-19 vaccine (CoronaVac) in adult population in Indonesia",
-    "rel_date": "2022-02-04",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.02.22270351",
-    "rel_abs": "BackgroundInactivated SARS-CoV-2 vaccine has been included in the national COVID-19 vaccination program in Indonesia since January 2021. The study aims to assess the impacts of inactivated COVID-19 vaccine on infection, hospitalization, and death among adult population aged [&ge;]18 years in Bali, Indonesia.\n\nMethodsTest-negative, case control study was conducted by linking SARS-CoV-2 laboratory records, vaccination, and health administrative data for the period of January 13 to June 30, 2021. Case-subjects were defined as individuals who had a positive RT-PCR test for SARS-CoV-2 during the period; they were matched with controls (tested negative) (1:1) based on age, sex, district of residence, and week of testing. We estimated the odds of vaccination in PCR confirmed, hospitalization and death due to COVID-19, accounting for the presence of comorbidities and prior infection. Vaccine effectiveness was estimated as (1-odds ratio) x 100%.\n\nResultsTotal 109,050 RT-PCR test results were retrieved during the January 13 to June 30, 2021. Of these, 14,168 subjects were eligible for inclusion in the study. Total 5518 matched case-control pairs were analyzed. Adjusted vaccine effectiveness (VE) against laboratory-confirmed SARS-CoV-2 infection was 14.5% (95% confidence interval -11 to 34.2) at 0-13 days after the first dose; 66.7% (95% CI: 58.1-73.5) at [&ge;]14 days after the second dose. The adjusted effectiveness against hospitalization and COVID-19-associated death was 71.1% (95% CI: 62.9-77.6) and 87.4% (95% CI: 65.1-95.4%) at [&ge;]14 days after receiving the second dose, respectively.\n\nConclusionsTwo-dose of inactivated CoronaVac vaccine showed high effectiveness against laboratory confirmed COVID-19 infection, hospitalization, and death associated with COVID-19 among adults aged [&ge;]18 years.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Anton Suryatma",
-        "author_inst": "National Agency for Research and Innovation"
-      },
-      {
-        "author_name": "Raras Anasi",
-        "author_inst": "Ministry of Health of Indonesia"
-      },
-      {
-        "author_name": "Miko Hananto",
-        "author_inst": "Ministry of Health of Indonesia"
-      },
-      {
-        "author_name": "Asep Hermawan",
-        "author_inst": "National Agency for Research and Innovation"
-      },
-      {
-        "author_name": "Ririn Ramadhany",
-        "author_inst": "Ministry of Health of Indonesia"
-      },
-      {
-        "author_name": "Irene Lorinda Indalao",
-        "author_inst": "Ministry of Health of Indonesia"
-      },
-      {
-        "author_name": "Agustiningsih Agustiningsih",
-        "author_inst": "National Agency for Research and Innovation"
-      },
-      {
-        "author_name": "Ely Hujjatul Fikriyah",
-        "author_inst": "Ministry of Health of Indonesia"
-      },
-      {
-        "author_name": "Kristina Lumban Tobing",
-        "author_inst": "National Agency for Research and Innovation"
-      },
-      {
-        "author_name": "Teti Tejayanti",
-        "author_inst": "Ministry of Health of Indonesia"
-      },
-      {
-        "author_name": "Rustika Rustika",
-        "author_inst": "National Agency for Research and Innovation"
-      },
-      {
-        "author_name": "Pandji Wibawa Dhewantara",
-        "author_inst": "National Agency for Research and Innovation"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.02.03.22270389",
     "rel_title": "Risk of severe COVID-19 from the Delta and Omicron variants in relation to vaccination status, sex, age and comorbidities: surveillance results from southern Sweden",
@@ -394384,6 +393131,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "dentistry and oral medicine"
   },
+  {
+    "rel_doi": "10.1101/2022.02.02.22269952",
+    "rel_title": "Serious hospital events following symptomatic infection with Sars-CoV-2 Omicron and Delta variants: an exposed-unexposed cohort study in December 2021 from the COVID-19 surveillance databases in France",
+    "rel_date": "2022-02-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.02.22269952",
+    "rel_abs": "BackgroundA rapid increase in incidence of the SARS-CoV-2 Omicron variant occurred in France in December 2021, while the Delta variant was prevailing since July 2021. We aimed to determine whether the risk of a severe hospital event following symptomatic SARS-CoV-2 infection differs for Omicron versus Delta.\n\nMethodsWe conducted a retrospective cohort study to compare severe hospital events (admission to intensive care unit or death) between Omicron and Delta symptomatic cases matched according to week of virological diagnosis and age. The analysis was adjusted for age, sex, vaccination status, presence of comorbidities and region of residence, using Cox proportional hazards model.\n\nFindingsBetween 06/12/2021-28/01/2022, 184 364 cases were included, of which 931 had a severe hospital event (822 Delta, 109 Omicron). The risk of severe event was lower among Omicron versus Delta cases; the difference in severity between the two variants decreased with age (aHR=0{middle dot}11 95%CI: 0{middle dot}07-0{middle dot}17 among 40-64 years, aHR=0{middle dot}51 95%CI: 0{middle dot}26-1{middle dot}01 among 80+ years). The risk of severe event increased with the presence of comorbidities (for very-high-risk comorbidity, aHR=4{middle dot}18 95%CI: 2{middle dot}88-6{middle dot}06 among 40-64 years) and in males (aHR=2{middle dot}29 95%CI: 1{middle dot}83-2{middle dot}86 among 40-64 years) and was higher in unvaccinated compared to primo-vaccinated (aHR=6{middle dot}90 95%CI: 5{middle dot}26-9{middle dot}05 among 40-64 years). A booster dose reduced the risk of severe hospital event in 80+ years infected with Omicron (aHR=0{middle dot}27; 95%CI: 0{middle dot}11-0{middle dot}65).\n\nInterpretationThis study confirms the lower severity of Omicron compared to Delta. However, the difference in disease severity is less marked in the elderly.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Vincent Auvigne",
+        "author_inst": "Sante publique France"
+      },
+      {
+        "author_name": "Sophie Vaux",
+        "author_inst": "Sante publique France"
+      },
+      {
+        "author_name": "Yann Le Strat",
+        "author_inst": "Sante publique France"
+      },
+      {
+        "author_name": "Justine Schaeffer",
+        "author_inst": "Sante publique France"
+      },
+      {
+        "author_name": "Lucie Fournier",
+        "author_inst": "Sante publique France"
+      },
+      {
+        "author_name": "Cynthia Tamandjou",
+        "author_inst": "Sante publique France"
+      },
+      {
+        "author_name": "Charline Montagnat",
+        "author_inst": "Sully"
+      },
+      {
+        "author_name": "Bruno Coignard",
+        "author_inst": "Sante publique France"
+      },
+      {
+        "author_name": "Daniel Levy-Bruhl",
+        "author_inst": "Sante publique France"
+      },
+      {
+        "author_name": "Isabelle Parent du Chatelet",
+        "author_inst": "Sante publique France"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2022.02.02.22270222",
     "rel_title": "Pediatric Croup during the COVID-19 Omicron Variant Surge",
@@ -395965,69 +394767,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2022.02.02.22270309",
-    "rel_title": "The Longitudinal Aging Study Amsterdam COVID-19 exposure index: a cross-sectional analysis of the impact of the pandemic on daily functioning of older adults",
-    "rel_date": "2022-02-03",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.02.22270309",
-    "rel_abs": "ObjectivesThe aim of this study was to develop an index to measure older adults exposure to the COVID-19 pandemic, and to study its association with various domains of functioning.\n\nDesignCross-sectional study.\n\nSettingThe Longitudinal Aging Study Amsterdam (LASA), a cohort study in the Netherlands.\n\nParticipantsCommunity dwelling older adults aged 62-102 years (n=1089) who participated in the LASA COVID-19 study (June-September 2020), just after the first wave of the pandemic.\n\nPrimary outcome measuresA 35-item COVID-19 exposure index with a score ranging between 0 and 1 was developed, including items that assess the extent to which the COVID-19 situation affected daily lives of older adults. Descriptive characteristics of the index were studied, stratified by several socio-demographic factors. Logistic regression analyses were performed to study associations between the exposure index and several indicators of functioning (functional limitations, anxiety, depression, and loneliness).\n\nResultsThe mean COVID-19 exposure index score was 0.20 (SD 0.10). Scores were relatively high among women and in the southern region of the Netherlands. In models adjusted for socio-demographic factors and pre-pandemic functioning (2018-2019), those with scores in the highest tertile of the exposure index were more likely to report functional limitations (OR: 2.23; 95% CI: 1.48 to 3.38), anxiety symptoms (OR: 3.87; 95% CI: 2.27 to 6.61), depressive symptoms (OR: 2.45; 95% CI: 1.53 to 3.93) and loneliness (OR: 2.97; 95% CI: 2.08-4.26) than those in the lowest tertile.\n\nConclusionsAmong older adults in the Netherlands, those with higher scores on a COVID-19 exposure index reported worse functioning in the physical, mental and social domain. The index may be used to identify persons for whom targeted interventions are needed to maintain or improve functioning during the pandemic or post-pandemic.\n\nStrengths and limitations of this studyO_LIThis study was based on a representative sample of older adults from three culturally different regions in the Netherlands.\nC_LIO_LIThe Longitudinal Aging Study Amsterdam COVID-19 study provides unique data on functioning of older adults in various life domains during the COVID-19 pandemic.\nC_LIO_LIThe items of the COVID-19 exposure index that was developed were based on self-report, more objective sources such as medical records were lacking.\nC_LIO_LIThe study covered the first months of the pandemic in the Netherlands, longitudinal data is needed to monitor functioning of older adults in later stages of the pandemic.\nC_LI",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Emiel O Hoogendijk",
-        "author_inst": "Amsterdam UMC - location VU University medical center"
-      },
-      {
-        "author_name": "Noah A Schuster",
-        "author_inst": "Amsterdam UMC - location VU University medical center"
-      },
-      {
-        "author_name": "Theo G van Tilburg",
-        "author_inst": "VU University Amsterdam"
-      },
-      {
-        "author_name": "Laura A Schaap",
-        "author_inst": "VU University Amsterdam"
-      },
-      {
-        "author_name": "Bianca Suanet",
-        "author_inst": "VU University Amsterdam"
-      },
-      {
-        "author_name": "Sascha de Breij",
-        "author_inst": "Amsterdam UMC - location VU University medical center"
-      },
-      {
-        "author_name": "Almar AL Kok",
-        "author_inst": "Amsterdam UMC - location VU University medical center"
-      },
-      {
-        "author_name": "Natasja M van Schoor",
-        "author_inst": "Amsterdam UMC - location VU University medical center"
-      },
-      {
-        "author_name": "Erik J Timmermans",
-        "author_inst": "University Medical Center Utrecht"
-      },
-      {
-        "author_name": "Renate T de Jongh",
-        "author_inst": "Amsterdam UMC - location VU University medical center"
-      },
-      {
-        "author_name": "Marjolein Visser",
-        "author_inst": "VU University Amsterdam"
-      },
-      {
-        "author_name": "Martijn Huisman",
-        "author_inst": "Amsterdam UMC - location VU University medical center"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.02.02.22270342",
     "rel_title": "Occurrence of relative bradycardia and relative tachycardia in individuals diagnosed with COVID-19",
@@ -396334,6 +395073,85 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.02.01.22270285",
+    "rel_title": "Association study of HLA with the kinetics of SARS-CoV-2 spike specific IgG antibody responses to BNT162b2 mRNA vaccine",
+    "rel_date": "2022-02-02",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.01.22270285",
+    "rel_abs": "BNT162b2, an mRNA-based SARS-CoV-2 vaccine (Pfizer-BioNTech), is one of the most effective COVID-19 vaccines and has been approved by more than 130 countries worldwide. However, several studies have reported that the COVID-19 vaccine shows high interpersonal variability in terms of humoral and cellular responses, such as those with respect to SARS-CoV-2 spike protein immunoglobulin (Ig)G, IgA, IgM, neutralizing antibodies, and CD4+ & CD8+ T cells. The objective of this study is to investigate the kinetic changes in anti-SARS-CoV-2 spike IgG (IgG-S) profiles and adverse reactions and their associations with HLA profiles among 100 hospital workers from the Center Hospital of the National Center for Global Health and Medicine (NCGM), Tokyo, Japan. DQA1*03:03:01 (P = 0.017; Odd ratio (OR) 2.80, 95%Confidence interval (CI) 1.05-7.25) was significantly associated with higher IgG-S production after two doses of BNT162b2 while DQB1*06:01:01:01 (P = 0.028, OR 0.27, 95%CI 0.05-0.94) was significantly associated with IgG-S declines after two doses of BNT162b2. No HLA alleles were significantly associated with either local symptoms or fever. However, C*12:02:02 (P = 0.058; OR 0.42, 95%CI 0.15-1.16), B*52:01:01 (P = 0.031; OR 0.38, 95%CI 0.14-1.03), DQA1*03:02:01 (P = 0.028; OR 0.39, 95%CI 0.15-1.00) and DPB1*02:01:02 (P = 0.024; OR 0.45, 95%CI 0.21-0.97) appeared significantly associated with protection against systemic symptoms after two doses of BNT162b2 vaccination. Further studies with larger sample sizes are clearly warranted to determine HLA allele associations with the production and long-term sustainability of IgG-S after COVID-19 vaccination.",
+    "rel_num_authors": 16,
+    "rel_authors": [
+      {
+        "author_name": "Seik-Soon Khor",
+        "author_inst": "Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan"
+      },
+      {
+        "author_name": "Yosuke Omae",
+        "author_inst": "Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan"
+      },
+      {
+        "author_name": "Junko S. Takeuchi",
+        "author_inst": "Department of Academic-Industrial Partnerships Promotion, Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan"
+      },
+      {
+        "author_name": "Ami Fukunaga",
+        "author_inst": "Department of Epidemiology and Prevention, Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan"
+      },
+      {
+        "author_name": "Shohei Yamamoto",
+        "author_inst": "Department of Epidemiology and Prevention, Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan"
+      },
+      {
+        "author_name": "Akihito Tanaka",
+        "author_inst": "Department of Laboratory Testing, Center Hospital of the National Center for the Global Health and Medicine, Tokyo, Japan"
+      },
+      {
+        "author_name": "Kouki Matsuda",
+        "author_inst": "Department of Refractory Viral Infection, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan"
+      },
+      {
+        "author_name": "Moto Kimura",
+        "author_inst": "Department of Academic-Industrial Partnerships Promotion, Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan"
+      },
+      {
+        "author_name": "Kenji Maeda",
+        "author_inst": "Department of Refractory Viral Infection, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan"
+      },
+      {
+        "author_name": "Gohzoh Ueda",
+        "author_inst": "Division of Core Diagnostics, Abbott Japan LLC, Tokyo, Japan"
+      },
+      {
+        "author_name": "Tetsuya Mizoue",
+        "author_inst": "Department of Epidemiology and Prevention, Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan"
+      },
+      {
+        "author_name": "Mugen Ujiie",
+        "author_inst": "Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan"
+      },
+      {
+        "author_name": "Hiroaki Mitsuya",
+        "author_inst": "Department of Refractory Viral Infection, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan"
+      },
+      {
+        "author_name": "Norio Ohmagari",
+        "author_inst": "Disease Control and Prevention Center, National Center for Global Health and Medicine, Tokyo, Japan"
+      },
+      {
+        "author_name": "Wataru Sugiura",
+        "author_inst": "Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan"
+      },
+      {
+        "author_name": "Katsushi Tokunaga",
+        "author_inst": "Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.01.29.22270016",
     "rel_title": "Exposing and Overcoming Limitations of Clinical Laboratory Tests in COVID-19 by Adding Immunological Parameters",
@@ -397707,65 +396525,6 @@
     "type": "new results",
     "category": "pharmacology and toxicology"
   },
-  {
-    "rel_doi": "10.1101/2022.02.01.478724",
-    "rel_title": "Metabolic dyshomeostasis induced by SARS-CoV-2 structural proteins reveals immunological insights into viral olfactory interactions",
-    "rel_date": "2022-02-02",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.01.478724",
-    "rel_abs": "One of the most common symptoms in COVID-19 is a sudden loss of smell. SARS-CoV-2 has been detected in the olfactory bulb (OB) from animal models and sporadically in COVID-19 patients. To decipher the specific role over the SARS-CoV-2 proteome at olfactory level, we characterized the in-depth molecular imbalance induced by the expression of GFP-tagged SARS-CoV-2 structural proteins (M, N, E, S) on mouse OB cells. Transcriptomic and proteomic trajectories uncovered a widespread metabolic remodeling commonly converging in extracellular matrix organization, lipid metabolism and signaling by receptor tyrosine kinases. The molecular singularities and specific interactome expression modules were also characterized for each viral structural factor. The intracellular molecular imbalance induced by each SARS-CoV-2 structural protein was accompanied by differential activation dynamics in survival and immunological routes in parallel with a differentiated secretion profile of chemokines in OB cells. Machine learning through a proteotranscriptomic data integration uncovered TGF-beta signaling as a confluent activation node by the SARS-CoV-2 structural proteome. Taken together, these data provide important avenues for understanding the multifunctional immunomodulatory properties of SARS-CoV-2 M, N, S and E proteins beyond their intrinsic role in virion formation, deciphering mechanistic clues to the olfactory inflammation observed in COVID-19 patients.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Mercedes Lachen-Montes",
-        "author_inst": "Navarrabiomed"
-      },
-      {
-        "author_name": "Naroa Mendizuri",
-        "author_inst": "Navarrabiomed"
-      },
-      {
-        "author_name": "Karina Ausin",
-        "author_inst": "Navarrabiomed"
-      },
-      {
-        "author_name": "Miriam Echaide",
-        "author_inst": "Navarrabiomed"
-      },
-      {
-        "author_name": "Ester Blanco",
-        "author_inst": "Navarrabiomed"
-      },
-      {
-        "author_name": "Luisa Chocarro",
-        "author_inst": "Navarrabiomed"
-      },
-      {
-        "author_name": "Maria De Toro",
-        "author_inst": "CIBIR"
-      },
-      {
-        "author_name": "David Escors",
-        "author_inst": "Navarrabiomed"
-      },
-      {
-        "author_name": "Joaquin Fernandez-Irigoyen",
-        "author_inst": "Navarrabiomed"
-      },
-      {
-        "author_name": "Grazyna Kochan",
-        "author_inst": "Navarrabiomed"
-      },
-      {
-        "author_name": "Enrique Santamaria",
-        "author_inst": "Navarrabiomed"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "systems biology"
-  },
   {
     "rel_doi": "10.1101/2022.02.02.478775",
     "rel_title": "Intracellular flow cytometry complements RT-qPCR detection of circulating SARS-CoV-2 variants of concern",
@@ -398072,6 +396831,33 @@
     "type": "new results",
     "category": "biophysics"
   },
+  {
+    "rel_doi": "10.1101/2022.01.30.478380",
+    "rel_title": "Using Unassigned NMR Chemical Shifts to Model RNA Secondary Structure",
+    "rel_date": "2022-02-01",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.30.478380",
+    "rel_abs": "NMR-derived chemical shifts are sensitive probes of RNA structure. However, the need to assign NMR spectra hampers their utility as a direct source of structural information. In this report, we describe a simple method that uses unassigned 2D NMR spectra to model the secondary structure of RNAs. Similar to assigned chemical shifts, we could use unassigned chemical shift data to reweight conformational libraries such that the highest weighted structure closely resembles their reference NMR structure. Furthermore, the application of our approach to the 3- and 5-UTR of the SARS-CoV-2 genome yields structures that are, for the most part, consistent with the secondary structure models derived from chemical probing data. Therefore, we expect the framework we describe here will be useful as a general strategy for rapidly generating preliminary structural RNA models directly from unassigned 2D NMR spectra. As we demonstrated for the 337-nt and 472-nt UTRs of SARS-CoV-2, our approach could be especially valuable for modeling the secondary structures of large RNA.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Neel Moudgal",
+        "author_inst": "Saline High School"
+      },
+      {
+        "author_name": "Grace Arhin",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Aaron Terrence Frank",
+        "author_inst": "University of Michigan"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "biophysics"
+  },
   {
     "rel_doi": "10.1101/2022.01.31.478476",
     "rel_title": "SARS-CoV-2 invades cognitive centers of the brain and induces Alzheimer's-like neuropathology",
@@ -399709,29 +398495,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.01.29.22270077",
-    "rel_title": "The course of COVID-19 in patients with chronic spontaneous urticaria receiving omalizumab treatment",
-    "rel_date": "2022-02-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.29.22270077",
-    "rel_abs": "IntroductionAlthough there are case reports and guideline recommendations that states omalizumab can be used in chronic spontaneous urticaria (CSU) patients during SARS-CoV-2 pandemic, there are scarce studies showing the course of Coronavirus disease 2019 (COVID-19) in CSU patients receiving omalizumab.\n\nMaterials and MethodsA total of 370 patients with chronic urticaria were included in the study between June 2020 and December 31, 2020.\n\nResultsSixty patients (16.2%) became infected with the SARS-CoV-2. The rate of pneumonia and hospitalization were 4.1% and 1.9%. There was no significant difference was determined between the CSU patients with omalizumab treatment and the non-receivers in regard to the rate of SARS-CoV-2 (+) (p: 0.567) and in regard to the rate of SARS-CoV-2 related pneumonia and hospitalization (p: 0.331 and p: 0.690). Gender, duration of CSU, serum IgE levels, omalizumab treatment, and atopy were not found to be associated with an increased risk for SARS-CoV-2 positivity in patients with CSU.\n\nConclusionOur study shows that the use of omalizumab does not increase the risk of COVID-19 infection, COVID-19-related pneumonia and hospitalizations in CSU patients and supports the views that omalizumab can be used safely in patients with CSU during the COVID-19 pandemic.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "EMEL ATAYIK",
-        "author_inst": "University of Health Science, Konya City Hospital Department of Allergy and Clinical Immunology, Konya, Turkey"
-      },
-      {
-        "author_name": "Gokhan Aytekin",
-        "author_inst": "University of Health Science, Konya City Hospital Department of Allergy and Clinical Immunology, Konya, Turkey"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "allergy and immunology"
-  },
   {
     "rel_doi": "10.1101/2022.01.31.22269194",
     "rel_title": "An outbreak of SARS-CoV-2 in a public-facing office in England, 2021",
@@ -400086,6 +398849,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2022.01.29.22269971",
+    "rel_title": "Estimating COVID-19 Vaccination Effectiveness Using Electronic Health Records of an Academic Medical Center in Michigan",
+    "rel_date": "2022-01-31",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.29.22269971",
+    "rel_abs": "ImportanceSystematic characterization of the protective effect of vaccinations across time and at-risk populations is needed to inform public health guidelines and personalized interventions.\n\nObjectiveTo evaluate the vaccine effectiveness (VE) over time and determine differences across demographic and clinical risk factors of COVID-19.\n\nDesign, Setting, and ParticipantsThis test negative design consisted of adult patients who were tested or diagnosed for COVID-19 at Michigan Medicine in 2021. Variables extracted from Electronic Health Records included vaccination status, age, gender, race/ethnicity, comorbidities, body mass index, residential-level socioeconomic characteristics, past COVID-19 infection, being immunosuppressed, and health care worker status.\n\nExposureThe primary exposure was vaccination status and was categorized into fully vaccinated with and without booster, partially vaccinated, or unvaccinated.\n\nMain Outcomes and MeasuresThe main outcomes were infection with COVID-19 (positive test or diagnosis) and having severe COVID-19, i.e., either being hospitalized or deceased. Based on these, VE was calculated by quarter, vaccine, and patient characteristics.\n\nResultsOf 170,487 COVID-19 positive adult patients, 78,002 (45.8%) were unvaccinated, and 92,485 (54.2%) were vaccinated, among which 74,060 (80.1%) were fully vaccinated. COVID-19 positivity and severity rates were substantially higher among unvaccinated (12.1% and 1.4%, respectively) compared to fully vaccinated individuals (4.7% and 0.4%, respectively). Among 7,187 individuals with a booster, only 18 (0.3%) had a severe outcome. The covariate-adjusted VE against an infection was 62.1% (95%CI 60.3-63.8%), being highest in the Q2 of 2021 (90.9% [89.5-92.1%]), lowest in Q3 (60.1% [55.9-64.0%]), and rebounding in Q4 to 68.8% [66.3- 71.1%]). Similarly, VE against severe COVID-19 overall was 73.7% (69.6-77.3%) and remained high throughout 2021: 87.4% (58.1-96.3%), 92.2% (88.3-94.8%), 74.4% (64.8-81.5%) and 83.0% (78.8-86.4%), respectively. Data on fully vaccinated individuals from Q4 indicated additional protection against infection with an additional booster dose (VE-Susceptibility: 64.0% [61.1-66.7%] vs. 87.3% [85.0-89.2%]) and severe outcomes (VE-Severity: 78.8% [73.5-83.0%] vs. 94.0% [89.5-96.6%]). Comparisons between Pfizer-BioNTech and Moderna vaccines indicated similar protection against susceptibility (82.9% [80.7-84.9%] versus 88.1% [85.5- 90.2%]) and severity (87.1% [80.3-91.6%]) vs. (84.9% [76.2-90.5%]) after controlling for vaccination timing and other factors. There was no significant effect modification by all the factors we examined.\n\nConclusions and RelevanceOur findings suggest that COVID-19 vaccines offered high protection against infection and severe COVID-19, and showed decreasing effectiveness over time and improved protection with a booster.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSHow do the rates of COVID-19 outcomes (infections or mild/severe disease) compare across vaccination status and quarters of 2021, after adjusting for confounders?\n\nFindingsIn this cohort of 170,487 adult patients tested for or diagnosed with COVID-19 during 2021, both COVID-19 positivity and severity rates were substantially higher in unvaccinated compared to fully vaccinated individuals. Vaccine effectiveness estimation was adjusted for covariates potentially related to both being vaccinated and COVID-19 outcomes; this also allowed us to determine if effectiveness differed across patient subgroups. The estimated vaccine effectiveness across the four quarters of 2021 was 62.1% against infection and was 73.7% against severe COVID-19 (defined as hospitalization, ICU admission, or death). There was no significant effect modification by all the factors we examined.\n\nMeaningThese findings suggest COVID-19 vaccines had relatively high protection against infection and severe COVID-19 during 2021 for those who received two doses of an mRNA vaccine (Moderna or Pfizer-BioNTech) or one dose of the Janssen vaccine, of which the effectiveness decreased over time and improved with a booster.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Emily Roberts",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Tian Gu",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Bhramar Mukherjee",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Lars G. Fritsche",
+        "author_inst": "University of Michigan School of Public Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.01.29.22270080",
     "rel_title": "Are high urea values before intravenous immunoglobulin replacement a risk factor for COVID-related mortality?",
@@ -401419,101 +400213,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2022.01.20.22269581",
-    "rel_title": "Occurrence and transmission potential of asymptomatic and presymptomatic SARS-CoV-2 infections: a living systematic review and meta-analysis",
-    "rel_date": "2022-01-30",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.20.22269581",
-    "rel_abs": "BACKGROUNDDebate about the level of asymptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection continues. The amount of evidence is increasing and study designs have changed over time. We updated a living systematic review to address three questions: (1) Amongst people who become infected with SARS-CoV-2, what proportion does not experience symptoms at all during their infection? (2) What is the infectiousness of asymptomatic and presymptomatic, compared with symptomatic, SARS-CoV-2 infection? (3) What proportion of SARS-CoV-2 transmission in a population is accounted for by people who are asymptomatic or presymptomatic?\n\nMETHODS AND FINDINGSThe protocol was first published on 1 April 2020 and last updated on 18 June 2021. We searched PubMed, Embase, bioRxiv and medRxiv, aggregated in a database of SARS-CoV-2 literature, most recently on 6 July 2021. Studies of people with PCR-diagnosed SARS-CoV-2, which documented symptom status at the beginning and end of follow-up, or mathematical modelling studies were included. Studies restricted to people already diagnosed, of single individuals or families, or without sufficient follow-up were excluded. One reviewer extracted data and a second verified the extraction, with disagreement resolved by discussion or a third reviewer. Risk of bias in empirical studies was assessed with a bespoke checklist and modelling studies with a published checklist. All data syntheses were done using random effects models. Review question (1): We included 130 studies.\n\nHeterogeneity was high so we did not estimate a mean proportion of asymptomatic infections overall (interquartile range 14-50%, prediction interval 2-90%), or in 84 studies based on screening of defined populations (interquartile range 20-65%, prediction interval 4-94%). In 46 studies based on contact or outbreak investigations, the summary proportion asymptomatic was 19% (95% CI 15-25%, prediction interval 2-70%). (2) The secondary attack rate in contacts of people with asymptomatic infection compared with symptomatic infection was 0.32 (95% CI 0.16-0.64, prediction interval 0.11-0-95, 8 studies). (3) In 13 modelling studies fit to data, the proportion of all SARS-CoV-2 transmission from presymptomatic individuals was higher than from asymptomatic individuals. Limitations of the evidence include high heterogeneity and high risks of selection and information bias in studies that were not designed to measure persistently asymptomatic infection, and limited information about variants of concern or in people who have been vaccinated.\n\nCONCLUSIONSBased on studies published up to July 2021, most SARS-CoV-2 infections were not persistently asymptomatic and asymptomatic infections were less infectious than symptomatic infections. Summary estimates from meta-analysis may be misleading when variability between studies is extreme and prediction intervals should be presented. Future studies should determine the asymptomatic proportion of SARS-CoV-2 infections caused by variants of concern and in people with immunity following vaccination or previous infection. Without prospective longitudinal studies with methods that minimise selection and measurement biases, further updates with the study types included in this living systematic review are unlikely to be able to provide a reliable summary estimate of the proportion of asymptomatic infections caused by SARS-CoV-2.\n\nREVIEW PROTOCOLOpen Science Framework (https://osf.io/9ewys/)\n\nAUTHOR SUMMARYO_ST_ABSWhy was this study done?C_ST_ABS{blacksquare} The proportion of people who will remain asymptomatic throughout the course of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (covid-19), is debated.\n{blacksquare}Studies that assess people at just one time point overestimate the proportion of true asymptomatic infection because those who go on to develop covid-19 symptoms will be wrongly classified as asymptomatic, but other types of study might underestimate the proportion if, for example, people with symptoms are more likely to be included in a study population.\n{blacksquare}The number of published studies about SARS-CoV-2 is increasing continuously, types of studies are changing and, since 2021, vaccines have become available, and variants of concern have emerged.\n\n\nWhat did the researchers do and find?{blacksquare} We updated a living systematic review through 6 July 2021, using automated workflows that speed up the review processes, and allow the review to be updated when relevant new evidence becomes available.\n{blacksquare}In 130 studies, we found an interquartile range of 14-50% (prediction interval 2-90%) of people with SARS-CoV-2 infection that was persistently asymptomatic; owing to heterogeneity, we did not estimate a summary proportion.\n{blacksquare}Contacts of people with asymptomatic SARS-CoV-2 infection are less likely to become infected than contacts of people with symptomatic infection (risk ratio 0.38, 95% CI 0.16-0.64, prediction interval 0.11-0.95, 8 studies).\n\n\nWhat do these findings mean?O_LI{blacksquare} Up to mid-2021, most people with SARS-CoV-2 were not persistently asymptomatic and asymptomatic infection was less infectious than symptomatic infection.\nC_LIO_LI{blacksquare} In the presence of high between-study variability, summary estimates from meta-analysis may be misleading and prediction intervals should be presented.\nC_LIO_LI{blacksquare} Future studies about asymptomatic SARS-CoV-2 infections caused by variants of concern and in people with immunity following vaccination or previous infection should be specifically designed, using methods to minimise biases in the selection of study participants and in ascertainment, classification and follow-up of symptom status.\nC_LI",
-    "rel_num_authors": 20,
-    "rel_authors": [
-      {
-        "author_name": "Diana Buitrago-Garcia",
-        "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland"
-      },
-      {
-        "author_name": "Aziz Mert Ipekci",
-        "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland"
-      },
-      {
-        "author_name": "Leonie Heron",
-        "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland"
-      },
-      {
-        "author_name": "Hira Imeri",
-        "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland"
-      },
-      {
-        "author_name": "Lucia Araujo-Chaveron",
-        "author_inst": "EHESP French School of Public Health La Plaine St Denis, Rennes, France ; Institut Pasteur, Paris, France"
-      },
-      {
-        "author_name": "Ingrid Arevalo-Rodriguez",
-        "author_inst": "Hospital Universitario Ramon y Cajal (IRYCIS)"
-      },
-      {
-        "author_name": "Agustin Ciapponi",
-        "author_inst": "Instituto de Efectividad Clinica y Sanitaria (IECS-CONICET), Buenos Aires, Argentina"
-      },
-      {
-        "author_name": "Muge Cevik",
-        "author_inst": "University of St Andrews"
-      },
-      {
-        "author_name": "Anthony Hauser",
-        "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Switzerland"
-      },
-      {
-        "author_name": "Muhammad Irfanul Alam",
-        "author_inst": "House 1066, 08 Lovelane, Chittagong 4000, Bangladesh"
-      },
-      {
-        "author_name": "Kaspar Meili",
-        "author_inst": "Department of Epidemiology and Global Health, Umea University, Umea, Sweden"
-      },
-      {
-        "author_name": "Eric A Meyerowitz",
-        "author_inst": "Montefiore Medical Center"
-      },
-      {
-        "author_name": "Nirmala Prajapati",
-        "author_inst": "Universite Paris-Saclay, Paris, France"
-      },
-      {
-        "author_name": "Xueting Qiu",
-        "author_inst": "Harvard T.H. Chan School of Public Health"
-      },
-      {
-        "author_name": "Aaron Richterman",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "William Gildardo Robles-Rodriguez",
-        "author_inst": "Fundacion Universitaria de Ciencias de la Salud. Bogota, Colombia"
-      },
-      {
-        "author_name": "Shabnam Thapa",
-        "author_inst": "Manchester Centre for Health Economics, University of Manchester, Manchester, United Kingdom"
-      },
-      {
-        "author_name": "Ivan Zhelyazkov",
-        "author_inst": "University of Sheffield, Sheffield, United Kingdom"
-      },
-      {
-        "author_name": "Georgia Salanti",
-        "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland"
-      },
-      {
-        "author_name": "Nicola Low",
-        "author_inst": "University of Bern"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.01.27.22269840",
     "rel_title": "Identification of thresholds on population density for understanding transmission of COVID-19",
@@ -401860,6 +400559,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.01.29.22270066",
+    "rel_title": "Evaluation of the systemic and mucosal immune response induced by COVID-19 and the BNT162b2 mRNA vaccine for SARS-CoV-2",
+    "rel_date": "2022-01-30",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.29.22270066",
+    "rel_abs": "BackgroundCurrently used vaccines to protect from COVID-19 mostly focus on the receptor-binding domain (RBD) of the viral spike protein, and induced neutralizing antibodies have shown to be protective. However, functional relevance of vaccine-generated antibodies are poorly understood on variants-of-concern (VOCs) and mucosal immunity.\n\nMethodsWe compared specific antibody production against the S1 subunit and the RBD of the spike protein, the whole virion of SARS-CoV-2, and monitored neutralizing antibodies in sera and saliva of 104 BNT162b2 vaccinees and 57 individuals with natural SARS-CoV-2 infection. Furthermore, we included a small cohort of 11 individuals which received a heterologous ChAdOx1-S/BNT162b2 prime-boost vaccination.\n\nResultsVaccinated individuals showed higher S1-IgG antibodies in comparison to COVID-19 patients, followed by a significant decrease 3 months later. Neutralizing antibodies (nAbs) were poorly correlated with initial S1-IgG levels, indicating that these might largely be non-neutralizing. In contrast, RBD IgGAM was strongly correlated to nAbs, suggesting that RBD-IgGAM is a surrogate marker to estimate nAb concentrations after vaccination. The protective effect of vaccine- and infection-induced nAbs was found reduced towards B.1.617.2 and B.1.351 VOCs. NAb titers are significantly higher after third vaccination compared to second vaccination. In contrast to COVID-19 patients, no relevant levels of RBD specific antibodies were detected in saliva samples from vaccinees.\n\nConclusionsOur data demonstrate that BNT162b2 vaccinated individuals generate relevant neutralizing antibodies, which begin to decrease within three months after immunization and show lower neutralizing potential to VOCs as compared to the original Wuhan virus strain. A third booster vaccination provides a stronger nAb antibody response than the second vaccination. The systemic vaccine does not seem to elicit readily detectable mucosal immunity.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Olaf Nickel",
+        "author_inst": "Klinikum Sankt Georg gGmbH Akademisches Lehrkrankenhaus der Universitat Leipzig: Klinikum Sankt Georg gGmbH"
+      },
+      {
+        "author_name": "Alexandra Rockstroh",
+        "author_inst": "Fraunhofer Institute for Cell Therapy and Immunology IZI: Fraunhofer-Institut fur Zelltherapie und Immunologie IZI"
+      },
+      {
+        "author_name": "Johannes Wolf",
+        "author_inst": "Klinikum Sankt Georg gGmbH Akademisches Lehrkrankenhaus der Universitat Leipzig: Klinikum Sankt Georg gGmbH"
+      },
+      {
+        "author_name": "Susann Landgraf",
+        "author_inst": "Klinikum Sankt Georg gGmbH Akademisches Lehrkrankenhaus der Universitat Leipzig: Klinikum Sankt Georg gGmbH"
+      },
+      {
+        "author_name": "Sven Kalbitz",
+        "author_inst": "Klinikum Sankt Georg gGmbH Akademisches Lehrkrankenhaus der Universitat Leipzig: Klinikum Sankt Georg gGmbH"
+      },
+      {
+        "author_name": "Nils Kellner",
+        "author_inst": "Klinikum Sankt Georg gGmbH Akademisches Lehrkrankenhaus der Universitat Leipzig: Klinikum Sankt Georg gGmbH"
+      },
+      {
+        "author_name": "Michael Borte",
+        "author_inst": "Klinikum Sankt Georg gGmbH Akademisches Lehrkrankenhaus der Universitat Leipzig: Klinikum Sankt Georg gGmbH"
+      },
+      {
+        "author_name": "Jasmin Fertey",
+        "author_inst": "Fraunhofer Institute for Cell Therapy and Immunology: Fraunhofer-Institut fur Zelltherapie und Immunologie IZI"
+      },
+      {
+        "author_name": "Christoph L\u00fcbbert",
+        "author_inst": "Klinikum Sankt Georg gGmbH Akademisches Lehrkrankenhaus der Universitat Leipzig: Klinikum Sankt Georg gGmbH"
+      },
+      {
+        "author_name": "Sebastian Ulbert",
+        "author_inst": "Fraunhofer Institute for Cell Therapy and Immunology: Fraunhofer-Institut fur Zelltherapie und Immunologie IZI"
+      },
+      {
+        "author_name": "Stephan Borte",
+        "author_inst": "Klinikum Sankt Georg gGmbH Akademisches Lehrkrankenhaus der Universitat Leipzig: Klinikum Sankt Georg gGmbH"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.01.28.22269987",
     "rel_title": "Genome surveillance of SARS-CoV-2 variants and their role in pathogenesis focusing on second wave of COVID-19 in India",
@@ -403285,53 +402043,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
-  {
-    "rel_doi": "10.1101/2022.01.28.22269911",
-    "rel_title": "Wastewater surveillance for COVID-19 response at multiple geographic scales: Aligning wastewater and clinical results at the census-block level and addressing pervasiveness of qPCR non-detects",
-    "rel_date": "2022-01-29",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.28.22269911",
-    "rel_abs": "Wastewater surveillance is a useful complement to clinical testing for managing COVID-19. While good agreement has been found between community-scale wastewater and clinical data, little is known about sub-community relationships between the two data types. Moreover, effects of non-detects in qPCR wastewater data have been largely overlooked. We used data collected from September 2020-June 2021 in Davis, California (USA) to address these gaps. By applying a predictive probability model to spatially disaggregate clinical results, we compared wastewater and clinical data at the community scale, in 16 sampling zones isolating city sub-regions, and in seven zones isolating high-priority building complexes or neighborhoods. We found reasonable agreement between wastewater and clinical data at all scales. Greater activity (i.e., more frequent detections) in clinical data tended to be mirrored in wastewater data. Small, isolated clinical-data spikes were often matched as well. We also developed a method for handling such non-detects using multiple imputation and compared results to (i) single imputation using half the qPCR limit of detection, (ii) single imputation using maximum qPCR cycle number, and (iii) non-detect censoring. Apparent wastewater trends were significantly influenced by non-detect handling. Multiple imputation improved correlation relative to single imputation, though not necessarily relative to censoring.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC=\"FIGDIR/small/22269911v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (31K):\norg.highwire.dtl.DTLVardef@5a57f5org.highwire.dtl.DTLVardef@144cf73org.highwire.dtl.DTLVardef@8fa56borg.highwire.dtl.DTLVardef@b52587_HPS_FORMAT_FIGEXP  M_FIG C_FIG",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Hannah Safford",
-        "author_inst": "University of California, Davis"
-      },
-      {
-        "author_name": "Rogelio E. Zuniga-Montanez",
-        "author_inst": "University of California, Davis"
-      },
-      {
-        "author_name": "Minji Kim",
-        "author_inst": "University of California, Davis"
-      },
-      {
-        "author_name": "Xiaoliu Wu",
-        "author_inst": "University of California, Davis"
-      },
-      {
-        "author_name": "Lifeng Wei",
-        "author_inst": "University of California, Davis"
-      },
-      {
-        "author_name": "James Sharpnack",
-        "author_inst": "University of California, Davis"
-      },
-      {
-        "author_name": "Karen Shapiro",
-        "author_inst": "University of California, Davis"
-      },
-      {
-        "author_name": "Heather Bischel",
-        "author_inst": "University of California, Davis"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.01.25.477724",
     "rel_title": "Distinct genetic determinants and mechanisms of SARS-CoV-2 resistance to remdesivir",
@@ -403638,6 +402349,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "rehabilitation medicine and physical therapy"
   },
+  {
+    "rel_doi": "10.1101/2022.01.27.22269909",
+    "rel_title": "How dangerous is omicron and how effective are vaccinations?",
+    "rel_date": "2022-01-28",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.27.22269909",
+    "rel_abs": "The sharp increase in the number of new COVID-19 cases in late 2021 and early 2022, which is associated with the spread of a new strain of coronavirus - omicron - is of great concern and makes it necessary to make at least approximate forecasts for the pandemic dynamics of the epidemic. As this rapid growth occurs even in countries with high levels of vaccinations, the question arises as to their effectiveness. The smoothed daily number of new cases and deaths per capita and the ratio of these characteristics were used to reveal the appearance of new coronavirus strains and to estimate the effectiveness of quarantine, testing and vaccination. The third year of the pandemic allowed us to compare the pandemic dynamics in the period from September 2020 to January 2021 with the same period one year later for Ukraine, EU, the UK, USA, India, Brazil, South Africa, Argentina, Australia, and in the whole world. Record numbers of new cases registered in late 2021 and early 2022 once again proved that existing vaccines cannot prevent new infections, and vaccinated people can spread the infection as intensively as non-vaccinated ones. Fortunately, the daily number of new cases already diminishes in EU, the UK, USA, South Africa, and Australia. In late January - early February 2022,the maximum averaged numbers of new cases are expected in Brazil, India, EU, and worldwide. \"Omicron\" waves can increase the numbers of deaths per capita, but in highly vaccinated countries, the deaths per case ratio significantly decreases.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Igor Nesteruk",
+        "author_inst": "Institute of Hydromechanics National Academy of sciences of Ukraine"
+      },
+      {
+        "author_name": "Oleksii Rodionov",
+        "author_inst": "Private consulting office, Kyiv, Ukraine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2022.01.25.22269808",
     "rel_title": "The inactivated NDV-HXP-S COVID-19 vaccine induces a significantly higher ratio of neutralizing to non-neutralizing antibodies in humans as compared to mRNA vaccines",
@@ -405259,53 +403993,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.01.26.22269805",
-    "rel_title": "Analysis of Fatality Impact and Seroprevalence Surveys in a Community Sustaining a SARS-CoV-2 Superspreading Event",
-    "rel_date": "2022-01-28",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.26.22269805",
-    "rel_abs": "There is ongoing debate on the COVID-19 infection fatality rate (IFR) and the impact of COVID-19 on overall population mortality. Here, we addressed these issues in a community in Germany with a major superspreader event analyzing deaths over time as well as auditing death certificates in the community.18 deaths that occurred within the first 6 months of the pandemic in the community had a positive test for SARS-CoV-2. Six out of 18 SARS-CoV-2+ deaths had non-COVID-19 related causes of death (COD). Individuals with confirmed infection and COVID-19 COD typically died of respiratory failure (75%) and tended to have fewer reported comorbidities (p=0.029). Duration between first confirmed infection and death was negatively associated to COVID-19 being COD (p=0.04). Repeated seroprevalence essays on an original sample of 587 individuals in three visits showed modest increases in seroprevalence over time, and substantial seroreversion (30% [27/90] (95% CI: [20.5%; 39.5%])). IFR estimates accordingly varied depending on COVID-19 death attribution and seroprevalence caveats. Careful ascertainment and audit of COVID-19 deaths are important in understanding the impact of the pandemic.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Enrico Richter",
-        "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany and German Center for Infection Research (DZIF), partner site Bonn-Cologne"
-      },
-      {
-        "author_name": "Dominik Liebl",
-        "author_inst": "Institute of Finance and Statistics and Hausdorff Center for Mathematics, University of Bonn, Germany"
-      },
-      {
-        "author_name": "Bianca Schulte",
-        "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany and German Center for Infection Research (DZIF), partner site Bonn-Cologne"
-      },
-      {
-        "author_name": "Nils Lehmann",
-        "author_inst": "Institute of Medical Informatics, Biometry und Epidemiology (IMIBE), University Hospital Essen, Germany"
-      },
-      {
-        "author_name": "Christine Fuhrmann",
-        "author_inst": "Clinical Study Core Unit, Study Center Bonn (SZB), Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Germany"
-      },
-      {
-        "author_name": "Karl-Heinz Joeckel",
-        "author_inst": "Institute of Medical Informatics, Biometry und Epidemiology (IMIBE), University Hospital Essen, Germany"
-      },
-      {
-        "author_name": "John Ioannidis",
-        "author_inst": "Departments of Medicine, of Epidemiology and Population Health, of Biomedical Data Science, and of Statistics, Stanford University, Stanford, USA"
-      },
-      {
-        "author_name": "Hendrik Streeck",
-        "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany and German Center for Infection Research (DZIF), partner site Bonn-Cologne"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.01.27.22269904",
     "rel_title": "Screening for SARS-CoV-2 in close contacts of individuals with confirmed infection: performance and operational considerations",
@@ -405812,6 +404499,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.01.27.22269299",
+    "rel_title": "Detection of SARS-CoV-2 Omicron, Delta, Alpha and Gamma variants using a rapid antigen test",
+    "rel_date": "2022-01-28",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.27.22269299",
+    "rel_abs": "Throughout the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have emerged with different infection and disease dynamics. Testing strategies, including clinical diagnosis, surveillance, and screening, have been deployed to help limit the spread of SARS-CoV-2 variants. Rapid antigen tests, in particular, have been approved for self-testing in many countries and governments are supporting their manufacturing and distribution. However, studies demonstrating the accuracy of rapid antigen tests in detecting SARS-CoV-2 variants, especially the new Omicron variant, are limited. We determined the analytical sensitivity of a CE-marked rapid antigen test against the Omicron, Delta, Alpha and Gamma variants. The rapid antigen test had the most sensitive limit of detection (10 plaque forming units [PFU]/mL) when tested with the Alpha and Gamma variants, followed by the Omicron (100 PFU/mL) and Delta (1,000 PFU/mL) variants. Given the increasing numbers of breakthrough infections and the need to surveil infectiousness, rapid antigen tests are effective public health tools to detect SARS-CoV-2 variants.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Nol Salcedo",
+        "author_inst": "E25Bio, Inc."
+      },
+      {
+        "author_name": "Nidhi Nandu",
+        "author_inst": "E25Bio, Inc."
+      },
+      {
+        "author_name": "Julie Boucau",
+        "author_inst": "Ragon Institute of MGH, Harvard and MIT"
+      },
+      {
+        "author_name": "Bobby Brooke Herrera",
+        "author_inst": "E25Bio, Inc."
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2022.01.26.22269917",
     "rel_title": "Viral Cultures for Assessing Fomites Transmission of SARS-CoV-2: a Systematic Review Protocol",
@@ -407325,149 +406043,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.01.27.22269895",
-    "rel_title": "Breakthrough infections with the omicron and delta variants of SARS-CoV-2 result in similar re-activation of vaccine-induced immunity",
-    "rel_date": "2022-01-27",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.27.22269895",
-    "rel_abs": "BackgroundThe Omicron variant of SARS-CoV-2 is now overtaking the Delta variant in many countries. Results showing that sera from double vaccinated individuals have minimal neutralizing activity against Omicron may indicate that the higher rate of transmission is due to evasion from vaccine-induced immunity. However, there is little information about activation of recall responses to Omicron in vaccinated individuals.\n\nMethodsWe measured inflammatory mediators, antibodies to the SARS-CoV-2 spike and nucleocapsid proteins, and spike peptide-induced release of interferon gamma in whole blood in 51 vaccinated individuals infected with Omicron, in 14 infected with Delta, and in 18 healthy controls. The median time points for the first and second samples were 7 and 14 days after symptom onset, respectively.\n\nFindingsInfection with Omicron or Delta led to a rapid and similar increase in antibodies to the SARS-CoV-2 spike and nucleocapsid proteins and spike peptide-induced interferon gamma in whole blood. Both the Omicron and the Delta infected patients had a mild and transient increase in inflammatory parameters.\n\nInterpretationThe results suggest that vaccine-induced immunological memory yields similar coverage for the Omicron and Delta variants.",
-    "rel_num_authors": 32,
-    "rel_authors": [
-      {
-        "author_name": "Arne Soraas",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "Gunnveig Grodeland",
-        "author_inst": "UNIVERSITETET I OSLO"
-      },
-      {
-        "author_name": "Beate Kiland Granerud",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "Thor Ueland",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "Andreas Lind",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "Borre Fevang",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "Sarah Murphy",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "Camilla Huse",
-        "author_inst": "University of Oslo"
-      },
-      {
-        "author_name": "Anders Benteson Nygaard",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "Anne Katrine Steffensen",
-        "author_inst": "University of Oslo"
-      },
-      {
-        "author_name": "Huda al-Baldawi",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "Mona Holberg-Petersen",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "Lise Lima Andresen",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "Camilla Agnes",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "Trine Ranheim",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "Ylva Schanke",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "Mette Istre",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "John Arne Dahl",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "Adity Chopra",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "Susanne Dudman",
-        "author_inst": "University of Oslo"
-      },
-      {
-        "author_name": "Mari Kaarbo",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "Jan Terje Andersen",
-        "author_inst": "University of Oslo"
-      },
-      {
-        "author_name": "Eline Benno Vaage",
-        "author_inst": "University of Oslo"
-      },
-      {
-        "author_name": "Trung The Tran",
-        "author_inst": "University of Oslo"
-      },
-      {
-        "author_name": "John Torgils Vaage",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "Annika Michelsen",
-        "author_inst": "University of Oslo"
-      },
-      {
-        "author_name": "Fredrik Muller",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "Pal Aukrust",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "Bente Halvorsen",
-        "author_inst": "University of Oslo"
-      },
-      {
-        "author_name": "Tuva Borresdatter Dahl",
-        "author_inst": "University of Oslo"
-      },
-      {
-        "author_name": "Jan Cato Holter",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "Fridtjof Lund-Johansen",
-        "author_inst": "Oslo University Hospital"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.01.26.22269877",
     "rel_title": "The impacts of increased global vaccine sharing on the COVID-19 pandemic; a retrospective modelling study",
@@ -407894,6 +406469,109 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.01.25.22269670",
+    "rel_title": "TNF\u03b1-producing CD4+ T cells dominate the SARS-CoV-2-specific T cell response in COVID-19 outpatients and are associated with durable antibodies",
+    "rel_date": "2022-01-26",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.25.22269670",
+    "rel_abs": "SARS-CoV-2-specific CD4+ T cells are likely important in immunity against COVID-19, but our understanding of CD4+ longitudinal dynamics following infection and specific features that correlate with the maintenance of neutralizing antibodies remains limited. We characterized SARS-CoV-2-specific CD4+ T cells in a longitudinal cohort of 109 COVID-19 outpatients. The quality of the SARS-CoV-2-specific CD4+ response shifted from cells producing IFN{gamma} to TNF+ from five days to four months post-enrollment, with IFN{gamma}-IL21-TNF+ CD4+ T cells the predominant population detected at later timepoints. Greater percentages of IFN{gamma}-IL21-TNF+ CD4+ T cells on day 28 correlated with SARS-CoV-2 neutralizing antibodies measured seven months post-infection ({rho}=0.4, P=0.01). mRNA vaccination following SARS-CoV-2 infection boosted both IFN{gamma} and TNF producing, spike protein-specific CD4+ T cells. These data suggest that SARS-CoV-2-specific, TNF-producing CD4+ T cells may play an important role in antibody maintenance following COVID-19.",
+    "rel_num_authors": 22,
+    "rel_authors": [
+      {
+        "author_name": "Kattria van der Ploeg",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Adam S Kirosingh",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Diego A M Mori",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Saborni Chakraborty",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Zicheng Hu",
+        "author_inst": "University of California, San Francisco; Bakar Computational Health Sciences Institute"
+      },
+      {
+        "author_name": "Benjamin L Seivers",
+        "author_inst": "J. Craig Venter Institute"
+      },
+      {
+        "author_name": "Karen B Jacobson",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Hector Bonilla",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Julie Parsonnet",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Jason R Andrews",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Kathleen D Press",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Maureen C Ty",
+        "author_inst": "Stanford university"
+      },
+      {
+        "author_name": "Daniel R Ruiz-Betancourt",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Lauren de la Parte",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Gene S Tan",
+        "author_inst": "J. Craig Venter Institute"
+      },
+      {
+        "author_name": "Catherine A Blish",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Saki Takahashi",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Isabel Rodriguez-Barraquer",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Bryan Greenhouse",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Upinder Singh",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Taia T Wang",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Prasanna Jagannathan",
+        "author_inst": "Stanford University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.01.24.22269791",
     "rel_title": "Predictive and analysis of COVID-19 cases cumulative total\uff1aARIMA model based on machine learning",
@@ -409579,69 +408257,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.01.14.21267257",
-    "rel_title": "A qualitative process analysis of DCT as an alternative to self-isolation following close contact with a confirmed case of COVID-19",
-    "rel_date": "2022-01-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.14.21267257",
-    "rel_abs": "BackgroundIn July 2021, a randomised controlled trial was conducted to compare the effect on SARS-CoV-2 transmission of seven days of daily contact testing (DCT) using lateral flow devise (LFT) and 2 PCR tests as an alternative to 10 days of standard self-isolation with 1 PCR, following close contact with a confirmed case of COVID-19. DCT appeared equivalent to self-isolation in terms of transmission in the trial, however it was not clear how tests were viewed and used in practice. In this qualitative study, we used a nested process to aid interpretation of the trial and provide insight into factors influencing use of tests, understanding of test results, and how tests were used to inform behavioural decisions.\n\nMethodsInterviews were conducted with 60 participants (42 randomised to DCT and 18 randomised to self-isolation) who had been in close contact with a confirmed positive case of COVID-19 and had consented to take part in the trial.\n\nResultsSub-themes emerging from the data were organised into three overarching themes: (1) assessing the risks and benefits of DCT; (2) use of testing during the study period and (3) future use of testing. Attitudes toward DCT as an alternative to self-isolation, and behaviour during the testing period appeared to be informed by an assessment of the associated risks and benefits. Participants reported how important it was for them to avoid isolation, how necessary self-isolation was considered to be, and the ability of LFTs to detect infection. Behaviour during the testing period was modified to reduce risks and harms as much as possible. Testing was considered a potential compromise, reducing both risk of transmission and the negative impact of self-isolation and was highly regarded as a way to  return to new normal.\n\nConclusionParticipants in this study viewed DCT as a sensible, feasible and welcome means of avoiding unnecessary self-isolation. Although negative LFTs provided reassurance, most people still restricted their activity as recommended. DCT was also highly valued by those in vulnerable households as a means of providing reassurance of the absence of infection, and as an important means of detecting infection and prompting self-isolation when necessary.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Sarah Denford",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Alex F Martin",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Lauren Towler",
-        "author_inst": "University of Southampton"
-      },
-      {
-        "author_name": "Fiona Mowbray",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Rosie Essery",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Rachael Bloomer",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Derren R Ready",
-        "author_inst": "UK Health Security Agency"
-      },
-      {
-        "author_name": "Nicola K Love",
-        "author_inst": "UK Health Security Agency"
-      },
-      {
-        "author_name": "Richard Amlot",
-        "author_inst": "UK Health Security Agency"
-      },
-      {
-        "author_name": "Isabel Oliver",
-        "author_inst": "UK Health Security Agency"
-      },
-      {
-        "author_name": "James Rubin",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Lucy Yardley",
-        "author_inst": "University of Bristol"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.01.22.22269686",
     "rel_title": "Border closure and travel restrictions to control the spread of COVID-19: an update to a Cochrane review",
@@ -409848,6 +408463,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.01.24.477469",
+    "rel_title": "Design of immunogens for eliciting antibody responses that may protect against SARS-CoV-2 variants",
+    "rel_date": "2022-01-25",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.24.477469",
+    "rel_abs": "The rise of SARS-CoV-2 variants and the history of outbreaks caused by zoonotic coronaviruses point to the need for next-generation vaccines that confer protection against variant strains. Here, we combined analyses of diverse sequences and structures of coronavirus spikes with data from deep mutational scanning to design SARS-CoV-2 variant antigens containing the most significant mutations that may emerge. We trained a neural network to predict RBD expression and ACE2 binding from sequence, which allowed us to determine that these antigens are stable and bind to ACE2. Thus, they represent viable variants. We then used a computational model of affinity maturation (AM) to study the antibody response to immunization with different combinations of the designed antigens. The results suggest that immunization with a cocktail of the antigens is likely to promote evolution of higher titers of antibodies that target SARS-CoV-2 variants than immunization or infection with the wildtype virus alone. Finally, our analysis of 12 coronaviruses from different genera identified the S2 cleavage site and fusion peptide as potential pan-coronavirus vaccine targets.\n\nAuthor SummarySARS-CoV-2 variants have already emerged and future variants may pose greater threats to the efficacy of current vaccines. Rather than using a reactive approach to vaccine development that would lag behind the evolution of the virus, such as updating the sequence in the vaccine with a current variant, we sought to use a proactive approach that predicts some of the mutations that could arise that could evade current immune responses. Then, by including these mutations in a new vaccine antigen, we might be able to protect against those potential variants before they appear. Toward this end, we used various computational methods including sequence analysis and machine learning to design such antigens. We then used simulations of antibody development, and the results suggest that immunization with our designed antigens is likely to result in an antibody response that is better able to target SARS-CoV-2 variants than current vaccines. We also leveraged our sequence analysis to suggest that a particular site on the spike protein could serve as a useful target for a pan-coronavirus vaccine.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Eric Wang",
+        "author_inst": "Massachusetts Institute of Technology"
+      },
+      {
+        "author_name": "Arup K Chakraborty",
+        "author_inst": "Massachusetts Institute of Technology"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2022.01.20.477163",
     "rel_title": "Mutations of SARS-CoV-2 variants of concern escaping Spike-specific T cells",
@@ -411185,49 +409823,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.01.24.22269699",
-    "rel_title": "SARS-CoV-2 antibody profile of naturally infected and vaccinated individuals detected using qualitative, semi-quantitative and multiplex immunoassays",
-    "rel_date": "2022-01-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.24.22269699",
-    "rel_abs": "Antibody profiling of vaccinated versus naturally infected individuals is important in evaluating immunity and aiding diagnosis and booster strategies. This study measured antibodies against different antigen targets in healthcare workers (HCW) who have been fully vaccinated with mRNA vaccines, recovered from natural infection, or patients during active infection. All vaccinated individuals were positive for anti-RBD, anti-S1, and anti-S2 antibodies. The median index and interquartile range (IQR) by the Atellica IgG assay were 179 and 140-291 respectively. Among the different antigen targets within the Bioplex assay, the levels of anti-RBD were highest (median >3200 U/mL; IQR >3200 to >3200 U/mL), followed by anti-S1 (median 2132 U/mL; IQR 1649->3200 U/mL) and anti-S2 (median=42 U/mL; IQR=24-76 U/mL). The non-vaccinated recovered cohort showed 90% seropositivity (median index >10; IQR 3.6->10) by Atellica total antibody, 73% by Atellica IgG (median index 3.3; IQR 0.9-9.4), 84% by Bioplex anti-RBD (median 62; IQR 12-269 U/mL), 77% by Bioplex anti-S1 (median 45; IQR 10-83 U/mL), 37% by Bioplex anti-S2 (median 7; IQR 1-12 U/mL), and 79% by Bioplex anti-nucleocapsid (median 69; IQR 20-185U/mL) respectively. The active infection cohort exhibited a similar pattern as the recovered cohort. About 88% and 78% of the recovered and active infection cohort produced both anti-spike and anti-N antibodies with Anti-S1/anti-N ratios ranging from 0.07-16.26. In summary, fully vaccinated individuals demonstrated an average of 50-fold higher antibody levels than naturally infected unvaccinated individuals with immune reactivity strongly towards RBD/S1 and a weak response to S2. The results support vaccination regardless of previous COVID-infection status.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Jamie Meyers",
-        "author_inst": "University Hospitals Cleveland Medical Center"
-      },
-      {
-        "author_name": "Anne Windau",
-        "author_inst": "University Hospitals Cleveland Medical Center"
-      },
-      {
-        "author_name": "Elie Saade",
-        "author_inst": "University Hospitals Cleveland Medical Center"
-      },
-      {
-        "author_name": "Christine Schmotzer",
-        "author_inst": "University Hospitals Cleveland Medical Center"
-      },
-      {
-        "author_name": "Jaime Noguez",
-        "author_inst": "University Hospitals Cleveland Medical Center"
-      },
-      {
-        "author_name": "Lisa Stempak",
-        "author_inst": "University Hospitals Cleveland Medical Center"
-      },
-      {
-        "author_name": "Xiaochun Zhang",
-        "author_inst": "University Hospitals Cleveland Medical Center"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.01.24.22269785",
     "rel_title": "Clinical evaluation of the Diagnostic Analyzer for Selective Hybridization (DASH): a point-of-care PCR test for rapid detection of SARS-CoV-2 infection",
@@ -411690,6 +410285,101 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "geriatric medicine"
   },
+  {
+    "rel_doi": "10.1101/2022.01.20.477164",
+    "rel_title": "Severe acute respiratory disease in American mink (Neovison vison) experimentally infected with SARS-CoV-2",
+    "rel_date": "2022-01-24",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.20.477164",
+    "rel_abs": "An animal model that fully recapitulates severe COVID-19 presentation in humans has been a top priority since the discovery of SARS-CoV-2 in 2019. Although multiple animal models are available for mild to moderate clinical disease, a non-transgenic model that develops severe acute respiratory disease has not been described. Mink experimentally infected with SARS-CoV-2 developed severe acute respiratory disease, as evident by clinical respiratory disease, radiological, and histological changes. Virus was detected in nasal, oral, rectal, and fur swabs. Deep sequencing of SARS-CoV-2 from oral swabs and lung tissue samples showed repeated enrichment for a mutation in the gene encoding for nonstructural protein 6 in open reading frame 1a/1ab. Together, these data indicate that American mink develop clinical features characteristic of severe COVID19 and as such, are uniquely suited to test viral countermeasures.\n\nOne Sentence SummarySARS-CoV-2 infected mink develop severe respiratory disease that recapitulates some components of severe acute respiratory disease, including ARDS.",
+    "rel_num_authors": 20,
+    "rel_authors": [
+      {
+        "author_name": "Danielle R Adney",
+        "author_inst": "Lovelace Biomedical Research Institute"
+      },
+      {
+        "author_name": "Jamie Lovaglio",
+        "author_inst": "National Institute of Allergy and Infectious Diseases"
+      },
+      {
+        "author_name": "Jonathan E Schulz",
+        "author_inst": "National Institute of Allergy and Infectious Diseases"
+      },
+      {
+        "author_name": "Claude Kwe Yinda",
+        "author_inst": "National Institute of Allergy and Infectious Diseases"
+      },
+      {
+        "author_name": "Victoria A Avanzato",
+        "author_inst": "National Institute of Allergy and Infectious Diseases"
+      },
+      {
+        "author_name": "Elaine Haddock",
+        "author_inst": "National Institute of Allergy and Infectious Diseases"
+      },
+      {
+        "author_name": "Julia R Port",
+        "author_inst": "National Institute of Allergy and Infectious Diseases"
+      },
+      {
+        "author_name": "Myndi Holbrook",
+        "author_inst": "National Institute of Allergy and Infectious Diseases"
+      },
+      {
+        "author_name": "Patrick W Hanley",
+        "author_inst": "National Institute of Allergy and Infectious Diseases"
+      },
+      {
+        "author_name": "Greg Saturday",
+        "author_inst": "National Institute of Allergy and Infectious Diseases"
+      },
+      {
+        "author_name": "Dana Scott",
+        "author_inst": "National Institute of Allergy and Infectious Diseases"
+      },
+      {
+        "author_name": "Jessica R Spengler",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Cassandra Tansey",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Caitlin Cossaboom",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Natalie Wendling",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Craig Martens",
+        "author_inst": "National Institute of Allergy and Infectious Diseases"
+      },
+      {
+        "author_name": "John Easley",
+        "author_inst": "Mink Veterinary Consulting and Research Service"
+      },
+      {
+        "author_name": "Seng Wai Yap",
+        "author_inst": "University of Wisconsin-Madison"
+      },
+      {
+        "author_name": "Stephanie N. Seifert",
+        "author_inst": "Washington State University"
+      },
+      {
+        "author_name": "Vincent J Munster",
+        "author_inst": "National Institute of Allergy and Infectious Diseases"
+      }
+    ],
+    "version": "1",
+    "license": "cc0",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2022.01.21.477274",
     "rel_title": "Host Chitinase 3-like-1 is a Universal Therapeutic Target for the Delta, Omicron and Other SARS-CoV-2 Viral Variants in COVID 19",
@@ -412839,53 +411529,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2022.01.22.22269545",
-    "rel_title": "Remdesivir for the Treatment of COVID-19: An Updated Systematic Review and Meta-Analysis",
-    "rel_date": "2022-01-23",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.22.22269545",
-    "rel_abs": "BackgroundThe benefits of remdesivir in the treatment of hospitalized patients with Covid-19 remain debated with the National Institutes of Health and the World Health Organization providing contradictory recommendations for and against use.\n\nMethodsWe performed a systematic review of randomized controlled trials (RCTs) of remdesivir for the treatment of hospitalized patients with COVID-19. The primary outcome was mortality, stratified by oxygen use (none, supplemental oxygen without mechanical ventilation, and mechanical ventilation). We conducted a frequentist random effects meta-analysis on the risk ratio (RR) scale and, to better contextualize the probabilistic benefits, we also performed a bayesian random effects meta-analysis on the risk difference scale.\n\nResultsWe identified 8 randomized trials, totaling 9157 participants. The RR for mortality comparing remdesivir versus control was 0.71 (95% confidence interval [CI] 0.42-1.22; I2=0.0%) in the patients who did not require supplemental oxygen; 0.83 (95%CI 0.73-0.95; I2=0.0%) for nonventilated patients requiring oxygen; and 1.19 (95%CI 0.98-1.44 I2=0.0%) in the setting of mechanical ventilation. Using neutral priors, the probabilities that remdesivir reduces mortality were 74.7%, 96.9% and 8.9%, respectively. The probability that remdesivir reduced mortality by more than 1% was 88.1% for nonventilated patients requiring oxygen.\n\nConclusionBased on this meta-analysis, there is a high probability that remdesivir reduces mortality for nonventilated patients with COVID-19 requiring supplemental oxygen therapy.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Todd C Lee",
-        "author_inst": "McGill University, Montreal, Canada"
-      },
-      {
-        "author_name": "Srinivas Murthy",
-        "author_inst": "University of British Columbia, Vancouver, Canada"
-      },
-      {
-        "author_name": "Olivier C Del Corpo",
-        "author_inst": "McGill University, Montreal, Canada"
-      },
-      {
-        "author_name": "Julien Senecal",
-        "author_inst": "McGill University, Montreal, Canada"
-      },
-      {
-        "author_name": "Guillaume Butler-Laporte",
-        "author_inst": "McGill University, Montreal, Canada"
-      },
-      {
-        "author_name": "Zahra N Sohani",
-        "author_inst": "McGill University, Montreal, Canada"
-      },
-      {
-        "author_name": "James M Brophy",
-        "author_inst": "McGill University, Montreal, Canada"
-      },
-      {
-        "author_name": "Emily G McDonald",
-        "author_inst": "McGill University, Montreal, Canada"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.01.20.22269539",
     "rel_title": "Comparison between mid-nasal swabs and buccal swabs for SARS-CoV-2 detection in mild COVID-19 patients",
@@ -413320,6 +411963,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2022.01.18.22269467",
+    "rel_title": "The Effects of Messaging on Expectations and Understanding of Long COVID: An Online Randomised Trial",
+    "rel_date": "2022-01-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.18.22269467",
+    "rel_abs": "ObjectivesWe examined whether providing different types of information about Long COVID would affect expectations about the illness.\n\nDesignA 2 (Illness description: Long COVID vs ongoing COVID-19 recovery) x 2 (Illness uncertainty: uncertainty emphasised vs uncertainty not emphasised) x 2 (Efficacy of support: enhanced support vs basic support) between-subjects randomised online experimental study.\n\nSettingThe online platform Prolific, collected in October 2021.\n\nParticipantsA representative sample of 1110 members of the public in the UK.\n\nInterventionsParticipants were presented with a scenario describing a positive COVID-19 test result and then presented with one of eight scenarios describing a Long COVID diagnosis.\n\nPrimary and Secondary Outcome MeasuresVarious outcome measures relating to illness expectations were captured including: symptom severity, symptom duration, quality of life, personal control, treatment control and illness coherence.\n\nResultsWe ran a series of 2 x 2 x 2 ANOVAs on the outcome variables. We found a main effect of illness description: individuals reported longer symptom duration and less illness coherence when the illness was described as Long COVID (compared to ongoing COVID-19 recovery). There was a main effect of illness uncertainty: when uncertainty was emphasised, participants reported longer expected symptom duration, less treatment control, and less illness coherence than when uncertainty was not emphasised. There was also a main effect of efficacy of support: participants reported higher personal control and higher treatment control when support was enhanced (compared to basic support). We also found an interaction between illness description and efficacy of support: when support was enhanced, participants reported less illness coherence for Long COVID (compared to ongoing COVID-19 recovery).\n\nConclusionsCommunications around Long COVID should not emphasise symptom uncertainty and should provide people with information on how they can facilitate their recovery and where they can access additional support. The findings also suggest that use of the term ongoing COVID-19 recovery, where possible, may reduce negative expectations associated with the illness.\n\nStrengths and Limitations of this studyO_LIThis is one of the first experimental designed studies to assess the impact of different types of communication about Long COVID.\nC_LIO_LIParticipants were a UK representative sample, although these findings are not necessarily applicable to all population groups (i.e., ethnic minorities).\nC_LIO_LIThis study is one of the first applications of the IPQ-R in a hypothetical, online experiment, with high reliability.\nC_LIO_LIThis was an online experiment, with hypothetical scenarios and participants with no experience of COVID-19 or Long COVID, therefore outcomes may be different in a real-world context.\nC_LI",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Jaskiran Kaur Bhogal",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Freya Mills",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Amelia Dennis",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Cristina Spoiala",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Joanna Milward",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Sidra Saeed",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Leah Ffion Jones",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Dale Weston",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Holly Carter",
+        "author_inst": "UK Health Security Agency"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2022.01.21.22269631",
     "rel_title": "Proteomic deconvolution reveals distinct immune cell fractions in different body sites in SARS-Cov-2 positive individuals",
@@ -414937,69 +413631,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2022.01.21.476344",
-    "rel_title": "Neutralization of Omicron SARS-CoV-2 by 2 or 3 doses of BNT162b2 vaccine",
-    "rel_date": "2022-01-22",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.21.476344",
-    "rel_abs": "We report the antibody neutralization against Omicron SARS-CoV-2 after 2 and 3 doses of BNT162b2 mRNA vaccine. Vaccinated individuals were serially tested for their neutralization against wild-type SARS-CoV-2 (strain USA-WA1/2020) and an engineered USA-WA1/2020 bearing the Omicron spike glycoprotein. Plaque reduction neutralization results showed that at 2 or 4 weeks post-dose-2, the neutralization geometric mean titers (GMTs) were 511 and 20 against the wild-type and Omicron-spike viruses, respectively, suggesting that two doses of BNT162b2 were not sufficient to elicit robust neutralization against Omicron; at 1 month post-dose-3, the neutralization GMTs increased to 1342 and 336, respectively, indicating that three doses of vaccine increased the magnitude and breadth of neutralization against Omicron; at 4 months post-dose-3, the neutralization GMTs decreased to 820 and 171, respectively, suggesting similar neutralization decay kinetics for both variants. The data support a three-dose vaccine strategy and provide the first glimpse of the neutralization durability against Omicron.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Hongjie Xia",
-        "author_inst": "University of Texas Medical Branch"
-      },
-      {
-        "author_name": "Jing Zou",
-        "author_inst": "University of Texas Medical Branch"
-      },
-      {
-        "author_name": "Chaitanya Kurhade",
-        "author_inst": "University of Texas Medical Branch"
-      },
-      {
-        "author_name": "Hui Cai",
-        "author_inst": "Pfizer Vaccines Research & Development"
-      },
-      {
-        "author_name": "Qi Yang",
-        "author_inst": "Pfizer Vaccines Research & Development"
-      },
-      {
-        "author_name": "Mark Cutler",
-        "author_inst": "Pfizer Vaccines Research & Development"
-      },
-      {
-        "author_name": "David Cooper",
-        "author_inst": "Pfizer Vaccines Research & Development"
-      },
-      {
-        "author_name": "Alexander Muik",
-        "author_inst": "BioNTech SE"
-      },
-      {
-        "author_name": "Kathrin U. Jansen",
-        "author_inst": "Pfizer Vaccines Research & Development"
-      },
-      {
-        "author_name": "Xuping Xie",
-        "author_inst": "University of Texas Medical Branch"
-      },
-      {
-        "author_name": "Kena A. Swanson",
-        "author_inst": "Pfizer Vaccines Research & Development"
-      },
-      {
-        "author_name": "Pei-Yong Shi",
-        "author_inst": "University of Texas Medical Branch"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2022.01.20.477115",
     "rel_title": "ESCPE-1 Mediates Retrograde Endosomal Sorting of the SARS-CoV-2 Host Factor Neuropilin-1",
@@ -415374,6 +414005,97 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.01.19.22269510",
+    "rel_title": "Microbial GWAS studies revealing combinations of Omicron RBD mutations existed and may contribute to antibody evasion and ACE2 binding",
+    "rel_date": "2022-01-21",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.19.22269510",
+    "rel_abs": "Since Omicron variant of SARS-CoV-2 was first detected in South Africa (SA), it has now dominated in United Kingdom (UK) of Europe and United State (USA) of North America. A prominent feature of this variant is the gathering of spike protein mutations, in particularly at the receptor binding domain (RBD). These RBD mutations essentially contribute to antibody resistance of current immune approaches. During global spillover, combinations of RBD mutations may exist and synergistically contribute to antibody resistance in fact. Using three geographic-stratified genome wide association studies (GWAS), we observed that RBD combinations exhibited a geographic pattern and genetical associated, such as five common mutations in both UK and USA Omicron, six or two specific mutations in UK or USA Omicron. Although the UK specific RBD mutations can be further classified into two separated sub-groups of combination based on linkage disequilibrium analysis. Functional analysis indicated that the common RBD combinations (fold change, -11.59) alongside UK or USA specific mutations significantly reduced neutralization (fold change, -38.72, -18.11). As RBD overlaps with angiotensin converting enzyme 2(ACE2) binding motif, protein-protein contact analysis indicated that the common RBD mutations enhanced ACE2 binding accessibility and were further strengthened by UK or USA-specific RBD mutations. Spatiotemporal evolution analysis indicated that UK-specific RBD mutations largely contribute to global spillover. Collectively, we have provided genetic evidence of RBD combinations and estimated their effects on antibody evasion and ACE2 binding accessibility.",
+    "rel_num_authors": 19,
+    "rel_authors": [
+      {
+        "author_name": "Xumin Ou",
+        "author_inst": "Sichuan Agricultural University"
+      },
+      {
+        "author_name": "Zhishuang Yang",
+        "author_inst": "College of Veterinary Medicine, Sichuan Agricultural University"
+      },
+      {
+        "author_name": "Dekang Zhu",
+        "author_inst": "SICAU"
+      },
+      {
+        "author_name": "Sai Mao",
+        "author_inst": "SICAU"
+      },
+      {
+        "author_name": "Mingshu Wang",
+        "author_inst": "SICAU"
+      },
+      {
+        "author_name": "Renyong Jia",
+        "author_inst": "Sichuan Agricultural University"
+      },
+      {
+        "author_name": "Shun Chen",
+        "author_inst": "SICAU"
+      },
+      {
+        "author_name": "Mafeng Liu",
+        "author_inst": "SICAU"
+      },
+      {
+        "author_name": "Qiao Yang",
+        "author_inst": "SICAU"
+      },
+      {
+        "author_name": "Ying Wu",
+        "author_inst": "SICAU"
+      },
+      {
+        "author_name": "Xinxin Zhao",
+        "author_inst": "SICAU"
+      },
+      {
+        "author_name": "Shaqiu Zhang",
+        "author_inst": "SICAU"
+      },
+      {
+        "author_name": "Juan Huang",
+        "author_inst": "SICAU"
+      },
+      {
+        "author_name": "Qun Gao",
+        "author_inst": "SICAU"
+      },
+      {
+        "author_name": "Yunya Liu",
+        "author_inst": "SICAU"
+      },
+      {
+        "author_name": "Ling Zhang",
+        "author_inst": "SICAU"
+      },
+      {
+        "author_name": "Maikel Peppelenbosch",
+        "author_inst": "Erasmus MC"
+      },
+      {
+        "author_name": "Qiuwei Pan",
+        "author_inst": "Erasmus MC"
+      },
+      {
+        "author_name": "An-chun Cheng",
+        "author_inst": "Sichuan Agricultural University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2022.01.20.477056",
     "rel_title": "Sialic acid and fucose residues on the SARS-CoV-2 receptor binding domain modulate IgG reactivity",
@@ -416643,113 +415365,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.01.18.22269300",
-    "rel_title": "Capturing intrahost recombination of SARS-CoV-2 during superinfection with Alpha and Epsilon variants in New York City",
-    "rel_date": "2022-01-21",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.18.22269300",
-    "rel_abs": "Recombination is an evolutionary process by which many pathogens generate diversity and acquire novel functions. Although a common occurrence during coronavirus replication, recombination can only be detected when two genetically distinct viruses contemporaneously infect the same host. Here, we identify an instance of SARS-CoV-2 superinfection, whereby an individual was simultaneously infected with two distinct viral variants: Alpha (B.1.1.7) and Epsilon (B.1.429). This superinfection was first noted when an Alpha genome sequence failed to exhibit the classic S gene target failure behavior used to track this variant. Full genome sequencing from four independent extracts revealed that Alpha variant alleles comprised between 70-80% of the genomes, whereas the Epsilon variant alleles comprised between 20-30% of the sample. Further investigation revealed the presence of numerous recombinant haplotypes spanning the genome, specifically in the spike, nucleocapsid, and ORF 8 coding regions. These findings support the potential for recombination to reshape SARS-CoV-2 genetic diversity.",
-    "rel_num_authors": 23,
-    "rel_authors": [
-      {
-        "author_name": "Joel O. Wertheim",
-        "author_inst": "UC San Diego"
-      },
-      {
-        "author_name": "Jade C. Wang",
-        "author_inst": "New York City Department of Health and Mental Hygiene"
-      },
-      {
-        "author_name": "Mindy Leelawong",
-        "author_inst": "New York City Department of Health and Mental Hygiene"
-      },
-      {
-        "author_name": "Darren P. Martin",
-        "author_inst": "University of Cape Town"
-      },
-      {
-        "author_name": "Jennifer L. Havens",
-        "author_inst": "UC San Diego"
-      },
-      {
-        "author_name": "Moinuddin A. Chowdhury",
-        "author_inst": "New York City Department of Health and Mental Hygiene"
-      },
-      {
-        "author_name": "Jonathan Pekar",
-        "author_inst": "UC San Diego"
-      },
-      {
-        "author_name": "Helly Amin",
-        "author_inst": "New York City Department of Health and Mental Hygiene"
-      },
-      {
-        "author_name": "Anthony Arroyo",
-        "author_inst": "New York City Department of Health and Mental Hygiene"
-      },
-      {
-        "author_name": "Gordon A. Awandare",
-        "author_inst": "University of Ghana"
-      },
-      {
-        "author_name": "Hoi Yan Chow",
-        "author_inst": "New York City Department of Health and Mental Hygiene"
-      },
-      {
-        "author_name": "Edimarlyn Gonzalez",
-        "author_inst": "New York City Department of Health and Mental Hygiene"
-      },
-      {
-        "author_name": "Elizabeth Luoma",
-        "author_inst": "New York City Department of Health and Mental Hygiene"
-      },
-      {
-        "author_name": "Collins M. Morang'a",
-        "author_inst": "University of Ghana"
-      },
-      {
-        "author_name": "Anton Nekrutenko",
-        "author_inst": "The Pennsylvania State University"
-      },
-      {
-        "author_name": "Stephen D. Shank",
-        "author_inst": "Temple University"
-      },
-      {
-        "author_name": "Peter K. Quashie",
-        "author_inst": "University of Ghana"
-      },
-      {
-        "author_name": "Jennifer L. Rakeman",
-        "author_inst": "New York City Department of Health and Mental Hygiene"
-      },
-      {
-        "author_name": "Victoria Ruiz",
-        "author_inst": "New York City Department of Health and Mental Hygiene"
-      },
-      {
-        "author_name": "Lucia V. Torian",
-        "author_inst": "New York City Department of Health and Mental Hygiene"
-      },
-      {
-        "author_name": "Tetyana I. Vasylyeva",
-        "author_inst": "UC San Diego"
-      },
-      {
-        "author_name": "Sergei L. Kosakovsky Pond",
-        "author_inst": "Temple University"
-      },
-      {
-        "author_name": "Scott Hughes",
-        "author_inst": "New York City Department of Health and Mental Hygiene"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.01.20.22269491",
     "rel_title": "Antigenic determinants of SARS-CoV-2-specific CD4+ T cell lines reveals M protein-driven dysregulation of interferon signaling",
@@ -417112,6 +415727,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2022.01.21.22269636",
+    "rel_title": "Using Survey Data to Estimate the Impact of the Omicron Variant on Vaccine Efficacy against COVID-19 Infection",
+    "rel_date": "2022-01-21",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.21.22269636",
+    "rel_abs": "Data collected in the Global COVID-19 Trends and Impact Surveys (UMD Global CTIS), and data on variants sequencing from GISAID, are used to evaluate the impact of the Omicron variant (in South Africa and other countries) on the prevalence of COVID-19 among unvaccinated and vaccinated population, in general and discriminating by the number of doses. In South Africa, we observe that the prevalence of COVID-19 in December (with strong presence of Omicron) among the unvaccinated population is comparable to the prevalence during the previous wave (in August-September), in which Delta was the variant with the largest presence. However, among vaccinated, the prevalence of COVID-19 in December is much higher than in the previous wave. In fact, a significant reduction of the vaccine efficacy is observed from August-September to December. For instance, the efficacy drops from 0.81 to 0.30 for those vaccinated with 2 doses, and from 0.51 to 0.09 for those vaccinated with one dose. The study is then extended to other countries in which Omicron has been detected, comparing the situation in October (before Omicron) with that of December. While the reduction measured is smaller than in South Africa, we still found, for instance, an average drop in vaccine efficacy from 0.53 to 0.45 among those vaccinated with two doses. Moreover, we found a significant negative (Pearson) correlation of around -0.6 between the measured prevalence of Omicron and the vaccine efficacy.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Jesus Rufino",
+        "author_inst": "IMDEA Networks Institute & CoronaSurveys Team, Spain"
+      },
+      {
+        "author_name": "Carlos Baquero",
+        "author_inst": "U. Porto & INESC TEC, Portugal, & CoronaSurveys Team"
+      },
+      {
+        "author_name": "Davide Frey",
+        "author_inst": "Univ Rennes, IRISA, CNRS, Inria, 35042 Rennes, France & CoronaSurveys Team"
+      },
+      {
+        "author_name": "Christin A. Glorioso",
+        "author_inst": "Academics for the Future of Science, Inc.  & U. of California San Francisco, USA, & CoronaSurveys Team"
+      },
+      {
+        "author_name": "Antonio Ortega",
+        "author_inst": "U. Southern California, USA, & CoronaSurveys Team"
+      },
+      {
+        "author_name": "Nina Rescic",
+        "author_inst": "Jozef Stefan Institute, Department of Intelligent Systems, Ljubljana, Slovenia, & CoronaSurveys Team"
+      },
+      {
+        "author_name": "Julian Charles Roberts",
+        "author_inst": "Gearu LTD, UK, & CoronaSurveys Team"
+      },
+      {
+        "author_name": "Rosa E. Lillo",
+        "author_inst": "U. Carlos III de Madrid, Spain, & CoronaSurveys Team"
+      },
+      {
+        "author_name": "Raquel Menezes",
+        "author_inst": "Centre of Mathematics of U. Minho, Portugal, & CoronaSurveys Team"
+      },
+      {
+        "author_name": "Jaya Prakash Champati",
+        "author_inst": "IMDEA Networks Institute, Spain, & CoronaSurveys Team"
+      },
+      {
+        "author_name": "Antonio Fernandez Anta",
+        "author_inst": "IMDEA Networks Institute, Spain, & CoronaSurveys Team"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2022.01.18.22269349",
     "rel_title": "Long-Term Persistence of IgG Antibodies in recovered COVID-19 individuals at 18 months and the impact of two-dose BNT162b2 (Pfizer-BioNTech) mRNA vaccination on the antibody response",
@@ -418649,113 +417323,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.01.19.22269531",
-    "rel_title": "Cross-sectional study to assess the efficacy of SARS-CoV-2 vaccination in patients with monoclonal gammopathies",
-    "rel_date": "2022-01-19",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.19.22269531",
-    "rel_abs": "SARS-CoV-2 vaccination is the most effective strategy to protect patients with haematologic malignancies against severe COVID-19, but primary vaccine responses are less effective in this population. Here, we characterized the humoral responses following 3 months after mRNA-based vaccines in patients at different stages of the same plasma cell diseases, including monoclonal gammopathy of undetermined significance (MGUS), smoldering multiple myeloma (SMM) and multiple myeloma on first line therapy (MM), compared to a healthy control population matched by sex and age. We observed that plasmas from uninfected MM patients after 3 months post-vaccine have lower SARS-CoV-2 specific IgG and IgA antibodies and decreased neutralization capacity compared with MGUS and SMM individuals, and a group of healthy controls. Importantly, we detected significantly higher plasma neutralization capacity in MM individuals who recovered from COVID-19 compared to their uninfected counterparts, highlighting that hybrid immunity elicit stronger immune responses even in this immunocompromised population. In contrast to MM group, no differences in the vaccine-induced humoral response were observed between uninfected MGUS, SMM and healthy individuals. In conclusion, a booster vaccine dose is recommended in uninfected MM patients to develop an adequate and effective humoral response to SARS-CoV-2 vaccine.",
-    "rel_num_authors": 23,
-    "rel_authors": [
-      {
-        "author_name": "Eugenia Abella",
-        "author_inst": "Department of Hematology, Hospital del Mar-IMIM"
-      },
-      {
-        "author_name": "Macedonia Trigueros",
-        "author_inst": "IrsiCaixa-AIDS Research Institute and Germans Trias i Pujol Health Research Institute (IGTP)"
-      },
-      {
-        "author_name": "Edwards Pradenas",
-        "author_inst": "IrsiCaixa-AIDS Research Institute and Germans Trias i Pujol Health Research Institute (IGTP)"
-      },
-      {
-        "author_name": "Francisco Munoz Lopez",
-        "author_inst": "IrsiCaixa-AIDS Research Institute and Germans Trias i Pujol Health Research Institute (IGTP)"
-      },
-      {
-        "author_name": "Francesc Garcia Pallarols",
-        "author_inst": "Department of Hematology, Hospital del Mar IMIM"
-      },
-      {
-        "author_name": "Randa Ben Azaiz Ben Lahsen",
-        "author_inst": "Department of Hematology, Hospital del Mar IMIM"
-      },
-      {
-        "author_name": "Benjamin Trinite",
-        "author_inst": "IrsiCaixa-AIDS Research Institute and Germans Trias i Pujol Health Research Institute (IGTP)"
-      },
-      {
-        "author_name": "Victor Urrea",
-        "author_inst": "IrsiCaixa-AIDS Research Institute and Germans Trias i Pujol Health Research Institute (IGTP)"
-      },
-      {
-        "author_name": "Silvia Marfil",
-        "author_inst": "IrsiCaixa-AIDS Research Institute and Germans Trias i Pujol Health Research Institute (IGTP)"
-      },
-      {
-        "author_name": "Carla Rovirosa",
-        "author_inst": "IrsiCaixa-AIDS Research Institute and Germans Trias i Pujol Health Research Institute (IGTP)"
-      },
-      {
-        "author_name": "Teresa Puig",
-        "author_inst": "IrsiCaixa-AIDS Research Institute and Germans Trias i Pujol Health Research Institute (IGTP)"
-      },
-      {
-        "author_name": "Eulalia Grau",
-        "author_inst": "IrsiCaixa-AIDS Research Institute and Germans Trias i Pujol Health Research Institute (IGTP)"
-      },
-      {
-        "author_name": "Anna Chamorro",
-        "author_inst": "Infectious Diseases Department, Fight against AIDS Foundation (FLS), Germans Trias i Pujol Hospital,"
-      },
-      {
-        "author_name": "Ruth Toledo",
-        "author_inst": "Infectious Diseases Department, Fight against AIDS Foundation (FLS), Germans Trias i Pujol Hospital,"
-      },
-      {
-        "author_name": "Marta Font",
-        "author_inst": "Infectious Diseases Department, Fight against AIDS Foundation (FLS), Germans Trias i Pujol Hospital,"
-      },
-      {
-        "author_name": "Dolors Palacin",
-        "author_inst": "Direccio d Atencio Primaria   Metropolitana Nord"
-      },
-      {
-        "author_name": "Francesc Lopez Segui",
-        "author_inst": "Infectious Diseases Department, Fight against AIDS Foundation (FLS), Germans Trias i Pujol Hospital,"
-      },
-      {
-        "author_name": "Jorge Carrillo",
-        "author_inst": "IrsiCaixa-AIDS Research Institute and Germans Trias i Pujol Health Research Institute (IGTP)"
-      },
-      {
-        "author_name": "Nuria Prat",
-        "author_inst": "Direccio d Atencio Primaria  Metropolitana Nord"
-      },
-      {
-        "author_name": "Lourdes Mateu",
-        "author_inst": "Infectious Diseases Department, Fight against AIDS Foundation (FLS), Germans Trias i Pujol Hospital"
-      },
-      {
-        "author_name": "Bonaventura Clotet",
-        "author_inst": "IrsiCaixa-AIDS Research Institute and Germans Trias i Pujol Health Research Institute (IGTP)"
-      },
-      {
-        "author_name": "Julia Blanco",
-        "author_inst": "IrsiCaixa-AIDS Research Institute and Germans Trias i Pujol Health Research Institute (IGTP)"
-      },
-      {
-        "author_name": "Marta Massanella",
-        "author_inst": "IrsiCaixa-AIDS Research Institute and Germans Trias i Pujol Health Research Institute (IGTP)"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.01.17.476677",
     "rel_title": "Prediction and validation of host cleavage targets of SARS-CoV-2 3C like protease",
@@ -419162,6 +417729,93 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.01.18.476863",
+    "rel_title": "SARS-CoV-2 Delta variant induces enhanced pathology and inflammatory responses in K18-hACE2 mice",
+    "rel_date": "2022-01-19",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.18.476863",
+    "rel_abs": "The COVID-19 pandemic has been fueled by novel variants of concern (VOC) that have increased transmissibility, receptor binding affinity, and other properties that enhance disease. The goal of this study is to characterize unique pathogenesis of the Delta VOC strain in the K18-hACE2-mouse challenge model. Challenge studies suggested that the lethal dose of Delta was higher than Alpha or Beta strains. To characterize the differences in the Delta strains pathogenesis, a time-course experiment was performed to evaluate the overall host response to Alpha or Delta variant challenge. qRT-PCR analysis of Alpha- or Delta- challenged mice revealed no significant difference between viral RNA burden in the lung, nasal wash or brain. However, histopathological analysis revealed high lung tissue inflammation and cell infiltration following Delta- but not Alpha-challenge at day 6. Additionally, pro-inflammatory cytokines were highest at day 6 in Delta-challenged mice suggesting enhanced pneumonia. Total RNA-sequencing analysis of lungs comparing infected to uninfected mice revealed that Alpha-challenged mice have more total genes differentially activated, conversely, Delta-challenged mice have a higher magnitude of differential gene expression. Delta-challenged mice have increased interferon-dependent gene expression and IFN-{gamma} production compared to Alpha. Analysis of TCR clonotypes suggested that Delta challenged mice have increased T-cell infiltration compared to Alpha challenged. Our data suggest that Delta has evolved to engage interferon responses in a manner that may enhance pathogenesis. The in vivo and in silico observations of this study underscore the need to conduct experiments with VOC strains to best model COVID-19 when evaluating therapeutics and vaccines.\n\nImportanceThe Delta variant of SARS-CoV-2 is known to be more transmissible and cause severe disease in human hosts due to mutations in its genome that are divergent from previous variants of concern (VOC). Our study evaluates the pathogenesis of Delta in the K18-hACE2 mouse model compared to the Alpha VOC. We observed that relative to Alpha, Delta challenge results in enhanced inflammation and tissue damage with stronger antiviral responses. These observations provide insight into Deltas unique pathogenesis.",
+    "rel_num_authors": 18,
+    "rel_authors": [
+      {
+        "author_name": "Katherine S Lee",
+        "author_inst": "West Virginia University"
+      },
+      {
+        "author_name": "Ting Y. Wong",
+        "author_inst": "West Virginia University"
+      },
+      {
+        "author_name": "Brynnan P Russ",
+        "author_inst": "West Virginia University"
+      },
+      {
+        "author_name": "Alexander M Horspool",
+        "author_inst": "West Virginia University"
+      },
+      {
+        "author_name": "Olivia Miller",
+        "author_inst": "West Virginia University"
+      },
+      {
+        "author_name": "Nathaniel Rader",
+        "author_inst": "West Virginia University"
+      },
+      {
+        "author_name": "Jerome P Givi",
+        "author_inst": "West Virginia University"
+      },
+      {
+        "author_name": "Michael T Winters",
+        "author_inst": "West Virginia University"
+      },
+      {
+        "author_name": "Zeriel YA Wong",
+        "author_inst": "West Virginia University"
+      },
+      {
+        "author_name": "Holly A. Cyphert",
+        "author_inst": "Marshall University"
+      },
+      {
+        "author_name": "James Denvir",
+        "author_inst": "Marshall University"
+      },
+      {
+        "author_name": "Peter G Stoilov",
+        "author_inst": "West Virginia University"
+      },
+      {
+        "author_name": "Mariette Barbier",
+        "author_inst": "West Virginia University"
+      },
+      {
+        "author_name": "Nadia Roan",
+        "author_inst": "Gladstone Institutes"
+      },
+      {
+        "author_name": "Md Shahrier Amin",
+        "author_inst": "West Virginia University"
+      },
+      {
+        "author_name": "Ivan Martinez",
+        "author_inst": "West Virginia University Cancer Institute"
+      },
+      {
+        "author_name": "Justin R. Bevere",
+        "author_inst": "West Virginia University"
+      },
+      {
+        "author_name": "F. Heath Damron",
+        "author_inst": "West Virginia University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2022.01.17.22269263",
     "rel_title": "Multisystemic inflammatory syndrome following COVID-19 mRNA vaccine in children: a national post-authorization pharmacovigilance study",
@@ -420550,37 +419204,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.01.16.22269390",
-    "rel_title": "Pooled RNA: extraction free testing of saliva for SARS-CoV-2 detection",
-    "rel_date": "2022-01-17",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.16.22269390",
-    "rel_abs": "The key to limiting SARS-CoV-2 spread is to identify virus-infected individuals (both symptomatic and asymptomatic) and isolate them from the general population. Hence, routine weekly testing for SARS-CoV-2 in all asymptomatic (capturing both infected and non-infected) individuals is considered critical in situations where a large number of individuals congregate such as schools, prisons, aged care facilities and industrial workplaces. Such testing is hampered by operational issues such as cost, test availability, access to healthcare workers and throughput. We developed the SalivaDirect RT-qPCR assay to increase access to SARS-CoV-2 testing via a low-cost, streamlined protocol using self-collected saliva. To expand the single sample testing protocol, we explored multiple extraction-free pooled saliva testing workflows prior to testing with the SalivaDirect assay. A pool size of five, with or without heat inactivation at 65{degrees}C for 15 minutes prior to testing resulted in a positive agreement of 98% and 89%, respectively, and an increased Ct value shift of 1.37 and 1.99 as compared to individual testing of the positive clinical saliva specimens. Applying this shift in Ct value to 316 individual, sequentially collected, SARS-CoV-2 positive saliva specimen results reported from six clinical laboratories using the original SalivaDirect assay, 100% of the samples would have been detected (Ct value >45) had they been tested in the 1:5 pool strategy. The availability of multiple pooled testing workflows for laboratories can increase test turnaround time, permitting results in a more actionable time frame while minimizing testing costs and changes to laboratory operational flow.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Orchid M Allicock",
-        "author_inst": "Yale school of Public Health"
-      },
-      {
-        "author_name": "Devyn Yolda-Carr",
-        "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA"
-      },
-      {
-        "author_name": "John Todd",
-        "author_inst": "Flambeau Diagnostics, Madison WI 53719, USA"
-      },
-      {
-        "author_name": "Anne L Wyllie",
-        "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.01.16.22269388",
     "rel_title": "Sero-Prevalence of Covid-19 among workers in Malaysia",
@@ -421027,6 +419650,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
+  {
+    "rel_doi": "10.1101/2022.01.17.22269412",
+    "rel_title": "EFCAB4B (CRACR2A) genetic variants associated with COVID-19 fatality",
+    "rel_date": "2022-01-17",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.17.22269412",
+    "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in more than 235 million cases worldwide and 4.8 million deaths (October 2021). Severe COVID-19 is characterised in part by vascular thrombosis and a cytokine storm due to increased plasma concentrations of factors secreted from endothelial and T-cells. Here, using patient data recorded in the UK Biobank, we demonstrate the importance of variations in Rab46 (CRACR2A) with clinical outcomes. Using logistic regression analysis, we determined that three single nucleotide polymorphisms (SNPs) in the gene EFCAB4B cause missense mutations in Rab46, which are associated with COVID-19 fatality independently of risk factors. All three SNPs cause changes in amino acid residues that are highly conserved across species, indicating their importance in protein structure and function. Two SNPs, rs17836273 (A98T) and rs36030417 (H212Q), cause amino acid substitutions in important functional domains: the EF-hand and coiled-coil domain respectively. By using molecular modelling, we suggest that the substitution of threonine at position 98 causes structural changes in the EF-hand calcium binding domain. Since Rab46 is a Rab GTPase that regulates both endothelial cell secretion and T-cell signalling, these missense variations may play a role in the molecular mechanisms underlying the thrombotic and inflammatory characteristics observed in patients with severe COVID-19 outcomes.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Dapeng Wang",
+        "author_inst": "Imperial"
+      },
+      {
+        "author_name": "Sabina D Wiktor",
+        "author_inst": "University of Leeds"
+      },
+      {
+        "author_name": "Chew W Cheng",
+        "author_inst": "University of Leeds"
+      },
+      {
+        "author_name": "Katie J Simmons",
+        "author_inst": "University of Leeds"
+      },
+      {
+        "author_name": "Ashley Money",
+        "author_inst": "University of Leeds"
+      },
+      {
+        "author_name": "Lucia Pedicini",
+        "author_inst": "University of Leeds"
+      },
+      {
+        "author_name": "Asya Carlton",
+        "author_inst": "University of Leeds"
+      },
+      {
+        "author_name": "Alexander L Breeze",
+        "author_inst": "University of Leeds"
+      },
+      {
+        "author_name": "Lynn McKeown",
+        "author_inst": "University of Leeds"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "genetic and genomic medicine"
+  },
   {
     "rel_doi": "10.1101/2022.01.17.22269136",
     "rel_title": "Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants.",
@@ -422148,41 +420822,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2022.01.14.22269288",
-    "rel_title": "Characterizing features of outbreak duration for novel SARS-CoV-2 variants of concern",
-    "rel_date": "2022-01-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.14.22269288",
-    "rel_abs": "Characterizing the dynamics of epidemic trajectories is critical to understanding the potential impacts of emerging outbreaks and to designing appropriate mitigation strategies. As the COVID-19 pandemic evolves, however, the emergence of SARS-CoV-2 variants of concern has complicated our ability to assess in real-time the potential effects of imminent outbreaks, such as those presently caused by the Omicron variant. Here, we report that SARS-CoV-2 outbreaks across regions exhibit strain-specific times from onset to peak, specifically for Delta and Omicron variants. Our findings may facilitate real-time identification of peak medical demand and may help fine-tune ongoing and future outbreak mitigation deployment efforts.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Alex D. Washburne",
-        "author_inst": "Selva Analytics"
-      },
-      {
-        "author_name": "Nathaniel Hupert",
-        "author_inst": "Weill Cornell Medicine"
-      },
-      {
-        "author_name": "Nicole Kogan",
-        "author_inst": "Department of Epidemiology, Harvard T. Chan School of Public Health"
-      },
-      {
-        "author_name": "William Hanage",
-        "author_inst": "Department of Epidemiology, Harvard T. Chan School of Public Health"
-      },
-      {
-        "author_name": "Mauricio Santillana",
-        "author_inst": "Harvard Medical School"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.01.13.22269102",
     "rel_title": "Effects of medical school on mental health and sleep habits",
@@ -422549,6 +421188,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "neurology"
   },
+  {
+    "rel_doi": "10.1101/2022.01.13.21268270",
+    "rel_title": "Health and Economic Consequences of Universal Paid Sick Leave Policies During the COVID-19 Pandemic",
+    "rel_date": "2022-01-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.13.21268270",
+    "rel_abs": "ImportanceUniversal paid sick-leave (PSL) policies have been implemented in jurisdictions to mitigate the spread of SARS-CoV-2. However empirical data regarding health and economic consequences of PSL policies is scarce.\n\nObjectiveTo estimate effects of a universal PSL policy in Ontario, Canadas most populous province.\n\nDesignAn agent-based model (ABM) to simulate SARS-CoV-2 transmission informed by data from Statistics Canada, health administrative sources, and from the literature.\n\nSettingOntario from January 1st to May 1st, 2021.\n\nParticipantsA synthetic population (1 million) with occupation and household characteristics representative of Ontario residents (14.5 million).\n\nExposureA base case of existing employer-based PSL alone versus the addition of a 3-or 10-day universal PSL policy to facilitate testing and self-isolation among workers infected with SARS-CoV-2 themselves or because of infected household members.\n\nMain Outcome(s) and Measure(s)Number of SARS-CoV-2 infections and COVID-19 hospitalizations, worker productivity, lost wages, and presenteeism (going to a workplace while infected).\n\nResultsIf a 3- and 10-day universal PSL were implemented over the 4-month study period, then compared with the base-case, the PSL policies were estimated to reduce cumulative SARS-CoV-2 cases by 85,531 (95% credible interval, CrI -2,484; 195,318) and 215,302 (81,500; 413,742), COVID-19 hospital admissions by 1,307 (-201; 3,205) and 3,352 (1,223; 6,528), numbers of workers forgoing wages by 558 (-327;1,608) and 7,406 (6,764; 8,072), and numbers of workers engaged in presenteeism by 24,499 (216; 54,170) and 279,863 (262,696; 295,449). Hours of productivity loss were estimated to be 10,854,379 (10,212,304; 11,465,635) in the base case, 17,446,525 (15,934,321; 18,854,683) in the 3-day scenario, and 26,127,165 (20,047,239; 29,875,161) in the 10-day scenario. Lost wages were $5,256,316 ($4,077,280; $6,804,983) and $12,610,962 ($11,463,128; $13,724,664) lower in the 3 day and 10 day scenarios respectively, relative to the base case.\n\nConclusions and RelevanceExpanded access to PSL is estimated to reduce total numbers of COVID-19 cases, reduce presenteeism of workers with SARS-CoV-2 at workplaces, and mitigate wage loss experienced by workers.\n\nCompeting interestsThe authors have no competing interests relevant to this article to disclose.\n\nFundingSupported by COVID-19 Rapid Research Funding (C-291-2431272-SANDER). This research was further supported, in part, by a Canada Research Chair in Economics of Infectious Diseases held by Beate Sander (CRC-950-232429). The study sponsor had no role in the design, collection, analysis, interpretation of the data, manuscript preparation or the decision to submit for publication.\n\nAuthor ContributionsConceptualization: PP, JDR, BS, DN\n\nData Curation: PP, JDR, BS, DN\n\nFormal Analysis: PP, JDR, DN\n\nMethodology: PP, JDR, BS, DN\n\nSupervision: PP, DN, BS\n\nValidation: PP, JDR, BS, DN\n\nFirst Draft: PP, JDR, BS, DN\n\nReview and Edit\n\nPP, JDR, BS, DN\n\nKey pointsO_ST_ABSQuestionC_ST_ABSWhat could be the health and economic consequence of more generous paid sick leave policies in the context of the COVID-19 pandemic?\n\nFindingsMore generous policies are estimated to reduce SARS-CoV-2 infections (and thus COVID-19 hospitalizations), lost wages and presence of individuals with infection at workplaces.\n\nMeaningMore generous paid sick leave can be a valuable addition to other COVID-19 public health interventions.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "David MJ Naimark",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Juan David Rios",
+        "author_inst": "The Hospital for Sick Children"
+      },
+      {
+        "author_name": "Sharmistha Mihsra",
+        "author_inst": "St. Michael's Hospital, Unity Health Toronto, Toronto, Canada"
+      },
+      {
+        "author_name": "Beate Sander",
+        "author_inst": "University Health Network"
+      },
+      {
+        "author_name": "Petros Pechlivanoglou",
+        "author_inst": "THE HOSPITAL FOR SICK CHILDREN"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health economics"
+  },
   {
     "rel_doi": "10.1101/2022.01.13.22268948",
     "rel_title": "Algorithmic Fairness and Bias Mitigation for Clinical Machine Learning: Insights from Rapid COVID-19 Diagnosis by Adversarial Learning",
@@ -424322,109 +422996,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2022.01.12.473243",
-    "rel_title": "COVID-19 vaccine booster induces a strong CD8+ T cell response against Omicron variant epitopes in HLA-A*02:01+ individuals",
-    "rel_date": "2022-01-13",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.12.473243",
-    "rel_abs": "The >30 mutated residues in the Omicron spike protein have led to its rapid classification as a new SARS-CoV-2 variant of concern. As a result, Omicron may escape from the immune system, decreasing the protection provided by COVID-19 vaccines. Preliminary data shows a weaker neutralizing antibody response to Omicron compared to the ancestral SARS-CoV-2 virus, which can be increased after a booster vaccine. Here, we report that CD8+ T cells can recognize Omicron variant epitopes presented by HLA-A*02:01 in both COVID-19 recovered and vaccinated individuals, even 6 months after infection or vaccination. Additionally, the T cell response was stronger for Omicron variant epitopes after the vaccine booster. Altogether, T cells can recognize Omicron variants, especially in vaccinated individuals after the vaccine booster.\n\nOne-Sentence SummaryCD8+ T cells response against Omicron variant epitopes is stronger after the vaccine booster.",
-    "rel_num_authors": 22,
-    "rel_authors": [
-      {
-        "author_name": "Andrea T. Nguyen",
-        "author_inst": "Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia; Department of Biochemis"
-      },
-      {
-        "author_name": "Christopher Szeto",
-        "author_inst": "Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia; Department of Biochemis"
-      },
-      {
-        "author_name": "Demetra S.M. Chatzileontiadou",
-        "author_inst": "Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia; Department of Biochemis"
-      },
-      {
-        "author_name": "Zhen Wei Marcus Tong",
-        "author_inst": "School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane Australia"
-      },
-      {
-        "author_name": "Michael J. Dewar-Oldis",
-        "author_inst": "Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia"
-      },
-      {
-        "author_name": "Lucy Cooper",
-        "author_inst": "Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia;Immunity Program, Biomedicine Discovery Institute, Monash Univ"
-      },
-      {
-        "author_name": "Lawton D. Murdolo",
-        "author_inst": "Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia"
-      },
-      {
-        "author_name": "Keng Yih Chew",
-        "author_inst": "Faculty of Medicine, The University of Queensland, Brisbane,"
-      },
-      {
-        "author_name": "Katie E. Lineburg",
-        "author_inst": "QIMR Berghofer Medical Research Institute - QIMR Berghofer Centre for Immunotherapy and Vaccine Development Brisbane, Queensland, Australia;"
-      },
-      {
-        "author_name": "Alan Riboldi-Tunicliffe",
-        "author_inst": "Australian Synchrotron, ANSTO, Clayton, Victoria, Australia;"
-      },
-      {
-        "author_name": "Rachel Williamson",
-        "author_inst": "Australian Synchrotron, ANSTO, Clayton, Victoria, Australia;"
-      },
-      {
-        "author_name": "Bradley J. Gardiner",
-        "author_inst": "Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia"
-      },
-      {
-        "author_name": "Dhilshan Jayasinghe",
-        "author_inst": "Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia;  Department of Biochemi"
-      },
-      {
-        "author_name": "Christian A. Lobos",
-        "author_inst": "Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia;  Department of Biochemi"
-      },
-      {
-        "author_name": "You Min Ahn",
-        "author_inst": "Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia"
-      },
-      {
-        "author_name": "Emma J. Grant",
-        "author_inst": "Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia;  Department of Biochemi"
-      },
-      {
-        "author_name": "Corey Smith",
-        "author_inst": "QIMR Berghofer Medical Research Institute - QIMR Berghofer Centre for Immunotherapy and Vaccine Development Brisbane, Queensland, Australia"
-      },
-      {
-        "author_name": "James McMahon",
-        "author_inst": "Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Australia;  Department of Infectious Diseases, Monash Medical Centre, Clayt"
-      },
-      {
-        "author_name": "Kim L. Good-Jacobson",
-        "author_inst": "Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia; Immunity Program, Biomedicine Discovery Institute, Monash Uni"
-      },
-      {
-        "author_name": "Peter J. Barnard",
-        "author_inst": "Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia"
-      },
-      {
-        "author_name": "Kirsty R. Short",
-        "author_inst": "Faculty of Medicine, The University of Queensland, Brisbane;  Australian Infectious Diseases Research Centre, The University of Queensland, Australia."
-      },
-      {
-        "author_name": "Stephanie Gras",
-        "author_inst": "Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia; Department of Biochemis"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2022.01.13.22269078",
     "rel_title": "COVID-19 infection and vaccination rates in healthcare workers in British Columbia, Canada: A Longitudinal Urban versus Rural Analysis of the Impact of the Vaccine Mandate",
@@ -424883,6 +423454,105 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "allergy and immunology"
   },
+  {
+    "rel_doi": "10.1101/2022.01.12.476120",
+    "rel_title": "An antibody targeting the N-terminal domain of SARS-CoV-2 disrupts the spike trimer",
+    "rel_date": "2022-01-13",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.12.476120",
+    "rel_abs": "The protective human antibody response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus focuses on the spike (S) protein which decorates the virion surface and mediates cell binding and entry. Most SARS-CoV-2 protective antibodies target the receptor- binding domain or a single dominant epitope ( supersite) on the N terminal domain (NTD). Here, using the single B cell technology LIBRA-seq, we isolated a large panel of NTD-reactive and SARS-CoV-2 neutralizing antibodies from an individual who had recovered from COVID-19. We found that neutralizing antibodies to the NTD supersite commonly are encoded by the IGHV1-24 gene, forming a genetic cluster that represents a public B cell clonotype. However, we also discovered a rare human antibody, COV2-3434, that recognizes a site of vulnerability on the SARS-CoV-2 S protein in the trimer interface and possesses a distinct class of functional activity. COV2-3434 disrupted the integrity of S protein trimers, inhibited cell-to-cell spread of virus in culture, and conferred protection in human ACE2 transgenic mice against SARS-CoV-2 challenge. This study provides insight about antibody targeting of the S protein trimer interface region, suggesting this region may be a site of virus vulnerability.",
+    "rel_num_authors": 21,
+    "rel_authors": [
+      {
+        "author_name": "Naveenchandra Suryadevara",
+        "author_inst": "Vanderbilt University Medical Center"
+      },
+      {
+        "author_name": "Andrea Shiakolas",
+        "author_inst": "Vanderbilt University"
+      },
+      {
+        "author_name": "Laura VanBlargan",
+        "author_inst": "Washington University in St. Louis"
+      },
+      {
+        "author_name": "Elad Binshtein",
+        "author_inst": "Vanderbilt University"
+      },
+      {
+        "author_name": "Rita Chen",
+        "author_inst": "Washington University in St. Louis"
+      },
+      {
+        "author_name": "James Brett Case",
+        "author_inst": "Washington University School of Medicine"
+      },
+      {
+        "author_name": "Kevin Kramer",
+        "author_inst": "Vanderbilt University"
+      },
+      {
+        "author_name": "Erica Armstrong",
+        "author_inst": "Vanderbilt University Medical Center"
+      },
+      {
+        "author_name": "Luke Myers",
+        "author_inst": "Vanderbilt University Medical Center"
+      },
+      {
+        "author_name": "Andrew Trivette",
+        "author_inst": "Vanderbilt University Medical Center"
+      },
+      {
+        "author_name": "Christopher Gainza",
+        "author_inst": "Vanderbilt University Medical Center"
+      },
+      {
+        "author_name": "Rachel Nargi",
+        "author_inst": "Vanderbilt University Medical Center"
+      },
+      {
+        "author_name": "Christopher Selverian",
+        "author_inst": "Integral Molecular"
+      },
+      {
+        "author_name": "Edgar Davidson",
+        "author_inst": "Integral Molecular"
+      },
+      {
+        "author_name": "Benjamin Doranz",
+        "author_inst": "Integral Molecular"
+      },
+      {
+        "author_name": "Summer Diaz",
+        "author_inst": "Vanderbilt University Medical Center"
+      },
+      {
+        "author_name": "Laura Handal",
+        "author_inst": "Vanderbilt University Medical Center"
+      },
+      {
+        "author_name": "Robert H. Carnahan",
+        "author_inst": "Vanderbilt University Medical Center"
+      },
+      {
+        "author_name": "Michael S. Diamond",
+        "author_inst": "Washington University in St. Louis"
+      },
+      {
+        "author_name": "Ivelin Georgiev",
+        "author_inst": "Vanderbilt University Medical Center"
+      },
+      {
+        "author_name": "James E. Crowe Jr.",
+        "author_inst": "Vanderbilt University Medical Center"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2022.01.13.475409",
     "rel_title": "Immunogenicity of convalescent and vaccinated sera against clinical isolates of ancestral SARS-CoV-2, beta, delta, and omicron variants",
@@ -426464,41 +425134,6 @@
     "type": "new results",
     "category": "biochemistry"
   },
-  {
-    "rel_doi": "10.1101/2022.01.11.475901",
-    "rel_title": "Effect of cannabidiol on apoptosis and cellular interferon and interferon-stimulated gene responses to the SARS-CoV-2 genes ORF8, ORF10 and M protein",
-    "rel_date": "2022-01-12",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.11.475901",
-    "rel_abs": "AimsTo study effects on cellular innate immune responses to novel genes ORF8 and ORF10, and the more conserved Membrane protein (M protein) from the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes COVID-19, either alone, or in combination with cannabidiol (CBD).\n\nMain MethodsHEK293 cells were transfected with a control plasmid, or plasmids expressing ORF8, ORF10, or M protein, and assayed for cell number and markers of apoptosis at 24 h, and expression of interferon and interferon-stimulated genes at 14 h.\n\nKey findingsA significant reduction in cell number, and increase in early and late apoptosis, was found after 24 h in cells where expression of viral genes was combined with 1-2 M CBD treatment, but not in control-transfected cells treated with CBD, or in cells expressing viral genes but treated only with vehicle. CBD (2 M) augmented expression of IFN{gamma}, IFN{lambda}1 and IFN{lambda}2/3, as well as the 2-5-oligoadenylate synthetase (OAS) family members OAS1, OAS2, OAS3, and OASL, in cells expressing ORF8, ORF10, and M protein. CBD also augmented expression of these genes in control cells not expressing viral genes, without enhancing apoptosis.\n\nSignificanceOur results demonstrate a poor ability of HEK293 cells to respond to SARS-CoV-2 genes alone, but suggest an augmented innate anti-viral response to these genes in the presence of CBD. Furthermore, our results indicate that CBD may prime components of the innate immune system, increasing readiness to respond to viral infection without activating apoptosis, and therefore could be studied for potential in prophylaxis.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Maria Fernanda Fernandes",
-        "author_inst": "University of Waterloo"
-      },
-      {
-        "author_name": "John Zewen Chan",
-        "author_inst": "University of Waterloo"
-      },
-      {
-        "author_name": "Chia Chun Joey Hung",
-        "author_inst": "University of Waterloo"
-      },
-      {
-        "author_name": "Michelle Victoria Tomczewski",
-        "author_inst": "University of Waterloo"
-      },
-      {
-        "author_name": "Robin Elaine Duncan",
-        "author_inst": "University of Waterloo"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "new results",
-    "category": "pharmacology and toxicology"
-  },
   {
     "rel_doi": "10.1101/2022.01.11.475889",
     "rel_title": "Favipiravir, umifenovir and camostat mesylate: a comparative study against SARS-CoV-2",
@@ -426769,6 +425404,225 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2022.01.10.22269002",
+    "rel_title": "Cardiopulmonary imaging utilization and findings among hospitalized COVID-19 patients in Latin America (From RIMAC: Registry IMAging Cardiopulmonary among hospitalized COVID-19 patients in LATAM)",
+    "rel_date": "2022-01-11",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.10.22269002",
+    "rel_abs": "ObjectivesTo describe the use and findings of cardiopulmonary imaging - chest X-ray (cX-ray), echocardiography (cEcho), chest CT (cCT), lung ultrasound (LUS)) and/or cardiac magnetic resonance imaging (cMRI) - in COVID-19-associated hospitalizations in Latin America (LATAM)\n\nBackgroundThe SARS-Cov-2 is one of the largest and most active threats to healthcare in living memory. There is an information gap on imaging services resources (ISR) used and their findings during the pandemic in LATAM.\n\nMethodsThis was a multicenter, prospective, observational study of COVID-19 inpatients conducted from March to December 2020 from 12 high-complexity centers in nine LATAM countries. Adults (> 18 yrs) with at least one imaging modality performed, followed from admission until discharge and/or in-hospital death, were included.\n\nResultsWe studied 1435 hospitalized patients (64% males) with a median age of 58 years classified into three regions: 262 from Mexico (Mx), 428 from Central America and Caribbean (CAC), and 745 from South America (SAm). More frequent comorbidities were overweight/obesity (61%), hypertension (45%), and diabetes (27%). During hospitalization, 58% were admitted to ICU. The in-hospital mortality was 28% (95%CI 25-30) highest in Mx (37%).\n\nThe most frequent cardiopulmonary imaging performed were cCT (61%)-more frequent in Mx and SAm-, and cX-ray (46%) -significantly used in CAC-. The cEcho was carried out in 18%, similarly among regions, and LUS in 7%, more frequently in Mx. The cMRI was performed in only one patient in the cohort. Abnormal findings on the cX-ray were related to peripheral (63%) or basal infiltrates (52%), and in cCT with ground glass infiltrates (89%). Both were more commonly in Mx. In LUS, interstitial syndrome (56%) was the most related abnormal finding, predominantly in Mx and CAC.\n\nConclusionsThe use and findings of cardiopulmonary imaging in LATAM varied between regions and may have been influenced by clinical needs, the personnel protection measures and/or hospitalization location.\n\nCondensed AbstractThe SARS-Cov-2 is one of the largest and most active threats to healthcare in living memory. There is limited information on imaging services resources (ISR) used and their findings during the pandemic in LATAM.\n\nTo our knowledge, RIMAC aimed the first international, multicenter study at registering the use and findings of cardiopulmonary imaging modalities performed for the diagnosis, prognosis, and treatment of patients hospitalized for infection with SARS-CoV-2 in Latin America. We studied their demographic parameters, comorbidities, in-hospital events, laboratory results, and treatments focusing on their impact in clinical complications.",
+    "rel_num_authors": 51,
+    "rel_authors": [
+      {
+        "author_name": "Salvador Vicente Spina",
+        "author_inst": "Hospital Aeronautico Central, Buenos Aires, Argentina"
+      },
+      {
+        "author_name": "Marcelo Luiz Campos Vieira",
+        "author_inst": "Hospital Israelita Albert Einstein, Sao Paulo, Brazil."
+      },
+      {
+        "author_name": "Cesar Herrera",
+        "author_inst": "CEDIMAT, Santo Domingo, Republica Dominicana"
+      },
+      {
+        "author_name": "Ana Munera Echeverri",
+        "author_inst": "Hospital General de Medellin, Medellin, Colombia"
+      },
+      {
+        "author_name": "Pamela Rojo",
+        "author_inst": "Clinica Davila, Santiago de Chile, Chile"
+      },
+      {
+        "author_name": "Alma Sthela Arrioja Salazar",
+        "author_inst": "Clinica Davila, Santiago de Chile, Chile."
+      },
+      {
+        "author_name": "Zuilma Vazquez Ortiz",
+        "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion   \"Salvador Zubiran\",      Ciudad de Mexico, Mexico"
+      },
+      {
+        "author_name": "Roberto Baltodano",
+        "author_inst": "HNG Almenara Irigoyen, Lima, Peru"
+      },
+      {
+        "author_name": "Graciela Reyes",
+        "author_inst": "Hospital El Cruce, Provincia Buenos Aires, Argentina"
+      },
+      {
+        "author_name": "Rocio Aceves Millan",
+        "author_inst": "Centro Medico Nacional 20 de Noviembre, Ciudad de Mexico, Mexico"
+      },
+      {
+        "author_name": "Juan Calderon Gonzalez",
+        "author_inst": "Hospital general de Zona Numero 4, Monterrey, Mexico"
+      },
+      {
+        "author_name": "Ana Camarozano",
+        "author_inst": "Hospital Nossa Senhora das Gracas y Universidade Federal do Parana, Brazil"
+      },
+      {
+        "author_name": "Edgar Aviles",
+        "author_inst": "Complejo Hospitalario Dr Arnulfo Arias Madrid, Ciudad de Panama, Panama"
+      },
+      {
+        "author_name": "Marco Antonio Cabrera",
+        "author_inst": "TECNISCAN Hospitalia, Ciudad de Guatemala, Guatemala"
+      },
+      {
+        "author_name": "Maria Florencia Grande Ratti",
+        "author_inst": "Internal Medicine Research Area, Hospital Italiano de Buenos Aires, Argentina"
+      },
+      {
+        "author_name": "Jorge Lowenstein",
+        "author_inst": "Instituto de Investigaciones Medicas, Buenos Aires, Argentina"
+      },
+      {
+        "author_name": "Rodrigo Hernandez Vyhmeister",
+        "author_inst": "Hospital de la Fuerza Aerea, Santiago de Chile, Chile"
+      },
+      {
+        "author_name": "Pamela Pina Santana",
+        "author_inst": "CEDIMAT, Santo Domingo, Republica Dominicana"
+      },
+      {
+        "author_name": "Jaime Ibarra Burgos",
+        "author_inst": "Medicina Interna Universidad CES, Medellin, Colombia"
+      },
+      {
+        "author_name": "Alejandra Rivera",
+        "author_inst": "Clinica Davila, Santiago de Chile, Chile."
+      },
+      {
+        "author_name": "Beatriz Fernandez Campos",
+        "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion \"Salvador Zubiran\",  Ciudad de Mexico, Mexico"
+      },
+      {
+        "author_name": "Kelly Cupe Chacalcaje",
+        "author_inst": "HNG Almenara Irigoyen, Lima, Peru"
+      },
+      {
+        "author_name": "Mariela De Santos",
+        "author_inst": "Hospital El Cruce, Provincia Buenos Aires, Argentina"
+      },
+      {
+        "author_name": "Tania Regina Afonso",
+        "author_inst": "Hospital Israelita Albert Einstein, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "Tomas Miranda Aquino",
+        "author_inst": "Centro Medico Nacional 20 de Noviembre, Ciudad de Mexico, Mexico"
+      },
+      {
+        "author_name": "Ana Lalyre Acosta",
+        "author_inst": "Complejo Hospitalario Dr Arnulfo Arias Madrid, Ciudad de Panama, Panama"
+      },
+      {
+        "author_name": "Beatriz Dominguez",
+        "author_inst": "TECNISCAN Hospitalia, Ciudad de Guatemala, Guatemala"
+      },
+      {
+        "author_name": "Federico Campos",
+        "author_inst": "CEDIMAT, Santo Domingo, Republica Dominicana"
+      },
+      {
+        "author_name": "Sergio Alday Ramirez",
+        "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion \"Salvador Zubiran\",  Ciudad de Mexico, Mexico"
+      },
+      {
+        "author_name": "Angela Cachicatari Beltran",
+        "author_inst": "HNG Almenara Irigoyen, Lima, Peru"
+      },
+      {
+        "author_name": "Daniela Alvarez",
+        "author_inst": "Hospital El Cruce, Provincia Buenos Aires, Argentina"
+      },
+      {
+        "author_name": "Patricia Oliveira Roveri",
+        "author_inst": "Hospital Israelita Albert Einstein, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "Carlos Rosales Ixcamparij",
+        "author_inst": "Centro Medico Nacional 20 de Noviembre, Ciudad de Mexico, Mexico"
+      },
+      {
+        "author_name": "Ender Otoniel Gonzalez",
+        "author_inst": "TECNISCAN Hospitalia, Ciudad de Guatemala, Guatemala"
+      },
+      {
+        "author_name": "Pedro Vargas",
+        "author_inst": "CEDIMAT, Santo Domingo, Republica Dominicana"
+      },
+      {
+        "author_name": "Maximiliano Flores Flamand",
+        "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion \"Salvador Zubiran\",     Ciudad de Mexico, Mexico"
+      },
+      {
+        "author_name": "Rosa Lopez Martinez",
+        "author_inst": "HNG Almenara Irigoyen, Lima, Peru"
+      },
+      {
+        "author_name": "Luciana Meza",
+        "author_inst": "Hospital El Cruce, Provincia Buenos Aires, Argentina"
+      },
+      {
+        "author_name": "Samira Saady Morthy",
+        "author_inst": "Hospital Israelita Albert Einstein, Sao Pablo, Brazil"
+      },
+      {
+        "author_name": "Rudy Ovalle",
+        "author_inst": "TECNISCAN Hospitalia, Ciudad de Guatemala, Guatemala"
+      },
+      {
+        "author_name": "Stalin Martinez",
+        "author_inst": "CEDIMAT, Santo Domingo, Republica Dominicana"
+      },
+      {
+        "author_name": "Oscar Perez Orpinel",
+        "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion \"Salvador Zubiran\", Ciudad  de Mexico, Mexico"
+      },
+      {
+        "author_name": "Mauricio Potito",
+        "author_inst": "Hospital El Cruce, Provincia Buenos Aires, Argentina"
+      },
+      {
+        "author_name": "Otto Orellana",
+        "author_inst": "TECNISCAN Hospitalia, Ciudad de Guatemala,"
+      },
+      {
+        "author_name": "Jorge Marte Baez",
+        "author_inst": "CEDIMAT, Santo Domingo, Republica Dominicana"
+      },
+      {
+        "author_name": "Consuelo Orihuela Sandoval",
+        "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion \"Salvador Zubiran\",    Ciudad de Mexico, Mexico"
+      },
+      {
+        "author_name": "Marcos Granillo Fernandez",
+        "author_inst": "Hospital El Cruce, Provincia Buenos Aires, Argentina"
+      },
+      {
+        "author_name": "Rohit Loomba",
+        "author_inst": "Advocate Children's Hospital/Rosalind Franklin University of Medicine and Science, Chicago, IL, USA"
+      },
+      {
+        "author_name": "Saul Flores",
+        "author_inst": "Texas Children's Hospital/Baylor School of Medicine, Houston, TX, USA"
+      },
+      {
+        "author_name": "Jose Maria Hernandez Hernandez",
+        "author_inst": "Cardiolink Estudios Cardiovasculares, Monterrey, Mexico"
+      },
+      {
+        "author_name": "Ricardo Pignatelli",
+        "author_inst": "Children`s Hospital, Baylor College of Medicine, Houston, USA"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "radiology and imaging"
+  },
   {
     "rel_doi": "10.1101/2022.01.10.22269033",
     "rel_title": "Analytic sensitivity of the Abbott BinaxNOW lateral flow immunochromatographic assay for the SARS-CoV-2 Omicron variant",
@@ -428130,37 +426984,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "allergy and immunology"
   },
-  {
-    "rel_doi": "10.1101/2022.01.08.22268942",
-    "rel_title": "Payments to key opinion leader physicians and drug sales of top pharmaceutical companies during the COVID-19 pandemic",
-    "rel_date": "2022-01-10",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.08.22268942",
-    "rel_abs": "BackgroundThe unprecedented context of the COVID-19 pandemic poses the opportunity to study several questions in circumstances that would probably not otherwise occur. We sought to determine the dynamics of pharmaceutical company drug sales revenue, market capitalization and payments to physicians during the pandemic, focusing on payments to so-called key opinion leaders (KOLs).\n\nMethodsWe analyzed the CMS Open Payments data of 15 top pharmaceutical company general payments to US physicians. We calculated total payments per year for all physicians, KOLs and 2018 KOLs in subsequent years. Drug-related fold changes in payments, drug revenues and company market capitation were calculated using Q1-2018 as reference. Yearly differences in payments, drug sales revenue and market capitalization were tested using generalized estimation equations (GEE). A double-sided p<0.05 was considered significant.\n\nResultsThe analyzed dataset comprised 8,563,872 payments to 382,779 physicians. In 2020, we observed a reduction in payments to physicians and KOLs compared to prior years. The total amount per KOL physician per company also decreased for each year for KOLs and the 2018 KOLs in the subsequent years. Payments per drug, but neither drug revenues nor pharmaceutical company market capitalization, followed a downward trend in 2020 compared to prior years. GEE analysis confirmed that, compared to 2018, the decrease in payments to KOLs overall and for the top drugs of each company was statistically significant. Yet, no significant differences in drug sales revenue and market capitalization was observed.\n\nConclusionsA substantial and significant reduction in payments to KOLs during the first fiscal year of the COVID-19 pandemic was not associated with a reduction in drug sales revenue of blockbuster drug products and the market capitalization of 15 top pharmaceutical companies. Overall, these findings suggest that a substantial part of pharmaceutical payments to KOLs do not appear to impact top drug sales revenues.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Jose L Sandoval",
-        "author_inst": "Geneva University Hospitals"
-      },
-      {
-        "author_name": "Alex Friedlaender",
-        "author_inst": "Geneva University Hospitals"
-      },
-      {
-        "author_name": "Alfredo Addeo",
-        "author_inst": "Geneva University Hospitals"
-      },
-      {
-        "author_name": "Glen J Weiss",
-        "author_inst": "MiRanostics Consulting, LLC"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "medical ethics"
-  },
   {
     "rel_doi": "10.1101/2022.01.08.22268611",
     "rel_title": "SARS-CoV-2-positive patients display considerable differences in proteome diversity in urine, nasopharyngeal, gargle solution and bronchoalveolar lavage fluid samples",
@@ -428555,6 +427378,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2022.01.08.22268950",
+    "rel_title": "Modelling COVID-19 Vaccine Breakthrough Infections in Highly Vaccinated Israel - the effects of waning immunity and third vaccination dose",
+    "rel_date": "2022-01-10",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.08.22268950",
+    "rel_abs": "In August 2021, a major wave of the SARS-CoV-2 Delta variant erupted in the highly vaccinated population of Israel. The Delta variant has a transmission advantage over the Alpha variant, and thus replaced it in approximately two months. The outbreak led to an unexpectedly large proportion of breakthrough infections (BTI)-- a phenomenon that received worldwide attention. The BTI proportion amongst cases in the age group of 60+ years reached levels as high as [~]85% in August 2021. Most of the Israeli population, especially those 60+ age, received their second dose of the vaccination, four months before the invasion of the Delta variant. Hence, either the vaccine induced immunity dropped significantly or the Delta variant possesses immunity escaping abilities. In this work, we analyzed and model age-structured cases, vaccination coverage, and vaccine BTI data obtained from the Israeli Ministry of Health, to help understand the epidemiological factors involved in the outbreak. We propose a mathematical model which captures a multitude of factors, including age structure, the time varying vaccine efficacy, time varying transmission rate, BTIs, reduced susceptibility and infectivity of vaccinated individuals, protection duration of the vaccine induced immunity, and the vaccine distribution. We fitted our model to the cases among vaccinated and unvaccinated, for <60 and 60+ age groups, to address the aforementioned factors. We found that the transmission rate was driven by multiple factors including the invasion of Delta variant and the mitigation measures. Through a model reconstruction of the reproductive number R0(t), it was found that the peak transmission rate of the Delta variant was 1.96 times larger than the previous Alpha variant. The model estimated that the vaccine efficacy dropped significantly from >90% to [~]40% over 6 months, and that the immunity protection duration has a peaked Gamma distribution (rather than exponential). We further performed model simulations quantifying the important role of the third vaccination booster dose in reducing the levels of breakthrough infections. This allowed us to explore \"what if\" scenarios should the booster not have been rolled out. Application of this framework upon invasion of new pathogens, or variants of concern, can help elucidate important factors in the outbreak dynamics and highlight potential routes of action to mitigate their spread.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Anyin Feng",
+        "author_inst": "Department of Applied Mathematics, The Hong Kong Polytechnic University, Hong Kong, China"
+      },
+      {
+        "author_name": "Uri Obolski",
+        "author_inst": "School of Public Health, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel"
+      },
+      {
+        "author_name": "Lewi Stone",
+        "author_inst": "Porter School of the Environment and Earth Sciences, Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel"
+      },
+      {
+        "author_name": "Daihai He",
+        "author_inst": "Department of Applied Mathematics, The Hong Kong Polytechnic University, Hong Kong, China"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2022.01.08.22268928",
     "rel_title": "Adaptation and validation of a scale to evaluate the quality of virtual courses developed for medical students in Peru during the COVID-19 pandemic",
@@ -429879,41 +428733,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2022.01.07.22268878",
-    "rel_title": "Granulocyte-macrophage colony-stimulating factor (GM-CSF) antibodies treatment for COVID-19 patients: a meta-analysis",
-    "rel_date": "2022-01-10",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.07.22268878",
-    "rel_abs": "ObjectiveWe performed a meta-analysis in order to determine safety of granulocyte-macrophage colony-stimulating factor (GM-CSF) antibodies on COVID-19.\n\nMethodsWe searched from the Cochrane Library, PubMed, Embase, biorxiv and medrxiv databases beginning in the COVID-19 outbreak on December 1, 2019 until August 29, 2021. The primary outcomes included death, the incidence of invasive mechanical ventilation (IMV), ventilation requirement, and secondary infection.\n\nResults6 eligible literature involving 1501 COVID-19 patients were recruited, and they were divided into experimental group (n = 736) and control group (n = 765). Using a random-effect model, we found that the GM-CSF antibodies treatment was associated with a 3.8-26.9% decline of the risk of mortality[odds ratio (OR) = 0.06, 95% confidence interval (CI): -0.11, -0.01, p =0.02], a 5.3-28.7% reduction of incidence of IMV [OR = 0.51, 95% CI: 0.28, 0.95, p =0.03], and a 23.3-50.0% enhancement of ventilation improvement [OR = 11.70, 95% CI: 1.99, 68.68, p=0.006]. There were no statistically significant differences in the association between two groups in second infection.\n\nConclusionSevere COVID-19 patients may benefit from GM-CSF antibodies.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "JinTao Guan",
-        "author_inst": "TaiZhou First people hopspital"
-      },
-      {
-        "author_name": "Anran Xi",
-        "author_inst": "Institute of TCM Clinical Basic Medicine, Zhejiang Chinese Medical University, Binwen Road 548, Hangzhou 310053, China"
-      },
-      {
-        "author_name": "DU Jin",
-        "author_inst": "First People Hospital of Taizhou, Zhejiang 318020, China"
-      },
-      {
-        "author_name": "XiaoYue Mou",
-        "author_inst": "First People Hospital of Taizhou, Zhejiang 318020, China"
-      },
-      {
-        "author_name": "Zhenghao Xu",
-        "author_inst": "Zhejiang Chinese Medical University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.01.08.22268865",
     "rel_title": "A method for variant agnostic detection of SARS-CoV-2, rapid monitoring of circulating variants, detection of mutations of biological significance, and early detection of emergent variants such as Omicron",
@@ -430496,6 +429315,105 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2022.01.05.22268777",
+    "rel_title": "Persistence of immunity and impact of a third (booster) dose of an inactivated SARS-CoV-2 vaccine, BBV152; a phase 2, double-blind, randomised controlled trial",
+    "rel_date": "2022-01-08",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.05.22268777",
+    "rel_abs": "BackgroundNeutralising antibody responses to SARS-CoV-2 vaccines have been reported to decline within 6 months of vaccination, particularly against Variants of Concern (VOC). We assessed the immunogenicity and safety of a booster dose of BBV152 administered 6 months after the second of a two-dose primary vaccination series.\n\nMethodsIn an ongoing phase 2 trial (ClinicalTrials.gov: NCT04471519) the protocol was amended after six months to re-consent and randomise 184 previously vaccinated participants to receive a third dose of vaccine or placebo on Day 215. The primary outcome was to measure neutralising antibody titres by plaque-reduction neutralisation test (PRNT50) four weeks after the booster; safety as serious adverse events (SAE) was the key secondary outcome.\n\nFindingsFour weeks after a second BBV152 vaccination geometric mean titres (GMTs) of neutralising antibodies were 197{middle dot}0 PRNT50 (95% CI: 155{middle dot}6-249{middle dot}4); this level declined to 23{middle dot}9 PRNT50 (14{middle dot}0-40{middle dot}6) six months later, with a seroconversion rate of 75{middle dot}4% (95% CI: 68{middle dot}4-81{middle dot}6). Four weeks after booster vaccination the GMT increased on Day 243 to 746{middle dot}6 PRNT50 (514{middle dot}9-1081) compared with 100{middle dot}7 PRNT50 (43{middle dot}6-232{middle dot}6) in the placebo group. Corresponding seroconversion rates were 98{middle dot}7% (92{middle dot}8-99{middle dot}9) and 79{middle dot}8% (69{middle dot}6-87{middle dot}8). Increased titres in the placebo group were attributed to natural infection as the study was conducted during the second wave of COVID-19 in India. PRNT50 titres against the SARS-CoV-2 variants increased--Alpha (32{middle dot}6-fold), Beta (161{middle dot}0-fold), Delta (264{middle dot}7-fold), and Delta plus (174{middle dot}2-fold)--after the booster vaccination. We found that vaccine induces both memory B and T cells with a distinct AIM+ specific CD4+T central and effector memory phenotype, including CD8+ TEMRA phenotype. Reactogenicity after vaccine and placebo was minimal and comparable, and no SAEs were reported.\n\nInterpretationSix months after a two-dose BBV152 vaccination series cell mediated immunity and neutralising antibodies to both homologous (D614G) and heterologous strains (Alpha, Beta, Delta and Delta plus) persisted above baseline, although the magnitude of the responses had declined. Neutralising antibodies against homologous and heterologous SARS-CoV-2 variants increased 19- to 97-fold after a third vaccination. Booster BBV152 vaccination is safe and may be necessary to ensure persistent immunity to prevent breakthrough infections.\n\nFundingThis work was supported and funded by Bharat Biotech International Limited.",
+    "rel_num_authors": 21,
+    "rel_authors": [
+      {
+        "author_name": "Krishna Mohan Vadrevu",
+        "author_inst": "Bharat Biotech"
+      },
+      {
+        "author_name": "Brunda Ganneru",
+        "author_inst": "Bharat Biotech"
+      },
+      {
+        "author_name": "Siddharth Reddy",
+        "author_inst": "Bharat Biotech"
+      },
+      {
+        "author_name": "Harsh Jogdand",
+        "author_inst": "Bharat Biotech"
+      },
+      {
+        "author_name": "Raju Dugyala",
+        "author_inst": "Bharat Biotech"
+      },
+      {
+        "author_name": "Usha Praturi",
+        "author_inst": "Bharat Biotech"
+      },
+      {
+        "author_name": "Gajanan N Sapkal",
+        "author_inst": "ICMR-National Institute of Virology"
+      },
+      {
+        "author_name": "Pragya Yadav",
+        "author_inst": "ICMR-National Institute of Virology"
+      },
+      {
+        "author_name": "Prabhakar Reddy",
+        "author_inst": "Nizam's Institute of Medical Sciences"
+      },
+      {
+        "author_name": "Savita Verma",
+        "author_inst": "P t B D Sharma, PGIMS/UHS Rohtak"
+      },
+      {
+        "author_name": "Chandramani Singh",
+        "author_inst": "AIIMS-Patna"
+      },
+      {
+        "author_name": "Sagar Vivek Redkar",
+        "author_inst": "Redkar Hospital"
+      },
+      {
+        "author_name": "Chandra Sekhar Gillurkar",
+        "author_inst": "Gillurkar Multispecilaity Hospitals, Nagpur"
+      },
+      {
+        "author_name": "Jitendra Singh Kushwaha",
+        "author_inst": "Prakhar Hospital"
+      },
+      {
+        "author_name": "Satyajit Mohapatra",
+        "author_inst": "SRM Medical College Hospital & Research center, Tamilnadu"
+      },
+      {
+        "author_name": "Amit Bhate",
+        "author_inst": "Jeevan Rekha Hospital, Belagavi"
+      },
+      {
+        "author_name": "Sanjay Rai",
+        "author_inst": "AIIMS-New Delhi"
+      },
+      {
+        "author_name": "Raches Ella",
+        "author_inst": "Independent Clinical Development Consultant"
+      },
+      {
+        "author_name": "Priya Abraham",
+        "author_inst": "Indian Council of Medical Research-National Institute of Virology"
+      },
+      {
+        "author_name": "Sai Prasad",
+        "author_inst": "Bharat Biotech"
+      },
+      {
+        "author_name": "Krishna Ella",
+        "author_inst": "Bharat Biotech"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2022.01.07.22268919",
     "rel_title": "Effectiveness of mRNA-1273 against SARS-CoV-2 omicron and delta variants",
@@ -431933,41 +430851,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "allergy and immunology"
   },
-  {
-    "rel_doi": "10.1101/2022.01.05.22268765",
-    "rel_title": "A Composite Ranking of Risk Factors for COVID-19 Time-To-Event Data from a Turkish Cohort",
-    "rel_date": "2022-01-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.05.22268765",
-    "rel_abs": "Having a complete and reliable list of risk factors from routine laboratory blood test for COVID-19 disease severity and mortality is important for patient care and hospital management. It is common to use meta-analysis to combine analysis results from different studies to make it more reproducible. In this paper, we propose to run multiple analyses on the same set of data to produce a more robust list of risk factors. With our time-to-event survival data, the standard survival analysis were extended in three directions. The first is to extend from tests and corresponding p-values to machine learning and their prediction performance. The second is to extend from single-variable to multiple-variable analysis. The third is to expand from analyzing time-to-decease data with death as the event of interest to analyzing time-to-hospital-release data to treat early recovery as a meaningful event as well. Our extension of the type of analyses leads to ten ranking lists. We conclude that 20 out of 30 factors are deemed to be reliably associated to faster-death or faster-recovery. Considering correlation among factors and evidenced by stepwise variable selection in random survival forest, 10[~]15 factors seem to be able to achieve the optimal prognosis performance. Our final list of risk factors contain calcium, white blood cell and neutrophils count, urea and creatine, d-dimer, red cell distribution widths, age, ferritin, glucose, lactate dehydrogenase, lymphocyte, basophils, anemia related factors (hemoglobin, hematocrit, mean corpuscular hemoglobin concentration), sodium, potassium, eosinophils, and aspartate aminotransferase.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Ayse Ulgen",
-        "author_inst": "Department of Biostatistics, Faculty of Medicine, Girne American University"
-      },
-      {
-        "author_name": "Sirin Cetin",
-        "author_inst": "Department of Biostatistics, Faculty of Medicine, Tokat GaziosmanPasa University, Turkey"
-      },
-      {
-        "author_name": "Meryem Cetin",
-        "author_inst": "Department of Medical Microbiology, Faculty of Medicine, Amasya University, Amasya, Turkey"
-      },
-      {
-        "author_name": "Hakan Sivgin",
-        "author_inst": "Department of Internal  Medicine, Faculty of Medicine, Tokat Gaziosmanpasa University, Tokat,  Turkey"
-      },
-      {
-        "author_name": "Wentian LI",
-        "author_inst": "Feinstein Institutes for Medical Research"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.01.05.22268782",
     "rel_title": "Protection afforded by prior infection against SARS-CoV-2 reinfection with the Omicron variant",
@@ -432274,6 +431157,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "primary care research"
   },
+  {
+    "rel_doi": "10.1101/2022.01.05.22268808",
+    "rel_title": "Adherence of SARS-CoV-2 delta variant to surgical mask and N95 respirators",
+    "rel_date": "2022-01-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.05.22268808",
+    "rel_abs": "The use of facial protection, including masks and respirators, has been adopted globally due to the COVID-19 pandemic. These products have been demonstrated to be effective in reducing the transmission of the virus. To determine whether or not the virus adheres to masks and respirators, we dissected four respirators and one surgical mask into layers. These individual layers were contaminated with the SARS-CoV-2 delta variant, and its release by vortexing was performed. Samples were used to infect Vero cells, and a plaque assay was used to determine to evaluate the adherence of the virus. Results showed that a cumulative log reduction of the layers reduced the load of the virus six-folds. Our study confirms the effectiveness of facial protection in reducing the transmission and or infection of the virus.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Ana C Lorenzo-Leal",
+        "author_inst": "University of British Columbia"
+      },
+      {
+        "author_name": "Selvarani Vimalanathan",
+        "author_inst": "University of British Columbia"
+      },
+      {
+        "author_name": "Horacio Bach",
+        "author_inst": "University of British Columbia"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2022.01.06.22268809",
     "rel_title": "Mental health assessment of Israeli adolescents before and during the COVID-19 pandemic",
@@ -433698,45 +432608,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "sports medicine"
   },
-  {
-    "rel_doi": "10.1101/2022.01.04.22268717",
-    "rel_title": "Performance evaluation of novel fluorescent-based lateral immune flow assay (LIFA) for rapid detection and quantitation of total anti-SARS-CoV-2 S-RBD binding antibodies in infected individuals",
-    "rel_date": "2022-01-05",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.04.22268717",
-    "rel_abs": "1.BackgroundThe vast majority of the commercially available LFIA is used to detect SARS-CoV-2 antibodies qualitatively. Recently, a novel fluorescence-based LIFA test was developed for quantitative measurement of the total binding antibody units (BAU/mL) against the receptor-binding domain of the SARS-CoV-2 spike protein (S-RBD).\n\nAimTo evaluate the performance of the fluorescence LIFA Finecare 2019-nCoV S-RBD test along with its reader (Model No.: FS-113).\n\nMethodsPlasma from 150 RT-PCR confirmed-positive individuals and 100 pre-pandemic samples were tested by FinCare to access sensitivity and specificity. For qualitative and quantitative validation of the FinCar measurements, the BAU/mL results of FinCare were compared with results of two reference assays: the surrogate virus-neutralizing test (sVNT, GenScript, USA), and the VIDAS(R)3 automated assay (BioMerieux, France).\n\nResultsFinecare showed 92% sensitivity and 100% specificity compared to PCR. Cohens Kappa statistic denoted moderate and excellent agreement with sVNT and VIDAS(R)3, ranging from 0.557 (95% CI: 0.32-0.78) to 0.731 (95% CI: 0.51-0.95), respectively. A strong correlation was observed between Finecare/sVNT (r=0.7, p<0.0001) and Finecare/VIDAS(R)3 (r=0.8, p<0.0001).\n\nConclusionFinecare is a reliable assay and can be used as a surrogate to assess binding and neutralizing antibody response post-infection or vaccination, particularly in none or small laboratory settings.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Farah M. Shurrab",
-        "author_inst": "Qatar University"
-      },
-      {
-        "author_name": "Nadin Younes",
-        "author_inst": "Qatar University"
-      },
-      {
-        "author_name": "Duaa W. Al-Sadeq",
-        "author_inst": "Qatar University"
-      },
-      {
-        "author_name": "Hamda Qotba",
-        "author_inst": "Primary health care corporation"
-      },
-      {
-        "author_name": "Laith J Abu-Raddad",
-        "author_inst": "Weill Cornell Medicine-Qatar"
-      },
-      {
-        "author_name": "Gheyath Nasrallah",
-        "author_inst": "Qatar University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.01.05.475037",
     "rel_title": "An elite broadly neutralizing antibody protects SARS-CoV-2 Omicron variant challenge",
@@ -434059,6 +432930,77 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2022.01.04.474979",
+    "rel_title": "SIRT5 is a proviral factor that interacts with SARS-CoV-2 Nsp14 protein",
+    "rel_date": "2022-01-05",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.04.474979",
+    "rel_abs": "SARS-CoV-2 non-structural protein Nsp14 is a highly conserved enzyme necessary for viral replication. Nsp14 forms a stable complex with non-structural protein Nsp10 and exhibits exoribonuclease and N7-methyltransferase activities. Protein-interactome studies identified human sirtuin 5 (SIRT5) as a putative binding partner of Nsp14. SIRT5 is an NAD-dependent protein deacylase critical for cellular metabolism that removes succinyl and malonyl groups from lysine residues. Here we investigated the nature of this interaction and the role of SIRT5 during SARS-CoV-2 infection. We showed that SIRT5 stably interacts with Nsp14, but not with Nsp10, suggesting that SIRT5 and Nsp10 are parts of separate complexes. We found that SIRT5 catalytic domain is necessary for the interaction with Nsp14, but that Nsp14 does not appear to be directly deacylated by SIRT5. Furthermore, knock-out of SIRT5 or treatment with specific SIRT5 inhibitors reduced SARS-CoV-2 viral levels in cell-culture experiments. SIRT5 knock-out cells expressed higher basal levels of innate immunity markers and mounted a stronger antiviral response. Our results indicate that SIRT5 is a proviral factor necessary for efficient viral replication, which opens novel avenues for therapeutic interventions.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Marius Walter",
+        "author_inst": "Buck Institute for Research on Aging, Novato, CA, United States."
+      },
+      {
+        "author_name": "Irene P Chen",
+        "author_inst": "Gladstone Institutes, San Francisco, CA, United States; University of California San Francisco, San Francisco, CA, United States."
+      },
+      {
+        "author_name": "Albert Vallejo-Gracia",
+        "author_inst": "Gladstone Institutes, San Francisco, CA, United States; University of California San Francisco, San Francisco, CA, United States."
+      },
+      {
+        "author_name": "Ik-Jung Kim",
+        "author_inst": "Buck Institute for Research on Aging, Novato, CA, United States."
+      },
+      {
+        "author_name": "Olga Bielska",
+        "author_inst": "Buck Institute for Research on Aging, Novato, CA, United States."
+      },
+      {
+        "author_name": "Victor L Lam",
+        "author_inst": "University of California San Francisco, San Francisco, CA, United States."
+      },
+      {
+        "author_name": "Jennifer M Hayashi",
+        "author_inst": "Gladstone Institutes, San Francisco, CA, United States; University of California San Francisco, San Francisco, CA, United States."
+      },
+      {
+        "author_name": "Andrew Cruz",
+        "author_inst": "Buck Institute for Research on Aging, Novato, CA, United States."
+      },
+      {
+        "author_name": "Samah Shah",
+        "author_inst": "Buck Institute for Research on Aging, Novato, CA, United States."
+      },
+      {
+        "author_name": "John D Gross",
+        "author_inst": "University of California San Francisco, San Francisco, CA, United States; Quantitative Biosciences Institute (QBI), University of California San Francisco, San "
+      },
+      {
+        "author_name": "Nevan J Krogan",
+        "author_inst": "University of California San Francisco, San Francisco, CA, United States; Quantitative Biosciences Institute (QBI), University of California San Francisco, San "
+      },
+      {
+        "author_name": "Birgit Schilling",
+        "author_inst": "Buck Institute for Research on Aging, Novato, CA, United States."
+      },
+      {
+        "author_name": "Melanie Ott",
+        "author_inst": "Gladstone Institutes, San Francisco, CA, United States; University of California San Francisco, San Francisco, CA, United States."
+      },
+      {
+        "author_name": "Eric Verdin",
+        "author_inst": "Buck Institute for Research on Aging, Novato, CA, United States."
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2022.01.05.22268626",
     "rel_title": "Fully Vaccinated and Boosted Patients Requiring Hospitalization for COVID-19: an Observational Cohort Analysis",
@@ -435400,105 +434342,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2022.01.04.22268747",
-    "rel_title": "Sub-optimal Neutralisation of Omicron (B.1.1.529) Variant by Antibodies induced by Vaccine alone or SARS-CoV-2 Infection plus Vaccine (Hybrid Immunity) post 6-months",
-    "rel_date": "2022-01-05",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.04.22268747",
-    "rel_abs": "BackgroundRapid expansion of the omicron SARS-CoV-2 variant of concern despite extensive vaccine coverage might be related to decreased neutralising ability of vaccine induced antibodies. The neutralising ability of different vaccines with or without natural SARS-CoV-2 infection against omicron is however not well known.\n\nMethodsWe tested the ability of vaccine and natural infection induced antibodies to neutralise omicron variant in a live virus neutralisation assay. Four groups of individuals were included: (i) complete vaccination with ChAdOx1 nCoV-19 (n=20), (ii) complete vaccination with ChAdOx1 nCoV-19 plus prior SARS-CoV-2 infection during the delta variant driven surge (n=20), (iii) complete vaccination with inactivated whole virus vaccine (BBV152) (n=20), (iv) complete vaccination with BBV152 plus prior SARS-CoV-2 infection (n=20). Primary outcome was fold-change in the virus neutralisation ability of plasma against the omicron variant compared with ancestral and delta variant.\n\nFindingsThe neutralisation geometric mean titre (GMT) was 384 (95% CI: 662, 223) against the ancestral virus with BBV152 vaccination alone and 383 (95% CI: 709, 207) with ChAdOx1 nCov-19 vaccination alone. The corresponding values for hybrid immunity groups were 795 (95% CI: 1302, 486) and 1424 (95% CI: 2581,786) respectively. Against the omicron variant, only 5 out of 20 in both BBV152 and ChAdOx1 nCoV-19 vaccine only groups, 5 out of 19 in BBV152 plus SARS-CoV-2 infection group, and 9 out of 20 in ChAdOx1 nCoV-19 plus SARS-CoV-2 infection group exhibited neutralisation titres above the lower limit of quantification (1:20) suggesting better neutralization in those with prior infection. The 50% neutralisation against ancestral strain and omicron demonstrated strong correlation with anti-RBD IgG levels [Pearson r: 0.94 (0.91, 0.96) p: <0.001 and 0.92 (0.88, 0.95) p:<0.001 respectively].\n\nInterpretationOmicron variant shows significant reduction in neutralising ability of both vaccine induced and hybrid immunity induced antibodies which might explain immune escape and high transmission even in the presence of widespread vaccine coverage.\n\nFundingDBT, India; GIISER-BMGF, USA\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThe Omicron variant of SARS-CoV-2 is fast becoming the dominant circulating strain world-wide. We did a literature search on PubMed between 01 November 2020 to 04 January 2022 using the terms \"Omicron\" and \"neutralisation\" and found 11 results for virus neutralisation against omicron by vaccine/natural infection induced antibodies. We identified two published and one preprint articles relevant to omicron virus neutralisation using live virus neutralization. Preliminary reports suggest that omicron variant is significantly less susceptible to in-vitro neutralisation by antibodies among recipients of mRNA vaccines (BNT162b2 and mRNA-1273), adenovirus vectored vaccine (ChAdOx1 nCoV-19 vaccines) and no virus neutralization was observed in subjects who received Coronavac (inactivated virus vaccine). Data regarding immune escape among those with natural SARS-CoV2 infection and vaccination are not available.\n\nAdded value of this studyWe report here that the proportion of neutralisers (those who demonstrated a FRNT50 titre >1:20) was significantly reduced against the omicron variant as compared to the ancestral and delta variant. The geometric mean titre of neutralisation among the vaccinated individuals without a history of previous natural infection was significantly reduced against the omicron variant as compared with ancestral and delta variants. The titres among the those with a history of previous infection also followed the same pattern, but the neutralising ability was better in them than those who did not have previous infection.\n\nImplications of all the available evidenceOmicron variant of SARS-CoV-2 is capable of escaping immunity provided by currently available vaccines and even natural infection due to significant mutations in its spike protein. The drop in neutralisation might be alarming, but the real-world impact of these reduced neutralisation titres on major public health indices like hospitalisation rates and mortality rates have to be interpreted along with the other factors such as inherent pathogenicity of the variant, immunization uptakes and seroprevalence from natural infection in different geographical regions and the expected role of cellular immune responses to the variant. Our data may guide policy on booster vaccination to deal with an impending public health emergency as a result of surge in omicron cases.",
-    "rel_num_authors": 21,
-    "rel_authors": [
-      {
-        "author_name": "Guruprasad R Medigeshi",
-        "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana, India"
-      },
-      {
-        "author_name": "Gaurav Batra",
-        "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana, India"
-      },
-      {
-        "author_name": "Deepika Rathna Murugesan",
-        "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana, India"
-      },
-      {
-        "author_name": "Ramachandran Thiruvengadam",
-        "author_inst": "Translational Health Science and Technology Institute, Faridabad"
-      },
-      {
-        "author_name": "Souvick Chattopadhyay",
-        "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana, India"
-      },
-      {
-        "author_name": "Bhabatosh Das",
-        "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana, India"
-      },
-      {
-        "author_name": "Mudita Gosain",
-        "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana, India"
-      },
-      {
-        "author_name": "Ayushi",
-        "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana, India"
-      },
-      {
-        "author_name": "Janmejay Singh",
-        "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana, India"
-      },
-      {
-        "author_name": "Ananthraj Anbalagan",
-        "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana, India"
-      },
-      {
-        "author_name": "Heena Shaman",
-        "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana, India"
-      },
-      {
-        "author_name": "Kamal Pargai",
-        "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana, India"
-      },
-      {
-        "author_name": "Farha Mehdi",
-        "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana, India"
-      },
-      {
-        "author_name": "Soon Jyoti Das",
-        "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana, India"
-      },
-      {
-        "author_name": "Namrata Kahlon",
-        "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana, India"
-      },
-      {
-        "author_name": "Savita Singh",
-        "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana, India"
-      },
-      {
-        "author_name": "Pallavi Kshetrapal",
-        "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana, India"
-      },
-      {
-        "author_name": "Nitya Wadhwa",
-        "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana, India"
-      },
-      {
-        "author_name": "Anil K Pandey",
-        "author_inst": "ESIC Medical College and Hospital, Faridabad, Haryana, India"
-      },
-      {
-        "author_name": "Shinjini Bhatnagar",
-        "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana, India"
-      },
-      {
-        "author_name": "Pramod Kumar Garg",
-        "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana, India"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2022.01.05.22268786",
     "rel_title": "Narrowing gap in regional and age-specific excess mortality in the first year and a half of COVID-19 in Hungary",
@@ -435941,6 +434784,77 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2022.01.04.474803",
+    "rel_title": "A synthetic bispecific antibody capable of neutralizing SARS-CoV-2 Delta and Omicron",
+    "rel_date": "2022-01-04",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.04.474803",
+    "rel_abs": "Bispecific antibodies have emerged as a promising strategy for curtailing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immune escape. This brief report highlights RBT-0813 (also known as TB493-04), a synthetic, humanized, receptor-binding domain (RBD)-targeted bispecific antibody that retains picomolar affinity to the Spike (S) trimers of all major variants of concern and neutralizes both SARS-CoV-2 Delta and Omicron in vitro.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Tom Z Yuan",
+        "author_inst": "Twist Bioscience"
+      },
+      {
+        "author_name": "Carolina Lucas",
+        "author_inst": "Yale University"
+      },
+      {
+        "author_name": "Valter S Monteiro",
+        "author_inst": "Yale University"
+      },
+      {
+        "author_name": "Akiko Iwasaki",
+        "author_inst": "Yale University, Howard Huges Medical Institute"
+      },
+      {
+        "author_name": "Marisa L Yang",
+        "author_inst": "Twist Bioscience"
+      },
+      {
+        "author_name": "Hector F Nepita",
+        "author_inst": "Twist Bioscience"
+      },
+      {
+        "author_name": "Ana G Lujan Hernandez",
+        "author_inst": "Twist Bioscience"
+      },
+      {
+        "author_name": "Joseph M Taft",
+        "author_inst": "EHT Zurich"
+      },
+      {
+        "author_name": "Lester Frei",
+        "author_inst": "ETH Zurich"
+      },
+      {
+        "author_name": "Sai T Reddy",
+        "author_inst": "ETH Zurich"
+      },
+      {
+        "author_name": "Cedric Weber",
+        "author_inst": "Alloy Therapeutics"
+      },
+      {
+        "author_name": "Kevin P Malobisky",
+        "author_inst": "Revelar Biotherapeutics"
+      },
+      {
+        "author_name": "Rodrigo Mesquita",
+        "author_inst": "Revelar Biotherapeutics"
+      },
+      {
+        "author_name": "Aaron Sato",
+        "author_inst": "Twist Bioscience"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2022.01.03.474779",
     "rel_title": "Host kinase CSNK2 is a target for inhibition of pathogenic \u03b2-coronaviruses including SARS-CoV-2",
@@ -437498,89 +436412,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.12.30.21267090",
-    "rel_title": "Statistical and agent-based modelling of the transmissibility of different SARS-CoV-2 variants in England and impact of different interventions",
-    "rel_date": "2022-01-03",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.30.21267090",
-    "rel_abs": "The English SARS-CoV-2 epidemic has been affected by the emergence of new viral variants such as B.1.177, Alpha and Delta, and changing restrictions. We used statistical models and calibration of an stochastic agent-based model Covasim to estimate B.1.177 to be 20% more transmissible than the wild type, Alpha to be 50-80% more transmissible than B.1.177 and Delta to be 65-90% more transmissible than Alpha. We used these estimates in Covasim (calibrated between September 01, 2020 and June 20, 2021), in June 2021, to explore whether planned relaxation of restrictions should proceed or be delayed. We found that due to the high transmissibility of Delta, resurgence in infections driven by the Delta variant would not be prevented, but would be strongly reduced by delaying the relaxation of restrictions by one month and with continued vaccination.",
-    "rel_num_authors": 17,
-    "rel_authors": [
-      {
-        "author_name": "Jasmina Panovska-Griffiths",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Ben Swallow",
-        "author_inst": "University of Glasgow"
-      },
-      {
-        "author_name": "Robert Hinch",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Jamie A Cohen",
-        "author_inst": "Institute for Disease Modeling"
-      },
-      {
-        "author_name": "Katherine Rosenfeld",
-        "author_inst": "Institute for Disease Modeling"
-      },
-      {
-        "author_name": "Robyn M Stuart",
-        "author_inst": "University of Copenhagen"
-      },
-      {
-        "author_name": "Luca Ferretti",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Francesco Di Lauro",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Chris Wymant",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Amanda Izzo",
-        "author_inst": "Institute for Diseases Modeling"
-      },
-      {
-        "author_name": "William Waites",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Russell M Viner",
-        "author_inst": "UCL Great Ormond St. Institute of Child Health"
-      },
-      {
-        "author_name": "Chris Bonell",
-        "author_inst": "LSHTM"
-      },
-      {
-        "author_name": "- The COVID-19 Genomics UK (COG-UK) consortium",
-        "author_inst": "-"
-      },
-      {
-        "author_name": "Christophe Fraser",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Daniel J Klein",
-        "author_inst": "Institute for Disease Modelling"
-      },
-      {
-        "author_name": "Cliff Kerr",
-        "author_inst": "Institute for Disease Modeling"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2022.01.02.22268641",
     "rel_title": "Integrin/TGF-Beta1 inhibitor GLPG-0187 blocks SARS-CoV-2 Delta and Omicron pseudovirus infection of airway epithelial cells which could attenuate disease severity",
@@ -437891,6 +436722,41 @@
     "type": "new results",
     "category": "bioinformatics"
   },
+  {
+    "rel_doi": "10.1101/2021.12.30.474580",
+    "rel_title": "SARS-CoV-2 entry sites are present in all structural elements of the human glossopharyngeal and vagal nerves: clinical implications",
+    "rel_date": "2022-01-03",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.30.474580",
+    "rel_abs": "Severe acute respiratory syndrome coronavirus (SARS-CoV-2) infections result in the temporary loss of smell and taste (anosmia and dysgeusia) in about one third of confirmed cases. Several investigators have reported that the viral spike protein receptor is present in olfactory neurons. However, no study has been published to date showing the presence of viral entry sites angiotensin-converting enzyme 2 (ACE2), neuropilin1 (NRP1), and TMPRSS2, the serine protease necessary for priming the viral proteins, in human nerves that are responsible for taste sensation (cranial nerves: VII, IX and X). We used immunocytochemistry to examine three postmortem donor samples of the IXth (glossopharyngeal) and Xth (vagal) cranial nerves where they leave/join the medulla from three donors to confirm the presence of ACE2, NRP1 and TMPRSS2. Two samples were paraffin embedded; one was a frozen sample. In addition to staining sections from the latter, we isolated RNA from it, made cDNA, and performed PCR to confirm the presence of the mRNAs that encode the proteins visualized. All three of the proteins required for SARS-CoV-2 infections appear to be present in the human IXth and Xth nerves near the medulla. Direct infection of these nerves by the COVID-19 virus is likely to cause the loss of taste experienced by many patients. In addition, potential viral spread through these nerves into the adjacent brainstem respiratory centers might also aggravate the respiratory problems patients are experiencing.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Lynn Vitale-Cross",
+        "author_inst": "NIDCR, NIH"
+      },
+      {
+        "author_name": "Ildiko Szalayova",
+        "author_inst": "NIDCR, NIH"
+      },
+      {
+        "author_name": "Aiden Scoggins",
+        "author_inst": "NIDCR, NIH"
+      },
+      {
+        "author_name": "Miklos Palkovits",
+        "author_inst": "Human Brain Tissue Bank, Semmelweis University, Budapest, Hungary"
+      },
+      {
+        "author_name": "Eva Mezey",
+        "author_inst": "NIDCR, NIH"
+      }
+    ],
+    "version": "1",
+    "license": "cc0",
+    "type": "new results",
+    "category": "neuroscience"
+  },
   {
     "rel_doi": "10.1101/2021.12.30.474613",
     "rel_title": "Nonself Mutations in the Spike Protein Suggest an Increase in the Antigenicity and a Decrease in the Virulence of the Omicron Variant of SARS-CoV-2",
@@ -439436,37 +438302,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.12.29.21268526",
-    "rel_title": "Predicting the impact of COVID-19 vaccination campaigns - a flexible age-dependent, spatially-stratified predictive model, accounting for multiple viral variants and vaccines",
-    "rel_date": "2022-01-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.29.21268526",
-    "rel_abs": "BackgroundAfter COVID-19 vaccines received approval, vaccination campaigns were launched worldwide. Initially, these were characterized by a shortage of vaccine supply, and specific risk groups were prioritized. Once supply was guaranteed and vaccination coverage saturated, the focus shifted from risk groups to anti-vaxxers, the underaged population, and regions of low coverage. At the same time, hopes to reach herd immunity by vaccination campaigns were put into perspective by the emergence and spread of more contagious and aggressive viral variants. Particularly, concerns were raised that not all vaccines protect against the new-emerging variants.\n\nMethods and findingsA model designed to predict the effect of vaccination campaigns on the spread of viral variants is introduced. The model is a comprehensive extension of the model underlying the pandemic preparedness tool CovidSim 2.0 (http://covidsim.eu/). The model is age and spatially stratified, incorporates a finite (but arbitrary) number of different viral variants, and incorporates different vaccine products. The vaccines are allowed to differ in their vaccination schedule, vaccination rates, the onset of vaccination campaigns, and their effectiveness. These factors are also age and/or location dependent. Moreover, the effectiveness and the immunizing effect of vaccines are assumed to depend on the interaction of a given vaccine and viral variant. Importantly, vaccines are not assumed to immunize perfectly. Individuals can be immunized completely, only partially, or fail to be immunized against one or many viral variants. Not all individuals in the population are vaccinable. The model is formulated as a high-dimensional system of differential equations, which is implemented efficiently in the programming language Julia.\n\nAs an example, the model was parameterized to reflect the epidemic situation in Germany until November 2021 and predicted the future dynamics of the epidemic under different interventions. In particular, without tightening contact reductions, a strong epidemic wave is predicted. At the current state, mandatory vaccination would be too late to have a strong effect on reducing the number of infections. However, it would reduce mortality. An emergency brake, i.e., an incidence-based stepwise lockdown would be efficient to reduce the number of infections and mortality. Furthermore, to specifically account for mobility between regions, the model was applied to two German provinces of particular interest: Saxony, which currently has the lowest vaccine rollout in Germany and high incidence, and Schleswig-Holstein, which has high vaccine rollout and low incidence.\n\nConclusionsA highly sophisticated and flexible but easy-to-parameterize model for the ongoing COVID-19 pandemic is introduced. The model is capable of providing useful predictions for the COVID-19 pandemic, and hence provides a relevant tool for epidemic decision-making. The model can be adjusted to any country, to derive the demand for hospital and ICU capacities as well as economic collateral damages.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Kristan Alexander Schneider",
-        "author_inst": "Hochschule Mittweida"
-      },
-      {
-        "author_name": "Henri Christian Junior Tsoungui Obama",
-        "author_inst": "Hochschule Mittweida"
-      },
-      {
-        "author_name": "Nessma Adil Mahmoud Yousif",
-        "author_inst": "Hochschule Mittweida"
-      },
-      {
-        "author_name": "Pierre Marie Ngougoue Ngougoue",
-        "author_inst": "Hochschule Mittweida"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.12.30.21267519",
     "rel_title": "Antibody binding and ACE2 binding inhibition is significantly reduced for the Omicron variant compared to all other variants of concern",
@@ -440005,6 +438840,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.12.31.21268596",
+    "rel_title": "Social isolation and psychological distress among southern US college students in the era of COVID-19",
+    "rel_date": "2022-01-01",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.31.21268596",
+    "rel_abs": "ObjectiveTo examine the prevalence of psychological distress and its association with social isolation among University of North Carolina Chapel Hill (UNC-CH) students.\n\nMethodsA cross-sectional survey was emailed to all students in June 2020. Students reported self-isolating none, some, most, or all of the time and were screened for clinically significant symptoms of depression (CSSD). Data were weighted to the UNC-CH population.\n\nResults7,012 students completed surveys-64% reported self-isolating most or all of the time and 64% reported CSSD. Compared to those self-isolating none of the time, students self-isolating some of the time were 1.78 (95% CI 1.37-2.30) times as likely to report CSSD, and students self-isolating most and all of the time were 2.12 (95% CI 1.64-2.74) and 2.27 (95% CI 1.75-2.94) times as likely to report CSSD, respectively.\n\nConclusionsUniversities should prioritize student mental health and prepare support services to mitigate mental health consequences of the pandemic.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Danielle Giovenco",
+        "author_inst": "University of North Carolina at Chapel Hill"
+      },
+      {
+        "author_name": "Bonnie E Shook-Sa",
+        "author_inst": "University of North Carolina at Chapel Hill"
+      },
+      {
+        "author_name": "Bryant Hutson",
+        "author_inst": "University of North Carolina at Chapel Hill"
+      },
+      {
+        "author_name": "Laurie Buchanan",
+        "author_inst": "University of North Carolina at Chapel Hill"
+      },
+      {
+        "author_name": "Edwin B Fisher",
+        "author_inst": "University of North Carolina at Chapel Hill"
+      },
+      {
+        "author_name": "Audrey Pettifor",
+        "author_inst": "University of North Carolina at Chapel Hill"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "psychiatry and clinical psychology"
+  },
   {
     "rel_doi": "10.1101/2021.12.29.21268505",
     "rel_title": "Head-to-head comparison of nasal and nasopharyngeal sampling using SARS-CoV-2 rapid antigen testing in Lesotho",
@@ -441654,37 +440528,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.12.29.21268521",
-    "rel_title": "Forecasting COVID-19 infection trends and new hospital admissions in England due to SARS-CoV-2 Variant of Concern Omicron",
-    "rel_date": "2021-12-30",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.29.21268521",
-    "rel_abs": "ObjectivesOn November 26, 2021, WHO designated the variant B.1.1.529 as a new SARS-CoV-2 variant of concern (VoC), named Omicron, originally identified in South Africa. Several mutations in Omicron indicate that it may have an impact on how it spreads, resistance to vaccination, or the severity of illness it causes. We used our previous modelling algorithms to forecast the spread of Omicron in England.\n\nDesignWe followed EQUATORs TRIPOD guidance for multivariable prediction models.\n\nSettingEngland.\n\nParticipantsNot applicable.\n\nInterventionsNon-interventional, observational study with a predicted forecast of outcomes.\n\nMain outcome measuresTrends in daily COVID-19 cases with a 7-day moving average and of new hospital admissions.\n\nMethodsModelling included a third-degree polynomial curve in existing epidemiological trends on the spread of Omicron and a new Gaussian curve to estimate a downward trend after a peak in England.\n\nResultsUp to February 15, 2022, we estimated a projection of 250,000 COVID-19 daily cases of Omicron spread in the worse scenario, and 170,000 in the \"best\" scenario. Omicron might represent a relative increase from the background daily rates of COVID-19 infection in England of mid December 2021 of 1.9 to 2.8-fold. With a 5-day lag-time, daily new hospital admissions would peak at around 5,063 on January 23, 2022 in the worse scenario.\n\nConclusionThis warning of pandemic surge of COVID-19 due to Omicron is calling for further reinforcing in England and elsewhere of universal hygiene interventions (indoor ventilation, social distance, and face masks), and anticipating the need of new total or partial lockdowns in England.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Alberto Giovanni Gerli",
-        "author_inst": "Universita degli Studi di Milano"
-      },
-      {
-        "author_name": "Stefano Centanni",
-        "author_inst": "San Paolo Hospital"
-      },
-      {
-        "author_name": "Joan B Soriano",
-        "author_inst": "Hospital Universitario de La Princesa"
-      },
-      {
-        "author_name": "Julio Ancochea",
-        "author_inst": "Hospital Universitario La Princesa"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.12.29.474402",
     "rel_title": "Structural and functional characterizations of altered infectivity and immune evasion of SARS-CoV-2 Omicron variant",
@@ -442051,6 +440894,109 @@
     "type": "new results",
     "category": "bioinformatics"
   },
+  {
+    "rel_doi": "10.1101/2021.12.30.474453",
+    "rel_title": "Preserved T cell reactivity to the SARS-CoV-2 Omicron variant indicates continued protection in vaccinated individuals.",
+    "rel_date": "2021-12-30",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.30.474453",
+    "rel_abs": "ImportanceThe emergence of the highly contagious Omicron variant of SARS-CoV-2 and the findings of a significantly reduced neutralizing potency of sera from convalescent or vaccinated individuals imposes the study of cellular immunity to predict the degree of immune protection to the yet again new coronavirus.\n\nDesignProspective monocentric observational study.\n\nSettingConducted between December 20-21 at the Santa Lucia Foundation IRCCS.\n\nParticipants61 volunteers (Mean age 41.62, range 21-62; 38F/23M) with different vaccination and SARS-CoV-2 infection backgrounds donated 15 ml of blood. Of these donors, one had recently completed chemotherapy, and one was undergoing treatment with monoclonal antibodies; the others reported no known health issue.\n\nMain Outcome(s) and Measure(s)The outcomes were the measurement of T cell reactivity to the mutated regions of the Spike protein of the Omicron SARS-CoV-2 variant and the assessment of remaining T cell immunity to the spike protein by stimulation with peptide libraries.\n\nResultsLymphocytes from freshly drawn blood samples were isolated and immediately tested for reactivity to the Spike protein of SARS-CoV-2. T cell responses to peptides covering the mutated regions in the Omicron variant were decreased by over 47% compared to the same regions of the ancestral vaccine strain. However, overall reactivity to the peptide library of the full-length protein was largely maintained (estimated 83%). No significant differences in loss of immune recognition were identified between groups of donors with different vaccination and/or infection histories.\n\nConclusions and RelevanceWe conclude that despite the mutations in the Spike protein, the SARS-CoV-2 Omicron variant is nonetheless recognized by the cellular component of the immune system. It is reasonable to assume that protection from hospitalization and severe disease is maintained.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSDoes the Omicron variant of SARS-CoV-2 escape cellular immunity?\n\nFindingsThis observational study was performed on 61 vaccinated donors with established immunity to SARS-CoV-2. Cellular responses to the mutated regions of the Omicron Spike protein were detected in 80% of donors. The mutations reduced T cell recognition by 47% compared to the vaccine strain. Reactivity to the whole Spike protein, however, was present in 100% of donors, and the fraction of remaining immunity to SARS-CoV-2 was estimated to be 83%.\n\nMeaningCellular immunity to the Omicron variant is maintained despite the mutations in its Spike protein, and may thus confer protection from severe COVID-19 in vaccinated individuals.",
+    "rel_num_authors": 22,
+    "rel_authors": [
+      {
+        "author_name": "Lorenzo De Marco",
+        "author_inst": "Santa Lucia Foundation IRCCS; Rome, Italy."
+      },
+      {
+        "author_name": "Marta Pirronello",
+        "author_inst": "Santa Lucia Foundation IRCCS; Rome, Italy."
+      },
+      {
+        "author_name": "Alice Verdiani",
+        "author_inst": "Santa Lucia Foundation IRCCS; Rome, Italy."
+      },
+      {
+        "author_name": "Andrea Termine",
+        "author_inst": "Fondazione Santa Lucia IRCCS, Rome, Italy"
+      },
+      {
+        "author_name": "Carlo Fabrizio",
+        "author_inst": "Santa Lucia Foundation, Rome, Italy"
+      },
+      {
+        "author_name": "Alessia Capone",
+        "author_inst": "Santa Lucia Foundation, Rome, Italy"
+      },
+      {
+        "author_name": "Andrea Sabatini",
+        "author_inst": "Santa Lucia Foundation, Rome, Italy"
+      },
+      {
+        "author_name": "Gisella Guerrera",
+        "author_inst": "Santa Lucia Foundation, Rome, Italy"
+      },
+      {
+        "author_name": "Roberta Placido",
+        "author_inst": "Santa Lucia Foundation, Rome, Italy"
+      },
+      {
+        "author_name": "Manolo Sambucci",
+        "author_inst": "Santa Lucia Foundation, Rome, Italy"
+      },
+      {
+        "author_name": "Daniela F Angelini",
+        "author_inst": "Santa Lucia Foundation, Rome, Italy"
+      },
+      {
+        "author_name": "Flavia Giannessi",
+        "author_inst": "Santa Lucia Foundation, Rome, Italy"
+      },
+      {
+        "author_name": "Mario Picozza",
+        "author_inst": "Santa Lucia Foundation, Rome, Italy"
+      },
+      {
+        "author_name": "Carlo Caltagirone",
+        "author_inst": "Santa Lucia Foundation, Rome, Italy"
+      },
+      {
+        "author_name": "Antonino Salvia",
+        "author_inst": "Santa Lucia Foundation, Rome, Italy"
+      },
+      {
+        "author_name": "Elisabetta Volpe",
+        "author_inst": "Santa Lucia Foundation, Rome, Italy"
+      },
+      {
+        "author_name": "Maria Pia Balice",
+        "author_inst": "Santa Lucia Foundation, Rome, Italy"
+      },
+      {
+        "author_name": "Angelo Rossini",
+        "author_inst": "Santa Lucia Foundation, Rome, Italy"
+      },
+      {
+        "author_name": "Olaf Rotzschke",
+        "author_inst": "Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore"
+      },
+      {
+        "author_name": "Emiliano Giardina",
+        "author_inst": "Santa Lucia Foundation, Rome, Italy; Tor Vergata University, Rome, Italy"
+      },
+      {
+        "author_name": "Luca Battistini",
+        "author_inst": "Santa Lucia Foundation, Rome, Italy"
+      },
+      {
+        "author_name": "Giovanna Borsellino",
+        "author_inst": "Santa Lucia Foundation, Rome, Italy"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2021.12.29.474491",
     "rel_title": "Molecular probes of spike ectodomain and its subdomains for SARS-CoV-2 variants, Alpha through Omicron",
@@ -443728,85 +442674,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.12.23.21268188",
-    "rel_title": "Characteristics and outcomes of cases of children and adolescents with pediatric inflammatory multisystem syndrome in a tertiary care centre in Mexico City.",
-    "rel_date": "2021-12-29",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.23.21268188",
-    "rel_abs": "Backgroundpediatric inflammatory multisystem syndrome (PIMS) is a complication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in children that resembles Kawasaki syndrome and places them at high risk of cardiorespiratory instability and/or cardiac damage. This study aims to describe the clinical presentation and outcomes of patients with PIMS in Mexico City.\n\nMethodsThis was an observational study of children hospitalized for PIMS based on the Centers for Disease Control and Prevention case definition criteria, in a single tertiary care pediatric center in Mexico City between May 1, 2020, and September 30, 2021. Demographic characteristics, epidemiological data, medical history, laboratory tests, cardiology evaluations, treatment, and clinical outcomes were analyzed.\n\nResultsSeventy-five cases fulfilled the case definition criteria for PIMS (median age: 10.9 years, Interquartile range [IQR]: 5.6-15.6). Fifteen (20%) patients had a severe underlying disease, 48 (64%) were admitted to the intensive care unit, 33 (44%) required invasive mechanical ventilation and 39 (52%) received vasopressor support. The patients were clustered through latent class analysis based on identified symptoms: Cluster 1 had rash or gastrointestinal symptoms (n = 60) and cluster 2 were those with predominantly respiratory manifestations (n = 15). Two patients (2.7%) died, and both had severe underlying conditions. Five patients (6.7%), all from cluster 1, developed coronary aneurysms.\n\nConclusionThere were a high proportion of patients with severe respiratory involvement and positive RT-PCR SARS-CoV-2 and very few cases of coronary aneurysms in our study which suggests that a high proportion of the children had severe acute COVID-19. The clinical manifestations and outcomes are comparable to previously reported international studies.",
-    "rel_num_authors": 16,
-    "rel_authors": [
-      {
-        "author_name": "Ricardo Gil Guevara",
-        "author_inst": "Emergency Medicine Department, Hospital Infantil de Mexico Federico Gomez Instituto Nacional de Salud, Mexico City, Mexico"
-      },
-      {
-        "author_name": "Maria de Lourdes Marroquin Yanez",
-        "author_inst": "Pediatric Intensive Care Unit, Hospital Infantil de Mexico Instituto Nacional de Salud , Mexico City, Mexico"
-      },
-      {
-        "author_name": "Rodolfo Norberto Jimenez-Juarez",
-        "author_inst": "Infectious Diseases Department, Hospital Infantil de Mexico Federico Gomez Instituto Nacional de Salud , Mexico City, Mexico.  Department of Pediatrics,  CMN La"
-      },
-      {
-        "author_name": "Victor Olivar Lopez",
-        "author_inst": "Emergency Medicine,  Hospital Infantil de Mexico Federico Gomez Instituto Nacional de Salud, Mexico City, Mexico"
-      },
-      {
-        "author_name": "Adrian Chavez Lopez",
-        "author_inst": "Pediatric Intensive Care Untit,  Hospital Infantil de Mexico Federico Gomez Instituto Nacional de Salud , Mexico City, Mexico"
-      },
-      {
-        "author_name": "Juan Jose Luis Sienra Monge",
-        "author_inst": "Ambulatory Pediatrics,  Hospital Infantil de Mexico Federico Gomez Instituto Nacional de Salud Instituto Nacional de Salud , Mexico City, Mexico."
-      },
-      {
-        "author_name": "Julio Erdmenger Orellana",
-        "author_inst": "Cardiology Department, Hospital Infantil de Mexico Federico Gomez Instituto Nacional de Salud, Mexico City, Mexico"
-      },
-      {
-        "author_name": "Lourdes Maria del Carmen Jamaica Balderas",
-        "author_inst": "Respiratory Medicine Department, Hospital Infantil de Mexico Federico Gomez Instituto Nacional de Salud , Mexico City, Mexico."
-      },
-      {
-        "author_name": "Silvia Alexandra Martinez Herrera",
-        "author_inst": "Emergency Medicine Department, Hospital Infantil de Mexico Federico Gomez Instituto Nacional de Salud, Mexico City, Mexico"
-      },
-      {
-        "author_name": "Clemen Dominguez-Barrera",
-        "author_inst": "Department of Infectious Diseases, Hospital Infantil de Mexico Federico Gomez Instituto Nacional de Salud , Mexico City, Mexico"
-      },
-      {
-        "author_name": "Horacio Marquez Gonzalez",
-        "author_inst": "Department of Clinical Research,  Hospital Infantil de Mexico Federico Gomez Instituto Nacional de Salud , Mexico City, Mexico"
-      },
-      {
-        "author_name": "Miguel Klunder-Klunder",
-        "author_inst": "Research Division, Hospital Infantil de Mexico Federico Gomez Instituto Nacional de Salud , Mexico City, Mexco"
-      },
-      {
-        "author_name": "Jaime Nieto-Zermeno",
-        "author_inst": "Hospital Infantil de Mexcio Federico Gomez Instituto Nacional de Salud , Mexico City, Mexico"
-      },
-      {
-        "author_name": "Monica Villa Guillen",
-        "author_inst": "Hospital Infantil de Mexico Federico Gomez Instituto Nacional de Salud  Instituto Nacional de Salud,  Mexico City, Mexico"
-      },
-      {
-        "author_name": "Nadia Gonzalez Garcia",
-        "author_inst": "Neruosciences Research Laboratory, Hospital Infantil de Mexico Federico Gomez Instituto Nacional de Salud, Mexico City, Mexico"
-      },
-      {
-        "author_name": "Maria Fernanda Castilla Peon",
-        "author_inst": "Research Division, Hospital Infantil de Mexico Federico Gomez Instituto Nacional de Salud"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "pediatrics"
-  },
   {
     "rel_doi": "10.1101/2021.12.27.21268348",
     "rel_title": "COVID-19 in children in NSW, Australia, during the 2021 Delta outbreak: Severity and Disease spectrum",
@@ -444125,6 +442992,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.12.28.21268472",
+    "rel_title": "Neutralizing antibody responses to SARS-CoV-2: a population based seroepidemiological analysis in Delhi, India",
+    "rel_date": "2021-12-29",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.28.21268472",
+    "rel_abs": "We conducted this study to estimate seroprevalence of neutralizing antibodies in the general population and to further correlate it with the IgG SARS-CoV-2 IgG levels. This present cross-sectional analysis was conducted as a sequel to a state level community-based seroepidemiological study in Delhi, India. A total of 2564 seropositive samples were selected from 25622 seropositive samples through simple random sampling. Neutralizing capacity was estimated by performing a surrogate virus neutralization test with the sVNT (GenScript) assay. Neutralizing antibody against the SARS-CoV-2 virus was operationally considered as detected when the signal inhibition was [&ge;]30%.\n\nA total of 2233 (87.1%, 95% C.I. 85.7, 88.3) of the 2564 SARS-CoV-2 seropositive samples had detectable neutralizing antibodies. On bi-variate analysis but not on adjusted analysis, Covid-19 vaccination showed a statistically significant association with the presence of neutralizing antibodies (p<0.001). The signal/ cut off (S/CO) of SARS-CoV-2 IgG ranged from 1.00 to 22.8 (median 11.40). In samples with S/CO [&ge;]4.00, the neutralizing antibodies ranged from 94.5 to 100%, while in samples with S/CO <4.00, it ranged from 52.0 to 79.2%. The neutralizing antibody seroprevalence strongly correlated with the S/CO range (r=0.62, p=0.002). In conclusion, in populations with high SARS-CoV-2 seroprevalence, neutralizing antibodies are generated in nearly 9 of 10 seropositive individuals.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Pragya Sharma",
+        "author_inst": "Maulana Azad Medical College, New Delhi"
+      },
+      {
+        "author_name": "Ekta Gupta",
+        "author_inst": "Institute of Liver and Biliary Sciences"
+      },
+      {
+        "author_name": "Saurav Basu",
+        "author_inst": "Maulana Azad Medical College, New Delhi; Indian Institute of Public Health - Delhi"
+      },
+      {
+        "author_name": "Reshu Aggarwal",
+        "author_inst": "Institute of Liver and Biliary Sciences"
+      },
+      {
+        "author_name": "Suruchi Mishra",
+        "author_inst": "Maulana Azad Medical College, New Delhi"
+      },
+      {
+        "author_name": "Pratibha Kale",
+        "author_inst": "Institute of Liver and Biliary Sciences, New Delhi"
+      },
+      {
+        "author_name": "Nutan Mundeja",
+        "author_inst": "Directorate General Health Services, Government of NCT, Delhi"
+      },
+      {
+        "author_name": "B S Charan",
+        "author_inst": "Directorate General Health Services, Government of NCT, Delhi"
+      },
+      {
+        "author_name": "Gautam Kumar Singh",
+        "author_inst": "Directorate General Health Services, Government of NCT, Delhi"
+      },
+      {
+        "author_name": "Mongjam MEGHACHANDRA SINGH",
+        "author_inst": "Maulana Azad Medical College, New Delhi"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.12.22.21268176",
     "rel_title": "A preliminary study of commercially available general-purpose chest radiography artificial intelligence-based software for detecting airspace opacity lesions in COVID-19 patients",
@@ -445818,109 +444740,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2021.12.28.474326",
-    "rel_title": "Intranasal inhibitor blocks Omicron and other variants of SARS-CoV-2",
-    "rel_date": "2021-12-28",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.28.474326",
-    "rel_abs": "The recent emergence of novel SARS-CoV-2 variants capable of efficiently escaping neutralizing antibodies emphasizes the need for prophylactic strategies to complement vaccination in fighting the COVID-19 pandemic. Nasal epithelium is rich in the ACE2 receptor and important for SARS-CoV-2 transmission by supporting early viral replication before seeding to the lung1. Intranasal administration of SARS-CoV-2 neutralizing antibodies or antibody fragments has shown encouraging potential as a protective measure in animal models2-5. However, there remains a dire need for SARS-CoV-2 blocking agents that are less vulnerable to mutational variation in the neutralization epitopes of the viral spike glycoprotein and more economical to produce in large scale. Here we describe TriSb92, a highly manufacturable and extremely stable trimeric human SH3 domain-derived antibody mimetic targeted against a conserved region in the receptor-binding domain of spike. TriSb92 potently neutralizes SARS-CoV-2 and its variants of concern, including Omicron BA.5 as well as the latest and most immunoevasive variants like BF.7, XBB, and BQ.1.1. Intranasal administration of a modest dose of TriSb92 (5 or 50 micrograms) as early as eight hours before a challenge with SARS-CoV-2 efficiently protected mice from infection, and was still effective even when given 4 h after the viral challenge. The target epitope of TriSb92 was defined by cryo-EM, which revealed triggering of a conformational shift in the spike trimer rather than competition for ACE2 binding as the molecular basis of its strong inhibitory action. The high potency and robust biochemical properties of TriSb92 together with the remarkable resistance of its inhibitory action against viral sequence evolution suggest that TriSb92 could be useful as a nasal spray for protecting susceptible individuals from SARS-CoV-2 infection.",
-    "rel_num_authors": 22,
-    "rel_authors": [
-      {
-        "author_name": "Anna R M\u00e4kel\u00e4",
-        "author_inst": "University of Helsinki"
-      },
-      {
-        "author_name": "Hasan U\u011furlu",
-        "author_inst": "University of Helsinki"
-      },
-      {
-        "author_name": "Liina Hannula",
-        "author_inst": "University of Helsinki"
-      },
-      {
-        "author_name": "Petja Salminen",
-        "author_inst": "University of Helsinki"
-      },
-      {
-        "author_name": "Ravi Kant",
-        "author_inst": "University of Helsinki"
-      },
-      {
-        "author_name": "Riku Fagerlund",
-        "author_inst": "University of Helsinki"
-      },
-      {
-        "author_name": "Sanna M\u00e4ki",
-        "author_inst": "University of Helsinki"
-      },
-      {
-        "author_name": "Anu Haveri",
-        "author_inst": "Finnish Institute for Health and Welfare"
-      },
-      {
-        "author_name": "Tomas Strandin",
-        "author_inst": "University of Helsinki"
-      },
-      {
-        "author_name": "Lauri Kareinen",
-        "author_inst": "University of Helsinki"
-      },
-      {
-        "author_name": "Jussi Hepojoki",
-        "author_inst": "University of Helsinki"
-      },
-      {
-        "author_name": "Lev Levanov",
-        "author_inst": "University of Helsinki"
-      },
-      {
-        "author_name": "Arja Pasternack",
-        "author_inst": "University of Helsinki"
-      },
-      {
-        "author_name": "Rauno A Naves",
-        "author_inst": "University of Helsinki"
-      },
-      {
-        "author_name": "Olli Ritvos",
-        "author_inst": "University of Helsinki"
-      },
-      {
-        "author_name": "Pamela \u00d6sterlund",
-        "author_inst": "Finnish Institute for Health and Welfare"
-      },
-      {
-        "author_name": "Tarja Sironen",
-        "author_inst": "University of Helsinki"
-      },
-      {
-        "author_name": "Olli Vapalahti",
-        "author_inst": "University of Helsinki"
-      },
-      {
-        "author_name": "Anja Kipar",
-        "author_inst": "University of Zurich"
-      },
-      {
-        "author_name": "Juha T Huiskonen",
-        "author_inst": "University of Helsinki"
-      },
-      {
-        "author_name": "Ilona Rissanen",
-        "author_inst": "University of Helsinki"
-      },
-      {
-        "author_name": "Kalle Saksela",
-        "author_inst": "University of Helsinki"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2021.12.28.474338",
     "rel_title": "Improved binding affinity of the Omicron's spike protein with hACE2 receptor is the key factor behind its increased virulence",
@@ -446255,6 +445074,125 @@
     "type": "new results",
     "category": "bioinformatics"
   },
+  {
+    "rel_doi": "10.1101/2021.12.27.474273",
+    "rel_title": "Structures of the Omicron Spike trimer with ACE2 and an anti-Omicron antibody",
+    "rel_date": "2021-12-28",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.27.474273",
+    "rel_abs": "The Omicron variant of SARS-CoV-2 has rapidly become the dominant infective strain and the focus efforts against the ongoing COVID-19 pandemic. Here we report an extensive set of structures of the Omicron spike trimer by its own or in complex with ACE2 and an anti-Omicron antibody. These structures reveal that most Omicron mutations are located on the surface of the spike protein, which confer stronger ACE2 binding by nearly 10 folds but become inactive epitopes resistant to many therapeutic antibodies. Importantly, both RBD and the closed conformation of the Omicron spike trimer are thermodynamically unstable, with the melting temperature of the Omicron RBD decreased by as much as 7{degrees}C, making the spiker trimer prone to random open conformations. An unusual RBD-RBD interaction in the ACE2-spike complex unique to Omicron is observed to support the open conformation and ACE2 binding, serving the basis for the higher infectivity of Omicron. A broad-spectrum therapeutic antibody JMB2002, which has completed Phase 1 clinical trial, is found to interact with the same two RBDs to inhibit ACE2 binding, in a mode that is distinguished from all previous antibodies, thus providing the structural basis for the potent inhibition of Omicron by this antibody. Together with biochemical data, our structures provide crucial insights into higher infectivity, antibody evasion and inhibition of Omicron.",
+    "rel_num_authors": 26,
+    "rel_authors": [
+      {
+        "author_name": "Wanchao Yin",
+        "author_inst": "Shanghai Institute of Materia Medica"
+      },
+      {
+        "author_name": "Youwei Xu",
+        "author_inst": "Shanghai Institute of Materia Medica"
+      },
+      {
+        "author_name": "Peiyu Xu",
+        "author_inst": "Shanghai Institute of Materia Medica"
+      },
+      {
+        "author_name": "Xiaodan Cao",
+        "author_inst": "Jemincare"
+      },
+      {
+        "author_name": "Canrong Wu",
+        "author_inst": "Shanghai"
+      },
+      {
+        "author_name": "Chunyin Gu",
+        "author_inst": "Shanghai Jemincare Pharmaceuticals Co., Ltd."
+      },
+      {
+        "author_name": "Xinheng He",
+        "author_inst": "Shanghai Institute of Materia Medica"
+      },
+      {
+        "author_name": "Xiaoxi Wang",
+        "author_inst": "Shanghai Institute of Materia Medica Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Sijie Huang",
+        "author_inst": "Shanghai Institute of Materia Medica"
+      },
+      {
+        "author_name": "Qingning Yuan",
+        "author_inst": "The Shanghai Advanced Electron Microscope Center"
+      },
+      {
+        "author_name": "Kai Wu",
+        "author_inst": "The Shanghai Advanced Electron Microscope Center"
+      },
+      {
+        "author_name": "Wen Hu",
+        "author_inst": "The Shanghai Advanced Electron Microscope Center"
+      },
+      {
+        "author_name": "Zifu Huang",
+        "author_inst": "Shanghai Institute of Materia Medica"
+      },
+      {
+        "author_name": "Jia Liu",
+        "author_inst": "Shanghai Jemincare Pharmaceuticals Co., Ltd."
+      },
+      {
+        "author_name": "Zongda Wang",
+        "author_inst": "Shanghai Jemincare Pharmaceuticals Co., Ltd."
+      },
+      {
+        "author_name": "Fangfang Jia",
+        "author_inst": "Shanghai Jemincare Pharmaceuticals Co., Ltd."
+      },
+      {
+        "author_name": "Kaiwen Xia",
+        "author_inst": "Shanghai Jemincare Pharmaceuticals Co., Ltd."
+      },
+      {
+        "author_name": "Peipei Liu",
+        "author_inst": "Shanghai Jemincare Pharmaceuticals Co., Ltd."
+      },
+      {
+        "author_name": "Xueping Wang",
+        "author_inst": "Shanghai Jemincare Pharmaceuticals Co., Ltd."
+      },
+      {
+        "author_name": "Bin Song",
+        "author_inst": "Immunological Disease Research Center"
+      },
+      {
+        "author_name": "Jie Zheng",
+        "author_inst": "Immunological Disease Research Center"
+      },
+      {
+        "author_name": "Hualiang Jiang",
+        "author_inst": "Shanghai Institute of Materia Medica"
+      },
+      {
+        "author_name": "Xi Cheng",
+        "author_inst": "Shanghai Institute of Materia Medica"
+      },
+      {
+        "author_name": "Yi Jiang",
+        "author_inst": "Shanghai Institute of Materia Medica Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Su-Jun Deng",
+        "author_inst": "Shanghai Jemincare Pharmaceuticals Co., Ltd."
+      },
+      {
+        "author_name": "H. Eric Xu",
+        "author_inst": "Shanghai Institute of Materia Medica"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "new results",
+    "category": "biophysics"
+  },
   {
     "rel_doi": "10.1101/2021.12.28.474359",
     "rel_title": "In contrast to TH2-biased approaches, TH1 COVID-19 vaccines protect Syrian hamsters from severe disease in the absence of dexamethasone-treatable vaccine-associated enhanced respiratory pathology",
@@ -448412,57 +447350,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.12.22.21268059",
-    "rel_title": "A model based on a high-resolution flux matrix explains the spread of diseases in a spatial network and the effect of mitigation strategies",
-    "rel_date": "2021-12-27",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.22.21268059",
-    "rel_abs": "Propagation of an epidemic across a spatial network of communities is described by a variant of the SIR model accompanied by an intercommunity infectivity matrix. This matrix is estimated from fluxes between communities, obtained from cell-phone tracking data recorded in the USA between March 2020 and February 2021. We apply this model to the SARS-CoV-2 pandemic by fitting just one global parameter representing the frequency of interaction between individuals. We find that the predicted infections agree reasonably well with the reported cases. We clearly see the effect of \"shelter-in-place\" policies introduced at the onset of the pandemic. Interestingly, a model with uniform transmission rates produces similar results, suggesting that the epidemic transmission was deeply influenced by air travel. We then study the effect of alternative mitigation policies, in particular restricting long-range travel. We find that this policy is successful in decreasing the epidemic size and slowing down the spread, but less effective than the shelter-in-place policy. This policy can result in a pulled wave of infections. We express its velocity and characterize the shape of the traveling front as a function of the epidemiological parameters. Finally, we discuss a policy of selectively constraining travel based on an edge-betweenness criterion.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Guillaume Le Treut",
-        "author_inst": "Chan-Zuckerberg Biohub"
-      },
-      {
-        "author_name": "Greg Huber",
-        "author_inst": "Chan-Zuckerberg Biohub"
-      },
-      {
-        "author_name": "Mason Kamb",
-        "author_inst": "Chan-Zuckerberg Biohub"
-      },
-      {
-        "author_name": "Kyle Kawagoe",
-        "author_inst": "University of Chicago"
-      },
-      {
-        "author_name": "Aaron McGeever",
-        "author_inst": "Chan-Zuckerberg Biohub"
-      },
-      {
-        "author_name": "Jonathan Miller",
-        "author_inst": "Okinawa Institute of Science and Technology"
-      },
-      {
-        "author_name": "Reuven Pnini",
-        "author_inst": "Okinawa Institute of Science and Technology"
-      },
-      {
-        "author_name": "Boris Veytsman",
-        "author_inst": "Chan Zuckerberg Initiative"
-      },
-      {
-        "author_name": "David Yllanes",
-        "author_inst": "Chan-Zuckerberg Biohub"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.12.24.21268382",
     "rel_title": "Early estimates of SARS-CoV-2 Omicron variant severity based on a matched cohort study, Ontario, Canada",
@@ -448837,6 +447724,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "neurology"
   },
+  {
+    "rel_doi": "10.1101/2021.12.20.21268066",
+    "rel_title": "Persisting Chemosensory Impairments in 366 Healthcare Workers Following COVID-19: An 11-Month Follow-up.",
+    "rel_date": "2021-12-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.20.21268066",
+    "rel_abs": "Background and ObjectivesOlfactory and gustatory dysfunctions (OD, GD) are prevalent symptoms following COVID-19 and persist in 6%-44% of individuals in the first months after the infection. As only few reports have described their prognosis more than 6 months later, the main objective of this study was to assess the prevalence of OD and GD 11 months after COVID-19. We also aimed to determine test-retest reliability of subjective chemosensory ratings for the follow-up of chemosensory sensitivity, as this measure is often used for remote follow-up.\n\nMethodsInclusion criteria included a PCR-confirmed SARS-CoV-2 infection; exclusion criteria were the presence of other respiratory infections and chronic sinusitis. To assess whether OD and GD had changed compared to pre-pandemic levels, we designed an observational study and distributed an online questionnaire assessing quantitative chemosensory function to healthcare workers 5 and 11 months after COVID-19. Specifically, we assessed olfaction, gustation, and trigeminal sensitivity (10-point visual analog scale) and function (4-point Likert scale) separately. We further assessed clinically relevant OD using the Chemosensory Perception Test, a psychophysical test designed to provide a reliable remote olfactory evaluation. Qualitative chemosensory dysfunction was also assessed.\n\nResultsWe included a total of 366 participants (mean age of 44.8 years old (SD: 11.7)). They completed the last online questionnaire 10.6 months (SD: 0.7) after the onset of COVID-19 symptoms. Of all participants, 307 (83.9%) and 301 (82.2%) individuals retrospectively reported lower olfactory or gustatory sensitivity during the acute phase of COVID-19. Eleven months later, 184 (50.3%) and 163 (44.5%) indicated reduced chemosensory sensitivity, 32.2% reported impairment of olfactory function while 24.9% exhibited clinically relevant OD. Three variables predicted OD at follow-up, namely chest pain and GD during COVID-19 and presence of phantosmia at 5 months. Olfactory sensitivity ratings had a high test-retest reliability (intraclass correlation coefficient: 0.818 (95% CI: 0.760 - 0.860))\n\nDiscussionThis study suggests that chemosensory dysfunctions persist in a third of COVID-19 patients 11 months after COVID-19. Subjective measures have a high test-retest reliability and thus can be used to monitor post-COVID-19 OD. OD appears to be a common long-term symptom of COVID-19 important to consider when treating patients.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Nicholas Bussiere",
+        "author_inst": "Universite du Quebec a Trois-Rivieres"
+      },
+      {
+        "author_name": "Jie Mei",
+        "author_inst": "Universite du Quebec a Trois-Rivieres"
+      },
+      {
+        "author_name": "Cindy Levesque-Boissonneault",
+        "author_inst": "Universite du Quebec a Trois-Rivieres"
+      },
+      {
+        "author_name": "Mathieu Blais",
+        "author_inst": "Centre de recherche CHU de Quebec Universite Laval"
+      },
+      {
+        "author_name": "Sara Carazo",
+        "author_inst": "Centre de Recherche CHU de Quebec - Universite Laval"
+      },
+      {
+        "author_name": "Francois Gros-Louis",
+        "author_inst": "Centre de recherche CHU de Quebec Universite Laval"
+      },
+      {
+        "author_name": "Robert Laforce Jr.",
+        "author_inst": "Centre de recherche CHU de Quebec Universite Laval"
+      },
+      {
+        "author_name": "Gaston DeSerres",
+        "author_inst": "Centre de recherche CHU de Quebec Universite Laval"
+      },
+      {
+        "author_name": "Nicolas Dupre",
+        "author_inst": "Centre de recherche CHU de Quebec Universite Laval"
+      },
+      {
+        "author_name": "Johannes Frasnelli",
+        "author_inst": "Universite du Quebec a Trois-Rivieres"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "otolaryngology"
+  },
   {
     "rel_doi": "10.1101/2021.12.26.21268358",
     "rel_title": "Can individuals with low antibody responses to vaccines against other viruses acquire adequate SARS-CoV-2 antibody after vaccination with the BNT162b2 mRNA vaccine?",
@@ -450278,41 +449220,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
-  {
-    "rel_doi": "10.1101/2021.12.24.21268317",
-    "rel_title": "COMPARATIVE ANALYSIS OF ANTIBODY RESPONSES FROM COVID-19 CONVALESCENTS RECEIVING VARIOUS VACCINES REVEALS CONSISTENT HIGH NEUTRALIZING ACTIVITY FOR SARS-CoV-2 VARIANT OF CONCERN OMICRON.",
-    "rel_date": "2021-12-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.24.21268317",
-    "rel_abs": "The latest SARS-CoV-2 variant of concern Omicron, with its immune escape from therapeutic anti-Spike monoclonal antibodies and WA-1 vaccine-elicited sera, demonstrates the continued relevance of COVID- 19 convalescent plasma (CCP) therapies. Lessons learnt from previous usage of CCP suggests focusing on early outpatients and immunocompromised recipients, with high neutralizing antibody (nAb) titer units. In this analysis we systematically reviewed Omicron-neutralizing plasma activity data, and found that approximately 47% (424/902) of CCP from unvaccinated pre-Omicron donors neutralizes Omicron BA.1 with a very low geomean of geometric mean titers for 50% neutralization GM(GMT50) of about 13, representing a more than 20-fold reduction from WA-1 neutralization. Two doses of mRNA vaccines in nonconvalescent subjects had a similar 50% percent neutralization with Omicron BA.1 neutralization GM(GMT(50)) of about 27. However, plasma from vaccinees recovered from either previous pre-Omicron variants of concern infection, Omicron BA.1 infection, or third-dose uninfected vaccinees was nearly 100% neutralizing against Omicron BA.1, BA.2 and BA.4/5 with GM(GMT(50)) all over 189, 10 times higher than pre-Omicron CCP. Fully vaccinated and post-BA.1 plasma (Vax-CCP) had GM(GMT50) over 450 for BA.4/5 and over 1500 for BA.1 and BA.2. These findings have implications for both CCP stocks collected in prior pandemic periods and plans to restart CCP collections. Thus, Vax-CCP provides an effective tool to combat ongoing variants that defeat therapeutic monoclonal antibodies.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "David J Sullivan",
-        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
-      },
-      {
-        "author_name": "Massimo Franchini",
-        "author_inst": "Division of Transfusion Medicine, Carlo Poma Hospital, 46100 Mantua, Italy"
-      },
-      {
-        "author_name": "Michael J Joyner",
-        "author_inst": "Department of Anesthesiology & Perioperative Medicine, Mayo Clinic, Rochester, MN 55902, USA"
-      },
-      {
-        "author_name": "Arturo Casadevall",
-        "author_inst": "Johns Hopkins School of Public Health"
-      },
-      {
-        "author_name": "Daniele Focosi",
-        "author_inst": "Pisa University Hospital"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.12.24.21268367",
     "rel_title": "Genomic surveillance reveals the emergence of SARS-CoV-2 Lineage A from Islamabad Pakistan",
@@ -450659,6 +449566,77 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "cardiovascular medicine"
   },
+  {
+    "rel_doi": "10.1101/2021.12.23.21268276",
+    "rel_title": "Risk of myocarditis following sequential COVID-19 vaccinations by age and sex",
+    "rel_date": "2021-12-25",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.23.21268276",
+    "rel_abs": "In an updated self-controlled case series analysis of 42,200,614 people aged 13 years or more, we evaluate the association between COVID-19 vaccination and myocarditis, stratified by age and sex, including 10,978,507 people receiving a third vaccine dose. Myocarditis risk was increased during 1-28 days following a third dose of BNT162b2 (IRR 2.02, 95%CI 1.40, 2.91). Associations were strongest in males younger than 40 years for all vaccine types with an additional 3 (95%CI 1, 5) and 12 (95% CI 1,17) events per million estimated in the 1-28 days following a first dose of BNT162b2 and mRNA-1273, respectively; 14 (95%CI 8, 17), 12 (95%CI 1, 7) and 101 (95%CI 95, 104) additional events following a second dose of ChAdOx1, BNT162b2 and mRNA-1273, respectively; and 13 (95%CI 7, 15) additional events following a third dose of BNT162b2, compared with 7 (95%CI 2, 11) additional events following COVID-19 infection. An association between COVID-19 infection and myocarditis was observed in all ages for both sexes but was substantially higher in those older than 40 years. These findings have important implications for public health and vaccination policy.\n\nFundingHealth Data Research UK.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Martina Patone",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Winnie Xue Mei",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Lahiru Handunnetthi",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Sharon Dixon",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Francesco Zaccardi",
+        "author_inst": "University of Leicester"
+      },
+      {
+        "author_name": "Manu Shankar-Hari",
+        "author_inst": "University of Edinburgh"
+      },
+      {
+        "author_name": "Peter Watkinson",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Kamlesh Khunti",
+        "author_inst": "University of Leicester"
+      },
+      {
+        "author_name": "Anthony Harnden",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Carol AC Coupland",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Keith M. Channon",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Nicholas L Mills",
+        "author_inst": "University of Edinburgh"
+      },
+      {
+        "author_name": "Aziz Sheikh",
+        "author_inst": "University of Edinburgh"
+      },
+      {
+        "author_name": "Julia Hippisley-Cox",
+        "author_inst": "University of Oxford"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.12.24.21268373",
     "rel_title": "Are COVID-19 data reliable? The case of the European Union",
@@ -452088,53 +451066,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.12.22.21268273",
-    "rel_title": "Neutralizing antibodies to SARS-CoV-2 Omicron variant after 3rd mRNA vaccination in health care workers and elderly subjects and response to a single dose in previously infected adults",
-    "rel_date": "2021-12-24",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.22.21268273",
-    "rel_abs": "The emergence of SARS-CoV-2 Omicron variant (B.1.1.529) with major spike protein mutations has raised concern over potential neutralization escape and breakthrough infections among vaccinated and previously SARS-CoV-2 infected subjects. We measured cross-protective antibodies against variants in health care workers (HCW, n=20) and nursing home residents (n=9) from samples collected 1-2 months following the booster (3rd) dose. We also assessed the antibody responses in prior to Omicron era infected subjects (n=38) with subsequent administration of a single mRNA vaccine dose. Following booster vaccination HCWs had high IgG antibody concentrations to the spike protein and neutralizing antibodies (NAb) were detectable against all variants. IgG concentrations among the elderly remained lower, and some lacked NAbs against the Beta and Omicron variants. NAb titers were significantly reduced against Delta, Beta and Omicron compared to wild-type virus regardless of age. Vaccination induced high IgG concentrations and variable titers of cross-reactive NAbs in previously infected subjects, whereas NAb titers against Omicron were barely detectable 1-month post-infection. High IgG concentrations with cross-protective neutralizing activity were detected after three COVID-19 vaccine doses in HCWs. However, lower NAb titers seen in the frail elderly suggest inadequate protection against Omicron breakthrough infections, yet protection against severe COVID-19 is expected.\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@84f4c4org.highwire.dtl.DTLVardef@e1a056org.highwire.dtl.DTLVardef@e5a4ecorg.highwire.dtl.DTLVardef@ae8370org.highwire.dtl.DTLVardef@137480e_HPS_FORMAT_FIGEXP  M_TBL O_FLOATNOTable 1.C_FLOATNO O_TABLECAPTIONGeometric mean IgG concentrations, GMC [95% CI] expressed as BAU/ml for spike proteins (SFL and RBD) and geometric mean titers, GMT [95% CI] of neutralizing antibodies (NAb) against wild-type (WT) virus and three variants of concern Delta (B.1.617.2), Beta (B.1.351) and Omicron (B.1.1.529) in elderly (n=7-9) and health care workers (HCW) 21-42 (n=7) or 43-77 (n=8) days post booster mRNA vaccination (3rd dose of Comirnaty).\n\nC_TABLECAPTION C_TBL Clinical trial registrationEudraCT 2021-004788-29",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Anu Haveri",
-        "author_inst": "Finnish Institute for Health and Welfare"
-      },
-      {
-        "author_name": "Anna Solastie",
-        "author_inst": "Finnish Institute for Health and Welfare"
-      },
-      {
-        "author_name": "Nina Ekstr\u00f6m",
-        "author_inst": "Finnish Institute for Health and Welfare"
-      },
-      {
-        "author_name": "Pamela \u00d6sterlund",
-        "author_inst": "Finnish Institute for Health and Welfare"
-      },
-      {
-        "author_name": "Hanna Nohynek",
-        "author_inst": "Finnish Institute for Health and Welfare"
-      },
-      {
-        "author_name": "Tuomo Nieminen",
-        "author_inst": "Finnish Institute for Health and Welfare"
-      },
-      {
-        "author_name": "Arto A Palmu",
-        "author_inst": "Finnish Institute for Health and Welfare"
-      },
-      {
-        "author_name": "Merit Melin",
-        "author_inst": "Finnish Institute for Health and Welfare"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.12.23.21268293",
     "rel_title": "Neutralising antibody activity against SARS-CoV-2 variants, including Omicron, in an elderly cohort vaccinated with BNT162b2",
@@ -452485,6 +451416,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pharmacology and therapeutics"
   },
+  {
+    "rel_doi": "10.1101/2021.12.22.21268045",
+    "rel_title": "Essential Workers COVID-19 Vaccine Hesitancy, Misinformation and Informational Needs in the Republic of North Macedonia.",
+    "rel_date": "2021-12-24",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.22.21268045",
+    "rel_abs": "IntroductionThe COVID-19 pandemic is a global health crisis that as of December 2021 has resulted in the death of over 5.2 million people. Despite the unprecedented development and distribution of vaccines, hesitancy to take the vaccine remains a wide-spread public health challenge, especially in Eastern European countries. In this study we focus on a sample of essential workers living in the Republic of North Macedonia to: 1) Describe rates of vaccine acceptance, risk perception and sources of COVID-19 information, 2) Explore predictors of vaccine hesitancy, and 3) Describe informational needs of hesitant and non-hesitant workers.\n\nMethodsDescriptive statistics were used to present frequencies of vaccine acceptance. Logistic regression was used to explore predictors of vaccine hesitancy based on sociodemographic characteristics, hesitancy to take other vaccines in the past, previous diagnosis of COVID-19, and individual risk perception of getting COVID-19. Chi square analysis was used to compare differences in informational needs between hesitant and non-hesitant individuals across socio-demographic groups.\n\nResultsFrom a sample of 1003 individuals, 439 (44%) reported that they were very likely to get the vaccine, and the rest (66%) reported some level of hesitancy. Older age, Albanian ethnicity, post-secondary school education, previous diagnosis of COVID-19, previous vaccine acceptance of other vaccines, and increased risk perception of COVID-19 infection were all found to be negatively associated with vaccine hesitancy. In particular hesitant individuals, compared to the non-hesitant, wanted to have more information and reassurance that all main international agencies (i.e. FDA, WHO, EMA) were all in accordance in recommending the vaccine and that they would be free to choose if getting the vaccine or not without consequences (p<0.01).",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Stephen Fucaloro",
+        "author_inst": "Harvard T.H. Chan School of Public Health"
+      },
+      {
+        "author_name": "Vahe Yacoubian",
+        "author_inst": "Harvard T.H. Chan School of Public Health"
+      },
+      {
+        "author_name": "Nigel Harriman",
+        "author_inst": "Harvard T.H. Chan School of Public Health"
+      },
+      {
+        "author_name": "Rachael Pitch-Loeb",
+        "author_inst": "Harvard T.H. Chan School of Public Health"
+      },
+      {
+        "author_name": "Metodi Hadji-Janev",
+        "author_inst": "University Goce Delcev"
+      },
+      {
+        "author_name": "Tea Burmaz",
+        "author_inst": "Harvard T.H. Chan School of Public Health"
+      },
+      {
+        "author_name": "Elena Savoia",
+        "author_inst": "Harvard T.H. Chan School of Public Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.12.22.21268268",
     "rel_title": "CMV seropositivity is a potential novel risk factor for severe COVID-19 in non-geriatric patients",
@@ -454065,89 +453039,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "cardiovascular medicine"
   },
-  {
-    "rel_doi": "10.1101/2021.12.21.21268214",
-    "rel_title": "Comparative effectiveness of ChAdOx1 versus BNT162b2 vaccines against SARS-CoV-2 infections in England and Wales: A cohort analysis using trial emulation in the Virus Watch community data",
-    "rel_date": "2021-12-23",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.21.21268214",
-    "rel_abs": "IntroductionInfections of SARS-CoV-2 in vaccinated individuals have been increasing globally. Understanding the associations between vaccine type and a post-vaccination infection could help prevent further COVID-19 waves. In this paper, we use trial emulation to understand the impact of a phased introduction of the vaccine in the UK driven by vulnerability and exposure status. We estimate the comparative effectiveness of COVID-19 vaccines (ChAdOx1 versus BNT162b2) against post-vaccination infections of SARS-CoV-2 in a community setting in England and Wales.\n\nMethodTrial emulation was conducted by pooling results from six cohorts whose recruitment was staggered between 1st January 2021 and 31st March 2021 and followed until 12th November 2021. Eligibility for each trial was based upon age (18+ at the time of vaccination), without prior signs of infection or an infection within the first 14 days of the first dose. Time from vaccination of ChAdOx1 or BNT162b2 until SARS-CoV-2 infection (positive polymerase chain reaction or lateral flow test after 14 of the vaccination) was modelled using Cox proportional hazards model for each cohort and adjusted for age at vaccination, gender, minority ethnic status, clinically vulnerable status and index of multiple deprivation quintile. For those without SARS-CoV-2 infection during the study period, follow-up was until loss-of-follow-up or end of study (12th November 2021). Pooled hazard ratios were generated using random-effects meta-analysis.\n\nResultsAcross six cohorts, there were a total of 21,283 participants who were eligible and vaccinated with either ChAdOx1 (n = 13,813) or BNT162b2 (n = 7,470) with a median follow-up time of 266 days (IQR: 235 - 282). By November 12th 2021, 750 (5.4%) adults who had ChAdOx1 as their vaccine experienced a SARS-CoV-2 infection, compared to 296 (4.0%) who had BNT162b2. We found that people who received ChAdOx1 vaccinations had 10.54 per 1000 people higher cumulative incidence for SARS-CoV-2 infection compared to BNT162b2 for infections during a maximum of 315 days of follow-up. When adjusted for age at vaccination, sex, minority ethnic status, index of multiple deprivation, and clinical vulnerability status, we found a pooled adjusted hazard ratio of 1.35 [HR: 1.35, 95%CI: 1.15 - 1.58], demonstrating a 35% increase in SARS-CoV-2 infections in people who received ChAdOx1 compared to BNT162b2.\n\nDiscussionWe found evidence of greater effectiveness of receiving BNT162b2 compared to ChAdOx1 vaccines against SARS-CoV-2 infection in England and Wales during a time period when Delta became the most prevalent variant of concern. Our findings demonstrate the importance of booster (third) doses to maintain protection and suggest that these should be prioritised to those who received ChAdOx1 as their primary course.",
-    "rel_num_authors": 17,
-    "rel_authors": [
-      {
-        "author_name": "Vincent Grigori Nguyen",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Alexei Yavlinsky",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Sarah Beale",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Susan J Hoskins",
-        "author_inst": "Univerity College London"
-      },
-      {
-        "author_name": "Vasileios Lampos",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Isobel Braithwaite",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Thomas Edward Byrne",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Wing Lam Erica Fong",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Ellen Fragaszy",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Cyril Geismar",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Jana Kovar",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Annalan M D Navaratnam",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Parth Patel",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Madhumita Shrotri",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Sophie Weber",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Andrew Hayward",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Robert W Aldridge",
-        "author_inst": "University College London"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.12.23.21267953",
     "rel_title": "Covid Vaccines for Children with Developmental Disabilities: Parent Survey of Willingness and Concerns",
@@ -454574,6 +453465,77 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2021.12.20.473471",
+    "rel_title": "Nucleocapsid 203 mutations enhance SARS-CoV-2 immune evasion",
+    "rel_date": "2021-12-23",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.20.473471",
+    "rel_abs": "Previous work indicated that the nucleocapsid 203 mutation increase the virulence and transmission of the SARS-CoV-2 Alpha variant. However, Delta later outcompeted Alpha and other lineages, promoting a new wave of infections. Delta also possesses a nucleocapsid 203 mutation, R203M. Large-scale epidemiological analyses suggest a synergistic effect of the 203 mutation and the spike L452R mutation, associated with Delta expansion. Viral competition experiments demonstrate the synergistic effect in fitness and infectivity. More importantly, we found that the combination of R203M and L452R brings in a 3.2-fold decrease in neutralizing titers to the neutralizing serum relative to L452R-only virus. R203M/L452R show an increased fitness after the initiation of global vaccination programmes, possibly associated with the enhanced immune evasion. Another rapidly emerging variant Omicron also bears the 203 mutation. Thus, we proposed that nucleocapsid mutations play an essential role for the rise and predominance of variants in concern.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Xiaoyuan Lin",
+        "author_inst": "School of Life Sciences, Chongqing University"
+      },
+      {
+        "author_name": "Weiwei Xue",
+        "author_inst": "School of Pharmaceutical Sciences, Chongqing University"
+      },
+      {
+        "author_name": "Yueping Zhang",
+        "author_inst": "College of Veterinary Medicine, China Agricultural University"
+      },
+      {
+        "author_name": "Beibei Fu",
+        "author_inst": "School of Life Sciences, Chongqing University"
+      },
+      {
+        "author_name": "Jakob Trimpert",
+        "author_inst": "Institute of Virology, Free University of Berlin"
+      },
+      {
+        "author_name": "Na Xing",
+        "author_inst": "Institute of Virology, Free University of Berlin"
+      },
+      {
+        "author_name": "Dusan Kunec",
+        "author_inst": "Institute of Virology, Free University of Berlin"
+      },
+      {
+        "author_name": "Wanyan Tang",
+        "author_inst": "Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital"
+      },
+      {
+        "author_name": "Yang Xiao",
+        "author_inst": "School of Life Sciences, Chongqing University"
+      },
+      {
+        "author_name": "Kaiwen Meng",
+        "author_inst": "College of Veterinary Medicine, China Agricultural University"
+      },
+      {
+        "author_name": "Shuobo Shi",
+        "author_inst": "College of Life Science and Technology, Beijing University of Chemical Technology"
+      },
+      {
+        "author_name": "Haibo Wu",
+        "author_inst": "School of Life Sciences, Chongqing University"
+      },
+      {
+        "author_name": "Geng Meng",
+        "author_inst": "College of Veterinary Medicine, China Agricultural University"
+      },
+      {
+        "author_name": "Zhenglin Zhu",
+        "author_inst": "School of Life Sciences, Chongqing University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2021.12.21.473268",
     "rel_title": "Efficacy of antiviral drugs against the omicron variant of SARS-CoV-2.",
@@ -456291,89 +455253,6 @@
     "type": "new results",
     "category": "biochemistry"
   },
-  {
-    "rel_doi": "10.1101/2021.12.18.473326",
-    "rel_title": "The P3 O-Tert-Butyl-Threonine is Key to High Cellular and Antiviral Potency for Aldehyde-Based SARS-CoV-2 Main Protease Inhibitors",
-    "rel_date": "2021-12-21",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.18.473326",
-    "rel_abs": "As an essential enzyme to SARS-CoV-2, main protease (MPro) is a viable target to develop antivirals for the treatment of COVID-19. By varying chemical compositions at both P2 and P3 sites and the N-terminal protection group, we synthesized a series of MPro inhibitors that contain {beta}-(S-2-oxopyrrolidin-3-yl)-alaninal at the P1 site. These inhibitors have a large variation of determined IC50 values that range from 4.8 to 650 nM. The determined IC50 values reveal that relatively small side chains at both P2 and P3 sites are favorable for achieving high in vitro MPro inhibition potency, the P3 site is tolerable toward unnatural amino acids with two alkyl substituents on the -carbon, and the inhibition potency is sensitive toward the N-terminal protection group. X-ray crystal structures of MPro bound with 16 inhibitors were determined. All structures show similar binding patterns of inhibitors at the MPro active site. A covalent interaction between the active site cysteine and a bound inhibitor was observed in all structures. In MPro, large structural variations were observed on residues N142 and Q189. All inhibitors were also characterized on their inhibition of MPro in 293T cells, which revealed their in cellulo potency that is drastically different from their in vitro enzyme inhibition potency. Inhibitors that showed high in cellulo potency all contain O-tert-butyl-threonine at the P3 site. Based on the current and a previous study, we conclude that O-tert-butyl-threonine at the P3 site is a key component to achieve high cellular and antiviral potency for peptidyl aldehyde inhibitors of MPro. This finding will be critical to the development of novel antivirals to address the current global emergency of concerning the COVID-19 pandemic.",
-    "rel_num_authors": 17,
-    "rel_authors": [
-      {
-        "author_name": "Yuying Ma",
-        "author_inst": "Texas A&M University"
-      },
-      {
-        "author_name": "Kai Yang",
-        "author_inst": "Texas A&M University"
-      },
-      {
-        "author_name": "Zhi Zachary Geng",
-        "author_inst": "Texas A&M University"
-      },
-      {
-        "author_name": "Yugendar R. Alugubellia",
-        "author_inst": "Texas A&M University"
-      },
-      {
-        "author_name": "Namir Shaabani",
-        "author_inst": "Sorrento Therapeutics"
-      },
-      {
-        "author_name": "Erol C. Vatansever",
-        "author_inst": "Texas A&M University"
-      },
-      {
-        "author_name": "Xinyu R. Ma",
-        "author_inst": "Texas A&M University"
-      },
-      {
-        "author_name": "Chia-Chuan Cho",
-        "author_inst": "Texas A&M University"
-      },
-      {
-        "author_name": "Kaustav Khatua",
-        "author_inst": "Texas A&M University"
-      },
-      {
-        "author_name": "Lauren Blankenship",
-        "author_inst": "Texas A&M University"
-      },
-      {
-        "author_name": "Ge Yu",
-        "author_inst": "Texas A&M University"
-      },
-      {
-        "author_name": "Banumathi Sankaran",
-        "author_inst": "Laurence Berkeley National Laboratory"
-      },
-      {
-        "author_name": "Pingwei Li",
-        "author_inst": "Texas A&M University"
-      },
-      {
-        "author_name": "Robert Allen",
-        "author_inst": "Sorrento Therapeutics"
-      },
-      {
-        "author_name": "Henry Ji",
-        "author_inst": "Sorrento Therapeutics"
-      },
-      {
-        "author_name": "Shiqing Xu",
-        "author_inst": "Texas A&M University"
-      },
-      {
-        "author_name": "Wenshe Ray Liu",
-        "author_inst": "Texas A&M University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "biochemistry"
-  },
   {
     "rel_doi": "10.1101/2021.12.20.473401",
     "rel_title": "Arsenal of Nanobodies for Broad-Spectrum Countermeasures against Current and Future SARS-CoV-2 Variants of Concerns",
@@ -457100,6 +455979,29 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2021.12.19.21268042",
+    "rel_title": "Government messaging about COVID-19 vaccination in Canada and Australia: a Narrative Policy Framework study",
+    "rel_date": "2021-12-21",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.19.21268042",
+    "rel_abs": "BackgroundStorytelling and narratives are critical components to public policy and have been central to public policy communicators throughout the COVID-19 pandemic.\n\nAimThis study applied the Narrative Policy Framework to compare and contrast the policy narratives of the Canadian and Australian Prime Ministers regarding COVID-19 vaccination.\n\nMethodsOfficial media releases, transcripts and speeches published on the websites of Prime Minister Morrison and Prime Minister Trudeau between 31 August 2020 and 10 September 2021 relating to COVID-19 vaccines were thematically analysed according to the Narrative Policy Framework.\n\nResultsThe policy narratives of Scott Morrison and Justin Trudeau tended towards describing both governments as heroes for securing and rolling out vaccines. Trudeau tended to focus on the villain of COVID-19 while Morrison regularly described other countries as victims of COVID-19 to position Australia as superior in its decision-making. These findings also demonstrate how narratives shifted over time due to changing COVID-19 case numbers, emergence of rare complications associated with the AstraZeneca vaccine and as new information arose.\n\nConclusionThese findings offer lessons for COVID-19 times as well as future pandemics and disease outbreaks by providing insight into how policy narratives influenced policy processes in both Australia and Canada.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Freya Saich",
+        "author_inst": "University of Sydney"
+      },
+      {
+        "author_name": "Alexandra Martiniuk",
+        "author_inst": "University of Sydney"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health policy"
+  },
   {
     "rel_doi": "10.1101/2021.12.17.21267976",
     "rel_title": "Sputnik Light booster after Sputnik V vaccination induces robust neutralizing antibody response to B.1.1.529 (Omicron) SARS-CoV-2 variant",
@@ -458644,45 +457546,6 @@
     "type": "new results",
     "category": "biochemistry"
   },
-  {
-    "rel_doi": "10.1101/2021.12.19.21268060",
-    "rel_title": "Orthostatic intolerance in adults with long COVID was not associated with postural orthostatic tachycardia syndrome",
-    "rel_date": "2021-12-21",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.19.21268060",
-    "rel_abs": "In this observational cross-sectional study, we investigated predictors of orthostatic intolerance (OI) in adults with long COVID. Participants underwent a 3-minute active stand (AS) with Finapres(R) NOVA, followed by a 10-minute unmedicated 70-degree head-up tilt test. 85 participants were included (mean age 46 years, range 25-78; 74% women), of which 56 (66%) reported OI during AS (OIAS). OIAS seemed associated with female sex, more fatigue and depressive symptoms, and greater inability to perform activities of daily living (ADL), as well as a higher heart rate (HR) at the lowest systolic blood pressure (SBP) point before the 1st minute post-stand (mean HRnadir: 88 vs 75 bpm, P=0.004). In a regression model also including age, sex, fatigue, depression, ADL inability, and peak HR after the nadir SBP, HRnadir was the only OIAS predictor (OR=1.09, 95% CI: 1.01-1.18, P=0.027). 22 participants had initial (iOH) and 5 classical (cOH) orthostatic hypotension, but neither correlated with OIAS. 71 participants proceeded to tilt, of which 28 had OI during tilt (OItilt). Of the 53 who had a 10-minute tilt, 7 (13%) fulfilled hemodynamic postural orthostatic tachycardia syndrome (POTS) criteria, but 6 did not report OItilt. OIAS was associated with a higher initial HR on AS, which after 1 minute equalized with the non-OIAS group. Despite these initial orthostatic HR differences, POTS was infrequent and largely asymptomatic. ClinicalTrials.gov Identifier: NCT05027724 (retrospectively registered on August 30, 2021).",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Ann Monaghan",
-        "author_inst": "Trinity College Dublin"
-      },
-      {
-        "author_name": "Glenn Jennings",
-        "author_inst": "Trinity College Dublin"
-      },
-      {
-        "author_name": "Feng Xue",
-        "author_inst": "Trinity College Dublin"
-      },
-      {
-        "author_name": "Lisa Byrne",
-        "author_inst": "St James's Hospital, Dublin"
-      },
-      {
-        "author_name": "Eoin Duggan",
-        "author_inst": "Trinity College Dublin"
-      },
-      {
-        "author_name": "Roman Romero-Ortuno",
-        "author_inst": "Trinity College Dublin"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "cardiovascular medicine"
-  },
   {
     "rel_doi": "10.1101/2021.12.16.21267766",
     "rel_title": "High-Quality and Easy-to-Regenerate Personal Filter",
@@ -459297,6 +458160,125 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.12.18.21267628",
+    "rel_title": "RESISTANCE CONFERRING MUTATIONS IN SARS-CoV-2 DELTA FOLLOWING SOTROVIMAB INFUSION",
+    "rel_date": "2021-12-21",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.18.21267628",
+    "rel_abs": "Several Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) neutralising monoclonal antibodies (mAbs) have received emergency use authorisation by regulatory agencies for treatment and prevention of Coronavirus Disease 2019 (COVID-19), including in patients at risk for progression to severe disease. Here we report the persistence of viable SARS-CoV-2 in patients treated with sotrovimab and the rapid development of spike gene mutations that have been shown to confer high level resistance to sotrovimab in vitro. We highlight the need for SARS-CoV-2 genomic surveillance in at risk individuals to inform stewardship of mAbs use and prevent potential treatment failures.",
+    "rel_num_authors": 26,
+    "rel_authors": [
+      {
+        "author_name": "Rebecca J Rockett",
+        "author_inst": "Sydney Institute of Infectious Diseases, University of Sydney, Sydney, New South Wales, Australia"
+      },
+      {
+        "author_name": "Kerri Basile",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology, Institute for Clinical Pathology and Medical Research, We"
+      },
+      {
+        "author_name": "Susan Maddocks",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology, Institute for Clinical Pathology and Medical Research, We"
+      },
+      {
+        "author_name": "Winkie Fong",
+        "author_inst": "Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia"
+      },
+      {
+        "author_name": "Jessica E Agius",
+        "author_inst": "Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia"
+      },
+      {
+        "author_name": "Jessica Johnson-Mackinnon",
+        "author_inst": "Sydney Institute of Infectious Diseases, University of Sydney, Sydney, New South Wales, Australia"
+      },
+      {
+        "author_name": "Alicia Arnott",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology, Institute for Clinical Pathology and Medical Research, We"
+      },
+      {
+        "author_name": "Shona Chandra",
+        "author_inst": "Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia"
+      },
+      {
+        "author_name": "Mailie Gall",
+        "author_inst": "Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia"
+      },
+      {
+        "author_name": "Jenny L Draper",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology, Institute for Clinical Pathology and Medical Research, We"
+      },
+      {
+        "author_name": "Elena Martinez",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology, Institute for Clinical Pathology and Medical Research, We"
+      },
+      {
+        "author_name": "Eby M Sim",
+        "author_inst": "Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia"
+      },
+      {
+        "author_name": "Clement Lee",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology, Institute for Clinical Pathology and Medical Research, We"
+      },
+      {
+        "author_name": "Christine Ngo",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology, Institute for Clinical Pathology and Medical Research, We"
+      },
+      {
+        "author_name": "Marc Ramsperger",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology, Institute for Clinical Pathology and Medical Research, We"
+      },
+      {
+        "author_name": "Andrew N Ginn",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology, Institute for Clinical Pathology and Medical Research, We"
+      },
+      {
+        "author_name": "Qinning Wang",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology, Institute for Clinical Pathology and Medical Research, We"
+      },
+      {
+        "author_name": "Michael Fennell",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology, Institute for Clinical Pathology and Medical Research, We"
+      },
+      {
+        "author_name": "Danny Ko",
+        "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, New South Wales Health Pathology, Institute for Clinical Pathology and Medical Research, We"
+      },
+      {
+        "author_name": "Ling Lim",
+        "author_inst": "Parramatta Public Health Unit, Western Sydney Local Health District, Parramatta, New South Wales, Australia"
+      },
+      {
+        "author_name": "Nicky Gilroy",
+        "author_inst": "Department of Infectious Diseases, Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia"
+      },
+      {
+        "author_name": "Matthew VN Sullivan",
+        "author_inst": "Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia"
+      },
+      {
+        "author_name": "Sharon C-A Chen",
+        "author_inst": "Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia"
+      },
+      {
+        "author_name": "Jen Kok",
+        "author_inst": "Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia"
+      },
+      {
+        "author_name": "Dominic E Dwyer",
+        "author_inst": "Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia"
+      },
+      {
+        "author_name": "Vitali L Sintchenko",
+        "author_inst": "Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, Australia"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.12.17.21267927",
     "rel_title": "Evaluation of the Roche SARS-CoV-2 Rapid Antibody Test in samples from vaccinated individuals",
@@ -460762,29 +459744,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.12.20.473542",
-    "rel_title": "Structural flexibility of the SARS-CoV-2 genome relevant to variation, replication, pathogenicity, and immune evasion.",
-    "rel_date": "2021-12-21",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.20.473542",
-    "rel_abs": "The SARS-CoV-2 pandemic continues to be driven by viral variants. Most research has focused on structural proteins and on site-specific mutations. Here, we describe recombination events involving genomic terminal sequences in SARS-CoV-2 and related viruses leading to structural rearrangements in terminal and coding regions and discuss their potential contributions to viral variation, replication, pathogenicity, and immune evasion.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Roberto Patarca",
-        "author_inst": "ACCESS Health International"
-      },
-      {
-        "author_name": "William A. Haseltine",
-        "author_inst": "ACCESS Health International"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2021.12.16.472391",
     "rel_title": "Reduced sera neutralization to Omicron SARS-CoV-2 by bothinactivated and protein subunit vaccines and the convalescents",
@@ -461087,6 +460046,25 @@
     "type": "new results",
     "category": "biophysics"
   },
+  {
+    "rel_doi": "10.1101/2021.12.17.473179",
+    "rel_title": "Disrupted Peyer's patch microanatomy in COVID-19 including germinal centre atrophy independent of local virus",
+    "rel_date": "2021-12-20",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.17.473179",
+    "rel_abs": "Confirmed SARS-coronavirus-2 infection with gastrointestinal symptoms and changes in microbiota associated with coronavirus disease 2019 (COVID-19) severity have been previously reported, but the disease impact on the architecture and cellularity of ileal Peyers patches (PP) remains unknown. Here we analysed post-mortem tissues from throughout the gastrointestinal (GI) tract of patients who died with COVID-19. When virus was detected by PCR in the GI tract, immunohistochemistry identified virus in epithelium and lamina propria macrophages, but not in lymphoid tissues. Immunohistochemistry and imaging mass cytometry (IMC) analysis of ileal PP revealed depletion of germinal centres (GC), disruption of B cell/T cell zonation and decreased potential B and T cell interaction and lower nuclear density in COVID-19 patients. This occurred independent of the local viral levels. The changes in PP demonstrate that the ability to mount an intestinal immune response is compromised in severe COVID-19, which could contribute to observed dysbiosis.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Manu Shankar-Hari",
+        "author_inst": "The University of Edinburgh"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2021.12.17.473180",
     "rel_title": "Insights into standards of care: dexamethasone and antibodies against COVID-19 in hamster models",
@@ -462524,37 +461502,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.12.17.21267995",
-    "rel_title": "Syndromic Surveillance-Based Estimates of Vaccine Efficacy Against COVID-Like Illness from Emerging Omicron and COVID-19 Variants",
-    "rel_date": "2021-12-18",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.17.21267995",
-    "rel_abs": "New infections from the omicron variant of SARS-CoV-2 have been increasing dramatically in South Africa since first identification in November 2021. Despite increasing uptake of COVID-19 vaccine, there are concerns vaccine protection against omicron may be reduced compared to other variants. We sought to characterize a surrogate measure of vaccine efficacy in Gauteng, South Africa by leveraging real-time syndromic surveillance data. The University of Maryland Global COVID Trends and Impact Survey (UMD-CTIS) is an online, cross-sectional survey conducted among users sampled from the Facebook active user base. We derived three COVID-like illness (CLI) definitions (stringent, classic, and broad) using combinations of self-reported symptoms (present or not in the prior 24 hours) that broadly tracked with reported COVID-19 cases during June 18, 2021 - December 14, 2021 (inclusive of the delta wave and up-trend of the omicron wave). We used syndromic-surveillance-based CLI prevalence measures among the vaccinated (PV) and unvaccinated (PU) respondents to estimate V ECLIP = 1 - (PV /PU), a proxy for vaccine efficacy, during the delta (June 18-July 18, N= 9,387 surveys) and omicron (December 4-14, N= 2,389 surveys) wave periods. We assume no waning immunity, CLI prevalence approximates incident infection with each variant, and vaccinated and unvaccinated survey respondents in the two variant wave periods are exchangeable. The vaccine appears to have consistently lower V ECLIP against omicron, compared to delta, regardless of the CLI definition used. Stringent CLI (i.e. anosmia plus fever, cough and/or myalgias) yielded a delta V ECLIP = 0.85 [0.54, 0.95] higher than omicron V ECLIP = 0.62 [0.46, 0.72]. Classic CLI (cough plus anosmia, fever, and/or myalgias) gave lower estimates (delta V ECLIP = 0.76 [0.54, 0.87], omicron V ECLIP = 0.51 [0.42, 0.59]), but omicron was still lower than delta. We acknowledge the potential for measurement, confounding, and selection bias, as well as limitations for generalizability for these self-reported, syndromic surveillance-based V ECLIP measures. Thus V ECLIP as estimates of true, population-level vaccine efficacy should therefore be taken with caution. Nevertheless, these preliminary findings demonstrating declining V ECLIP raise concern for a true decline in vaccine efficacy versus waning immunity as a potential contributor to the omicron variant taking hold in Gauteng and elsewhere.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Tanner J Varrelman",
-        "author_inst": "Boston Children's Hospital"
-      },
-      {
-        "author_name": "Benjamin M Rader",
-        "author_inst": "Boston University"
-      },
-      {
-        "author_name": "Christina M Astley",
-        "author_inst": "Boston Children's Hospital"
-      },
-      {
-        "author_name": "John S Brownstein",
-        "author_inst": "Boston Children's Hospital"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.12.17.21267997",
     "rel_title": "Perceptions and Attitudes Towards COVID-19 Vaccination Amongst Pregnant and Postpartum Individuals",
@@ -462841,6 +461788,125 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.12.15.472838",
+    "rel_title": "A third vaccination with a single T cell epitope protects against SARS-CoV-2 infection in the absence of neutralizing antibodies",
+    "rel_date": "2021-12-18",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.15.472838",
+    "rel_abs": "Understanding the mechanisms and impact of booster vaccinations can facilitate decisions on vaccination programmes. This study shows that three doses of the same synthetic peptide vaccine eliciting an exclusive CD8+ T cell response against one SARS-CoV-2 Spike epitope protected all mice against lethal SARS-CoV-2 infection in the K18-hACE2 transgenic mouse model in the absence of neutralizing antibodies, while only a second vaccination with this T cell vaccine was insufficient to provide protection. The third vaccine dose of the single T cell epitope peptide resulted in superior generation of effector-memory T cells in the circulation and tissue-resident memory T (TRM) cells, and these tertiary vaccine-specific CD8+ T cells were characterized by enhanced polyfunctional cytokine production. Moreover, fate mapping showed that a substantial fraction of the tertiary effector-memory CD8+ T cells developed from remigrated TRM cells. Thus, repeated booster vaccinations quantitatively and qualitatively improve the CD8+ T cell response leading to protection against otherwise lethal SARS-CoV-2 infection.\n\nSummaryA third dose with a single T cell epitope-vaccine promotes a strong increase in tissue-resident memory CD8+ T cells and fully protects against SARS-CoV-2 infection, while single B cell epitope-eliciting vaccines are unable to provide protection.",
+    "rel_num_authors": 26,
+    "rel_authors": [
+      {
+        "author_name": "Iris N. Pardieck",
+        "author_inst": "Leiden University Medical Center"
+      },
+      {
+        "author_name": "Esme T.I. van der Gracht",
+        "author_inst": "Leiden University Medical Center"
+      },
+      {
+        "author_name": "Dominique M.B. Veerkamp",
+        "author_inst": "Leiden University Medical Center"
+      },
+      {
+        "author_name": "Felix M. Behr",
+        "author_inst": "Leiden University Medical Center"
+      },
+      {
+        "author_name": "Suzanne van Duikeren",
+        "author_inst": "Leiden University Medical Center"
+      },
+      {
+        "author_name": "Guillaume Beyrend",
+        "author_inst": "Leiden University Medical Center"
+      },
+      {
+        "author_name": "Jasper Rip",
+        "author_inst": "Leiden University Medical Center"
+      },
+      {
+        "author_name": "Reza Nadafi",
+        "author_inst": "Leiden University Medical Center"
+      },
+      {
+        "author_name": "Tetje C. van der Sluis",
+        "author_inst": "Leiden University Medical Center"
+      },
+      {
+        "author_name": "Elham Beyranvand Nejad",
+        "author_inst": "Leiden University Medical Center"
+      },
+      {
+        "author_name": "Nils Mulling",
+        "author_inst": "Leiden University Medical Center"
+      },
+      {
+        "author_name": "Dena J. Brasem",
+        "author_inst": "Leiden University Medical Center"
+      },
+      {
+        "author_name": "Marcel G.M. Camps",
+        "author_inst": "Leiden University Medical Center"
+      },
+      {
+        "author_name": "Sebenzile K. Myeni",
+        "author_inst": "Leiden University Medical Center"
+      },
+      {
+        "author_name": "Peter J. Bredenbeek",
+        "author_inst": "Leiden University Medical Center"
+      },
+      {
+        "author_name": "Marjolein Kikkert",
+        "author_inst": "Leiden University Medical Center"
+      },
+      {
+        "author_name": "Yeonsu Kim",
+        "author_inst": "Helmholtz Centre for Infection Research"
+      },
+      {
+        "author_name": "Luka Cicin-Sain",
+        "author_inst": "Helmholtz Centre for Infection Research"
+      },
+      {
+        "author_name": "Tamim Abdelaal",
+        "author_inst": "Leiden University Medical Center"
+      },
+      {
+        "author_name": "Klaas P.J.M. van Gisbergen",
+        "author_inst": "Sanquin Research and Landsteiner Laboratory"
+      },
+      {
+        "author_name": "Kees L.M.C. Franken",
+        "author_inst": "Leiden University Medical Center"
+      },
+      {
+        "author_name": "Jan Wouter Drijfhout",
+        "author_inst": "Leiden University Medical Center"
+      },
+      {
+        "author_name": "Cornelius J.M. Melief",
+        "author_inst": "ISA Pharmaceuticals"
+      },
+      {
+        "author_name": "Gerben C.M. Zondag",
+        "author_inst": "Immunetune"
+      },
+      {
+        "author_name": "Ferry Ossendorp",
+        "author_inst": "Leiden University Medical Center"
+      },
+      {
+        "author_name": "Ramon Arens",
+        "author_inst": "Leiden University Medical Center"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2021.12.16.21267959",
     "rel_title": "Social mixing patterns relevant to infectious diseases spread by close contact in urban Blantyre, Malawi.",
@@ -464518,53 +463584,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.12.15.472864",
-    "rel_title": "A recurring YYDRxG pattern in broadly neutralizing antibodies to a conserved site on SARS-CoV-2, variants of concern, and related viruses",
-    "rel_date": "2021-12-17",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.15.472864",
-    "rel_abs": "Studying the antibody response to SARS-CoV-2 informs on how the human immune system can respond to antigenic variants as well as other SARS-related viruses. Here, we structurally and functionally characterized a potent human antibody ADI-62113 that also neutralizes SARS-CoV- 2 variants of concern and cross-reacts with many other sarbecoviruses. A YYDRxG motif encoded by IGHD3-22 in CDR H3 facilitates targeting to a highly conserved epitope on the SARS-CoV-2 receptor binding domain. A computational search for a YYDRxG pattern in publicly available sequences identified many antibodies with broad neutralization activity against SARS-CoV-2 variants and SARS-CoV. Thus, the YYDRxG motif represents a common convergent solution for the human humoral immune system to counteract sarbecoviruses. These findings also suggest an epitope targeting strategy to identify potent and broadly neutralizing antibodies that can aid in the design of pan-sarbecovirus vaccines and antibody therapeutics.\n\nShort SummaryDecryption of a recurrent sequence feature in anti-SARS-CoV-2 antibodies identifies how potent pan-sarbecovirus antibodies target a conserved epitope on the receptor binding domain.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Hejun Liu",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "Chengzi I. Kaku",
-        "author_inst": "Adimab, LLC"
-      },
-      {
-        "author_name": "Ge Song",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "Meng Yuan",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "Raiees Andrabi",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "Dennis R. Burton",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "Laura M. Walker",
-        "author_inst": "Adimab, LLC"
-      },
-      {
-        "author_name": "Ian A. Wilson",
-        "author_inst": "The Scripps Research Institute"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2021.12.15.472874",
     "rel_title": "Distinguishing COVID-19 infection and vaccination history by T cell reactivity",
@@ -464931,6 +463950,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "intensive care and critical care medicine"
   },
+  {
+    "rel_doi": "10.1101/2021.12.16.472920",
+    "rel_title": "Amyloidogenesis of SARS-CoV-2 Spike Protein",
+    "rel_date": "2021-12-17",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.16.472920",
+    "rel_abs": "SARS-CoV-2 infection is associated with a surprising number of morbidities. Uncanny similarities with amyloid-disease associated blood coagulation and fibrinolytic disturbances together with neurologic and cardiac problems led us to investigate the amyloidogenicity of the SARS-CoV-2 Spike protein (S-protein). Amyloid fibril assays of peptide library mixtures and theoretical predictions identified seven amyloidogenic sequences within the S-protein. All seven peptides in isolation formed aggregates during incubation at 37{degrees}C. Three 20-amino acid long synthetic Spike peptides (sequence 191-210, 599-618, 1165-1184) fulfilled three amyloid fibril criteria: nucleation dependent polymerization kinetics by ThT, Congo red positivity and ultrastructural fibrillar morphology. Full-length folded S-protein did not form amyloid fibrils, but amyloid-like fibrils with evident branching were formed during 24 hours of S-protein co-incubation with the protease neutrophil elastase (NE) in vitro. NE efficiently cleaved S-protein rendering exposure of amyloidogenic segments and accumulation of the peptide 193-202, part of the most amyloidogenic synthetic Spike peptide. NE is overexpressed at inflamed sites of viral infection and at vaccine injection sites. Our data propose a molecular mechanism for amyloidogenesis of SARS-CoV-2 S-protein in humans facilitated by endoproteolysis. The potential implications of S-protein amyloidogenesis in COVID-19 disease associated pathogenesis and consequences following S-protein based vaccines should be addressed in understanding the disease, long COVID-19, and vaccine side effects.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Sofie Nystrom",
+        "author_inst": "Linkoping University"
+      },
+      {
+        "author_name": "Per Hammarstrom",
+        "author_inst": "Linkoping University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "biochemistry"
+  },
   {
     "rel_doi": "10.1101/2021.12.14.21267810",
     "rel_title": "Early detection and improved genomic surveillance of SARS-CoV-2 variants from deep sequencing data",
@@ -466204,45 +465246,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "respiratory medicine"
   },
-  {
-    "rel_doi": "10.1101/2021.12.15.21267872",
-    "rel_title": "Epidemiological analysis of hospitalized cases of COVID-19 in in-digenous people in an Amazonian region: cross-sectional study with data from the surveillance of acute and severe respiratory syn-dromes in Brazil",
-    "rel_date": "2021-12-16",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.15.21267872",
-    "rel_abs": "Indigenous people are considered more vulnerable to new infectious agents. In view of the novel coronavirus causing COVID-19, health authorities are concerned about the possible impact of the pandemic on reaching vulnerable populations, such as the indigenous people of the Brazilian Amazon. Thus, we aimed to carry out an epidemiological analysis of serious cases and deaths from COVID-19 in indigenous population in the state of Para, Brazil. The data was obtained from the public Ministry of Health platform. Data analysis was performed using the Statistical Package for the Social Sciences 20, Chi-square of adherence, the independence test and G test. For spatial distribution was used ArcGIS. We observed 123 COVID-19 cases: 46 deaths (37.40%), male gender (76-61.79%), age above 60 years (61-49.6%), the most frequent risk factor was chronic cardiovascular disease (18-14.63%). The predictors of death were: invasive ventilation has (10.73) more chances for the outcome death, those not vaccinated against influenza have (3.41) and age (1.4). COVID-19 occurrence was higher in municipalities that have villages with health care or commerce, or with migrants from the Warao ethnic group. Notifications should take into consideration the specific issues of indigenous people so that effective control measures can be defined.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Ana Lucia da Silva Ferreira",
-        "author_inst": "Universidade do Estado do Para"
-      },
-      {
-        "author_name": "Daniele Melo Sardinha",
-        "author_inst": "Instituto Evandro Chagas"
-      },
-      {
-        "author_name": "Claudia Ozela El-husny",
-        "author_inst": "Universidade do Estado do Para"
-      },
-      {
-        "author_name": "Carmem Aliandra Freire de Sa",
-        "author_inst": "Instituto Evandro Chagas"
-      },
-      {
-        "author_name": "Emilyn Costa Conceicao",
-        "author_inst": "Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa"
-      },
-      {
-        "author_name": "Karla Valeria Batista Lima",
-        "author_inst": "Universidade do Estado do Para"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "respiratory medicine"
-  },
   {
     "rel_doi": "10.1101/2021.12.15.21267794",
     "rel_title": "Changing of therapeutic trends between the 1st and 2nd wave did not reduce COVID-19 related mortality of renal transplant recipients: a national registry study.",
@@ -466609,6 +465612,69 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.12.14.21267199",
+    "rel_title": "The COVID-19 pandemic amplified long-standing racial disparities in the United States criminal justice system",
+    "rel_date": "2021-12-16",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.14.21267199",
+    "rel_abs": "The criminal legal system in the United States drives an incarceration rate that is the highest on the planet, with disparities by class and race among its signature features [1-3]. During the first year of the COVID-19 pandemic, the number of incarcerated people in the U.S. decreased by at least 17%--the largest, fastest reduction in prison population in American history [4]. In this study, we ask how this reduction influenced the racial com-position of U.S. prisons, and consider possible mechanisms for these dynamics. Using an original dataset curated from public sources on prison demographics across all 50 states and the District of Columbia, we show that incarcerated white people benefited disproportionately from the decrease in the U.S. prison population, and that the fraction of incarcerated Black and Latino people sharply increased. This pattern of increased racial disparity exists across prison systems in nearly every state and reverses a decades-long trend before 2020 and the onset of COVID-19, when the proportion of incarcerated white people was increasing amid declining numbers of incarcerated Black people [5]. Although a variety of factors underlie these trends, we find that racial inequities in average sentence length are a major contributor. Ultimately, this study reveals how disruptions caused by COVID-19 exacer-bated racial inequalities in the criminal legal system, and highlights key forces that sustain mass incarceration.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Brennan Klein",
+        "author_inst": "Northeastern University Network Science Institute"
+      },
+      {
+        "author_name": "C. Brandon Ogbunugafor",
+        "author_inst": "Yale University"
+      },
+      {
+        "author_name": "Benjamin J. Schafer",
+        "author_inst": "Yale University"
+      },
+      {
+        "author_name": "Zarana Bhadricha",
+        "author_inst": "Northeastern University"
+      },
+      {
+        "author_name": "Preeti Kori",
+        "author_inst": "Northeastern University"
+      },
+      {
+        "author_name": "Jim Sheldon",
+        "author_inst": "Northeastern University"
+      },
+      {
+        "author_name": "Nitish Kaza",
+        "author_inst": "Northeastern University"
+      },
+      {
+        "author_name": "Arush Sharma",
+        "author_inst": "Northeastern University"
+      },
+      {
+        "author_name": "Emily A. Wang",
+        "author_inst": "Yale University"
+      },
+      {
+        "author_name": "Tina Eliassi-Rad",
+        "author_inst": "Northeastern University Network Science Institute"
+      },
+      {
+        "author_name": "Samuel V. Scarpino",
+        "author_inst": "Northeastern University"
+      },
+      {
+        "author_name": "Elizabeth Hinton",
+        "author_inst": "Yale University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.12.14.21267809",
     "rel_title": "mRNA COVID-19 vaccine effectiveness against SARS-CoV-2 infection in a prospective community cohort, rural Wisconsin, November 2020-December 2021",
@@ -468485,161 +467551,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
-  {
-    "rel_doi": "10.1101/2021.12.14.21267689",
-    "rel_title": "Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and SARS-CoV-2 variants",
-    "rel_date": "2021-12-15",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.14.21267689",
-    "rel_abs": "The COVID-19 pandemic has demonstrated a clear need for high-throughput, multiplexed, and sensitive assays for detecting SARS-CoV-2 and other respiratory viruses as well as their emerging variants. Here, we present microfluidic CARMEN (mCARMEN), a cost-effective virus and variant detection platform that combines CRISPR-based diagnostics and microfluidics with a streamlined workflow for clinical use. We developed the mCARMEN respiratory virus panel (RVP) and demonstrated its diagnostic-grade performance on 533 patient specimens in an academic setting and then 166 specimens in a clinical setting. We further developed a panel to distinguish 6 SARS-CoV-2 variant lineages, including Delta and Omicron, and evaluated it on 106 patient specimens, with near-perfect concordance to sequencing-based variant classification. Lastly, we implemented a combined Cas13 and Cas12 approach that enables quantitative measurement of viral copies in samples. mCARMEN enables high-throughput surveillance of multiple viruses and variants simultaneously.",
-    "rel_num_authors": 35,
-    "rel_authors": [
-      {
-        "author_name": "Nicole L Welch",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard; Harvard Program in Virology"
-      },
-      {
-        "author_name": "Meilin Zhu",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard"
-      },
-      {
-        "author_name": "Catherine Hau",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard"
-      },
-      {
-        "author_name": "Juliane Weller",
-        "author_inst": "Wellcome Sanger Institute"
-      },
-      {
-        "author_name": "Marzieh Ezzaty Mirhashemi",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard"
-      },
-      {
-        "author_name": "Sreekar Mantena",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard"
-      },
-      {
-        "author_name": "Tien G Nguyen",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard"
-      },
-      {
-        "author_name": "Bennett Shaw",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard; Massachusetts General Hospital"
-      },
-      {
-        "author_name": "Cheri M Ackerman",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard"
-      },
-      {
-        "author_name": "Sri Gowtham Thakku",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard"
-      },
-      {
-        "author_name": "Megan W Tse",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard"
-      },
-      {
-        "author_name": "Jared Kehe",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard"
-      },
-      {
-        "author_name": "Matthew R Bauer",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard"
-      },
-      {
-        "author_name": "Maria-Martine Uwera",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard"
-      },
-      {
-        "author_name": "Jacqueline S Eversley",
-        "author_inst": "Massachusetts General Hospital"
-      },
-      {
-        "author_name": "Derek A Bielawski",
-        "author_inst": "Massachusetts General Hospital"
-      },
-      {
-        "author_name": "Graham McGrath",
-        "author_inst": "Massachusetts General Hospital"
-      },
-      {
-        "author_name": "Joseph Braidt",
-        "author_inst": "Massachusetts General Hospital"
-      },
-      {
-        "author_name": "Jeremy Johnson",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard"
-      },
-      {
-        "author_name": "Felecia Cerrato",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard"
-      },
-      {
-        "author_name": "Brittany A Petros",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard"
-      },
-      {
-        "author_name": "Gabi L Gionet",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard"
-      },
-      {
-        "author_name": "Samantha K Jalbert",
-        "author_inst": "Harvard Medical School"
-      },
-      {
-        "author_name": "Michael L Cleary",
-        "author_inst": "Harvard Medical School"
-      },
-      {
-        "author_name": "Katherine J Siddle",
-        "author_inst": "Broad Institute"
-      },
-      {
-        "author_name": "Christain T Happi",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard; African Centre of Excellence for Genomics of Infectious Diseases (ACEGID)"
-      },
-      {
-        "author_name": "Deborah T Hung",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard"
-      },
-      {
-        "author_name": "Michael Springer",
-        "author_inst": "Harvard Medical School"
-      },
-      {
-        "author_name": "Bronwyn MacInnis",
-        "author_inst": "Broad Institute"
-      },
-      {
-        "author_name": "Jacob Lemieux",
-        "author_inst": "Broad Institute"
-      },
-      {
-        "author_name": "Eric S Rosenberg",
-        "author_inst": "Massachusetts General Hospital"
-      },
-      {
-        "author_name": "John A Branda",
-        "author_inst": "Massachusetts General Hospital"
-      },
-      {
-        "author_name": "Paul C Blainey",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard"
-      },
-      {
-        "author_name": "Pardis Sabeti",
-        "author_inst": "Harvard University; The Broad Institute or MIT and Harvard; Howard Hughes Medical Institute"
-      },
-      {
-        "author_name": "Cameron Myhrvold",
-        "author_inst": "Princeton University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.12.14.21267783",
     "rel_title": "Dynamics of anti-Spike IgG antibody level after full BNT162b2 COVID-19 vaccination in health care workers",
@@ -469038,6 +467949,81 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "allergy and immunology"
   },
+  {
+    "rel_doi": "10.1101/2021.12.14.21267460",
+    "rel_title": "Differential Risk of SARS-CoV-2 Infection by Occupation: Evidence from the Virus Watch prospective cohort study in England and Wales",
+    "rel_date": "2021-12-15",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.14.21267460",
+    "rel_abs": "BackgroundWorkers differ in their risk of SARS-CoV-2 infection according to their occupation, but the direct contribution of occupation to this relationship is unclear. This study aimed to investigate how infection risk differed across occupational groups in England and Wales up to April 2022, after adjustment for potential confounding and stratification by pandemic phase.\n\nMethodsData from 15,190 employed/self-employed participants in the Virus Watch prospective cohort study were used to generate risk ratios for virologically- or serologically-confirmed SARS-CoV-2 infection using robust Poisson regression, adjusting for socio-demographic and health-related factors and non-work public activities. We calculated attributable fractions (AF) amongst the exposed for belonging to each occupational group based on adjusted risk ratios (aRR).\n\nFindingsIncreased risk was seen in nurses (aRR=1.44, 1.25-1.65; AF=30%, 20-39%), doctors (aRR=1.33, 1.08-1.65; AF=25%, 7-39%), carers (1.45, 1.19-1.76; AF=31%, 16-43%), primary school teachers (aRR=1.67, 1.42-1.96; AF=40%, 30-49%), secondary school teachers (aRR=1.48, 1.26-1.72; AF=32%, 21-42%), and teaching support occupations (aRR=1.42, 1.23-1.64; AF=29%, 18-39%) compared to office-based professional occupations. Differential risk was apparent in the earlier phases (Feb 2020 - May 2021) and attenuated later (June - October 2021) for most groups, although teachers and teaching support workers demonstrated persistently elevated risk across waves.\n\nInterpretationOccupational differentials in SARS-CoV-2 infection risk vary over time and are robust to adjustment for socio-demographic, health-related, and non-workplace activity-related potential confounders. Direct investigation into workplace factors underlying elevated risk and how these change over time is needed to inform occupational health interventions.",
+    "rel_num_authors": 15,
+    "rel_authors": [
+      {
+        "author_name": "Sarah Beale",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Susan J Hoskins",
+        "author_inst": "Univerity College London"
+      },
+      {
+        "author_name": "Thomas Edward Byrne",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Erica Wing Lam Fong",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Ellen Fragaszy",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Cyril Geismar",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Jana Kovar",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Annalan MD Navaratnam",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Vincent Nguyen",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Parth Patel",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Alexei Yavlinsky",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Anne Johnson",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Martie Van Tongeren",
+        "author_inst": "University of Manchester"
+      },
+      {
+        "author_name": "Robert W Aldridge",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Andrew Hayward",
+        "author_inst": "University College London"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.12.14.21267771",
     "rel_title": "Final sizes and durations of new COVID-19 pandemic waves in Poland and Germany predicted by generalized SIR model",
@@ -470767,93 +469753,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.12.13.21267729",
-    "rel_title": "Interdependencies between cellular and humoral immune responses in heterologous and homologous SARS-CoV-2 vaccination",
-    "rel_date": "2021-12-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.13.21267729",
-    "rel_abs": "BackgroundHomologous and heterologous SARS-CoV-2-vaccinations yield different spike protein-directed humoral and cellular immune responses. However, their interdependencies remain elusive.\n\nMethodsCOV-ADAPT is a prospective, observational cohort study of 417 healthcare workers who received homologous vaccination with Astra (ChAdOx1-S; AstraZeneca) or BNT (BNT162b2; Biontech/Pfizer) or heterologous vaccination with Astra/BNT. We assessed the humoral (anti-spike-RBD-IgG, neutralizing antibodies, antibody avidity) and cellular (spike-induced T cell interferon-{gamma} release) immune response in blood samples up to 2 weeks before (T1) and 2 to 12 weeks following secondary immunization (T2).\n\nFindingsInitial vaccination with Astra resulted in lower anti-spike-RBD-IgG responses compared to BNT (70{+/-}114 vs. 226{+/-}279 BAU/ml, p<0.01) at T1, whereas T cell activation did not differ significantly. Booster vaccination with BNT proved superior to Astra at T2 (anti-spike-RBD-IgG: Astra/BNT 2387{+/-}1627 and BNT/BNT 3202{+/-}2184 vs. Astra/Astra 413{+/-}461 BAU/ml, both p<0.001; spike-induced T cell interferon-{gamma} release: Astra/BNT 5069{+/-}6733 and BNT/BNT 4880{+/-}7570 vs. Astra/Astra 1152{+/-}2243 mIU/ml, both p<0.001). No significant differences were detected between BNT-boostered groups at T2. For Astra, we observed no booster effect on T cell activation. We found associations between anti-spike-RBD-IgG levels (Astra/BNT and BNT/BNT) and T cell responses (Astra/Astra and Astra/BNT) from T1 to T2. There were also links between levels of anti-spike-RBD-IgG and T cell at both time points (all groups combined). All regimes yielded neutralizing antibodies and increased antibody avidity at T2.\n\nInterpretationInterdependencies between humoral and cellular immune responses differ between common SARS-CoV-2 vaccination regimes. T cell activation is unlikely to compensate for poor humoral responses.\n\nFundingDeutsche Forschungsgemeinschaft (DFG), ER723/3-1\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched Pubmed for papers published between 01/01/2019 and 14/05/2021 with the search terms \"covid-19\" combined with \"vaccination\" and \"heterologous\", excluding \"BCG\". Of the 41 papers found, none addressed the combination of ChAdOx1-S by AstraZeneca (Astra) and BNT162b2 by Biontech/Pfizer (BNT). After our study was initiated, the CombiVacS trial reported a significant booster effect when BNT was given after initial vaccination with Astra.1 The investigators of the CoCo trial subsequently published data on heterologous immunization in comparison to homologous Astra in a small population (n=87), with the heterologous immunization scheme showing a superior humoral and cellular immune response.2 Further studies investigated heterologous vaccinations with Astra and BNT as well as homologous Astra and BNT regimes and also found superior humoral and cellular immune responses in the heterologous regimes compared to homologous Astra, and comparable or slightly superior immune responses when compared to homologous BNT vaccination.3-6 The body of research covering the effects of heterologous immunization regimes has recently been aggregated in a systematic review.7\n\nAdded value of this studyTo our knowledge, this is the first study that evaluates the interdependencies of cellular and humoral immune responses following heterologous vaccination with Astra/BNT in a large group of individuals. Our data show strong correlations between humoral and cellular immune responses with the prime-boost combination Astra/BNT. The findings suggest that individuals with a robust initial response developed strong humoral and cellular immune responses after booster immunization.\n\nImplications of all the available evidenceOur study and the available data suggest that due to its superior capacity to elicit a humoral and cellular immune response, mRNA-based vaccines such as BNT should be chosen for booster vaccination rather than Astra. This seems to be particularly important in individuals whose immune response was poor after initial vaccination with Astra.\n\nWe demonstrate here an association between humoral and cellular immune responses following vaccination. Our findings suggest that distinct differences between common COVID-19 vaccination regimes should be taken into account in population-based vaccine programs. The present data indicate that a poor humoral immune response is unlikely to be mitigated by a strong cellular immune response.",
-    "rel_num_authors": 18,
-    "rel_authors": [
-      {
-        "author_name": "Moritz M Hollstein",
-        "author_inst": "Department of Dermatology, Venereology and Allergology, University Medical Center Goettingen, Germany"
-      },
-      {
-        "author_name": "Lennart Muensterkoetter",
-        "author_inst": "Institute of Medical Microbiology and Virology, University Medical Center Goettingen, Germany"
-      },
-      {
-        "author_name": "Michael P Schoen",
-        "author_inst": "Department of Dermatology, Venereology and Allergology, University Medical Center Goettingen, Germany"
-      },
-      {
-        "author_name": "Armin Bergmann",
-        "author_inst": "Department of Dermatology, Venereology and Allergology, University Medical Center Goettingen, Germany"
-      },
-      {
-        "author_name": "Thea M Husar",
-        "author_inst": "Department of Dermatology, Venereology and Allergology, University Medical Center Goettingen, Germany"
-      },
-      {
-        "author_name": "Anna Abratis",
-        "author_inst": "Institute for Clinical Chemistry, University Medical Center Goettingen, Germany"
-      },
-      {
-        "author_name": "Abass Eidizadeh",
-        "author_inst": "Institute for Clinical Chemistry, University Medical Center Goettingen, Germany"
-      },
-      {
-        "author_name": "Meike Schaffrinski",
-        "author_inst": "Department of Dermatology, Venereology and Allergology, University Medical Center Goettingen, Germany"
-      },
-      {
-        "author_name": "Karolin Zachmann",
-        "author_inst": "Department of Dermatology, Venereology and Allergology, University Medical Center Goettingen, Germany"
-      },
-      {
-        "author_name": "Anne Schmitz",
-        "author_inst": "Department of Dermatology, University of Muenster, Muenster, Germany"
-      },
-      {
-        "author_name": "Jason S Holsapple",
-        "author_inst": "Department of Dermatology, University of Muenster, Muenster, Germany"
-      },
-      {
-        "author_name": "Hedwig Stanisz-Bogeski",
-        "author_inst": "Department of Dermatology, Venereology and Allergology, University Medical Center Goettingen, Germany"
-      },
-      {
-        "author_name": "Julie Schanz",
-        "author_inst": "Institute for Clinical Chemistry, University Medical Center Goettingen, Germany"
-      },
-      {
-        "author_name": "Uwe Gross",
-        "author_inst": "Institute of Medical Microbiology and Virology, University Medical Center Goettingen, Germany"
-      },
-      {
-        "author_name": "Andreas Leha",
-        "author_inst": "Department of Medical Statistics, University Medical Centre Goettingen, Germany"
-      },
-      {
-        "author_name": "Andreas E Zautner",
-        "author_inst": "Institute of Medical Microbiology and Virology, University Medical Center Goettingen, Germany"
-      },
-      {
-        "author_name": "Moritz Schnelle",
-        "author_inst": "Institute for Clinical Chemistry, University Medical Center Goettingen, Germany"
-      },
-      {
-        "author_name": "Luise Erpenbeck",
-        "author_inst": "Department of Dermatology, University of Muenster, Muenster, Germany"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.12.13.21267727",
     "rel_title": "Adult life-course trajectories of psychological distress and economic outcomes in midlife during the COVID-19 pandemic",
@@ -471180,6 +470079,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.12.12.21267681",
+    "rel_title": "COVID-19 in French Nursing Homes during the Second Pandemic Wave: A Mixed-Methods Cross-Sectional Study",
+    "rel_date": "2021-12-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.12.21267681",
+    "rel_abs": "IntroductionFrench nursing homes were deeply affected by the first wave of the COVID-19 pandemic, with 38% of all residents infected and 5% dying. Yet, little was done to prepare these facilities for the second pandemic wave, and subsequent outbreak response strategies largely duplicated what had been done in the spring of 2020, regardless of the unique needs of the care home environment.\n\nMethodsA cross-sectional, mixed-methods study using retrospective, quantitative data from residents of 14 nursing homes between November 2020 and mid-January 2021. Four facilities were purposively selected as qualitative study sites for additional in-person, in-depth interviews in January and February 2021.\n\nResultsThe average attack rate in the 14 participating nursing facilities was 39% among staff and 61% among residents. One-fifth (20) of infected residents ultimately died from COVID-19 and its complications. Failure-to-Thrive-Syndrome (FTTS) was diagnosed in 23% of COVID-positive residents. Those at highest risk of death were men (HR=1.78; IC95: 1.18 - 2.70; p=0.006) with FTTS (HR=4.04; IC95: 1.93 - 8.48; p<0.001) in facilities with delayed implementation of universal FFP2 masking policies (HR=1.05; IC95: 1.02 - 1.07; p<0.001). The lowest mortality was found in residents of facilities with a partial (HR=0.30; IC95: 0.18 - 0.51; p<0.001) or full-time physician on staff (HR=0.20; IC95: 0.08 - 0.53; p=0.001). Significant themes emerging from qualitative analysis centered on (i) the structural, chronic neglect of nursing homes, (ii) the negative effects of the top-down, bureaucratic nature of COVID-19 crisis response, and (iii) the counterproductive effects of lockdowns on both residents and staff.\n\nConclusionDespite high resident mortality during the first pandemic wave, French nursing homes were ill-prepared for the second, with risk factors (especially staffing, lack of medical support, isolation/quarantine policy etc) that affected case fatality and residents and caregivers overall well-being and mental health.\n\nSUMMARY BOXO_ST_ABSWhat is already known?C_ST_ABSO_LIThough much was learned about COVID-19 in nursing homes during the first pandemic wave (Spring 2020), descriptions of the second wave in these facilities is nearly absent from the scientific literature.\nC_LIO_LIPrior COVID-19 research in nursing homes has rarely been qualitative and has almost never interviewed care home residents themselves.\nC_LIO_LIFirst-wave research indicated that much stronger outbreak and infection prevention was urgently needed to bolster nursing facilities preparedness. Higher staff-to-resident ratios, less staff turnover, more masks, better organization, more medical support, and more epidemiological tools were found to reduce COVID-19s impact.\nC_LI\n\nWhat are the new findings?O_LIOur results document a lack of preparedness for the second wave, with attack rates among staff (39% overall) and residents (61% overall) similar to levels seen during the first wave peak.\nC_LIO_LIDespite authorities claims to have reinforced these structures readiness, and despite much research into the needs in these environments, preventive measures (like strict lockdowns) remained largely unchanged and had a direct impact on residents, with 23% of COVID-positives also diagnosed with Failure-to-Thrive Syndrome.\nC_LIO_LIQualitative results detailed how ill-suited and inflexible some preventive measures were for residents and staff alike. Participants described precarious and understaffed living and working conditions as substantial and long-standing difficulties that became critical risks during the COVID-19 outbreak, and compromised the response.\nC_LI\n\nWhat do the new findings imply?O_LIThese results suggest that knowledge gained during the first pandemic wave was not consistently applied to care home policy or practice in France, and that these nursing homes were not always safe environments that considered residents mental health and well-being alongside infection prevention.\nC_LIO_LIDespite the high mortality of the first pandemic wave, French nursing homes were ill-prepared for the second. As a 5th wave descends on France (albeit with much higher COVID-19 vaccination rates), applying the lessons from previous periods (especially with regard to staffing, isolation of the elderly, medical supplies, standard of care procedures) must be prioritized.\nC_LI",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Morgane Dujmovic",
+        "author_inst": "Epicentre"
+      },
+      {
+        "author_name": "Thomas Roederer",
+        "author_inst": "Epicentre"
+      },
+      {
+        "author_name": "Severine Frison",
+        "author_inst": "Epicentre"
+      },
+      {
+        "author_name": "Carla Melki",
+        "author_inst": "Medecins Sans Frontieres - France"
+      },
+      {
+        "author_name": "Thomas Lauvin",
+        "author_inst": "Medecins Sans Frontieres - France"
+      },
+      {
+        "author_name": "Emmanuel Grellety-Bosviel",
+        "author_inst": "Epicentre"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.12.13.21267267",
     "rel_title": "Genomics-informed outbreak investigations of SARS-CoV-2 using civet",
@@ -472717,53 +471655,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.12.13.472454",
-    "rel_title": "TopHap: Rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity",
-    "rel_date": "2021-12-14",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.13.472454",
-    "rel_abs": "MotivationBuilding reliable phylogenies from very large collections of sequences with a limited number of phylogenetically informative sites is challenging because sequencing errors and recurrent/backward mutations interfere with the phylogenetic signal, confounding true evolutionary relationships. Massive global efforts of sequencing genomes and reconstructing the phylogeny of SARS-CoV-2 strains exemplify these difficulties since there are only hundreds of phylogenetically informative sites and millions of genomes. For such datasets, we set out to develop a method for building the phylogenetic tree of genomic haplotypes consisting of positions harboring common variants to improve the signal-to-noise ratio for more accurate phylogenetic inference of resolvable phylogenetic features.\n\nResultsWe present the TopHap approach that determines spatiotemporally common haplotypes of common variants and builds their phylogeny at a fraction of the computational time of traditional methods. To assess topological robustness, we develop a bootstrap resampling strategy that resamples genomes spatiotemporally. The application of TopHap to build a phylogeny of 68,057 genomes (68KG) produced an evolutionary tree of major SARS-CoV-2 haplotypes. This phylogeny is concordant with the mutation tree inferred using the co-occurrence pattern of mutations and recovers key phylogenetic relationships from more traditional analyses. We also evaluated alternative roots of the SARS-CoV-2 phylogeny and found that the earliest sampled genomes in 2019 likely evolved by four mutations of the most recent common ancestor of all SARS-CoV-2 genomes. An application of TopHap to more than 1 million genomes reconstructed the most comprehensive evolutionary relationships of major variants, which confirmed the 68KG phylogeny and provided evolutionary origins of major variants of concern.\n\nAvailabilityTopHap is available on the web at https://github.com/SayakaMiura/TopHap.\n\nContacts.kumar@temple.edu",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Marcos A. Caraballo-Ortiz",
-        "author_inst": "Temple University"
-      },
-      {
-        "author_name": "Sayaka Miura",
-        "author_inst": "Temple University"
-      },
-      {
-        "author_name": "Maxwell Sanderford",
-        "author_inst": "Temple University"
-      },
-      {
-        "author_name": "Tenzin Dolker",
-        "author_inst": "Temple University"
-      },
-      {
-        "author_name": "Qiqing Tao",
-        "author_inst": "Temple University"
-      },
-      {
-        "author_name": "Steven Weaver",
-        "author_inst": "Temple University"
-      },
-      {
-        "author_name": "Sergei  L Kosakovsky Pond",
-        "author_inst": "Temple University Institute for Genomics and Evolutionary Medicine"
-      },
-      {
-        "author_name": "Sudhir Kumar",
-        "author_inst": "Temple University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "new results",
-    "category": "bioinformatics"
-  },
   {
     "rel_doi": "10.1101/2021.12.10.471928",
     "rel_title": "Language Models for the Prediction of SARS-CoV-2 Inhibitors",
@@ -473078,6 +471969,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.12.11.21267259",
+    "rel_title": "Time-Varying Mortality Risk Suggests Increased Impact of Thrombosis in Hospitalized Covid-19 Patients",
+    "rel_date": "2021-12-13",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.11.21267259",
+    "rel_abs": "Treatment protocols, treatment availability, disease understanding, and viral characteristics have changed over the course of the Covid-19 pandemic; as a result, the risks associated with patient comorbidities and biomarkers have also changed. We add to the ongoing conversation regarding inflammation, hemostasis and vascular function in Covid-19 by performing a time-varying observational analysis of over 4000 patients hospitalized for Covid-19 in a New York City hospital system from March 2020 to August 2021 to elucidate the changing impact of thrombosis, inflammation, and other risk factors on in-hospital mortality. We find that the predictive power of biomarkers of thrombosis risk have increased over time, suggesting an opportunity for improved care by identifying and targeting therapies for patients with elevated thrombophilic propensity.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Benjamin J Lengerich",
+        "author_inst": "MIT"
+      },
+      {
+        "author_name": "Mark E. Nunnally",
+        "author_inst": "NYU Langone Health"
+      },
+      {
+        "author_name": "Yin J Aphinyanaphongs",
+        "author_inst": "NYU Langone Health"
+      },
+      {
+        "author_name": "Rich Caruana",
+        "author_inst": "Microsoft Research"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.12.10.21267523",
     "rel_title": "Human serum from SARS-CoV-2 vaccinated and COVID-19 patients shows reduced binding to the RBD of SARS-CoV-2 Omicron variant in comparison to the original Wuhan strain and the Beta and Delta variants",
@@ -474395,45 +473317,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.12.09.471941",
-    "rel_title": "ClusTRace, a bioinformatic pipeline for analyzing clusters in virus phylogenies",
-    "rel_date": "2021-12-12",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.09.471941",
-    "rel_abs": "SummarySARS-CoV-2 is the highly transmissible etiologic agent of coronavirus disease 2019 (COVID-19) and has become a global scientific and public health challenge since December 2019. Several new variants of SARS-CoV-2 have emerged globally raising concern about prevention and treatment of COVID-19. Early detection and in depth analysis of the emerging variants allowing pre-emptive alert and mitigation efforts are thus of paramount importance.\n\nHere we present ClusTRace, a novel bioinformatic pipeline for a fast and scalable analysis of sequence clusters or clades in large viral phylogenies. ClusTRace offers several high level functionalities including outlier filtering, aligning, phylogenetic tree reconstruction, cluster or clade extraction, variant calling, visualization and reporting. ClusTRace was developed as an aid for COVID-19 transmission chain tracing in Finland and the main emphasis has been on fast and unsupervised screening of phylogenies for markers of super-spreading events and other features of concern, such as high rates of cluster growth and/or accumulation of novel mutations.\n\nAvailabilityAll code is freely available from https://bitbucket.org/plyusnin/clustrace/",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Ilya Plyusnin",
-        "author_inst": "University of Helsinki"
-      },
-      {
-        "author_name": "Phuoc Thien Truong Nguyen",
-        "author_inst": "University of Helsinki"
-      },
-      {
-        "author_name": "Tarja Sironen",
-        "author_inst": "University of Helsinki"
-      },
-      {
-        "author_name": "Olli Vapalahti",
-        "author_inst": "University of Helsinki"
-      },
-      {
-        "author_name": "Teemu Smura",
-        "author_inst": "University of Helsinki"
-      },
-      {
-        "author_name": "Ravi Kant",
-        "author_inst": "University of Helsinki"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "bioinformatics"
-  },
   {
     "rel_doi": "10.1101/2021.12.09.21267556",
     "rel_title": "Predicted Symptomatic Effectiveness of Pfizer-BioNTech BNT162b2 Vaccine Against Omicron Variant of SARS-CoV-2",
@@ -475004,6 +473887,113 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.12.09.21267539",
+    "rel_title": "Food for thought: Eating before saliva collection and interference with SARS-CoV-2 detection",
+    "rel_date": "2021-12-11",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.09.21267539",
+    "rel_abs": "BackgroundSaliva is an optimal specimen for detection of viruses that cause upper respiratory infections including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) due to its cost-effectiveness and non-invasive collection. However, together with intrinsic enzymes and oral microbiota, childrens unique dietary habits may introduce substances that interfere with diagnostic testing.\n\nMethodsTo determine whether childrens dietary choices impact SARS-CoV-2 detection in saliva, we performed a diagnostic study that simulates testing of real-life specimens provided from healthy children (n=5) who self-collected saliva at home before and at 0, 20, and 60 minutes after eating from 20 foods they selected. Each of seventy-two specimens was split into two volumes and spiked with SARS-CoV-2-negative or -positive standards prior to side-by-side testing by reverse-transcription polymerase chain reaction matrix-assisted laser desorption ionization time-of-flight (RT-PCR/MALDI-TOF) assay.\n\nResultsDetection of internal extraction control and SARS-CoV-2 nucleic acids was reduced in replicates of saliva collected at 0 minutes after eating 11 of 20 foods. Interference resolved at 20 and 60 minutes after eating all foods except hot dog in one participant. This represented a significant improvement in detection of nucleic acids compared to saliva collected at 0 minutes after eating (P=0.0005).\n\nConclusionsWe demonstrate successful detection of viral nucleic acids in saliva self-collected by children before and after eating a variety of foods. Fasting is not required before saliva collection for SARS-CoV-2 testing by RT-PCR/MALDI-TOF, but waiting 20 minutes after eating is sufficient for accurate testing. These findings should be considered for SARS-CoV-2 testing and broader viral diagnostics in saliva specimens.",
+    "rel_num_authors": 23,
+    "rel_authors": [
+      {
+        "author_name": "Matthew M. Hernandez",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Mariawy Riollano-Cruz",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Mary C. Boyle",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Radhika Banu",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Paras Shrestha",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Brandon Gray",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Liyong Cao",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Feng Chen",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Huanzhi Shi",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Daniel E. Paniz-Perez",
+        "author_inst": "Department of Pathology, Molecular and Cell-Based Medicine, Kids Laboratory and Science Hub, Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Paul A. Paniz-Perez",
+        "author_inst": "Department of Pathology, Molecular and Cell-Based Medicine, Kids Laboratory and Science Hub, Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Aryan L. Rishi",
+        "author_inst": "Department of Pathology, Molecular and Cell-Based Medicine, Kids Laboratory and Science Hub, Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Jacob Dubinsky",
+        "author_inst": "Department of Pathology, Molecular and Cell-Based Medicine, Kids Laboratory and Science Hub, Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Dylan Dubinsky",
+        "author_inst": "Department of Pathology, Molecular and Cell-Based Medicine, Kids Laboratory and Science Hub, Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Owen Dubinsky",
+        "author_inst": "Department of Pathology, Molecular and Cell-Based Medicine, Kids Laboratory and Science Hub, Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Sophie Baine",
+        "author_inst": "Department of Pathology, Molecular and Cell-Based Medicine, Kids Laboratory and Science Hub, Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Lily Baine",
+        "author_inst": "Department of Pathology, Molecular and Cell-Based Medicine, Kids Laboratory and Science Hub, Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Suzanne Arinsburg",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Ian Baine",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Juan David Ramirez",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Carlos Cordon-Cardo",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Emilia M Sordillo",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Alberto E Paniz Mondolfi",
+        "author_inst": "Icahn School of Medicine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.12.08.21267491",
     "rel_title": "SARS-CoV-2 B.1.1.529 variant (Omicron) evades neutralization by sera from vaccinated and convalescent individuals",
@@ -476585,161 +475575,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.12.08.21267430",
-    "rel_title": "Cytokine release syndrome-like serum responses after COVID-19 vaccination are frequent but clinically inapparent in cancer patients under immune checkpoint therapy",
-    "rel_date": "2021-12-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.08.21267430",
-    "rel_abs": "Cancer patients frequently receive immune checkpoint therapies (ICT) which may modulate immune responses to COVID-19 vaccines. Recently, cytokine release syndrome (CRS) was observed in a cancer patient who received the BTN162b2 vaccine under ICT. Here, we analyzed adverse events (AEs) in patients of various solid tumor types undergoing (n=64) or not undergoing (n=26) COVID-19 vaccination under ICT as an exploratory endpoint of a prospectively planned cohort study. We did not observe clinically relevant CRS after vaccination (95% CI [0,0.056]). Short term (<4 weeks) serious AEs were rare (12.5%) and overall AEs under ICT were comparable to unvaccinated patients. Despite the absence of CRS symptoms, we observed a pairwise-correlated set of CRS-associated cytokines upregulated in 42% of patients after vaccination and ICT (>1.5fold). Hence, clinically meaningful CRS appears to be rare in cancer patients under ICT and elevated serum cytokine levels are common but not sufficient to establish CRS diagnosis.",
-    "rel_num_authors": 35,
-    "rel_authors": [
-      {
-        "author_name": "Thomas Walle",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg"
-      },
-      {
-        "author_name": "Sunanjay Bajaj",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg"
-      },
-      {
-        "author_name": "Joscha A Kraske",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg"
-      },
-      {
-        "author_name": "Thomas Roesner",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Christiane Sophie Cussigh",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Katharina Anna Kaelber",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Lisa Jasmin Mueller",
-        "author_inst": "Department of Hematology, University Hospital Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Sophia Boyoung Strobel",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Jana Burghaus",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Stefan Kallenberger",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Christoph Stein-Thoeringer",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Maximilian Jenzer",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Antonia Schubert",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Steffen Kahle",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Anja Williams",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Birgit Hoyler",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Lin Zielske",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Renate Skatula",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Stefanie Sawall",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Mathias Felix Leber",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Russell Z Kunes",
-        "author_inst": "Department of Statistics, Columbia University, New York, NY 10027, USA"
-      },
-      {
-        "author_name": "Johannes Krisam",
-        "author_inst": "Institute of Medical Biometry, Heidelberg University, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Carlo Fremd",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Andreas Schneeweiss",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Juergen Krauss",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Anne Katrin Berger",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Georg Martin Haag",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Stefanie Zschaebitz",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Niels Halama",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Christoph Springfeld",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Romy Kirsten",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Jessica C Hassel",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Dirk Jaeger",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      },
-      {
-        "author_name": "- NCT ANTICIPATE Investigators",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Guy Ungerechts",
-        "author_inst": "National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "oncology"
-  },
   {
     "rel_doi": "10.1101/2021.12.08.21267433",
     "rel_title": "A Phenome Wide Association Study of Severe COVID-19 Genetic Risk Variants",
@@ -477022,6 +475857,105 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.12.09.21267355",
+    "rel_title": "Estimating Active Cases of COVID-19",
+    "rel_date": "2021-12-10",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.09.21267355",
+    "rel_abs": "Having accurate and timely data on active COVID-19 cases is challenging, since it depends on the availability of an appropriate infrastructure to perform tests and aggregate their results. In this paper, we consider a case to be active if it is infectious, and we propose methods to estimate the number of active infectious cases of COVID-19 from the official data (of confirmed cases and fatalities) and from public survey data. We show that the latter is a viable option in countries with reduced testing capacity or infrastructures.",
+    "rel_num_authors": 21,
+    "rel_authors": [
+      {
+        "author_name": "Javier Alvarez",
+        "author_inst": "IMDEA Networks Institute, Spain"
+      },
+      {
+        "author_name": "Carlos Baquero",
+        "author_inst": "U. Porto & INESC TEC, Portugal"
+      },
+      {
+        "author_name": "Elisa Cabana",
+        "author_inst": "IMDEA Networks Institute, Spain"
+      },
+      {
+        "author_name": "Jaya Prakash Champati",
+        "author_inst": "IMDEA Networks Institute, Spain"
+      },
+      {
+        "author_name": "Antonio Fernandez Anta",
+        "author_inst": "IMDEA Networks Institute, Spain"
+      },
+      {
+        "author_name": "Davide Frey",
+        "author_inst": "Univ. Rennes, IRISA, CNRS, INRIA, France"
+      },
+      {
+        "author_name": "Augusto Garcia-Agundez Garcia",
+        "author_inst": "Brown University, USA"
+      },
+      {
+        "author_name": "Chryssis Georgiou",
+        "author_inst": "U. of Cyprus, Cyprus"
+      },
+      {
+        "author_name": "Mathieu Goessens",
+        "author_inst": "Consulting, France"
+      },
+      {
+        "author_name": "Harold Hernandez",
+        "author_inst": "U. Carlos III de Madrid, Spain"
+      },
+      {
+        "author_name": "Rosa Lillo",
+        "author_inst": "U. Carlos III de Madrid, Spain"
+      },
+      {
+        "author_name": "Raquel Menezes",
+        "author_inst": "U. Minho, Portugal"
+      },
+      {
+        "author_name": "Raul Moreno",
+        "author_inst": "Madox Viajes, Spain"
+      },
+      {
+        "author_name": "Nicolas Nicolaou",
+        "author_inst": "Algolysis Ltd, Cyprus"
+      },
+      {
+        "author_name": "Oluwasegun Ojo",
+        "author_inst": "IMDEA Networks Institute & U. Carlos III de Madrid, Spain"
+      },
+      {
+        "author_name": "Antonio Ortega",
+        "author_inst": "U. Southern California, USA"
+      },
+      {
+        "author_name": "Estrella Rausell",
+        "author_inst": "U. Autonoma de Madrid, Spain"
+      },
+      {
+        "author_name": "Jesus Rufino",
+        "author_inst": "IMDEA Network Institute, Spain"
+      },
+      {
+        "author_name": "Efstathios Stavrakis",
+        "author_inst": "Algolysis Ltd, Cyprus"
+      },
+      {
+        "author_name": "Govind Jeevan",
+        "author_inst": "Academics for the Future of Science, Inc. & DICE Institute, Pathcheck Foundation, USA"
+      },
+      {
+        "author_name": "Christin Glorioso",
+        "author_inst": "Academics for the Future of Science, Inc., University of California San Francisco, & DICE Institute, Pathcheck Foundation, USA"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health informatics"
+  },
   {
     "rel_doi": "10.1101/2021.12.06.471527",
     "rel_title": "SARS-CoV-2 variants of concern are dependent on IFITM2 for efficient replication in human lung cells",
@@ -478451,93 +477385,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
-  {
-    "rel_doi": "10.1101/2021.12.08.21267439",
-    "rel_title": "Safety and Immunogenicity of SARS-CoV-2 S-2P Protein Vaccine MVC-COV1901 in People Living with HIV",
-    "rel_date": "2021-12-09",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.08.21267439",
-    "rel_abs": "ObjectivesTo provide data on the immune response to COVID-19 vaccines in people living with HIV (PWH), MVC-COV1901, a recombinant protein vaccine containing S-2P protein adjuvanted with CpG 1018 and aluminium hydroxide, was assessed.\n\nMethodsA total of 57 PWH of [&ge;] 20 years of age who are on stable antiretroviral therapy and with CD4+ T cell [&ge;] 350 cells/mm3 and HIV viral load < 103 copies/ml were compared with 882 HIV-negative participants. Participants received 2 doses of MVC-COV1901 28 days apart. Safety and the immunogenicity were evaluated.\n\nResultsNo vaccine-related serious adverse events (SAEs) were recorded. Seroconversion rates (SCRs) of 100% and 99.8% were achieved in people living with HIV (PWH) and comparators, respectively, 28 days after second dose. The geometric mean titers (GMTs) (95% confidence interval [CI]) against wild type SARS-CoV-2 virus were 136.62 IU/mL (WHO Standardized International Unit) (95% CI 114.3-163.3) and 440.41 IU/mL (95% CI 421.3-460.4), for PWH and control groups, respectively, after adjusting for sex, age, BMI category, and comorbidity, and the adjusted GMT ratio of comparator/PWH was 3.22 (95% CI 2.6-4.1). A higher CD4/CD8 ratio was associated with a higher GMT (R=0.27, p=0.039).\n\nConclusionsMVC-COV1901 has shown robust safety but weaker immunogenicity responses in PWH. As a result, a third dose or booster doses of MVC-COV1901 may be appropriate for PWH.",
-    "rel_num_authors": 18,
-    "rel_authors": [
-      {
-        "author_name": "Shu-Hsing Cheng",
-        "author_inst": "Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan; School of Public Health, Taipei Medical University"
-      },
-      {
-        "author_name": "Chia En Lien",
-        "author_inst": "Medigen Vaccine Biologics Corp., Taipei, Taiwan; Institute of Public Health, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan"
-      },
-      {
-        "author_name": "Szu-Min Hsieh",
-        "author_inst": "Department of Internal Medicine, Division of Infectious Diseases, National Taiwan University Hospital, Taipei, Taiwan; College of Medicine, National Taiwan Univ"
-      },
-      {
-        "author_name": "Chien-Yu Cheng",
-        "author_inst": "Department of Infectious Diseases, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan; School of Public Health, National Yang Ming Chiao "
-      },
-      {
-        "author_name": "Wang-Da Liu",
-        "author_inst": "Department of Internal Medicine, Division of Infectious Diseases, National Taiwan University Hospital, Taipei, Taiwan; Department of Medicine, National Taiwan U"
-      },
-      {
-        "author_name": "Ching-Lung Lo",
-        "author_inst": "Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan; Department of Medicine, College of Medicine, National Cheng Kung Unive"
-      },
-      {
-        "author_name": "Wen-chien Ko",
-        "author_inst": "Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan; Department of Medicine, College of Medicine, National Cheng Kung Unive"
-      },
-      {
-        "author_name": "Yen-Hsu Chen",
-        "author_inst": "Department of Internal Medicine, Division of Infectious Diseases, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; School of Medicine, Graduate Institu"
-      },
-      {
-        "author_name": "Ching-Tai Huang",
-        "author_inst": "Department of Infectious Diseases, Chang Gung Memorial Hospital, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan"
-      },
-      {
-        "author_name": "Hsiao-Ting Chang",
-        "author_inst": "Department of Family Medicine, Taipei Veterans General Hospital ; School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan"
-      },
-      {
-        "author_name": "Shinn-Jang Hwang",
-        "author_inst": "Department of Family Medicine, Taipei Veterans General Hospital; School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan"
-      },
-      {
-        "author_name": "Ning-Chi Wang",
-        "author_inst": "Tri-Service General Hospital, Taipei, Taiwan"
-      },
-      {
-        "author_name": "Ming-Che Liu",
-        "author_inst": "Clinical Research Centre, Taipei Medical University Hospital, Taipei, Taiwan; School of Dental Technology, College of Oral Medicine"
-      },
-      {
-        "author_name": "Yu-Lin Lee",
-        "author_inst": "Department of Internal Medicine, Changhua Christian Hospital, Changhua, Taiwan; Program in Medical Biotechnology, National Chung Hsing University, Taichung, Tai"
-      },
-      {
-        "author_name": "I-Chen Tai",
-        "author_inst": "Medigen Vaccine Biologics Corp., Taipei, Taiwan"
-      },
-      {
-        "author_name": "Josue Antonio Garcia Estrada",
-        "author_inst": "Medigen Vaccine Biologics Corp., Taipei, Taiwan"
-      },
-      {
-        "author_name": "Tzou-Yien Lin",
-        "author_inst": "College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Paediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan"
-      },
-      {
-        "author_name": "Wen-Sen Lee",
-        "author_inst": "Division of Infectious Disease, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan; Department of Internal Medicine, "
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "hiv aids"
-  },
   {
     "rel_doi": "10.1101/2021.12.08.21267502",
     "rel_title": "Measurement of SARS-CoV-2 antigens in plasma of pediatric patients with acute COVID-19 or MIS-C using an ultrasensitive and quantitative immunoassay",
@@ -478836,6 +477683,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.12.09.21267516",
+    "rel_title": "Changes in the trajectory of Long Covid symptoms following COVID-19 vaccination: community-based cohort study",
+    "rel_date": "2021-12-09",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.09.21267516",
+    "rel_abs": "ObjectiveTo estimate associations between COVID-19 vaccination and Long Covid symptoms in adults who were infected with SARS-CoV-2 prior to vaccination.\n\nDesignObservational cohort study using individual-level interrupted time series analysis.\n\nSettingRandom sample from the community population of the UK.\n\nParticipants28,356 COVID-19 Infection Survey participants (mean age 46 years, 56% female, 89% white) aged 18 to 69 years who received at least their first vaccination after test-confirmed infection.\n\nMain outcome measuresPresence of long Covid symptoms at least 12 weeks after infection over the follow-up period 3 February to 5 September 2021.\n\nResultsMedian follow-up was 141 days from first vaccination (among all participants) and 67 days from second vaccination (84% of participants). First vaccination was associated with an initial 12.8% decrease (95% confidence interval: -18.6% to -6.6%) in the odds of Long Covid, but increasing by 0.3% (-0.6% to +1.2%) per week after the first dose. Second vaccination was associated with an 8.8% decrease (-14.1% to -3.1%) in the odds of Long Covid, with the odds subsequently decreasing by 0.8% (-1.2% to -0.4%) per week. There was no statistical evidence of heterogeneity in associations between vaccination and Long Covid by socio-demographic characteristics, health status, whether hospitalised with acute COVID-19, vaccine type (adenovirus vector or mRNA), or duration from infection to vaccination.\n\nConclusionsThe likelihood of Long Covid symptoms reduced after COVID-19 vaccination, and the improvement was sustained over the follow-up period after the second dose. Vaccination may contribute to a reduction in the population health burden of Long Covid, though longer follow-up time is needed.\n\nSummary boxWhat is already known on this topic\n\nO_LICOVID-19 vaccines are effective at reducing rates of SARS-CoV-2 infection, transmission, hospitalisation, and death\nC_LIO_LIThe incidence of Long Covid may be reduced if infected after vaccination, but the relationship between vaccination and pre-existing long COVID symptoms is unclear, as published studies are generally small and with self-selected participants\nC_LI\n\nWhat this study adds\n\nO_LIThe likelihood of Long Covid symptoms reduced after COVID-19 vaccination, and the improvement was sustained over the follow-up period after the second dose\nC_LIO_LIThere was no evidence of differences in this relationship by socio-demographic characteristics, health-related factors, vaccine type, or duration from infection to vaccination\nC_LIO_LIAlthough causality cannot be inferred from this observational evidence, vaccination may contribute to a reduction in the population health burden of Long Covid; further research is needed to understand the biological mechanisms that may ultimately contribute to the development of therapeutics for Long Covid\nC_LI",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Daniel Ayoubkhani",
+        "author_inst": "Office for National Statistics"
+      },
+      {
+        "author_name": "Charlotte Bermingham",
+        "author_inst": "Office for National Statistics"
+      },
+      {
+        "author_name": "Koen B Pouwels",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Myer Glickman",
+        "author_inst": "Office for National Statistics"
+      },
+      {
+        "author_name": "Vahe Nafilyan",
+        "author_inst": "Office for National Statistics"
+      },
+      {
+        "author_name": "Francesco Zaccardi",
+        "author_inst": "University of Leicester"
+      },
+      {
+        "author_name": "Kamlesh Khunti",
+        "author_inst": "University of Leicester"
+      },
+      {
+        "author_name": "Nisreen A Alwan",
+        "author_inst": "University of Southampton"
+      },
+      {
+        "author_name": "Ann Sarah Walker",
+        "author_inst": "University of Oxford"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.12.09.21267507",
     "rel_title": "Superspreading of SARS-CoV-2 infections: A Systematic Review and Meta-analysis",
@@ -479913,37 +478811,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.12.07.21267381",
-    "rel_title": "COVID-19 clusters in schools: frequency, size, and transmission rates from crowdsourced exposure reports",
-    "rel_date": "2021-12-08",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.07.21267381",
-    "rel_abs": "The role of schools in the spread of the COVID-19 pandemic is controversial, with some claiming they are an important driver of the pandemic and others arguing that transmission in schools is negligible. School cluster reports that have been collected in various jurisdictions are a source of data about transmission in schools. These reports consist of the name of a school, a date, and the number of students known to be infected. We provide a simple model for the frequency and size of clusters in this data, based on random arrivals of index cases at schools who then infect their classmates with a highly variable rate, fitting the overdispersion evident in the data. We fit our model to reports from four Canadian provinces, providing estimates of mean and dispersion for cluster size, whilst factoring in imperfect ascertainment. Our parameter estimates are robust to variations in ascertainment fraction. We use these estimates in two ways: i) to explore how uneven the distribution of cases is among different clusters in different jurisdictions (that is, what fraction of cases are in the 20% largest clusters), and ii) to determine the distribution of instantaneous transmission rate {beta} among different index cases. We show how these latter distributions can be used in simulations of school transmission where we explore the effect of different interventions, in the context of highly variable transmission rates.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Paul F Tupper",
-        "author_inst": "Simon Fraser University"
-      },
-      {
-        "author_name": "Shraddha Pai",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "- COVID Schools Canada",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Caroline Colijn",
-        "author_inst": "Simon Fraser University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.12.06.21267388",
     "rel_title": "Deviations in Predicted COVID-19 cases in the US during early months of 2021 relate to rise in B.1.526 and its family of variants",
@@ -480350,6 +479217,149 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "genetic and genomic medicine"
   },
+  {
+    "rel_doi": "10.1101/2021.12.08.21266760",
+    "rel_title": "Humoral and cellular responses to SARS-CoV-2 vaccination in patients with lymphoid malignancies",
+    "rel_date": "2021-12-08",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.08.21266760",
+    "rel_abs": "SARS-CoV-2 vaccination protects against COVID-19. Antibodies and antigen-specific T-cell responses against the spike domain can be used to measure vaccine immune response. Individuals with lymphoma have defects in humoral and cellular immunity that may compromise vaccine response. In this prospective observational study of 457 participants with lymphoma, 52% of participants vaccinated on treatment had undetectable anti-spike IgG antibodies compared to 9% who were not on treatment. Marked impairment was observed in those receiving anti- CD20 antibody within 12 months where 60% had undetectable antibodies compared to 11% on chemotherapy, which persisted despite three vaccine doses. Overall, 63% had positive T-cell responses irrespective of treatment. Individuals with indolent B-cell lymphoma have impaired antibody and cellular responses that were independent of treatment. The significant reduction and heterogeneity in immune responses in these individuals emphasise the urgent need for immune response monitoring and alternative prophylactic strategies to protect against COVID- 19.",
+    "rel_num_authors": 32,
+    "rel_authors": [
+      {
+        "author_name": "Sean Hua Lim",
+        "author_inst": "University of Southampton"
+      },
+      {
+        "author_name": "Nicola Campbell",
+        "author_inst": "University Hospital Southampton NHS Foundation Trust"
+      },
+      {
+        "author_name": "Beth Stuart",
+        "author_inst": "Southampton Clinical Trials Unit, University of Southampton"
+      },
+      {
+        "author_name": "Marina Johnson",
+        "author_inst": "Great Ormond Street Institute Of Child Health Biomedical Research Centre, University College London"
+      },
+      {
+        "author_name": "Debora Joseph-Pietras",
+        "author_inst": "NIHR/Cancer Research UK Southampton Experimental Cancer Medicine Centre, WISH Laboratory"
+      },
+      {
+        "author_name": "Adam Kelly",
+        "author_inst": "NIHR/Cancer Research UK Southampton Experimental Cancer Medicine Centre, WISH Laboratory"
+      },
+      {
+        "author_name": "Danielle Jeffrey",
+        "author_inst": "NIHR/Cancer Research UK Southampton Experimental Cancer Medicine Centre, WISH Laboratory"
+      },
+      {
+        "author_name": "Anna H Turaj",
+        "author_inst": "University of Southampton"
+      },
+      {
+        "author_name": "Kate Rolfvondenbaumen",
+        "author_inst": "NIHR/Cancer Research UK Southampton Experimental Cancer Medicine Centre, WISH Laboratory"
+      },
+      {
+        "author_name": "Celine Galloway",
+        "author_inst": "NIHR/Cancer Research UK Southampton Experimental Cancer Medicine Centre, WISH Laboratory"
+      },
+      {
+        "author_name": "Thomas Wynn",
+        "author_inst": "NIHR/Cancer Research UK Southampton Experimental Cancer Medicine Centre, WISH Laboratory"
+      },
+      {
+        "author_name": "Adam R Coleman",
+        "author_inst": "NIHR/Cancer Research UK Southampton Experimental Cancer Medicine Centre, WISH Laboratory"
+      },
+      {
+        "author_name": "Ben Ward",
+        "author_inst": "NIHR/Cancer Research UK Southampton Experimental Cancer Medicine Centre, WISH Laboratory"
+      },
+      {
+        "author_name": "Karen Long",
+        "author_inst": "University of Southampton Clinical Informatics Research Unit"
+      },
+      {
+        "author_name": "Andrew T Bates",
+        "author_inst": "University Hospital Southampton NHS Foundation Trust"
+      },
+      {
+        "author_name": "Diana Ayres",
+        "author_inst": "University Hospital Southampton NHS Foundation Trust"
+      },
+      {
+        "author_name": "Robert Lown",
+        "author_inst": "University Hospital Southampton NHS Foundation Trust"
+      },
+      {
+        "author_name": "Janlyn Falconer",
+        "author_inst": "University Hospital Southampton NHS Foundation Trust"
+      },
+      {
+        "author_name": "Oliver Brake",
+        "author_inst": "University Hospital Southampton NHS Foundation Trust"
+      },
+      {
+        "author_name": "James Batchelor",
+        "author_inst": "University of Southampton Clinical Informatic Research Unit"
+      },
+      {
+        "author_name": "Victoria Willimott",
+        "author_inst": "Norfolk and Norwich University Hospital NHS Foundation Trust"
+      },
+      {
+        "author_name": "Anna Bowzyk Al-Naeeb",
+        "author_inst": "Bedford Hospital"
+      },
+      {
+        "author_name": "Lisa Robinson",
+        "author_inst": "County Hospital Hereford"
+      },
+      {
+        "author_name": "Ann O'Callaghan",
+        "author_inst": "Portsmouth Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "Graham P Collins",
+        "author_inst": "Oxford University Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "Tobias Menne",
+        "author_inst": "Newcastle upon Tyne Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "Saul Faust",
+        "author_inst": "NIHR Southampton Clinical Research Facility and NIHR Southampton Biomedical Research Centre"
+      },
+      {
+        "author_name": "Christopher P Fox",
+        "author_inst": "Nottingham University Hospital NHS Trust"
+      },
+      {
+        "author_name": "Matthew Ahearne",
+        "author_inst": "University Hospitals Leicester NHS Trust"
+      },
+      {
+        "author_name": "Peter W.M. Johnson",
+        "author_inst": "University of Southampton"
+      },
+      {
+        "author_name": "Andrew J Davies",
+        "author_inst": "University of Southampton"
+      },
+      {
+        "author_name": "David Goldblatt",
+        "author_inst": "Great Ormond Street Institute of Child Health Biomedical Research Centre, University College London"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "hematology"
+  },
   {
     "rel_doi": "10.1101/2021.12.08.21267458",
     "rel_title": "Relative contribution of leaving home for work or education, transport, shopping and other activities on risk of acquiring COVID-19 infection outside the household in the second wave of the pandemic in England and Wales",
@@ -481819,313 +480829,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2021.12.03.471045",
-    "rel_title": "Receptor binding and escape from Beta antibody responses drive Omicron-B.1.1.529 evolution",
-    "rel_date": "2021-12-07",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.03.471045",
-    "rel_abs": "On the 24th November 2021 the sequence of a new SARS CoV-2 viral isolate spreading rapidly in Southern Africa was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titres of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic as well as Alpha, Beta, Gamma, Delta are substantially reduced or fail to neutralize. Titres against Omicron are boosted by third vaccine doses and are high in cases both vaccinated and infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of a large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses, combining mutations conferring tight binding to ACE2 to unleash evolution driven by immune escape, leading to a large number of mutations in the ACE2 binding site which rebalance receptor affinity to that of early pandemic viruses.",
-    "rel_num_authors": 73,
-    "rel_authors": [
-      {
-        "author_name": "Wanwisa Dejnirattisai",
-        "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK"
-      },
-      {
-        "author_name": "Jiandong Huo",
-        "author_inst": "Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK"
-      },
-      {
-        "author_name": "Daming Zhou",
-        "author_inst": "Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK."
-      },
-      {
-        "author_name": "Jiri Zahradni_k",
-        "author_inst": "Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel"
-      },
-      {
-        "author_name": "Piyada Supasa",
-        "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK"
-      },
-      {
-        "author_name": "Chang Liu",
-        "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK"
-      },
-      {
-        "author_name": "Helen M. E. Duyvesteyn",
-        "author_inst": "Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK."
-      },
-      {
-        "author_name": "Helen Ginn",
-        "author_inst": "Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK."
-      },
-      {
-        "author_name": "Alexander J. Mentzer",
-        "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK"
-      },
-      {
-        "author_name": "Aekkachai Tuekprakhon",
-        "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK"
-      },
-      {
-        "author_name": "Rungtiwa Nutalai",
-        "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK"
-      },
-      {
-        "author_name": "Beibei - Wang",
-        "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK"
-      },
-      {
-        "author_name": "Aiete Dijokaite",
-        "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK"
-      },
-      {
-        "author_name": "Suman Khan",
-        "author_inst": "Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel"
-      },
-      {
-        "author_name": "Ori Avinoam",
-        "author_inst": "Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel"
-      },
-      {
-        "author_name": "Mohammad Bahar",
-        "author_inst": "Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK"
-      },
-      {
-        "author_name": "Donal Skelly",
-        "author_inst": "Peter Medawar Building for Pathogen Research,Nuffield Deptment of Medicine, University of Oxford, UK"
-      },
-      {
-        "author_name": "Sandra Adele",
-        "author_inst": "Peter Medawar Building for Pathogen Research, Oxford, UK"
-      },
-      {
-        "author_name": "Sile Johnson",
-        "author_inst": "Peter Medawar Building for Pathogen Research"
-      },
-      {
-        "author_name": "Ali Amini",
-        "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, UK"
-      },
-      {
-        "author_name": "Thomas Ritter",
-        "author_inst": "Oxford University Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Chris Mason",
-        "author_inst": "Oxford University Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Christina Dold",
-        "author_inst": "Oxford Vaccine Group, Department of Paediatrics,  University of Oxford, Oxford, OX3 7LE, UK."
-      },
-      {
-        "author_name": "Danile Pan",
-        "author_inst": "Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust"
-      },
-      {
-        "author_name": "Sara Assadi",
-        "author_inst": "Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust"
-      },
-      {
-        "author_name": "Adam Bellass",
-        "author_inst": "Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust"
-      },
-      {
-        "author_name": "Nikki Omo-Dare",
-        "author_inst": "Department of Infectious Diseases and HIV Medicine, University Hospitals of Leicester NHS Trust"
-      },
-      {
-        "author_name": "David Koeckerling",
-        "author_inst": "Medical Sciences Division, University of Oxford"
-      },
-      {
-        "author_name": "Amy Flaxman",
-        "author_inst": "Jenner Institute, Nuffield Department of Medicine, University of Oxford, UK"
-      },
-      {
-        "author_name": "Daniel Jenkin",
-        "author_inst": "Jenner Institute, Nuffield Department of Medicine, University of Oxford, UK"
-      },
-      {
-        "author_name": "Parvinder K Aley",
-        "author_inst": "Oxford Vaccine Group, Department of Paediatrics,  University of Oxford, Oxford, OX3 7LE, UK."
-      },
-      {
-        "author_name": "Merryn Voysey",
-        "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, OX3 7LE"
-      },
-      {
-        "author_name": "Sue Ann Costa Clemens",
-        "author_inst": "Institute of Global Health, University of Siena, Siena, Brazil; Department of Paediatrics, University of Oxford, Oxford, UK."
-      },
-      {
-        "author_name": "Felipe Gomes Naveca",
-        "author_inst": "Laborato rio de Ecologia de Doencas Transmissveis na Amazonia, Instituto Leonidas e Maria Deane, FIOCRUZ, Manaus, Amazonas, Brazil"
-      },
-      {
-        "author_name": "Valdinete Nascimento",
-        "author_inst": "Laborato rio de Ecologia de Doencas Transmissveis na Amazonia, Instituto Leonidas e Maria Deane, FIOCRUZ, Manaus, Amazonas, Brazil"
-      },
-      {
-        "author_name": "Fernanda Nascimento",
-        "author_inst": "Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia, Instituto Leonidas e Maria Deane, FIOCRUZ, Manaus, Amazonas, Brazil"
-      },
-      {
-        "author_name": "Cristiano Fernandes da Costa",
-        "author_inst": "Fundacao de Vigilancia em Saude do Amazonas, Manaus, Amazonas, Brazil"
-      },
-      {
-        "author_name": "Paola Cristina Resende",
-        "author_inst": "Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil"
-      },
-      {
-        "author_name": "Alex Pauvolid-Correa",
-        "author_inst": "Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil"
-      },
-      {
-        "author_name": "Marilda M. Siqueira",
-        "author_inst": "Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil"
-      },
-      {
-        "author_name": "Vicky Baillie",
-        "author_inst": "South African MRC, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, J"
-      },
-      {
-        "author_name": "Natali Serafin",
-        "author_inst": "South African MRC, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, J"
-      },
-      {
-        "author_name": "Zanele Ditse",
-        "author_inst": "South African MRC, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, J"
-      },
-      {
-        "author_name": "Kelly Da Silva",
-        "author_inst": "South African MRC, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, J"
-      },
-      {
-        "author_name": "Shabir Madhi",
-        "author_inst": "South African MRC, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, J"
-      },
-      {
-        "author_name": "Marta C Nunes",
-        "author_inst": "South African MRC, Vaccines and Infectious Diseases Analytics Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, J"
-      },
-      {
-        "author_name": "Tariq Malik",
-        "author_inst": "National Infection Service, Public Health England (PHE), Porton Down, Salisbury, UK"
-      },
-      {
-        "author_name": "Peter JM Openshaw",
-        "author_inst": "National Heart & Lung Institute, Imperial College London"
-      },
-      {
-        "author_name": "J Kenneth Baillie",
-        "author_inst": "Genetics and Genomics, Roslin Institute, University of Edinburgh, Edinburgh, UK"
-      },
-      {
-        "author_name": "Malcolm G Semple",
-        "author_inst": "NIHR Health Protection Research Unit, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, "
-      },
-      {
-        "author_name": "Alain R Townsend",
-        "author_inst": "MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK"
-      },
-      {
-        "author_name": "Kuan-Ying A. Huang",
-        "author_inst": "Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan."
-      },
-      {
-        "author_name": "Tiong Kit Tan",
-        "author_inst": "MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK"
-      },
-      {
-        "author_name": "Miles W. Carroll",
-        "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK"
-      },
-      {
-        "author_name": "Paul Klenerman",
-        "author_inst": "Peter Medawar Building for Pathogen Research,Nuffield Deptment of Medicine, University of Oxford, UK"
-      },
-      {
-        "author_name": "Eleanor Barnes",
-        "author_inst": "Peter Medawar Building for Pathogen Research, Nuffield Deptment of Medicine, University of Oxford, UK"
-      },
-      {
-        "author_name": "Susanna J. Dunachie",
-        "author_inst": "Peter Medawar Building for Pathogen Research,Nuffield Deptment of Medicine, University of Oxford, UK"
-      },
-      {
-        "author_name": "Bede Constantinides",
-        "author_inst": "Nuffield Department of Medicine, University of Oxford, Oxford, UK."
-      },
-      {
-        "author_name": "Hermione Webster",
-        "author_inst": "Nuffield Department of Medicine, University of Oxford, Oxford, UK."
-      },
-      {
-        "author_name": "Derrick Crook",
-        "author_inst": "Nuffield Department of Medicine, University of Oxford, Oxford, UK."
-      },
-      {
-        "author_name": "Andrew J. Pollard",
-        "author_inst": "Oxford Vaccine Group, Department of Paediatrics,  University of Oxford, Oxford, OX3 7LE, UK."
-      },
-      {
-        "author_name": "Teresa Lambe",
-        "author_inst": "Oxford Vaccine Group, Department of Paediatrics,  University of Oxford, Oxford, OX3 7LE, UK."
-      },
-      {
-        "author_name": "- OPTIC Consortium",
-        "author_inst": "-"
-      },
-      {
-        "author_name": "- ISARIC4C",
-        "author_inst": "-"
-      },
-      {
-        "author_name": "Neil G. Paterson",
-        "author_inst": "Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK."
-      },
-      {
-        "author_name": "Mark A. Williams",
-        "author_inst": "Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK."
-      },
-      {
-        "author_name": "David R. Hall",
-        "author_inst": "Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK."
-      },
-      {
-        "author_name": "Elizabeth E Fry",
-        "author_inst": "Division of Structural Biology, Nuffield Department of Medicine,"
-      },
-      {
-        "author_name": "Juthathip Mongkolsapaya",
-        "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK"
-      },
-      {
-        "author_name": "Jingshan Ren",
-        "author_inst": "Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK."
-      },
-      {
-        "author_name": "Gideon Schreiber",
-        "author_inst": "Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel"
-      },
-      {
-        "author_name": "David I. Stuart",
-        "author_inst": "Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Headington, Oxford, UK."
-      },
-      {
-        "author_name": "Gavin R. Screaton",
-        "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2021.12.05.471310",
     "rel_title": "A sarbecovirus found in Russian bats uses human ACE2",
@@ -482420,6 +481123,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.12.04.471153",
+    "rel_title": "Elucidating design principles for engineering cell-derived vesicles to inhibit SARS-CoV-2 infection",
+    "rel_date": "2021-12-07",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.04.471153",
+    "rel_abs": "The ability of pathogens to develop drug resistance is a global health challenge. The SARS-CoV-2 virus presents an urgent need wherein several variants of concern resist neutralization by monoclonal antibody therapies and vaccine-induced sera. Decoy nanoparticles--cell-mimicking particles that bind and inhibit virions--are an emerging class of therapeutics that may overcome such drug resistance challenges. To date, we lack quantitative understanding as to how design features impact performance of these therapeutics. To address this gap, here we perform a systematic, comparative evaluation of various biologically-derived nanoscale vesicles, which may be particularly well-suited to sustained or repeated administration in the clinic due to low toxicity, and investigate their potential to inhibit multiple classes of model SARS-CoV-2 virions. A key finding is that such particles exhibit potent antiviral efficacy across multiple manufacturing methods, vesicle subclasses, and virus-decoy binding affinities. In addition, these cell-mimicking vesicles effectively inhibit model SARS-CoV-2 variants that evade monoclonal antibodies and recombinant protein-based decoy inhibitors. This study provides a foundation of knowledge that may guide the design of decoy nanoparticle inhibitors for SARS-CoV-2 and other viral infections.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Taylor Franklin Gunnels",
+        "author_inst": "Northwestern University"
+      },
+      {
+        "author_name": "Devin M Stranford",
+        "author_inst": "Northwestern University"
+      },
+      {
+        "author_name": "Roxana E Mitrut",
+        "author_inst": "Northwestern University"
+      },
+      {
+        "author_name": "Neha Kamat",
+        "author_inst": "Northwestern University"
+      },
+      {
+        "author_name": "Joshua Nathaniel Leonard",
+        "author_inst": "Northwestern University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "bioengineering"
+  },
   {
     "rel_doi": "10.1101/2021.12.06.471394",
     "rel_title": "Insertions in the SARS-CoV-2 Spike N-Terminal Domain May Aid COVID-19 Transmission",
@@ -483809,25 +482547,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "radiology and imaging"
   },
-  {
-    "rel_doi": "10.1101/2021.12.07.21267405",
-    "rel_title": "SIR Modeling the Dual Disaster Impacts of Omicron B.1.1.529 and Natural Disaster Events on Simulated 6 Months (from December 2021 to May 2022) Healthcare System Resiliences in Fragile SE Asia Ring of Fire Ecosystems",
-    "rel_date": "2021-12-07",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.07.21267405",
-    "rel_abs": "For some countries that have experienced numerous natural disasters, including massive earthquakes and tsunamis, managing the COVID-19 pandemic can be very challenging. This situation arises considering that the disaster can directly and indirectly affect the healthcare system s capacity to serve the COVID-19 cases. With severely damaged healthcare facilities due to the disaster, there will be severely ill COVID-19 cases unmanaged. The coupling and interplay between these two phenomena can indeed be catastrophic. One of the regions where this issue becomes concerned is in Southeast Asia, where most of the Asian countries lie in the fragile ring of fire ecosystem, contributing to the high tsunami and earthquake disasters in the world. At the same time, Asia is one of the regions that have been severely impacted due to the current COVID-19 Delta Variant. Recently, a more contagious Omicron Variant has emerged and put a more massive burden on the healthcare facilities that are impacted by disasters. Then, in this situation, this paper aims to assess healthcare resilience in managing the Omicron pandemic amid disaster impacts. SIR simulation was used to determine whether severely ill Omicron cases were below or above healthcare and ICU capacity under different vaccination coverage. Our result confirms that vaccination coverage was the imminent factor in reducing the severely ill cases in every healthcare facility, whether the facilities were damaged or not. Increasing vaccination coverage from 30% to 60% will significantly reduce the number of severely ill cases that fall below the capacity of healthcare. Based on the current SIR model on the Omicron epidemic variables and Ro, it is estimated that the Omicron will reach its peak after 180 days in February 2022 and will totally disappear in May 2022 in this modeled area. When healthcare system facilities were fully operational and no disaster happened, combined with 60% vaccination rates, all Omicron case numbers were below and under the available hospital beds and even available ICU beds. While the situation is changed when a disaster occurs and causes 30% damage or reduction to healthcare facilities. In this situation, there are portions of Omicron cases that cannot be managed by the healthcare system since the cases have exceeded the available beds. The situations become more apparent where the healthcare facilities are severely damaged and lose 60% of their functionality. In this situation, all modeled Omicron cases and even the severe cases have exceeded the ICU capacity.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Andri A Wibowo",
-        "author_inst": "University of Indonesia"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health informatics"
-  },
   {
     "rel_doi": "10.1101/2021.12.06.21267084",
     "rel_title": "Predicted CTL responses from pressured epitopes in SARS-CoV-2 correlate with COVID-19 severity",
@@ -484290,6 +483009,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pediatrics"
   },
+  {
+    "rel_doi": "10.1101/2021.12.06.21267391",
+    "rel_title": "The Impact of Mass Exodus on the Resurgence of COVID19 Cases: Study Case of Regions in Indonesia",
+    "rel_date": "2021-12-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.06.21267391",
+    "rel_abs": "The inclusion of the human mobility aspect is essential for understanding the behavior of COVID-19 spread, especially when millions of people travel across borders near Eid Al-Fitr. This study aims at grasping the effect of mass exodus among regions on the active cases of COVID-19 in a mathematical perspective. We construct a multi-region SIQRD (Susceptible-Infected-Quarantined-Recovered-Death) model that accommodates the direct transfer of people from one region to others. The mobility rate is estimated using the proposed Dawson-like function, which requires the Origin-Destination Matrix data. Assuming only susceptible, unapparent infected, and recovered individuals travel near Eid Al-Fitr, the rendered model is well-depicting the actual data at that time, giving either a significant spike or decline in the number of active cases due to the mass exodus. Most agglomerated regions like Jakarta and Depok City experienced the fall of active cases number, both in actual data and the simulated model. However, most rural areas experienced the opposite, like Bandung District and Cimahi City. This study should confirm that most travelers originated from big cities to the rural regions and scientifically justifies that massive mobility affects the COVID-19 transmission among areas.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Nuning Nuraini",
+        "author_inst": "Institut Teknologi Bandung"
+      },
+      {
+        "author_name": "Kamal Khairudin Sukandar",
+        "author_inst": "Institut Teknologi Bandung"
+      },
+      {
+        "author_name": "Wirdatul Aini",
+        "author_inst": "Institut Teknologi Bandung"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.12.04.471206",
     "rel_title": "Engineering RNA viruses with unnatural amino acid to evoke adjustable immune response in mice",
@@ -485651,29 +484397,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.12.03.21267195",
-    "rel_title": "Worldwide routine immunisation coverage regressed during the first year of the COVID-19 pandemic",
-    "rel_date": "2021-12-05",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.03.21267195",
-    "rel_abs": "We modelled historical, country-specific routine immunisation trends using publicly available vaccination coverage data for diphtheria, tetanus and pertussis-containing vaccine first-dose (DTP1) and third-dose (DTP3) from 2000 to 2019. We evaluate changes in coverage in 2020 by comparing model predictions to WUENIC-reported coverage. We report a 2.9% (95%CI: [2.2%; 3.6%]) global decline in DTP3 coverage, and important increases in missed immunisations in some countries with middle-income countries, and the Americas, being most affected.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Beth Evans",
-        "author_inst": "London School of Hygiene and Tropical Medicine (LSHTM)"
-      },
-      {
-        "author_name": "Thibaut Jombart",
-        "author_inst": "London School of Hygiene and Tropical Medicine (LSHTM)"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.12.02.21267210",
     "rel_title": "Post-traumatic Stress Risk among COVID-19 Survivors in Colombia",
@@ -485988,6 +484711,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.12.02.21267164",
+    "rel_title": "Estimation of heterogeneous instantaneous reproduction numbers with application to characterize SARS-CoV-2 transmission in Massachusetts counties",
+    "rel_date": "2021-12-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.02.21267164",
+    "rel_abs": "The reproductive number is an important metric that has been widely used to quantify the infectiousness of communicable diseases. The time-varying instantaneous reproductive number is useful for monitoring the real time dynamics of a disease to inform policy making for disease control. Local estimation of this metric, for instance at a county or city level, allows for more targeted interventions to curb transmission. However, simultaneous estimation of local reproductive numbers must account for potential sources of heterogeneity in these time-varying quantities - a key element of which is human mobility. We develop a statistical method that incorporates human mobility between multiple regions for estimating region-specific instantaneous reproductive numbers. The model also can account for exogenous cases imported from outside of the regions of interest. We propose two approaches to estimate the reproductive numbers, with mobility data used to adjust incidence in the first approach and to inform a formal priori distribution in the second (Bayesian) approach. Through a simulation study, we show that region-specific reproductive numbers can be well estimated if human mobility is reasonably well approximated by available data. We use this approach to estimate the instantaneous reproductive numbers of COVID-19 for 14 counties in Massachusetts using CDC case report data and the human mobility data collected by SafeGraph. We found that, accounting for mobility, our method produces estimates of reproductive numbers that are distinct across counties. In contrast, independent estimation of county-level reproductive numbers tends to produce similar values, as trends in county case-counts for the state are fairly concordant. These approaches can also be used to estimate any heterogeneity in transmission, for instance, age-dependent instantaneous reproductive number estimates. As people are more mobile and interact frequently in ways that permit transmission, it is important to account for this in the estimation of the reproductive number.\n\nAuthor summaryTo control the spreading of an infectious disease, it is very important to understand the real-time infectiousness of the pathogen that causes the disease. An existing metric called instantaneous reproductive number is often used to quantify the average number of secondary cases generated by individuals who are infectious at a certain time point, assuming no changes to current conditions. In practice, we might be interested in using the metric to describe the infectiousness in multiple regions. However, this is challenging when there are visitors traveling between these regions, since this could lead to a misclassification of where an individual is actually infected and create biased estimates for the instantaneous reproductive numbers. We developed a method that takes account of human mobility to estimate the instantaneous reproductive numbers for multiple regions simultaneously, which could reveal the heterogeneity of the metric. This method aims to provide helpful information on region-specific infectiousness for disease control measures that focus on the region with higher pathogen infectiousness. This approach is also applicable for estimating the reproductive number in the presence of other sources of heterogeneity, including by age.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Zhenwei Zhou",
+        "author_inst": "Boston University"
+      },
+      {
+        "author_name": "Eric Kolaczyk",
+        "author_inst": "Boston University"
+      },
+      {
+        "author_name": "Robin N Thompson",
+        "author_inst": "University of Warwick"
+      },
+      {
+        "author_name": "Laura F White",
+        "author_inst": "Boston University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.12.01.21266960",
     "rel_title": "Comparative magnitude and persistence of SARS-CoV-2 vaccination responses on a population level in Germany",
@@ -487469,41 +486223,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.12.01.470802",
-    "rel_title": "Delta variant with P681R critical mutation revealed by ultra-large atomic-scale ab initio simulation: Implications for the fundamentals of biomolecular interactions",
-    "rel_date": "2021-12-03",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.01.470802",
-    "rel_abs": "SARS-CoV-2 Delta variant is emerging as a globally dominant strain. Its rapid spread and high infection rate are attributed to a mutation in the spike protein of SARS-CoV-2 allowing the virus to invade human cells much faster and with increased efficiency. Particularly, an especially dangerous mutation P681R close to the furin cleavage site has been identified as responsible for increasing the infection rate. Together with the earlier reported mutation D614G in the same domain, it offers an excellent instance to investigate the nature of mutations and how they affect the interatomic interactions in the spike protein. Here, using ultra large-scale ab initio computational modeling, we study the P681R and D614G mutations in the SD2-FP domain including the effect of double mutation and compare the results with the wild type. We have recently developed a method of calculating the amino acid-amino acid bond pairs (AABP) to quantitatively characterize the details of the interatomic interactions, enabling us to explain the nature of mutation at the atomic resolution. Our most significant find is that the mutations reduce the AABP value, implying a reduced bonding cohesion between interacting residues and increasing the flexibility of these amino acids to cause the damage. The possibility of using this unique mutation quantifiers in a machine learning protocol could lead to the prediction of emerging mutations.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Puja Adhikari",
-        "author_inst": "University of Missouri-Kansas City"
-      },
-      {
-        "author_name": "Bahaa Jawad",
-        "author_inst": "University of Missouri-Kansas City"
-      },
-      {
-        "author_name": "Praveen Rao",
-        "author_inst": "University of Missouri-Columbia"
-      },
-      {
-        "author_name": "Rudolf Podgornik",
-        "author_inst": "University of Chinese Academy of Sciences"
-      },
-      {
-        "author_name": "Wai-Yim Ching",
-        "author_inst": "University of Missouri-Kansas City"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "biochemistry"
-  },
   {
     "rel_doi": "10.1101/2021.12.01.470353",
     "rel_title": "Possible Interference in Protein - Protein interaction as a new approach in microinhibition of respiratory pathogens on nasal- oral epithelium: An early on-screen study with reference toSARS-Cov-2-ACE2 binding interference",
@@ -487850,6 +486569,73 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2021.12.01.470697",
+    "rel_title": "Macaque-human differences in SARS-CoV-2 Spike antibody response elicited by vaccination or infection",
+    "rel_date": "2021-12-03",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.01.470697",
+    "rel_abs": "Macaques are a commonly used model for studying immunity to human viruses, including for studies of SARS-CoV-2 infection and vaccination. However, it is unknown whether macaque antibody responses recapitulate, and thus appropriately model, the response in humans. To answer this question, we employed a phage-based deep mutational scanning approach (Phage- DMS) to compare which linear epitopes are targeted on the SARS-CoV-2 Spike protein in humans and macaques following either vaccination or infection. We also used Phage-DMS to determine antibody escape pathways within each epitope, enabling a granular comparison of antibody binding specificities at the locus level. Overall, we identified some common epitope targets in both macaques and humans, including in the fusion peptide (FP) and stem helix- heptad repeat 2 (SH-H) regions. Differences between groups included a response to epitopes in the N-terminal domain (NTD) and C-terminal domain (CTD) in vaccinated humans but not vaccinated macaques, as well as recognition of a CTD epitope and epitopes flanking the FP in convalescent macaques but not convalescent humans. There was also considerable variability in the escape pathways among individuals within each group. Sera from convalescent macaques showed the least variability in escape overall and converged on a common response with vaccinated humans in the SH-H epitope region, suggesting highly similar antibodies were elicited. Collectively, these findings suggest that the antibody response to SARS-CoV-2 in macaques shares many features with humans, but with substantial differences in the recognition of certain epitopes and considerable individual variability in antibody escape profiles, suggesting a diverse repertoire of antibodies that can respond to major epitopes in both humans and macaques.\n\nAuthor summaryNon-human primates, including macaques, are considered the best animal model for studying infectious diseases that infect humans. Vaccine candidates for SARS-CoV-2 are first tested in macaques to assess immune responses prior to advancing to human trials, and macaques are also used to model the human immune response to SARS-CoV-2 infection. However, there may be differences in how macaque and human antibodies recognize the SARS-CoV-2 entry protein, Spike. Here we characterized the locations on Spike that are recognized by antibodies from vaccinated or infected macaques and humans. We also made mutations to the viral sequence and assessed how these affected antibody binding, enabling a comparison of antibody binding requirements between macaques and humans at a very precise level. We found that macaques and humans share some responses, but also recognize distinct regions of Spike. We also found that in general, antibodies from different individuals had unique responses to viral mutations, regardless of species. These results will yield a better understanding of how macaque data can be used to inform human immunity to SARS-CoV-2.",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Alexandra Willcox",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      },
+      {
+        "author_name": "Kevin Sung",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      },
+      {
+        "author_name": "Meghan  E. Garrett",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      },
+      {
+        "author_name": "Jared  G. Galloway",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      },
+      {
+        "author_name": "Megan  A. O\u2019Connor",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Jesse  H. Erasmus",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Jennifer  K. Logue",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "David  W. Hawman",
+        "author_inst": "National Institute of Allergy and Infectious Diseases Division of Intramural Research"
+      },
+      {
+        "author_name": "Helen  Y. Chu",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Kim  J. Hasenkrug",
+        "author_inst": "National Institute of Allergy and Infectious Diseases Division of Intramural Research"
+      },
+      {
+        "author_name": "Deborah  H. Fuller",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Frederick  A. Matsen",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      },
+      {
+        "author_name": "Julie Overbaugh",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      }
+    ],
+    "version": "1",
+    "license": "cc0",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2021.12.02.470930",
     "rel_title": "Investigating the human host - ssRNA virus interaction landscape using the SMEAGOL toolbox",
@@ -489163,33 +487949,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "primary care research"
   },
-  {
-    "rel_doi": "10.1101/2021.12.01.21267158",
-    "rel_title": "Changes Over Time in COVID-19 Vaccination Inequalities in Eight Large U.S. Cities",
-    "rel_date": "2021-12-02",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.01.21267158",
-    "rel_abs": "We estimate the associations between community socioeconomic composition and changes in COVID-19 vaccination levels in eight large cities at three time points. Between March and April, low SES communities had significantly lower change in percent vaccinated than high SES communities. Between April and May, this difference was not significant. Thus, the large vaccination gap between communities during restricted vaccine eligibility did not narrow when eligibility opened up. The link between COVID-19 vaccination and community disadvantage may lead to a bifurcated recovery where advantaged communities move on from the pandemic more quickly while disadvantaged communities continue to suffer.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "S. Michael Gaddis",
-        "author_inst": "University of California, Los Angeles"
-      },
-      {
-        "author_name": "Colleen M. Carey",
-        "author_inst": "Cornell University"
-      },
-      {
-        "author_name": "Nicholas V DiRago",
-        "author_inst": "University of California, Los Angeles"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.11.30.21267085",
     "rel_title": "TREATMENT COSTS FOR COVID-19 PATIENTS IN A TERTIARY HOSPITAL FROM SERBIA",
@@ -489412,6 +488171,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
+  {
+    "rel_doi": "10.1101/2021.12.01.21267147",
+    "rel_title": "Comparison of Saliva and Mid-Turbinate Swabs for Detection of COVID-19",
+    "rel_date": "2021-12-02",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.01.21267147",
+    "rel_abs": "BackgroundSaliva is an attractive sample for detecting SARS-CoV-2. However, contradictory reports exist concerning the sensitivity of saliva versus nasal swabs.\n\nMethodsWe followed close contacts of COVID-19 cases for up to 14 days from last exposure and collected self-reported symptoms, mid-turbinate swabs (MTS), and saliva every two or three days. Ct values, viral load, and frequency of viral detection by MTS and saliva were compared.\n\nResults58 contacts provided 200 saliva-MTS pairs; 14 contacts (13 with symptoms) had one or more positive samples. Saliva and MTS had similar rates of viral detection (p=0.78) and substantial agreement ({kappa}=0.83). However, sensitivity varied significantly with time since symptom onset. Early on (days -3 to 2), saliva had 12 times (95%CI: 1.2, 130) greater likelihood of viral detection and 3.2 times (95% CI: 2.8, 3.8) higher RNA copy numbers compared to MTS. After day 2 post-symptoms, there was a non-significant trend toward greater sensitivity using MTS.\n\nConclusionSaliva and MTS demonstrated high agreement making saliva a suitable alternative to MTS for COVID-19 detection. Saliva was more sensitive early in the infection when transmission is most likely to occur, suggesting that it may be a superior and cost-effective screening tool for COVID-19.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Jianyu Lai",
+        "author_inst": "Department of Epidemiology and Biostatistics, University of Maryland School of Public Health, College Park, Maryland, USA"
+      },
+      {
+        "author_name": "Jennifer Rebecca German",
+        "author_inst": "Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Ma"
+      },
+      {
+        "author_name": "Filbert H. Hong",
+        "author_inst": "Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Ma"
+      },
+      {
+        "author_name": "S.-H. Sheldon Tai",
+        "author_inst": "Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Ma"
+      },
+      {
+        "author_name": "Kathleen M. McPhaul",
+        "author_inst": "Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Ma"
+      },
+      {
+        "author_name": "Donald K. Milton",
+        "author_inst": "Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Ma"
+      },
+      {
+        "author_name": "- University of Maryland StopCOVID Research Group",
+        "author_inst": ""
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.11.29.21267028",
     "rel_title": "A simple model of COVID-19 explains disease severity and the effect of treatments",
@@ -491013,49 +489815,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.11.30.21267043",
-    "rel_title": "Identification of susceptibility loci for adverse events following COVID-19 vaccination in the Japanese population: A web-based genome-wide association study.",
-    "rel_date": "2021-11-30",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.30.21267043",
-    "rel_abs": "The novel coronavirus disease 2019 (COVID-19) pandemic has spread rapidly worldwide. To prevent the spread of COVID-19, mRNA-based vaccines made by Pfizer/BioNTech (BNT162b1) and Moderna (mRNA-1273) have been widely used worldwide, including in Japan. Various adverse events after COVID-19 mRNA vaccinations have been reported, with differences observed among individuals. However, the analysis on the genetic background for susceptibility to side effects has been limited. In the present work, we performed genome-wide association studies (GWAS) for self-reported adverse events of COVID-19 mRNA vaccination in 4,545 Japanese individuals and identified 14 associated loci. Among these, 6p21 was associated with 37.5{degrees}C or higher fever, 38 {degrees}C or higher fever, and muscle pain. Our results may enable one to prepare for and manage side effects by knowing their susceptibility to the occurrence of adverse events. Furthermore, we obtained valuable data that can lead to the understanding of the mechanism of action of COVID-19 mRNA vaccines.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Shun Nogawa",
-        "author_inst": "Genequest Inc."
-      },
-      {
-        "author_name": "Hajime Kanamori",
-        "author_inst": "Tohoku University Graduate School of Medicine"
-      },
-      {
-        "author_name": "Koichi Tokuda",
-        "author_inst": "Tohoku University Graduate School of Medicine"
-      },
-      {
-        "author_name": "Kaoru Kawafune",
-        "author_inst": "Genequest Inc."
-      },
-      {
-        "author_name": "Miyuki Chijiiwa",
-        "author_inst": "Genequest Inc."
-      },
-      {
-        "author_name": "Kenji Saito",
-        "author_inst": "Genequest Inc."
-      },
-      {
-        "author_name": "Shoko Takahashi",
-        "author_inst": "Genequest Inc."
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.11.30.21267048",
     "rel_title": "Risk of Hospitalization, severe disease, and mortality due to COVID-19 and PIMS-TS in children with SARS-CoV-2 infection in Germany",
@@ -491626,6 +490385,109 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2021.11.28.468932",
+    "rel_title": "Case Study of High-Throughput Drug Screening and Remote Data Collection for SARS-CoV-2 Main Protease by Using Serial Femtosecond X-ray Crystallography",
+    "rel_date": "2021-11-30",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.28.468932",
+    "rel_abs": "Since early 2020, COVID-19 has grown to affect the lives of billions globally. A worldwide investigation has been ongoing for characterizing the virus and also for finding an effective drug and developing vaccines. As time has been of the essence, a crucial part of this research has been drug repurposing; therefore, confirmation of in-silico drug screening studies has been carried out for this purpose. Here we demonstrated the possibility of screening a variety of drugs efficiently by leveraging a high data collection rate of 120 images/second with the new low-noise, high dynamic range ePix10k2M Pixel Array Detector installed at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Linac Coherent Light Source (LCLS). The X-ray Free-Electron Laser (XFEL) is used for remote high-throughput data collection for drug repurposing of the main protease (Mpro) of SARS-CoV-2 at ambient temperature with mitigated X-ray radiation damage. We obtained multiple structures soaked with 9 drug candidate molecules in two crystal forms. Although our drug binding attempts failed, we successfully established a high-throughput Serial Femtosecond X-ray crystallographic (SFX) data collection protocol.",
+    "rel_num_authors": 22,
+    "rel_authors": [
+      {
+        "author_name": "Omur Guven",
+        "author_inst": "Koc University"
+      },
+      {
+        "author_name": "Mehmet Gul",
+        "author_inst": "Koc University"
+      },
+      {
+        "author_name": "Esra Ayan",
+        "author_inst": "Koc University"
+      },
+      {
+        "author_name": "J. Austin Johnson",
+        "author_inst": "Koc University"
+      },
+      {
+        "author_name": "Baris Cakilkaya",
+        "author_inst": "Koc University"
+      },
+      {
+        "author_name": "Gozde Usta",
+        "author_inst": "Koc University"
+      },
+      {
+        "author_name": "Fatma Betul Ertem",
+        "author_inst": "Koc University"
+      },
+      {
+        "author_name": "Nurettin Tokay",
+        "author_inst": "Koc University"
+      },
+      {
+        "author_name": "Busra Yuksel",
+        "author_inst": "Koc University"
+      },
+      {
+        "author_name": "Oktay Gocenler",
+        "author_inst": "Koc University"
+      },
+      {
+        "author_name": "Cengizhan Buyukdag",
+        "author_inst": "Koc University"
+      },
+      {
+        "author_name": "Sabine Botha",
+        "author_inst": "Arizona State University"
+      },
+      {
+        "author_name": "Gihan Ketawala",
+        "author_inst": "Arizona State University"
+      },
+      {
+        "author_name": "Zhen Su",
+        "author_inst": "SLAC National Accelerator Laboratory"
+      },
+      {
+        "author_name": "Brandon Hayes",
+        "author_inst": "SLAC National Accelerator Laboratory"
+      },
+      {
+        "author_name": "Frederic Poitevin",
+        "author_inst": "SLAC National Accelerator Laboratory"
+      },
+      {
+        "author_name": "Alexander Batyuk",
+        "author_inst": "SLAC National Accelerator Laboratory"
+      },
+      {
+        "author_name": "Chun Hong Yoon",
+        "author_inst": "SLAC National Accelerator Laboratory"
+      },
+      {
+        "author_name": "Christopher Kupitz",
+        "author_inst": "SLAC National Accelerator Laboratory"
+      },
+      {
+        "author_name": "Serdar Durdagi",
+        "author_inst": "Bahcesehir University"
+      },
+      {
+        "author_name": "Raymond G. Sierra",
+        "author_inst": "SLAC National Accelerator Laboratory"
+      },
+      {
+        "author_name": "Hasan DeMirci",
+        "author_inst": "SLAC National Laboratory"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "molecular biology"
+  },
   {
     "rel_doi": "10.1101/2021.11.28.470226",
     "rel_title": "Main protease mutants of SARS-CoV-2 variants remain susceptible to PF-07321332",
@@ -492735,45 +491597,6 @@
     "type": "new results",
     "category": "genomics"
   },
-  {
-    "rel_doi": "10.1101/2021.11.29.21266906",
-    "rel_title": "Diagnostic performance of attenuated total reflection Fourier-transform infrared spectroscopy for detecting COVID-19 from routine nasopharyngeal swab samples",
-    "rel_date": "2021-11-29",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.29.21266906",
-    "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing global COVID-19 pandemic since 2019 has led to increasing amount of research to study how to do fast screening and diagnosis to efficiently detect COVID-19 positive cases, and how to prevent spreading of the virus. Our research objective was to study whether SARS-CoV-2 could be detected from routine nasopharyngeal swab samples by using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy coupled with partial least squares discriminant analysis (PLS-DA). The advantage of ATR-FTIR is that measurements can be conducted without any sample preparation and no reagents are needed. Our study included 558 positive and 558 negative samples collected from Northern Finland. Overall, we found moderate diagnostic performance for ATR-FTIR when polymerase chain reaction (PCR) was used as the gold standard: the average area under the receiver operating characteristics curve (AUROC) was 0.67-0.68 (min. 0.65, max. 0.69) with 20, 10 and 5 k-fold cross validations. Mean accuracy, sensitivity and specificity was 0.62-0.63 (min. 0.60, max. 0.65), 0.61 (min. 0.58, max. 0.65) and 0.64 (min. 0.59, max. 0.67) with 20, 10 and 5 k-fold cross validations. As a conclusion, our study with relatively large sample set clearly indicate that measured ATR-FTIR spectrum contains specific information for SARS-CoV-2 infection (P<0.001 in label permutation test). However, the diagnostic performance of ATR-FTIR remained only moderate, potentially due to low concentration of viral particles in the transport medium. Further studies are needed before ATR-FTIR can be recommended for fast screening of SARS-CoV-2 from routine nasopharyngeal swab samples.\n\nImportanceAttenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy coupled with machine learning-based analysis was applied to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from nasopharyngeal swab samples originally collected and processed for polymerase chain reaction (PCR) analysis. Even though our results showed moderate performance, we think that our carefully designed and conducted work is valuable in the field of SARS-CoV-2 diagnostics as there were as many as 1116 nasopharyngeal swab samples (558 negative and 558 positive) collected from individual patients in a real clinical setting. The Real clinical setting refers to the fact that the nasopharyngeal swab samples were collected from people with symptoms typical for COVID-19 or asymptomatic individuals exposed to SARS-CoV-2. The presented technique could be relatively easy to use for point-of-care testing, as ATR-FTIR can be performed with a portable machine without sample preparation and machine learning-based model could give a result immediately after ATR-FTIR measurement.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Helin\u00e4 Heino",
-        "author_inst": "University of Oulu"
-      },
-      {
-        "author_name": "Lassi Rieppo",
-        "author_inst": "University of Oulu"
-      },
-      {
-        "author_name": "Tuija M\u00e4nnist\u00f6",
-        "author_inst": "Northern Finland Laboratory Centre NordLab"
-      },
-      {
-        "author_name": "Mikko Sillanp\u00e4\u00e4",
-        "author_inst": "University of Oulu"
-      },
-      {
-        "author_name": "Vesa M\u00e4ntynen",
-        "author_inst": "Northern Finland Laboratory Centre NordLab"
-      },
-      {
-        "author_name": "Simo Saarakkala",
-        "author_inst": "University of Oulu, Oulu University Hospital"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.11.29.21266109",
     "rel_title": "A case series of SARS-CoV-2 reinfections caused by the variant of concern Gamma in Brazil",
@@ -493280,6 +492103,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.11.25.470044",
+    "rel_title": "Anticipating future SARS-CoV-2 variants of concern through ab initio quantum mechanical modeling",
+    "rel_date": "2021-11-29",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.25.470044",
+    "rel_abs": "Evolved SARS-CoV-2 variants are currently challenging the efficacy of first-generation vaccines, largely through the emergence of spike protein mutants. Among these variants, Delta is presently the most concerning. We employ an ab initio quantum mechanical model based on Density Functional Theory to characterize the spike protein Receptor Binding Domain (RBD) interaction with host cells and gain mechanistic insight into SARS-CoV-2 evolution. The approach is illustrated via a detailed investigation of the role of the E484K RBD mutation, a signature mutation of the Beta and Gamma variants. The simulation is employed to: predict the depleting effect of the E484K mutation on binding the RBD with select antibodies; identify residue E484 as a weak link in the original interaction with the human receptor hACE2; and describe SARS-CoV-2 Wuhan strand binding to the bat Rhinolophus macrotis ACE2 as more optimized than the human counterpart. Finally, we predict the hACE2 binding efficacy of a hypothetical E484K mutation added to the Delta variant RBD, identifying a potential future variant of concern. Results can be generalized to other mutations, and provide useful information to complement existing experimental datasets of the interaction between randomly generated libraries of hACE2 and viral spike mutants. We argue that ab initio modeling is at the point of being aptly employed to inform and predict events pertinent to viral and general evolution.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Marco Zaccaria",
+        "author_inst": "Boston College"
+      },
+      {
+        "author_name": "Luigi Genovese",
+        "author_inst": "CEA, Grenoble, France"
+      },
+      {
+        "author_name": "Michael Farzan",
+        "author_inst": "The Scripps Research Institute"
+      },
+      {
+        "author_name": "William Dawson",
+        "author_inst": "RIKEN Center for Computational Science, Kobe, Japan"
+      },
+      {
+        "author_name": "Takahito Nakajima",
+        "author_inst": "RIKEN Center for Computational Science, Kobe, Japan"
+      },
+      {
+        "author_name": "Welkin E Johnson",
+        "author_inst": "Boston College"
+      },
+      {
+        "author_name": "Babak Momeni",
+        "author_inst": "Boston College"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "biophysics"
+  },
   {
     "rel_doi": "10.1101/225151",
     "rel_title": "Proof of concept continuous event logging in living cells",
@@ -494685,37 +493551,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "cardiovascular medicine"
   },
-  {
-    "rel_doi": "10.1101/2021.11.21.21262716",
-    "rel_title": "Covid-19 vaccination coverage and break through infections in urban slums of Bengaluru, India: A cross sectional study.",
-    "rel_date": "2021-11-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.21.21262716",
-    "rel_abs": "BackgroundThe ongoing pandemic of Corona virus disease 2019(covid-19) is caused by severe acute respiratory syndrome Corona virus 2(SAR-COV-2). The world health organization declared it as public health emergency of international concern on January 2020, and later declared as pandemic on 11 March 2020.One of the high-risk groups for COVID-19 disease are people residing in urban overcrowded slums and as most of the population is migrant, they are less aware of the pandemic and have less access to health care facilities.\n\nVaccinating these high-risk groups can decrease disease burden and control the ongoing pandemic.\n\nObjectives1] To estimate COVID 19 vaccination coverage 2] To assess the factors responsible for COVID - 19 vaccination coverage and vaccine hesitancy 3] To study AEFI pattern following COVID-19 vaccination 4] To determine the prevalence of breakthrough infections after COVID - 19 Vaccination in urban slums of Bengaluru, India.\n\nMethodologyA community based cross sectional study was conducted in Urban slums belonging to Urban Health and Training Centre, Department of community medicine, Akash Institute of Medical Sciences and Research Centre, Bengaluru Rural District, Karnataka, India. After obtaining Institutional ethical clearance and informed consent from study participants, data was collected from 1638 participants, fulfilling inclusion criteria using a predesigned, pretested, structured questionnaire. Data was entered in Microsoft excel and analyzed using SPSS version 24. Chi square test and Fischers exact test was applied and p <0.05 considered as statistically significant.\n\nResultsIn the present study, 35.5% (583 out of 1638) of the study participants had taken COVID Vaccine, of which 533 (91.42%) were partially vaccinated and remaining 50 (8.5%) were fully Vaccinated. Majority i.e., 98.45% have taken vaccine at Govt health centers. 63.65% vaccinated with Covishield reported adverse events, whereas 18.6% vaccinated with Covaxin reported adverse events. Adverse events were more likely to be reported by women (74.7%) compared to men (58.6%), this observation was consistent across all age groups. Vaccination coverage was high among 18 - 45 years age group (37.75%), males (64.86%), Christians (47.05%) followed by Hindus (43.56%), graduates (95.67%), clerical and skilled workers (70.75%), Upper middle socioeconomic class (72.41%). This difference was statistically significant. Our study reported Break through infections in 7 out of total 583 vaccinated with a prevalence of 1.2%. The break through infections was very high among partially vaccinated (85.71%) as compared to fully vaccinated individuals (14.28%). This was observed among those vaccinated with Covaxin only.\n\nConclusionThe COVID vaccine coverage was low in urban slums. The prevalence of Break through infections in our study was higher as compared to available data/reports in the country. Break through infections was very high among partially vaccinated as compared to fully vaccinated individuals. This study on break through infections on COVID vaccination is first study in South India on general population. The most important factor for vaccine hesitancy is the occurrence of mild or serious adverse effects following immunization, and this may be the biggest challenge in the global response against the pandemic.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Sunil Kumar D.R.",
-        "author_inst": "Akash Institute of Medical Sciences and Research Centre, Bengaluru, India"
-      },
-      {
-        "author_name": "Srividya J",
-        "author_inst": "Akash Institute of Medical Sciences and Research Centre, Bengaluru, India"
-      },
-      {
-        "author_name": "Apoorva E Patel",
-        "author_inst": "Akash Institute of Medical Sciences and Research Centre, Bengaluru, India"
-      },
-      {
-        "author_name": "Vidya R",
-        "author_inst": "Akash Institute of Medical Sciences and Research Centre, Bengaluru, India"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.11.24.21266831",
     "rel_title": "Germany's current COVID-19 crisis is mainly driven by the unvaccinated",
@@ -495238,6 +494073,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.11.24.21266837",
+    "rel_title": "Changes in antidepressant use in Australia: A nationwide analysis prior to and during the COVID-19 pandemic (2015-2021)",
+    "rel_date": "2021-11-26",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.24.21266837",
+    "rel_abs": "BackgroundDepression and anxiety affect 4% to 14% of Australians every year; symptoms may have been exacerbated during the COVID-19 pandemic. We examined recent patterns of antidepressant use in Australia in the period 2015 to 2021, which includes the first year of the pandemic.\n\nMethodsWe used national dispensing claims for people aged [&ge;]10 years to investigate annual trends in prevalent and new antidepressant use (no antidepressants dispensed in the year prior). We conducted stratified analyses by sex, age group and antidepressant class. We report outcomes from 2015 to 2019 and used time series analysis to quantify changes during the first year of the COVID-19 pandemic (March 2020 to February 2021).\n\nResultsIn 2019 the annual prevalence of antidepressant use was 170.4 per 1,000 women and 101.8 per 1,000 men, an increase of 7.0% and 9.2% from 2015, respectively. New antidepressant use also increased for both sexes (3.0% for women and 4.9% for men) and across most age groups, particularly among adolescents (aged 10-17 years; 46%-57%). During the first year of the COVID-19 pandemic, we observed higher than expected prevalent use (+2.2%, 95%CI 0.3%, 4.2%) among females, corresponding to a predicted excess of 45,217 (95%CI 5,819, 84,614) females dispensed antidepressants. The largest increases during the first year of the pandemic occurred among female adolescents for both prevalent (+11.7%, 95%CI 4.1%, 20.5%) and new antidepressant use (+15.6%, 95%CI 8.5%, 23.7%).\n\nConclusionAntidepressant use continues to increase in Australia overall and especially among young people. We found a differential impact of the COVID-19 pandemic in treated depression and anxiety, greater among females than males, and greater among young females than other age groups, suggesting an increased mental health burden in populations already on a trajectory of increased use of antidepressants prior to the pandemic. Reasons for these differences require further investigation.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Juliana de Oliveira Costa",
+        "author_inst": "Medicines Policy Research Unit, Centre for Big Data Research in Health,  Faculty of Medicine/ UNSW Sydney"
+      },
+      {
+        "author_name": "Malcolm B. Gilles",
+        "author_inst": "Medicines Policy Research Unit, Centre for Big Data Research in Health, Faculty of Medicine/ UNSW Sydney"
+      },
+      {
+        "author_name": "Andrea L Schaffer",
+        "author_inst": "Medicines Policy Research Unit, Centre for Big Data Research in Health, Faculty of Medicine/ UNSW Sydney"
+      },
+      {
+        "author_name": "David Peiris",
+        "author_inst": "The George Institute for Global Health, Faculty of Medicine/ UNSW Sydney"
+      },
+      {
+        "author_name": "Helga Zoega",
+        "author_inst": "Medicines Policy Research Unit, Centre for Big Data Research in Health, Faculty of Medicine/ UNSW Sydney. Centre of Public Health Sciences, Faculty of Medicine,"
+      },
+      {
+        "author_name": "Sallie-Anne Pearson",
+        "author_inst": "Medicines Policy Research Unit, Centre for Big Data Research in Health, Faculty of Medicine/ UNSW Sydney"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.11.25.21266856",
     "rel_title": "The COVID-19 pandemic and temporal change in metabolic risk factors for cardiovascular disease: a natural experiment within the HELIUS study.",
@@ -496575,101 +495449,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.11.22.21266681",
-    "rel_title": "In vitro, classical complement activation differs by disease severity and between SARS-CoV-2 antigens",
-    "rel_date": "2021-11-24",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.22.21266681",
-    "rel_abs": "Antibodies specific for the spike glycoprotein (S) and nucleocapsid (N) SARS-CoV-2 proteins are typically present during severe COVID-19, and induced to S after vaccination. The binding of viral antigens by antibody can initiate the classical complement pathway. Since complement could play pathological or protective roles at distinct times during SARS-CoV-2 infection we determined levels of antibody-dependent complement activation along the complement cascade. Here, we used an ELISA assay to assess complement protein binding (C1q) and the deposition of C4b, C3b, and C5b to S and N antigens in the presence of anti-SARS-CoV-2 antibodies from different test groups: non-infected, single and double vaccinees, non-hospitalised convalescent (NHC) COVID-19 patients and convalescent hospitalised (ITU-CONV) COVID-19 patients. C1q binding correlates strongly with antibody responses, especially IgG1 levels. However, detection of downstream complement components, C4b, C3b and C5b shows some variability associated with the antigen and subjects studied. In the ITU-CONV, detection of C3b-C5b to S was observed consistently, but this was not the case in the NHC group. This is in contrast to responses to N, where median levels of complement deposition did not differ between the NHC and ITU-CONV groups. Moreover, for S but not N, downstream complement components were only detected in sera with higher IgG1 levels. Therefore, the classical pathway is activated by antibodies to multiple SARS-CoV-2 antigens, but the downstream effects of this activation may differ depending on the specific antigen targeted and the disease status of the subject.\n\nO_LISpike- and nucleocapsid-specific antibodies activate complement in vitro\nC_LIO_LIC1q binding correlates with IgG1 antibody levels\nC_LIO_LIGeneration of C4b, C3b and C5b relates to the antigen targeted and the patient group tested\nC_LI",
-    "rel_num_authors": 20,
-    "rel_authors": [
-      {
-        "author_name": "Rachel E Lamerton",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Edith Marcial Juarez",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Sian E Faustini",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Marisol E Perez-Toledo",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Margaret Goodall",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Sian E Jossi",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Maddy L Newby",
-        "author_inst": "University of Southampton"
-      },
-      {
-        "author_name": "Iain Chapple",
-        "author_inst": "University of Birmingham and Birmingham Community Healthcare NHS Trust"
-      },
-      {
-        "author_name": "Thomas Dietrich",
-        "author_inst": "University of Birmingham and Birmingham Community Healthcare NHS Trust"
-      },
-      {
-        "author_name": "Tonny Veenith",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Adrian M Shields",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Lorraine Harper",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Ian R Henderson",
-        "author_inst": "University of Queensland"
-      },
-      {
-        "author_name": "Julie Rayes",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "David C Wraith",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Steve P Watson",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Max Crispin",
-        "author_inst": "University of Southampton"
-      },
-      {
-        "author_name": "Mark T Drayson",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Alex G Richter",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Adam F Cunningham",
-        "author_inst": "University of Birmingham"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "allergy and immunology"
-  },
   {
     "rel_doi": "10.1101/2021.11.22.21266721",
     "rel_title": "Simulating the impact of vaccination rates on the initial stages of a COVID-19 outbreak in New Zealand (Aotearoa) with a stochastic model",
@@ -496912,6 +495691,77 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.11.23.21266734",
+    "rel_title": "Establishing and characterising large COVID-19 cohorts after mapping the Information System for Research in Primary Care in Catalonia to the OMOP Common Data Model",
+    "rel_date": "2021-11-24",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.23.21266734",
+    "rel_abs": "BackgroundFew datasets have been established that capture the full breadth of COVID-19 patient interactions with a health system. Our first objective was to create a COVID-19 dataset that linked primary care data to COVID-19 testing, hospitalisation, and mortality data at a patient level. Our second objective was to provide a descriptive analysis of COVID-19 outcomes among the general population and describe the characteristics of the affected individuals.\n\nMethodsWe mapped patient-level data from Catalonia, Spain, to the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM). More than 3,000 data quality checks were performed to assess the readiness of the database for research. Subsequently, to summarise the COVID-19 population captured, we established a general population cohort as of the 1st March 2020 and identified outpatient COVID-19 diagnoses or positive test results for SARS-CoV-2, hospitalisations with COVID-19, and COVID-19 deaths during follow-up, which went up until 30th June 2021.\n\nFindingsMapping data to the OMOP CDM was performed and high data quality was observed. The mapped database was used to identify a total of 5,870,274 individuals, who were included in the general population cohort as of 1st March 2020. Over follow up, 604,472 had either an outpatient COVID-19 diagnosis or positive test result, 58,991 had a hospitalisation with COVID-19, 5,642 had an ICU admission with COVID-19, and 11,233 had a COVID-19 death. People who were hospitalised or died were more commonly older, male, and with more comorbidities. Those admitted to ICU with COVID-19 were generally younger and more often male than those hospitalised in general and those who died.\n\nInterpretationWe have established a comprehensive dataset that captures COVID-19 diagnoses, test results, hospitalisations, and deaths in Catalonia, Spain. Extensive data checks have shown the data to be fit for use. From this dataset, a general population cohort of 5.9 million individuals was identified and their COVID-19 outcomes over time were described.\n\nFundingGeneralitat de Catalunya and European Health Data and Evidence Network (EHDEN).",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Edward Burn",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Sergio Fern\u00e1ndez-Bertol\u00edn",
+        "author_inst": "IDIAPJGol, Barcelona, Spain"
+      },
+      {
+        "author_name": "Erica A Voss",
+        "author_inst": "Janssen Pharmaceutical Research and Development, Titusville, NJ, USA"
+      },
+      {
+        "author_name": "Clair Blacketer",
+        "author_inst": "Janssen Pharmaceutical Research and Development, Titusville, NJ, USA"
+      },
+      {
+        "author_name": "Maria Arag\u00f3n",
+        "author_inst": "IDIAPJGol, Barcelona, Spain"
+      },
+      {
+        "author_name": "Martina Recalde",
+        "author_inst": "IDIAPJGol, Barcelona, Spain"
+      },
+      {
+        "author_name": "Elena Roel",
+        "author_inst": "IDIAPJGol, Barcelona, Spain"
+      },
+      {
+        "author_name": "Andrea Pistillo",
+        "author_inst": "IDIAPJGol, Barcelona, Spain"
+      },
+      {
+        "author_name": "Berta Ravent\u00f3s",
+        "author_inst": "IDIAPJGol, Barcelona, Spain"
+      },
+      {
+        "author_name": "Carlen Reyes",
+        "author_inst": "IDIAPJGol, Barcelona, Spain"
+      },
+      {
+        "author_name": "Sebastiaan van Sandijk",
+        "author_inst": "Odysseus Data Services s.r.o., Prague, Czech Republic"
+      },
+      {
+        "author_name": "Lars Halvorsen",
+        "author_inst": "edenceHealth NV, Kontich, Belgium"
+      },
+      {
+        "author_name": "Peter R Rijnbeek",
+        "author_inst": "Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands"
+      },
+      {
+        "author_name": "Talita Duarte-Salles",
+        "author_inst": "IDIAPJGol, Barcelona, Spain"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.11.21.21266655",
     "rel_title": "Determining international spread of novel B.1.1.523 SARS-CoV-2 lineage",
@@ -498285,41 +497135,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.11.23.21266574",
-    "rel_title": "Reinfection with SARS-CoV-2: outcome, risk factors and vaccine efficacy in a Scottish cohort",
-    "rel_date": "2021-11-24",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.23.21266574",
-    "rel_abs": "BackgroundThe objective of this study was to investigate how protection against COVID-19 conferred by previous infection is modified by vaccination.\n\nMethodsIn a cohort of all 152655 individuals in Scotland alive at 90 days after a positive test for SARS-CoV-2 (confirmed by cycle threshold < 30, or two tests) followed till 22 September 2021, rate ratios for reinfection were estimated with calendar time or tests as timescale.\n\nFindingsRates of detected and hospitalised reinfection with COVID-19 while unvaccinated were respectively 6.8 (95% CI 6.4 to 7.2) and 0.18 (95% CI 0.12 to 0.25) per 1000 person-months. These rates were respectively 68% and 74% lower than in a matched cohort of individuals who had not previously tested positive. Efficacy of two doses of vaccine in those with previous infection was estimated as as 84% (95 percent CI 81% to 86%) against detected reinfection and 71% (95 percent CI 29% to 88%) against hospitalised or fatal reinfection. The rate of detected reinfection after two doses of vaccine was 1.35 (95% CI 1.02 to 1.78) times higher in those vaccinated before first infection than in those unvaccinated at first infection.\n\nInterpretationThe combination of natural infection and vaccination provides maximal protection against new infection with SARS-CoV-2: prior vaccination does not impair this protection.\n\nFundingNo specific funding was received for this work.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSIn a recent systematic review of cohort studies reported up to July 2021, the average reduction in COVID-19 infection rates in those with previous infection compared with those without evidence of previous infection was 90%. There is little information about the protective effect of previous infection against severe COVID-19, or about how the protective effects of previous infection against reinfection and severe disease are modified by vaccination.\n\nWhat this paper addsIn unvaccinated individuals the protection against hospitalised COVID-19 conferred by previous infection is similar to that induced by vaccination. In those with previous infection, vaccination reduces the rates of reinfection and hospitalised COVID-19 by about 70%.\n\nImplications of all the available evidenceThe combination of natural infection and vaccination provides maximal protection against COVID-19: prior vaccination does not seriously impair this protection.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Paul M McKeigue",
-        "author_inst": "University of Edinburgh"
-      },
-      {
-        "author_name": "David McAllister",
-        "author_inst": "University of Glasgow"
-      },
-      {
-        "author_name": "Chris Robertson",
-        "author_inst": "University of Strathclyde"
-      },
-      {
-        "author_name": "Diane Stockton",
-        "author_inst": "Public Health Scotland"
-      },
-      {
-        "author_name": "Helen Colhoun",
-        "author_inst": "University of Edinburgh"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.11.23.21266775",
     "rel_title": "Recurring Spatiotemporal Patterns of COVID-19 in the United States",
@@ -498598,6 +497413,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.11.17.21266441",
+    "rel_title": "Pausing methotrexate improves immunogenicity of COVID-19 vaccination in patients with rheumatic diseases",
+    "rel_date": "2021-11-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.17.21266441",
+    "rel_abs": "ObjectiveTo study the effect of methotrexate (MTX) and its discontinuation on the humoral immune response after COVID-19 vaccination in patients with autoimmune rheumatic diseases (AIRD).\n\nMethodsIn this retrospective study, neutralising SARS-CoV-2 antibodies were measured after second vaccination in 64 rheumatic patients on methotrexate therapy, 31 of whom temporarily paused medication without a fixed regimen. The control group consisted of 21 AIRD patients without immunosuppressive medication.\n\nResultsMTX patients showed a significantly lower mean antibody response compared to AIRD patients without immunosuppressive therapy (71.8 % vs 92.4 %, p<0.001). For patients taking MTX, age correlated negatively with immune response (r=-0.49; p<0.001). All nine patients with antibody levels below the cut-off were older than 60 years. Patients who held MTX during at least one vaccination showed significantly higher mean neutralising antibody levels after second vaccination, compared to patients who continued MTX therapy during both vaccinations (83.1 % vs 61.2 %, p=0.001). This effect was particularly pronounced in patients older than 60 years (80.8 % vs 51.9 %, p=0.001). The impact of the time period after vaccination was greater than of the time before vaccination with the critical cut-off being 10 days.\n\nConclusionMTX reduces the immunogenicity of SARS-CoV-2 vaccination in an age-dependent manner. Our data further suggest that holding MTX for at least 10 days after vaccination significantly improves the antibody response in patients over 60 years of age.",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Amanthi Nadira Arumahandi de Silva",
+        "author_inst": "Department of Rheumatology and Clinical Immunology, Charite University Hospital, Chariteplatz 1, 10117 Berlin, Germany"
+      },
+      {
+        "author_name": "Leonie Maria Frommert",
+        "author_inst": "Department of Rheumatology and Clinical Immunology, Charite University Hospital, Chariteplatz 1, 10117 Berlin, Germany"
+      },
+      {
+        "author_name": "Fredrik N Albach",
+        "author_inst": "Department of Rheumatology and Clinical Immunology, Charite University Hospital, Chariteplatz 1, 10117 Berlin, Germany"
+      },
+      {
+        "author_name": "Jens Klotsche",
+        "author_inst": "German Rheumatism Research Center Berlin, Chariteplatz 1, 10117 Berlin, Germany"
+      },
+      {
+        "author_name": "Veronika Scholz",
+        "author_inst": "Department of Rheumatology and Clinical Immunology, Charite University Hospital, Chariteplatz 1, 10117 Berlin, Germany"
+      },
+      {
+        "author_name": "Alexander ten Hagen",
+        "author_inst": "Department of Rheumatology and Clinical Immunology, Charite University Hospital, Chariteplatz 1, 10117 Berlin, Germany"
+      },
+      {
+        "author_name": "Lara Maria Jeworowski",
+        "author_inst": "Institute of Virology, Charite University Hospital, Chariteplatz 1, 10117 Berlin, Germany"
+      },
+      {
+        "author_name": "Tatjana Schwarz",
+        "author_inst": "Institute of Virology, Charite University Hospital, Chariteplatz 1, 10117 Berlin, Germany"
+      },
+      {
+        "author_name": "Jan Zernicke",
+        "author_inst": "Department of Rheumatology and Clinical Immunology, Charite University Hospital, Chariteplatz 1, 10117 Berlin, Germany"
+      },
+      {
+        "author_name": "Victor Max Corman",
+        "author_inst": "Institute of Virology, Charite University Hospital, Chariteplatz 1, 10117 Berlin, Germany"
+      },
+      {
+        "author_name": "Christian Drosten",
+        "author_inst": "Institute of Virology, Charite University Hospital, Chariteplatz 1, 10117 Berlin, Germany"
+      },
+      {
+        "author_name": "Gerd Ruediger Burmester",
+        "author_inst": "Department of Rheumatology and Clinical Immunology, Charite University Hospital, Chariteplatz 1, 10117 Berlin, Germany"
+      },
+      {
+        "author_name": "Robert Biesen",
+        "author_inst": "Department of Rheumatology and Clinical Immunology, Charite University Hospital, Chariteplatz 1, 10117 Berlin, Germany"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "rheumatology"
+  },
   {
     "rel_doi": "10.1101/2021.11.20.469409",
     "rel_title": "Airway epithelial interferon response to SARS-CoV-2 is inferior to rhinovirus and heterologous rhinovirus infection suppresses SARS-CoV-2 replication",
@@ -500087,65 +498969,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health systems and quality improvement"
   },
-  {
-    "rel_doi": "10.1101/2021.11.18.21266478",
-    "rel_title": "Serum SARS-CoV-2 Antigens for the Determination of COVID-19 Severity",
-    "rel_date": "2021-11-21",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.18.21266478",
-    "rel_abs": "The diagnostic of SARS-CoV-2 infection relies on reverse transcriptase polymerase chain reactions (RT-PCR) performed on nasopharyngeal (NP) swabs. Nevertheless, false negative results can be obtained with inadequate sampling procedures making the use of other matrices of interest. This study aims at evaluating the kinetic of serum N antigen in severe and non-severe patients and compare the clinical performance of serum antigenic assays with NP RT-PCR. Ninety patients were included and monitored for several days. Disease severity was determined according to the WHO clinical progression scale. The serum N antigen was measured with a chemiluminescent assay (CLIA) and the Single Molecular Array (Simoa). Thresholds for severity were determined. In severe patients, the peak antigen response was observed 7 days after the onset of symptoms followed by a decline. No peak response was observed in non-severe patients. Severity threshold for the Simoa and the CLIA provided positive likelihood ratio of 30.0 and 10.9 for the timeframe between day 2 and day 14, respectively. Compared to NP RT-PCR, antigenic assays were able to discriminate the severity of the disease (p = 0.0174, 0.0310 and p = 0.1551 with the Simoa, the CLIA and the NP RT-PCR, respectively). Sensitive N antigen detection in serum thus provides a valuable new marker for COVID-19 diagnosis and evaluation of disease severity. When assessed during the first 2 weeks since the onset of symptoms, it may help in identifying patients at risk of developing severe COVID-19 to optimize better intensive care utilization.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Julien Favresse",
-        "author_inst": "SLBO"
-      },
-      {
-        "author_name": "Jean-Louis Bayart",
-        "author_inst": "CSPO"
-      },
-      {
-        "author_name": "Clara David",
-        "author_inst": "QualiBlood"
-      },
-      {
-        "author_name": "Constant Gillot",
-        "author_inst": "UNamur"
-      },
-      {
-        "author_name": "Gr\u00e9goire Wie\u00ebrs",
-        "author_inst": "CSPO"
-      },
-      {
-        "author_name": "Gatien Roussel",
-        "author_inst": "Clinique Saint-Pierre Ottignies"
-      },
-      {
-        "author_name": "Guillaume Sondag",
-        "author_inst": "SLBO"
-      },
-      {
-        "author_name": "Marc Elsen",
-        "author_inst": "SLBO"
-      },
-      {
-        "author_name": "Christine Eucher",
-        "author_inst": "SLBO"
-      },
-      {
-        "author_name": "Jean-Michel Dogn\u00e9",
-        "author_inst": "UNamur"
-      },
-      {
-        "author_name": "Jonathan Douxfils",
-        "author_inst": "University of Namur"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.11.19.21266588",
     "rel_title": "Longitudinal SARS-CoV-2 RNA Wastewater Monitoring Across a Range of Scales Correlates with Total and Regional COVID-19 Burden in a Well-Defined Urban Population",
@@ -500640,6 +499463,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.11.20.21266644",
+    "rel_title": "Immunogenicity of heterologous prime/boost inactivated and mRNA COVID-19 vaccine",
+    "rel_date": "2021-11-21",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.20.21266644",
+    "rel_abs": "IntroductionIn August 2021, Thailand imported the BNT162b2 mRNA COVID-19 vaccine. The prioritised group to receive the BNT162b2 vaccine were health professionals. The BNT162b2 vaccine scheduled for healthcare workers were two-dose regimen administered three weeks apart, the third dose booster in two-dose inactivated CoronaVac vaccine recipients or as a second dose in health professionals who had received the CoronaVac or adenoviral-vectored (ChAdOx1-S) vaccine as the first dose regardless of the interval between the first and second dose.\n\nMethodsThis study aims to evaluate the immunogenicity of the heterologous prime boost CoronaVac followed by BNT162b2 in health professionals.\n\nResultsThe CoronaVac/BNT162b2 vaccine recipients elicited higher neutralizing activity against the original Wuhan and all variants of concern than in the recipients of the two-dose CoronaVac.\n\nConclusionsThe heterologous CoronaVac/BNT162b2 could be used as an alternative regimen in countries experiencing the vaccine shortages and in individuals experiencing the adverse events following CoronaVac.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Nasamon Wanlapakorn",
+        "author_inst": "Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand."
+      },
+      {
+        "author_name": "Ritthideach Yorsaeng",
+        "author_inst": "Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand"
+      },
+      {
+        "author_name": "Harit Phowatthanasathian",
+        "author_inst": "Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand"
+      },
+      {
+        "author_name": "Nungruthai Suntronwong",
+        "author_inst": "Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand"
+      },
+      {
+        "author_name": "Sitthichai Kanokudom",
+        "author_inst": "Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand"
+      },
+      {
+        "author_name": "Natthinee Sudhinaraset",
+        "author_inst": "Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand"
+      },
+      {
+        "author_name": "Yong Poovorawan",
+        "author_inst": "Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand, FRS(T), the Royal Society"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "allergy and immunology"
+  },
   {
     "rel_doi": "10.1101/2021.11.19.21266605",
     "rel_title": "Myocarditis and Pericarditis following COVID-19 Vaccination: Rapid Systematic Review of Incidence, Risk Factors, and Clinical Course",
@@ -501865,45 +500731,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.11.17.21266445",
-    "rel_title": "Evaluation of a novel direct capture method for virus concentration n wastewater from COVID-19 infectious ward and correlation analysis with the number of inpatients.",
-    "rel_date": "2021-11-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.17.21266445",
-    "rel_abs": "The global outbreak of the SARS-CoV-2 pandemic has increased the focus of Wastewater-based epidemiology (WBE) studies as a tool for understanding the epidemic and risk management. A highly sensitive and rapid method for the virus concentration from wastewater is needed to obtain the accurate information for early detection of SARS-CoV-2 outbreak and epidemic. In this study, we evaluated the efficiency of the direct capture method provided from Promega, based on column adsorption using the wastewater from actual infectious diseases ward. The efficiency of the nucleic acid extraction-purification process was also evaluated by Maxwell(R) RSC instrument (fully automated extraction) and QIAamp Viral RNA mini kit (manual extraction). The obtained SARS-CoV-2 data from wastewater were analyzed with the number of inpatients which is the consideration of the severity and the days of onset. The combination of direct capture and Maxwells method (DC-MW) was suggested to be a highly sensitive and simple method with better concentration efficiency and quantification than other methods. Moreover, the inpatient conditions (severity and days of after onset) should be considered to accurately understand the actual status of the correlation between the number of inpatients and SARS-CoV-2 concentration in wastewater. The highly sensitive method of DC-MW was suggested to assess more actual situation of SARS-CoV-2 shedding into the wastewater.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Manami Inaba",
-        "author_inst": "Yamaguchi University"
-      },
-      {
-        "author_name": "Ryohei Nakao",
-        "author_inst": "Yamaguchi University"
-      },
-      {
-        "author_name": "Fumiko Imamura",
-        "author_inst": "NIPPON KOEI CO., Research & Development Center Center for Advanced Research"
-      },
-      {
-        "author_name": "Yutaka Nakashima",
-        "author_inst": "Yamaguchi Prefectural Grand Medical Center"
-      },
-      {
-        "author_name": "Seiji Miyazono",
-        "author_inst": "Yamaguchi University"
-      },
-      {
-        "author_name": "Yoshihisa Akamatsu",
-        "author_inst": "Yamaguchi University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.11.15.21266335",
     "rel_title": "A SARS-CoV-2 Delta Variant Containing Mutation in the Probe Binding Region Used for qRT-PCR Test in Japan Exhibited Atypical PCR Amplification and Might Induce False Negative Result",
@@ -502214,6 +501041,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.11.17.21266410",
+    "rel_title": "COVID-19 management in social care in England: a systematic review of changing policies and newspaper reported staff perspectives.",
+    "rel_date": "2021-11-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.17.21266410",
+    "rel_abs": "Adult social care has been a major focus of public attention and infection control guidance during the COVID-19 pandemic, with a high mortality both for carers and those receiving care. To protect themselves and others from infection, staff in residential and domiciliary care settings had to quickly adapt to infection control measures that heavily impacted on their working and every-day life, whilst navigating new responsibilities, uncertainties and anxieties. We sought to explore the production and reception of guidance and look at ways these can be adapted to improve the working life of care staff in domiciliary and residential care whilst reducing the risk of SARS-CoV-2 transmission amid this pandemic and of future emerging infections.\n\nWe conducted two complementary and integrated systematic reviews of published documents in the pre-vaccination era: (1) National guidance for social care (conducted between 29 July to 28 October 2020), and (2) Newspaper coverage of infection control issues in social care (conducted between 27th July to 10th September 2020).\n\nThree higher order common themes emerged in the integrated systematic review of guidance documents and newspaper articles: a) Testing, b) Personal Protective Equipment, c) Employment. The reviews revealed a sharp disjunction between the content of infection control guidance and its usability and applicability in social care settings. We suggest that infection control guidance needs to be better adapted to social care settings and informed by the sector. The practicalities of care work and care settings need to be at the core of the process for guidance to be relevant and effective. Modes and timings of communications also need to be optimised.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Lavinia Bertini",
+        "author_inst": "Department of Primary Care and Public Health, Brighton and Sussex Medical School, Falmer, UK."
+      },
+      {
+        "author_name": "Leanne Bogen-Johnston",
+        "author_inst": "School of Psychology, University of Sussex, Falmer, UK"
+      },
+      {
+        "author_name": "Jo Middleton",
+        "author_inst": "Department of Primary Care and Public Health, Brighton and Sussex Medical School, Falmer, UK."
+      },
+      {
+        "author_name": "Wendy Wood",
+        "author_inst": "School of Health Sciences, University of Brighton, UK."
+      },
+      {
+        "author_name": "Shanu Sadhwani",
+        "author_inst": "Department of Primary Care and Public Health, Brighton and Sussex Medical School, Falmer, UK."
+      },
+      {
+        "author_name": "Julien Forder",
+        "author_inst": "Personal Social Services Research Unit, University of Kent, Canterbury, UK."
+      },
+      {
+        "author_name": "Daniel Roland",
+        "author_inst": "Personal Social Services Research Unit, University of Kent, Canterbury, UK."
+      },
+      {
+        "author_name": "Rebecca Sharp",
+        "author_inst": "Kent Surrey Sussex Academic Health Science Network, Worthing, West Sussex, UK."
+      },
+      {
+        "author_name": "John Drury",
+        "author_inst": "School of Psychology, University of Sussex, Falmer, UK."
+      },
+      {
+        "author_name": "Jackie A Cassell",
+        "author_inst": "Department of Primary Care and Public Health, Brighton and Sussex Medical School, Falmer, UK."
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.11.17.21266392",
     "rel_title": "Impact of dexamethasone on persistent symptoms of COVID-19: an observational study",
@@ -503507,65 +502389,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.11.17.21265440",
-    "rel_title": "COVID-19 first and delta waves in relation to ACEI, ARB, Influenza vaccination, and comorbidity in a North Metropolitan Barcelona Health Consortium",
-    "rel_date": "2021-11-17",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.17.21265440",
-    "rel_abs": "BACKGROUNDSome authors have reported that angiotensin converter enzyme inhibitors (ACEI) and angiotensin receptor blockers (ARB) improve clinical outcomes in hypertensive COVID-19 patients, and others have proposed cross-protection for influenza vaccination. This study explores the impact of these variables on the evolution of hospitalized patients, focusing in the first wave and the Delta wave.\n\nMETHODSHospitalizations (n=1888) from March 1, 2020, to July 31, 2021, in the Hospital of Terrassa, the referral center for the free access Terrassa Health Consortium in the North Metropolitan Barcelona Health Region (population=167,386) were studied. The number of chronic treatments and conditions of patients from the initial outbreak (n=184) and the Delta outbreak (n=158) were recorded.\n\nRESULTSOf the non-survivors, 96.3% were aged >60 years in the first wave and 100% were aged >70 years in the Delta wave. In non-survival hospitalized patients aged >60 years, the percentage treated with ACEI was similar to general population but was significantly different for ARB treatments of influenza vaccination, although associated to a higher comorbidity and age. In July 2021, the number of hospitalizations for patients aged <50 years was higher than March 2020 and 22% of hospitalized patients without chronic treatments and conditions needed admission to the intensive care unit. Mortality was reduced in the groups with most comorbidities who received influenza and SARS-CoV2 vaccination.\n\nCONCLUSIONSIn COVID-19 infection, age and comorbidity are related to survival, ACEI use is safe. A high proportion of patients without comorbidity require hospitalization and intensive care.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Marta Juanes-Gonzalez",
-        "author_inst": "Terrassa Health Consortium"
-      },
-      {
-        "author_name": "Ana Calderon-Valdiviezo",
-        "author_inst": "Terrassa Health Consortium"
-      },
-      {
-        "author_name": "Helena Losa-Puig",
-        "author_inst": "Terrassa Health Consortium. Now at Hospital Alvaro Cunqueiro."
-      },
-      {
-        "author_name": "Roger Valls-Foix",
-        "author_inst": "Terrassa Health Consortium"
-      },
-      {
-        "author_name": "Marta Gonzalez-Salvador",
-        "author_inst": "Terrassa Health Consortium"
-      },
-      {
-        "author_name": "Marc Leon-Perez",
-        "author_inst": "Terrassa Health Consortium"
-      },
-      {
-        "author_name": "Luis Pueyo Anton",
-        "author_inst": "Terrassa Health Consortium"
-      },
-      {
-        "author_name": "Celia Lozano-Paz",
-        "author_inst": "Terrassa Health Consortium"
-      },
-      {
-        "author_name": "Maite Franco-Romero",
-        "author_inst": "Terrassa Health Consortium"
-      },
-      {
-        "author_name": "Josep Vidal-Alaball",
-        "author_inst": "Catalan Health Institute, Foundation University Institute for Primary Health Care Research Jordi Gol i Gurina, University of Vic-Central University of Catalonia"
-      },
-      {
-        "author_name": "Anna Puigdellivol-Sanchez",
-        "author_inst": "Consorci Sanitari de Terrassa"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.11.17.21266455",
     "rel_title": "Estimating COVID-19-induced Excess Mortality in Lombardy",
@@ -503784,6 +502607,97 @@
     "type": "new results",
     "category": "bioinformatics"
   },
+  {
+    "rel_doi": "10.1101/2021.11.15.468720",
+    "rel_title": "Susceptibility of sheep to experimental co-infection with the ancestral lineage of SARS-CoV-2 and its alpha variant",
+    "rel_date": "2021-11-17",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.15.468720",
+    "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for a global pandemic that has had significant impacts on human health and economies worldwide. SARS-CoV-2 is highly transmissible and the cause of coronavirus disease 2019 (COVID-19) in humans. A wide range of animal species have also been shown to be susceptible to SARS-CoV-2 infection by experimental and/or natural infections. Domestic and large cats, mink, ferrets, hamsters, deer mice, white-tailed deer, and non-human primates have been shown to be highly susceptible, whereas other species such as mice, dogs, pigs, and cattle appear to be refractory to infection or have very limited susceptibility. Sheep (Ovis aries) are a commonly farmed domestic ruminant that have not previously been thoroughly investigated for their susceptibility to SARS-CoV-2. Therefore, we performed in vitro and in vivo studies which consisted of infection of ruminant-derived cell cultures and experimental challenge of sheep to investigate their susceptibility to SARS-CoV-2. Our results showed that sheep-derived cell cultures support SARS-CoV-2 replication. Furthermore, experimental challenge of sheep demonstrated limited infection with viral RNA shed in nasal and oral swabs primarily at 1-day post challenge (DPC), and also detected in the respiratory tract and lymphoid tissues at 4 and 8 DPC. Sero-reactivity was also observed in some of the principal infected sheep but not the contact sentinels, indicating that transmission to co-mingled naive sheep was not highly efficient; however, viral RNA was detected in some of the respiratory tract tissues of sentinel animals at 21 DPC. Furthermore, we used challenge inoculum consisting of a mixture of two SARS-CoV-2 isolates, representatives of the ancestral lineage A and the B.1.1.7-like alpha variant of concern (VOC), to study competition of the two virus strains. Our results indicate that sheep show low susceptibility to SARS-CoV-2 infection, and that the alpha VOC outcompeted the ancestral lineage A strain.",
+    "rel_num_authors": 19,
+    "rel_authors": [
+      {
+        "author_name": "Natasha N Gaudreault",
+        "author_inst": "Kansas State University College of Veterinary Medicine"
+      },
+      {
+        "author_name": "Konner Cool",
+        "author_inst": "Kansas State University"
+      },
+      {
+        "author_name": "Jessie D Trujillo",
+        "author_inst": "Kansas State University College of Veterinary Medicine"
+      },
+      {
+        "author_name": "Igor Morozov",
+        "author_inst": "Kansas State University College of Veterinary Medicine"
+      },
+      {
+        "author_name": "David A Meekins",
+        "author_inst": "Kansas State University College of Veterinary Medicine"
+      },
+      {
+        "author_name": "Chester D McDowell",
+        "author_inst": "Kansas State University College of Veterinary Medicine"
+      },
+      {
+        "author_name": "Dashzeveg Bold",
+        "author_inst": "Kansas State University College of Veterinary Medicine"
+      },
+      {
+        "author_name": "Mariano Carossino",
+        "author_inst": "Louisiana State University"
+      },
+      {
+        "author_name": "Velmurugan Balaraman",
+        "author_inst": "Kanasas State University"
+      },
+      {
+        "author_name": "Dana Mitzel",
+        "author_inst": "ARS-USDA"
+      },
+      {
+        "author_name": "Taeyong Kwon",
+        "author_inst": "Kansas State University"
+      },
+      {
+        "author_name": "Daniel W Madden",
+        "author_inst": "Kansas State University"
+      },
+      {
+        "author_name": "Bianca Libanori Artiaga",
+        "author_inst": "Kansas State University"
+      },
+      {
+        "author_name": "Roman Pogranichniy",
+        "author_inst": "Kansas State University"
+      },
+      {
+        "author_name": "Gleyder Roman-Sosa",
+        "author_inst": "Kansas State University; Institut fur Virologie, Justus-Liebig-Universitat"
+      },
+      {
+        "author_name": "William C Wilson",
+        "author_inst": "USDA-ARS"
+      },
+      {
+        "author_name": "Udeni BR Balasuriya",
+        "author_inst": "Louisiana State University"
+      },
+      {
+        "author_name": "Adolfo Garcia-Sastre",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Juergen A Richt",
+        "author_inst": "Kansas State University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2021.11.15.468761",
     "rel_title": "Microglia do not restrict SARS-CoV-2 replication following infection of the central nervous system of K18-hACE2 transgenic mice",
@@ -505097,45 +504011,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "respiratory medicine"
   },
-  {
-    "rel_doi": "10.1101/2021.11.15.21266341",
-    "rel_title": "Effectiveness of BNT162b2 (Comirnaty, Pfizer-BioNTech) COVID-19 booster vaccine against covid-19 related symptoms in England: test negative case-control study",
-    "rel_date": "2021-11-15",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.15.21266341",
-    "rel_abs": "BackgroundIn September 2021, the UK Government introduced a booster programme targeting individuals over 50 and those in a clinical risk group. Individuals were offered either a full dose of the BNT162b2 (Comirnaty, Pfizer-BioNTech) vaccine or a half dose of the mRNA-1273 (Spikevax, Moderna) vaccine, irrespective of the vaccine received as the primary course\n\nMethodsWe used a test-negative case-control design to estimate the Vaccine Effectiveness (VE) of the booster dose BNT162b2 (Comirnaty, Pfizer-BioNTech) in those aged over 50 against symptomatic disease in post booster time intervals compared to individuals at least 140 days post a second dose with no booster dose recorded. In a secondary analysis, we also compared to unvaccinated individuals and to the 2 to 6 day period after a booster dose was received. Analyses were stratified by which primary doses had been received and any mixed primary courses were excluded.\n\nResultsThe relative VE estimate in the 14 days after the BNT162b2 (Comirnaty, Pfizer-BioNTech) booster dose, compared to individuals that received a two-dose primary course, was 87.4 (95% confidence interval 84.9-89.4) in those individuals who received two doses ChAdOx1-S (Vaxzevria, AstraZeneca) as a primary course and 84.4 (95% confidence interval 82.8-85.8) in those individuals who received two doses of BNT162b2 (Comirnaty, Pfizer-BioNTech) as a primary course. Using the 2-6 day period post the booster dose as the baseline gave similar results. The absolute VE from 14 days after the booster, using the unvaccinated baseline, was 93.1(95% confidence interval 91.7-94.3) in those with ChAdOx1-S (Vaxzevria, AstraZeneca) as their primary course and 94.0 (93.4-94.6) for BNT162b2 (Comirnaty, Pfizer-BioNTech) as their primary course.\n\nConclusionsOur study provides real world evidence of significant increased protection from the booster vaccine dose against symptomatic disease in those aged over 50 year of age irrespective of which primary course was received.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Nick Andrews",
-        "author_inst": "UK health Security Agency"
-      },
-      {
-        "author_name": "Julia Stowe",
-        "author_inst": "UK health Security Agency"
-      },
-      {
-        "author_name": "Freja Kirsebom",
-        "author_inst": "UK health Security Agency"
-      },
-      {
-        "author_name": "Charlotte Gower",
-        "author_inst": "UK health Security Agency"
-      },
-      {
-        "author_name": "Mary Ramsay",
-        "author_inst": "UK health Security Agency"
-      },
-      {
-        "author_name": "Jamie Lopez Bernal",
-        "author_inst": "UK health Security Agency"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.11.15.21266317",
     "rel_title": "Effect of COVID-19 vaccination on menstrual periods in a retrospectively recruited cohort",
@@ -505730,6 +504605,25 @@
     "type": "new results",
     "category": "biophysics"
   },
+  {
+    "rel_doi": "10.1101/2021.11.15.468283",
+    "rel_title": "Mutagenic distinction between the receptor-binding and fusion subunits of the SARS-CoV-2 spike glycoprotein",
+    "rel_date": "2021-11-15",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.15.468283",
+    "rel_abs": "We observe that a residue R of the spike glycoprotein of SARS-CoV-2 which has mutated in one or more of the current Variants of Concern or Interest or under Monitoring rarely participates in a backbone hydrogen bond if R lies in the S1 subunit and usually participates in one if R lies in the S2 subunit. A partial explanation for this based upon free energy is explored as a potentially general principle in the mutagenesis of viral glycoproteins. This observation could help target future vaccine cargos for the evolving coronavirus as well as more generally. A study of the Delta and Omicron variants suggests that Delta was an energetically necessary intermediary in the evolution from Wuhan-Hu-1 to Omicron.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Robert Clark Penner",
+        "author_inst": "Institut des Hautes Etudes Scientifiques"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2021.11.12.468374",
     "rel_title": "Full protection against all four SARS-CoV-2 variants of concern (VOC) in hamsters requires revision of spike antigen used for vaccination.",
@@ -507363,93 +506257,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.11.11.21266241",
-    "rel_title": "Finger stick blood test to assess post vaccination SARS-CoV-2 neutralizing antibody response against variants",
-    "rel_date": "2021-11-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.11.21266241",
-    "rel_abs": "There is clinical need for a quantifiable point-of-care (PoC) SARS-CoV-2 neutralizing antibody (nAb) test that is adaptable with the pandemics changing landscape. Here, we present a rapid and semi-quantitative nAb test that uses finger stick or venous blood to assess the nAb response of vaccinated population against wild-type, alpha, beta, gamma, and delta variant receptor binding domains. It captures a clinically relevant range of nAb levels, and effectively differentiates pre-vaccination, post 1st dose and post 2nd dose vaccination samples within 10 minutes. The data observed against alpha, beta, gamma, and delta variants agrees with published results evaluated in established serology tests. Finally, our test revealed a substantial reduction in nAb level for beta, gamma, and delta variants between early BNT162b2 vaccination group (within 3 months) and later vaccination group (post 3 months). This test is highly suited for PoC settings and provides an insightful nAb response in a post-vaccinated population.",
-    "rel_num_authors": 18,
-    "rel_authors": [
-      {
-        "author_name": "Rachel Lim",
-        "author_inst": "Singapore-MIT Alliance in Research and Technology"
-      },
-      {
-        "author_name": "Hoi Lok Cheng",
-        "author_inst": "Singapore-MIT Alliance in Research and Technology"
-      },
-      {
-        "author_name": "Jia Huan",
-        "author_inst": "Singapore-MIT Alliance in Research and Technology"
-      },
-      {
-        "author_name": "Patthara Kongsuphol",
-        "author_inst": "Singapore-MIT Alliance in Research and Technology"
-      },
-      {
-        "author_name": "Bhuvaneshwari D/O Shunmuganath",
-        "author_inst": "National University of Singapore"
-      },
-      {
-        "author_name": "Wei Chen Ming",
-        "author_inst": "Nanyang Technological University"
-      },
-      {
-        "author_name": "Say Yong Ng",
-        "author_inst": "Singapore-MIT Alliance in Research and Technology"
-      },
-      {
-        "author_name": "Xiaohong Gao",
-        "author_inst": "Nanyang Technological University"
-      },
-      {
-        "author_name": "Shuvan Prashant Turaga",
-        "author_inst": "Attonics System Pte"
-      },
-      {
-        "author_name": "Sascha P Heussler",
-        "author_inst": "Attonics System Pte"
-      },
-      {
-        "author_name": "Joyti Somani",
-        "author_inst": "National University Hospital"
-      },
-      {
-        "author_name": "Sharmila Sengupta",
-        "author_inst": "National University Hospital"
-      },
-      {
-        "author_name": "Dousabel MY Tay",
-        "author_inst": "MIT"
-      },
-      {
-        "author_name": "Megan E McBee",
-        "author_inst": "Singapore-MIT Alliance in Research and Technology"
-      },
-      {
-        "author_name": "Barnaby Young",
-        "author_inst": "National Centre for Infectious Diseases"
-      },
-      {
-        "author_name": "Paul A MacAry",
-        "author_inst": "National University of Singapore"
-      },
-      {
-        "author_name": "HAdley D Sikes",
-        "author_inst": "Singapore-MIT Alliance in Research and Technology"
-      },
-      {
-        "author_name": "Peter Preiser",
-        "author_inst": "Nanyang Technological University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.11.10.21265739",
     "rel_title": "Limited impact of contact tracing in a University setting for COVID-19 due to asymptomatic transmission and social distancing",
@@ -507844,6 +506651,109 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.11.10.467646",
+    "rel_title": "Total virome characterizations of game animals in China reveals a spectrum of emerging viral pathogens",
+    "rel_date": "2021-11-12",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.10.467646",
+    "rel_abs": "Game animals are wildlife species often traded and consumed as exotic food, and are potential reservoirs for SARS-CoV and SARS-CoV-2. We performed a meta-transcriptomic analysis of 1725 game animals, representing 16 species and five mammalian orders, sampled across China. From this we identified 71 mammalian viruses, with 45 described for the first time. Eighteen viruses were considered as potentially high risk to humans and domestic animals. Civets (Paguma larvata) carried the highest number of potentially high risk viruses. We identified the transmission of Bat coronavirus HKU8 from a bat to a civet, as well as cross-species jumps of coronaviruses from bats to hedgehogs and from birds to porcupines. We similarly identified avian Influenza A virus H9N2 in civets and Asian badgers, with the latter displaying respiratory symptoms, as well as cases of likely human-to-wildlife virus transmission. These data highlight the importance of game animals as potential drivers of disease emergence.\n\nHighlightsO_LI1725 game animals from five mammalian orders were surveyed for viruses\nC_LIO_LI71 mammalian viruses were discovered, 18 with a potential risk to humans\nC_LIO_LICivets harbored the highest number of potential  high risk viruses\nC_LIO_LIA species jump of an alphacoronavirus from bats to a civet was identified\nC_LIO_LIH9N2 influenza virus was detected in a civet and an Asian badger\nC_LIO_LIHumans viruses were also identified in game animals\nC_LI",
+    "rel_num_authors": 22,
+    "rel_authors": [
+      {
+        "author_name": "Wan-Ting He",
+        "author_inst": "Nanjing Agricultural University"
+      },
+      {
+        "author_name": "Xin Hou",
+        "author_inst": "Sun Yat-sen University"
+      },
+      {
+        "author_name": "Jin Zhao",
+        "author_inst": "Nanjing Agricultural University"
+      },
+      {
+        "author_name": "Jiumeng Sun",
+        "author_inst": "Nanjing Agricultural University"
+      },
+      {
+        "author_name": "Haijian He",
+        "author_inst": "Agricultural College, Jinhua Polytechnic"
+      },
+      {
+        "author_name": "Wei Si",
+        "author_inst": "Zhejiang University"
+      },
+      {
+        "author_name": "Jing Wang",
+        "author_inst": "Sun Yat-sen University"
+      },
+      {
+        "author_name": "Zhiwen Jiang",
+        "author_inst": "Nanjing Agricultural University"
+      },
+      {
+        "author_name": "Ziqing Yan",
+        "author_inst": "Nanjing Agricultural University"
+      },
+      {
+        "author_name": "Gang Xing",
+        "author_inst": "Zhejiang University"
+      },
+      {
+        "author_name": "Meng Lu",
+        "author_inst": "Nanjing Agricultural University"
+      },
+      {
+        "author_name": "Marc A Suchard",
+        "author_inst": "University of California Los Angeles"
+      },
+      {
+        "author_name": "Xiang Ji",
+        "author_inst": "University of California Los Angeles & Tulane University"
+      },
+      {
+        "author_name": "Wenjie Gong",
+        "author_inst": "Chinese Academy of Agricultural Sciences"
+      },
+      {
+        "author_name": "Biao He",
+        "author_inst": "Chinese Academy of Agricultural Sciences"
+      },
+      {
+        "author_name": "Jun Li",
+        "author_inst": "City University of Hong Kong"
+      },
+      {
+        "author_name": "Philippe Lemey",
+        "author_inst": "KU Leuven"
+      },
+      {
+        "author_name": "Deyin Guo",
+        "author_inst": "Sun Yat-sen University"
+      },
+      {
+        "author_name": "Changchun Tu",
+        "author_inst": "Chinese Academy of Agricultural Sciences"
+      },
+      {
+        "author_name": "Edward C Holmes",
+        "author_inst": "University of Sydney"
+      },
+      {
+        "author_name": "Mang Shi",
+        "author_inst": "Sun Yat-sen University"
+      },
+      {
+        "author_name": "Shuo Su",
+        "author_inst": "Nanjing Agricultural University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "zoology"
+  },
   {
     "rel_doi": "10.1101/2021.11.10.468174",
     "rel_title": "Serum from COVID-19 patients early in the pandemic shows limited evidence of cross-neutralization against variants of concern",
@@ -509133,45 +508043,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.11.06.21265955",
-    "rel_title": "Using mobile phone data to estimate dynamic population changes and improve the understanding of a pandemic: A case study in Andorra",
-    "rel_date": "2021-11-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.06.21265955",
-    "rel_abs": "Compartmental models are often used to understand and predict the progression of an infectious disease such as COVID-19. The most basic of these models consider the total population of a region to be closed. Many incorporate human mobility into their transmission dynamics, usually based on static and aggregated data. However, mobility can change dramatically during a global pandemic as seen with COVID-19, making static data unsuitable. Recently, large mobility datasets derived from mobile devices have been used, along with COVID-19 infections data, to better understand the relationship between mobility and COVID-19. However, studies to date have relied on data that represent only a fraction of their target populations, and the data from mobile devices have been used for measuring mobility within the study region, without considering changes to the population as people enter and leave the region.\n\nThis work presents a unique case study in Andorra, with comprehensive datasets that include telecoms data covering 100% of mobile subscribers in the country, and results from a serology testing program that more than 90% of the population voluntarily participated in. We use the telecoms data to both measure mobility within the country and to provide a real-time census of people entering, leaving and remaining in the country. We develop multiple SEIR (compartmental) models parameterized on these metrics and show how dynamic population metrics can improve the models. We find that total daily trips did not have predictive value in the SEIR models while country entrances did. As a secondary contribution of this work, we show how Andorras serology testing program was likely impacted by people leaving the country. Overall, this case study suggests how using mobile phone data to measure dynamic population changes could improve studies that rely on more commonly used mobility metrics and the overall understanding of a pandemic.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Alex A Berke",
-        "author_inst": "Massachusetts Institute of Technology"
-      },
-      {
-        "author_name": "Ronan Doorley",
-        "author_inst": "Massachusetts Institute of Technology"
-      },
-      {
-        "author_name": "Luis Alonso",
-        "author_inst": "Massachusetts Institute of Technology"
-      },
-      {
-        "author_name": "Marc Pons",
-        "author_inst": "Andorra Recerca + Innovacio"
-      },
-      {
-        "author_name": "Vanesa Arroyo",
-        "author_inst": "Andorra Recerca + Innovacio"
-      },
-      {
-        "author_name": "Kent Larson",
-        "author_inst": "Massachusetts Institute of Technology"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.11.10.21266188",
     "rel_title": "A study of the benefits of vaccine mandates and vaccine passports for SARS-CoV-2",
@@ -509446,6 +508317,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.11.10.21266195",
+    "rel_title": "Disparities in COVID-19 Fatalities among Working Californians",
+    "rel_date": "2021-11-11",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.10.21266195",
+    "rel_abs": "BackgroundInformation on the occupational distribution of COVID-19 mortality is limited.\n\nObjectiveTo characterize COVID-19 fatalities among working Californians.\n\nDesignRetrospective study of laboratory-confirmed COVID-19 fatalities with dates of death from January 1 to December 31, 2020.\n\nSettingCalifornia.\n\nParticipantsCOVID-19 accounted for 8,050 (9.9%) of 81,468 fatalities among Californians 18-64 years old. Of these decedents, 2,486 (30.9%) were matched to state employment records and classified as \"confirmed working.\" The remainder were classified as \"likely working\" (n=4,121 [51.2%]) or \"not working\" (n=1,443 [17.9%]) using death certificate and case registry data.\n\nMeasurementsWe calculated age-adjusted overall and occupation-specific COVID-19 mortality rates using 2019 American Community Survey denominators.\n\nResultsConfirmed and likely working COVID-19 decedents were predominantly male (76.3%), Latino (68.7%), and foreign-born (59.6%), with high school or less education (67.9%); 7.8% were Black. The overall age-adjusted COVID-19 mortality rate was 30.0 per 100,000 workers (95% confidence interval [CI], 29.3-30.8). Workers in nine occupational groups had mortality rates higher than this overall rate, including those in farming (78.0; 95% CI, 68.7-88.2); material moving (77.8; 95% CI, 70.2-85.9); construction (62.4; 95% CI, 57.7-67.4); production (60.2; 95% CI, 55.7-65.0); and transportation (57.2; 95% CI, 52.2-62.5) occupations. While occupational differences in mortality were evident across demographic groups, mortality rates were three-fold higher for male compared with female workers and three- to seven-fold higher for Latino and Black workers compared with Asian and White workers.\n\nLimitationsThe requirement that fatalities be laboratory-confirmed and the use of 2019 denominator data may underestimate the occupational burden of COVID-19 mortality.\n\nConclusionCalifornians in manual labor and in-person service occupations experienced disproportionate COVID-19 mortality, with the highest rates observed among male, Latino, and Black workers.",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Kristin J Cummings",
+        "author_inst": "California Department of Public Health"
+      },
+      {
+        "author_name": "John Beckman",
+        "author_inst": "California Department of Public Health"
+      },
+      {
+        "author_name": "Matthew Frederick",
+        "author_inst": "California Department of Public Health"
+      },
+      {
+        "author_name": "Robert Harrison",
+        "author_inst": "California Department of Public Health"
+      },
+      {
+        "author_name": "Alyssa Nguyen",
+        "author_inst": "California Department of Public Health"
+      },
+      {
+        "author_name": "Robert Snyder",
+        "author_inst": "California Department of Public Health"
+      },
+      {
+        "author_name": "Elena Chan",
+        "author_inst": "California Department of Public Health"
+      },
+      {
+        "author_name": "Kathryn Gibb",
+        "author_inst": "California Department of Public Health"
+      },
+      {
+        "author_name": "Andrea Rodriguez",
+        "author_inst": "California Department of Public Health"
+      },
+      {
+        "author_name": "Jessie Wong",
+        "author_inst": "California Department of Public Health"
+      },
+      {
+        "author_name": "Erin L Murray",
+        "author_inst": "California Department of Public Health"
+      },
+      {
+        "author_name": "Seema Jain",
+        "author_inst": "California Department of Public Health"
+      },
+      {
+        "author_name": "Ximena Vergara",
+        "author_inst": "California Department of Public Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.11.10.21266168",
     "rel_title": "Antibody decay, T cell immunity and breakthrough infections following two SARS-CoV-2 vaccine doses in infliximab- and vedolizumab-treated patients",
@@ -511051,109 +509989,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2021.11.09.467981",
-    "rel_title": "LRRC15 suppresses SARS-CoV-2 infection and controls collagen production",
-    "rel_date": "2021-11-10",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.09.467981",
-    "rel_abs": "Although ACE2 is the primary receptor for SARS-CoV-2 infection, a systematic assessment of host factors that regulate binding to SARS-CoV-2 spike protein has not been described. Here we use whole genome CRISPR activation to identify host factors controlling cellular interactions with SARS-CoV-2. Our top hit was a TLR-related cell surface receptor called leucine-rich repeat-containing protein 15 (LRRC15). LRRC15 expression was sufficient to promote SARS-CoV-2 Spike binding where they form a cell surface complex. LRRC15 mRNA is expressed in human collagen-producing lung myofibroblasts and LRRC15 protein is induced in severe COVID-19 infection where it can be found lining the airways. Mechanistically, LRRC15 does not itself support SARS-CoV-2 infection, but fibroblasts expressing LRRC15 can suppress both pseudotyped and authentic SARS-CoV-2 infection in trans. Moreover, LRRC15 expression in fibroblasts suppresses collagen production and promotes expression of IFIT, OAS, and MX-family antiviral factors. Overall, LRRC15 is a novel SARS-CoV-2 spike-binding receptor that can help control viral load and regulate antiviral and antifibrotic transcriptional programs in the context of COVID-19 infection.",
-    "rel_num_authors": 22,
-    "rel_authors": [
-      {
-        "author_name": "Lipin Loo",
-        "author_inst": "Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, and School of Life and Environmental Sciences, University of S"
-      },
-      {
-        "author_name": "Matthew A. Waller",
-        "author_inst": "Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, and School of Life and Environmental Sciences, University of S"
-      },
-      {
-        "author_name": "Cesar L. Moreno",
-        "author_inst": "Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, and School of Life and Environmental Sciences, University of S"
-      },
-      {
-        "author_name": "Alexander J. Cole",
-        "author_inst": "Centenary Institute and Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, 2006, Australia"
-      },
-      {
-        "author_name": "Alberto O. Stella",
-        "author_inst": "The Kirby Institute, University of New South Wales, New South Wales, Australia"
-      },
-      {
-        "author_name": "Oltin-Tiberiu Pop",
-        "author_inst": "Institute for Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland"
-      },
-      {
-        "author_name": "Ann-Kristin Jochum",
-        "author_inst": "Institute for Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland; Institute for Pathology, Kantonsspital St. Gallen, St. Gallen, Switzerland"
-      },
-      {
-        "author_name": "Omar Hasan Ali",
-        "author_inst": "Institute for Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland; Department of Medical Genetics, Life Sciences Institute, University of British C"
-      },
-      {
-        "author_name": "Christopher E. Denes",
-        "author_inst": "Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, and School of Life and Environmental Sciences, University of S"
-      },
-      {
-        "author_name": "Zina Hamoudi",
-        "author_inst": "Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, and School of Life and Environmental Sciences, University of S"
-      },
-      {
-        "author_name": "Felicity Chung",
-        "author_inst": "Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, and School of Life and Environmental Sciences, University of S"
-      },
-      {
-        "author_name": "Anupriya Aggarwal",
-        "author_inst": "The Kirby Institute, University of New South Wales, New South Wales, Australia"
-      },
-      {
-        "author_name": "Jason K.K. Low",
-        "author_inst": "School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia."
-      },
-      {
-        "author_name": "Karishma Patel",
-        "author_inst": "School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia."
-      },
-      {
-        "author_name": "Rezwan Siddique",
-        "author_inst": "School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia."
-      },
-      {
-        "author_name": "Taeyoung Kang",
-        "author_inst": "Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia"
-      },
-      {
-        "author_name": "Suresh Mathivanan",
-        "author_inst": "Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia."
-      },
-      {
-        "author_name": "Joel Mackay",
-        "author_inst": "School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales 2006, Australia."
-      },
-      {
-        "author_name": "Lukas Flatz",
-        "author_inst": "Institute for Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland; Center for Dermatooncology, Department of Dermatology, Eberhard Karls University"
-      },
-      {
-        "author_name": "Stuart Turville",
-        "author_inst": "The Kirby Institute, University of New South Wales, New South Wales, Australia"
-      },
-      {
-        "author_name": "Daniel Hesselson",
-        "author_inst": "Centenary Institute and Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, 2006, Australia"
-      },
-      {
-        "author_name": "G Gregory Neely",
-        "author_inst": "Charles Perkins Centre, Dr. John and Anne Chong Lab for Functional Genomics, Centenary Institute, and School of Life and Environmental Sciences, University of S"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "cell biology"
-  },
   {
     "rel_doi": "10.1101/2021.11.10.468037",
     "rel_title": "Potent antibody immunity to SARS-CoV-2 variants elicited by a third dose of inactivated vaccine",
@@ -511479,6 +510314,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.11.04.21265951",
+    "rel_title": "Validation of a rapid and sensitive SARS-CoV-2 screening system developed for pandemic-scale infection surveillance",
+    "rel_date": "2021-11-09",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.04.21265951",
+    "rel_abs": "Without any realistic prospect of comprehensive global vaccine coverage and lasting immunity, control of pandemics such as COVID-19 will require implementation of large-scale, rapid identification and isolation of infectious individuals to limit further transmission. Here, we describe an automated, high-throughput integrated screening platform, incorporating saliva-based loop-mediated isothermal amplification (LAMP) technology, that is designed for population-scale sensitive detection of infectious carriers of SARS-CoV-2 RNA. Central to this surveillance system is the \"Sentinel\" testing instrument, which is capable of reporting results within 25 minutes of saliva sample collection with a throughput of up to 3,840 results per hour. It incorporates continuous flow loading of samples at random intervals to cost-effectively adjust for fluctuations in testing demand. Independent validation of our saliva-based RT-LAMP technology on an automated LAMP instrument coined the \"Sentinel\", found 98.7% sensitivity, 97.6% specificity, and 98% efficiency against a RT-PCR comparator assay, confirming its suitability for surveillance screening. This Sentinel surveillance system offers a feasible and scalable approach to complement vaccination, to curb the spread of COVID-19 variants, and control future pandemics to save lives.\n\nOne-Sentence SummaryDevelopment of a high-throughput LAMP-based automated continuous flow, random access SARS-CoV-2 screening platform with sufficient sensitivity and specificity to enable pandemic-scale population testing of infectious individuals using saliva sampling.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Robert Dewhurst",
+        "author_inst": "Perron Institute for Neurological and Translational Science"
+      },
+      {
+        "author_name": "Tatjana Heinrich",
+        "author_inst": "Perron Institute for Neurological and Translational Science"
+      },
+      {
+        "author_name": "Paul Watt",
+        "author_inst": "Avicena Systems"
+      },
+      {
+        "author_name": "Paul Ostergaard",
+        "author_inst": "Avicena Systems"
+      },
+      {
+        "author_name": "Jose Maria Marimon",
+        "author_inst": "Donostialdea Integrated Health Organization"
+      },
+      {
+        "author_name": "Mariana Moreira",
+        "author_inst": "Lancs Lamp Laboratory"
+      },
+      {
+        "author_name": "Philip E Houldsworth",
+        "author_inst": "Lancs Lamp Laboratory"
+      },
+      {
+        "author_name": "Jack Dylan Rudrum",
+        "author_inst": "Perron Institute for Neurological and Translational Science"
+      },
+      {
+        "author_name": "David Wood",
+        "author_inst": "University of Western Australia"
+      },
+      {
+        "author_name": "Sulev Koks",
+        "author_inst": "Perron Institute for Neurological and Translational Science"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.11.05.21265961",
     "rel_title": "Three doses of COVID-19 mRNA vaccination are safe based on adverse events reported in electronic health records",
@@ -512636,25 +511526,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.11.08.21266087",
-    "rel_title": "Vaccine effectiveness of Pfizer-BioNTech and Oxford-AstraZeneca to prevent severe COVID-19 in Costa Rica by September and October 2021: A nationwide, observational study of hospitalisations prevalence.",
-    "rel_date": "2021-11-09",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.08.21266087",
-    "rel_abs": "ObjectiveTo estimate the dose-dependent effectiveness of coronavirus disease (COVID-19) vaccines to prevent severe illness in real-world conditions of Costa Rica, after the Delta variant became dominant.\n\nDesignObservational study; secondary analysis of hospitalisation prevalence.\n\nSettingNationwide adult population, Costa Rica.\n\nParticipantsAll 3.67 million adults residents in Costa Rica by mid-2021. Public aggregated data of 5978 hospital records from 14th September to 20th October, 2021 and 6.1 million vaccination doses administered.\n\nInterventionsVaccination with Pfizer-BioNTech (78%) and Oxford-AstraZeneca (22%).\n\nMain outcome measuresPrevalence of COVID-19-related hospitalisations\n\nResultsVaccine effectiveness to prevent hospitalisation (VEH) was estimated as 93.4% (95% confidence interval [CI]: 93.0 to 93.9) for complete vaccination and 76.7% (CI: 75.0 to 78.3) for single-dose vaccination among adults of all ages. VEH was lower and more uncertain among older adults aged 58 years and above: 92% (CI: 91% to 93%) for those who had received full vaccination and 64% (CI: 58% to 69%) for those who had received partial vaccination. Single-dose VEH declined over time during the study period, especially in the older age group. Estimates were sensitive to possible errors in the population count used to determine the residual number of unvaccinated people in groups with high vaccine coverage.\n\nConclusionThe Costa Rican vaccination programme that administered Pfizer and Oxford vaccines are highly effective to prevent COVID-19-related hospitalisations after the Delta variant had become dominant. Moreover, a single dose is reasonably effective, justifying the continuation of the national policy of postponing the application for the second dose of the Pfizer vaccine to accelerate the vaccination and increase the number of people being vaccinated. Timely monitoring of vaccine effectiveness is important to detect eventual failures and motivate the public based on information that the vaccinations are effective.\n\nSummary BoxO_ST_ABSWhat is already known on the topicC_ST_ABSO_LIThe Costa Rican Social Security Fund provides vaccinations in Costa Rica, and they use Pfizer-BioNTech and Oxford-AstraZeneca for the vaccinations. The Delta variant became predominant in Costa Rica by September 2021\nC_LIO_LIReal-world estimates of these vaccines effectiveness to prevent hospitalisations range from 90% to 98% for two doses and from 70% to 91% for a single dose. Almost all of these estimates predate the Delta variant.\nC_LIO_LIThere are controversies regarding the effectiveness of a single dose of COVID-19 vaccine after the emergence of the Delta variant.\nC_LI\n\nWhat this study addsO_LIVaccine effectiveness to prevent hospitalisation as estimated as 93.4% (95% CI: 93.0 to 93.9) for complete vaccination and 76.7% (CI: 75.0 to 78.3) for single-dose vaccination among adults of all ages by October 2021.\nC_LIO_LIThese study findings suggest that a single dose of COVID-19 vaccination is reasonably effective to prevent hospitalisations.\nC_LIO_LITherefore, the application for the second dose of the Pfizer vaccine can be postponed beyond the three weeks recommended by the fabricant to accelerate vaccination coverage.\nC_LI",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Luis Rosero-Bixby",
-        "author_inst": "Universidad de Costa Rica"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.11.08.21265312",
     "rel_title": "Understanding COVID-19 trajectories from a nationwide linked electronic health record cohort of 56 million people: phenotypes, severity, waves & vaccination",
@@ -513009,6 +511880,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.11.08.467648",
+    "rel_title": "Phage-like particle vaccines are highly immunogenic and protect against pathogenic coronavirus infection and disease",
+    "rel_date": "2021-11-09",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.08.467648",
+    "rel_abs": "The response by vaccine developers to the COVID-19 pandemic has been extraordinary with effective vaccines authorized for emergency use in the U.S. within one year of the appearance of the first COVID-19 cases. However, the emergence of SARS-CoV-2 variants and obstacles with the global rollout of new vaccines highlight the need for platforms that are amenable to rapid tuning and stable formulation to facilitate the logistics of vaccine delivery worldwide. We developed a \"designer nanoparticle\" platform using phage-like particles (PLPs) derived from bacteriophage lambda for multivalent display of antigens in rigorously defined ratios. Here, we engineered PLPs that display the receptor binding domain (RBD) protein from SARS-CoV-2 and MERS-CoV, alone (RBDSARS-PLPs, RBDMERS-PLPs) and in combination (hCoV-RBD PLPs). Functionalized particles possess physiochemical properties compatible with pharmaceutical standards and retain antigenicity. Following primary immunization, BALB/c mice immunized with RBDSARS- or RBDMERS-PLPs display serum RBD-specific IgG endpoint and live virus neutralization titers that, in the case of SARS-CoV-2, were comparable to those detected in convalescent plasma from infected patients. Further, these antibody levels remain elevated up to 6 months post-prime. In dose response studies, immunization with as little as one microgram of RBDSARS-PLPs elicited robust neutralizing antibody responses. Finally, animals immunized with RBDSARS-PLPs, RBDMERS-PLPs, and hCoV-RBD PLPs were protected against SARS-CoV-2 and/or MERS-CoV lung infection and disease. Collectively, these data suggest that the designer PLP system provides a platform for facile and rapid generation of single and multi-target vaccines.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Bennett J Davenport",
+        "author_inst": "University of Colorado School of Medicine"
+      },
+      {
+        "author_name": "Alexis Catala",
+        "author_inst": "University of Colorado School of Medicine"
+      },
+      {
+        "author_name": "Stuart M Weston",
+        "author_inst": "University of Maryland School of Medicine"
+      },
+      {
+        "author_name": "Robert M Johnson",
+        "author_inst": "University of Maryland School of Medicine"
+      },
+      {
+        "author_name": "Jeremy Ardunay",
+        "author_inst": "University of Maryland School of Medicine"
+      },
+      {
+        "author_name": "Holly L Hammond",
+        "author_inst": "University of Maryland School of Medicine"
+      },
+      {
+        "author_name": "Carly Dillen",
+        "author_inst": "University of Maryland School of Medicine"
+      },
+      {
+        "author_name": "Matthew B Frieman",
+        "author_inst": "University of Maryland School of Medicine"
+      },
+      {
+        "author_name": "Carlos E Catalano",
+        "author_inst": "University of Colorado Skaggs School of Pharmacy and Pharmaceutical Sciences"
+      },
+      {
+        "author_name": "Thomas E Morrison",
+        "author_inst": "University of Colorado School of Medicine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2021.11.05.21265977",
     "rel_title": "Waning, Boosting and a Path to Endemicity for SARS-CoV-2.",
@@ -514658,61 +513584,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.11.05.467529",
-    "rel_title": "Structural basis of main proteases of coronavirus bound to drug candidate PF-07321332",
-    "rel_date": "2021-11-08",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.05.467529",
-    "rel_abs": "The high mutation rate of COVID-19 and the prevalence of multiple variants strongly support the need for pharmacological options to complement vaccine strategies. One region that appears highly conserved among different genus of coronaviruses is the substrate binding site of the main protease (Mpro or 3CLpro), making it an attractive target for the development of broad-spectrum drugs for multiple coronaviruses. PF-07321332 developed by Pfizer is the first orally administered inhibitor targeting the main protease of SARS-CoV-2, which also has shown potency against other coronaviruses. Here we report three crystal structures of main protease of SARS-CoV-2, SARS-CoV and MERS-CoV bound to the inhibitor PF-07321332. The structures reveal a ligand-binding site that is conserved among SARS-CoV-2, SARS-CoV and MERS-CoV, providing insights into the mechanism of inhibition of viral replication. The long and narrow cavity in the cleft between domains I and II of main protease harbors multiple inhibitor binding sites, where PF-07321332 occupies subsites S1, S2 and S4 and appears more restricted compared with other inhibitors. A detailed analysis of these structures illuminated key structural determinants essential for inhibition and elucidated the binding mode of action of main proteases from different coronaviruses. Given the importance of main protease for the treatment of SARS-CoV-2 infection, insights derived from this study should accelerate the design of safer and more effective antivirals.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Jian Li",
-        "author_inst": "College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China."
-      },
-      {
-        "author_name": "Cheng Lin",
-        "author_inst": "School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China."
-      },
-      {
-        "author_name": "Xuelan Zhou",
-        "author_inst": "Shenzhen Crystalo Biopharmaceutical Co., Ltd, Shenzhen 518118, China."
-      },
-      {
-        "author_name": "Fanglin Zhong",
-        "author_inst": "Jiangxi Jmerry Biopharmaceutical Co., Ltd, Ganzhou 341000, China."
-      },
-      {
-        "author_name": "Pei Zeng",
-        "author_inst": "Jiangxi Jmerry Biopharmaceutical Co., Ltd, Ganzhou 341000, China."
-      },
-      {
-        "author_name": "Haihai Jiang",
-        "author_inst": "School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China."
-      },
-      {
-        "author_name": "Yang Yang",
-        "author_inst": "Shenzhen Crystalo Biopharmaceutical Co., Ltd, Shenzhen 518118, China."
-      },
-      {
-        "author_name": "Peter McCormick",
-        "author_inst": "William Harvey Research Institute, Queen Mary University of London"
-      },
-      {
-        "author_name": "Yang Fu",
-        "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China 518055"
-      },
-      {
-        "author_name": "Jin Zhang",
-        "author_inst": "School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China."
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "biophysics"
-  },
   {
     "rel_doi": "10.1101/2021.11.07.21266027",
     "rel_title": "Ethnicity and outcomes in COVID-19 in the United Kingdom: a systematic review and meta-analysis",
@@ -515027,6 +513898,101 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.11.04.21265780",
+    "rel_title": "Immunogenicity and safety of the homogenous booster shot of a recombinant fusion protein vaccine (V-01) against COVID-19 in healthy adult participants primed with a two-dose regimen",
+    "rel_date": "2021-11-08",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.04.21265780",
+    "rel_abs": "BackgroundRising concerns over waning immunity and reduction in neutralizing activity against variants of concern (VOCs) have contributed to deploying booster doses by different strategies to tackle the COVID-19 pandemic. Preliminary findings from Phase I and II have shown that V-01, a recombinant fusion protein vaccine against COVID-19, exhibited favorable safety and immunogenicity profiles in 1060 adult participants of both younger and senior age. Herein, we aimed to assess the immunogenicity and safety for a booster dose in participants previously primed with a two-dose 10g V-01 regimen (day 0, 21) from phase I trial, providing reassuring data for necessity and feasibility of a homogenous booster dose.\n\nMethodsWe conducted a single-arm, open-label trial at the Guangdong Provincial Center for Disease Control and Prevention (Gaozhou, China). Forty-three eligible participants who were previously primed 4-5 months earlier with two-dose 10g V-01 regimen from phase I trial received booster vaccination. We primarily assessed the immunogenicity post-booster vaccination, measured by RBD-binding antibodies using ELISA and neutralizing activity against wild-type SARS-CoV-2 and emerging variants of concern (VOCs) using neutralization assays. We secondarily assessed the safety and reactogenicity of the booster vaccination.\n\nResultsThe third dose of V-01 exhibited significant boosting effects of humoral immune response in participants primed with two-dose 10g V-01 regimen regarding both wild-type SARS-CoV-2 and VOCs. We observed a 60.4-folds increase in neutralizing titres against SARS-CoV-2 of younger adults, with GMTs of 17 (95%CI: 12-23) prior to booster vaccination in comparison to 1017 (95%CI: 732-1413) at day 14 post booster vaccination; and a 53.6-folds increase in that of older adults, with GMTs of 14 (95%CI: 9-20) before booster vaccination in comparison to 729(95%CI: 397-1339) at day 14 post-booster vaccination. The neutralizing titres against SARS-CoV-2 Delta strain also demonstrated a sharp increase from the day of pre booster vaccination to day 14 post booster vaccination, with GMTs of 11 (95%CI:8-15) versus 383 (95%CI:277-531) in younger adults (35.4-folds increase), and 6.5(95%CI: 5-8) versus 300(95%CI:142-631) in older adults (46.0-folds increase), respectively. We also observed a considerable and consistent increase of pseudovirus neutralizing titres against emerging VOCs from day 28 post second vaccination to day 14 post booster vaccination, with GMTs of 206 (95%CI:163-259) versus 607 (95%CI: 478-771) for Alpha strain, 54 (95%CI:38-77) versus 329 (95%CI: 255-425) for Beta strain, 219 (95%CI:157-306) versus 647 (95%CI: 484-865) for Delta strain. Our preliminary findings indicate a homogenous booster dose of V-01 was safe and well-tolerated, with overall adverse reactions being absent or mild-to-moderate in severity, and no grade 3 or worse AEs were related to booster vaccination.\n\nConclusionsA homogenous booster immunization in participants receiving a primary series of two-dose V-01 elicited a substantial humoral immune response against wild-type SARS-CoV-2 and emerging VOCs, along with a favorable safety and reactogenicity profile. Our study provided promising data for a homogenous prime-boost strategy using recombinant protein vaccine to tackle the ongoing pandemic, potentially providing broad protection against emerging VOCs and overcoming waning immunity.",
+    "rel_num_authors": 20,
+    "rel_authors": [
+      {
+        "author_name": "Yuan Li",
+        "author_inst": "Guangdong Provincial Institute of Biological Products and Materia Medica, Guangzhou, China"
+      },
+      {
+        "author_name": "Xin Fang",
+        "author_inst": "National Institutes for Food and Drug Control, Beijing, China"
+      },
+      {
+        "author_name": "Rongjuan Pei",
+        "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China"
+      },
+      {
+        "author_name": "Renfeng Fan",
+        "author_inst": "Guangdong Provincial Institute of Biological Products and Materia Medica, Guangzhou, China"
+      },
+      {
+        "author_name": "Shaomin Chen",
+        "author_inst": "Guangdong Provincial Institute of Biological Products and Materia Medica, Guangzhou, China"
+      },
+      {
+        "author_name": "Peiyu Zeng",
+        "author_inst": "Gaozhou Center for Disease Control and Prevention, Maoming, China"
+      },
+      {
+        "author_name": "Zhiqiang Ou",
+        "author_inst": "Guangdong Provincial Institute of Biological Products and Materia Medica, Guangzhou, China"
+      },
+      {
+        "author_name": "Jinglong Deng",
+        "author_inst": "Gaozhou Center for Disease Control and Prevention, Maoming, China"
+      },
+      {
+        "author_name": "Jian Zhou",
+        "author_inst": "Gaozhou Center for Disease Control and Prevention, Maoming, China"
+      },
+      {
+        "author_name": "Zehui Sun",
+        "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China"
+      },
+      {
+        "author_name": "Lishi Liu",
+        "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China"
+      },
+      {
+        "author_name": "Hua Peng",
+        "author_inst": "Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China"
+      },
+      {
+        "author_name": "Xujia Chen",
+        "author_inst": "LivzonBio Inc., Zhuhai, China"
+      },
+      {
+        "author_name": "Zhipeng Su",
+        "author_inst": "LivzonBio Inc., Zhuhai, China"
+      },
+      {
+        "author_name": "Xi Chen",
+        "author_inst": "LivzonBio Inc.,  Zhuhai, China"
+      },
+      {
+        "author_name": "Jianfeng He",
+        "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China"
+      },
+      {
+        "author_name": "Wuxiang Guan",
+        "author_inst": "Wuhan Institute of Virology Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Zhongyu Hu",
+        "author_inst": "National Institutes for Food and Drug Control, Beijing, China"
+      },
+      {
+        "author_name": "Yang-Xin Fu",
+        "author_inst": "Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China"
+      },
+      {
+        "author_name": "Jikai Zhang",
+        "author_inst": "Guangdong Provincial Institute of Biological Products and Materia Medica, Guangzhou, China"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "allergy and immunology"
+  },
   {
     "rel_doi": "10.1101/2021.11.04.21265924",
     "rel_title": "Can I Afford To Be On Campus?: Do College Students with Disabilities Understand COVID-19 Vaccination Costs?",
@@ -516352,165 +515318,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.11.03.21265769",
-    "rel_title": "Autoantibodies Detected in MIS-C Patients due to Administration of Intravenous Immunoglobulin",
-    "rel_date": "2021-11-04",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.03.21265769",
-    "rel_abs": "The autoantibody profile associated with known autoimmune diseases in patients with COVID-19 or multisystem inflammatory syndrome in children (MIS-C) remains poorly defined. Here we show that adults with COVID-19 had a moderate prevalence of autoantibodies against the lung antigen KCNRG, and SLE-associated Smith autoantigen. Children with COVID-19 rarely had autoantibodies; one of 59 children had GAD65 autoantibodies associated with acute insulin-dependent diabetes. While autoantibodies associated with SLE/Sjogrens syndrome (Ro52, Ro60, and La) and/or autoimmune gastritis (gastric ATPase) were detected in 74% (40/54) of MIS-C patients, further analysis of these patients and of children with Kawasaki disease (KD), showed that the administration of intravenous immunoglobulin (IVIG) was largely responsible for detection of these autoantibodies in both groups of patients. Monitoring in vivo decay of the autoantibodies in MIS-C children showed that the IVIG-derived Ro52, Ro60, and La autoantibodies declined to undetectable levels by 45-60 days, but gastric ATPase autoantibodies declined more slowly requiring >100 days until undetectable. Together these findings demonstrate that administration of high-dose IVIG is responsible for the detection of several autoantibodies in MIS-C and KD. Further studies are needed to investigate autoantibody production in MIS-C patients, independently from IVIG administration.",
-    "rel_num_authors": 36,
-    "rel_authors": [
-      {
-        "author_name": "Peter D. Burbelo",
-        "author_inst": "National Institute of Dental and Craniofacial Research, NIH, Bethesda, Maryland, 20892, USA"
-      },
-      {
-        "author_name": "Riccardo Castagnoli",
-        "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD. USA"
-      },
-      {
-        "author_name": "Chisato Shimizu",
-        "author_inst": "Department of Pediatrics, Rady Children's Hospital, University of California San Diego, San Diego, CA, USA"
-      },
-      {
-        "author_name": "Ottavia M. Delmonte",
-        "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, 20892, USA"
-      },
-      {
-        "author_name": "Kerry Dobbs",
-        "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, 20892, USA"
-      },
-      {
-        "author_name": "Valentina Discepolo",
-        "author_inst": "Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, Naples, Italy"
-      },
-      {
-        "author_name": "Andrea Lo Vecchio",
-        "author_inst": "Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, Naples, Italy"
-      },
-      {
-        "author_name": "Alfredo Guarino",
-        "author_inst": "Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, Naples, Italy"
-      },
-      {
-        "author_name": "Francesco Licciardi",
-        "author_inst": "Division of Pediatric Immunology and Rheumatology, Department of Public Health and Pediatric Sciences, Regina Margherita Childrens Hospital, University of Turin"
-      },
-      {
-        "author_name": "Ugo Ramenghi",
-        "author_inst": "Division of Pediatric Immunology and Rheumatology, Department of Public Health and Pediatric Sciences, Regina Margherita Childrens Hospital, University of Turin"
-      },
-      {
-        "author_name": "Emma Rey",
-        "author_inst": "Instituto de Ciencias e Innovacion en Medicina (ICIM), Clinica Alemana Universidad del Desarrollo, Santiago, Chile"
-      },
-      {
-        "author_name": "Maria Cecilia Vial",
-        "author_inst": "Instituto de Ciencias e Innovacion en Medicina, Clinica Alemana Universidad del Desarrollo, Santiago, Chile"
-      },
-      {
-        "author_name": "Gian Luigi Marseglia",
-        "author_inst": "Department of Pediatrics, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy"
-      },
-      {
-        "author_name": "Amelia Licari",
-        "author_inst": "Department of Pediatrics, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy"
-      },
-      {
-        "author_name": "Daniela Montagna",
-        "author_inst": "Department of Pediatrics, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy"
-      },
-      {
-        "author_name": "Camillo Rossi",
-        "author_inst": "Direzione Sanitaria, ASST Spedali Civili, Piazzale Spedali Civili 1, 25123 Brescia, Italy"
-      },
-      {
-        "author_name": "Gina A. Montealegre Sanchez",
-        "author_inst": "Intramural Clinical Management and Operations Branch (ICMOB). Division of Clinical   Research, NIAID, NIH"
-      },
-      {
-        "author_name": "Karyl Barron",
-        "author_inst": "Division of Intramural Research, National Institute of Allergy and Infectious Disease, NIH, Bethesda, MD 20892, USA"
-      },
-      {
-        "author_name": "Blake M. Warner",
-        "author_inst": "National Institute of Dental and Craniofacial Research, NIH, Bethesda, Maryland 20892, USA"
-      },
-      {
-        "author_name": "John A. Chiorini",
-        "author_inst": "National Institute of Dental and Craniofacial Research, NIH, Bethesda, Maryland 20892, USA"
-      },
-      {
-        "author_name": "Yazmin Espinosa",
-        "author_inst": "Hospital Roberto del Rio, Santiago, Chile"
-      },
-      {
-        "author_name": "Loreani Noguera",
-        "author_inst": "Instituto de Ciencias e Innovacion en Medicina (ICIM), Clinica Alemana Universidad del Desarrollo, Santiago, Chile"
-      },
-      {
-        "author_name": "Lesia Dropulic",
-        "author_inst": "Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892, USA"
-      },
-      {
-        "author_name": "Meng Truong",
-        "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892, USA"
-      },
-      {
-        "author_name": "Dana Gerstbacher",
-        "author_inst": "Pediatric Rheumatology, Stanford Childrens Hospital, Stanford, CA, USA"
-      },
-      {
-        "author_name": "Sayonara Mato",
-        "author_inst": "Pediatric Infectious Diseases, Randall Childrens Hospital at Legacy Emanuel, Portland, OR, USA"
-      },
-      {
-        "author_name": "John Kanegaye",
-        "author_inst": "Department of Pediatrics, Rady Childrens Hospital, University of California San Diego, San Diego, CA, USA"
-      },
-      {
-        "author_name": "Adriana H. Tremoulet",
-        "author_inst": "Department of Pediatrics, Rady Childrens Hospital, University of California San Diego, San Diego, CA, USA"
-      },
-      {
-        "author_name": "- Pediatric Emergency Medicine Kawasaki Group",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Eli M. Eisenstein",
-        "author_inst": "Department of Pediatrics, Hadassah Medical Center, Faculty of Medicine, Hebrew University, Jerusalem, Israel"
-      },
-      {
-        "author_name": "Helen C. Su",
-        "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892, USA"
-      },
-      {
-        "author_name": "Luisa Imberti",
-        "author_inst": "CREA Laboratory, Diagnostic Department, ASST Spedali Civili di Brescia, Piazzale Spedali Civili 1, 25123 Brescia, Italy"
-      },
-      {
-        "author_name": "Maria Cecilia Poli",
-        "author_inst": "Instituto de Ciencias e Innovacion en Medicina (ICIM), Clinica Alemana Universidad del Desarrollo, Santiago, Chile and Hospital Roberto del Rio, Santiago, Chile"
-      },
-      {
-        "author_name": "Jane C. Burns",
-        "author_inst": "Department of Pediatrics, Rady Childrens Hospital, University of California San Diego, San Diego, CA, USA"
-      },
-      {
-        "author_name": "Luigi D. Notarangelo",
-        "author_inst": "Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892, USA"
-      },
-      {
-        "author_name": "Jeffrey I. Cohen",
-        "author_inst": "Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland 20892, USA"
-      }
-    ],
-    "version": "1",
-    "license": "cc0",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.11.03.21265791",
     "rel_title": "Cohort study of Covid-19 vaccine effectiveness among healthcare workers in Finland, December 2020 - October 2021",
@@ -516789,6 +515596,121 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "medical education"
   },
+  {
+    "rel_doi": "10.1101/2021.11.02.21265778",
+    "rel_title": "Plasma markers of neurologic injury and systemic inflammation in individuals with self-reported neurologic post-acute sequelae of SARS-CoV-2 infection (PASC)",
+    "rel_date": "2021-11-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.02.21265778",
+    "rel_abs": "BackgroundThe biologic mechanisms underlying neurologic post-acute-sequelae of SARS-CoV-2 infection (PASC) are incompletely understood.\n\nMethodsWe measured markers of neuronal injury (glial fibrillary acidic protein [GFAP], neurofilament light chain [NfL]) and soluble markers of inflammation among a cohort of people with prior confirmed SARS-CoV-2 infection at early and late recovery following the initial illness (defined as less than and greater than 90 days, respectively). The primary clinical outcome was the presence of self-reported central nervous system (CNS) PASC symptoms during the late recovery timepoint. We compared fold-changes in marker values between those with and without CNS PASC symptoms using linear mixed effects models and examined relationships between neurologic and immunologic markers using rank linear correlations.\n\nResultsOf 121 individuals, 52 reported CNS PASC symptoms. During early recovery, those who went on to report CNS PASC symptoms had elevations in GFAP (1.3-fold higher mean ratio, 95% CI 1.04-1.63, p=0.02), but not NfL (1.06-fold higher mean ratio, 95% CI 0.89-1.26, p=0.54). During late recovery, neither GFAP nor NfL levels were elevated among those with CNS PASC symptoms. Although absolute levels of NfL did not differ, those who reported CNS PASC symptoms demonstrated a stronger downward trend over time in comparison to those who did not report CNS PASC symptoms (p=0.041). Those who went on to report CNS PASC also exhibited elevations in IL-6 (48% higher during early recovery and 38% higher during late recovery), MCP-1 (19% higher during early recovery), and TNF-alpha (19% higher during early recovery and 13% higher during late recovery). GFAP and NfL correlated with levels of several immune activation markers during early recovery; these correlations were attenuated during late recovery.\n\nConclusionsSelf-reported neurologic symptoms present >90 days following SARS-CoV-2 infection are associated with elevations in markers of neurologic injury and inflammation at early recovery timepoints, suggesting that early injury can result in long-term disease. The correlation of GFAP and NfL with markers of systemic immune activation suggests one possible mechanism that might contribute to these symptoms. Additional work is needed to better characterize these processes and to identify interventions to prevent or treat this condition.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSDo individuals with and without self-reported neurologic symptoms following SARS-CoV-2 infection have different levels of biomarkers of neurologic injury or immune activationa\n\nFindingsIn this cohort study of 121 adults, individuals reporting neurologic symptoms beyond 90 days following SARS-CoV-2 infection had higher levels of glial fibrillary acidic protein but not neurofilament light chain. Levels of several markers of inflammation including interleukin-6, tumor necrosis factor-alpha, and monocyte chemoattractant protein-1 were also elevated.\n\nMeaningPost-acute neurologic symptoms following SARS-CoV-2 infection are associated with significant differences in levels of certain biomarkers. Further investigation may provide clues to the biologic pathways underlying these symptoms.",
+    "rel_num_authors": 25,
+    "rel_authors": [
+      {
+        "author_name": "Michael J Peluso",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Hannah M Sans",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Carrie A Forman",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Alyssa N Nylander",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Hsi-en Ho",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Scott Lu",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Sarah A Goldberg",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Rebecca Hoh",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Viva Tai",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Sadie E Munter",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Ahmed Chenna",
+        "author_inst": "Monogram Biosciences Inc."
+      },
+      {
+        "author_name": "Brandon C Yee",
+        "author_inst": "Monogram Biosciences Inc."
+      },
+      {
+        "author_name": "John W Winslow",
+        "author_inst": "Monogram Biosciences Inc."
+      },
+      {
+        "author_name": "Christos J Petropoulos",
+        "author_inst": "Monogram Biosciences Inc."
+      },
+      {
+        "author_name": "Jeffrey N Martin",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "J. Daniel Kelly",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Matthew S Durstenfeld",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Priscilla Y Hsue",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Peter W Hunt",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Meredith Greene",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Felicia C Chow",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Joanna Hellmuth",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Timothy J Henrich",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "David V Glidden",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Steven G Deeks",
+        "author_inst": "University of California, San Francisco"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.11.04.21265921",
     "rel_title": "Prevalence of Antibodies to SARS-CoV-2 following natural infection and vaccination in Irish Hospital Healthcare Workers; changing epidemiology as the pandemic progresses",
@@ -518114,93 +517036,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.11.03.21265877",
-    "rel_title": "REACT-1 round 15 interim report: High and rising prevalence of SARS-CoV-2 infection in England from end of September 2021 followed by a fall in late October 2021",
-    "rel_date": "2021-11-03",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.03.21265877",
-    "rel_abs": "BackgroundThe third wave of COVID-19 in England coincided with the rapid spread of the Delta variant of SARS-CoV-2 from the end of May 2021. Case incidence data from the national testing programme (Pillar 2) in England may be affected by changes in testing behaviour and other biases. Community surveys may provide important contextual information to inform policy and the public health response.\n\nMethodsWe estimated patterns of community prevalence of SARS-CoV-2 infection in England using RT-PCR swab-positivity, demographic and other risk factor data from round 15 (interim) of the REal-time Assessment of Community Transmission-1 (REACT-1) study (round 15a, carried out from 19 to 29 October 2021). We compared these findings with those from round 14 (9 to 27 September 2021).\n\nResultsDuring mid- to late-October 2021 (round 15a) weighted prevalence was 1.72% (1.61%, 1.84%) compared to 0.83% (0.76%, 0.89%) in September 2021 (round 14). The overall reproduction number (R) from round 14 to round 15a was 1.12 (1.11, 1.14) with increases in prevalence over this period (September to October) across age groups and regions except Yorkshire and The Humber. However, within round 15a (mid- to late-October) there was evidence of a fall in prevalence with R of 0.76 (0.65, 0.88). The highest weighted prevalence was observed among children aged 5 to 12 years at 5.85% (5.10%, 6.70%) and 13 to 17 years at 5.75% (5.02%, 6.57%). At regional level, there was an almost four-fold increase in weighted prevalence in South West from round 14 at 0.59% (0.43%,0.80%) to round 15a at 2.18% (1.84%, 2.58%), with highest smoothed prevalence at subregional level also found in South West in round 15a. Age, sex, key worker status, and presence of children in the home jointly contributed to the risk of swab-positivity. Among the 126 sequenced positive swabs obtained up until 23 October, all were Delta variant; 13 (10.3%) were identified as the AY.4.2 sub-lineage.\n\nDiscussionWe observed the highest overall prevalence of swab-positivity seen in the REACT-1 study in England to date in round 15a (October 2021), with a two-fold rise in swab-positivity from round 14 (September 2021). Despite evidence of a fall in prevalence from mid- to late-October 2021, prevalence remains high, particularly in school-aged children, with evidence also of higher prevalence in households with one or more children. Thus, vaccination of children aged 12 and over remains a high priority (with possible extension to children aged 5-12) to help reduce within-household transmission and disruptions to education, as well as among adults, to lessen the risk of serious disease among those infected.",
-    "rel_num_authors": 18,
-    "rel_authors": [
-      {
-        "author_name": "Marc Chadeau-Hyam",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Oliver Eales",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Barbara Bodinier",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Haowei Wang",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "David J Haw",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Matthew Whitaker",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Caroline E Walters",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Christina J Atchison",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Peter J Diggle",
-        "author_inst": "Lancaster University"
-      },
-      {
-        "author_name": "Andrew J Page",
-        "author_inst": "Quadram Institute"
-      },
-      {
-        "author_name": "Deborah Ashby",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Wendy Barclay",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Graham P Taylor",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Graham Cooke",
-        "author_inst": "Imperial College"
-      },
-      {
-        "author_name": "Helen Ward",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Ara Darzi",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Christl A. Donnelly",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Paul Elliott",
-        "author_inst": "Imperial College London School of Public Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.10.29.466402",
     "rel_title": "Inhibition of SAR S-CoV-2 infection and replication by lactoferrin, MUC1 and \u03b1-lactalbumin identified in human breastmilk",
@@ -518775,6 +517610,393 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "genetic and genomic medicine"
   },
+  {
+    "rel_doi": "10.1101/2021.11.01.21265527",
+    "rel_title": "Effectiveness, Explainability and Reliability of Machine Meta-Learning Methods for Predicting Mortality in Patients with COVID-19: Results of the Brazilian COVID-19 Registry",
+    "rel_date": "2021-11-02",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.01.21265527",
+    "rel_abs": "ObjectiveTo provide a thorough comparative study among state-of-the-art machine learning methods and statistical methods for determining in-hospital mortality in COVID-19 patients using data upon hospital admission; to study the reliability of the predictions of the most effective methods by correlating the probability of the outcome and the accuracy of the methods; to investigate how explainable are the predictions produced by the most effective methods.\n\nMaterials and MethodsDe-identified data were obtained from COVID-19 positive patients in 36 participating hospitals, from March 1 to September 30, 2020. Demographic, comorbidity, clinical presentation and laboratory data were used as training data to develop COVID-19 mortality prediction models. Multiple machine learning and traditional statistics models were trained on this prediction task using a folded cross-validation procedure, from which we assessed performance and interpretability metrics.\n\nResultsThe Stacking of machine learning models improved over the previous state-of-the-art results by more than 26% in predicting the class of interest (death), achieving 87.1% of AUROC and macro F1 of 73.9%. We also show that some machine learning models can be very interpretable and reliable, yielding more accurate predictions while providing a good explanation for the  why.\n\nConclusionThe best results were obtained using the meta-learning ensemble model - Stacking. State-of the art explainability techniques such as SHAP-values can be used to draw useful insights into the patterns learned by machine-learning algorithms. Machine-learning models can be more explainable than traditional statistics models while also yielding highly reliable predictions.",
+    "rel_num_authors": 93,
+    "rel_authors": [
+      {
+        "author_name": "Bruno Barbosa Miranda de Paiva Sr.",
+        "author_inst": "Computer Science Department, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Polianna Delfino Pereira Sr.",
+        "author_inst": "Internal Medicine Department, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Institute for Health Technology Assessment (IATS/CNPq)"
+      },
+      {
+        "author_name": "Claudio Moises Valiense de Andrade",
+        "author_inst": "Computer Science Department, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Virginia Mara Reis Gomes Sr.",
+        "author_inst": "Centro Universitario de Belo Horizonte (UniBH), Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Maria Clara Pontello Barbosa Lima Sr.",
+        "author_inst": "Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Maira Viana Rego Souza Silva Sr.",
+        "author_inst": "Medical School and University Hospital, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Marcelo Carneiro Sr.",
+        "author_inst": "Hospital Santa Cruz, Santa Cruz do Sul, Rio Grande do Sul, Brazil"
+      },
+      {
+        "author_name": "Karina Paula Medeiros Prado Martins Sr.",
+        "author_inst": "Medical School and University Hospital, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Thais Lorenna Souza Sales Sr.",
+        "author_inst": "Universidade Federal de Sao Joao del Rey. R, Divinopolis, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Rafael Lima Rodrigues de Carvalho Sr.",
+        "author_inst": "Institute for Health Technology Assessment (IATS/CNPq), Porto Alegre, Rio Grande do Sul, Brazil"
+      },
+      {
+        "author_name": "Magda C. Pires",
+        "author_inst": "Department of Statistics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Lucas Emanuel F Ramos",
+        "author_inst": "Department of Statistics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Rafael T Silva Sr.",
+        "author_inst": "Department of Statistics, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Adriana Falangola Benjamin Bezerra",
+        "author_inst": "Hospital das Clinicas da Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil"
+      },
+      {
+        "author_name": "Alexandre Vargas Schwarzbold",
+        "author_inst": "Hospital Universitario de Santa Maria, Santa Maria, Rio Grande do Sul, Brazil"
+      },
+      {
+        "author_name": "Aline Gabrielle Sousa Nunes",
+        "author_inst": "Hospital UNIMED BH, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Amanda de Oliveira Maurilio",
+        "author_inst": "Hospital Sao Joao de Deus, Sao Joao de Deus, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Ana Luiza Bahia Alves Scotton",
+        "author_inst": "Hospital Regional Antonio Dias, Patos de Minas, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Andre Soares de Moura Costa",
+        "author_inst": "Hospitais da Rede Mater Dei, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Andriele Abreu Castro",
+        "author_inst": "Hospital Moinhos de Vento, Porto Alegre, Rio Grande do Sul, Brazil"
+      },
+      {
+        "author_name": "Barbara Lopes Farace",
+        "author_inst": "Risoleta Tolentino Neves, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Christiane Correa Rodrigues Cimini",
+        "author_inst": "Mucuri Medical School, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Teofilo Otoni, Minas Gerais, Brazil; Hospital Santa Rosalia, Teofilo Otoni, Min"
+      },
+      {
+        "author_name": "Cintia Alcantara De Carvalho",
+        "author_inst": "Hospital Joao XXIII, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Daniel Vitorio Silveira",
+        "author_inst": "Hospital UNIMED BH, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Daniela Ponce",
+        "author_inst": "Faculdade de Medicina de Botucatu - Universidade Estadual Paulista Julio de Mesquita Filho, Botucatu, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "Elayne Crestani Pereira",
+        "author_inst": "Universidade do Sul de Santa Catarina (UNISUL), Florianopolis, Santa Catarina, Brazil; Hospital SOS Cardio, Florianopolis, Santa Catarina, Brazil"
+      },
+      {
+        "author_name": "Euler Roberto Fernandes Manenti",
+        "author_inst": "Hospital Mae de Deus, Porto Alegre, Rio Grande do Sul, Brazil"
+      },
+      {
+        "author_name": "Evelin Paola de Almeida Cenci",
+        "author_inst": "Hospital Universitario Canoas, Canoas, Rio Grande do Sul, Brazil"
+      },
+      {
+        "author_name": "Fernanda Barbosa Lucas",
+        "author_inst": "Hospital Santo Antonio, Curvelo, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Fernanda D'Athayde Rodrigues",
+        "author_inst": "Hospital de Clinicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil"
+      },
+      {
+        "author_name": "Fernando Anschau",
+        "author_inst": "Hospital Nossa Senhora da Conceicao, Porto Alegre, Rio Grande do Sul, Brazil; Hospital Cristo Redentor, Porto Alegre, Rio Grande do Sul, Brazil"
+      },
+      {
+        "author_name": "Fernando Antonio Botoni",
+        "author_inst": "Medical School and University Hospital, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Fernando Graca Aranha",
+        "author_inst": "Hospital SOS Cardio, Florianopolis, Santa Catarina, Brazil"
+      },
+      {
+        "author_name": "Frederico Bartolazzi",
+        "author_inst": "Hospital Santo Antonio, Curvelo, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Gisele Alsina Nader Bastos",
+        "author_inst": "Hospital Moinhos de Vento, Porto Alegre, Rio Grande do Sul, Brazil"
+      },
+      {
+        "author_name": "Giovanna Grunewald Vietta",
+        "author_inst": "Universidade do Sul de Santa Catarina (UNISUL), Florianopolis, Santa Catarina, Brazil; Hospital SOS Cardio, Florianopolis, Santa Catarina, Brazil"
+      },
+      {
+        "author_name": "Guilherme Fagundes Nascimento",
+        "author_inst": "Hospital UNIMED BH, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Helena Carolina Noal",
+        "author_inst": "Hospital Universitario de Santa Maria, Santa Maria, Rio Grande do Sul, Brazil"
+      },
+      {
+        "author_name": "Helena Duani",
+        "author_inst": "Medical School and University Hospital, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Heloisa Reniers Vianna",
+        "author_inst": "Universitario Ciencias Medicas, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Henrique Cerqueira Guimaraes",
+        "author_inst": "Risoleta Tolentino Neves, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Isabela Moraes Gomes",
+        "author_inst": "Medical School and University Hospital, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Jamille Hemetrio Salles Martins Costa",
+        "author_inst": "Hospital Marcio Cunha, Ipatinga, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Jessica Rayane Correa Silva da Fonseca",
+        "author_inst": "Hospital Semper, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Julia Di Sabatino Santos Guimaraes",
+        "author_inst": "Pontifica Universidade Catolica de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Julia Drumond Parreiras de Morais",
+        "author_inst": "Universitario Ciencias Medicas, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Juliana Machado Rugolo",
+        "author_inst": "Faculdade de Medicina de Botucatu - Universidade Estadual Paulista Julio de Mesquita Filho, Botucatu, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "Joanna D'arc Lyra Batista",
+        "author_inst": "Universidade Federal da Fronteira Sul, Chapeco, Santa Catarina, Brazil"
+      },
+      {
+        "author_name": "Joice Coutinho de Alvarenga",
+        "author_inst": "Hospital Joao XXIII, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Jose Miguel Chatkin",
+        "author_inst": "Schoolof Medicine, Pontificia Universidade Catolica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil; Hospital Sao Lucas PUCRS, Porto Alegre, Brazi"
+      },
+      {
+        "author_name": "Karen Brasil Ruschel",
+        "author_inst": "Institute for Health Technology Assessment (IATS/CNPq), Porto Alegre, Rio Grande do Sul, Brazil; Hospital Mae de Deus, Porto Alegre, Rio Grande do Sul, Brazil; "
+      },
+      {
+        "author_name": "Leila Beltrami Moreira",
+        "author_inst": "Hospital de Clinicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil"
+      },
+      {
+        "author_name": "Leonardo Seixas de Oliveira",
+        "author_inst": "Hospital Bruno Born, Lajeado, Rio Grande do Sul,Brazil"
+      },
+      {
+        "author_name": "Liege Barella Zandona",
+        "author_inst": "Hospital Bruno Born, Lajeado, Rio Grande do Sul,Brazil"
+      },
+      {
+        "author_name": "Lilian Santos Pinheiro",
+        "author_inst": "Mucuri Medical School, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Teofilo Otoni, Minas Gerais, Brazil; Hospital Santa Rosalia, Teofilo Otoni, Min"
+      },
+      {
+        "author_name": "Luanna da Silva Monteiro",
+        "author_inst": "Hospital Metropolitano Odilon Behrens, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Lucas de Deus Sousa",
+        "author_inst": "Hospital Regional Antonio Dias, Patos de Minas, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Luciane Kopittke",
+        "author_inst": "Hospital Nossa Senhora da Conceicao, Porto Alegre, Rio Grande do Sul, Brazil; Hospital Cristo Redentor, Porto Alegre, Rio Grande do Sul, Brazil"
+      },
+      {
+        "author_name": "Luciano de Souza Viana",
+        "author_inst": "Hospital Marcio Cunha, Ipatinga, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Luis Cesar de Castro",
+        "author_inst": "Hospital Tacchini, Bento Goncalves, Rio Grande do Sul, Brazil"
+      },
+      {
+        "author_name": "Luisa Argolo Assis",
+        "author_inst": "Pontifica Universidade Catolica de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Luisa Elem Almeida Santos",
+        "author_inst": "Centro Universitario de Patos de Minas, Patos de Minas, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Maderson Alvares de Souza Cabral",
+        "author_inst": "Hospital Moinhos de Vento, Porto Alegre, Rio Grande do Sul, Brazil"
+      },
+      {
+        "author_name": "Magda Cesar Raposo",
+        "author_inst": "Universidade Federal de Sao Joao del Rey. R, Divinopolis, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Maiara Anschau Floriani",
+        "author_inst": "Moinhos Research Institute, Porto Alegre, Rio Grande do Sul, Brazil"
+      },
+      {
+        "author_name": "Maria Angelica Pires Ferreira",
+        "author_inst": "Hospital de Clinicas de Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil"
+      },
+      {
+        "author_name": "Maria Aparecida Camargos Bicalho",
+        "author_inst": "Fundacao Hospitalar do Estado de Minas Gerais (FHEMIG), Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Mariana Frizzo de Godoy",
+        "author_inst": "Hospital Sao Lucas PUCRS, Porto Alegre, Brazil. Rua Joao Cateano, 79/503. Porto Alegre, Rio Grande do Sul, Brazil"
+      },
+      {
+        "author_name": "Matheus Carvalho Alves Nogueira",
+        "author_inst": "Hospitais da Rede Mater Dei, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Meire Pereira de Figueiredo",
+        "author_inst": "Hospital Santo Antonio, Curvelo, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Milton Henriques Guimaraes Junior",
+        "author_inst": "Hospital Marcio Cunha, Ipatinga, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Monica Aparecida de Paula De Sordi",
+        "author_inst": "Faculdade de Medicina de Botucatu - Universidade Estadual Paulista Julio de Mesquita Filho, Botucatu, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "Natalia da Cunha Severino Sampaio",
+        "author_inst": "Hospital Eduardo de Menezes, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Neimy Ramos de Oliveira",
+        "author_inst": "Hospital Eduardo de Menezes, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Pedro Ledic Assaf",
+        "author_inst": "Hospital Metropolitano Doutor Celio de Castro, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Raquel Lutkmeier",
+        "author_inst": "Hospital Nossa Senhora da Conceicao, Porto Alegre, Rio Grande do Sul, Brazil; Hospital Cristo Redentor, Porto Alegre, Rio Grande do Sul, Brazil"
+      },
+      {
+        "author_name": "Reginaldo Aparecido Valacio",
+        "author_inst": "Hospital Metropolitano Odilon Behrens, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Renan Goulart Finger",
+        "author_inst": "Hospital Regional do Oeste, Chapeco, Santa Catarina,Brazil"
+      },
+      {
+        "author_name": "Roberta Senger",
+        "author_inst": "Hospital Universitario de Santa Maria, Santa Maria, Rio Grande do Sul, Brazil"
+      },
+      {
+        "author_name": "Rochele Mosmann Menezes",
+        "author_inst": "Hospital Santa Cruz, Santa Cruz do Sul, Rio Grande do Sul, Brazil"
+      },
+      {
+        "author_name": "Rufino de Freitas Silva",
+        "author_inst": "Hospital Sao Joao de Deus, Sao Joao de Deus, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Saionara Cristina Francisco",
+        "author_inst": "Hospital Metropolitano Doutor Celio de Castro, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Silvana Mangeon Mereilles Guimaraes",
+        "author_inst": "Hospital Marcio Cunha, Ipatinga, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Silvia Ferreira Araujo",
+        "author_inst": "Hospital Marcio Cunha, Ipatinga, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Talita Fischer Oliveira",
+        "author_inst": "Hospital Santa Cruz, Santa Cruz do Sul, Rio Grande do Sul, Brazil"
+      },
+      {
+        "author_name": "Tatiana Kurtz",
+        "author_inst": "Hospital Santa Cruz, Santa Cruz do Sul, Rio Grande do Sul, Brazil"
+      },
+      {
+        "author_name": "Tatiani Oliveira Fereguetti",
+        "author_inst": "Hospital Eduardo de Menezes, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Thainara Conceicao de Oliveira",
+        "author_inst": "Hospital Universitario Canoas, Canoas, Rio Grande do Sul, Brazil"
+      },
+      {
+        "author_name": "Thulio Henrique Oliveira Diniz",
+        "author_inst": "Hospital Sao Joao de Deus, Sao Joao de Deus, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Yara Neves Marques Barbosa Ribeiro",
+        "author_inst": "Hospital Metropolitano Doutor Celio de Castro, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Yuri Carlotto Ramires",
+        "author_inst": "Hospital Bruno Born, Lajeado, Rio Grande do Sul,Brazil"
+      },
+      {
+        "author_name": "Marcos Andre Goncalves",
+        "author_inst": "Computer Science Department, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil"
+      },
+      {
+        "author_name": "Milena Soriano Marcolino",
+        "author_inst": "Institute for Health Technology Assessment (IATS/CNPq), Porto Alegre, Rio Grande do Sul, Brazil; Medical School and University Hospital, Universidade Federal de"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health informatics"
+  },
   {
     "rel_doi": "10.1101/2021.11.02.21265755",
     "rel_title": "A combination of variant genotypes at two loci in the APOL1 gene is associated with adverse outcomes in SARS-CoV-2: a UK Biobank study.",
@@ -520112,65 +519334,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.05.17.444407",
-    "rel_title": "Structure-function analysis of the nsp14 N7-guanine methyltransferase reveals an essential role in Betacoronavirus replication",
-    "rel_date": "2021-11-01",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.17.444407",
-    "rel_abs": "As coronaviruses (CoVs) replicate in the host cell cytoplasm, they rely on their own capping machinery to ensure the efficient translation of their mRNAs, protect them from degradation by cellular 5 exoribonucleases, and escape innate immune sensing. The CoV nonstructural protein 14 (nsp14) is a bi-functional replicase subunit harboring an N-terminal 3'-to-5' exoribonuclease (ExoN) domain and a C-terminal (N7-guanine)-methyltransferase (N7-MTase) domain that is presumably involved in viral mRNA capping. Here, we aimed to integrate structural, biochemical, and virological data to assess the importance of conserved N7-MTase residues for nsp14s enzymatic activities and virus viability. We revisited the crystal structure of severe acute respiratory syndrome (SARS)-CoV nsp14 to perform an in silico comparative analysis between betacoronaviruses. We identified several residues likely involved in the formation of the N7-MTase catalytic pocket, which presents a fold distinct from the Rossmann fold observed in most known MTases. Next, for SARS-CoV and Middle East respiratory syndrome-CoV, site-directed mutagenesis of selected residues was used to assess their importance for in vitro enzymatic activity. Most of the engineered mutations abolished N7-MTase activity, while not affecting nsp14-ExoN activity. Upon reverse engineering of these mutations into different betacoronavirus genomes, we identified two substitutions (R310A and F426A in SARS-CoV nsp14) abrogating virus viability and one mutation (H424A) yielding a crippled phenotype across all viruses tested. Our results identify the N7-MTase as a critical enzyme for betacoronavirus replication and define key residues of its catalytic pocket that can be targeted to design inhibitors with a potential pan-coronaviral activity spectrum.\n\nSignificance StatementThe ongoing SARS-CoV-2 pandemic emphasizes the urgent need to develop efficient broad-spectrum anti-CoV drugs. The structure-function characterization of conserved CoV replicative enzymes is key to identifying the most suitable drug targets. Using a multidisciplinary comparative approach and different betacoronaviruses, we characterized the key conserved residues of the nsp14 (N7-guanine)-methyltransferase, a poorly defined subunit of the CoV mRNA-synthesizing machinery. Our study highlights the unique structural features of this enzyme and establishes its essential role in betacoronavirus replication, while identifying two residues that are critical for the replication of the four betacoronaviruses tested, including SARS-CoV-2.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Natacha S. Ogando",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Priscila El Kazzi",
-        "author_inst": "CNRS"
-      },
-      {
-        "author_name": "Jessika  C. Zevenhoven-Dobbe",
-        "author_inst": "Leids Universitair Medisch Centrum"
-      },
-      {
-        "author_name": "Brenda w. Bontes",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Alice Decombe",
-        "author_inst": "CNRS"
-      },
-      {
-        "author_name": "Clara C S. Posthuma Ph.D.",
-        "author_inst": "Department of Medical Microbiology; Leiden University Medical Center"
-      },
-      {
-        "author_name": "Volker Thiel Ph.D.",
-        "author_inst": "Institute for Virology and Immunology"
-      },
-      {
-        "author_name": "Bruno Canard",
-        "author_inst": "CNRS"
-      },
-      {
-        "author_name": "Francois Ferron",
-        "author_inst": "CNRS"
-      },
-      {
-        "author_name": "Etienne Decroly",
-        "author_inst": "CNRS"
-      },
-      {
-        "author_name": "Eric J Snijder",
-        "author_inst": "Leiden University Medical Center"
-      }
-    ],
-    "version": "2",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "molecular biology"
-  },
   {
     "rel_doi": "10.1101/2021.10.31.21265703",
     "rel_title": "Efficacy and Safety of SOBERANA 02, a COVID-19 conjugate vaccine in heterologous three doses combination",
@@ -520625,6 +519788,29 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2021.10.29.466519",
+    "rel_title": "A biosafety level 2 surrogate for studying SARS-CoV-2 survival in food processing environmental biofilms",
+    "rel_date": "2021-11-01",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.29.466519",
+    "rel_abs": "Meat processing plants have been at the center of the SARS-CoV-2 pandemic. There are several factors that contribute to the persistence of SARS-CoV-2 in meat processing plants and one of the factors is the formation of a multi-species biofilm with virus. Biofilm can act as a reservoir in protecting, harboring, and dispersing SARS-CoV-2 from biofilm to the meat processing facility environment. We used Murine Hepatitis Virus (MHV) as a surrogate for SARS-CoV-2 virus and meat processing facility drain samples to develop mixed-species biofilms on commonly found materials in processing facilities (Stainless-Steel (SS), PVC and tiles). The results showed that MHV was able to integrate into the environmental biofilm and survived for a period of 5 days at 7{degrees}C. There was no significate difference between the viral-environmental biofilm biovolumes developed on different materials SS, PVC, and tiles. There was a 2-fold increase in the virus-environmental biofilm biovolume when compared to environmental biofilm by itself. These results indicate a complex virus-environmental biofilm interaction which is providing enhanced protection for the survival of viral particles with the environmental biofilm community.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Austin Blake Featherstone",
+        "author_inst": "Texas A&M"
+      },
+      {
+        "author_name": "Sapna Chitlapilly Dass",
+        "author_inst": "Texas A&M"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2021.10.29.466418",
     "rel_title": "SARS-CoV-2 mechanistic correlates of protection: insight from modelling response to vaccines",
@@ -521866,61 +521052,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pediatrics"
   },
-  {
-    "rel_doi": "10.1101/2021.10.28.21265578",
-    "rel_title": "Impact of the COVID-19 pandemic on routine immunization coverage in children under 2 years old in Ontario, Canada: A retrospective cohort study",
-    "rel_date": "2021-10-29",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.28.21265578",
-    "rel_abs": "BackgroundThe COVID-19 pandemic has caused a disruption in childhood immunization coverage around the world. This study aimed to determine the change in immunization coverage for children under 2 years old in Ontario, Canada, comparing time periods pre-pandemic to during the pandemic.\n\nMethodsWe conducted an observational retrospective open cohort study, using primary care electronic medical record data from the University of Toronto Practice-Based Research Network (UTOPIAN) database, from January 2019 to December 2020. Children under 2 years old who had at least 2 visits recorded in UTOPIAN were included. We measured up-to-date (UTD) immunization coverage rates, overall and by type of vaccine (DTaP-IPV-Hib, Pneu-C-13, Rot, Men-C-C, MMR, Var), and on-time immunization coverage rates by age milestone (2, 4, 6, 12, 15 and 18 months). We compared average coverage rates over 3 periods of time: January 2019-March 2020 (T1); March-July 2020 (T2); and August-December 2020 (T3).\n\nResults12,313 children were included. Overall UTD coverage for all children was 71.0% in T1, dropped by 5.7% (95% CI: -6.2, -5.1) in T2, slightly increased in T3 but remained lower than in T1. MMR vaccine UTD coverage slightly decreased in T2 and T3 by approximately 2%. The largest decreases were seen at ages 15-month and 18-month old, with drops in on-time coverage of 14.7% (95% CI: -18.7, -10.6) and 16.4% (95% CI: -20.0, -12.8) respectively during T2. When stratified by sociodemographic characteristics, no specific subgroup of children was found to have been differentially impacted by the pandemic.\n\nConclusionChildhood immunization coverage rates for children under 2 years in Ontario decreased significantly during the early period of the COVID-19 pandemic and only partially recovered during the rest of 2020. Public health and educational interventions for providers and parents are needed to ensure adequate catch-up of delayed/missed immunizations to prevent potential outbreaks of vaccine-preventable diseases.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Catherine Ji",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Pierre-Philippe Piche-Renaud",
-        "author_inst": "The Hospital for Sick Children"
-      },
-      {
-        "author_name": "Jemisha Apajee",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Ellen Stephenson",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Milena Forte",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Jeremy N Friedman",
-        "author_inst": "The Hospital for Sick Children"
-      },
-      {
-        "author_name": "Michelle Science",
-        "author_inst": "The Hospital for Sick Children"
-      },
-      {
-        "author_name": "Stanley Zlotkin",
-        "author_inst": "The Hospital for Sick Children"
-      },
-      {
-        "author_name": "Shaun K Morris",
-        "author_inst": "The Hospital for Sick Children"
-      },
-      {
-        "author_name": "Karen Tu",
-        "author_inst": "North York General Hospital"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "primary care research"
-  },
   {
     "rel_doi": "10.1101/2021.10.28.21265604",
     "rel_title": "Transferability of Psychological Interventions from Disaster-Exposed Employees to Healthcare Workers Working during the COVID-19 Pandemic",
@@ -522267,6 +521398,69 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.10.29.21265248",
+    "rel_title": "Safety and immunogenicity of a high-dose quadrivalent influenza vaccine administered concomitantly with a third dose of the mRNA-1273 SARS-CoV-2 vaccine in adults >= 65 years of age: a Phase II, open-label study",
+    "rel_date": "2021-10-29",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.29.21265248",
+    "rel_abs": "BackgroundConcomitant seasonal influenza vaccination with a COVID-19 vaccine booster could help to minimise potential disruption to the seasonal influenza vaccination campaign and maximise protection against both diseases among individuals at risk of severe disease and hospitalisation. This study assesses the safety and immunogenicity of concomitant administration of high-dose quadrivalent influenza vaccine (QIV-HD) and a mRNA-1273 vaccine booster dose in older adults.\n\nMethodsThis is an ongoing Phase II, multi-centre, open-label study (NCT04969276). We describe interim results up to 21 days after vaccination (July 2021-August 2021). Adults aged [&ge;] 65 years living in the community, who were to have received a second mRNA-1273 dose at least five months previously, were randomised (1:1:1) to concomitant QIV-HD and mRNA-1273 vaccination (Coad), QIV-HD alone, or mRNA-1273 vaccine alone. Unsolicited adverse events (AEs) occurring immediately, solicited local and systemic reactions up to day (D)8, and unsolicited AEs, serious AEs (SAEs), AEs of special interest (AESIs) and medically attended AEs (MAAEs) up to D22 were reported. Haemagglutination inhibition (HAI) antibody responses to influenza A/H1N1, A/H3N2, B/Yamagata and B/Victoria strains and SARS CoV-2 binding antibody responses (SARS-CoV-2 Pre-Spike IgG ELISA) were assessed at D1 and D22.\n\nFindingsOf 306 participants randomised, 296 were included for analysis (Coad, n=100; QIV-HD, n=92; mRNA-1273, n=104). Reactogenicity profiles were similar between the Coad and mRNA-1273 groups, with lower reactogenicity rates in the QIV-HD group (frequency [95% CIs] of solicited injection site reactions: 86{middle dot}0% [77{middle dot}6-92{middle dot}1], 91{middle dot}3% [84{middle dot}2-96{middle dot}0] and 61{middle dot}8% [50{middle dot}9-71{middle dot}9]; solicited systemic reactions: 80{middle dot}0% [70{middle dot}8-87{middle dot}3], 83{middle dot}7% [75{middle dot}1-90{middle dot}2] and 49{middle dot}4% [38{middle dot}7-60{middle dot}2], respectively). Up to D22, unsolicited AEs were reported for 17{middle dot}0% and 14{middle dot}4% participants in the Coad and mRNA-1273 groups, respectively, with a lower rate (10{middle dot}9%) in the QIV-HD group. Seven MAAEs were reported (Coad, n=3; QIV-HD, n=1; mRNA-1273, n=3). There were no SAEs, AESIs or deaths. HAI antibody geometric mean titres (GMTs) increased from D1 to D22 to similar levels for each influenza strain in the Coad and QIV-HD groups (GMTs [95% confidence interval], range across strains: Coad, 286 [233-352] to 429 [350-525]; QIV-HD, 315 [257-386] to 471 [378-588]). SARS-CoV-2 binding antibody geometric mean concentrations (GMCs) also increased to similar levels in the Coad and mRNA-1273 groups (D22 GMCs [95% confidence interval]: 7634 [6445-9042] and 7904 [6883- 9077], respectively).\n\nInterpretationNo safety concerns or immune interference were observed for concomitant administration of QIV-HD with mRNA-1273 booster in adults aged [&ge;] 65 years, supporting co-administration recommendations.\n\nFundingSanofi Pasteur",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Ruvim Izikson",
+        "author_inst": "Sanofi Pasteur, Swiftwater, Pennsylvania, USA"
+      },
+      {
+        "author_name": "Daniel Brune",
+        "author_inst": "Accelerated Enrollment Solutions, Peoria, Illinois, USA"
+      },
+      {
+        "author_name": "Jean-S\u00e9bastien Bolduc",
+        "author_inst": "Sanofi Pasteur, Marcy l Etoile, France"
+      },
+      {
+        "author_name": "Pierre Bourron",
+        "author_inst": "Sanofi Pasteur, Lyon, France"
+      },
+      {
+        "author_name": "Marion Fournier",
+        "author_inst": "Sanofi Pasteur, Lyon, France"
+      },
+      {
+        "author_name": "Tamala Mallett Moore",
+        "author_inst": "Sanofi Pasteur, Swiftwater, Pennsylvania, USA"
+      },
+      {
+        "author_name": "Aseem Pandey",
+        "author_inst": "Sanofi Pasteur, Swiftwater, Pennsylvania, USA"
+      },
+      {
+        "author_name": "Lucia Perez",
+        "author_inst": "Sanofi Pasteur, Swiftwater, Pennsylvania, USA"
+      },
+      {
+        "author_name": "Nessryne Sater",
+        "author_inst": "Sanofi Pasteur, Marcy l Etoile, France"
+      },
+      {
+        "author_name": "Anju Shrestha",
+        "author_inst": "Sanofi Pasteur, Swiftwater, Pennsylvania, USA"
+      },
+      {
+        "author_name": "Sophie Wague",
+        "author_inst": "Sanofi Pasteur, Lyon, France"
+      },
+      {
+        "author_name": "Sandrine I Samson",
+        "author_inst": "Sanofi Pasteur, Lyon, France"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.10.28.21265616",
     "rel_title": "Risk factors for severe PCR-positive SARS-CoV-2 infection in hospitalized children: a multicenter cohort study",
@@ -523724,129 +522918,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2021.10.27.21265561",
-    "rel_title": "Kinetics of immune responses to the AZD1222/Covishield vaccine with varying dose intervals in Sri Lankan individuals",
-    "rel_date": "2021-10-27",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.27.21265561",
-    "rel_abs": "BackgroundTo understand the kinetics of immune responses with different dosing gaps of the AZD1222 vaccine, we compared antibody and T cell responses in two cohorts with two different dosing gaps.\n\nMethodsAntibodies to the SARS-CoV-2 virus were assessed in 297 individuals with a dosing gap of 12 weeks, sampled at 12 weeks post second dose (cohort 1) and in 77 individuals with a median dosing gap of 21.4 weeks (cohort 2) sampled 6 weeks post second dose. ACE2 receptor blocking antibodies (ACE2R-Abs), antibodies to the receptor binding domain (RBD) of the virus and variants of concern (VOC) and ex vivo T cell responses were assessed in a sub cohort.\n\nResultsAll individuals (100%) had SARS-CoV-2 specific total antibodies and 94.2% of cohort 1 and 97.1% of cohort 2 had ACE2R-blocking Abs. There was no difference in antibody titres or positivity rates in different age groups in both cohorts. The ACE2R-blocking Abs (p<0.0001) and antibodies to the RBD of the VOCs were significantly higher in cohort 2, compared to cohort 1. 41.2% to 65.8% of different age groups gave a positive response by the haemagglutination assay to the RBD of the ancestral virus and VOCs in cohort 1, while 53.6% to 90% gave a positive response in cohort 2. 17/57 (29.8%) of cohort 1 and 17/29 (58.6%) of cohort 2 had ex vivo IFN{gamma} ELISpot responses above the positive threshold. The ACE2R-blocking antibodies and ex vivo IFN{gamma} ELISpot responses at 12 weeks post-first dose, significantly correlated with levels 12 weeks post second dose (Spearmans r=0.46, p=0.008) and (Spearmans r=0.71, p<0.0001) respectively.\n\nConclusionsBoth dosing schedules resulted in high levels of antibody and T cell responses post vaccination, although those with a longer dosing gap had a higher magnitude of responses, possibly as immune responses were measured 6 weeks post second dose compared to 12 weeks post second dose.",
-    "rel_num_authors": 27,
-    "rel_authors": [
-      {
-        "author_name": "Chandima Jeewandara",
-        "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka."
-      },
-      {
-        "author_name": "Inoka Aberathna",
-        "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka."
-      },
-      {
-        "author_name": "Laksiri Gomes",
-        "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka."
-      },
-      {
-        "author_name": "Pradeep Pushpakumara",
-        "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka."
-      },
-      {
-        "author_name": "Saubhagya Danasekara",
-        "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka."
-      },
-      {
-        "author_name": "Dinuka Guruge",
-        "author_inst": "Colombo Municipal Council, Colombo, Sri Lanka."
-      },
-      {
-        "author_name": "Thushali Ranasinghe",
-        "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka."
-      },
-      {
-        "author_name": "Banuri Gunasekara",
-        "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka."
-      },
-      {
-        "author_name": "Achala Kamaladasa",
-        "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka."
-      },
-      {
-        "author_name": "Heshan Kuruppu",
-        "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka."
-      },
-      {
-        "author_name": "Gayasha Somathilaka",
-        "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka."
-      },
-      {
-        "author_name": "Osanda Dissanayaka",
-        "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka."
-      },
-      {
-        "author_name": "Nayanathara Gamalath",
-        "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka."
-      },
-      {
-        "author_name": "Dinithi Ekanayaka",
-        "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka."
-      },
-      {
-        "author_name": "Jeewantha Jayamali",
-        "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka."
-      },
-      {
-        "author_name": "Deshni Jayathilaka",
-        "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka."
-      },
-      {
-        "author_name": "Anushika Mudunkotuwa",
-        "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka."
-      },
-      {
-        "author_name": "Michael Harvie",
-        "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka."
-      },
-      {
-        "author_name": "Thashmi Nimasha",
-        "author_inst": "Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka."
-      },
-      {
-        "author_name": "Ruwan Wijayamuni",
-        "author_inst": "Colombo Municipal Council, Colombo, Sri Lanka."
-      },
-      {
-        "author_name": "Lisa Schimanski",
-        "author_inst": "Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK.\""
-      },
-      {
-        "author_name": "Pramila Rijal",
-        "author_inst": "Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK.\""
-      },
-      {
-        "author_name": "Tiong Tan",
-        "author_inst": "Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford,UK"
-      },
-      {
-        "author_name": "Tao Tong",
-        "author_inst": "Centre for Translational Immunology, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK.\""
-      },
-      {
-        "author_name": "Alain Townsend",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Graham Ogg",
-        "author_inst": "MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK."
-      },
-      {
-        "author_name": "Gathsaurie Neelika Malavige",
-        "author_inst": "University of Sri Jayewardenepura"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "allergy and immunology"
-  },
   {
     "rel_doi": "10.1101/2021.10.26.21265531",
     "rel_title": "Boosting of the SARS-CoV-2-specific immune response after vaccination with single-dose Sputnik Light vaccine",
@@ -524185,6 +523256,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.10.23.21265429",
+    "rel_title": "Use of serology immunoassays for predicting SARS-CoV-2 infection: a serology-based diagnostic algorithm",
+    "rel_date": "2021-10-26",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.23.21265429",
+    "rel_abs": "BackgroundDetection of viral RNA by nucleic acid amplification testing (NAAT) remains the gold standard for diagnosis of SARS-CoV-2 infection but is limited by high cost and other factors. Whether serology-based assays can be effectively incorporated into a diagnostic algorithm remains to be determined. Herein we describe the development of a serology-based testing algorithm for SARS-CoV-2 infection.\n\nPatients and MethodsBetween July 2020 and February 2021, we included symptomatic unvaccinated patients evaluated in the Emergency Department of our institution for suspected SARS-CoV-2. All patients had testing by real-time Reverse Transcription Polymerase Chain Reaction. The performance characteristics of five commercial enzymatic serology assays testing for different antibody isotypes were evaluated in a derivation cohort and the assay with the best performance was further tested on a validation cohort. Optimal cut-off points were determined using receiver operating characteristic (ROC) curves and further tested using logistic regression.\n\nResultsThe derivation and validations cohorts included 72 and 319 patients, respectively. Based on its initial performance, the Elecsys Anti-SARS-CoV-2 assay (Roche Diagnostics) was further tested in the validation cohort. Using ROC curve analysis, we estimated the diagnostic performance for different cut-off points assuming a prevalence of positive tests of 5%. At any given cut-off point the NPV was over 97%.\n\nDiscussionThis study suggests that an initial diagnostic strategy using the Elecsys Anti-SARS-CoV-2 serology test in symptomatic unvaccinated patients could help to rule out an acute SARS-CoV2 infection and potentially lead to appropriately tailored infection control measures or rational guidance for further testing with a potential cost reduction and increased availability.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Alejandro Lazo-Langner MD MSc",
+        "author_inst": "Division of Hematology, Department of Medicine, Western University, London, Ontario, Canada"
+      },
+      {
+        "author_name": "Benjamin Chin-Yee MD",
+        "author_inst": "Division of Hematology, Department of Medicine, Western University, London, Ontario, Canada"
+      },
+      {
+        "author_name": "Jaryd Tong BMSc",
+        "author_inst": "Department of Pathology and Laboratory Medicine, Western University, and London Health Sciences Centre, London, Ontario, Canada"
+      },
+      {
+        "author_name": "Lori Lowes PhD",
+        "author_inst": "Department of Pathology and Laboratory Medicine, Western University, and London Health Sciences Centre, London, Ontario, Canada"
+      },
+      {
+        "author_name": "Benjamin D. Hedley PhD",
+        "author_inst": "Department of Pathology and Laboratory Medicine, Western University, and London Health Sciences Centre, London, Ontario, Canada"
+      },
+      {
+        "author_name": "Michael Silverman MD",
+        "author_inst": "Division of Infectious Diseases, Department of Medicine, Western University, London, Ontario, Canada"
+      },
+      {
+        "author_name": "Johan Delport MBChB",
+        "author_inst": "Department of Pathology and Laboratory Medicine, Western University, and London Health Sciences Centre, London, Ontario, Canada"
+      },
+      {
+        "author_name": "Vipin Bhayana PhD",
+        "author_inst": "Department of Pathology and Laboratory Medicine, Western University, and London Health Sciences Centre, London, Ontario, Canada"
+      },
+      {
+        "author_name": "Michael Knauer PhD",
+        "author_inst": "Department of Pathology and Laboratory Medicine, Western University, and London Health Sciences Centre, London, Ontario, Canada"
+      },
+      {
+        "author_name": "Ian Chin-Yee MD",
+        "author_inst": "Department of Pathology and Laboratory Medicine, Western University, and London Health Sciences Centre, London, Ontario, Canada"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.10.21.21265140",
     "rel_title": "Seroprevalence, prevalence, and genomic surveillance: monitoring the initial phases of the SARS-CoV-2 pandemic in Betim, Brazil",
@@ -525534,101 +524660,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.10.20.21265247",
-    "rel_title": "Leveraging machine learning and self-administered tests to predict COVID-19:An olfactory and gustatory dysfunction assessment through crowd-sourced data in India",
-    "rel_date": "2021-10-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.20.21265247",
-    "rel_abs": "It has been established that smell and taste loss are frequent symptoms during COVID-19 onset. Most evidence stems from medical exams or self-reports. The latter is particularly confounded by the common confusion of smell and taste. Here, we tested whether practical smelling and tasting with household items can be used to assess smell and taste loss. We conducted an online survey and asked participants to use common household items to perform a smell and taste test. We also acquired generic information on demographics, health issues including COVID-19 diagnosis, and current symptoms. We developed several machine learning models to predict COVID-19 diagnosis. We found that the random forest classifier consistently performed better than other models like support vector machines or logistic regression. The smell and taste perception of self-administered household items were statistically different for COVID-19 positive and negative participants. The most frequently selected items that also discriminated between COVID-19 positive and negative participants were clove, coriander seeds, and coffee for smell and salt, lemon juice, and chillies for taste. Our study shows that the results of smelling and tasting household items can be used to predict COVID-19 illness and highlight the potential of a simple home-test to help identify the infection and prevent the spread.",
-    "rel_num_authors": 20,
-    "rel_authors": [
-      {
-        "author_name": "Ritesh Kumar",
-        "author_inst": "CSIR-Central Scientific Instruments Organisation, Chandigarh, India"
-      },
-      {
-        "author_name": "Maneet Singh",
-        "author_inst": "Indian Institute of Technology Ropar"
-      },
-      {
-        "author_name": "Prateek Singh",
-        "author_inst": "CSIR-Institute of Genomics and Integrative Biology, New-Delhi, India"
-      },
-      {
-        "author_name": "Valentina Parma",
-        "author_inst": "Monell Chemical Senses Center, Philadelphia, USA"
-      },
-      {
-        "author_name": "Kathrin Ohla",
-        "author_inst": "Institute of Neuroscience and Medicine (INM-3),Research Center Julich"
-      },
-      {
-        "author_name": "Shannon B Olsson",
-        "author_inst": "National Centre for Biological Sciences, Tata Institute of Fundamental Research,Bengaluru, India"
-      },
-      {
-        "author_name": "Varun Saini",
-        "author_inst": "CSIR-Central Scientific Instruments Organisation, Chandigarh, India"
-      },
-      {
-        "author_name": "Jyotsna Rani",
-        "author_inst": "Indira Gandhi Institute of Medical Sciences, Patna, India"
-      },
-      {
-        "author_name": "Kunal Kishore",
-        "author_inst": "Shree Narayan Medical Institute & Hospital, Bihar, India"
-      },
-      {
-        "author_name": "Priyanka Kumari",
-        "author_inst": "Narayan Medical College & Hospital, Bihar,India"
-      },
-      {
-        "author_name": "Parul Ichhpujani",
-        "author_inst": "Government Medical College & Hospital, Chandigarh, India"
-      },
-      {
-        "author_name": "Anupma Sharma",
-        "author_inst": "CSIR-Central Scientific Instruments Organisation, Chandigarh, India"
-      },
-      {
-        "author_name": "Saurav Kumar",
-        "author_inst": "CSIR-Central Scientific Instruments Organisation, Chandigarh, India"
-      },
-      {
-        "author_name": "Manu Sharma",
-        "author_inst": "CSIR-Central Scientific Instruments Organisation, Chandigarh, India"
-      },
-      {
-        "author_name": "Amol P Bhondekar",
-        "author_inst": "CSIR-Central Scientific Instruments Organisation, Chandigarh, India"
-      },
-      {
-        "author_name": "Anamika Kothari",
-        "author_inst": "CSIR-Central Scientific Instruments Organisation, Chandigarh, India"
-      },
-      {
-        "author_name": "Viren Sardana",
-        "author_inst": "CSIR-Institute of Genomics and Integrative Biology, New-Delhi, India"
-      },
-      {
-        "author_name": "Sudarshan Iyengar",
-        "author_inst": "Indian Institute of Technology Ropar"
-      },
-      {
-        "author_name": "Debasis Dash",
-        "author_inst": "CSIR-Institute of Genomics and Integrative Biology, New-Delhi, India"
-      },
-      {
-        "author_name": "Rishemjit Kaur",
-        "author_inst": "CSIR-Central Scientific Instruments Organisation, Chandigarh, India"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.10.22.21265255",
     "rel_title": "Clinical performance characteristics of the Swift Normalase Amplicon Panel for sensitive recovery of SARS-CoV-2 genomes",
@@ -525899,6 +524930,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.10.25.21265493",
+    "rel_title": "Modeling the impact of vaccination strategies for nursing homes in the context of increased SARS-CoV-2 community transmission and variants",
+    "rel_date": "2021-10-26",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.25.21265493",
+    "rel_abs": "Nursing homes (NH) were among the first settings to receive COVID-19 vaccines in the United States, but staff vaccination coverage remains low at an average of 64%. Using an agent-based model, we examined the impact of community prevalence, the Delta variant, staff vaccination coverage, and boosters for residents on outbreak dynamics in nursing homes. We found that increased staff primary series coverage and high booster vaccine effectiveness (VE) in residents leads to fewer infections and that the cumulative incidence is highly dependent on community transmission. Despite high VE, high community transmission resulted in continued symptomatic infections in NHs.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Inga Holmdahl",
+        "author_inst": "Harvard T.H. Chan School of Public Health"
+      },
+      {
+        "author_name": "Rebecca Kahn",
+        "author_inst": "Harvard T.H. Chan School of Public Health"
+      },
+      {
+        "author_name": "Kara Jacobs Slifka",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Kathleen Dooling",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Rachel B Slayton",
+        "author_inst": "Centers for Disease Control and Prevention"
+      }
+    ],
+    "version": "1",
+    "license": "cc0",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.10.24.21265444",
     "rel_title": "A biological variation-based approach to the day-to-day changes of D-dimer, Fibrinogen, and Ferritin levels that are crucial in the clinical course of COVID-19 in healthy smokers and non-smokers",
@@ -527644,73 +526710,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "medical ethics"
   },
-  {
-    "rel_doi": "10.1101/2021.10.21.21265339",
-    "rel_title": "Comparative Effectiveness of BNT162b2 versus Ad26.COV2.S for the Prevention of COVID-19 among Dialysis Patients",
-    "rel_date": "2021-10-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.21.21265339",
-    "rel_abs": "BackgroundmRNA-based SARS-CoV-2 vaccines have been shown to be highly effective among dialysis patients. Because individual vaccines may be differentially available or acceptable to patients, it is important to understand comparative effectiveness of other vaccines, such those based on adeno-virus technologies.\n\nMethodsThis retrospective study compared the clinical effectiveness of Ad26.COV2.S (Janssen/Johnson and Johnson) to BNT162b2 among dialysis patients. Patients initiating BNT162b2 (Pfizer/BioNTech) were matched 1:1 to Ad26.COV2.S recipients based on age, race, US state of residence, calendar week of first vaccine receipt, and history of COVID-19. The primary outcome was the comparative rate of COVID-19 considered over 3 follow-up intervals: weeks 1-3, 4-6, and [&ge;] 7 post-vaccination. In a subset of consented Ad26.COV2.S patients, blood samples were collected [&ge;]28 days after vaccination and anti-SARS-Cov-2 immunoglobulin G antibodies were measured.\n\nResultsThere were 2659 matched pairs of patients who received a first dose of each vaccine. During weeks 1-3, incidence rates were 1.13 vs 1.39 per 1000 patient-weeks (pt-wks) for BNT162b2 and Ad26.COV2.S recipients, respectively (incident rate difference [IRD]: 0.25; 95% CI: -0.90, 1.36). During weeks 4-6, incidence rates were 0.78 vs 0.39 per 1000 pt-wks for BNT162b2 and Ad26.COV2.S recipients, respectively (IRD: -0.39; 95% CI: -1.16, 0.38). After week 7, incidence rates were 1.29 vs 1.39 per 1000 pt-wks for BNT162b2 and Ad26.COV2.S recipients, respectively (IRD: 0.10; 95% CI: -0.35, 0.55). Results were similar when considering only patients without a history of COVID-19 and among matched pairs in which BNT162b2 recipients completed the 2-dose regimen. SARS-CoV-2 antibodies were detected in 59.4% (95% CI: 53.0%-65.5%) of Ad26.COV2.S patients.\n\nConclusionIn a large real-world cohort of dialysis patients, no difference was detected in the clinical effectiveness of BNT162b2 and Ad26.COV2.S, despite an inconsistent antibody response to the latter. These data support the use of either agent in ongoing vaccination efforts in this population.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Steven M Brunelli",
-        "author_inst": "DaVita Clinical Research"
-      },
-      {
-        "author_name": "Scott Sibbel",
-        "author_inst": "DaVita Clinical Research"
-      },
-      {
-        "author_name": "Steph Karpinski",
-        "author_inst": "DaVita Clinical Research"
-      },
-      {
-        "author_name": "Gilbert Marlowe",
-        "author_inst": "DaVita Clinical Research"
-      },
-      {
-        "author_name": "Adam G Walker",
-        "author_inst": "DaVita Clinical Research"
-      },
-      {
-        "author_name": "Jeffrey Giullian",
-        "author_inst": "DaVita, Inc."
-      },
-      {
-        "author_name": "David Van Wyck",
-        "author_inst": "DaVita, Inc."
-      },
-      {
-        "author_name": "Tara Kelley",
-        "author_inst": "DaVita Clinical Research"
-      },
-      {
-        "author_name": "Rachael Lazar",
-        "author_inst": "DaVita, Inc."
-      },
-      {
-        "author_name": "Meredith L Zywno",
-        "author_inst": "DaVita, Inc."
-      },
-      {
-        "author_name": "Jeffrey J Connaire",
-        "author_inst": "DaVita Clinical Research"
-      },
-      {
-        "author_name": "Amy Young",
-        "author_inst": "DaVita Clinical Research"
-      },
-      {
-        "author_name": "Francesca Tentori",
-        "author_inst": "DaVita Clinical Research"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "nephrology"
-  },
   {
     "rel_doi": "10.1101/2021.10.21.21265318",
     "rel_title": "The impact of vaccinating adolescents and children on COVID-19 disease outcomes",
@@ -528049,6 +527048,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.10.22.21265371",
+    "rel_title": "Social mixing patterns in the UK following the relaxation of COVID-19 pandemic restrictions: a cross-sectional online survey",
+    "rel_date": "2021-10-25",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.22.21265371",
+    "rel_abs": "BackgroundSince 23 March 2020, social distancing measures have been implemented in the UK to reduce SARS-CoV-2 transmission. We conducted a cross-sectional survey to quantify and characterize non-household contact and to identify the effect of shielding and isolating on contact patterns.\n\nMethodsThrough an online questionnaire, the CoCoNet study measured daily interactions and mobility of 5143 participants between 28 July and 14 August 2020. Negative binomial regression modelling identified participant characteristics associated with contact rates.\n\nResultsThe mean rate of non-household contacts per person was 2.9 d-1. Participants attending a workplace (adjusted incidence rate ratio (aIRR) 3.33, 95%CI 3.02 to 3.66), self-employed (aIRR 1.63, 95%CI 1.43 to 1.87) or working in healthcare (aIRR 5.10, 95%CI 4.29 to 6.10) reported significantly higher non-household contact rates than those working from home. Participants self-isolating as a precaution or following Test and Trace instructions had a lower non-household contact rate than those not self-isolating (aIRR 0.58, 95%CI 0.43 to 0.79). We found limited evidence that those shielding had reduced non-household contacts compared to non-shielders.\n\nConclusionThe daily rate of non-household interactions remains lower than pre-pandemic levels, suggesting continued adherence to social distancing guidelines. Individuals attending a workplace in-person or employed as healthcare professionals were less likely to maintain social distance and had a higher non-household contact rate, possibly increasing their infection risk. Shielding and self-isolating individuals required greater support to enable them to follow the government guidelines and reduce non-household contact and therefore their risk of infection.\n\nSummary boxO_ST_ABSWhat is already known on this subject?C_ST_ABSO_LIThe introduction of social distancing guidelines in March 2020 reduced social contact rates in the UK.\nC_LIO_LIEvidence of low levels of adherence to self-isolation.\nC_LI\n\nWhat does this study add?O_LIThis study provides quantitative insight into the social mixing patterns in the UK at the beginning of the second wave of SARS-CoV2 infection.\nC_LIO_LIHealthcare professionals and individuals attending their workplace in-person were less able to follow social distancing guidelines and made more contact with people outside their household than those working from home.\nC_LIO_LIShielding individuals did not make fewer non-household contacts than those not shielding.\nC_LI",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Jessica R E Bridgen",
+        "author_inst": "Lancaster University"
+      },
+      {
+        "author_name": "Chris P Jewell",
+        "author_inst": "Lancaster University"
+      },
+      {
+        "author_name": "Jonathan M Read",
+        "author_inst": "Lancaster University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.10.22.21264706",
     "rel_title": "Modeling the impact of school reopening and contact tracing strategies on Covid-19 dynamics in different epidemiologic settings in Brazil",
@@ -529962,45 +528988,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2021.10.21.465386",
-    "rel_title": "Variations in cell-surface ACE2 levels alter direct binding of SARS-CoV-2 Spike protein and viral infectivity: Implications for measuring Spike protein interactions with animal ACE2 orthologs",
-    "rel_date": "2021-10-23",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.21.465386",
-    "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of COVID-19, the most severe pandemic in a century. The virus gains access to host cells when the viral Spike protein (S-protein) binds to the host cell-surface receptor angiotensin-converting enzyme 2 (ACE2). Studies have attempted to understand SARS-CoV-2 S-protein interaction with vertebrate orthologs of ACE2 by expressing ACE2 orthologs in mammalian cells and measuring viral infection or S-protein binding. Often these cells only transiently express ACE2 proteins and levels of ACE2 at the cell surface are not quantified. Here, we describe a cell-based assay that uses stably transfected cells expressing ACE2 proteins in a bi-cistronic vector with an easy to quantify reporter protein to normalize ACE2 expression. We found that both binding of the S-protein receptor-binding domain (RBD) and infection with a SARS-CoV-2 pseudovirus is proportional to the amount of human ACE2 expressed at the cell surface, which can be inferred by quantifying the level of reporter protein, Thy1.1. We also compared different ACE2 orthologs which were expressed in stably transfected cells expressing equivalent levels of Thy1.1. When ranked for either viral infectivity or RBD binding, mouse ACE2 had a weak to undetectable affinity for S-protein while human ACE2 was the highest level detected and feline ACE2 had an intermediate phenotype. The generation of stably transfected cells whose ACE2 level can be normalized for cross-ortholog comparisons allows us to create a reusable cellular library useful for measuring emerging SARS-CoV-2 variants ability to potentially infect different animals.\n\nImportanceSARS-CoV-2 is a zoonotic virus responsible for the worst global pandemic in a century. An understanding of how the virus can infect other vertebrate species is important for controlling viral spread and understanding the natural history of the virus. Here we describe a method to generate cells stably expressing equivalent levels of different ACE2 orthologs, the receptor for SARS-CoV-2, on the surface of a human cell line. We find that both binding of the viral Spike protein receptor binding domain (RBD) and infection of cells with a SARS-CoV-2 pseudovirus are proportional to ACE2 levels at the cell surface. Adaptation of this method will allow for the creation of a library of stable transfected cells expressing equivalent levels of different vertebrate ACE2 orthologs which can be repeatedly used for identifying vertebrate species which may be susceptible to infection with SARS-CoV-2 and its many variants.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Soheila Kazemi",
-        "author_inst": "Oregon State University"
-      },
-      {
-        "author_name": "Alberto Domingo L\u00f3pez-Mu\u0144oz",
-        "author_inst": "Centro de Biolog\u00eda Molecular Severo Ochoa"
-      },
-      {
-        "author_name": "Jaroslav Holl\u00fd",
-        "author_inst": "National Institutes of Allergy and Infectious Diseases"
-      },
-      {
-        "author_name": "Ling Jin",
-        "author_inst": "Oregon State University"
-      },
-      {
-        "author_name": "Jonathan W. Yewdell",
-        "author_inst": "National Institute of Allergy and Infectious Diseases"
-      },
-      {
-        "author_name": "Brian P. Dolan",
-        "author_inst": "Oregon State University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2021.10.19.21265093",
     "rel_title": "The Mask-Wearing Bias In The Estimates Of Vaccine Efficacy",
@@ -530339,6 +529326,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.10.21.21265216",
+    "rel_title": "Generation time of the Alpha and Delta SARS-CoV-2 variants",
+    "rel_date": "2021-10-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.21.21265216",
+    "rel_abs": "BackgroundIn May 2021, the Delta SARS-CoV-2 variant became dominant in the UK. This variant is associated with increased transmissibility compared to the Alpha variant that was previously dominant. To understand ongoing transmission and interventions, a key question is whether the Delta variant generation time (the time between infections in infector- infectee pairs) is typically shorter-i.e., transmissions are happening more quickly-or whether infected individuals simply generate more infections.\n\nMethodsWe analysed transmission data from a UK Health Security Agency household study. By fitting a mathematical transmission model to the data, we estimated the generation times for the Alpha and Delta variants.\n\nResultsThe mean intrinsic generation time (the generation time if there had been a constant supply of susceptibles throughout infection) was shorter for the Delta variant (4{middle dot}6 days, 95% CrI 4{middle dot}0-5{middle dot}4 days) than the Alpha variant (5{middle dot}5 days, 95% CrI 4{middle dot}6-6{middle dot}4 days), although within uncertainty ranges. However, there was a larger difference in the realised mean household generation time between the Delta (3{middle dot}2 days, 95% CrI 2{middle dot}4-4{middle dot}2 days) and Alpha (4{middle dot}5 days, 95% CrI 3{middle dot}7-5{middle dot}4 days) variants. This is because higher transmissibility led to faster susceptible depletion in households, in addition to the reduced intrinsic generation time.\n\nConclusionsThe Delta variant transmits more quickly than previously circulating variants. This has implications for interventions such as contact tracing, testing and isolation, which are less effective if the virus is transmitted quickly. Epidemiological models of interventions should be updated to include the shorter generation time of the Delta variant.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "William S Hart",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Liz Miller",
+        "author_inst": "LSHTM"
+      },
+      {
+        "author_name": "Nick J Andrews",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Pauline Waight",
+        "author_inst": "UK Health Security Agency"
+      },
+      {
+        "author_name": "Philip K Maini",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Seb Funk",
+        "author_inst": "LSHTM"
+      },
+      {
+        "author_name": "Robin N Thompson",
+        "author_inst": "University of Warwick"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.10.20.21265288",
     "rel_title": "COVID-19 Vaccine Perceptions and Uptake in a National Prospective Cohort of Essential Workers",
@@ -531803,49 +530833,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2021.10.21.465254",
-    "rel_title": "Gramicidin S and Melittin - Potential anti-viral therapeutic peptides to treat SARS-CoV-2 infection",
-    "rel_date": "2021-10-22",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.21.465254",
-    "rel_abs": "The COVID19 pandemic has resulted in multipronged approaches for treatment of the disease. Since de novo discovery of drugs is time consuming, repurposing of molecules is now considered as one of the alternative strategies to treat COVID19. Antibacterial peptides are being recognized as attractive candidates for repurposing to treat viral infections. In this study, we describe the anti-SARS-CoV-2 activity of gramicidin S and melittin peptides obtained from Bacillus brevis and bee venom respectively. Our in vitro antiviral assay results showed significant decrease in the viral load compared to the untreated group with no/very less cytotoxicity. The EC50 values for gramicidin S and melittin are calculated as 1.571g and 0.656g respectively. Both the peptides treated to the SARS-CoV-2 infected Vero cells showed viral clearance from 12 hours onwards with a maximal clearance after 24 hours post infection. Based on proteome analysis it was found that more than 250 proteins were found to be differentially regulated in the gramicidin S and melittin treated SARS-CoV-2 infected Vero cells against control SARS-CoV-2 infected Vero cells after 24 and 48 hours post infection. The identified proteins were found to be associated in the metabolic and mRNA processing of the Vero cells post-treatment and infection. Both these peptides could be attractive candidates for repurposing to treat SARS-CoV-2 infection.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Mohammed Ghalib Enayathullah",
-        "author_inst": "CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India"
-      },
-      {
-        "author_name": "Yash Parekh",
-        "author_inst": "CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India."
-      },
-      {
-        "author_name": "Sarena Banu",
-        "author_inst": "CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India."
-      },
-      {
-        "author_name": "Sushma Ram",
-        "author_inst": "CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India."
-      },
-      {
-        "author_name": "Ramakrishnan Nagaraj",
-        "author_inst": "CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India."
-      },
-      {
-        "author_name": "Bokara Kiran Kumar",
-        "author_inst": "CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India."
-      },
-      {
-        "author_name": "Mohammed M Idris",
-        "author_inst": "CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India."
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "cell biology"
-  },
   {
     "rel_doi": "10.1101/2021.10.22.465411",
     "rel_title": "Underlying selection for the diversity of Spike protein sequences of SARS-CoV-2",
@@ -532108,6 +531095,69 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.10.20.21265269",
+    "rel_title": "Effect of the third dose of BNT162b2 vaccine in quantitative SARS-CoV-2 spike 1-2 IgG antibody titers in healthcare workers",
+    "rel_date": "2021-10-21",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.20.21265269",
+    "rel_abs": "BackgroundVaccination is our main strategy to control SARS-CoV-2 infection. Given a decrease in the quantitative SARS-CoV-2 spike 1-2 IgG antibody titers three months following the second BNT162b2 dose, healthcare workers got a third booster dose after six months of completing the original scheme. This study aimed to analyze quantitative SARS-CoV-2 spike 1-2 IgG antibody titers and safety of the third dose.\n\nMaterial and methodsA prospective longitudinal cohort study included healthcare workers who received a third booster dose after six months of the complete BNT162b2 regimen. We assessed the quantitative SARS-CoV-2 spike 1-2 IgG antibody titers 21-28 days after the first and second dose, three months after the complete scheme, 1-7 days following the third dose, and 21-28 days after the boost.\n\nResultsThe cohort comprised 168 non-immunocompromised participants of 41(10) years old, 67% being women. The third dose was associated with increasing the quantitative antibody titers, regardless of previous SARS-CoV-2 history. In negative SARS-CoV-2 history, the median (IQR) antibody titers increased from 379 (645.4) to 2960 (2010), while in positive SARS-CoV-2 history, from 590 (1262) to 3090 (2080). The third dose had less number of total side effects compared to the other two shots. The most common side effect after the third BNT162b2 shot was pain at the injection site (n=82, 84.5%), followed by tiredness (n=45, 46.4%), with a mild severity (n=36, 37.1%). Tiredness, myalgias, arthralgias, fever, and adenopathy were proportionally higher following the third dose than the two-dose regimen (p<0.05).\n\nConclusionThe third dose applied after six months of the original BNT162b2 regimen provided a good humoral immune response by elevating the quantitative SARS-CoV-2 spike 1-2 IgG antibody titers. The booster dose was well tolerated with no severe side effects after the additional BNT162b2 dose.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Maria Elena Romero-Ibarguengoitia",
+        "author_inst": "Hospital Clinica Nova de Monterrey and Vicerrectoria de Ciencias de la Salud, Escuela de Medicina, Universidad de Monterrey"
+      },
+      {
+        "author_name": "Diego Rivera-Salinas",
+        "author_inst": "Hospital Clinica Nova de Monterrey and Vicerrectoria de Ciencias de la Salud, Escuela de Medicina, Universidad de Monterrey"
+      },
+      {
+        "author_name": "Yodira Guadalupe Hernandez-Ruiz",
+        "author_inst": "Hospital Clinica Nova  de Monterrey and Vicerrectoria de Ciencias de la Salud, Escuela de Medicina, Universidad de Monterrey"
+      },
+      {
+        "author_name": "Ana Gabriela Armendariz-Vazquez",
+        "author_inst": "Hospital Clinica Nova de Monterrey and Vicerrectoria de Ciencias de la Salud, Escuela de Medicina, Universidad de Monterrey"
+      },
+      {
+        "author_name": "Arnulfo Gonzalez-Cantu",
+        "author_inst": "Hospital Clinica Nova de Monterrey and Vicerrectoria de Ciencias de la Salud, Escuela de Medicina, Universidad de Monterrey"
+      },
+      {
+        "author_name": "Irene Antonieta Barco-Flores",
+        "author_inst": "Hospital Clinica Nova de Monterrey"
+      },
+      {
+        "author_name": "Rosalinda Gonzalez-Facio",
+        "author_inst": "Hospital Clinica Nova de Monterrey"
+      },
+      {
+        "author_name": "Laura Patricia Montelongo-Cruz",
+        "author_inst": "Hospital Clinica Nova de Monterrey and Vicerrectoria de Ciencias de la Salud, Escuela de Medicina, Universidad de Monterrey"
+      },
+      {
+        "author_name": "Gerardo Francisco Del Rio-Parra",
+        "author_inst": "Hospital Clinica Nova de Monterrey and Vicerrectoria de Ciencias de la Salud, Escuela de Medicina, Universidad de Monterrey"
+      },
+      {
+        "author_name": "Mauricio Rene Garza-Herrera",
+        "author_inst": "Hospital Clinica Nova de Monterrey and Vicerrectoria de Ciencias de la Salud, Escuela de Medicina, Universidad de Monterrey"
+      },
+      {
+        "author_name": "Jessica Andrea Leal Melendez",
+        "author_inst": "Hospital Clinica Nova de Monterrey and Vicerrectoria de Ciencias de la Salud, Escuela de Medicina, Universidad de Monterrey"
+      },
+      {
+        "author_name": "Miguel Angel Sanz-Sanchez",
+        "author_inst": "Hospital Clinica Nova de Monterrey and Vicerrectoria de Ciencias de la Salud, Escuela de Medicina, Universidad de Monterrey"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.10.18.21264783",
     "rel_title": "SARS-CoV-2 variant transmission in a community-health population (Mexico City, Mexico)",
@@ -533785,205 +532835,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.10.19.21265226",
-    "rel_title": "Wastewater and surface monitoring to detect COVID-19 in elementary school settings: The Safer at School Early Alert project",
-    "rel_date": "2021-10-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.19.21265226",
-    "rel_abs": "BackgroundSchools are high-risk settings for SARS-CoV-2 transmission, but necessary for childrens educational and social-emotional wellbeing. Previous research suggests that wastewater monitoring can detect SARS-CoV-2 infections in controlled residential settings with high levels of accuracy. However, its effective accuracy, cost, and feasibility in non-residential community settings is unknown.\n\nMethodsThe objective of this study was to determine the effectiveness and accuracy of community-based passive wastewater and surface (environmental) surveillance to detect SARS-CoV-2 infection in neighborhood schools compared to weekly diagnostic (PCR) testing. We implemented an environmental surveillance system in nine elementary schools with 1700 regularly present staff and students in southern California. The system was validated from November 2020 - March 2021.\n\nFindingsIn 447 data collection days across the nine sites 89 individuals tested positive for COVID-19, and SARS-CoV-2 was detected in 374 surface samples and 133 wastewater samples. Ninety-three percent of identified cases were associated with an environmental sample (95% CI: 88% - 98%); 67% were associated with a positive wastewater sample (95% CI: 57% - 77%), and 40% were associated with a positive surface sample (95% CI: 29% - 52%). The techniques we utilized allowed for near-complete genomic sequencing of wastewater and surface samples.\n\nInterpretationPassive environmental surveillance can detect the presence of COVID-19 cases in non-residential community school settings with a high degree of accuracy.\n\nFundingCounty of San Diego, Health and Human Services Agency, National Institutes of Health, National Science Foundation, Centers for Disease Control",
-    "rel_num_authors": 46,
-    "rel_authors": [
-      {
-        "author_name": "Rebecca K Fielding-Miller",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Smruthi Karthikeyan",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Tommi Gaines",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Richard S Garfein",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Rodolfo A Salido",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Victor Cantu",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Laura Kohn",
-        "author_inst": "Kohn Educational Consulting"
-      },
-      {
-        "author_name": "Fitri C Wijaya",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Marlene Flores",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Vinton Omaleki",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Araz Majnoonian",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Natasha K Martin",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Dahl Austin",
-        "author_inst": "Independent consultant"
-      },
-      {
-        "author_name": "Louise C Laurent",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Adriane Wynne",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Patricia Gonzalez-Zuniga",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Megan Nguyen",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Anh V Vo",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Tina T Le",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Dawn Duong",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Ashkan Hassani",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Samantha Tweeten",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Kristen Jepsen",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Benjamin Henson",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Abbas Hakim",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Amanda Birmingham",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Adam M Mark",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Chanond A Nasamran",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Sara B Rosenthal",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Niema Moshiri",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Kathleen M Fisch",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Greg Humphrey",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Sawyer Farmer",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Helena Tubb",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Tommy Valles",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Justin Morris",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Jaeyoung Kang",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Behnam Khaleghi",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Colin Young",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Ameen D Akel",
-        "author_inst": "Micron Technology"
-      },
-      {
-        "author_name": "Sean Eilert",
-        "author_inst": "Micron Technology"
-      },
-      {
-        "author_name": "Justin Eno",
-        "author_inst": "Micron Technology"
-      },
-      {
-        "author_name": "Ken Curewitz",
-        "author_inst": "Micron Technology"
-      },
-      {
-        "author_name": "Tajana Rosing",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "- SEARCH",
-        "author_inst": "-"
-      },
-      {
-        "author_name": "Rob Knight",
-        "author_inst": "University of California, San Diego"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.10.20.21265279",
     "rel_title": "Factors affecting the mental health of pregnant women using UK maternity services during the COVID-19 pandemic: A qualitative interview study.",
@@ -534270,6 +533121,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.10.11.21264694",
+    "rel_title": "A cohort of 222 anti-CD20 treated patients with multiple sclerosis followed through the COVID-19 pandemic: Attenuated humoral but robust cellular immune responses after vaccination and infection",
+    "rel_date": "2021-10-19",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.11.21264694",
+    "rel_abs": "ObjectiveTo analyze humoral and cellular immune responses to SARS-CoV-2 vaccinations and infections in anti-CD20 treated patients with multiple sclerosis (pwMS).\n\nMethods181 pwMS on anti-CD20 therapy and 41 pwMS who began anti-CD20 therapy were included in a prospective, observational, single-center cohort study between March 2020 and August 2021. 51 pwMS under anti-CD20 treatment, 14 anti-CD20 therapy-naive pwMS and 19 healthy controls (HC) were vaccinated twice against SARS-CoV-2. We measured SARS-CoV-2 spike protein (full-length, S1 domain and receptor binding domain) immunoglobulin (Ig)G and S1 IgA and virus neutralizing capacity and avidity of SARS-CoV-2 antibodies. SARS-CoV-2 specific T cells were determined by interferon-{gamma} release assays.\n\nResultsFollowing two SARS-CoV-2 vaccinations, levels of IgG and IgA antibodies to SARS-CoV-2 spike protein as well as neutralizing capacity and avidity of SARS-CoV-2 IgG were lower in anti-CD20 treated pwMS than in anti-CD20 therapy-naive pwMS and in HC (p<0.003 for all pairwise comparisons). However, in all anti-CD20 treated pwMS vaccinated twice (n=26) or infected with SARS-CoV-2 (n=2), in whom SARS-CoV-2 specific T cells could be measured, SARS-CoV-2 specific T cells were detectable, at levels similar to those of twice-vaccinated anti-CD20 therapy-naive pwMS (n=7) and HC (n=19). SARS-CoV-2 S1 IgG levels (r=0.42, p=0.002), antibody avidity (r=0.7, p<0.001) and neutralizing capacity (r=0.44, p=0.03) increased with time between anti-CD20 infusion and second vaccination. Based on detection of SARS-CoV-2 antibodies, SARS-CoV-2 infections occurred in 4/175 (2.3%) anti-CD20 treated pwMS, all of whom recovered fully.\n\nInterpretationThese findings should inform treatment decisions and SARS-CoV-2 vaccination management in pwMS.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Tatjana Schwarz",
+        "author_inst": "Institute of Virology, Charite - Universitaetsmedizin"
+      },
+      {
+        "author_name": "Carolin Otto",
+        "author_inst": "Department of Neurology, Charite - Universitaetsmedizin"
+      },
+      {
+        "author_name": "Terry C Jones",
+        "author_inst": "Institute of Virology, Charite - Universitaetsmedizin"
+      },
+      {
+        "author_name": "Florence Pache",
+        "author_inst": "Department of Neurology, Charite - Universitaetsmedizin Berlin"
+      },
+      {
+        "author_name": "Patrick Schindler",
+        "author_inst": "Department of Neurology, Charite - Universitaetsmedizin Berlin"
+      },
+      {
+        "author_name": "Moritz Niederschweiberer",
+        "author_inst": "Department of Neurology, Charite - Universitaetsmedizin Berlin"
+      },
+      {
+        "author_name": "Felix Schmidt",
+        "author_inst": "Department of Neurology, Charite- Universitaetsmedizin"
+      },
+      {
+        "author_name": "Christian Drosten",
+        "author_inst": "Institute of Virology, Charite Universitaetsmedizin Berlin"
+      },
+      {
+        "author_name": "Victor M Corman",
+        "author_inst": "Institute of Virology, Charite - Universitaetsmedizin Berlin"
+      },
+      {
+        "author_name": "Klemens Ruprecht",
+        "author_inst": "Department of Neurology, Charite - Universitaetsmedizin Berlin"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "neurology"
+  },
   {
     "rel_doi": "10.1101/2021.10.16.464647",
     "rel_title": "BugSplit: highly accurate taxonomic binning of metagenomic assemblies enables genome-resolved metagenomics",
@@ -535618,49 +534524,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.10.13.21264921",
-    "rel_title": "Predicting COVID-19 Vaccine Efficacy from Neutralizing Antibody Levels",
-    "rel_date": "2021-10-18",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.13.21264921",
-    "rel_abs": "Recent studies using data accrued from global SARS-CoV-2 vaccination efforts have demonstrated that breakthrough infections are correlated with levels of neutralizing antibodies. The decrease in neutralizing antibody titers of vaccinated individuals over time, combined with the emergence of more infectious variants of concern has resulted in waning vaccine efficacy against infection and a rise in breakthrough infections. Here we use a combination of neutralizing antibody measurements determined by a high throughput surrogate viral neutralization test (sVNT) together with published data from vaccine clinical trials and comparative plaque reduction neutralization test (PRNT) between SARS-CoV-2 variants to develop a model for vaccine efficacy (VE) against symptomatic infection. Vaccine efficacy estimates using this model show good concordance with real world data from the US and Israel. Our work demonstrates that appropriately calibrated neutralizing antibody measurements determined by high throughput sVNT can be used to provide a semi-quantitative estimate of protection against infection. Given the highly variable antibody levels among the vaccinated population, this model may be of use in identification of individuals with an elevated risk of breakthrough infections.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Majid R. Abedi",
-        "author_inst": "DxTerity Diagnostics, Rancho Dominguez, CA"
-      },
-      {
-        "author_name": "Samuel Dixon",
-        "author_inst": "DxTerity Diagnostics, Rancho Dominguez, CA"
-      },
-      {
-        "author_name": "Timothy Guyon",
-        "author_inst": "DxTerity Diagnostics, Rancho Dominguez, CA"
-      },
-      {
-        "author_name": "Serene Hsu",
-        "author_inst": "DxTerity Diagnostics, Rancho Dominguez, CA"
-      },
-      {
-        "author_name": "Aviva R. Jacobs",
-        "author_inst": "DxTerity Diagnostics, Rancho Dominguez, CA"
-      },
-      {
-        "author_name": "Lakshmi Nair",
-        "author_inst": "Thermo Fisher Scientific, South San Francisco, CA"
-      },
-      {
-        "author_name": "Robert Terbrueggen",
-        "author_inst": "DxTerity Diagnostics, Rancho Dominguez, CA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.10.13.21264946",
     "rel_title": "Clinical observation of high-flow nasal cannula (HFNC) with non-rebreather mask (NRM) use on severe or critically ill COVID-19 diabetic patients",
@@ -535911,6 +534774,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.10.15.21265059",
+    "rel_title": "CoWWAn: Model-based assessment of COVID-19 epidemic dynamics by wastewater analysis",
+    "rel_date": "2021-10-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.15.21265059",
+    "rel_abs": "We present COVID-19 Wastewater Analyser (CoWWAn) to reconstruct the epidemic dynamics from SARS-CoV-2 viral load in wastewater. As demonstrated for various regions and sampling protocols, this mechanistic model-based approach quantifies the case numbers, provides epidemic indicators and accurately infers future epidemic trends. In situations of reduced testing capacity, analysing wastewater data with CoWWAn is a robust and cost-effective alternative for real-time surveillance of local COVID-19 dynamics.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Daniele Proverbio",
+        "author_inst": "University of Luxembourg"
+      },
+      {
+        "author_name": "Fran\u00e7oise Kemp",
+        "author_inst": "University of Luxembourg"
+      },
+      {
+        "author_name": "Stefano Magni",
+        "author_inst": "University of Luxembourg"
+      },
+      {
+        "author_name": "Leslie Ogorzaly",
+        "author_inst": "Luxembourg Institute of Science and Technology"
+      },
+      {
+        "author_name": "Henry-Michel Cauchie",
+        "author_inst": "Luxembourg Institute of Scienceand Technology"
+      },
+      {
+        "author_name": "Jorge Gon\u00e7alves",
+        "author_inst": "University of Luxembourg"
+      },
+      {
+        "author_name": "Alexander Skupin",
+        "author_inst": "University of Luxembourg"
+      },
+      {
+        "author_name": "Atte Aalto",
+        "author_inst": "University of Luxembourg"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.10.14.21264980",
     "rel_title": "Incidence of SARS-CoV-2 infection in a cohort of workers from the University of Porto",
@@ -537128,61 +536038,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.10.15.464595",
-    "rel_title": "Mitoxantrone modulates a glycosaminoglycan-spike complex to inhibit SARS-CoV-2 infection",
-    "rel_date": "2021-10-18",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.15.464595",
-    "rel_abs": "Spike-mediated entry of SARS-CoV-2 into human airway epithelial cells is an attractive therapeutic target for COVID-19. In addition to protein receptors, the SARS-CoV-2 spike (S) protein also interacts with heparan sulfate, a negatively charged glycosaminoglycan (GAG) attached to certain membrane proteins on the cell surface. This interaction facilitates the engagement of spike with a downstream receptor to promote viral entry. Here, we show that Mitoxantrone, an FDA-approved topoisomerase inhibitor, targets a spike-GAG complex to compromise the fusogenic function of spike in viral entry. As a single agent, Mitoxantrone inhibits the infection of an authentic SARS-CoV-2 strain in a cell-based model and in human lung EpiAirway 3D tissues. Gene expression profiling supports the plasma membrane as a major target of Mitoxantrone but also underscores an undesired activity targeting nucleosome dynamics. We propose that Mitoxantrone analogs bearing similar GAG-binding activities but with reduced affinity for DNA topoisomerase may offer an alternative therapy to overcome breakthrough infections in the post-vaccine era.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Qi Zhang",
-        "author_inst": "NIH/NCATS"
-      },
-      {
-        "author_name": "Peter Radvak",
-        "author_inst": "Center for Biologics Evaluation and Research, US Food and Drug Administration"
-      },
-      {
-        "author_name": "Juhyung Lee",
-        "author_inst": "NIH/NIDDK"
-      },
-      {
-        "author_name": "Yue Xu",
-        "author_inst": "NIH/NIDDK"
-      },
-      {
-        "author_name": "Vivian Cao-Dao",
-        "author_inst": "NIH/NIDDK"
-      },
-      {
-        "author_name": "Miao Xu",
-        "author_inst": "NIH/NCATS"
-      },
-      {
-        "author_name": "Wei Zheng",
-        "author_inst": "NIH/NCATS"
-      },
-      {
-        "author_name": "Catherine Z Chen",
-        "author_inst": "NIH/NCATS"
-      },
-      {
-        "author_name": "Hang Xie",
-        "author_inst": "Center for Biologics Evaluation and Research, US Food and Drug Administration"
-      },
-      {
-        "author_name": "Yihong Ye",
-        "author_inst": "NIH/NIDDK"
-      }
-    ],
-    "version": "1",
-    "license": "cc0",
-    "type": "new results",
-    "category": "cell biology"
-  },
   {
     "rel_doi": "10.1101/2021.10.17.21265123",
     "rel_title": "Long-term manifestations and modifiers of prevalence estimates of the post-COVID-19 syndrome: A systematic review and meta-analysis.",
@@ -537533,6 +536388,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
+  {
+    "rel_doi": "10.1101/2021.10.13.21264894",
+    "rel_title": "Memory B cell and humoral responses elicited by Sputnik V in nai\u0308ve and COVID-19-recovered vaccine recipients",
+    "rel_date": "2021-10-17",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.13.21264894",
+    "rel_abs": "The development of effective vaccines against SARS-CoV-2 remains a global health priority. Despite extensive use, the effects of Sputnik V on B cell immunity need to be explored in detail. We show that B memory cell (MBC) and antibody responses to Sputnik V were heavily dependent on whether the vaccinee had a history of SARS-CoV-2 infection or not. In vitro stimulated MBCs from previously infected recipients of Sputnik V secreted a significant amount of anti-RBD IgG both on days 28 and 85 from the beginning of vaccination. These antibodies demonstrated robust neutralization of the Wuhan Spike-pseudotyped lentivirus. In the naive group of vaccinees, the level of anti-RBD IgG secretion was five- to six-fold reduced compared to that of the recovered group, and maximum virus neutralization (Wuhan spike) was achieved only on day 85. Sera from all the recovered and most naive Sputnik V recipients were neutralizing against the ancestral Wuhan and mutant B.1.351 viruses. Thus, our in-depth analysis of MBC responses in Sputnik V vaccinees complements traditional serological approaches and may provide important outlook into future B cell responses upon re-encounter with the emerging variants of SARS-CoV-2.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Maria G Byazrova",
+        "author_inst": "Institute of Immunology Moscow"
+      },
+      {
+        "author_name": "Sergey V Kulemzin",
+        "author_inst": "Institute of Molecular and Cellular Biology"
+      },
+      {
+        "author_name": "Ekaterina A Astakhova",
+        "author_inst": "Institute of Immunology Moscow"
+      },
+      {
+        "author_name": "Tatyana N Belovezhets",
+        "author_inst": "Institute of Molecular and Cellular Biology"
+      },
+      {
+        "author_name": "Grigory A Efimov",
+        "author_inst": "National Research Center for Hematology"
+      },
+      {
+        "author_name": "Anton N Chikaev",
+        "author_inst": "Institute of Molecular and Cellular Biology"
+      },
+      {
+        "author_name": "Ilya O Kolotygin",
+        "author_inst": "Institute of Molecular and Cellular Biology"
+      },
+      {
+        "author_name": "Andrey A Gorchakov",
+        "author_inst": "Institute of Molecular and Cellular Biology"
+      },
+      {
+        "author_name": "Alexander V Taranin",
+        "author_inst": "Institute of Molecular and Cellular Biology"
+      },
+      {
+        "author_name": "Alexander V Filatov",
+        "author_inst": "Institute of Immunology Moscow"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "allergy and immunology"
+  },
   {
     "rel_doi": "10.1101/2021.10.14.21264861",
     "rel_title": "Interactions among common non-SARS-CoV-2 respiratory viruses and influence of the COVID-19 pandemic on their circulation in New York City",
@@ -539229,57 +538139,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.10.11.21264820",
-    "rel_title": "Comparison of endoscopic activity before and during the covid pandemic at a tertiary care hospital in South Punjab",
-    "rel_date": "2021-10-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.11.21264820",
-    "rel_abs": "IntroductionCoronavirus disease 2019 (COVID-19) has resulted in dramatic changes to health-care delivery. Endoscopic activity has had frequent disruptions during this pandemic. The objective of the study was to see the influence of pandemic over the endoscopic activity.\n\nMethodsThis retrospective analysis of endoscopic activity was undertaken at Nishtar Hospital Multan. Procedural analysis was done in the three months immediately after covid lockdown (1st April till 30th June 2020) and was compared to a similar period one year back.\n\nResultsFive hundred and fifty-four (68.5%) patients underwent endoscopic procedures during the three months of pre-COVID era, while this number reduced to half (n=255, 31.5%) patients during the covid pandemic. Even though the absolute number of Esophagogastroduodenoscopies (EGDs) reduced during the pandemic, patients were more likely to undergo EGDs during the COVID pandemic in contrast to the era before the pandemic (79% versus 66%, p = 0.002). The most common indication for EGD was upper gastrointestinal bleeding (UGIB). The percentage of EGDs done for UGIB rose from almost 60% to 80% during the covid pandemic (p < 0.001). The most common findings were esophageal varices and portal gastropathy (non-significant difference during and before the pandemic). Percentage of ERCPs done for obstructive jaundice doubled during the COVID pandemic (33% versus 65%, p = 0.002).The most common indication for sigmoidoscopy or colonoscopy was lower gastrointestinal bleeding. However, no significant difference was found before and during the covid pandemic (41.7% and 45.8% respectively, p=0.72). Internal hemorrhoids were the most common endoscopic finding. Colon cancer diagnosis reduced from 10% to undetected during the pandemic period.\n\nConclusionCOVID pandemic resulted in considerable reduction in all type of endoscopic procedures. Majority of procedures were done for emergency indications like gastrointestinal bleeding. Rates of cancer detection was significantly reduced.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Farooq Mohyud Din",
-        "author_inst": "Nishtar Medical University and Hospital"
-      },
-      {
-        "author_name": "Muhammad Asif Gul",
-        "author_inst": "Nishtar Medical University & Hospital"
-      },
-      {
-        "author_name": "Nouman Hameed",
-        "author_inst": "Nishtar Medical University & Hospital"
-      },
-      {
-        "author_name": "Rizwan Hameed",
-        "author_inst": "Nishtar Medical University & Hospital"
-      },
-      {
-        "author_name": "Yasir Zaidi",
-        "author_inst": "Nishtar Medical University & Hospital"
-      },
-      {
-        "author_name": "Shehryar Kanju",
-        "author_inst": "Nishtar Medical University & Hospital"
-      },
-      {
-        "author_name": "Ahsan Tameez-ud-din",
-        "author_inst": "Rawalpindi Medical University"
-      },
-      {
-        "author_name": "Syeda Manal Altaf",
-        "author_inst": "Rawalpindi Medical University"
-      },
-      {
-        "author_name": "Asma Tameez Ud Din",
-        "author_inst": "Shahida Islam Medical College"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "gastroenterology"
-  },
   {
     "rel_doi": "10.1101/2021.10.12.21264903",
     "rel_title": "Leaders gender and the fight against COVID-19: investigation, replication, and a possible explanation",
@@ -539658,6 +538517,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.10.11.21264869",
+    "rel_title": "Modeling and analysis of COVID-19 infected persons during repeated waves in Japan",
+    "rel_date": "2021-10-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.11.21264869",
+    "rel_abs": "A model for estimating the number of COVID-19 infected persons (infecteds) is proposed based on the exponential function law of the SIR model. This model is composed of several equations expressing the number of infecteds, considering the onset after an incubation period, infectivity, wavy infection persistence with repeated infection spread and convergence with insufficient quarantine. This model is applied to the infection in Japan, which is currently suffering from the 5th wave, and the initial number of infecteds and various related parameters are calculated by curve fitting of the cumulative number of infecteds to the total cases in the database. As a minimum boundary of the number of infecteds for the infection continuation up to the 5th wave, the initial number of infecteds at the outbreak of infection is more than an order of magnitude higher than the actual initial cases. A convergence ratio (cumulative number of infecteds / total cases) at the end of the first wave is obtained as 1.5. The quarantine rate and social distancing ratio based on the SIQR model are evaluated, and the social distancing ratio increases sharply just after the governments declaration of emergency. The quarantine rate closely equals the positive rate by PCR tests, meaning that the number of infecteds, which had been unknown, is on the order of almost the same as the number of tests.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Koichi Hashiguchi",
+        "author_inst": "None"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.10.14.21264959",
     "rel_title": "Vaccine effectiveness against SARS-CoV-2 transmission to household contacts during dominanceof Delta variant (B.1.617.2), August-September 2021, the Netherlands",
@@ -541115,33 +539993,6 @@
     "type": "new results",
     "category": "molecular biology"
   },
-  {
-    "rel_doi": "10.1101/2021.10.11.21264836",
-    "rel_title": "Mechanism of optimal time-course COVID-19 vaccine prioritization based on non-Markovian steady-state prediction",
-    "rel_date": "2021-10-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.11.21264836",
-    "rel_abs": "Vaccination is essential for controlling the coronavirus disease (COVID-19) pandemic. An effective time-course strategy for the allocation of COVID-19 vaccines is crucial given that the global vaccine supply will still be limited in some countries/regions in the near future and that mutant strains have emerged and will continue to spread worldwide. Both asymptomatic and symptomatic transmission have played major roles in the COVID-19 pandemic, which can only be properly described as a typical non-Markovian process. However, the prioritization of vaccines in the non-Markovian framework still lacks sufficient research, and the underlying mechanism of the time-course vaccine allocation optimization has not yet been uncovered. In this paper, based on an age-stratified compartmental model calibrated through clinical and epidemiological data, we propose optimal vaccination strategies (OVS) through steady-state prediction in the non-Markovian framework. This OVS outperforms other empirical vaccine prioritization approaches in minimizing cumulative infections, cumulative deaths, or years of life lost caused by the pandemic. We found that there exists a fast decline in the prevention efficiency of vaccination if vaccines are solely administered to a selected age group, which indicates that the widely adopted strategy to continuously vaccinate high-risk group is not optimal. Through mathematical analysis of the model, we reveal that dynamic vaccine allocations to combinations of different age groups is necessary to achieve optimal vaccine prioritization. Our work not only provides meaningful references for vaccination in countries currently lacking vaccines and for vaccine allocation strategies to prevent mutant strains in the future, but also reveals the mechanism of dynamic vaccine allocation optimization, forming a theoretical and modelling framework empirically applicable to the optimal time-course prioritization.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Mi Feng",
-        "author_inst": "Hong Kong Baptist University"
-      },
-      {
-        "author_name": "Liang Tian",
-        "author_inst": "Hong Kong Baptist University"
-      },
-      {
-        "author_name": "Changsong Zhou",
-        "author_inst": "Hong Kong Baptist University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.10.13.21264960",
     "rel_title": "Evaluation of real-life use of Point-Of-Care Rapid Antigen TEsting for SARS-CoV-2 in schools for outbreak control (EPOCRATES)",
@@ -541584,6 +540435,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.10.10.21264821",
+    "rel_title": "Modelling the effect of COVID-19 mass vaccination on acute admissions in a major English healthcare system",
+    "rel_date": "2021-10-13",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.10.21264821",
+    "rel_abs": "BackgroundManaging high levels of severe COVID-19 in the acute setting can impact upon the quality of care provided to both affected patients and those requiring other hospital services. Mass vaccination has offered a route to reduce societal restrictions while protecting hospitals from being overwhelmed. Yet, early in the mass vaccination effort, the possible effect on future bed pressures remained subject to considerable uncertainty. This paper provides an account of how, in one healthcare system, operational decision-making and bed planning was supported through modelling the effect of a range of vaccination scenarios on future COVID-19 admissions.\n\nMethodsAn epidemiological model of the Susceptible-Exposed-Infectious-Recovered (SEIR) type was fitted to local data for the one-million resident healthcare system located in South West England. Model parameters and vaccination scenarios were calibrated through a system-wide multi-disciplinary working group, comprising public health intelligence specialists, healthcare planners, epidemiologists, and academics. From 4 March 2021 (the time of the study), scenarios assumed incremental relaxations to societal restrictions according to the envisaged UK Government timeline, with all restrictions to be removed by 21 June 2021.\n\nResultsAchieving 95% vaccine uptake in adults by 31 July 2021 would not avert a third wave in autumn 2021 but would produce a median peak bed requirement approximately 6% (IQR: 1% to 24%) of that experienced during the second wave (January 2021). A two-month delay in vaccine rollout would lead to significantly higher peak bed occupancy, at 66% (11% to 146%) of that of the second wave. If only 75% uptake was achieved (the amount typically associated with vaccination campaigns) then the second wave peak for acute and intensive care beds would be exceeded by 4% and 19% respectively, an amount which would seriously pressure hospital capacity.\n\nConclusionModelling provided support to senior managers in setting the number of acute and intensive care beds to make available for COVID-19 patients, as well as highlighting the importance of public health in promoting high vaccine uptake among the population. Forecast accuracy has since been supported by actual data collected following the analysis, with observed peak bed occupancy falling comfortably within the inter-quartile range of modelled projections.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Ross D Booton",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Anna L Powell",
+        "author_inst": "UK National Health Service"
+      },
+      {
+        "author_name": "Katy ME Turner",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Richard M Wood",
+        "author_inst": "UK National Health Service"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health informatics"
+  },
   {
     "rel_doi": "10.1101/2021.10.10.21264817",
     "rel_title": "Child mental and behavioral health services during the COVID-19 pandemic: Trends and implications for service outcomes during telehealth expansion",
@@ -542937,85 +541819,6 @@
     "type": "new results",
     "category": "biophysics"
   },
-  {
-    "rel_doi": "10.1101/2021.10.10.21264589",
-    "rel_title": "Impact of Antibody Cocktail Therapy Combined with Casirivimab and Imdevimab on Clinical Outcome for Covid-19 patients in A Real-Life Setting: A Single Institute Analysis",
-    "rel_date": "2021-10-12",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.10.21264589",
-    "rel_abs": "BackgroundRecent data from clinical trial suggest that antibody cocktail therapy, a combination of the monoclonal antibodies casirivimab and imdevimab, has been shown to rapidly reduce the viral load and markedly decrease the risk of hospitalization or death among high-risk patients with coronavirus disease 2019 (Covid-19). However, it remains unclear how effective in a real-life clinical setting the therapy is.\n\nMethodsWe retrospectively analyzed mild to moderate Covid-19 patients with one or more high-risk factors for severe disease who consecutively underwent the antibody cocktail therapy of the disease in our institute in June 2021 through early September 2021, compared to those with high-risk factors who were isolated in non-medical facilities consecutively during the same period, thereby being not given the antibody cocktail therapy there. The key outcome was the percentage of patients with Covid-19-related deterioration which needed additional medical interventions, such as oxygen support or other antiviral therapies.\n\nResultsData from 55 patients with initially receiving antibody cocktail therapy and 53 patients with isolation into non-medical facilities are analyzed. 22 (41.5 %) of 53 patients with isolation facilities were finally hospitalized to receive medical interventions. On the other hand, 13 (23.6 %) of 55 patients with antibody cocktail therapy in our hospital subsequently underwent further medical interventions because of the progression. In multivariate analysis with variables of age, BMI, and high-risk factors, the antibody cocktail therapy significantly reduced 70 % in the need for further medical interventions compared to the initial isolation in the non-medical facilities (odds ratio=0.30, 95%CI [0.10-0.87], p=0.027). Furthermore, patients with 96% or above of SPO2 were significantly more favorable for the therapy than those with 95% or below of SPO2.\n\nConclusionThe treatment of antibody cocktail was closely linked to reduction in the need for further medical interventions. The result indicates that the antibody cocktail therapy is associated with reducing the strain on hospitals, which is related to the improvement of medical management for public health care in Covid-19 pandemic era.",
-    "rel_num_authors": 16,
-    "rel_authors": [
-      {
-        "author_name": "Yasutaka Kakinoki",
-        "author_inst": "Asahikawa City Hospital"
-      },
-      {
-        "author_name": "Kazuki Yamada",
-        "author_inst": "Division of Internal Medicine, Asahikawa City Hospital, Asahikawa, Japan"
-      },
-      {
-        "author_name": "Yoko Tanino",
-        "author_inst": "Division of Internal Medicine, Asahikawa City Hospital, Asahikawa, Japan"
-      },
-      {
-        "author_name": "Keiko Suzuki",
-        "author_inst": "Division of Internal Medicine, Asahikawa City Hospital, Asahikawa, Japan"
-      },
-      {
-        "author_name": "Takaya Ichikawa",
-        "author_inst": "Division of Internal Medicine, Asahikawa City Hospital, Asahikawa, Japan"
-      },
-      {
-        "author_name": "Naoki Suzuki",
-        "author_inst": "Asahikawa City Health Center"
-      },
-      {
-        "author_name": "Go Asari",
-        "author_inst": "Asahikawa City Health Center"
-      },
-      {
-        "author_name": "Ai Nakamura",
-        "author_inst": "Division of Internal Medicine, Asahikawa City Hospital, Asahikawa, Japan"
-      },
-      {
-        "author_name": "Shin Kukita",
-        "author_inst": "Division of Internal Medicine, Asahikawa City Hospital, Asahikawa, Japan"
-      },
-      {
-        "author_name": "Akito Uehara",
-        "author_inst": "Division of Internal Medicine, Asahikawa City Hospital, Asahikawa, Japan"
-      },
-      {
-        "author_name": "Seisuke Saito",
-        "author_inst": "Division of Internal Medicine, Asahikawa City Hospital, Asahikawa, Japan"
-      },
-      {
-        "author_name": "Shohei Kuroda",
-        "author_inst": "Division of Internal Medicine, Asahikawa City Hospital, Asahikawa, Japan"
-      },
-      {
-        "author_name": "Hidemitsu Sakagami",
-        "author_inst": "Division of Internal Medicine, Asahikawa City Hospital, Asahikawa, Japan"
-      },
-      {
-        "author_name": "Yuuki Nagashima",
-        "author_inst": "Division of Internal Medicine, Asahikawa City Hospital, Asahikawa, Japan"
-      },
-      {
-        "author_name": "Kae Takahashi",
-        "author_inst": "Division of Internal Medicine, Asahikawa City Hospital, Asahikawa, Japan"
-      },
-      {
-        "author_name": "Satoshi Suzuki",
-        "author_inst": "Division of Internal Medicine, Asahikawa City Hospital, Asahikawa, Japan"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.10.07.21257459",
     "rel_title": "Cellular and Antibody Immunity after COVID-19 Vaccination at >4-Month Follow Up in Immunocompetent and Immunocompromised Subjects",
@@ -543265,6 +542068,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
+  {
+    "rel_doi": "10.1101/2021.10.08.21264765",
+    "rel_title": "The impact of heating, ventilation, and air conditioning design features on the transmission of viruses, including the 2019 novel coronavirus: a systematic review of ventilation and coronavirus",
+    "rel_date": "2021-10-11",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.08.21264765",
+    "rel_abs": "Aerosol transmission has been a pathway for virus spread for many viruses. Similarly, emerging evidence regarding SARS-CoV-2, and the resulting pandemic as declared by WHO in March 2020, determined aerosol transmission for SARS-CoV-2 to be significant. As such, public health officials and professionals have sought data regarding the effect of Heating, Ventilation, and Air Conditioning (HVAC) features to control and mitigate viruses, particularly coronaviruses. A systematic review was conducted using international standards to identify and comprehensively synthesize research examining the effectiveness of ventilation for mitigating transmission of coronaviruses. The results from 32 relevant studies showed that: increased ventilation rate was associated with decreased transmission, transmission probability/risk, infection probability/risk, droplet persistence, virus concentration, and increased virus removal and virus particle removal efficiency; increased ventilation rate decreased risk at longer exposure times; some ventilation was better than no ventilation; airflow patterns affected transmission; ventilation feature (e.g., supply/exhaust, fans) placement influenced particle distribution. Some studies provided qualitative recommendations; however, few provided specific quantitative ventilation parameters suggesting a significant gap in current research. Adapting HVAC ventilation systems to mitigate virus transmission is not a one-solution-fits-all approach but instead requires consideration of factors such as ventilation rate, airflow patterns, air balancing, occupancy, and feature placement.\n\nPractical ImplicationsIncreasing ventilation, whether through ventilation rates (ACH, m3/h, m3/min, L/min) or as determined by CO2 levels (ppm), is associated with decreased transmission, transmission probability/risk, infection probability/risk, droplet persistence, and virus concentration, and increased virus removal and efficiency of virus particle removal. As well, professionals should consider the fact that changing ventilation rate or using mixing ventilation is not always the only way to mitigate and control viruses as varying airflow patterns and the use of ventilation resulted in better outcomes than situations without ventilation. Practitioners also need to consider occupancy, ventilation feature (supply/exhaust and fans) placement, and exposure time in conjunction with both ventilation rates and airflow patterns. Some recommendations with quantified data were made, including using an air change rate of 9 h-1 for a hospital ward; waiting six air changes or 2.5 hours before allowing different individuals into an unfiltered office with [~]2 fresh air changes (FCH) and one air change for a high-efficiency MERV or HEPA filtered laboratory; and using a pressure difference between -2 and -25 Pa in negative pressure isolation spaces. Other recommendations for practice included using or increasing ventilation, introducing fresh air, using maximum supply rates, avoiding poorly ventilated spaces, assessing fan placement and potentially increasing ventilation locations, and employing ventilation testing and air balancing checks.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Gail M. Thornton",
+        "author_inst": "University of Alberta"
+      },
+      {
+        "author_name": "Brian A Fleck",
+        "author_inst": "University of Alberta"
+      },
+      {
+        "author_name": "Emily Kroeker",
+        "author_inst": "University of Alberta"
+      },
+      {
+        "author_name": "Dhyey Dandnayak",
+        "author_inst": "University of Alberta"
+      },
+      {
+        "author_name": "Natalie Fleck",
+        "author_inst": "University of Alberta"
+      },
+      {
+        "author_name": "Lexuan Zhong",
+        "author_inst": "University of Alberta"
+      },
+      {
+        "author_name": "Lisa A Hartling",
+        "author_inst": "University of Alberta"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health systems and quality improvement"
+  },
   {
     "rel_doi": "10.1101/2021.10.08.21264708",
     "rel_title": "The effect of training and workstation adjustability on teleworker discomfort during the COVID-19 pandemic",
@@ -544830,89 +543676,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2021.10.08.463665",
-    "rel_title": "SARS-CoV-2 infection induces inflammatory bone loss in golden Syrian hamsters",
-    "rel_date": "2021-10-09",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.08.463665",
-    "rel_abs": "Extrapulmonary complications of different organ systems have been increasingly recognized in patients with severe or chronic Coronavirus Disease 2019 (COVID-19). However, limited information on the skeletal complications of COVID-19 is known, even though inflammatory diseases of the respiratory tract have been known to perturb bone metabolism and cause pathological bone loss. In this study, we characterized the effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on bone metabolism in an established golden Syrian hamster model for COVID-19. SARS-CoV-2 causes significant multifocal loss of bone trabeculae in the long bones and lumbar vertebrae of all infected hamsters. The bone loss progressively worsens from the acute phase to the post-recovery phase. Mechanistically, the bone loss was associated with SARS-CoV-2-induced cytokine dysregulation which upregulates osteoclastic differentiation of monocyte-macrophage lineage. The pro-inflammatory cytokines further trigger a second wave of cytokine storm in the skeletal tissues to augment their pro-osteoclastogenesis effect. Our findings in this established hamster model suggest that pathological bone loss may be a neglected complication which warrants more extensive investigations during the long-term follow-up of COVID-19 patients. The benefits of potential prophylactic and therapeutic interventions against pathological bone loss should be further evaluated.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=188 HEIGHT=200 SRC=\"FIGDIR/small/463665v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (81K):\norg.highwire.dtl.DTLVardef@ada9b8org.highwire.dtl.DTLVardef@1617fcaorg.highwire.dtl.DTLVardef@cdcd3org.highwire.dtl.DTLVardef@75a0ab_HPS_FORMAT_FIGEXP  M_FIG C_FIG Graphical abstractSARS-CoV-2 infection causes pathological bone loss in golden Syrian hamsters through induction of cytokine storm and inflammation-induced osteoclastogenesis.",
-    "rel_num_authors": 17,
-    "rel_authors": [
-      {
-        "author_name": "Wei Qiao",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Hui En Lau",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Huizhi Xie",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Vincent K.M. Poon",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Chris C.S. Chan",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Hin Chu",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Shuofeng Yuan",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Terrence T.T. Yuen",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Kenn K.H. Chik",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Jessica O.L. Tsang",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Chris C.Y. Chan",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Jian-Piao Cai",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Cuiting Luo",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Kwok-Yong Yuen",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Kenneth M.C. Cheung",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Jasper F.W. Chan",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Kelvin W.K. Yeung",
-        "author_inst": "The University of Hong Kong"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2021.10.08.463613",
     "rel_title": "Gut Bacterial Dysbiosis and Instability is Associated with the Onset of Complications and Mortality in COVID-19",
@@ -545191,6 +543954,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.10.09.21264771",
+    "rel_title": "Taste loss as a distinct symptom of COVID-19: A systematic review and meta-analysis",
+    "rel_date": "2021-10-09",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.09.21264771",
+    "rel_abs": "Chemosensory scientists have been skeptical that reports of COVID-19 taste loss are genuine, in part because before COVID-19, taste loss was rare and often confused with smell loss. Therefore, to establish the predicted prevalence rate of taste loss in COVID-19 patients, we conducted a systematic review and meta-analysis of 376 papers published in 2020-2021, with 241 meeting all inclusion criteria. Additionally, we explored how methodological differences (direct vs. self-report measures) may affect these estimates. We hypothesized that direct prevalence measures of taste loss would be the most valid because they avoid the taste/smell confusion of self-report. The meta-analysis showed that, among 138,897 COVID-19-positive patients, 39.2% reported taste dysfunction (95% CI: 35.34-43.12%), and the prevalence estimates were slightly but not significantly higher from studies using direct (n = 18) versus self-report (n = 223) methodologies (Q = 0.57, df = 1, p = 0.45). Generally, males reported lower rates of taste loss than did females and taste loss was highest in middle-aged groups. Thus, taste loss is a bona fide symptom COVID-19, meriting further research into the most appropriate direct methods to measure it and its underlying mechanisms.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Mackenzie R Hannum",
+        "author_inst": "Monell Chemical Senses Center"
+      },
+      {
+        "author_name": "Riley Koch",
+        "author_inst": "Monell Chemical Senses Center"
+      },
+      {
+        "author_name": "Vicente Ramirez",
+        "author_inst": "Monell Chemical Senses Center"
+      },
+      {
+        "author_name": "Sarah Marks",
+        "author_inst": "Monell Chemical Senses Center"
+      },
+      {
+        "author_name": "Aurora Toskala",
+        "author_inst": "Monell Chemical Senses Center"
+      },
+      {
+        "author_name": "Riley Herriman",
+        "author_inst": "Monell Chemical Senses Center"
+      },
+      {
+        "author_name": "Cailu Lin",
+        "author_inst": "Monell Chemical Senses Center"
+      },
+      {
+        "author_name": "Paule Valery Joseph",
+        "author_inst": "NIH/NIAAA"
+      },
+      {
+        "author_name": "Danielle R Reed",
+        "author_inst": "Monell Chemical Senses Center"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "allergy and immunology"
+  },
   {
     "rel_doi": "10.1101/2021.10.06.463336",
     "rel_title": "Compositional analysis of Sindbis virus ribonucleoproteins reveals an extensive co-opting of key nuclear RNA-binding proteins",
@@ -546696,113 +545510,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.10.06.21264467",
-    "rel_title": "Illness characteristics of COVID-19 in children infected with the SARS-CoV-2 Delta variant",
-    "rel_date": "2021-10-07",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.06.21264467",
-    "rel_abs": "BackgroundThe Delta (B.1.617.2) SARS-CoV-2 variant became the predominant UK circulating strain in May 2021. Whether COVID-19 from Delta infection differs to infection with other variants in children is unknown.\n\nMethodsThrough the prospective COVID Symptom Study, 109,626 UK school-aged children were proxy-reported between December 28, 2020 and July 8, 2021. We selected all symptomatic children who tested positive for SARS-CoV-2 and were proxy-reported at least weekly, within two timeframes: December 28, 2020 to May 6, 2021 (Alpha (B.1.1.7) the main UK circulating variant); and May 26 to July 8, 2021 (Delta the main UK circulating variant). We assessed illness profiles (symptom prevalence, duration, and burden), hospital presentation, and presence of long ([&ge;]28 day) illness; and calculated odds ratios for symptoms presenting within the first 28 days of illness.\n\nFindings694 (276 younger [5-11 years], 418 older [12-17 years]) symptomatic children tested positive for SARS-CoV-2 with Alpha infection and 706 (227 younger and 479 older) children with Delta infection. Median illness duration was short with either variant (overall cohort: 5 days (IQR 2-9.75) with Alpha, 5 days (IQR 2-9) with Delta). The seven most prevalent symptoms were common to both variants. Symptom burden over the first 28 days was slightly greater with Delta compared with Alpha infection (in younger children, 3 (IQR 2-5) with Alpha, 4 (IQR 2-7) with Delta; in older children 5 (IQR 3-8) with Alpha and 6 (IQR 3-9) with Delta infection in older children). The odds of several symptoms were higher with Delta than Alpha infection, including headache and fever. Few children presented to hospital, and long illness duration was uncommon, with either variant.\n\nInterpretationCOVID-19 in UK school-aged children due to SARS-CoV-2 Delta strain B.1.617.2 resembles illness due to the Alpha variant B.1.1.7., with short duration and similar symptom burden.\n\nFundingZOE Limited, UK Government Department of Health and Social Care, Wellcome Trust, UK Engineering and Physical Sciences Research Council, UK Research and Innovation London Medical Imaging & Artificial Intelligence Centre for Value Based Healthcare, UK National Institute for Health Research, UK Medical Research Council, British Heart Foundation and Alzheimers Society.\n\nEthicsEthics approval was granted by KCL Ethics Committee (reference LRS-19/20-18210).\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSTo identify existing evidence for differences in COVID-19 due to infection with Alpha (B.1.1.7) or Delta (B.1.617.2) SARS-CoV-2 variants, we searched PubMed for peer-reviewed articles and medRxiv for preprint publications between March 1, and September 17, 2021 using keywords (\"SARS-CoV-2\" OR \"COVID-19\") AND (children OR p?ediatric*) AND (\"delta variant\" OR \"B.1.617.2\"). We did not restrict our search by language. Of twenty published articles identified in PubMed, we found one case study describing disease presentation associated with Delta variant infection in a child. Another study examining the increase in hospitalization rates of paediatric cases in USA from August 1, 2020 to August 27, 2021 stated that \"It is not known whether the B.1.617.2 (Delta) variant [...] causes different clinical outcomes in children and adolescents compared with variants that circulated earlier.\" Four studies reported cases of transmission of the Delta variant in school and community contexts; and two discussed screening testing in school-aged children (thus not directly relevant to the research question here). Remaining papers did not target paediatric age specifically. We found no studies investigating differences in COVID-19 presentation (e.g., duration, burden, individual symptoms) in school-aged children either in the UK or world-wide.\n\nAdded value of this studyWe describe and compare illness profiles in symptomatic UK school-aged children (aged 5-17 years) with COVID-19 when either Alpha or Delta strains were the predominant circulating SARS-CoV-2 variant. Our data, collected through one of the largest UK citizen science epidemiological initiatives, show that symptom profile and illness duration of COVID-19 are broadly similar between the strains. Although there were slightly more symptoms with Delta than with Alpha, particularly in older children, this was offset by similar symptom duration (whether considered for symptoms individually or for illness overall). Our study adds quantitative information to the debate on whether there are meaningful clinical differences in COVID-19 due to Alpha vs. Delta variants; and contributes to the discussion regarding rationale for vaccinating children (particularly younger children) against SARS-CoV-2.\n\nImplications of all the available evidenceOur data confirm that COVID-19 in UK school-aged children is usually of short duration and similar symptom burden, whether due to Delta or Alpha. Our data contribute to epidemiological surveillance from the wider UK population, and we capture common and generally mild paediatric presentations of COVID-19 that might be missed using clinician-based surveillance alone. Our data will also be useful for the vaccination debate.",
-    "rel_num_authors": 23,
-    "rel_authors": [
-      {
-        "author_name": "Erika Molteni",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Carole Helene Sudre",
-        "author_inst": "School of Biomedical Engineering & Imaging Sciences, Kings College London, London, UK."
-      },
-      {
-        "author_name": "Liane S Canas",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Sunil S Bhopal",
-        "author_inst": "Newcastle University"
-      },
-      {
-        "author_name": "Robert C Hughes",
-        "author_inst": "Department of Population Health, Faculty of Epidemiology & Population Health, London School of Hygiene & Tropical Medicine, Keppel Street, London, UK."
-      },
-      {
-        "author_name": "Liyuan Chen",
-        "author_inst": "School of Biomedical Engineering & Imaging Sciences, Kings College London, London, UK."
-      },
-      {
-        "author_name": "Jie Deng",
-        "author_inst": "School of Biomedical Engineering & Imaging Sciences, Kings College London, London, UK."
-      },
-      {
-        "author_name": "Benjamin Murray",
-        "author_inst": "School of Biomedical Engineering & Imaging Sciences, Kings College London, London, UK."
-      },
-      {
-        "author_name": "Eric Kerfoot",
-        "author_inst": "School of Biomedical Engineering & Imaging Sciences, Kings College London, London, UK."
-      },
-      {
-        "author_name": "Michela S Antonelli",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Mark S Graham",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Kerstin Klaser",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Anna May",
-        "author_inst": "ZOE Limited London, UK"
-      },
-      {
-        "author_name": "Christina Hu",
-        "author_inst": "ZOE Limited London, UK."
-      },
-      {
-        "author_name": "Joan Capdevila Pujol",
-        "author_inst": "ZOE Limited London, UK."
-      },
-      {
-        "author_name": "Jonathan Wolf",
-        "author_inst": "ZOE Limited London, UK."
-      },
-      {
-        "author_name": "Alexander Hammers",
-        "author_inst": "School of Biomedical Engineering & Imaging Sciences, Kings College London, London, UK."
-      },
-      {
-        "author_name": "Timothy D Spector",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Sebastien Ourselin",
-        "author_inst": "School of Biomedical Engineering & Imaging Sciences, Kings College London, London, UK."
-      },
-      {
-        "author_name": "Marc Modat",
-        "author_inst": "School of Biomedical Engineering & Imaging Sciences, Kings College London, London, UK."
-      },
-      {
-        "author_name": "Claire Steves",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Michael Absoud",
-        "author_inst": "Childrens Neurosciences, Evelina London Childrens Hospital, St Thomas Hospital, Kings Health Partners, Academic Health Science Centre, London, UK."
-      },
-      {
-        "author_name": "Emma L Duncan",
-        "author_inst": "Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK."
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "pediatrics"
-  },
   {
     "rel_doi": "10.1101/2021.10.05.21264160",
     "rel_title": "Internalizing Problems Before and During the COVID-19 Pandemic in Dutch Children and Adolescents with and without Pre-Existing Mental Health Problems",
@@ -547309,6 +546016,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "respiratory medicine"
   },
+  {
+    "rel_doi": "10.1101/2021.10.05.21264597",
+    "rel_title": "Effect of workplace infection control practices on workers' psychological distress: a large-scale cohort study during the COVID-19 second state of emergency in Japan",
+    "rel_date": "2021-10-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.05.21264597",
+    "rel_abs": "BackgroundThe COVID-19 pandemic has dramatically transformed the work environment and work practices worldwide. Long-term infection control practices may increase the psychological stress on workers, and conversely, inadequate infection control practices at the working place may increase the fear of infection. This study aimed to determine the relationship between infection control practices at the workplace and employee mental health during the COVID-19 pandemic in Japan.\n\nMethodsThis study was conducted in December 2020 and February 2021. The participants had undergone a preliminary survey, which revealed that they were in good mental health. Their psychological distress was investigated via a second survey, and the factors associated with distress were studied using a logistic model.\n\nResultsThe results of the second survey indicated that 15.1% of participants demonstrated psychological distress. This was associated with leave-of-absence instructions, instructions for shortening business hours, and requests to avoid the workplace in case of any symptoms.\n\nConclusionThe study found that while some infection control practices reduce workers distress, others worsen it. Employers need to consider infection control practices as well as the worsening mental health of employees following a decrease in income caused by such measures. Follow-up studies may be necessary to clarify the long-term effects on workers mental health.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Toyohiko Kodama",
+        "author_inst": "University of Occupational and Environmental Health, Japan"
+      },
+      {
+        "author_name": "Tomohiro Ishimaru",
+        "author_inst": "University of Occupational and Environmental Health, Japan"
+      },
+      {
+        "author_name": "Seiichiro Tateishi",
+        "author_inst": "University of Occupational and Environmental Health, Japan"
+      },
+      {
+        "author_name": "Ayako Hino",
+        "author_inst": "University of Occupational and Environmental Health, Japan"
+      },
+      {
+        "author_name": "Mayumi Tsuji",
+        "author_inst": "University of Occupational and Environmental Health, Japan"
+      },
+      {
+        "author_name": "Akira OGami",
+        "author_inst": "University of Occupational and Environmental Health, Japan"
+      },
+      {
+        "author_name": "Tomohisa Nagata",
+        "author_inst": "University of Occupational and Environmental Health, Japan"
+      },
+      {
+        "author_name": "Shinya Matsuda",
+        "author_inst": "University of Occupational and Environmental Health, Japan"
+      },
+      {
+        "author_name": "Yoshihisa Fujino",
+        "author_inst": "University of Occupational and Environmental Health, Japan"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "occupational and environmental health"
+  },
   {
     "rel_doi": "10.1101/2021.10.06.21264631",
     "rel_title": "Genetic risk factors and Covid-19 severity in Brazil: results from BRACOVID Study",
@@ -548858,61 +547616,6 @@
     "type": "new results",
     "category": "biophysics"
   },
-  {
-    "rel_doi": "10.1101/2021.10.06.462907",
-    "rel_title": "A cell-free assay for rapid screening of inhibitors of hACE2-receptor - SARS-CoV-2-Spike binding",
-    "rel_date": "2021-10-06",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.06.462907",
-    "rel_abs": "We present a cell-free assay for rapid screening of candidate inhibitors of protein binding, focusing on inhibition of the interaction between the SARS-CoV-2 Spike receptor binding domain (RBD) and human angiotensin-converting enzyme 2 (hACE2). The assay has two components: fluorescent polystyrene particles covalently coated with RBD, termed virion-particles (v-particles), and fluorescently-labeled hACE2 (hACE2F) that binds the v-particles. When incubated with an inhibitor, v-particle - hACE2F binding is diminished, resulting in a reduction in the fluorescent signal of bound hACE2F relative to the non-inhibitor control, which can be measured via flow cytometry or fluorescence microscopy. We determine the amount of RBD needed for v-particle preparation, v-particle incubation time with hACE2F, hACE2F detection limit, and specificity of v-particle binding to hACE2F. We measure the dose response of the v-particles to a known inhibitor. Finally, we demonstrate that RNA-hACE2F granules trap v-particles effectively, providing a basis for potential RNA-hACE2F therapeutics.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Nanami Kikuchi",
-        "author_inst": "Technion - Israel institute of technology"
-      },
-      {
-        "author_name": "Or Willinger",
-        "author_inst": "Technion - Israel institute of technology"
-      },
-      {
-        "author_name": "Naor Granik",
-        "author_inst": "Technion, Israel Institute of Technology"
-      },
-      {
-        "author_name": "Noa Navon",
-        "author_inst": "Technion - Israel institute of technology"
-      },
-      {
-        "author_name": "Shanny Ackerman",
-        "author_inst": "Technion - Israel institute of technology"
-      },
-      {
-        "author_name": "Ella Samuel",
-        "author_inst": "Technion - Israel institute of technology"
-      },
-      {
-        "author_name": "Tomer Antman",
-        "author_inst": "Technion - Israel institute of technology"
-      },
-      {
-        "author_name": "Noa Katz",
-        "author_inst": "Technion - Israel institute of technology"
-      },
-      {
-        "author_name": "Sarah Goldberg",
-        "author_inst": "Technion - Israel institute of technology"
-      },
-      {
-        "author_name": "Roee Amit",
-        "author_inst": "Technion - Israel institute of Technology"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "synthetic biology"
-  },
   {
     "rel_doi": "10.1101/2021.10.05.463271",
     "rel_title": "Clinical and immunological signatures of severe COVID-19 in previously healthy patients with clonal hematopoiesis",
@@ -549527,6 +548230,81 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.10.02.21264267",
+    "rel_title": "Year-long COVID-19 infection reveals within-host evolution of SARS-CoV-2 in a patient with B cell depletion",
+    "rel_date": "2021-10-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.02.21264267",
+    "rel_abs": "BackgroundB-cell depleting therapies may lead to protracted disease and prolonged viral shedding in individuals infected with SARS-CoV-2. Viral persistence in the setting of immunosuppression raises concern for viral evolution.\n\nMethodsAmplification of sub-genomic transcripts for the E gene (sgE) was done on nasopharyngeal samples over the course of 355 days in a patient infected with SARS-CoV-2 who had previously undergone CAR T cell therapy and had persistently positive SARS-CoV-2 nasopharyngeal swabs. Whole genome sequencing was performed on samples from the patients original presentation and 10 months later.\n\nResultsOver the course of almost a year, the virus accumulated a unique in-frame deletion in the amino-terminal domain of the spike protein, and complete deletion of ORF7b and ORF8, the first report of its kind in an immunocompromised patient. Also, minority variants that were identified in the early samples--reflecting the heterogeneity of the initial infection--were found to be fixed late in the infection. Remdesivir and high-titer convalescent plasma treatment were given, and the infection was eventually cleared after 335 days of infection.\n\nConclusionsThe unique viral mutations found in this study highlight the importance of analyzing viral evolution in protracted SARS-CoV-2 infection, especially in immunosuppressed hosts, and the implication of these mutations in the emergence of viral variants.\n\nSummaryWe report an immunocompromised patient with persistent symptomatic SARS-CoV-2 infection for 335 days. During this time, the virus accumulated a unique in-frame deletion in the spike, and a complete deletion of ORF7b and ORF8 which is the first report of its kind in an immunocompromised patient.",
+    "rel_num_authors": 15,
+    "rel_authors": [
+      {
+        "author_name": "Veronique Nussenblatt",
+        "author_inst": "National Institutes of Health"
+      },
+      {
+        "author_name": "Allison Roder",
+        "author_inst": "National Institute of Allergy and Infectious Diseases"
+      },
+      {
+        "author_name": "Sanchita Das",
+        "author_inst": "National Institutes of Health"
+      },
+      {
+        "author_name": "Emmie de Wit",
+        "author_inst": "NIAID, NIH"
+      },
+      {
+        "author_name": "Jung-Ho Youn",
+        "author_inst": "National Institutes of Health"
+      },
+      {
+        "author_name": "Stephanie Banakis",
+        "author_inst": "National Institutes of Health"
+      },
+      {
+        "author_name": "Alexandra Muchegian",
+        "author_inst": "National Institutes of Health"
+      },
+      {
+        "author_name": "Christopher Mederos",
+        "author_inst": "National Institutes of Health"
+      },
+      {
+        "author_name": "Wei Wang",
+        "author_inst": "National Institutes of Health"
+      },
+      {
+        "author_name": "Matt Chung",
+        "author_inst": "National Institutes of Health"
+      },
+      {
+        "author_name": "Lizette Perez-Perez",
+        "author_inst": "National Institutes of Health"
+      },
+      {
+        "author_name": "Tara Palmore",
+        "author_inst": "National Institutes of Health"
+      },
+      {
+        "author_name": "Jennifer Brudno",
+        "author_inst": "National Cancer Institute"
+      },
+      {
+        "author_name": "James Kochenderfer",
+        "author_inst": "National Cancer Institute"
+      },
+      {
+        "author_name": "Elodie Ghedin",
+        "author_inst": "National Institute of Allergy and Infectious Diseases"
+      }
+    ],
+    "version": "1",
+    "license": "cc0",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.10.02.21264415",
     "rel_title": "Acquisition and onward transmission of a SARS-CoV-2 E484K variant among household contacts of a bamlanivimab-treated patient",
@@ -551256,33 +550034,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2021.10.02.462863",
-    "rel_title": "Dynamic Allostery Highlights the Evolutionary Differences between the CoV-1 and CoV-2 Main Proteases",
-    "rel_date": "2021-10-04",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.02.462863",
-    "rel_abs": "The SARS-CoV-2 coronavirus has become one of the most immediate and widely-studied systems since its identification and subsequent global outbreak from 2019-2020. In an effort to understand the biophysical changes as a result of mutations, the mechanics of multiple different proteins within the SARS-CoV-2 virus have been studied and compared with SARS-CoV-1. Focusing on the main protease (mPro), we first explored the long range dynamic-relationship, particularly in cross-chain dynamics, using the Dynamic Coupling Index (DCI) to investigate the dynamic coupling between the catalytic site residues and the rest of the protein, both inter and intra chain for the CoV-1 and CoV-2 mPro. We found that there is significant cross-chain coupling between these active sites and distal residues in the CoV-2 mPro but it was missing in CoV-1. The enhanced long distance interactions, particularly between the two chains, suggest subsequently enhanced cooperativity for CoV-2. A further comparative analysis of the dynamic flexibility using the Dynamic Flexibility Index (DFI) between the CoV-1 and CoV-2 mPros shows that the inhibitor binding near active sites induces change in flexibility to a distal region of the protein, opposite in behavior between the two systems; this region becomes more flexible upon inhibitor binding in CoV-1 while it becomes less flexible in the CoV-2 mPro. Upon inspection, we show that, on average, the dynamic flexibility of the sites substituted from CoV-1 to CoV-2 changes significantly less than the average calculated across all residues within the structure, indicating that the differences in behaviors between the two systems is likely the result of allosteric influence, where the new substitutions in COV-2 induce flexibility and dynamical changes elsewhere in the structure.\n\nSIGNIFICANCEHere we have conducted a comparative analysis between the SARS-CoV-1 and SARS-CoV-2 mPro systems to shed mechanistic insight on the biophysical changes associated with the mutations between these two enzymes. Our work shows that the CoV-2 mPro system exhibits enhanced cross-chain communication between catalytic site residues and the rest of the structure. Further, both dynamic coupling and dynamic flexibility analyses indicates that, largely, the dynamic changes as evaluated by DCI and DFI occur at sites other than the mutation sites themselves, indicating that the functional differences between these two proteins are a result of dynamic allostery",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Paul Campitelli",
-        "author_inst": "Arizona State University"
-      },
-      {
-        "author_name": "Jin Lu",
-        "author_inst": "Arizona State University"
-      },
-      {
-        "author_name": "Sefika Banu Ozkan",
-        "author_inst": "Arizona State University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "biophysics"
-  },
   {
     "rel_doi": "10.1101/2021.10.01.21262806",
     "rel_title": "Frequency of surveillance testing necessary to reduce transmission of the Delta variant of SARS-CoV-2",
@@ -551501,6 +550252,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.10.02.21264454",
+    "rel_title": "COVID-19 Vaccine: Newspaper Coverage of the side effects of the vaccine in Nigeria",
+    "rel_date": "2021-10-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.02.21264454",
+    "rel_abs": "BackgroundCOVID-19 Vaccine hesitancy is increasing globally, and this threatens the worlds ability to bring the pandemic under control. The way the media reports on the vaccine may influence or affect how the population perceive the safety and efficacy of the vaccine.\n\nMethodsThe aim of this study was to determine how newspapers in Nigeria report stories about the vaccine and the side effects of the vaccine amidst the growing fear on the safety of the vaccine. A total of 4 national daily newspapers were randomly selected for the study. These are Leadership, Guardian, Nation and Punch newspapers. The study was anchored on agenda setting theory. Quantitative content analysis research was used for the study. The duration of the study was the day the vaccine was introduced in Nigeria: March 1st, 2021 to July 31st, 2021. An Excel sheet served as the instrument for data collection and analysis done using SPSS version 25 with the level of significance predetermined at a p-value <0.05.\n\nResultsKey findings from this research were: Government officials and technical experts were predominantly used by the newspapers as the source of their information. There was a mixed reporting of vaccine side effects with a significant difference between those newspaper publications that reported vaccine side effects and those that didnt. Amongst those that reported side effects, there was also a significant difference between those that communicated how and where to report the side effects as against those that didnt.\n\nConclusionAs part of the effort to curtail vaccine hesitancy, a continuous improvement in communicating the vaccine efficacy and safety is needed.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Kehinde Victor Soyemi",
+        "author_inst": "GlaxoSmithKline Pharrmaceuticals"
+      },
+      {
+        "author_name": "Olagoke A Ewedairo",
+        "author_inst": "Medical Affairs, Global Public Health, Johnson and Johnson Pharmaceutical"
+      },
+      {
+        "author_name": "Charles Oluwatemitope Olomofe",
+        "author_inst": "College of Public Health, East Tennessee State University, Johnson City, United States"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.10.02.21264456",
     "rel_title": "Using conditional inference to quantify interaction effects of socio-demographic covariates of US COVID-19 vaccine hesitancy",
@@ -552990,37 +551768,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.10.01.21264359",
-    "rel_title": "COVID-19 mortality in Italy varies by patient age, sex and pandemic wave",
-    "rel_date": "2021-10-02",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.01.21264359",
-    "rel_abs": "BackgroundSARS-CoV-2 has caused a worldwide epidemic of enormous proportions, which resulted in different mortality rates in different countries for unknown reasons.\n\nAimWe aimed to evaluate which independent parameters are associated with risk of mortality from COVID-19 in a series that includes all Italian cases, ie, more than 4 million individuals infected with the SARS-CoV-2 coronavirus.\n\nMethodsWe analyzed factors associated with mortality using data from the Italian national database of SARS-CoV-2-positive cases, including more than 4 million cases, >415 thousand hospitalized for coronavirus disease-19 (COVID-19) and >127 thousand deceased. For patients for whom age, sex and date of infection detection were available, we determined the impact of these variables on mortality 30 days after the date of diagnosis or hospitalization.\n\nResultsMultivariable Cox analysis showed that each of the analyzed variables independently affected COVID-19 mortality. Specifically, in the overall series, age was the main risk factor for mortality, with HR >100 in the age groups older than 65 years compared with a reference group of 15-44 years. Male sex presented an excess risk of death (HR = 2.1; 95% CI, 2.0-2.1). Patients infected in the first pandemic wave (before 30 June 2020) had a greater risk of death than those infected later (HR = 2.7; 95% CI, 2.7-2.8).\n\nConclusionsIn a series of all confirmed SARS-CoV-2-infected cases in an entire European nation, elderly age was by far the most significant risk factor for COVID-19 mortality, confirming that protecting the elderly should be a priority in pandemic management. Male sex and being infected during the first wave were additional risk factors associated with COVID-19 mortality.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Francesca Minnai",
-        "author_inst": "Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate (MI), Italy"
-      },
-      {
-        "author_name": "Gianluca De Bellis",
-        "author_inst": "Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate (MI), Italy"
-      },
-      {
-        "author_name": "Tommaso A Dragani",
-        "author_inst": "Fondazione IRCCS Istituto Nazionale dei Tumori"
-      },
-      {
-        "author_name": "Francesca Colombo",
-        "author_inst": "Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate (MI), Italy"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.09.28.21264245",
     "rel_title": "Disproportionality analysis of adverse neurological and psychiatric reactions with the ChAdOx1 (Oxford-AstraZeneca) and BNT162b2 (Pfizer-BioNTech) COVID-19 vaccines in the United Kingdom",
@@ -553411,6 +552158,81 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.09.29.21264199",
+    "rel_title": "Effectiveness of mRNA-1273 against Delta, Mu, and other emerging variants",
+    "rel_date": "2021-10-01",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.29.21264199",
+    "rel_abs": "BackgroundReal-world studies have found high vaccine effectiveness (VE) of mRNA-based COVID-19 vaccines, but reduced VE against the Delta variant and waning protection have been reported, with few studies examining mRNA-1273 variant-specific VE.\n\nMethodsWe conducted a test-negative case-control study at Kaiser Permanente Southern California. Whole genome sequencing was conducted for SARS-CoV-2 positive specimens collected from 3/1/2021 to 7/27/2021. Test-positive cases were matched 1:5 to test-negative controls on age, sex, race/ethnicity, and specimen collection date. Outcomes included SARS-CoV-2 infection and hospitalization. Exposures were 2 doses or 1 dose of mRNA-1273 [&ge;]14 days prior to specimen collection versus no COVID-19 vaccination. Conditional logistic regression was used to compare odds of vaccination among cases versus controls, adjusting for confounders. VE was calculated as (1-odds ratio)x100%.\n\nResultsThe study included 8,153 cases and their matched controls. Two-dose VE (95% confidence interval) was 86.7% (84.3-88.7%) against Delta infection, 98.4% (96.9-99.1%) against Alpha, 90.4% (73.9-96.5%) against Mu, 96-98% against other identified variants, and 79.9% (76.9-82.5%) against unidentified variants. VE against Delta declined from 94.1% (90.5-96.3%) 14-60 days after vaccination to 80.0% (70.2-86.6%) 151-180 days after vaccination. Waning was less pronounced for non-Delta variants. VE against Delta was lower among individuals aged [&ge;]65 years (75.2% [59.6-84.8%]) than those aged 18-64 years (87.9% [85.5-89.9%]). VE against Delta hospitalization was 97.6% (92.8-99.2%). One-dose VE was 77.0% (60.7-86.5%) against Delta infection.\n\nConclusionsTwo doses of mRNA-1273 were highly effective against all SARS-CoV-2 variants. However, VE against Delta moderately declined with increasing time since vaccination.\n\nTrial Registration NumberNot applicable\n\nFundingModerna Inc.",
+    "rel_num_authors": 15,
+    "rel_authors": [
+      {
+        "author_name": "Katia Bruxvoort",
+        "author_inst": "University of Alabama at Birmingham"
+      },
+      {
+        "author_name": "Lina S. Sy",
+        "author_inst": "Kaiser Permanente Southern California"
+      },
+      {
+        "author_name": "Lei Qian",
+        "author_inst": "Kaiser Permanente Southern California"
+      },
+      {
+        "author_name": "Bradley K. Ackerson",
+        "author_inst": "Kaiser Permanente Southern California"
+      },
+      {
+        "author_name": "Yi Luo",
+        "author_inst": "Kaiser Permanente Southern California"
+      },
+      {
+        "author_name": "Gina S. Lee",
+        "author_inst": "Kaiser Permanente Southern California"
+      },
+      {
+        "author_name": "Yun Tian",
+        "author_inst": "Kaiser Permanente Southern California"
+      },
+      {
+        "author_name": "Ana Florea",
+        "author_inst": "Kaiser Permanente Southern California"
+      },
+      {
+        "author_name": "Michael Aragones",
+        "author_inst": "Kaiser Permanente Southern California"
+      },
+      {
+        "author_name": "Julia E. Tubert",
+        "author_inst": "Kaiser Permanente Southern California"
+      },
+      {
+        "author_name": "Harpreet S. Takhar",
+        "author_inst": "Kaiser Permanente Southern California"
+      },
+      {
+        "author_name": "Jennifer H. Ku",
+        "author_inst": "Kaiser Permanente Southern California"
+      },
+      {
+        "author_name": "Yamuna D. Paila",
+        "author_inst": "Moderna Inc."
+      },
+      {
+        "author_name": "Carla A. Talarico",
+        "author_inst": "Moderna Inc."
+      },
+      {
+        "author_name": "Hung Fu Tseng",
+        "author_inst": "Kaiser Permanente Southern California"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.09.30.21264356",
     "rel_title": "Modelling of COVID-19 pandemic vis-a-vis some socioeconomic factors",
@@ -554652,45 +553474,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2021.09.28.21264186",
-    "rel_title": "Effect of common maintenance drugs on the risk and severity of COVID-19 in elderly patients",
-    "rel_date": "2021-10-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.28.21264186",
-    "rel_abs": "BackgroundMaintenance drugs are used to treat chronic conditions. Several classes of maintenance drugs have attracted attention because of their potential to affect susceptibility to and severity of COVID-19.\n\nMethodsUsing claims data on 20% random sample of Part D Medicare enrollees from April to December 2020, we identified patients diagnosed with COVID-19. Using a nested case-control design, non-COVID-19 controls were identified by 1:5 matching on age, race, sex, dual-eligibility status and geographical region. We identified usage of angiotensin-converting enzyme inhibitors (ACEI), angiotensin-receptor blockers (ARB), warfarin, direct factor Xa inhibitors, clopidogrel, famotidine and hydroxychloroquine based on Medicare prescription claims data. Using extended Cox regression models with time-varying propensity score adjustment we examined the independent effect of each study drug on contracting COVID-19. For severity of COVID-19, we performed extended Cox regressions on all COVID-19 patients, using COVID-19-related hospitalization and all-cause mortality as outcomes. Covariates included gender, age, race, geographic region, low-income indicator and co-morbidities. To compensate for indication bias related to the use of hydroxychloroquine for the prophylaxis or treatment of COVID-19, we censored patients who only started on hydroxychloroquine in 2020.\n\nResultsUp to December 2020, our sample contained 374,229 Medicare patients over 65 who were diagnosed with COVID-19. Among the COVID-19 patients, 209,208 (55.9%) were on at least one study drug. The three most common study drugs were ACEI 97,872 (26.1%), ARB 83,329 (22.3%) and clopidogrel 38,203 (10.2%). Current users of ACEI, ARB, warfarin, direct factor Xa inhibitor and clopidogrel were associated with reduced risk of getting COVID-19 (3-13%), and reduced risk of dying after a COVID-19 diagnosis (8-19%). Famotidine did not show consistent significant effects. Hydroxychloroquine did not show significant effects after censoring of recent starters.\n\nConclusionsMaintenance use of ACEI, ARB, warfarin, direct factor Xa inhibitor and clopidogrel was associated with reduction in risk of acquiring COVID-19 and dying from it.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Kin Wah Fung",
-        "author_inst": "National Library of Medicine, NIH"
-      },
-      {
-        "author_name": "Seo Baik",
-        "author_inst": "Lister Hill National Center for Biomedical Communications, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of Ame"
-      },
-      {
-        "author_name": "Fitsum Baye",
-        "author_inst": "Lister Hill National Center for Biomedical Communications, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of Ame"
-      },
-      {
-        "author_name": "Zhaonian Zheng",
-        "author_inst": "Lister Hill National Center for Biomedical Communications, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of Ame"
-      },
-      {
-        "author_name": "Vojtech Huser",
-        "author_inst": "Lister Hill National Center for Biomedical Communications, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of Ame"
-      },
-      {
-        "author_name": "Clem McDonald",
-        "author_inst": "Lister Hill National Center for Biomedical Communications, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of Ame"
-      }
-    ],
-    "version": "1",
-    "license": "cc0",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.09.28.21263671",
     "rel_title": "Standardized incidence ratio of the COVID-19 pandemic: a case study in a Midwestern state",
@@ -555113,6 +553896,101 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.09.30.462449",
+    "rel_title": "Pyronaridine Protects Against SARS-CoV-2 in Mouse",
+    "rel_date": "2021-09-30",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.30.462449",
+    "rel_abs": "There are currently relatively few small-molecule antiviral drugs that are either approved or emergency approved for use against SARS-CoV-2. One of these is remdesivir, which was originally repurposed from its use against Ebola and functions by causing early RNA chain termination. We used this as justification to evaluate three molecules we had previously identified computationally with antiviral activity against Ebola and Marburg. Out of these we previously identified pyronaridine, which inhibited the SARS-CoV-2 replication in A549-ACE2 cells. Herein, the in vivo efficacy of pyronaridine has now been assessed in a K18-hACE transgenic mouse model of COVID-19. Pyronaridine treatment demonstrated a statistically significant reduction of viral load in the lungs of SARS CoV-2 infected mice. Furthermore, the pyronaridine treated group reduced lung pathology, which was also associated with significant reduction in the levels of pro-inflammatory cytokines/chemokine and cell infiltration. Notably, pyronaridine inhibited the viral PLpro activity in vitro (IC50 of 1.8 {micro}M) without any effect on Mpro, indicating a possible molecular mechanism involved in its ability to inhibit SARS-CoV-2 replication. Interestingly, pyronaridine also selectively inhibits the host kinase CAMK1 (IC50 of 2.4 {micro}M). We have also generated several pyronaridine analogs to assist in understanding the structure activity relationship for PLpro inhibition. Our results indicate that pyronaridine is a potential therapeutic candidate for COVID-19.\n\nOne sentence summaryThere is currently intense interest in discovering small molecules with direct antiviral activity against the severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2). Pyronaridine, an antiviral drug with in vitro activity against Ebola, Marburg and SARS-CoV-2 has now statistically significantly reduced the viral load in mice along with IL-6, TNF-, and IFN-{beta} ultimately demonstrating a protective effect against lung damage by infection to provide a new potential treatment for testing clinically.",
+    "rel_num_authors": 20,
+    "rel_authors": [
+      {
+        "author_name": "Ana C. Puhl",
+        "author_inst": "Collaborations Pharmaceuticals"
+      },
+      {
+        "author_name": "Giovanni F. Gomes",
+        "author_inst": "Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo"
+      },
+      {
+        "author_name": "Samara Damasceno",
+        "author_inst": "Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo"
+      },
+      {
+        "author_name": "Andre Schutzer de Godoy",
+        "author_inst": "University of Sao Paulo"
+      },
+      {
+        "author_name": "Gabriela D. Noske",
+        "author_inst": "University of Sao Paulo"
+      },
+      {
+        "author_name": "Aline M. Nakamura",
+        "author_inst": "University of Sao Paulo"
+      },
+      {
+        "author_name": "Victor O. Gawrijuk",
+        "author_inst": "University of Sao Paulo"
+      },
+      {
+        "author_name": "Rafaela S. Fernandes",
+        "author_inst": "University of Sao Paulo"
+      },
+      {
+        "author_name": "Natalia Monakhova",
+        "author_inst": "Research Center of Biotechnology RAS, 119071 Moscow, Russia."
+      },
+      {
+        "author_name": "Olga Riabova",
+        "author_inst": "Federal Research Center Fundamentals of Biotechnology Russian Academy of Science"
+      },
+      {
+        "author_name": "Thomas R Lane",
+        "author_inst": "Collaborations Pharmaceuticals Inc."
+      },
+      {
+        "author_name": "Vadim Makarov",
+        "author_inst": "Federal Research Center Fundamentals of Biotechnology Russian Academy of Science"
+      },
+      {
+        "author_name": "Flavio P. Veras",
+        "author_inst": "Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo"
+      },
+      {
+        "author_name": "Sabrina S. Batah",
+        "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo"
+      },
+      {
+        "author_name": "Alexandre T. Fabro",
+        "author_inst": "Department of Pathology and Legal Medicine, Ribeirao Preto Medical School, University of Sao Paulo"
+      },
+      {
+        "author_name": "Glaucius Oliva",
+        "author_inst": "University of Sao Paulo"
+      },
+      {
+        "author_name": "Fernando Cunha",
+        "author_inst": "Universidade de Sao Paulo Campus de Ribeirao Preto"
+      },
+      {
+        "author_name": "Jose C. Alves-Filho",
+        "author_inst": "Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo"
+      },
+      {
+        "author_name": "Thiago M. Cunha",
+        "author_inst": "Center for Research in Inflammatory Diseases (CRID), Ribeirao Preto Medical School, University of Sao Paulo"
+      },
+      {
+        "author_name": "Sean Ekins",
+        "author_inst": "Collaborations Pharmaceuticals, Inc."
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "pharmacology and toxicology"
+  },
   {
     "rel_doi": "10.1101/2021.09.30.462488",
     "rel_title": "Durability of immune responses to the BNT162b2 mRNA vaccine",
@@ -556758,49 +555636,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.09.27.21264183",
-    "rel_title": "Predictors of parents intention to vaccinate their children against the COVID-19 in Greece: a cross-sectional study",
-    "rel_date": "2021-09-29",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.27.21264183",
-    "rel_abs": "BackgroundParents intention to vaccinate their children against the COVID-19 is envisaged as critical strategy to control the pandemic.\n\nObjectiveTo investigate the intention of parents to vaccinate their children against the COVID-19 and the factors influencing this intention.\n\nMethodsWe conducted an online cross-sectional study in Greece and we collected data during the first week of September 2021. A convenience sample was used by collecting questionnaires through social media. Our study population included adult parents with children aged 12-17 years who were eligible for a COVID-19 vaccine.\n\nResultsStudy population included 813 parents with a mean age of 42.3 years. Among parents, 36% reported that they will vaccinate their children against the COVID-19, 33.5% denied vaccination and 30.5% were undecided. Concerns about the safety, effectiveness and side effects of COVID-19 vaccines were the most important reasons for decline of COVID-19 vaccination. Parents who took the flu vaccine in 2020 and those who had more knowledge and fewer concerns about COVID-19 vaccines had a greater probability to vaccinate their children against the COVID-19. Increased self-perceived severity of COVID-19, and increased trust in COVID-19 vaccines and the government regarding the information about the COVID-19 vaccines were associated with parents intention to vaccinate their children. However, increased knowledge regarding COVID-19 was associated with decreased intention of parents to vaccinate their children.\n\nConclusionsParents intention to vaccinate their children against the COVID-19 was low. Our findings could contribute to the development of target strategies to implement adherence to COVID-19 vaccination campaigns.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Petros A Galanis",
-        "author_inst": "National and Kapodistrian University of Athens"
-      },
-      {
-        "author_name": "Irene Vraka",
-        "author_inst": "P & A Kyriakou Children's Hospital"
-      },
-      {
-        "author_name": "Olga Siskou",
-        "author_inst": "National and Kapodistrian University of Athens"
-      },
-      {
-        "author_name": "Olympia Konstantakopoulou",
-        "author_inst": "National and Kapodistrian University of Athens"
-      },
-      {
-        "author_name": "Aglaia Katsiroumpa",
-        "author_inst": "National and Kapodistrian University of Athens"
-      },
-      {
-        "author_name": "Ioannis Moisoglou",
-        "author_inst": "General Hospital of Lamia"
-      },
-      {
-        "author_name": "Daphne Kaitelidou",
-        "author_inst": "National and Kapodistrian University of Athens"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.09.28.21264265",
     "rel_title": "How a positive COVID-19 diagnosis affects the physical, social and psychological wellbeing of people in the United Arab Emirates? An Explorative Qualitative Study",
@@ -557315,6 +556150,113 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "hiv aids"
   },
+  {
+    "rel_doi": "10.1101/2021.09.28.21264250",
+    "rel_title": "Reduced antibody activity against SARS-CoV-2 B.1.617.2 Delta virus in serum of mRNA-vaccinated patients receiving TNF-alpha inhibitors",
+    "rel_date": "2021-09-29",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.28.21264250",
+    "rel_abs": "Although vaccines effectively prevent COVID-19 in healthy individuals, they appear less immunogenic in individuals with chronic inflammatory diseases (CID) and/or under chronic immunosuppression, and there is uncertainty of their activity against emerging variants of concern in this population. Here, we assessed a cohort of 74 CID patients treated as monotherapy with chronic immunosuppressive drugs for functional antibody responses in serum against historical and variant SARS-CoV-2 viruses after immunization with Pfizer mRNA BNT162b2 vaccine. Longitudinal analysis showed the greatest reductions in neutralizing antibodies and Fc effector function capacity in individuals treated with TNF- inhibitors, and this pattern appeared worse against the B.1.617.2 Delta virus. Within five months of vaccination, serum neutralizing titers of the majority of CID patients fell below the presumed threshold correlate for antibody-mediated protection. Thus, further vaccine boosting or administration of long-acting prophylaxis (e.g., monoclonal antibodies) likely will be required to prevent SARS-CoV-2 infection in this susceptible population.",
+    "rel_num_authors": 23,
+    "rel_authors": [
+      {
+        "author_name": "Rita E Chen",
+        "author_inst": "Washington University School of Medicine"
+      },
+      {
+        "author_name": "Matthew J Gorman",
+        "author_inst": "Ragon Institute"
+      },
+      {
+        "author_name": "Daniel Y Zhu",
+        "author_inst": "MIT"
+      },
+      {
+        "author_name": "Juan Manuel Carreno",
+        "author_inst": "Icahn School of Medicine"
+      },
+      {
+        "author_name": "Dansu Yuan",
+        "author_inst": "Ragon Institute"
+      },
+      {
+        "author_name": "Laura A VanBlargan",
+        "author_inst": "Washington University"
+      },
+      {
+        "author_name": "Samantha Burdess",
+        "author_inst": "Washington University"
+      },
+      {
+        "author_name": "Douglas A Lauffenburger",
+        "author_inst": "MIT"
+      },
+      {
+        "author_name": "Wooseob Kim",
+        "author_inst": "Washington University"
+      },
+      {
+        "author_name": "Jackson S Turner",
+        "author_inst": "Washington University"
+      },
+      {
+        "author_name": "Lindsay Droit",
+        "author_inst": "Washington University"
+      },
+      {
+        "author_name": "Scott A Handley",
+        "author_inst": "Washington University"
+      },
+      {
+        "author_name": "Salim Chahin",
+        "author_inst": "Washington University"
+      },
+      {
+        "author_name": "Parakkal Deepak",
+        "author_inst": "Washington University in St Louis School of Medicine"
+      },
+      {
+        "author_name": "Jane O'Halloran",
+        "author_inst": "Washington University in St. Louis School of Medicine"
+      },
+      {
+        "author_name": "Michael Paley",
+        "author_inst": "Washington University"
+      },
+      {
+        "author_name": "Rachel Presti",
+        "author_inst": "Wash U"
+      },
+      {
+        "author_name": "Gregory F Wu",
+        "author_inst": "Washington University"
+      },
+      {
+        "author_name": "Florian Krammer",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Galit Alter",
+        "author_inst": "Ragon Institute of MGH, MIT, and Harvard"
+      },
+      {
+        "author_name": "Ali Ellebedy",
+        "author_inst": "Washington University School of Medicine"
+      },
+      {
+        "author_name": "Alfred Hyoungju Kim",
+        "author_inst": "Washington University School of Medicine"
+      },
+      {
+        "author_name": "Michael S Diamond",
+        "author_inst": "Washington University School of Medicine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.09.28.21263911",
     "rel_title": "A MUC5B gene polymorphism, rs35705950-T, confers protective effects in COVID-19 infection",
@@ -558812,41 +557754,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health economics"
   },
-  {
-    "rel_doi": "10.1101/2021.09.18.21263605",
-    "rel_title": "The Kinetics of COVID-19 Vaccine Response in a Community Vaccinated Population",
-    "rel_date": "2021-09-28",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.18.21263605",
-    "rel_abs": "We used a noninvasive electrochemical quantitative assay for IgG antibodies to SARS-CoV-2 S1 in saliva to investigate the kinetics of antibody response in a community-based population who had received either the Pfizer or Moderna mRNA-based vaccines. Samples were received from a total of 97 individuals including a subset of 42 individuals who collected samples twice-weekly for 3 months or longer. In all, 840 samples were collected and analyzed. In all individuals, salivary antibody levels rose sharply in the 2-week period following their second vaccination, with peak antibody levels being at 10-20 days post-vaccination. We observed that 20%, 10% and 2.4% of individuals providing serial samples had a 90%, 95%, and 99% drop respectively from peak levels during the duration of monitoring and two patients fell to pre-vaccination levels (5%). The use of non-invasive quantitative salivary antibody measurement can allow widespread, cost-effective monitoring of vaccine response.\n\nArticle Summary LineCOVID-19 antibodies were measured in saliva and 20% of vaccinated subjects experienced a 90% drop in peak antibody levels over the course of monitoring.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Michael Tu",
-        "author_inst": "Liquid Diagnostics LLC"
-      },
-      {
-        "author_name": "Samantha H. Chiang",
-        "author_inst": "UCLA School of Dentistry"
-      },
-      {
-        "author_name": "Richard Bender",
-        "author_inst": "Liquid Diagnostic LLC"
-      },
-      {
-        "author_name": "David Wong",
-        "author_inst": "UCLA School of Dentistry"
-      },
-      {
-        "author_name": "Charles Strom",
-        "author_inst": "Liquid Diagnostics LLC"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "allergy and immunology"
-  },
   {
     "rel_doi": "10.1101/2021.09.27.21264188",
     "rel_title": "Bayesian Inference of State-Level COVID-19 Basic Reproduction Numbers across the United States",
@@ -559197,6 +558104,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.09.25.21264106",
+    "rel_title": "Functional Data Analysis: Transition from Daily Observation of COVID-19 Prevalence in France to Functional Curves",
+    "rel_date": "2021-09-28",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.25.21264106",
+    "rel_abs": "In this paper we use the technique of functional data analysis to model daily hospitalized, deceased, ICU cases and return home patient numbers along the COVID-19 outbreak, considered as functional data across different departments in France while our response variables are numbers of vaccinations, deaths, infected, recovered and tests in France. These sets of data were considered before and after vaccination started in France. We used some smoothing techniques to smooth our data set, then analysis based on functional principal components method was performed, clustering using k-means techniques was done to understand the dynamics of the pandemic in different French departments according to their geographical location on France map and we also performed canonical correlations analysis between variables. Finally, we made some predictions to assess the accuracy of the method using functional linear regression models.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Kayode Oshinubi",
+        "author_inst": "University Grenoble Alpes"
+      },
+      {
+        "author_name": "Firas Ibrahim",
+        "author_inst": "University Grenoble Alpes"
+      },
+      {
+        "author_name": "Mustapha Rachdi",
+        "author_inst": "University Grenoble Alpes"
+      },
+      {
+        "author_name": "Jacques Demongeot",
+        "author_inst": "University Grenoble Alpes"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.09.25.21264118",
     "rel_title": "Modeling of COVID-19 Transmission Dynamics on US Population: Inter-transfer Infection in Age Groups, Mutant Variants, and Vaccination Strategies",
@@ -560378,37 +559316,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.09.26.21264141",
-    "rel_title": "Clinician and patient experience of neurology telephone consultations during the COVID-19 pandemic",
-    "rel_date": "2021-09-27",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.26.21264141",
-    "rel_abs": "BackgroundTelephone consultations are already employed in specific neurological settings. At Cambridge University Hospitals, the COVID-19 pandemic initially prompted almost all face-to-face appointments to be delivered by telephone, providing a uniquely unselected population to assess.\n\nObjectivesWe explored patient and clinician experience of telephone consultations; and whether telephone consultations might be preferable for pre-identifiable subgroups of patients after the pandemic.\n\nMethodsClinicians delivering neurological consultations converted to telephone between April-July 2020 were invited to complete a questionnaire following each consult (430 respondents) and the corresponding patients were subsequently surveyed (290 respondents). The questionnaires assessed clinician and patient goal achievement (and the reasons for any dissatisfaction). Clinicians also described consultation duration (in comparison to face-to-face) while patients detailed comparative convenience and preference.\n\nResultsThe majority of clinicians (335/430, 78%) and patients (227/290, 78%) achieved their consultation goals by telephone, particularly during follow-up consultations (clinicians 272/329, 83%, patients 176/216, 81%) and in some disease subgroups (e.g. seizures/epilepsy (clinicians 114/122 (93%), patients 71/81 (88%)). 95% of telephone consultations were estimated to take the same or less time than an equivalent face-to-face consultation. Most patients found telephone consultations convenient (69%) with 149/211 (71%) indicating they would like telephone or video consultations to play some role in their future follow-up.\n\nConclusionTelephone consultations appear effective, convenient and popular in prespecified subgroups of neurological outpatients. Further work comparing telephone, video and face-to-face consultations across multiple centres is now needed.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Tagore Nakornchai",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Elena Conci",
-        "author_inst": "Cambridge University Hospitals"
-      },
-      {
-        "author_name": "Anke Hensiek",
-        "author_inst": "Cambridge University Hospitals"
-      },
-      {
-        "author_name": "J William L Brown",
-        "author_inst": "University of Cambridge"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "neurology"
-  },
   {
     "rel_doi": "10.1101/2021.09.26.21264152",
     "rel_title": "Intravenous Immunoglobulin (IVIG) in Treating Non-ventilated COVID-19 Patients with Moderate to Severe Hypoxia is Pharmacoeconomically Favorable When Appropriately Targeted",
@@ -560955,6 +559862,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "ophthalmology"
   },
+  {
+    "rel_doi": "10.1101/2021.09.23.21264036",
+    "rel_title": "Diagnostic Yield of Screening for SARS-CoV-2 among Patients Admitted for Alternate Diagnoses",
+    "rel_date": "2021-09-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.23.21264036",
+    "rel_abs": "ObjectivesTo determine the diagnostic yield of screening patients for SARS-CoV-2 who were admitted with a diagnosis unrelated to COVID-19, and identify risk factors for positive tests.\n\nDesignCohort from the Canadian COVID-19 Emergency Department Rapid Response Network (CCEDRRN) registry\n\nSetting30 acute care hospitals across Canada\n\nParticipantsPatients hospitalized for non-COVID-19 related diagnoses who were tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) between March 1, and December 29, 2020\n\nMain outcomePositive nucleic acid amplification test (NAAT) for SARS-CoV-2\n\nOutcome measureDiagnostic yield\n\nResultsWe enrolled 15,690 consecutive eligible adults who were admitted to hospital without clinically suspected COVID-19. Among these patients, 122 tested positive for COVID-19, resulting in a diagnostic yield of 0.8% (95% CI 0.64% - 0.92%). Factors associated with a positive test included presence of a fever, being a healthcare worker, having a positive household contact or institutional exposure, and living in an area with higher 7-day average incident COVID-19 cases.\n\nConclusionsUniversal screening of hospitalized patients for COVID-19 across two pandemic waves had a low diagnostic yield and should be informed by individual-level risk assessment in addition to regional COVID-19 prevalence.\n\nTrial registrationNCT04702945\n\nSUMMARY BOXESSection 1: Universal screening of admitted patients for SARS-CoV-2 was implemented in many hospitals at the beginning of the pandemic. The Infections Diseases Society of America (IDSA) recommended avoiding universal screening of asymptomatic hospitalized patients in areas and times of low-COVID prevalence (defined as <2% prevalence) with very low certainty of evidence, based on studies of COVID-19 prevalence among asymptomatic individuals in the community.\n\nSection 2: This study supports IDSA recommendations to avoid universal screening for COVID-19 in times and areas of low COVID prevalence and identifies patient-level risk factors strongly associated with positive testing that should be considered for screening.",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Phil Davis",
+        "author_inst": "Department of Emergency Medicine, University of Saskatchewan, Saskatoon, SK, Canada"
+      },
+      {
+        "author_name": "Rhonda J Rosychuk",
+        "author_inst": "Department of Pediatrics, University of Alberta, Edmonton, AB, Canada"
+      },
+      {
+        "author_name": "Jeffrey P Hau",
+        "author_inst": "Centre for Clinical Epidemiology and Evaluation, Vancouver Coastal Health Research Institute, 828 W 10th Ave, Vancouver BC V5Z1M9"
+      },
+      {
+        "author_name": "Ivy Cheng",
+        "author_inst": "Department of Emergency Medicine, Sunnybrook Health Sciences Center"
+      },
+      {
+        "author_name": "Andrew D McRae",
+        "author_inst": "Department of Emergency Medicine, University of Calgary"
+      },
+      {
+        "author_name": "Raoul Daoust",
+        "author_inst": "D\u00e9partement M\u00e9decine de Famille et M\u00e9decine d'Urgence, Facult\u00e9 de M\u00e9decine, Universit\u00e9 de Montr\u00e9al, Department of Emergency Medicine, Research Centre, CIUSSS-No"
+      },
+      {
+        "author_name": "Eddy Lang",
+        "author_inst": "Department of Emergency Medicine, University of Calgary"
+      },
+      {
+        "author_name": "Joel Turner",
+        "author_inst": "Department of Emergency Medicine, McGill University, Montreal, QC"
+      },
+      {
+        "author_name": "Jaspreet Khangura",
+        "author_inst": "Department of Emergency Medicine, University of British Columbia"
+      },
+      {
+        "author_name": "Patrick T Fok",
+        "author_inst": "Division of EMS, Department of Emergency Medicine, Dalhousie University"
+      },
+      {
+        "author_name": "Maja Stachura",
+        "author_inst": "Department of Emergency Medicine, University of British Columbia"
+      },
+      {
+        "author_name": "Baljeet Brar",
+        "author_inst": "Department of Emergency Medicine, University of British Columbia"
+      },
+      {
+        "author_name": "Corinne M Hohl",
+        "author_inst": "Department of Emergency Medicine, Faculty of Medicine, University of British Columbia, 2775 Laurel St., Vancouver BC V5Z 1M9."
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "emergency medicine"
+  },
   {
     "rel_doi": "10.1101/2021.09.23.21263715",
     "rel_title": "Prediction of long-term kinetics of vaccine-elicited neutralizing antibody and time-varying vaccine-specific efficacy against the SARS-CoV-2 Delta variant by clinical endpoint",
@@ -562552,109 +561526,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.09.22.21263949",
-    "rel_title": "Who is at risk of poor mental health following COVID-19 outpatient management?",
-    "rel_date": "2021-09-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.22.21263949",
-    "rel_abs": "BackgroundCOVID-19 convalescents are at risk of developing a de novo mental health disorder or of worsening of a pre-existing one. The objectives of our study was to phenotype individuals at highest risk of mental health disorders among COVID-19 outpatients.\n\nMethodsWe conducted a binational online survey study with adult non-hospitalized COVID-19 convalescents (Austria/AT: n=1157, Italy/IT: n= 893). Primary endpoints were positive screening for depression and anxiety (PHQ-4, Patient Health Questionnaire) and self-perceived overall mental health and quality of life rated with 4 point Likert scales. Psychosocial stress was surveyed with a modified PHQ stress module. Associations of the mental health with socio-demographic variables, COVID-19 course and recovery data were assessed by multi-parameter random forest and serial univariable modeling. Mental disorder risk subsets were defined by self-organizing map and hierarchical clustering algorithms. The survey analyses are publicly available (https://im2-ibk.shinyapps.io/mental_health_dashboard/).\n\nResultsIn the study cohorts, 4.6 (IT)/6% (AT) of participants reported depression and/or anxiety before to infection. At a median of 79 days (AT)/96 days (IT) post COVID-19 onset, 12.4 (AT)/19.3% (IT) of subjects were screened positive for anxiety and 17.3 (AT)/23.2% (IT) for depression. Over one-fifth of the respondents rated their overall mental health (AT: 21.8%, IT: 24.1%) or quality of life (AT: 20.3%, IT: 25.9%) as fair or poor. In both study collectives, psychosocial stress, high numbers of acute and persistent COVID-19 complaints and the presence of acute neurocognitive symptoms (impaired concentration, confusion, forgetfulness) were the strongest correlates of deteriorating mental health and poor quality of life. In clustering analysis, these variables defined a  high risk subset with particularly high propensity of post-COVID-19 mental health impairment and decreased quality of life. Pre-existing depression or anxiety was associated with an increased symptom burden during acute COVID-19 and recovery.\n\nConclusionOur study revealed a bidirectional relationship between COVID-19 symptoms and mental health. We put forward specific acute symptoms of the disease as  red flags of mental health deterioration which should prompt general practitioners to identify COVID-19 patients who may benefit from early psychological and psychiatric intervention.\n\nTrial registrationClinicalTrials.gov: NCT04661462.",
-    "rel_num_authors": 22,
-    "rel_authors": [
-      {
-        "author_name": "Katharina H\u00fcfner",
-        "author_inst": "Department of Psychiatry, Psychotherapy and Psychosomatics, University Hospital for Psychiatry II, Medical University of Innsbruck, Innsbruck, Austria"
-      },
-      {
-        "author_name": "Piotr Tymoszuk",
-        "author_inst": "Data Analytics As a Service Tirol"
-      },
-      {
-        "author_name": "Dietmar Ausserhofer",
-        "author_inst": "Institute of General Practice and Public Health, Claudiana Bolzano, Italy"
-      },
-      {
-        "author_name": "Sabina Sahanic",
-        "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria"
-      },
-      {
-        "author_name": "Alex Pizzini",
-        "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria"
-      },
-      {
-        "author_name": "Verena Rass",
-        "author_inst": "Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria"
-      },
-      {
-        "author_name": "Matyas Galffy",
-        "author_inst": "Department of Psychiatry, Psychotherapy and Psychosomatics, University Hospital for Psychiatry II, Medical University of Innsbruck, Innsbruck, Austria"
-      },
-      {
-        "author_name": "Anna B\u00f6hm",
-        "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria"
-      },
-      {
-        "author_name": "Katharina Kurz",
-        "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria"
-      },
-      {
-        "author_name": "Thomas Sonnweber",
-        "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria"
-      },
-      {
-        "author_name": "Ivan Tancevski",
-        "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria"
-      },
-      {
-        "author_name": "Stefan Kiechl",
-        "author_inst": "Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria"
-      },
-      {
-        "author_name": "Andreas Huber",
-        "author_inst": "Tyrolean Federal Institute for Integrated Care, Innsbruck, Austria"
-      },
-      {
-        "author_name": "Barbara Plagg",
-        "author_inst": "Institute of General Practice and Public Health, Claudiana Bolzano, Italy"
-      },
-      {
-        "author_name": "Christian Wiedermann",
-        "author_inst": "Institute of General Practice and Public Health, Claudiana Bolzano, Italy"
-      },
-      {
-        "author_name": "Rosa Bellmann-Weiler",
-        "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria"
-      },
-      {
-        "author_name": "Herbert Bachler",
-        "author_inst": "Institute of General Medicine, Medical University of Innsbruck, Innsbruck, Austria"
-      },
-      {
-        "author_name": "G\u00fcnter Weiss",
-        "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria"
-      },
-      {
-        "author_name": "Giuliano Piccoliori",
-        "author_inst": "Institute of General Practice and Public Health, Claudiana Bolzano, Italy"
-      },
-      {
-        "author_name": "Raimund Helbok",
-        "author_inst": "Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria"
-      },
-      {
-        "author_name": "Judith L\u00f6ffler-Ragg",
-        "author_inst": "Medical University of Innsbruck"
-      },
-      {
-        "author_name": "Barbara Sperner-Unterweger",
-        "author_inst": "Department of Psychiatry, Psychotherapy and Psychosomatics, University Hospital for Psychiatry II, Medical University of Innsbruck, Innsbruck, Austria"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.09.22.21263944",
     "rel_title": "The importance of sustained compliance with physical distancing during COVID-19 vaccination rollout",
@@ -562929,6 +561800,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.09.26.461851",
+    "rel_title": "Cytotoxic T-cell-based vaccine against SARS-CoV2: a hybrid immunoinformatic approach",
+    "rel_date": "2021-09-26",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.26.461851",
+    "rel_abs": "This paper presents an alternative vaccination platform that provides long-term cellular immune protection mediated by cytotoxic T-cells. The immune response via cellular immunity creates superior resistance to viral mutations, which are currently the greatest threat to the global vaccination campaign. Furthermore, we also propose a safer, more facile and physiologically appropriate immunization method using either intra-nasal or oral administration. The underlying technology is an adaptation of synthetic long peptides (SLPs) previously used in cancer immunotherapy. SLPs comprising HLA class I and class II epitopes are used to stimulate antigen cross-presentation and canonical class II presentation by dendritic cells. The result is a cytotoxic T cell-mediated prompt and specific immune response against the virus-infected epithelia and a rapid and robust virus clearance. Peptides isolated from COVID-19 convalescent patients were screened for the best HLA population coverage and were tested for toxicity and allergenicity. 3D peptide folding followed by molecular docking studies provided positive results, suggesting a favourable antigen presentation.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Alexandru Tirziu",
+        "author_inst": "\"Victor Babes\" University of Medicine and Pharmacy Timisoara"
+      },
+      {
+        "author_name": "Virgil Paunescu",
+        "author_inst": "OncoGen Association, Timisoara, Romania"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "bioinformatics"
+  },
   {
     "rel_doi": "10.1101/2021.09.25.461766",
     "rel_title": "Deactivation of SARS-CoV-2 surrogate porcine epidemic diarrhea virus with electron beam irradiation under the cold chain transportation condition",
@@ -564282,109 +563176,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.09.20.21263828",
-    "rel_title": "Colchicine for COVID-19 in adults in the community (PRINCIPLE): a randomised, controlled, adaptive platform trial",
-    "rel_date": "2021-09-23",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.20.21263828",
-    "rel_abs": "ObjectivesColchicine has been proposed as a COVID-19 treatment, but its effect on time to recovery is unknown. We aimed to determine whether colchicine is effective at reducing time to recovery and COVID-19 related hospitalisations/deaths among people in the community.\n\nDesignProspective, multicentre, open-label, multi-arm, adaptive Platform Randomised Trial of Treatments in the Community for Epidemic and Pandemic Illnesses (PRINCIPLE).\n\nSettingNational trial run remotely from a central trial site and at multiple primary care centres across the United Kingdom.\n\nParticipantsAdults aged [&ge;]65, or [&ge;]18 years with comorbidities or shortness of breath, and unwell [&le;]14 days with suspected COVID-19 in the community.\n\nInterventionsParticipants were randomised to usual care, usual care plus colchicine (500{micro}g daily for 14 days), or usual care plus other interventions.\n\nMain outcome measuresThe co-primary endpoints were time to first self-reported recovery, and hospitalisation/death related to COVID-19, within 28 days, analysed using Bayesian models. The hypothesis for the time to recovery endpoint is evaluated first, and if superiority is declared on time to recovery, the hypothesis for the second co-primary endpoint of hospitalisation/death is then evaluated. To determine futility, we pre-specified a clinically meaningful benefit in time to first reported recovery as a hazard ratio of 1.2 or larger (equating to approximately 1.5 days benefit in the colchicine arm, assuming 9 days recovery in the usual care arm).\n\nResultsThe trial opened on April 2, 2020, with randomisation to colchicine starting on March 04, 2021 and stopping on May 26, 2021, because the pre-specified time to recovery futility criterion was met. The primary analysis model included 2755 SARS-CoV-2 positive participants, randomised to colchicine (n=156), usual care (n=1145), and other treatments (n=1454). Time to first self-reported recovery was similar in the colchicine group compared with usual care with an estimated hazard ratio of 0.919 [95% credible interval 0.72 to 1.16] and an estimated increase of 1.14 days [-1.86 to 5.21] in median time to self-reported recovery for colchicine versus usual care. The probability of meaningful benefit in time to recovery was very low at 1.8%. Results were similar in comparisons with concurrent controls. COVID-19 related hospitalisations/deaths were similar in the colchicine group versus usual care, with an estimated odds ratio of 0.76 [0.28 to 1.89] and an estimated difference of -0.4% [-2.7% to 2.4]. One serious adverse event occurred in the colchicine group and one in usual care.\n\nConclusionsColchicine did not improve time to recovery in people at higher risk of complications with COVID-19 in the community.\n\nTrial registrationISRCTN86534580.",
-    "rel_num_authors": 22,
-    "rel_authors": [
-      {
-        "author_name": "- The PRINCIPLE Trial Collaborative Group",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Jienchi Dorward",
-        "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom and Centre for the AIDS Programme of Research in South Africa "
-      },
-      {
-        "author_name": "Ly-Mee Yu",
-        "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom"
-      },
-      {
-        "author_name": "Gail Hayward",
-        "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom"
-      },
-      {
-        "author_name": "Benjamin R Saville",
-        "author_inst": "Berry Consultants, Texas, USA and Department of Biostatistics, Vanderbilt University School of Medicine, Tennessee, USA"
-      },
-      {
-        "author_name": "Oghenekome Gbinigie",
-        "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom"
-      },
-      {
-        "author_name": "Oliver van Hecke",
-        "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom"
-      },
-      {
-        "author_name": "Emma Ogburn",
-        "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom"
-      },
-      {
-        "author_name": "Philip H Evans",
-        "author_inst": "College of Medicine and Health, University of Exeter and National Institute for Health Research, Clinical Research Network"
-      },
-      {
-        "author_name": "Nicholas PB Thomas",
-        "author_inst": "Royal College of General Practitioners, London, UK, and National Institute for Health Research, Clinical Research Network"
-      },
-      {
-        "author_name": "Mahendra G Patel",
-        "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom and School of Pharmacy and Medical Sciences, University of Bra"
-      },
-      {
-        "author_name": "Duncan Richards",
-        "author_inst": "Oxford Clinical Trials Research Unit, Botnar Research Centre, University of Oxford, Oxford, UK"
-      },
-      {
-        "author_name": "Nicholas Berry",
-        "author_inst": "Berry Consultants, Texas, USA"
-      },
-      {
-        "author_name": "Michelle A Detry",
-        "author_inst": "Berry Consultants, Texas, USA"
-      },
-      {
-        "author_name": "Christina Saunders",
-        "author_inst": "Berry Consultants, Texas, USA"
-      },
-      {
-        "author_name": "Mark Fitzgerald",
-        "author_inst": "Berry Consultants, Texas, USA"
-      },
-      {
-        "author_name": "Victoria Harris",
-        "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom"
-      },
-      {
-        "author_name": "Milensu Shanyinde",
-        "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom"
-      },
-      {
-        "author_name": "Simon de Lusignan",
-        "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom"
-      },
-      {
-        "author_name": "Monique I Andersson",
-        "author_inst": "Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom,"
-      },
-      {
-        "author_name": "Christopher C Butler",
-        "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom"
-      },
-      {
-        "author_name": "FD Richard Hobbs",
-        "author_inst": "Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.09.21.21262619",
     "rel_title": "Saliva-based detection of COVID-19 infection in a real-world setting using reagent-free Raman spectroscopy and machine learning",
@@ -564879,6 +563670,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.09.21.21263457",
+    "rel_title": "Real-world Effectiveness of 2-dose SARS-CoV-2 Vaccination in Kidney Transplant Recipients",
+    "rel_date": "2021-09-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.21.21263457",
+    "rel_abs": "The humoral response to two doses of SARS-CoV-2 (Covid-19) vaccine among transplant recipients is inferior to immunocompetent individuals.1 Data on the  real-world effectiveness of vaccination in kidney transplant recipients [KTRs] are lacking. We performed a cohort study to investigate the impact of vaccination on Covid-19 infection and outcomes in our kidney transplant program.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Caitriona M. McEvoy",
+        "author_inst": "St. Michael's Hospital and Temerty Faculty of Medicine, University of Toronto"
+      },
+      {
+        "author_name": "Anna Lee",
+        "author_inst": "Temerty Faculty of Medicine, University of Toronto"
+      },
+      {
+        "author_name": "Paraish S. Misra",
+        "author_inst": "Temerty Faculty of Medicine, University of Toronto"
+      },
+      {
+        "author_name": "Gerald Lebovic",
+        "author_inst": "Applied Health Research Centre, LKSKI, Unity Health Toronto"
+      },
+      {
+        "author_name": "Ron Wald",
+        "author_inst": "St. Michael's Hospital and Temerty Faculty of Medicine, University of Toronto"
+      },
+      {
+        "author_name": "Darren A. Yuen",
+        "author_inst": "St. Michael's Hospital and Temerty Faculty of Medicine, University of Toronto"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "transplantation"
+  },
   {
     "rel_doi": "10.1101/2021.09.19.21263799",
     "rel_title": "Spatial simulation of COVID-19 new cases development",
@@ -566052,49 +564882,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.09.19.21263800",
-    "rel_title": "Association of Initial Clinical Characteristics with the Need for the Intensive Care Unit and Hospitalization in Patients Presenting to the Emergency Department with Acute Symptomatic COVID-19",
-    "rel_date": "2021-09-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.19.21263800",
-    "rel_abs": "ObjectiveTo evaluate the association of initial clinical symptoms with need for hospitalization, intensive care, or death in ED patients within 30 days after presenting with acute symptomatic COVID-19.\n\nMethodsThis study is a retrospective case-series of patients presenting to a single ED with acute symptomatic COVID-19 from March 7-August 9, 2020. Symptomatic patients with laboratory-confirmed SARS-CoV-2 infection were eligible for this study. Patients who tested positive for COVID-19 due to screening tests but had no reasonably associated symptoms were excluded. Participants were analyzed by three categories representative of clinical severity: intensive care unit (ICU) care/death, general ward admission, and ED discharge/convalescence at home. Outcomes were ascertained 30 days after initial presentation to account for escalation in severity after the ED visit. We conducted univariate and multivariable logistic regression analyses to report odds ratios (OR) with 95% confidence intervals (CI) between hospital or ICU care/death versus convalescence at home and between ICU care/death versus general ward admission.\n\nResultsIn total, 994 patients were included in the study, of which, 551 (55.4%) patients convalesced at home, 314 (31.6%) patients required general ward admission, and 129 (13.0%) required ICU care or died. In the multivariable models, ED patients requiring hospital admission were more likely to be aged [&ge;] 65 years (adjusted OR [aOR] 7.4, 95% CI: 5.0, 10.8), Black/African American (aOR 3.0, 95% CI: 1.6, 5.8) or Asian/American Indian/Alaska Native/Other (aOR 2.2, 95% CI: 1.1, 4.3), and experience dyspnea (aOR 2.7, 95% CI: 2.0, 3.7) or diarrhea (aOR 1.6, 95% CI: 1.1, 2.2). However, they were less likely to experience sore throat (aOR 0.4, 95% CI: 0.2, 0.6), myalgia (aOR 0.5, 95% CI: 0.4, 0.7), headache (aOR 0.5, 95% CI: 0.4, 0.8), or olfactory/taste disturbance (aOR 0.5, 95% CI: 0.3, 0.8). ED patients who required ICU care or died were more likely to experience altered mental status (aOR 3.8, 95% CI: 2.1, 6.6), but were less likely to report history of fever (0.5, 95% CI: 0.3, 0.8).\n\nConclusionsCOVID-19 presents with a multitude of clinical symptoms and an understanding of the association of symptoms with clinical severity may be useful for predicting ultimate patient outcomes.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Benjamin Zollinger",
-        "author_inst": "The George Washington University, School of Medicine & Health Sciences, Department of Emergency Medicine"
-      },
-      {
-        "author_name": "Sophia Newton",
-        "author_inst": "The George Washington University, School of Medicine & Health Sciences, Department of Emergency Medicine"
-      },
-      {
-        "author_name": "Jincong Q. Freeman",
-        "author_inst": "George Washington University, Milken Institute School of Public Health, Department of Biostatistics and Bioinformatics"
-      },
-      {
-        "author_name": "Seamus Moran",
-        "author_inst": "The George Washington University, School of Medicine & Health Sciences, Department of Emergency Medicine"
-      },
-      {
-        "author_name": "Nataly Montano Vargas",
-        "author_inst": "The George Washington University, School of Medicine & Health Sciences, Department of Emergency Medicine"
-      },
-      {
-        "author_name": "Yan Ma",
-        "author_inst": "George Washington University, Milken Institute School of Public Health, Department of Biostatistics and Bioinformatics"
-      },
-      {
-        "author_name": "Andrew C. Meltzer",
-        "author_inst": "The George Washington University, School of Medicine & Health Sciences, Department of Emergency Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "emergency medicine"
-  },
   {
     "rel_doi": "10.1101/2021.09.18.21263783",
     "rel_title": "The Delta Variant Had Negligible Impact on COVID-19 Vaccine Effectiveness in the USA",
@@ -566381,6 +565168,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "gastroenterology"
   },
+  {
+    "rel_doi": "10.1101/2021.09.20.21263808",
+    "rel_title": "Human Milk Antibodies Elicited by BNT162b2 Vaccination Target have reduced activity against SARS-CoV-2 Variants of Concern",
+    "rel_date": "2021-09-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.20.21263808",
+    "rel_abs": "We detected the presence of SARS-CoV-2 specific IgA against all major VOCs in milk out to 6 weeks after D2 of BNT162b2. These likely confer some protection to the breastfed infants, who are ineligible for vaccination and are at risk of severe COVID-19.\n\nHowever, we detected significantly reduced milk IgA binding to VOCs, including the globally dominant Delta variant, suggesting reduced protection for breastfeeding infants. Additionally, these antibodies were significantly reduced by as early as 4-6 weeks after D2.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Jia Ming Low",
+        "author_inst": "National University Hospital of Singapore"
+      },
+      {
+        "author_name": "Yue Gu",
+        "author_inst": "Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore"
+      },
+      {
+        "author_name": "Melissa Shu Feng Ng",
+        "author_inst": "Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore"
+      },
+      {
+        "author_name": "Liang Wei Wang",
+        "author_inst": "Agency for Science, Technology and Research"
+      },
+      {
+        "author_name": "Amin Zubair",
+        "author_inst": "Department of Neonatology, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore"
+      },
+      {
+        "author_name": "Youjia Zhong",
+        "author_inst": "Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore"
+      },
+      {
+        "author_name": "Paul McAry",
+        "author_inst": "Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "pediatrics"
+  },
   {
     "rel_doi": "10.1101/2021.09.20.21263838",
     "rel_title": "Childhood Asthma and COVID-19: A Nested Case-Control Study",
@@ -567958,29 +566788,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2021.09.21.461322",
-    "rel_title": "Identification of HLA-A*24:02-restricted CTL candidate epitopes derived from the non-structural polyprotein 1a of SARS-CoV-2 and analysis of their conservation using the mutation database of SARS-CoV-2 variants",
-    "rel_date": "2021-09-22",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.21.461322",
-    "rel_abs": "COVID-19 vaccines are currently being administrated worldwide and playing a critical role in controlling the pandemic. They have been designed to elicit neutralizing antibodies against Spike protein of the original SARS-CoV-2, and hence they are less effective against SARS-CoV-2 variants with mutated Spike than the original virus. It is possible that novel variants with abilities of enhanced transmissibility and/or immunoevasion will appear in the near future and perfectly escape from vaccine-elicited immunity. Therefore, the current vaccines may need to be improved to compensate for the viral evolution. For this purpose, it may be beneficial to take advantage of CD8+ cytotoxic T lymphocytes (CTLs). Several lines of evidence suggest the contribution of CTLs on the viral control in COVID-19, and CTLs target a wide range of proteins involving comparatively conserved non-structural proteins. Here, we identified twenty-two HLA-A*24:02-restricted CTL candidate epitopes derived from the non-structural polyprotein 1a (pp1a) of SARS-CoV-2 using computational algorithms, HLA-A*24:02 transgenic mice and the peptide-encapsulated liposomes. We focused on pp1a and HLA-A*24:02 because pp1a is relatively conserved and HLA-A*24:02 is predominant in East Asians such as Japanese. The conservation analysis revealed that the amino acid sequences of 7 out of the 22 epitopes were hardly affected by a number of mutations in the Sequence Read Archive database of SARS-CoV-2 variants. The information of such conserved epitopes might be useful for designing the next-generation COVID-19 vaccine that is universally effective against any SARS-CoV-2 variants by the induction of both anti-Spike neutralizing antibodies and CTLs specific for conserved epitopes.\n\nImportanceCOVID-19 vaccines have been designed to elicit neutralizing antibodies against the Spike protein of the original SARS-CoV-2, and hence they are less effective against variants. It is possible that novel variants will appear and escape from vaccine-elicited immunity. Therefore, the current vaccines may need to be improved to compensate for the viral evolution. For this purpose, it may be beneficial to take advantage of CD8+ cytotoxic T lymphocytes (CTLs). Here, we identified twenty-two HLA-A*24:02-restricted CTL candidate epitopes derived from the non-structural polyprotein 1a (pp1a) of SARS-CoV-2. We focused on pp1a and HLA-A*24:02 because pp1a is conserved and HLA-A*24:02 is predominant in East Asians. The conservation analysis revealed that the amino acid sequences of 7 out of the 22 epitopes were hardly affected by mutations in the database of SARS-CoV-2 variants. The information might be useful for designing the next-generation COVID-19 vaccine that is universally effective against any variants.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Akira Takagi",
-        "author_inst": "Kohjin Bio Co., Ltd."
-      },
-      {
-        "author_name": "Masanori Matsui",
-        "author_inst": "Saitama Medical University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2021.09.18.21263775",
     "rel_title": "Detection of COVID-19 in smartphone-based breathing recordings using CNN-BiLSTM: a pre-screening deep learning tool",
@@ -568124,6 +566931,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.09.14.21263467",
+    "rel_title": "Information Theoretic Model Selection for Accurately Estimating Unreported COVID-19 Infections",
+    "rel_date": "2021-09-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.14.21263467",
+    "rel_abs": "One of the most significant challenges in the early combat against COVID-19 was the difficulty in estimating the true magnitude of infections. Unreported infections drove up disease spread in numerous regions, made it very hard to accurately estimate the infectivity of the pathogen, therewith hampering our ability to react effectively. Despite the use of surveillance-based methods such as serological studies, identifying the true magnitude is still challenging today. This paper proposes an information theoretic approach for accurately estimating the number of total infections. Our approach is built on top of Ordinary Differential Equations (ODE) based models, which are commonly used in epidemiology and for estimating such infections. We show how we can help such models to better compute the number of total infections and identify the parameterization by which we need the fewest bits to describe the observed dynamics of reported infections. Our experiments show that our approach leads to not only substantially better estimates of the number of total infections but also better forecasts of infections than standard model calibration based methods. We additionally show how our learned parameterization helps in modeling more accurate what-if scenarios with non-pharmaceutical interventions. Our results support earlier findings that most COVID-19 infections were unreported and non-pharmaceutical interventions indeed helped to mitigate the spread of the outbreak. Our approach provides a general method for improving epidemic modeling which is applicable broadly.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Jiaming Cui",
+        "author_inst": "Georgia Institute of Technology"
+      },
+      {
+        "author_name": "Arash Haddadan",
+        "author_inst": "University of Virginia"
+      },
+      {
+        "author_name": "A S M Ahsan-Ul Haque",
+        "author_inst": "University of Virginia"
+      },
+      {
+        "author_name": "Jilles Vreeken",
+        "author_inst": "CISPA Helmholtz Center for Information Security"
+      },
+      {
+        "author_name": "Bijaya Adhikari",
+        "author_inst": "The University of Iowa"
+      },
+      {
+        "author_name": "Anil Vullikanti",
+        "author_inst": "University of Virginia"
+      },
+      {
+        "author_name": "B. Aditya Prakash",
+        "author_inst": "Georgia Institute of Technology"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.09.14.21263578",
     "rel_title": "Monitoring the COVID-19 immunisation programme through a National Immunisation Management System- Englands experience",
@@ -569365,41 +568215,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.09.16.460616",
-    "rel_title": "A novel B.1.1.523 SARS-CoV-2 variant that combines many spike mutations linked to immune evasion with current variants of concern",
-    "rel_date": "2021-09-21",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.16.460616",
-    "rel_abs": "In the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic several variants have emerged that are linked to increased transmissibility and immune evasion. These variants are recognized as variants of concern (VOC). In this study, we describe a B.1.1.523 variant that shares many spike mutations with current VOC. Receptor-binding domain mutations E484K and S494P were observed but also a deletion (position 156-158) in the N-terminal antigenic supersite that is similar to the delta-variant. These mutations are linked to immune evasion in VOC that could lead to less effective vaccines. This variant has been reported in various different countries and continents despite the dominance of B.1.1.7 (alpha) and B.1.617.2 (delta) variant. Furthermore, the B.1.1.523 pangolin lineage as a whole is recognized as a variant under monitoring since 14th of July 2021.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Brian M.J.W. van der Veer",
-        "author_inst": "Maastricht University Medical Centre+"
-      },
-      {
-        "author_name": "Jozef Dingemans",
-        "author_inst": "Maastricht University Medical Centre+"
-      },
-      {
-        "author_name": "Lieke B van Alphen",
-        "author_inst": "Maastricht University Medical Centre"
-      },
-      {
-        "author_name": "Christian JPA Hoebe",
-        "author_inst": "South Limburg Public Health Service"
-      },
-      {
-        "author_name": "Paul H.M. Savelkoul",
-        "author_inst": "Maastricht University Medical Centre"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2021.09.19.460950",
     "rel_title": "IL13Pred: A method for predicting immunoregulatory cytokine IL-13 inducing peptides for managing COVID-19 severity.",
@@ -569670,6 +568485,169 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.09.17.21263532",
+    "rel_title": "Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a sixteen-week interval between doses",
+    "rel_date": "2021-09-21",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.17.21263532",
+    "rel_abs": "While the standard regimen of the BNT162b2 mRNA vaccine includes two doses administered three weeks apart, some public health authorities decided to space them, raising concerns about vaccine efficacy. Here, we analyzed longitudinal humoral responses including antibody binding, Fc-mediated effector functions and neutralizing activity against the D614G strain but also variants of concern and SARS-CoV-1 in a cohort of SARS-CoV-2 naive and previously infected individuals, with an interval of sixteen weeks between the two doses. While the administration of a second dose to previously infected individuals did not significantly improve humoral responses, we observed a significant increase of humoral responses in naive individuals after the 16-weeks delayed second shot, achieving similar levels as in previously infected individuals. We compared these responses to those elicited in individuals receiving a short (4-weeks) dose interval. For the naive donors, these responses were superior to those elicited by the short dose interval.",
+    "rel_num_authors": 37,
+    "rel_authors": [
+      {
+        "author_name": "Alexandra Tauzin",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Shang Yu Gong",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Guillaume Beaudoin-Bussieres",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Dani Vezina",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Romain Gasser",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Lauriane Nault",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Lorie Marchitto",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Mehdi Benlarbi",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Debashree Chatterjee",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Manon Nayrac",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Annemarie Laumaea",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Jeremie Prevost",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Marianne Boutin",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Geremy Sannier",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Alexandre Nicolas",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Catherine Bourassa",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Gabrielle Gendron-Lepage",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Halima Medjahed",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Guillaume Goyette",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Yuxia Bo",
+        "author_inst": "University of Ottawa"
+      },
+      {
+        "author_name": "Josee Perreault",
+        "author_inst": "Hema-Quebec"
+      },
+      {
+        "author_name": "Laurie Gokool",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Chantal Morrisseau",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Pascale Arlotto",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Renee Bazin",
+        "author_inst": "Hema-Quebec"
+      },
+      {
+        "author_name": "Mathieu Dube",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Gaston De Serres",
+        "author_inst": "INSPQ"
+      },
+      {
+        "author_name": "Nicholas Brousseau",
+        "author_inst": "INSPQ"
+      },
+      {
+        "author_name": "Jonathan Richard",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Roberta Rovito",
+        "author_inst": "University of Milan"
+      },
+      {
+        "author_name": "Marceline Cote",
+        "author_inst": "University of Ottawa"
+      },
+      {
+        "author_name": "Cecile Tremblay",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Giulia C Marchetti",
+        "author_inst": "University of Milan"
+      },
+      {
+        "author_name": "Ralf Duerr",
+        "author_inst": "New York University School of Medicine"
+      },
+      {
+        "author_name": "Valerie Martel-Laferriere",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Daniel E Kaufmann",
+        "author_inst": "CRCHUM"
+      },
+      {
+        "author_name": "Andres Finzi",
+        "author_inst": "CRCHUM"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.09.17.21263759",
     "rel_title": "Estimates of presumed population immunity to SARS-CoV-2 by state in the United States, August 2021",
@@ -570999,249 +569977,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.09.20.461025",
-    "rel_title": "Analysis of the upper respiratory tract microbiota in mild and severe COVID-19 patients",
-    "rel_date": "2021-09-20",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.20.461025",
-    "rel_abs": "The microbiota of the respiratory tract remains a relatively poorly studied subject. At the same time, like the intestinal microbiota, it is involved in modulating the immune response to infectious agents in the host organism. A causal relationship between the composition of the respiratory microbiota and the likelihood of development and the severity of COVID-19 may be hypothesized. We analyze biomaterial from nasopharyngeal smears from 336 patients with a confirmed diagnosis of COVID-19, selected during the first and second waves of the epidemic in Russia. Sequences from a similar study conducted in Spain were also included in the analysis. We investigated associations between disease severity and microbiota at the level of microbial community (community types) and individual microbes (differentially represented species). To search for associations, we performed multivariate analysis, taking into account comorbidities, type of community and lineage of the virus. We found that two out of six community types are associated with a more severe course of the disease, and one of the community types is characterized by high stability (very similar microbiota profiles in different patients) and low level of lung damage. Differential abundance analysis with respect to comorbidities and community type suggested association of Rothia and Streptococcus genera representatives with more severe lung damage, and Leptotrichia, unclassified Lachnospiraceae and Prevotella with milder forms of the disease.",
-    "rel_num_authors": 57,
-    "rel_authors": [
-      {
-        "author_name": "Vladislav Viktorovich Babenko",
-        "author_inst": "Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia"
-      },
-      {
-        "author_name": "Ramiz Romanovich Bakhtyev",
-        "author_inst": "City Clinical Hospital named after S.I. Spasokukotsky of Moscow Healthcare Department, Academic Consortium"
-      },
-      {
-        "author_name": "Vladimir Pavlovich Baklaushev",
-        "author_inst": "Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, Moscow, Russia"
-      },
-      {
-        "author_name": "Larisa Alexandrovna Balykova",
-        "author_inst": "City Clinical Hospital named after S.I. Spasokukotsky of Moscow Healthcare Department, Academic Consortium"
-      },
-      {
-        "author_name": "Pavel Viktorovich Bashkirov",
-        "author_inst": "Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia"
-      },
-      {
-        "author_name": "Julia Andreevna Bespyatykh",
-        "author_inst": "Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia"
-      },
-      {
-        "author_name": "Anna Sergeevna Blagonravova",
-        "author_inst": "Privolzhsky Research Medical University, Nizhny Novgorod, Russia"
-      },
-      {
-        "author_name": "Daria Igorevna Boldyreva",
-        "author_inst": "Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia"
-      },
-      {
-        "author_name": "Dmitry Evgenievich Fedorov",
-        "author_inst": "Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia"
-      },
-      {
-        "author_name": "Ilshat Rafkatovich Gafurov",
-        "author_inst": "Kazan Federal University, Kazan, Russia"
-      },
-      {
-        "author_name": "Raushaniya Faritovna Gaifullina",
-        "author_inst": "Kazan Federal University, Kazan, Russia"
-      },
-      {
-        "author_name": "Julia Sergeevna Galeeva",
-        "author_inst": "Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia"
-      },
-      {
-        "author_name": "Elena Anatolyevna Galova",
-        "author_inst": "Privolzhsky Research Medical University, Nizhny Novgorod, Russia"
-      },
-      {
-        "author_name": "Alina Vladimirovna Gospodaryk",
-        "author_inst": "Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia"
-      },
-      {
-        "author_name": "Elena Nikolaevna Ilina",
-        "author_inst": "Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia"
-      },
-      {
-        "author_name": "Konstantin Pavlovich Ivanov",
-        "author_inst": "Hospital of the Russian Academy of Sciences, Troitsk, Russia"
-      },
-      {
-        "author_name": "Daria Dmitrievna Kharlampieva",
-        "author_inst": "Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia"
-      },
-      {
-        "author_name": "Polina Andreevna Khromova",
-        "author_inst": "Scientific Centre for Family Health and Human Reproduction Problems, Irkutsk, Russia"
-      },
-      {
-        "author_name": "Ksenia Mikhailovna Klimina",
-        "author_inst": "Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia"
-      },
-      {
-        "author_name": "Konstantin Borisovich Kolontarev",
-        "author_inst": "City Clinical Hospital named after S.I. Spasokukotsky of Moscow Healthcare Department, Academic Consortium"
-      },
-      {
-        "author_name": "Nadezhda Aleksandrovna Kolyshkina",
-        "author_inst": "Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, Moscow, Russia"
-      },
-      {
-        "author_name": "Andrey Vladimirovich Koritsky",
-        "author_inst": "Hospital of the Russian Academy of Sciences, Troitsk, Russia"
-      },
-      {
-        "author_name": "Vyacheslav Alexandrovich Kuropatkin",
-        "author_inst": "Burnasyan Federal Medical Biophysical Center, Moscow, Russia"
-      },
-      {
-        "author_name": "Vasily Nikolaevich Lazarev",
-        "author_inst": "Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia"
-      },
-      {
-        "author_name": "Alexander Ivanovich Manolov",
-        "author_inst": "Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Age"
-      },
-      {
-        "author_name": "Valentin Alexandrovich Manuvera",
-        "author_inst": "Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia"
-      },
-      {
-        "author_name": "Daria Sergeevna Matyushkina",
-        "author_inst": "Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia"
-      },
-      {
-        "author_name": "Maxim Denisovich Morozov",
-        "author_inst": "Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia"
-      },
-      {
-        "author_name": "Ekaterina Vladimirovna Moskaleva",
-        "author_inst": "Scientific Centre for Family Health and Human Reproduction Problems, Irkutsk, Russia"
-      },
-      {
-        "author_name": "Varvara Alexandrovna Musarova",
-        "author_inst": "Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia"
-      },
-      {
-        "author_name": "Oleg Borisovich Ogarkov",
-        "author_inst": "Scientific Centre for Family Health and Human Reproduction Problems, Irkutsk, Russia"
-      },
-      {
-        "author_name": "Elizaveta Andreevna Orlova",
-        "author_inst": "Scientific Centre for Family Health and Human Reproduction Problems, Irkutsk, Russia"
-      },
-      {
-        "author_name": "Alexander Vladimirovich Pavlenko",
-        "author_inst": "Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia"
-      },
-      {
-        "author_name": "Alla Germanovna Petrova",
-        "author_inst": "Scientific Centre for Family Health and Human Reproduction Problems, Irkutsk, Russia"
-      },
-      {
-        "author_name": "Natalia Sergeevna Pozhenko",
-        "author_inst": "Hospital of the Russian Academy of Sciences, Troitsk, Russia"
-      },
-      {
-        "author_name": "Dmitry Yurievich Pushkar",
-        "author_inst": "City Clinical Hospital named after S.I. Spasokukotsky of Moscow Healthcare Department, Academic Consortium"
-      },
-      {
-        "author_name": "Alexander Grigorievich Rumyantsev",
-        "author_inst": "Russian Academy of Sciences, Russia"
-      },
-      {
-        "author_name": "Sergey Aleksandrovich Rumyantsev",
-        "author_inst": "Russian Academy of Sciences, Russia"
-      },
-      {
-        "author_name": "Vladimir Alexandrovich Rumyantsev",
-        "author_inst": "Hospital of the Russian Academy of Sciences, Troitsk, Russia"
-      },
-      {
-        "author_name": "Lyubov Vladimirovna Rychkova",
-        "author_inst": "Scientific Centre for Family Health and Human Reproduction Problems, Irkutsk, Russia"
-      },
-      {
-        "author_name": "Alexander Sergeevich Samoilov",
-        "author_inst": "Burnasyan Federal Medical Biophysical Center, Moscow, Russia"
-      },
-      {
-        "author_name": "Irina Yurievna Shirokova",
-        "author_inst": "Privolzhsky Research Medical University, Nizhny Novgorod, Russia"
-      },
-      {
-        "author_name": "Vyacheslav Vladimirovich Sinkov",
-        "author_inst": "Scientific Centre for Family Health and Human Reproduction Problems, Irkutsk, Russia"
-      },
-      {
-        "author_name": "Svetlana Vladimirovna Solovieva",
-        "author_inst": "Burnasyan Federal Medical Biophysical Center, Moscow, Russia"
-      },
-      {
-        "author_name": "Elizaveta Valentinovna Starikova",
-        "author_inst": "Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia"
-      },
-      {
-        "author_name": "Polina Olegovna Tikhonova",
-        "author_inst": "Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia"
-      },
-      {
-        "author_name": "Galina Sergeevna Trifonova",
-        "author_inst": "Privolzhsky Research Medical University, Nizhny Novgorod, Russia"
-      },
-      {
-        "author_name": "Alexander Vitalievich Troitsky",
-        "author_inst": "Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, Moscow, Russia"
-      },
-      {
-        "author_name": "Alexander Alekseevich Tulichev",
-        "author_inst": "Privolzhsky Research Medical University, Nizhny Novgorod, Russia"
-      },
-      {
-        "author_name": "Yuri Dmitrievich Udalov",
-        "author_inst": "Burnasyan Federal Medical Biophysical Center, Moscow, Russia"
-      },
-      {
-        "author_name": "Anna Mikhailovna Varizhuk",
-        "author_inst": "Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia"
-      },
-      {
-        "author_name": "Alexander Olegovich Vasiliev",
-        "author_inst": "City Clinical Hospital named after S.I. Spasokukotsky of Moscow Healthcare Department, Academic Consortium"
-      },
-      {
-        "author_name": "Rinat Irekovich Vereshchagin",
-        "author_inst": "Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia"
-      },
-      {
-        "author_name": "Vladimir Alexandrovich Veselovsky",
-        "author_inst": "Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia"
-      },
-      {
-        "author_name": "Alexey Igorevich Volnukhin",
-        "author_inst": "City Clinical Hospital named after S.I. Spasokukotsky of Moscow Healthcare Department, Academic Consortium"
-      },
-      {
-        "author_name": "Gaukhar Maratovna Yusubalieva",
-        "author_inst": "Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, Moscow, Russia"
-      },
-      {
-        "author_name": "Vadim Markovich Govorun",
-        "author_inst": "Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "molecular biology"
-  },
   {
     "rel_doi": "10.1101/2021.09.15.21263628",
     "rel_title": "COVID-19 Vaccination and Healthcare Demand",
@@ -571524,6 +570259,81 @@
     "type": "new results",
     "category": "biophysics"
   },
+  {
+    "rel_doi": "10.1101/2021.09.15.21263654",
+    "rel_title": "Correlates of COVID-19 vaccination status among college students",
+    "rel_date": "2021-09-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.15.21263654",
+    "rel_abs": "ObjectivesDespite the widespread availability of COVID-19 vaccines in the United States, vaccine hesitancy remains high among certain groups. This study examined the correlates of being unvaccinated among a sample of university students (N=2900) during the spring and summer of 2021, when the campus had been closed for over a year and students were preparing to return to in-person learning.\n\nMethodsStudents responded to an email invitation and completed electronic surveys. Results. In multivariable logistic regression analyses, students were more likely to be unvaccinated if they were African American, identified with any political affiliation other than Democrat, were undergraduates or international students, had not traveled outside the Los Angeles during the pandemic, and/or had previously been ill with COVID-19.\n\nConclusionFindings indicate that culturally resonant educational interventions, and possibly vaccine requirements, are needed to promote vaccination among university students.",
+    "rel_num_authors": 15,
+    "rel_authors": [
+      {
+        "author_name": "Michele Nicolo",
+        "author_inst": "University of Southern California"
+      },
+      {
+        "author_name": "Eric Kawaguchi",
+        "author_inst": "University of SouthernCalifornia"
+      },
+      {
+        "author_name": "Angie Ghanem-Uzqueda",
+        "author_inst": "University of Southern California"
+      },
+      {
+        "author_name": "Andre E Kim",
+        "author_inst": "University of Southern California"
+      },
+      {
+        "author_name": "Daniel Soto",
+        "author_inst": "University of Southern California"
+      },
+      {
+        "author_name": "Sohini Deva",
+        "author_inst": "University of SouthernCalifornia"
+      },
+      {
+        "author_name": "Kush R Shanker",
+        "author_inst": "University of Southern California"
+      },
+      {
+        "author_name": "Christopher Rogers",
+        "author_inst": "University of Southern California"
+      },
+      {
+        "author_name": "Ryan Lee",
+        "author_inst": "University of Southern California"
+      },
+      {
+        "author_name": "Frank Gilliland",
+        "author_inst": "University of Southern California"
+      },
+      {
+        "author_name": "Jeffrey Klausner",
+        "author_inst": "University of Southern California"
+      },
+      {
+        "author_name": "Andrea Kovacs",
+        "author_inst": "University of Southern California"
+      },
+      {
+        "author_name": "David V Conti",
+        "author_inst": "University of Southern California"
+      },
+      {
+        "author_name": "Howard Hu",
+        "author_inst": "University of Southern California"
+      },
+      {
+        "author_name": "Jennifer B Unger",
+        "author_inst": "University of Southern California"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.09.14.21263598",
     "rel_title": "EFFICACY OF THE MEASLES-MUMPS-RUBELLA (MMR) VACCINE IN THE REDUCING THE SEVERITY OF COVID-19: AN INTERIM ANALYSIS OF A RANDOMISED CONTROLLED CLINICAL TRIAL",
@@ -573377,53 +572187,6 @@
     "type": "new results",
     "category": "synthetic biology"
   },
-  {
-    "rel_doi": "10.1101/2021.09.14.460394",
-    "rel_title": "Anti-SARS-CoV-2 IgG and IgA antibodies in COVID-19 convalescent plasma do not facilitate antibody-dependent enhance of viral infection.",
-    "rel_date": "2021-09-16",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.14.460394",
-    "rel_abs": "The novel coronavirus SARS-CoV2, which causes COVID-19, has resulted in the death of nearly 4 million people within the last 18 months. While preventive vaccination and monoclonal antibody therapies have been rapidly developed and deployed, early in the pandemic the use of COVID-19 convalescent plasma (CCP) was a common means of passive immunization, with the theoretical risk of antibody-dependent enhancement (ADE) of viral infection remaining undetermined. Though vaccines elicit a strong and protective immune response, and transfusion of CCP with high titers of neutralization activity are correlated with better clinical outcomes, the question of whether antibodies in CCP can enhance infection of SARS-CoV2 has not been directly addressed. In this study, we analyzed for and observed passive transfer of neutralization activity with CCP transfusion. Furthermore, to specifically understand if antibodies against the spike protein (S) enhance infection, we measured the anti-S IgG, IgA, and IgM responses and adapted retroviral-pseudotypes to measure virus neutralization with target cells expressing the ACE2 virus receptor and the Fc alpha receptor (FcR) or Fc gamma receptor IIA (Fc{gamma}RIIA). Whereas neutralizing activity of CCP correlated best with higher titers of anti-S IgG antibodies, the neutralizing titer was not affected when Fc receptors were present on target cells. These observations support the absence of antibody-dependent enhancement of infection (ADE) by IgG and IgA isotypes found in CCP. The results presented, therefore, support the clinical use of currently available antibody-based treatment including the continued study of CCP transfusion strategies.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Natasha  M Clark",
-        "author_inst": "University of Wisconsin-Madison"
-      },
-      {
-        "author_name": "Sanath  Kumar Janaka",
-        "author_inst": "University of Wisconsin-Madison"
-      },
-      {
-        "author_name": "William Hartman",
-        "author_inst": "University of Wisconsin-Madison"
-      },
-      {
-        "author_name": "Susan Stramer",
-        "author_inst": "American Red Cross"
-      },
-      {
-        "author_name": "Erin Goodhue",
-        "author_inst": "American Red Cross"
-      },
-      {
-        "author_name": "John Weiss",
-        "author_inst": "American Red Cross"
-      },
-      {
-        "author_name": "David  T. Evans",
-        "author_inst": "University of Wisconsin-Madison"
-      },
-      {
-        "author_name": "Joseph  P. Connor",
-        "author_inst": "University of Wisconsin-Madison"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2021.09.13.21263365",
     "rel_title": "High Seroconversion Rates Amongst Black and Hispanics With Hematologic Malignancies after SARS-CoV-2 Vaccination",
@@ -573730,6 +572493,69 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.09.13.21262182",
+    "rel_title": "mRNA COVID-19 Vaccination and Development of CMR-confirmed Myopericarditis",
+    "rel_date": "2021-09-16",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.13.21262182",
+    "rel_abs": "During the process of open peer review on MedRxiv we quickly received a number of messages from reviewers concerned that there was a problem with our reported incidence of myocarditis post mRNA vaccination. Our reported incidence appeared vastly inflated by an incorrectly small denominator (ie number of doses administered over the time period of the study). We reviewed the data available at Open Ottawa and found that there had indeed been a major underestimation, with the actual number of administered doses being more than 800,000 (much higher than quoted in the paper).\n\nIn order to avoid misleading either colleagues or the general public and press, we the authors unanimously wish to withdraw this paper on the grounds of incorrect incidence data. We thank the many peer reviewers who went out of their way to contact us and point out our error. We apologize to anyone who may have been upset or disturbed by our report.\n\nIn summary, the authors have withdrawn this manuscript because of a major error pertaining to the quoted incidence data. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Tahir Kafil",
+        "author_inst": "Ottawa Heart Institute"
+      },
+      {
+        "author_name": "Mariana M Lamacie",
+        "author_inst": "Ottawa Heart Institute"
+      },
+      {
+        "author_name": "Sophie Chenier",
+        "author_inst": "Ottawa Heart Institute"
+      },
+      {
+        "author_name": "Heather Taggart",
+        "author_inst": "Ottawa Heart Institute"
+      },
+      {
+        "author_name": "Nina Ghosh",
+        "author_inst": "Ottawa Heart Institute"
+      },
+      {
+        "author_name": "Alexander Dick",
+        "author_inst": "Ottawa Heart Institute"
+      },
+      {
+        "author_name": "Gary Small",
+        "author_inst": "Ottawa Heart Institute"
+      },
+      {
+        "author_name": "Peter Liu",
+        "author_inst": "Ottawa Heart Institute"
+      },
+      {
+        "author_name": "Rob S Beanlands",
+        "author_inst": "Ottawa Heart Institute"
+      },
+      {
+        "author_name": "Lisa Mielniczuk",
+        "author_inst": "Ottawa Heart Institute"
+      },
+      {
+        "author_name": "David Birnie",
+        "author_inst": "Ottawa Heart Institute"
+      },
+      {
+        "author_name": "Andrew M Crean",
+        "author_inst": "Ottawa Heart Institute"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "cardiovascular medicine"
+  },
   {
     "rel_doi": "10.1101/2021.09.13.21262360",
     "rel_title": "Efficacy of two doses of COVID-19 vaccine against severe COVID-19 in those with risk conditions and residual risk to the clinically extremely vulnerable: the REACT-SCOT case-control study",
@@ -575383,45 +574209,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pediatrics"
   },
-  {
-    "rel_doi": "10.1101/2021.09.12.21263463",
-    "rel_title": "Bacterial and Fungal Co-Infections among ICU COVID-19 Hospitalized Patients in a Palestinian Hospital: Incidence and Antimicrobial Stewardship",
-    "rel_date": "2021-09-15",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.12.21263463",
-    "rel_abs": "Diagnosis of co-infections with multiple pathogens among hospitalized COVID-19 patients can be jointly challenging and very essential for appropriate treatment, shortening hospital stay and preventing antimicrobial resistance. This study proposes to investigate the burden of bacterial and fungal co-infections outcomes on COVID-19 patients. It is a single centre cross-sectional study of hospitalized COVID-19 patients at Beit-Jala hospital in Palestine. The study included 321 hospitalized patients admitted to the ICU between June 2020 and March 2021 aged [&ge;] 20 years, with a confirmed diagnosis of COVID-19 via RT-PCR conducted on a nasopharyngeal swab. The patients information was gathered using graded data forms from electronic medical reports. The diagnosis of bacterial and fungal infection was proved through the patients clinical presentation and positive blood or sputum culture results. All cases had received empirical antimicrobial therapy before the ICU admission, and different regimens during the ICU stay. The rate of bacterial co-infection was 51.1%, mainly from gram-negative isolates (Enterobacter species and K.pneumoniae). The rate of fungal co-infection caused by A.fumigatus was 48.9%, and the mortality rate was 8.1%. However, it is unclear if it had been attributed to SARS-CoV-2 or coincidental.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Hani Abdel Hafez Naseef shtaya",
-        "author_inst": "Birzeit University"
-      },
-      {
-        "author_name": "Ula Mohammad",
-        "author_inst": "Birzeit University"
-      },
-      {
-        "author_name": "Nimeh Al-Shami",
-        "author_inst": "Birzeit University"
-      },
-      {
-        "author_name": "Yousef Sahoury",
-        "author_inst": "Birzeit University"
-      },
-      {
-        "author_name": "Abdallah D Abukhalil",
-        "author_inst": "Birzeit University"
-      },
-      {
-        "author_name": "Mohammad Farraj",
-        "author_inst": "Birzeit University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.09.07.21263194",
     "rel_title": "COVID-19 convalescent plasma and randomized clinical trials: rebuilding confidence by explaining failures and finding signals of efficacy.",
@@ -575708,6 +574495,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "occupational and environmental health"
   },
+  {
+    "rel_doi": "10.1101/2021.09.12.21263475",
+    "rel_title": "Spike Protein NTD mutation G142D in SARS-CoV-2 Delta VOC lineages is associated with frequent back mutations, increased viral loads, and immune evasion",
+    "rel_date": "2021-09-15",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.12.21263475",
+    "rel_abs": "The significantly greater infectivity of the SARS-CoV-2 Delta variants of concern (VOC) is hypothesized to be driven by key mutations that result in increased transmissibility, viral load and/or evasion of host immune response. We surveyed the mutational profiles of Delta VOC genomes between September 2020 and mid-August 2021 and identified a previously unreported mutation pattern at amino acid position 142 in the N-terminal domain (NTD) of the spike protein which demonstrated multiple rounds of mutation from G142 to D142 and back. This pattern of frequent back mutations was observed at multiple time points and across Delta VOC sub-lineages. The etiology for these recurrent mutations is unclear but raises the possibility of host-directed editing of the SARS-CoV-2 genome. Within Delta VOC this mutation is associated with higher viral load, further enhanced in the presence of another NTD mutation (T95I) which was also frequently observed in these cases. Protein modeling of both mutations predicts alterations of the surface topography of the NTD by G142D, specifically disturbance of the  super site epitope that binds NTD-directed neutralizing antibodies (NAbs). The appearance of frequent and repeated G142D followed by D142G back mutations is previously unreported in SARS-CoV-2 and may represent viral adaptation to evolving host immunity characterized by increasing frequency of spike NAbs, from both prior infection and vaccine-based immunity. The emergence of alterations of the NTD in and around the main NAb epitope is a concerning development in the ongoing evolution of SARS-CoV-2 which may contribute to increased infectivity, immune evasion and  breakthrough infections characteristic of Delta VOC. Future vaccine and therapy development may benefit by recognizing the emergence of these novel spike NTD mutations and considering their impact on antibody recognition, viral neutralization, infectivity, replication, and viral load.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Lishuang Shen",
+        "author_inst": "Children's Hospital Los Angeles"
+      },
+      {
+        "author_name": "Timothy J Triche",
+        "author_inst": "Children's Hospital Los Angeles"
+      },
+      {
+        "author_name": "Jennifer Dien Bard",
+        "author_inst": "Children's Hospital Los Angeles"
+      },
+      {
+        "author_name": "Jaclyn A Biegel",
+        "author_inst": "Children's Hospital Los Angeles"
+      },
+      {
+        "author_name": "Alexander R Judkins",
+        "author_inst": "Children's Hospital Los Angeles"
+      },
+      {
+        "author_name": "Xiaowu Gai",
+        "author_inst": "Children's Hospital Los Angeles"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.09.12.21263453",
     "rel_title": "Spread of Gamma (P.1) sub-lineages carrying Spike mutations close to the furin cleavage site and deletions in the N-terminal domain drives ongoing transmission of SARS-CoV-2 in Amazonas, Brazil",
@@ -577121,65 +575947,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.09.09.21263341",
-    "rel_title": "Place, cause and expectedness of death and relationship to the deceased are associated with poorer experiences of end-of-life care and challenges in early bereavement: Risk factors from an online survey of people bereaved during the COVID-19 pandemic",
-    "rel_date": "2021-09-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.09.21263341",
-    "rel_abs": "ObjectivesTo identify clinical and demographic risk factors for sub-optimal end-of-life care and pandemic-related challenges prior to death and in early bereavement.\n\nDesignOnline open national survey of adults bereaved in the UK from 16 March 2020-5 January 2021, recruited via media, social media, national associations and organisations.\n\nSettingGeneral population, UK.\n\nParticipants711 participants, mean age 49.5 (SD 12.9, range 18-90). 395 (55.6%) had experienced the death of a parent, 152 (21.4%) a partner. 628 (88.6%) were female and 33 (4.7%) from a minority ethnic background. The mean age of the person who died was 72.2 (SD 16.1, range miscarriage to 102 years). 311 (43.8%) deaths were from confirmed/suspected COVID-19, and 410 (57.8%) deaths occurred in hospital.\n\nMain outcome measuresEnd-of-life care experiences (six items, e.g. involvement in care decisions) and pandemic-related challenges before and after death (six items, e.g. unable to visit prior to death).\n\nResultsDeaths in hospital/care home increased the likelihood of: unable to visit prior to death, unable to say goodbye as wanted, limited contact in last days of life (all P<0.001). Deaths in hospice/at home increased the likelihood of: involved in care decisions (P<0.001), well supported by healthcare professionals (HCPs) after the death (P=0.003). Hospice deaths increased the likelihood of being given bereavement support information, which was least likely for care home deaths (P<0.001). Hospital deaths decreased the likelihood of knowing the contact details for the responsible care professional (P=0.001). Bereavement due to COVID-19 decreased the likelihood of: involvement in care decisions (P<0.001), feeling well supported by HCPs after the death (P<0.001), and increased the likelihood of: being unable to say goodbye (OR=0.348; 95% CI: 0.2 to 0.605), social isolation and loneliness (OR=0.439; 95% CI: 0.261 to 0.739), limited contact with relatives/friends (OR=0.465; 95% CI: 0.254 to 0.852). Expected deaths were associated with higher likelihood of feeling involved, informed, and well supported by HCPs (all P<0.001). The deceased being a partner or child increased the likelihood of knowing the contact details for the responsible care professional (P=0.001), being able to visit (P<0.001) and given bereavement support information (P<0.001). Being a bereaved partner strongly increased odds of social isolation and loneliness, e.g. OR = 0.092 (95% CI: 0.028 to 0.297) partner versus distant family member.\n\nConclusionsFour clear risk factors were found for poorer end-of-life care and pandemic-related challenges in bereavement: place, cause and expectedness of death, and relationship to the deceased.\n\nO_TEXTBOXWhat is already known on this topic?O_LISince the start of the pandemic, over 20 million family members and friends have been bereaved due to COVID-19, with millions more bereaved due to other causes.\nC_LIO_LIBereavement of any cause during the COVID-19 pandemic is associated with specific challenges, including limited access to people before their death, pressure on health and social care providers, quarantining due to infection or exposure, lockdowns and social distancing.\nC_LIO_LIThere remains little evidence to inform optimal clinical practice, bereavement support and the policy response to COVID-19 as a mass bereavement event.\nC_LI\n\nWhat this study addsO_LIOur study highlights four risk factors for poorer end-of-life care and increased risk of pandemic-related challenges in early bereavement: place, cause and expectedness of death and relationship to the deceased.\nC_LIO_LICOVID-19 deaths, hospital and care home deaths and unexpected deaths were generally associated with poorer outcomes, while being a partner of the person who died (regardless of cause) and bereavement due to COVID-19 increased the odds of experiencing social isolation and loneliness in bereavement.\nC_LIO_LIThese factors should be taken into account in clinical practice, policy and bereavement support.\nC_LI\n\nC_TEXTBOX",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Lucy E Selman",
-        "author_inst": "University of Bristol, Palliative and End of Life Care Research Group, Population Health Sciences, Bristol Medical School, Bristol, UK"
-      },
-      {
-        "author_name": "Damian JJ Farnell",
-        "author_inst": "Cardiff University, School of Dentistry, Cardiff, UK"
-      },
-      {
-        "author_name": "Mirella Longo",
-        "author_inst": "Cardiff University, Marie Curie Research Centre, Cardiff, UK"
-      },
-      {
-        "author_name": "Silvia Goss",
-        "author_inst": "Cardiff University, Marie Curie Research Centre, Cardiff, UK"
-      },
-      {
-        "author_name": "Kathy Seddon",
-        "author_inst": "Wales Cancer Research Centre, Cardiff, UK"
-      },
-      {
-        "author_name": "Anna Torrens-Burton",
-        "author_inst": "Cardiff University, Marie Curie Research Centre, Cardiff, UK"
-      },
-      {
-        "author_name": "Catriona R Mayland",
-        "author_inst": "University of Sheffield, Department of Oncology and Metabolism, Sheffield, UK"
-      },
-      {
-        "author_name": "Donna Wakefield",
-        "author_inst": "North Tees and Hartlepool NHS Foundation Trust, Stockton-on-Tees, UK"
-      },
-      {
-        "author_name": "Bridget Johnston",
-        "author_inst": "University of Glasgow, School of Medicine, Dentistry and Nursing, Glasgow, UK"
-      },
-      {
-        "author_name": "Anthony Byrne",
-        "author_inst": "Cardiff University, Marie Curie Research Centre, Cardiff, UK"
-      },
-      {
-        "author_name": "Emily J Harrop",
-        "author_inst": "Cardiff University, Marie Curie Research Centre, Cardiff, UK"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "palliative medicine"
-  },
   {
     "rel_doi": "10.1101/2021.09.03.21262841",
     "rel_title": "COVID-19 Bimodal Clinical and Pathological Phenotypes",
@@ -577798,6 +576565,81 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.09.03.21262757",
+    "rel_title": "Asymptomatic SARS-CoV-2 infection and the demography of COVID-19",
+    "rel_date": "2021-09-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.03.21262757",
+    "rel_abs": "Asymptomatic individuals carrying SARS-CoV-2 can transmit the virus and contribute to outbreaks of COVID-19, but it is not yet clear how the proportion of asymptomatic infections varies by age and geographic location. Here we use detailed surveillance data gathered during COVID-19 resurgences in six cities of China at the beginning of 2021 to investigate this question. Data were collected by multiple rounds of city-wide PCR test with detailed contact tracing, where each patient was monitored for symptoms through the whole course of infection. We find that the proportion of asymptomatic infections declines with age (coefficient =-0.006, P<0.01), falling from 56% in age group 0-9 years to 12% in age group >60 years. Using an age-stratified compartment model, we show that this age-dependent asymptomatic pattern together with the age distribution of overall cases can explain most of the geographic differences in reported asymptomatic proportions. Combined with demography and contact matrices from other countries worldwide, we estimate that a maximum of 22%-55% of SARS-CoV-2 infections would come from asymptomatic cases in an uncontrolled epidemic based on asymptomatic proportions in China. Our analysis suggests that flare-ups of COVID-19 are likely if only adults are vaccinated and that surveillance and possibly control measures among children will be still needed in the future to contain epidemic resurgence.",
+    "rel_num_authors": 15,
+    "rel_authors": [
+      {
+        "author_name": "Zengmiao Wang",
+        "author_inst": "Beijing Normal University"
+      },
+      {
+        "author_name": "Peiyi Wu",
+        "author_inst": "Beijing Normal University"
+      },
+      {
+        "author_name": "Jingyuan Wang",
+        "author_inst": "Beihang University"
+      },
+      {
+        "author_name": "Jose Lourenco",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Bingying Li",
+        "author_inst": "Beijing Normal University"
+      },
+      {
+        "author_name": "Benjamin Rader",
+        "author_inst": "Boston University"
+      },
+      {
+        "author_name": "Marko Laine",
+        "author_inst": "Meteorological Research Unit"
+      },
+      {
+        "author_name": "Hui Miao",
+        "author_inst": "Ohio State University"
+      },
+      {
+        "author_name": "Ligui Wang",
+        "author_inst": "Center of Disease Control and Prevention, PLA"
+      },
+      {
+        "author_name": "Hongbin Song",
+        "author_inst": "Center of Disease Control and Prevention, PLA"
+      },
+      {
+        "author_name": "Nita Bharti",
+        "author_inst": "The Pennsylvania State University"
+      },
+      {
+        "author_name": "John Brownstein",
+        "author_inst": "Harvard University"
+      },
+      {
+        "author_name": "Ottar  N Bjornstad",
+        "author_inst": "Penn State University"
+      },
+      {
+        "author_name": "Christopher Dye",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Huaiyu Tian",
+        "author_inst": "Beijing Normal University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.09.09.21263342",
     "rel_title": "Reports of myocarditis and pericarditis following mRNA COVID-19 vaccines: A review of spontaneously reported data from the UK, Europe, and the US",
@@ -579263,73 +578105,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2021.09.12.459978",
-    "rel_title": "Structure-activity relationships of B.1.617 and other SARS-CoV-2 spike variants",
-    "rel_date": "2021-09-13",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.12.459978",
-    "rel_abs": "The surge of COVID-19 infection cases is spurred by emerging SARS-CoV-2 variants such as B.1.617. Here we report 38 cryo-EM structures, corresponding to the spike protein of the Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2) and Kappa (B.1.617.1) variants in different functional states with and without its receptor, ACE2. Mutations on the N-terminal domain not only alter the conformation of the highly antigenic supersite of the Delta variant, but also remodel the glycan shield by deleting or adding N-glycans of the Delta and Gamma variants, respectively. Substantially enhanced ACE2 binding was observed for all variants, whose mutations on the receptor binding domain modulate the electrostatics of the binding interfaces. Despite their abilities to escape host immunity, all variants can be potently neutralized by three unique antibodies.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Tzu-Jing Yang",
-        "author_inst": "Institute of Biological Chemistry, Academia Sinica, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan"
-      },
-      {
-        "author_name": "Pei-Yu Yu",
-        "author_inst": "Institute of Biological Chemistry, Academia Sinica"
-      },
-      {
-        "author_name": "Yuan-Chih Chang",
-        "author_inst": "Institute of Biological Chemistry, Academia Sinica, Taiwan; Academia Sinica Cryo-EM Center, Academia Sinica, Taipei, Taiwan"
-      },
-      {
-        "author_name": "Ning-En Chang",
-        "author_inst": "Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan"
-      },
-      {
-        "author_name": "Yu-Xi Tsai",
-        "author_inst": "Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan"
-      },
-      {
-        "author_name": "Kang-Hao Liang",
-        "author_inst": "Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan; Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, Taiwan"
-      },
-      {
-        "author_name": "Piotr Draczkowski",
-        "author_inst": "Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Faculty of Pharmacy, Medical University of Lublin, ul. W. Chodzki 4a, 20-093 Lublin, Poland"
-      },
-      {
-        "author_name": "Bertina Lin",
-        "author_inst": "Johns Hopkins University, Baltimore, MD, U.S.A."
-      },
-      {
-        "author_name": "Yong-Sheng Wang",
-        "author_inst": "Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan"
-      },
-      {
-        "author_name": "Yu-Chun Chien",
-        "author_inst": "Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan"
-      },
-      {
-        "author_name": "Kay-Hooi Khoo",
-        "author_inst": "Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan"
-      },
-      {
-        "author_name": "Han-Chung Wu",
-        "author_inst": "Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan; Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, Taiwan"
-      },
-      {
-        "author_name": "Shang-Te Danny Hsu",
-        "author_inst": "Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "new results",
-    "category": "biophysics"
-  },
   {
     "rel_doi": "10.1101/2021.09.11.459879",
     "rel_title": "Ultrafast, one-step, and microwave heating-based synthesis of DNA/RNA-AuNP conjugates",
@@ -579644,6 +578419,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.09.07.21263200",
+    "rel_title": "Distinguishing Incubation and Acute Disease Stages of Mild-to-Moderate COVID-19",
+    "rel_date": "2021-09-13",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.07.21263200",
+    "rel_abs": "ObjectiveWhile numerous studies have already compared the immune responses against SARS-CoV-2 in severely and mild-to-moderately ill COVID-19 patients, longitudinal trajectories are still scarce. We therefore set out to analyze serial blood samples from mild-to-moderately ill patients in order to define the immune landscapes for differently progressed disease stages.\n\nMethodsTwenty-two COVID-19 patients were subjected to consecutive venipuncture within seven days after diagnosis or admittance to hospital. Flow cytometry was performed to analyze peripheral blood immune cell compositions and their activation as were plasma levels of cytokines and SARS-CoV-2 specific immunoglobulins. Healthy donors served as controls.\n\nResultsIntegrating the kinetics of plasmablasts and SARS-CoV-2 specific antibodies allowed for the definition of three disease stages of early COVID-19. The incubation phase was characterized by a sharp increase in pro-inflammatory monocytes and terminally differentiated cytotoxic T cells. The latter correlated significantly with elevated concentrations of IP-10. Early acute infection featured a peak in PD-1+ cytotoxic T cells, plasmablasts and increasing titers of virus specific antibodies. During late acute infection, immature neutrophils were enriched whereas all other parameters returned to baseline.\n\nConclusionOur findings will help to define landmarks that are indispensable for the refinement of new anti-viral and anti-inflammatory therapeutics, and may also inform clinicians to optimize treatment and prevent fatal outcome.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Michael M\u00fcller",
+        "author_inst": "Rostock University Medical Center"
+      },
+      {
+        "author_name": "Johann Volzke",
+        "author_inst": "Rostock University Medical Center"
+      },
+      {
+        "author_name": "Behnam Subin",
+        "author_inst": "Rostock University Medical Center"
+      },
+      {
+        "author_name": "Christian Johann Schmidt",
+        "author_inst": "Rostock University Medical Center"
+      },
+      {
+        "author_name": "Hilte Geerdes-Fenge",
+        "author_inst": "Rostock University Medical Center"
+      },
+      {
+        "author_name": "Emil Christian Reisinger",
+        "author_inst": "Rostock University Medical Center"
+      },
+      {
+        "author_name": "Brigitte M\u00fcller-Hilke",
+        "author_inst": "Rostock Univsersity Medical Center"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.09.08.21263057",
     "rel_title": "State-wide Genomic Epidemiology Investigations of COVID-19 Infections in Healthcare Workers: Insights for Future Pandemic Preparedness",
@@ -580893,33 +579711,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.09.07.21263246",
-    "rel_title": "Prevalence and Incidence of Stress, Depression and Anxiety Symptoms among Brazilians in Quarantine across the early phases of the COVID-19 Crisis",
-    "rel_date": "2021-09-12",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.07.21263246",
-    "rel_abs": "ObjectiveThe present study aimed to measure the prevalence and incidence of stress, depression, and anxiety symptoms in Brazilians during the COVID-19 pandemic.\n\nMethodWe assessed 103 (54 women, 49 men) participants online in three periods of the pandemic: March 2020 (T1), April 2020 (T2), and June 2020 (T3). Prevalence and incidence were identified when mental health scores were two standard deviations above the mean compared to normative data. Mental health indicators were measured using the Perceived Stress Scale, the Filgueiras Depression Index, and the State-Trait Anxiety Inventory - State Subscale.\n\nResultsAt T1, 89% of individuals were below cut-off scores for stress, anxiety, and depression, which dropped to 35% by T3. Stress prevalence was 1.9% at T1, 7.8% at T2, and 28.2% at T3. Depression prevalence was 0% at T1, 23.3% at T2, and 25.2% at T3. State anxiety prevalence was 10.7% at T1, 11.7% at T2, and 45.6% at T3. Stress incidence increased by 7.8% from T1 to T2, and 23.3% from T2 to T3. Depression incidence increased by 23.3% from T1 to T2, and 15.5% from T2 to T3. Anxiety incidence increased by 9.7% from T1 to T2, and 39.8% from T2 to T3. Stress severity scores significantly increased from 16.1{+/-}8.7 at T1 to 23.5{+/-}8.4 at T2, and 30.3{+/-}6.0 at T3. Depression severity scores significantly increased from 48.5{+/-}20.5 at T1 to 64.7{+/-}30.2 at T2, and 75.9{+/-}26.1 at T3. Anxiety increased from 49.0{+/-}13.4 at T1 to 53.5{+/-}12.5 at T2 and 62.3{+/-}13.4 at T3. Females had significantly higher anxiety scores than males by T3 (66.7{+/-}11.8 vs. 57.4{+/-}13.5).\n\nConclusionPrevalence and incidence of stress, depression, and anxiety significantly increased throughout the pandemic. The largest increase in stress and anxiety occurred between T2 and T3, and between T1 and T2 for depression. Severity of stress, depression, and anxiety increased throughout the study.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Miguel Blacutt",
-        "author_inst": "Teachers College of Columbia University"
-      },
-      {
-        "author_name": "Alberto Filgueiras",
-        "author_inst": "Rio de Janeiro State University"
-      },
-      {
-        "author_name": "Matthew A Stults-Kolehmainen",
-        "author_inst": "Yale - New Haven Hospital"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "psychiatry and clinical psychology"
-  },
   {
     "rel_doi": "10.1101/2021.09.07.21263236",
     "rel_title": "Change in Measles Vaccine Coverage and Estimated Impact on Measles Mortality in Low and Middle Income Countries, 2020: An Investigation into Secondary Public Health Effects of the COVID-19 Pandemic Using the Lives Saved Tool",
@@ -581130,6 +579921,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.09.07.21263213",
+    "rel_title": "Comprehensive Evaluation of COVID-19 Patient Short- and Long-term Outcomes: Disparities in Healthcare Utilization and Post-Hospitalization Outcomes",
+    "rel_date": "2021-09-12",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.07.21263213",
+    "rel_abs": "BackgroundUnderstanding risk factors for short- and long-term COVID-19 outcomes have implications for current guidelines and practice. We study whether early identified risk factors for COVID-19 persist one year later and through varying disease progression trajectories.\n\nMethodsThis was a retrospective study of 6,731 COVID-19 patients presenting to Michigan Medicine between March 10, 2020 and March 10, 2021. We describe disease progression trajectories from diagnosis to potential hospital admission, discharge, readmission, or death. Outcomes pertained to all patients: rate of medical encounters, hospitalization-free survival, and overall survival, and hospitalized patients: discharge versus in-hospital death and readmission. Risk factors included patient age, sex, race, body mass index, and 29 comorbidity conditions.\n\nResultsYounger, non-Black patients utilized healthcare resources at higher rates, while older, male, and Black patients had higher rates of hospitalization and mortality. Diabetes with complications, coagulopathy, fluid and electrolyte disorders, and blood loss anemia were risk factors for these outcomes. Diabetes with complications, coagulopathy, fluid and electrolyte disorders, and blood loss were associated with lower discharge and higher inpatient mortality rates.\n\nConclusionsThis study found differences in healthcare utilization and adverse COVID-19 outcomes, as well as differing risk factors for short- and long-term outcomes throughout disease progression. These findings may inform providers in emergency departments or critical care settings of treatment priorities, empower healthcare stakeholders with effective disease management strategies, and aid health policy makers in optimizing allocations of medical resources.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Stephen Salerno Jr.",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Yuming Sun",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Emily L Morris",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Xinwei He",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Yajing Li",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Ziyang Pan Pan",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Peisong Han",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Jian Kang",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Michael W Sjoding",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Yi Li",
+        "author_inst": "University of Michigan"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.09.10.21263385",
     "rel_title": "Effectiveness of the Single-Dose Ad26.COV2.S COVID Vaccine",
@@ -582955,65 +581801,6 @@
     "type": "new results",
     "category": "biochemistry"
   },
-  {
-    "rel_doi": "10.1101/2021.09.10.459786",
-    "rel_title": "Computational drug repurposing against SARS-CoV-2 reveals plasma membrane cholesterol depletion as key factor of antiviral drug activity",
-    "rel_date": "2021-09-10",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.10.459786",
-    "rel_abs": "Comparing SARS-CoV-2 infection-induced gene expression signatures to drug treatment-induced gene expression signatures is a promising bioinformatic tool to repurpose existing drugs against SARS-CoV-2. The general hypothesis of signature based drug repurposing is that drugs with inverse similarity to a disease signature can reverse disease phenotype and thus be effective against it. However, in the case of viral infection diseases, like SARS-CoV-2, infected cells also activate adaptive, antiviral pathways, so that the relationship between effective drug and disease signature can be more ambiguous.\n\nTo address this question, we analysed gene expression data from in vitro SARS-CoV-2 infected cell lines, and gene expression signatures of drugs showing anti-SARS-CoV-2 activity. Our extensive functional genomic analysis showed that both infection and treatment with in vitro effective drugs leads to activation of antiviral pathways like NFkB and JAK-STAT. Based on the similarity - and not inverse similarity - between drug and infection-induced gene expression signatures, we were able to predict the in vitro antiviral activity of drugs. We also identified SREBF1/2, key regulators of lipid metabolising enzymes, as the most activated transcription factors by several in vitro effective antiviral drugs. Using a fluorescently labeled cholesterol sensor, we showed that these drugs decrease the cholesterol levels of plasma-membrane. Supplementing drug-treated cells with cholesterol reversed the in vitro antiviral effect, suggesting the depleting plasma-membrane cholesterol plays a key role in virus inhibitory mechanism.\n\nOur results can help to more effectively repurpose approved drugs against SARS-CoV-2, and also highlights key mechanisms behind their antiviral effect.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=171 HEIGHT=200 SRC=\"FIGDIR/small/459786v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (37K):\norg.highwire.dtl.DTLVardef@7cd823org.highwire.dtl.DTLVardef@51f699org.highwire.dtl.DTLVardef@114c555org.highwire.dtl.DTLVardef@a774ee_HPS_FORMAT_FIGEXP  M_FIG C_FIG",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Szilvia Barsi",
-        "author_inst": "Semmelweis University, Faculty of Medicine, Department of Physiology, Budapest, Hungary"
-      },
-      {
-        "author_name": "Henrietta Papp",
-        "author_inst": "National Laboratory of Virology, Szentagothai Research Centre, University of Pecs, Pecs, Hungary"
-      },
-      {
-        "author_name": "Alberto Valdeolivas Urbelz",
-        "author_inst": "Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Daniel J Toth",
-        "author_inst": "Semmelweis University, Faculty of Medicine, Department of Physiology, Budapest, Hungary"
-      },
-      {
-        "author_name": "Anett Kuczmog",
-        "author_inst": "National Laboratory of Virology, Szentagothai Research Centre, University of Pecs, Pecs, Hungary"
-      },
-      {
-        "author_name": "Monika Madai",
-        "author_inst": "National Laboratory of Virology, Szentagothai Research Centre, University of Pecs, Pecs, Hungary"
-      },
-      {
-        "author_name": "Laszlo Hunyady",
-        "author_inst": "Semmelweis University, Faculty of Medicine, Department of Physiology, Budapest, Hungary"
-      },
-      {
-        "author_name": "Peter Varnai",
-        "author_inst": "Semmelweis University, Faculty of Medicine, Department of Physiology, Budapest, Hungary"
-      },
-      {
-        "author_name": "Julio Saez-Rodriguez",
-        "author_inst": "Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany"
-      },
-      {
-        "author_name": "Ferenc Jakab",
-        "author_inst": "National Laboratory of Virology, Szentagothai Research Centre, University of Pecs, Pecs, Hungary"
-      },
-      {
-        "author_name": "Bence Szalai",
-        "author_inst": "Semmelweis University, Faculty of Medicine, Department of Physiology, Budapest, Hungary"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "systems biology"
-  },
   {
     "rel_doi": "10.1101/2021.09.09.459504",
     "rel_title": "Differential antibody dynamics to SARS-CoV-2 infection and vaccination",
@@ -583496,6 +582283,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pharmacology and therapeutics"
   },
+  {
+    "rel_doi": "10.1101/2021.09.08.459502",
+    "rel_title": "Digital Spatial Profiling of Collapsing Glomerulopathy",
+    "rel_date": "2021-09-09",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.08.459502",
+    "rel_abs": "Collapsing glomerulopathy is a histologically distinct variant of focal and segmental glomerulosclerosis that presents with heavy proteinuria and portends a poor prognosis. Collapsing glomerulopathy can be triggered by viral infections such as HIV and SARS-CoV-2. Transcriptional profiling of collapsing glomerulopathy lesions is difficult since only a few glomeruli may exhibit this histology within a kidney biopsy and the mechanisms driving this heterogeneity are unknown. Therefore, we used recently developed digital spatial profiling (DSP) technology which permits quantification of mRNA at the level of individual glomeruli. Using DSP, we profiled 1,852 transcripts in glomeruli from HIV and SARS-CoV-2 infected patients with biopsy confirmed collapsing glomerulopathy. The increased resolution of DSP uncovered heterogeneity in glomerular transcriptional profiles that were missed in early laser capture microdissection studies of pooled glomeruli. Focused validation using immunohistochemistry and RNA in situ hybridization showed good concordance with DSP results. Therefore, DSP represents a powerful method to dissect transcriptional programs of pathologically discernible kidney lesions.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Kelly D. Smith",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Kammi Henriksen",
+        "author_inst": "University of Chicago"
+      },
+      {
+        "author_name": "Roberto F. Nicosia",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Charles E. Alpers",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Shreeram Akilesh",
+        "author_inst": "University of Washington"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "pathology"
+  },
   {
     "rel_doi": "10.1101/2021.09.09.459634",
     "rel_title": "A thermostable oral SARS-CoV-2 vaccine induces mucosal and protective immunity",
@@ -585153,85 +583975,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2021.09.01.21262969",
-    "rel_title": "SARS-CoV-2 infected cells trigger an acute antiviral response mediated by Plasmacytoid dendritic cells in mild but not severe COVID-19 patients",
-    "rel_date": "2021-09-08",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.01.21262969",
-    "rel_abs": "Type I and III interferons (IFN-I/{lambda}) are key antiviral mediators against SARS-CoV-2 infection. Here, we demonstrate that plasmacytoid dendritic cells (pDCs) are the predominant IFN-I/{lambda} source following their sensing of SARS-CoV-2-infected cells. Mechanistically, this short-range sensing by pDCs requires sustained integrin-mediated cell adhesion with infected cells. In turn, pDCs restrict viral spread by an IFN-I/{lambda} response directed toward SARS-CoV-2-infected cells. This specialized function enables pDCs to efficiently turn-off viral replication, likely via a local response at the contact site with infected cells. By exploring the pDC response in SARS-CoV-2 patients, we further demonstrate that pDC responsiveness inversely correlates with the severity of the disease. The pDC response is particularly impaired in severe COVID-19 patients. Overall, we propose that pDC activation is essential to control SARS-CoV-2-infection. Failure to unfold this response could be key to understand severe cases of COVID-19.",
-    "rel_num_authors": 16,
-    "rel_authors": [
-      {
-        "author_name": "Manon Venet",
-        "author_inst": "CIRI; Inserm U1111; Universite Claude Bernard Lyon 1; CNRS, UMR5308; Ecole Normale Superieure de Lyon; Univ Lyon; France"
-      },
-      {
-        "author_name": "Margarida Sa Ribeiro",
-        "author_inst": "CIRI; Inserm U1111; Universite Claude Bernard Lyon 1; CNRS, UMR5308; Ecole Normale Superieure de Lyon; Univ Lyon; France"
-      },
-      {
-        "author_name": "Elodie Decembre",
-        "author_inst": "CIRI; Inserm U1111; Universite Claude Bernard Lyon 1; CNRS, UMR5308; Ecole Normale Superieure de Lyon; Univ Lyon; France"
-      },
-      {
-        "author_name": "Alicia Bellomo",
-        "author_inst": "CIRI; Inserm U1111; Universite Claude Bernard Lyon 1; CNRS, UMR5308; Ecole Normale Superieure de Lyon; Univ Lyon; France"
-      },
-      {
-        "author_name": "Garima Joshi",
-        "author_inst": "CIRI; Inserm U1111; Universite Claude Bernard Lyon 1; CNRS, UMR5308; Ecole Normale Superieure de Lyon; Univ Lyon; France"
-      },
-      {
-        "author_name": "Marine Villard",
-        "author_inst": "CIRI; Inserm U1111; Universite Claude Bernard Lyon 1; CNRS, UMR5308; Ecole Normale Superieure de Lyon; Univ Lyon; France"
-      },
-      {
-        "author_name": "David Cluet",
-        "author_inst": "Laboratoire de Biologie et Modelisation de la Cellule; University de Lyon; Ecole normale superieure de Lyon; Universite Claude Bernard Lyon 1; CNRS UMR 5239; IN"
-      },
-      {
-        "author_name": "Magali Perret",
-        "author_inst": "CIRI; Inserm U1111; Universite Claude Bernard Lyon 1; CNRS, UMR5308; Ecole Normale Superieure de Lyon; Univ Lyon; France"
-      },
-      {
-        "author_name": "Remi Pescamona",
-        "author_inst": "CIRI; Inserm U1111; Universite Claude Bernard Lyon 1; CNRS, UMR5308; Ecole Normale Superieure de Lyon; Univ Lyon; France"
-      },
-      {
-        "author_name": "Helena Paidassi",
-        "author_inst": "CIRI; Inserm U1111; Universite Claude Bernard Lyon 1; CNRS, UMR5308; Ecole Normale Superieure de Lyon; Univ Lyon; France"
-      },
-      {
-        "author_name": "Thierry Walzer",
-        "author_inst": "CIRI; Inserm U1111; Universite Claude Bernard Lyon 1; CNRS, UMR5308; Ecole Normale Superieure de Lyon; Univ Lyon; France"
-      },
-      {
-        "author_name": "Omran Allatif",
-        "author_inst": "CIRI; Inserm U1111; Universite Claude Bernard Lyon 1; CNRS, UMR5308; Ecole Normale Superieure de Lyon; Univ Lyon; France"
-      },
-      {
-        "author_name": "Alexandre Belot",
-        "author_inst": "CIRI; Inserm U1111; Universite Claude Bernard Lyon 1; CNRS, UMR5308; Ecole Normale Superieure de Lyon; Univ Lyon; France"
-      },
-      {
-        "author_name": "Sophie trouillet-assant",
-        "author_inst": "Hospices Civils de Lyon;CIRI; Inserm U1111; Universite Claude Bernard Lyon 1; CNRS, UMR5308; Ecole Normale Superieure de Lyon; Univ Lyon; France"
-      },
-      {
-        "author_name": "Emiliano Ricci",
-        "author_inst": "Laboratoire de Biologie et Modelisation de la Cellule; University de Lyon; Ecole normale superieure de Lyon; Universite Claude Bernard Lyon 1; CNRS UMR 5239; IN"
-      },
-      {
-        "author_name": "Marlene DREUX",
-        "author_inst": "CIRI; Inserm U1111; Universite Claude Bernard Lyon 1; CNRS, UMR5308; Ecole Normale Superieure de Lyon; Univ Lyon; France"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.09.03.21263083",
     "rel_title": "Suicide and self-harm in low- and middle- income countries during the COVID-19 pandemic: A systematic review",
@@ -585610,6 +584353,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "occupational and environmental health"
   },
+  {
+    "rel_doi": "10.1101/2021.09.02.21262599",
+    "rel_title": "Severe COVID-19 is associated with sustained biochemical disturbances and prolonged symptomatology; A retrospective single-centre cohort study",
+    "rel_date": "2021-09-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.02.21262599",
+    "rel_abs": "This manuscript has been withdrawn following a formal investigation by the Zan Mitrev Clinic Scientific Committee.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Marija Simjanoska",
+        "author_inst": "Columbia University in the City of New York"
+      },
+      {
+        "author_name": "Zan Mitrev",
+        "author_inst": "Zan Mitrev Clinic"
+      },
+      {
+        "author_name": "Gianluca Villa",
+        "author_inst": "University of Florence"
+      },
+      {
+        "author_name": "Daniel Griffin",
+        "author_inst": "Columbia University College of Physicians and Surgeons"
+      },
+      {
+        "author_name": "Rodney Rosalia",
+        "author_inst": "Zan Mitrev Clinic"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.09.02.21263046",
     "rel_title": "The early impact of vaccination against SARS-CoV-2 in Region Stockholm, Sweden",
@@ -586831,61 +585609,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "rehabilitation medicine and physical therapy"
   },
-  {
-    "rel_doi": "10.1101/2021.08.31.21262914",
-    "rel_title": "Association between City-wide Lockdown and COVID-19 Hospitalization Rates in Multigenerational Households in New York City",
-    "rel_date": "2021-09-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.31.21262914",
-    "rel_abs": "BackgroundCity-wide lockdowns and school closures have demonstrably impacted COVID-19 transmission. However, simulation studies have suggested an increased risk of COVID-19 related morbidity for older individuals inoculated by house-bound children. This study examines whether the March 2020 lockdown in New York City (NYC) was associated with higher COVID-19 hospitalization rates in neighborhoods with larger proportions of multigenerational households.\n\nMethodsWe obtained daily age-segmented COVID-19 hospitalization counts in each of 166 ZIP code tabulation areas (ZCTAs) in NYC. Using Bayesian Poisson regression models that account for spatiotemporal dependencies between ZCTAs, as well as socioeconomic risk factors, we conducted a difference-in-differences study amongst ZCTA-level hospitalization rates from February 23 to May 2, 2020. We compared ZCTAs in the lowest quartile of multigenerational housing to other quartiles before and after the lockdown.\n\nFindingsAmong individuals over 55 years, the lockdown was associated with higher COVID-19 hospitalization rates in ZCTAs with more multigenerational households. The greatest difference occurred three weeks after lockdown: Q2 vs. Q1: 54% increase (95% Bayesian credible intervals: 22 - 96%); Q3 vs. Q1: 48%, (17 - 89%); Q4 vs. Q1: 66%, (30 - 211%). After accounting for pandemic-related population shifts, a significant difference was observed only in Q4 ZCTAs: 37% (7 -76%).\n\nInterpretationBy increasing house-bound mixing across older and younger age groups, city-wide lockdown mandates imposed during the growth of COVID-19 cases may have inadvertently, but transiently, contributed to increased transmission in multigenerational households.\n\nFundingNational Center for Advancing Translational Sciences; Clinical and Translational Science Center at Weill Cornell Medical College.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Arnab K Ghosh",
-        "author_inst": "Weill Cornell Medical College"
-      },
-      {
-        "author_name": "Sara Venkataraman",
-        "author_inst": "Cornell University"
-      },
-      {
-        "author_name": "Evgeniya Reshetnyak",
-        "author_inst": "Weill Cornell Medical College"
-      },
-      {
-        "author_name": "Mangala Rajan",
-        "author_inst": "Weill Cornell Medical College"
-      },
-      {
-        "author_name": "Anjile An",
-        "author_inst": "Weill Cornell Medical College"
-      },
-      {
-        "author_name": "John K Chae",
-        "author_inst": "Weill Cornell Medical College"
-      },
-      {
-        "author_name": "Mark A Unruh",
-        "author_inst": "Weill Cornell Medical College"
-      },
-      {
-        "author_name": "David Abramson",
-        "author_inst": "New York University"
-      },
-      {
-        "author_name": "Charles K DiMaggio",
-        "author_inst": "New York University School of Medicine"
-      },
-      {
-        "author_name": "Nathaniel Hupert",
-        "author_inst": "Weill Cornell Medical College"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health policy"
-  },
   {
     "rel_doi": "10.1101/2021.09.02.21263042",
     "rel_title": "Local SARS-CoV-2 peptide-specific Immune Responses in Convalescent and Uninfected Human Lung Tissue Models",
@@ -587232,6 +585955,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.09.01.21262990",
+    "rel_title": "Impact and effectiveness of social distancing for COVID-19 mitigation -- A transnational and transregional study",
+    "rel_date": "2021-09-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.01.21262990",
+    "rel_abs": "We present an analysis of the relationship between SARS-CoV-2 infection rates and a social distancing metric from data for all the states and most populous cities in the United States and Brazil, all the 22 European Economic Community countries and the United Kingdom. We discuss why the infection rate, instead of the effective reproduction number or growth rate of cases, is a proper choice to perform this analysis when considering a wide span of time. We obtain a strong Spearmans rank order correlation between the social distancing metric and the infection rate in each locality. We show that mask mandates increase the values of Spearmans correlation in the United States, where a mandate was adopted. We also obtain an explicit numerical relation between the infection rate and the social distancing metric defined in the present work.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Tarcisio Marciano Rocha Jr.",
+        "author_inst": "Universidade de Brasilia"
+      },
+      {
+        "author_name": "Jose Fernando Mendes",
+        "author_inst": "Universidade de Aveiro"
+      },
+      {
+        "author_name": "Marcelo Albano Moret",
+        "author_inst": "Universidade do Estado da Bahia"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.09.02.21263018",
     "rel_title": "The pitfalls of inferring virus-virus interactions from co-detection prevalence data: Application to influenza and SARS-CoV-2",
@@ -588433,45 +587183,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2021.09.03.458946",
-    "rel_title": "Network analysis outlines strengths and weaknesses of emerging SARS-CoV-2 Spike variants",
-    "rel_date": "2021-09-04",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.03.458946",
-    "rel_abs": "The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has triggered myriad efforts to dissect and understand the structure and dynamics of this complex pathogen. The Spike glycoprotein of SARS-CoV-2 has received special attention as it is the means by which the virus enters the human host cells. The N-terminal domain (NTD) is one of the targeted regions of the Spike protein for therapeutics and neutralizing antibodies against COVID-19. Though its function is not well-understood, the NTD is reported to acquire mutations and deletions that can accelerate the evolutionary adaptation of the virus driving antibody escape. Cellular processes are known to be regulated by complex interactions at the molecular level, which can be characterized by means of a graph representation facilitating the identification of key residues and critical communication pathways within the molecular complex. From extensive all-atom molecular dynamics simulations of the entire Spike for the wild-type and the dominant variant, we derive a weighted graph representation of the protein in two dominant conformations of the receptor-binding-domain; all-down and one-up. We implement graph theory techniques to characterize the relevance of specific residues at facilitating roles of communication and control, while uncovering key implications for fitness and adaptation. We find that many of the reported high-frequency mutations tend to occur away from the critical residues highlighted by our graph theory analysis, implying that these mutations tend to avoid targeting residues that are most critical for protein allosteric communication. We propose that these critical residues could be candidate targets for novel antibody therapeutics. In addition, our analysis provides quantitative insights of the critical role of the NTD and furin cleavage site and their wide-reaching influence over the protein at large. Many of our conclusions are supported by empirical evidence while others point the way towards crucial simulation-guided experiments.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Pedro D Manrique",
-        "author_inst": "Los Alamos National Laboratory"
-      },
-      {
-        "author_name": "Srirupa Chakraborty",
-        "author_inst": "Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, U.S.A. Center for Nonlinear Studies, Los Alamos National Laborat"
-      },
-      {
-        "author_name": "Kien Nguyen",
-        "author_inst": "Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, U.S.A."
-      },
-      {
-        "author_name": "Rachael Mansbach",
-        "author_inst": "Physics Department, Concordia University, Montreal, Quebec, Canada, H4B IR6"
-      },
-      {
-        "author_name": "Bette Korber",
-        "author_inst": "Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, U.S.A."
-      },
-      {
-        "author_name": "S. Gnanakaran",
-        "author_inst": "Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, U.S.A."
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "molecular biology"
-  },
   {
     "rel_doi": "10.1101/2021.09.03.458953",
     "rel_title": "An Extended Coatomer Binding Motif in the SARS-CoV-2 Spike Protein",
@@ -588834,6 +587545,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.09.03.458829",
+    "rel_title": "Characterization of SARS-CoV-2 variants B.1.617.1 (Kappa), B.1.617.2 (Delta) and B.1.618 on cell entry, host range, and sensitivity to convalescent plasma and ACE2 decoy receptor",
+    "rel_date": "2021-09-03",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.03.458829",
+    "rel_abs": "Recently, highly transmissible SARS-CoV-2 variants B.1.617.1 (Kappa), B.1.617.2 (Delta) and B.1.618 were identified in India with mutations within the spike proteins. The spike protein of Kappa contains four mutations E154K, L452R, E484Q and P681R, and Delta contains L452R, T478K and P681R, while B.1.618 spike harbors mutations {Delta}145-146 and E484K. However, it remains unknown whether these variants have altered in their entry efficiency, host tropism, and sensitivity to neutralizing antibodies as well as entry inhibitors. In this study, we found that Kappa, Delta or B.1.618 spike uses human ACE2 with no or slightly increased efficiency, while gains a significantly increased binding affinity with mouse, marmoset and koala ACE2 orthologs, which exhibits limited binding with WT spike. Furthermore, the P618R mutation leads to enhanced spike cleavage, which could facilitate viral entry. In addition, Kappa, Delta and B.1.618 exhibits a reduced sensitivity to neutralization by convalescent sera owning to the mutation of E484Q, T478K, {Delta}145-146 or E484K, but remains sensitive to entry inhibitors-ACE2-lg decoy receptor. Collectively, our study revealed that enhanced human and mouse ACE2 receptor engagement, increased spike cleavage and reduced sensitivity to neutralization antibodies of Kappa, Delta and B.1.618 may contribute to the rapid spread of these variants and expanded host range. Furthermore, our result also highlighted that ACE2-lg could be developed as broad-spectrum antiviral strategy against SARS-CoV-2 variants.",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Wenlin Ren",
+        "author_inst": "Tsinghua University"
+      },
+      {
+        "author_name": "Xiaohui Ju",
+        "author_inst": "Tsinghua University"
+      },
+      {
+        "author_name": "Mingli Gong",
+        "author_inst": "Tsinghua University"
+      },
+      {
+        "author_name": "Jun Lan",
+        "author_inst": "Tsinghua University"
+      },
+      {
+        "author_name": "Yanying Yu",
+        "author_inst": "Tsinghua University"
+      },
+      {
+        "author_name": "Quanxin Long",
+        "author_inst": "Chongqing Medical University"
+      },
+      {
+        "author_name": "Yu Zhang",
+        "author_inst": "Tsinghua University"
+      },
+      {
+        "author_name": "Jin Zhong",
+        "author_inst": "Institut Pasteur of Shanghai"
+      },
+      {
+        "author_name": "Guocai Zhong",
+        "author_inst": "Shenzhen Bay Laboratory"
+      },
+      {
+        "author_name": "Xinquan Wang",
+        "author_inst": "Tsinghua University"
+      },
+      {
+        "author_name": "Ailong Huang",
+        "author_inst": "Chongqing Medical University"
+      },
+      {
+        "author_name": "Rong Zhang",
+        "author_inst": "Fudan University Shanghai Medical College"
+      },
+      {
+        "author_name": "Qiang Ding",
+        "author_inst": "Tsinghua University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2021.09.02.458667",
     "rel_title": "SARS-CoV-2 infection activates dendritic cells via cytosolic receptors rather than extracellular TLRs",
@@ -590339,49 +589117,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2021.09.01.458647",
-    "rel_title": "High diversity in Delta variant across countries revealed via genome-wide analysis of SARS-CoV-2 beyond the Spike protein",
-    "rel_date": "2021-09-02",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.01.458647",
-    "rel_abs": "The highly contagious Delta variant of SARS-CoV-2 has emerged as the new dominant global strain, and reports of reduced effectiveness of COVID-19 vaccines against the Delta variant are highly concerning. While there has been extensive focus on understanding the amino acid mutations in the Delta variant  s Spike protein, the mutational landscape of the rest of the SARS-CoV-2 proteome (25 proteins) remains poorly understood. To this end, we performed a systematic analysis of mutations in all the SARS-CoV-2 proteins from nearly 2 million SARS-CoV-2 genomes from 176 countries/territories. Six highly-prevalent missense mutations in the viral life cycle-associated Membrane (I82T), Nucleocapsid (R203M, D377Y), NS3 (S26L), and NS7a (V82A, T120I) proteins are almost exclusive to the Delta variant compared to other variants of concern (mean prevalence across genomes: Delta = 99.74%, Alpha = 0.06%, Beta = 0.09%, Gamma = 0.22%). Furthermore, we find that the Delta variant harbors a more diverse repertoire of mutations across countries compared to the previously dominant Alpha variant (cosine similarity: meanAlpha = 0.94, S.D.Alpha = 0.05; meanDelta = 0.86, S.D.Delta = 0.1; Cohen  s dAlpha-Delta = 1.17, p-value < 0.001). Overall, our study underscores the high diversity of the Delta variant between countries and identifies a list of targetable amino acid mutations in the Delta variant  s proteome for probing the mechanistic basis of pathogenic features such as high viral loads, high transmissibility, and reduced susceptibility against neutralization by vaccines.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Pritha Ghosh",
-        "author_inst": "nference Labs"
-      },
-      {
-        "author_name": "Rohit Suratekar",
-        "author_inst": "nference Labs"
-      },
-      {
-        "author_name": "Michiel J.M. Niesen",
-        "author_inst": "nference"
-      },
-      {
-        "author_name": "Praveen Anand",
-        "author_inst": "nference"
-      },
-      {
-        "author_name": "Gregory Donadio",
-        "author_inst": "nference"
-      },
-      {
-        "author_name": "Venky Soundararajan",
-        "author_inst": "nference"
-      },
-      {
-        "author_name": "AJ Venkatakrishnan",
-        "author_inst": "nference"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "genomics"
-  },
   {
     "rel_doi": "10.1101/2021.09.01.458653",
     "rel_title": "Nanobody-Functionalized Cellulose for Capturing and Containing SARS-CoV-2",
@@ -590944,6 +589679,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "intensive care and critical care medicine"
   },
+  {
+    "rel_doi": "10.1101/2021.08.29.21262798",
+    "rel_title": "Viral loads of Delta-variant SARS-CoV2 breakthrough infections following vaccination and booster with the BNT162b2 vaccine",
+    "rel_date": "2021-09-01",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.29.21262798",
+    "rel_abs": "The BNT162b2 vaccine showed high real-life effectiveness both at preventing disease and in reducing viral loads of breakthrough infections, but coincidental with the rise of the Delta-variant SARS-CoV2, these protective effects have been decreasing, prompting a third, booster, vaccine inoculation. Here, analyzing viral loads of over 11,000 infections during the current wave in Israel, we find that even though this wave is dominated by the Delta-variant, breakthrough infections in recently vaccinated patients, still within 2 months post their second vaccine inoculation, do have lower viral loads compared to unvaccinated patients, with the extent of viral load reduction similar to pre-Delta breakthrough observations. Yet, this infectiousness protection starts diminishing for patients two months post vaccination and ultimately vanishes for patients 6 months or longer post vaccination. Encouragingly, we find that this diminishing vaccine effectiveness on breakthrough infection viral loads is restored following the booster vaccine. These results suggest that the vaccine is initially effective in reducing infectiousness of breakthrough infections even with the Delta variant, and that while this protectiveness effect declines with time it can be restored, at least temporarily, with a booster vaccine.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Matan Levine-Tiefenbrun",
+        "author_inst": "Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel"
+      },
+      {
+        "author_name": "Idan Yelin",
+        "author_inst": "Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel"
+      },
+      {
+        "author_name": "Hillel Alapi",
+        "author_inst": "Maccabitech, Maccabi Health Services, Tel Aviv, Israel"
+      },
+      {
+        "author_name": "Rachel Katz",
+        "author_inst": "Maccabitech, Maccabi Health Services, Tel Aviv, Israel"
+      },
+      {
+        "author_name": "Esma Herzel",
+        "author_inst": "Maccabitech, Maccabi Health Services, Tel Aviv, Israel"
+      },
+      {
+        "author_name": "Jacob Kuint",
+        "author_inst": "Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel"
+      },
+      {
+        "author_name": "Gabriel Chodick",
+        "author_inst": "Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel"
+      },
+      {
+        "author_name": "Sivan Gazit",
+        "author_inst": "Maccabitech, Maccabi Health Services, Tel Aviv, Israel"
+      },
+      {
+        "author_name": "Tal Patalon",
+        "author_inst": "Maccabitech, Maccabi Health Services, Tel Aviv, Israel"
+      },
+      {
+        "author_name": "Roy Kishony",
+        "author_inst": "Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.08.30.21262862",
     "rel_title": "Sex-associated differences between body mass index and SARS-CoV-2 antibody titers following the BNT162b2 vaccine among 2,435 healthcare workers in Japan",
@@ -592273,45 +591063,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.08.29.21261803",
-    "rel_title": "COVID-19 vaccine hesitancy among Algerian medical students: a cross-sectional study in five universities.",
-    "rel_date": "2021-08-31",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.29.21261803",
-    "rel_abs": "Vaccine hesitancy is a limiting factor in global efforts to contain the current pandemic, wreaking havoc on public health. As todays students are tomorrows doctors, it is critical to understand their attitudes toward the COVID-19 vaccine. To our knowledge, this study was the first national one to look into the attitudes of Algerian medical students toward the SARS-CoV-2 vaccine using an electronic convenience survey.\n\n383 medical students from five Algerian universities were included, with a mean age of 21.02. 85.37% (n=327) of respondents had not taken the COVID-19 vaccine yet and were divided into three groups; the vaccine acceptance group (n=175, 53.51%), the vaccine-hesitant group (n=75, 22.93%), and the vaccine refusal group (n=77, 23.54%).\n\nGender, age, education level, university, and previous experience with COVID-19 were not significant predictors for vaccine acceptance. The confirmed barriers to the COVID-19 vaccine concern available information, effectiveness, safety, and adverse effects.\n\nThis work highlights the need for an educational strategy about the safety and effectiveness of the COVID-19 vaccine. Medical students should be educated about the benefits of vaccination for themselves and their families and friends.\n\nThe Vaccine acceptant students influence should not be neglected with a possible ambassador role to hesitant and resistant students.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC=\"FIGDIR/small/21261803v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (59K):\norg.highwire.dtl.DTLVardef@fa156forg.highwire.dtl.DTLVardef@95676forg.highwire.dtl.DTLVardef@b9b712org.highwire.dtl.DTLVardef@a2095f_HPS_FORMAT_FIGEXP  M_FIG C_FIG",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Mohamed amine Kerdoun",
-        "author_inst": "Department of Medicine, Faculty of medical sciences, Kasdi Merbah University, Ouargla, 30000, Algeria."
-      },
-      {
-        "author_name": "Hamza Abdellah Henni",
-        "author_inst": "Laboratory of dynamic interactions and reactivity of systems, Kasdi Merbah University, Ouargla, 30000, Algeria."
-      },
-      {
-        "author_name": "Assia Yamoun",
-        "author_inst": "Department of Medicine, Faculty of medical sciences, Abdelhamid Mira University, Bejaia, 06000, Algeria."
-      },
-      {
-        "author_name": "Amine Rahmani",
-        "author_inst": "Mohamed Boudiaf Public Hospital, Ouargla, 30000, Algeria."
-      },
-      {
-        "author_name": "Rym Messaouda Kerdoun",
-        "author_inst": "Laboratory of biology and environment, Constantine 1 University, Constantine, 25000, Algeria."
-      },
-      {
-        "author_name": "Nazia Elouar",
-        "author_inst": "EPSP Bechir Mentouri, Constantine, 25000, Algeria."
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.08.26.21262647",
     "rel_title": "Spatial equity of COVID-19 vaccination services in Aotearoa",
@@ -592806,6 +591557,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.08.30.21262821",
+    "rel_title": "The impact of pausing the Oxford-AstraZeneca COVID-19 vaccine on uptake in Europe: a difference-in-differences analysis",
+    "rel_date": "2021-08-31",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.30.21262821",
+    "rel_abs": "BackgroundSeveral countries paused their rollouts of the Oxford-AstraZeneca COVID-19 vaccine in mid-March 2021 due to concerns about vaccine-induced thrombosis and thrombocytopenia. Many warned that this risked damaging public confidence during a critical period of pandemic response. This study investigated whether the pause in the use of the Oxford-AstraZeneca vaccine had an impact on subsequent vaccine uptake in European countries.\n\nMethodsWe used a difference-in-differences approach capitalizing on the fact that some countries halted their rollouts whilst others did not. A longitudinal panel was constructed for European Economic Area countries spanning 15 weeks in early 2021. Media reports were used to identify countries that paused the Oxford-AstraZeneca vaccine and the timing of this. Data on vaccine uptake were available through the European Centre for Disease Control and Prevention COVID-19 Vaccine Tracker. Difference-in-differences linear regression models controlled for key confounders that could influence vaccine uptake, and country and week fixed effects. Further models and robustness checks were performed.\n\nResultsThe panel included 28 countries, with 19 in the intervention group and 9 in the control group. Pausing the Oxford-AstraZeneca vaccine was associated with a 0.52% decrease in uptake for the first dose of a COVID-19 vaccine and a 1.49% decrease in the uptake for both doses, comparing countries that paused to those that did not. These estimates are not statistically significant (p=0.86 and 0.39 respectively). For the Oxford-AstraZeneca vaccine only, the pause was associated with a 0.56% increase in uptake for the first dose and a 0.07% decrease in uptake for both doses. These estimates are also not statistically significant (p= 0.56 and 0.51 respectively). All our findings are robust to sensitivity analyses.\n\nConclusionAs new COVID-19 vaccines emerge, regulators should be cautious to deviate from usual protocols if further investigation on clinical or epidemiological grounds is warranted.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Vageesh Jain",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Paula Lorgelly",
+        "author_inst": "University College London"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health policy"
+  },
   {
     "rel_doi": "10.1101/2021.08.30.21262666",
     "rel_title": "AZD7442 demonstrates prophylactic and therapeutic efficacy in non-human primates and extended half-life in humans",
@@ -594419,41 +593193,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.08.30.21262826",
-    "rel_title": "Analysis of alternative Covid-19 mitigation measures in school classrooms: an agent-based model of SARS-CoV-2 transmission",
-    "rel_date": "2021-08-30",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.30.21262826",
-    "rel_abs": "1.The SARS-CoV-2 epidemic continues to have major impacts on childrens education, with schools required to implement infection control measures that have led to long periods of absence and classroom closures. We have developed an agent-based epidemiological model of SARS-CoV-2 transmission that allows us to quantify projected infection patterns within primary school classrooms, and related uncertainties; the basis of our approach is a contact model constructed using random networks, informed by structured expert judgement. The effectiveness of mitigation strategies are considered in terms of effectiveness at supressing infection outbreaks and limiting pupil absence. Covid-19 infections in schools in the UK in Autumn 2020 are re-examined and the model used for forecasting infection levels in autumn 2021, as the more infectious Delta-variant was emerging and school transmission thought likely to play a major role in an incipient new wave of the epidemic. Our results were in good agreement with available data. These findings indicate that testing-based surveillance of infections in the classroom population with isolation of positive cases is a more effective mitigation measure than bubble quarantine, both for reducing transmission in primary schools and for avoiding pupil absence, even accounting for insensitivity of self-administered tests. Bubble quarantine entails large numbers of pupils being absent from school, with only modest impact on classroom infection levels. However, maintaining reduced contact rates within the classroom can have a major beneficial impact for managing Covid-19 in school settings.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Mark J Woodhouse",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Willy P Aspinall",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Stephen RJ Sparks",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Ellen Brooks Pollock",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Caroline Relton",
-        "author_inst": "University of Bristol"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health policy"
-  },
   {
     "rel_doi": "10.1101/2021.08.24.21262423",
     "rel_title": "Waning immunity of the BNT162b2 vaccine: A nationwide study from Israel",
@@ -594688,6 +593427,69 @@
     "type": "new results",
     "category": "biochemistry"
   },
+  {
+    "rel_doi": "10.1101/2021.08.27.21262721",
+    "rel_title": "Short-Term Immune Response After Inactivated SARS-CoV-2 (CoronaVac, Sinovac) And ChAdOx1 nCoV-19 (Vaxzevria, Oxford-AstraZeneca) Vaccinations in Thai Health Care Workers",
+    "rel_date": "2021-08-30",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.27.21262721",
+    "rel_abs": "BackgroundInactivated SARS-CoV-2 (CoronaVac(R),Sinovac, or SV) and ChAdOx1 nCoV-19 (Vaxzevria(R),Oxford-Astra Zeneca, or AZ) vaccines have been administered to the health care workers (HCWs) in Thailand.\n\nObjectiveTo determine the short-term immune response after the SV and AZ vaccinations in HCWs.\n\nMethodsIn this prospective cohort study, HCWs who completed a 2-dose regimen of the SV or AZ were included. Immune response was evaluated by surrogate viral neutralization test (sVNT) and anti-SARS-CoV-2 total antibody. Blood samples were analyzed at 4 and 12 weeks after the complete SV vaccination and at 4 weeks after each dose of the AZ vaccination. The primary outcome was the seroconversion rate at 4-weeks after complete immunization.\n\nResultsOverall, 185 HCWs with a median (IQR) age of 40.5(30.3-55.8) years (94 HCWs in the SV group and 91 in the AZ group) were included. At 4 weeks after completing the SV vaccination, 60.6% (95%CI:50.0-70.6%) had seroconversion evaluated by sVNT([&ge;]68%inhibition), comparable to the patients recovered from mild COVID-19 infection(69.0%), with a rapid reduction to 12.2%(95%CI:6.3-20.8) at 12 weeks. In contrast, 85.7%(95%CI:76.8-92.2%) HCWs who completed the second dose of the AZ for 4 weeks had seroconversion, comparable to the COVID-19 pneumonia patients(92.5%). When using the anti-SAR-CoV-2 total antibody level([&ge;]132 U/ml) criteria, only 71.3% HCWs in the SV group had seroconversion, compared to 100% in the AZ group.\n\nConclusionA rapid decline of short-term immune response in the HCWs after the SV vaccination indicates the need for a vaccine booster, particularly during the ongoing spreading of the SAR-CoV-2 variants of concern.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Watsamon Jantarabenjakul",
+        "author_inst": "King Chulalongkorn Memorial Hospital"
+      },
+      {
+        "author_name": "Napaporn Chantasrisawad",
+        "author_inst": "King Chulalongkorn Memorial Hospital"
+      },
+      {
+        "author_name": "Thanyawee Puthanakit",
+        "author_inst": "Faculty of Medicine, Chulalongkorn University"
+      },
+      {
+        "author_name": "Supaporn Wacharapluesadee",
+        "author_inst": "King Chulalongkorn Memorial Hospital"
+      },
+      {
+        "author_name": "Nattiya Hirankarn",
+        "author_inst": "Faculty of Medicine, Chulalongkorn University"
+      },
+      {
+        "author_name": "Vichaya Ruenjaiman",
+        "author_inst": "Faculty of Medicine, Chulalongkorn University"
+      },
+      {
+        "author_name": "Leilani Paitoonpong",
+        "author_inst": "Faculty of Medicine, Chulalongkorn University"
+      },
+      {
+        "author_name": "Gompol Suwanpimolkul",
+        "author_inst": "Faculty of Medicine, Chulalongkorn University"
+      },
+      {
+        "author_name": "Pattama Torvorapanit",
+        "author_inst": "King Chulalongkorn Memorial Hospital"
+      },
+      {
+        "author_name": "Rakchanok Pradit",
+        "author_inst": "King Chulalongkorn Memorial Hospital"
+      },
+      {
+        "author_name": "Jiratchaya Sophonphan",
+        "author_inst": "Thai Red Cross AIDS Research Centre"
+      },
+      {
+        "author_name": "OPASS PUTCHAROEN",
+        "author_inst": "Faculty of Medicine, Chulalongkorn university"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.08.28.21262543",
     "rel_title": "Antibodies anti-SARS-CoV2 time-course in patients and vaccinated subjects: an evaluation of the harmonization of two different methods",
@@ -596177,45 +594979,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "respiratory medicine"
   },
-  {
-    "rel_doi": "10.1101/2021.08.26.21261149",
-    "rel_title": "Predicted long-term impact of COVID-19 pandemic-related care delays on cancer incidence and mortality in Canada",
-    "rel_date": "2021-08-28",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.26.21261149",
-    "rel_abs": "ObjectivesThe COVID-19 pandemic has affected cancer care worldwide. This study aimed to estimate the long-term impacts of the pandemic on cancer incidence and mortality in Canada using a mathematical model.\n\nMethodsWe developed a stochastic microsimulation model to estimate the cancer care disruptions and its long-term impact on cancer incidence and mortality in Canada. The model reproduces cancer incidence, survival, and epidemiology in Canada, by using cancer incidence, stage at diagnosis and survival data from the Canadian Cancer Registries. We modeled reported declines in cancer diagnoses and treatments recorded in provincial administrative datasets from March 2020-June 2021. We assumed that diagnostic and treatment delays lead to an increased rate of death. Based on the literature, we assumed each 4-week delay in diagnosis and treatment would lead to a 6% to 50% higher rate of cancer death. Results are the median predictions of 10 stochastic simulations.\n\nFindingsThe model predicts that cancer care disruptions during the COVID-19 pandemic could lead to 21,247 (2{middle dot}0%) more cancer deaths in Canada in 2020-2030, assuming treatment capacity is recovered to 2019 pre-pandemic levels in 2021. This represents 355,172 life years lost expected due to pandemic-related diagnostic and treatment delays. The highest absolute expected excess cancer mortality was predicted in breast, lung, and colorectal cancers, and in the provinces of Ontario, Quebec, and British Columbia. Diagnostic and treatment capacity in 2021 onwards highly influenced the number of predicted cancer deaths over the next decade.\n\nInterpretationCancer care disruptions during the Covid-19 pandemic could lead to significant life loss; however, most of these could be mitigated by increasing diagnostic and treatment capacity in the post-pandemic era to address the service backlog.\n\nFundingCanadian Institutes of Health Research\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe performed a review of modeling studies predicting the impact of pandemic-induced disruptions to cancer care on cancer survival outcomes. We searched MEDLINE on 2 July 2021 for records published from 1 January 2020 with no language restrictions. Our search consisted of index keywords [Cancer AND COVID-19 AND [(delay AND diagnosis) OR (delay AND screening) OR (delay AND treatment)] AND outcomes AND modelling study]. We identified 14 studies that model the long-term effect of disruptions to cancer screening programs, diagnostic intervals, and to treatment intervals for common cancers. Most studies (9/14) assessed the impact of cancer screening disruptions but did not assume any treatment disruptions. Disruptions to cancer screening services in high income health systems were estimated to lead to small increases in cancer incidence and mortality, even with immediate resumption of screening to services after disruption periods. Fewer studies examined the impact of diagnostic referral and treatment disruptions; these are similarly predicted to lead to increases in cancer incidence and mortality, with varying impacts depending on cancer site. Due to difficulties in obtaining real-time healthcare data, previous studies have relied on assumptions regarding the duration of health care disruptions (1-, 3-, 6-, 12-, to 24-months) rather than on empirical data. All studies restricted their analysis to the impact on a single or a few cancer sites.\n\nAdded value of this studyOur stochastic microsimulation model is the first to assess the population-level impact of diagnostic and treatment disruptions on overall cancer mortality across all sites. Using Canadian cancer statistics and expert validation of treatment modalities, we constructed a model that reproduced pre-pandemic cancer mortality data. An important added value of this analysis compared to previous studies was that we were able to integrate empirical data on cancer-related procedures during the pandemic era to model disruptions to cancer care.\n\nImplications of all the available evidenceWe estimate there could be a 2{middle dot}0% increase over expected cancer mortality between 2020-2030 in Canada due to pandemic-related disruptions to diagnostic and treatment intervals. Our results identified that a 10-20% increase in cancer care service capacity over pre-pandemic levels could prevent a considerable amount of the predicted excess cancer-related deaths by reducing diagnostic and treatment backlogs. By stratifying our reported outcomes by sex, age, province, and cancer site, we provide a long-term perspective that can inform post-pandemic public health policy or aid in prioritization of patients in the event of a resurgence of COVID-19. While our model is specific to Canada, it could be applied to countries that have experienced comparable COVID-19-related healthcare disruptions.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Tal\u00eda Malag\u00f3n",
-        "author_inst": "McGill University"
-      },
-      {
-        "author_name": "Jean Hai Ein Yong",
-        "author_inst": "Canadian Partnership Against Cancer"
-      },
-      {
-        "author_name": "Parker Tope",
-        "author_inst": "McGill University"
-      },
-      {
-        "author_name": "Wilson H. Miller Jr.",
-        "author_inst": "McGill University"
-      },
-      {
-        "author_name": "Eduardo L. Franco",
-        "author_inst": "McGill University"
-      },
-      {
-        "author_name": "- McGill Task Force on the Impact of COVID-19 on Cancer Control and Care",
-        "author_inst": ""
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "oncology"
-  },
   {
     "rel_doi": "10.1101/2021.08.26.21262694",
     "rel_title": "When do we need massive computations to perform detailed COVID-19 simulations?",
@@ -596658,6 +595421,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.08.25.21262627",
+    "rel_title": "History of suicide attempts and COVID-19 infection in Veterans with schizophrenia or schizoaffective disorder: effect modification by age and obesity",
+    "rel_date": "2021-08-28",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.25.21262627",
+    "rel_abs": "ImportanceAs patients with schizophrenia or schizoaffective disorder have a high risk of suicide, and a history of suicide attempt is a strong predictor of suicide, determining whether history of suicide attempt is associated with COVID-19 in patients with schizophrenia or schizoaffective disorder has implications for suicide prevention in this patient population.\n\nObjectiveTo determine whether a history of suicide attempt is associated with COVID-19 in Veterans with schizophrenia or schizoaffective disorder.\n\nDesignCross-sectional analyses of nation-wide electronic health records (EHR).\n\nSettingUnited States Veterans Health Administration.\n\nParticipantsVeterans with a diagnosis of schizophrenia or schizoaffective disorder that received treatment at any United States Veterans Affairs Medical Center from January 1, 2020 to January 31, 2021.\n\nExposureHistory of suicide attempt.\n\nMain OutcomeAdjusted and unadjusted odds ratios (ORs) for COVID-19 positivity in suicide attempters relative to non-attempters. Adjusted analyses included age, sex, race, marital status, BMI, and a medical comorbidity score.\n\nResultsA total of 101,032 Veterans [mean age 56.67 {+/-} 13.13 years; males 91,715 (90.8%)] were included in the analyses. There were 2,703 (2.7%) suicide attempters and 719 (0.7%) patients were positive for COVID-19. There was effect modification by age and BMI in the association of history of suicide attempt with COVID-19 positivity such that the association was only significant in obese (BMI [&ge;] 30) patients and patients younger than 59 years respectively. In the entire sample, the unadjusted OR for COVID-19 positivity in attempters was 1.42 (95% CI 0.97 to 2.10) and the adjusted odds ratio was 1.90 (95% CI 1.28 to 2.80). In patients younger than 59 years, and in the obese patients respectively, history of suicide attempt was associated with COVID-positive status in unadjusted analyses [OR 3.53 (95% CI 2.10 to 5.94); OR 2.22 (95% CI 1.29 to 3.81)] and adjusted analyses [OR 3.42 (95% CI 2.02 to 5.79); OR 2.85 (95% CI 1.65 to 4.94)].\n\nConclusions and RelevanceYoung or obese suicide attempters with a diagnosis of schizophrenia or schizoaffective disorders have higher rates of COVID-19 diagnosis; due to possible long-term neuropsychiatric sequelae of infection with SARS-CoV-2, such patients should be monitored closely.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Olaoluwa O Okusaga",
+        "author_inst": "Michael E. DeBakey VA Medical Center/Baylor College of Medicine"
+      },
+      {
+        "author_name": "Rachel L Kember",
+        "author_inst": "University of Pennsylvania"
+      },
+      {
+        "author_name": "Gina M Peloso",
+        "author_inst": "Department of Biostatistics, Boston University School of Public Health"
+      },
+      {
+        "author_name": "Roseann E Peterson",
+        "author_inst": "Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University"
+      },
+      {
+        "author_name": "Marijana Vujkovic",
+        "author_inst": "University of Pennsylvania"
+      },
+      {
+        "author_name": "Brian G Mitchell",
+        "author_inst": "Michael E. DeBakey VA Medical Center/Baylor College of Medicine"
+      },
+      {
+        "author_name": "Jared Bernard",
+        "author_inst": "Michael E. DeBakey VA Medical Center/Baylor College of Medicine"
+      },
+      {
+        "author_name": "Annette Walder",
+        "author_inst": "Michael E. DeBakey VA Medical Center/Baylor College of Medicine"
+      },
+      {
+        "author_name": "Tim B Bigdeli",
+        "author_inst": "SUNY Downstate Medical Center"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "psychiatry and clinical psychology"
+  },
   {
     "rel_doi": "10.1101/2021.08.26.21262693",
     "rel_title": "Socioeconomic and comorbid factors affecting mortality and length of stay in COVID-19",
@@ -598363,93 +597177,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.08.22.21262294",
-    "rel_title": "Retrospective mortality and prevalence of SARS-CoV-2 antibodies in greater Omdurman, Sudan: a population-based cross-sectional survey",
-    "rel_date": "2021-08-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.22.21262294",
-    "rel_abs": "BackgroundEven after adjusting for the expected lower severity due to the younger age of the population, relatively low SARS-CoV-2 incidence and mortality rates have been reported throughout Africa. For investigating whether this is truly the case, we conducted a survey to estimate the COVID-19 related mortality and cumulative incidence of SARS-CoV-2 infections in Omdurman the most populated city of the tripartite metropolis Khartoum in Sudan.\n\nMethodsA retrospective, cross-sectional, mortality and seroprevalence survey was conducted in Omdurman, Sudan, from March 1, until April 10 2021. A two-stage cluster sampling method was used to investigate the death rate for the pre-pandemic (January 1, 2019-February 29, 2020) and pandemic (March 1, 2020 - day of the survey) period using questionnaires. The seroprevalence survey was performed in a subset of households and all consenting members were tested with a rapid serological test (SD-Biosensor) and a subgroup additionally with ELISA (EUROIMMUN). Fishers exact test was used to assess differences between the pre-and pandemic periods and a random effect and Bayesian latent class model to adjust for test performance.\n\nFindingsData from 27315 people (3716 households) for the entire recall period showed a 67% (95% CI 32-110) increase in death rate between the pre-pandemic (0.12 deaths/10000 people/day [95% CI 0.10-0.14]) and pandemic (0.20 [0.16-0.23]) periods. Notably, a 74% (30-133) increase in death was observed among people aged [&ge;]50 years. The adjusted seroprevalence of SARS-CoV-2 was 54.6% (95% CI 51.4-57.8). The seroprevalence was significantly associated with age, increasing up to 80.7% (71.7-89.7) for the oldest age group ([&ge;]50 years).\n\nInterpretationOur results showed a significant elevated mortality for the pandemic period with a considerable excess mortality in Omdurman, Sudan. The overall high seroprevalence indicated a different age pattern compared to other countries, with a significant increase by age.\n\nFundingMedecins Sans Frontieres",
-    "rel_num_authors": 18,
-    "rel_authors": [
-      {
-        "author_name": "Wendelin Moser",
-        "author_inst": "M\u00e9decins Sans Fronti\u00e8res, Geneva, Switzerland"
-      },
-      {
-        "author_name": "Mohammed Ahmed Hassan Fahal",
-        "author_inst": "Directorate General of Emergency and Epidemics Control, Khartoum State Ministry of Health, Khartoum, Sudan"
-      },
-      {
-        "author_name": "Elamin Abualas",
-        "author_inst": "National Public Health Laboratory, Federal Ministry of Health, Khartoum, Sudan"
-      },
-      {
-        "author_name": "Shahinaz Bedri",
-        "author_inst": "National Public Health Laboratory, Federal Ministry of Health, Khartoum, Sudan"
-      },
-      {
-        "author_name": "Mahgoub Taj Elsir",
-        "author_inst": "Khartoum State Ministry of Health, Khartoum, Sudan"
-      },
-      {
-        "author_name": "Mona Fateh El Rahman Omer Mohamed",
-        "author_inst": "Khartoum State Ministry of Health, Khartoum, Sudan"
-      },
-      {
-        "author_name": "Abdelhalim Babiker Mahmoud",
-        "author_inst": "M\u00e9decins Sans Fronti\u00e8res, Khartoum, Sudan; Faculty of Pharmacy, University of Khartoum, Khartoum, Sudan"
-      },
-      {
-        "author_name": "Amna Ismail Ibrahim Ahmad",
-        "author_inst": "M\u00e9decins Sans Fronti\u00e8res, Khartoum, Sudan"
-      },
-      {
-        "author_name": "Mohammed A. Mohammed",
-        "author_inst": "M\u00e9decins Sans Fronti\u00e8res, Khartoum, Sudan; Faculty of Medicine, University of Khartoum, Khartoum, Sudan"
-      },
-      {
-        "author_name": "Sami Altalib",
-        "author_inst": "M\u00e9decins Sans Fronti\u00e8res, Khartoum, Sudan; Faculty of Medicine, University of Khartoum, Khartoum, Sudan"
-      },
-      {
-        "author_name": "Ola Adil DafaAllah",
-        "author_inst": "M\u00e9decins Sans Fronti\u00e8res, Khartoum, Sudan; National Public Health Laboratory, Federal Ministry of Health, Khartoum, Sudan"
-      },
-      {
-        "author_name": "Salahaldin Abdallah Hmed",
-        "author_inst": "M\u00e9decins Sans Fronti\u00e8res, Khartoum, Sudan"
-      },
-      {
-        "author_name": "Andrew S. Azman",
-        "author_inst": "M\u00e9decins Sans Fronti\u00e8res, Geneva, Switzerland; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, USA; Global Health Institute, Facult"
-      },
-      {
-        "author_name": "Iza Ciglenecki",
-        "author_inst": "M\u00e9decins Sans Fronti\u00e8res, Geneva, Switzerland"
-      },
-      {
-        "author_name": "Etienne Gignoux",
-        "author_inst": "Epicentre, Paris, France"
-      },
-      {
-        "author_name": "Alan Gonz\u00e1lez",
-        "author_inst": "M\u00e9decins Sans Fronti\u00e8res, Geneva, Switzerland"
-      },
-      {
-        "author_name": "Christine Mwongera",
-        "author_inst": "M\u00e9decins Sans Fronti\u00e8res, Geneva, Switzerland"
-      },
-      {
-        "author_name": "Manuel Albela",
-        "author_inst": "M\u00e9decins Sans Fronti\u00e8res, Geneva, Switzerland"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.08.24.21262535",
     "rel_title": "Correlation between Proinflammatory cytokines and severity of COVID-19 within Palestinian Population",
@@ -598840,6 +597567,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pharmacology and therapeutics"
   },
+  {
+    "rel_doi": "10.1101/2021.08.24.21262554",
+    "rel_title": "Impact of the early stages of the COVID-19 pandemic on coverage of RMNH interventions in Ethiopia",
+    "rel_date": "2021-08-26",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.24.21262554",
+    "rel_abs": "BackgroundThe COVID-19 pandemic and response have the potential to disrupt access and use of reproductive, maternal, and newborn health (RMNH) services. Numerous initiatives aim to gauge the indirect impact of COVID-19 on RMNH.\n\nMethodsWe assessed the impact of COVID-19 on RMNH coverage in the early stages of the pandemic using panel survey data from PMA-Ethiopia. Enrolled pregnant women were surveyed 6-weeks post-birth. We compared the odds of service receipt, coverage of RMNCH service indicators, and health outcomes within the cohort of women who gave birth prior to the pandemic and the COVID-19 affected cohort. We calculated impacts nationally and by urbanicity.\n\nResultsThis dataset shows little disruption of RMNH services in Ethiopia in the initial months of the pandemic. There were no significant reductions in women seeking health services or the content of services they received for either preventative or curative interventions. In rural areas, a greater proportion of women in the COVID-19 affected cohort sought care for peripartum complications, ANC, PNC, and care for sick newborns. Significant reductions in coverage of BCG vaccination and chlorohexidine use in urban areas were observed in the COVID-19 affected cohort. An increased proportion of women in Addis Ababa reported postpartum family planning in the COVID-19 affected cohort. Despite the lack of evidence of reduced health services, the data suggest increased stillbirths in the COVID-19 affected cohort.\n\nDiscussionThe government of Ethiopias response to control the COVID-19 pandemic and ensure continuity of essential health services appears to have successfully averted most negative impacts on maternal and neonatal care. This analysis cannot address the later effects of the pandemic and may not capture more acute or geographically isolated reductions in coverage. Continued efforts are needed to ensure that essential health services are maintained and even strengthened to prevent indirect loss of life.\n\nWhat is already known?O_LICOVID-19 pandemic and response have the potential to disrupt access and use of reproductive, maternal, and neonatal health services\nC_LIO_LIAnecdotal evidence suggests some disruptions to health system staffing and resources, service access, and health campaigns in Ethiopia early in the pandemic\nC_LI\n\nWhat are the new findings?O_LIOur analysis of PMA-Ethiopia panel survey data shows little disruption of RMNH services in Ethiopia in the initial months of the pandemic\nC_LIO_LICompared to immediately prior to the pandemic we observed an increase in care-seeking in rural areas, commodity-related intervention reductions in urban areas, and an increase in postpartum family planning in Addis Ababa\nC_LIO_LIDespite the lack of evidence of a reduction in health services, the data suggest increased stillbirths in the COVID-19 affected cohort\nC_LI\n\nWhat do the new findings imply?O_LIThe government of Ethiopia successfully maintained continuity of most RMNCH services during the early stages of the COVID-19 pandemic\nC_LIO_LIContinued efforts are needed to ensure that essential health services are maintained and even strengthened to prevent indirect loss of life\nC_LI",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Emily D Carter",
+        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
+      },
+      {
+        "author_name": "Linnea Zimmerman",
+        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
+      },
+      {
+        "author_name": "Ellie Qian",
+        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
+      },
+      {
+        "author_name": "Tim Roberton",
+        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
+      },
+      {
+        "author_name": "Assefa Seme",
+        "author_inst": "Addis Ababa University"
+      },
+      {
+        "author_name": "Solomon Shiferaw",
+        "author_inst": "Addis Ababa University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.08.24.21262336",
     "rel_title": "Enhanced neutrophil extracellular trap formation in COVID-19 is inhibited by the PKC inhibitor ruboxistaurin.",
@@ -600513,61 +599279,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.08.23.21262463",
-    "rel_title": "Prioritizing COVID-19 vaccination efforts and dose allocation within Madagascar",
-    "rel_date": "2021-08-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.23.21262463",
-    "rel_abs": "BackgroundWhile mass COVID-19 vaccination programs are underway in high-income countries, limited availability of doses has resulted in few vaccines administered in low and middle income countries (LMICs). The COVID-19 Vaccines Global Access (COVAX) is a WHO-led initiative to promote vaccine access equity to LMICs and is providing many of the doses available in these settings. However, initial doses are limited and countries, such as Madagascar, need to develop prioritization schemes to maximize the benefits of vaccination with very limited supplies. There is some consensus that dose deployment should initially target health care workers, and those who are more vulnerable including older individuals. However, questions of geographic deployment remain, in particular associated with limits around vaccine access and delivery capacity in underserved communities, for example in rural areas that may also include substantial proportions of the population.\n\nMethodsTo address these questions, we developed a mathematical model of SARS-CoV-2 transmission dynamics and simulated various vaccination allocation strategies for Madagascar. Simulated strategies were based on a number of possible geographical prioritization schemes, testing sensitivity to initial susceptibility in the population, and evaluating the potential of tests for previous infection.\n\nResultsUsing cumulative deaths due to COVID-19 as the main outcome of interest, our results indicate that distributing the number of vaccine doses according to the number of elderly living in the region or according to the population size results in a greater reduction of mortality compared to distributing doses based on the reported number of cases and deaths. The benefits of vaccination strategies are diminished if the burden (and thus accumulated immunity) has been greatest in the most populous regions, but the overall strategy ranking remains comparable. If rapid tests for prior immunity may be swiftly and effectively delivered, there is potential for considerable gain in mortality averted, but considering delivery limitations modulates this.\n\nConclusionAt a subnational scale, our results support the strategy adopted by the COVAX initiative at a global scale.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Fidisoa Rasambainarivo",
-        "author_inst": "Princeton University"
-      },
-      {
-        "author_name": "Tanjona Ramiadantsoa",
-        "author_inst": "University of Fianarantsoa"
-      },
-      {
-        "author_name": "Antso Raherinandrasana",
-        "author_inst": "Ministry of Health of Madagascar"
-      },
-      {
-        "author_name": "Santatra Randrianarisoa",
-        "author_inst": "Mahaliana Labs"
-      },
-      {
-        "author_name": "Benjamin L Rice",
-        "author_inst": "Princeton University"
-      },
-      {
-        "author_name": "Michelle V. Evans",
-        "author_inst": "MIVEGEC, Universite de Montpellier, CNRS, IRD"
-      },
-      {
-        "author_name": "Benjamin ROCHE",
-        "author_inst": "IRD"
-      },
-      {
-        "author_name": "Fidiniaina Mamy Randriatsrafara",
-        "author_inst": "Ministry of Health of Madagascar"
-      },
-      {
-        "author_name": "Amy Wesolowski",
-        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
-      },
-      {
-        "author_name": "C. Jessica E. Metcalf",
-        "author_inst": "Princeton University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.08.23.21262469",
     "rel_title": "The impact of the COVID-19 pandemic on adult mental health in the UK: A rapid systematic review",
@@ -600870,6 +599581,45 @@
     "type": "new results",
     "category": "genomics"
   },
+  {
+    "rel_doi": "10.1101/2021.08.23.457411",
+    "rel_title": "Woodsmoke particulates alter expression of antiviral host response genes in human nasal epithelial cells infected with SARS-CoV-2 in a sex-dependent manner",
+    "rel_date": "2021-08-25",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.23.457411",
+    "rel_abs": "We have previously shown that exposure to particulate air pollution, both from natural and anthropogenic sources, alters gene expression in the airways and increases susceptibility to respiratory viral infection. Additionally, we have shown that woodsmoke particulates (WSP) affect responses to influenza in a sex-dependent manner. In the present study, we used human nasal epithelial cells (hNECs) from both sexes to investigate how particulate exposure could modulate gene expression in the context of SARS-CoV-2 infection. We used diesel exhaust particulate (DEP) as well as WSP derived from eucalyptus or red oak wood. HNECs were exposed to particulates at a concentration of 22 g/cm2 for 2 h then immediately infected with SARS-CoV-2 at a MOI (multiplicity of infection) of 0.5. Exposure to particulates had no significant effects on viral load recovered from infected cells. Without particulate exposure, hNECs from both sexes displayed a robust upregulation of antiviral host response genes, though the response was greater in males. However, WSP exposure before infection dampened expression of genes related to the antiviral host response by 72 h post infection. Specifically, red oak WSP downregulated IFIT1, IFITM3, IFNB1, MX1, CCL3, CCL5, CXCL11, CXCL10, and DDX58, among others. After sex stratification of these results, we found that exposure to WSP prior to SARS-CoV-2 infection downregulated anti-viral gene expression in hNECs from females more so than males. These data indicate that WSP, specifically from red oak, alter virus-induced gene expression in a sex-dependent manner and potentially suppress antiviral host defense responses following SARS-CoV-2 infection.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Stephanie A Brocke",
+        "author_inst": "University of North Carolina at Chapel Hill"
+      },
+      {
+        "author_name": "Grant T Billings",
+        "author_inst": "North Carolina State University, Raleigh NC"
+      },
+      {
+        "author_name": "Sharon A Taft-Benz",
+        "author_inst": "University of North Carolina at Chapel Hill"
+      },
+      {
+        "author_name": "Neil E Alexis",
+        "author_inst": "University of North Carolina at Chapel Hill"
+      },
+      {
+        "author_name": "Mark T Heise",
+        "author_inst": "University of North Carolina at Chapel Hill"
+      },
+      {
+        "author_name": "Ilona Jaspers",
+        "author_inst": "University of North Carolina at Chapel Hill"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "pharmacology and toxicology"
+  },
   {
     "rel_doi": "10.1101/2021.08.24.457518",
     "rel_title": "Yeast-expressed Recombinant SARS-CoV-2 Receptor Binding Domain, RBD203-N1 as a COVID-19 Protein Vaccine Candidate",
@@ -602290,121 +601040,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.08.24.457187",
-    "rel_title": "Profiling Transcription Initiation in Peripheral Leukocytes Reveals Severity-Associated Cis-Regulatory Elements in Critical COVID-19",
-    "rel_date": "2021-08-24",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.24.457187",
-    "rel_abs": "The contribution of transcription factors (TFs) and gene regulatory programs in the immune response to COVID-19 and their relationship to disease outcome is not fully understood. Analysis of genome-wide changes in transcription at both promoter-proximal and distal cis-regulatory DNA elements, collectively termed the active cistrome, offers an unbiased assessment of TF activity identifying key pathways regulated in homeostasis or disease. Here, we profiled the active cistrome from peripheral leukocytes of critically ill COVID-19 patients to identify major regulatory programs and their dynamics during SARS-CoV-2 associated acute respiratory distress syndrome (ARDS). We identified TF motifs that track the severity of COVID- 19 lung injury, disease resolution, and outcome. We used unbiased clustering to reveal distinct cistrome subsets delineating the regulation of pathways, cell types, and the combinatorial activity of TFs. We found critical roles for regulatory networks driven by stimulus and lineage determining TFs, showing that STAT and E2F/MYB regulatory programs targeting myeloid cells are activated in patients with poor disease outcomes and associated with single nucleotide genetic variants implicated in COVID-19 susceptibility. Integration with single-cell RNA-seq found that STAT and E2F/MYB activation converged in specific neutrophils subset found in patients with severe disease. Collectively we demonstrate that cistrome analysis facilitates insight into disease mechanisms and provides an unbiased approach to evaluate global changes in transcription factor activity and stratify patient disease severity.",
-    "rel_num_authors": 25,
-    "rel_authors": [
-      {
-        "author_name": "Michael Tun Yin Lam",
-        "author_inst": "UC San Diego"
-      },
-      {
-        "author_name": "Sascha H Duttke",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Mazen Faris Odish",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Hiep D Le",
-        "author_inst": "Salk Institute of Biological Studies"
-      },
-      {
-        "author_name": "Emily A Hansen",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Celina T Nguyen",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Samantha Trescott",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Roy Kim",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Shaunak Deota",
-        "author_inst": "Salk Institute of Biological Studies"
-      },
-      {
-        "author_name": "Max W Chang",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Arjun Patel",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Mark Hepokoski",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Mona Alotaibi",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Mark Rolfsen",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Katherine Perofsky",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Anna S Warden",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Sydney I Ramirez",
-        "author_inst": "La Jolla Institute for Immunology"
-      },
-      {
-        "author_name": "Jennifer M Dan",
-        "author_inst": "La Jolla Institute for Immunology"
-      },
-      {
-        "author_name": "Robert Abbott",
-        "author_inst": "La Jolla Institute for Immunology"
-      },
-      {
-        "author_name": "Shane Crotty",
-        "author_inst": "La Jolla Institute For Immunology (LJI)"
-      },
-      {
-        "author_name": "Laura E Crotty-Alexander",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Atul Malhotra",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Satchidananda Panda",
-        "author_inst": "Salk Institute of Biological Studies"
-      },
-      {
-        "author_name": "Christopher W Benner",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Nicole G Coufal",
-        "author_inst": "University of California, San Diego"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "genomics"
-  },
   {
     "rel_doi": "10.1101/2021.08.23.457434",
     "rel_title": "Structure-based design of antisense oligonucleotides that inhibit SARS-CoV-2 replication",
@@ -602771,6 +601406,49 @@
     "type": "new results",
     "category": "biophysics"
   },
+  {
+    "rel_doi": "10.1101/2021.08.19.21262310",
+    "rel_title": "Predicting SARS-CoV-2 infections for children and youth with single symptom screening",
+    "rel_date": "2021-08-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.19.21262310",
+    "rel_abs": "Symptom-based SARS-CoV-2 screening and testing decisions in children have important implications on daycare and school exclusion policies. Single symptoms account for a substantial volume of testing and disruption to in-person learning and childcare, yet their predictive value is unclear, given the clinical overlap with other circulating respiratory viruses and non-infectious etiologies. We aimed to determine the relative frequency and predictive value of single symptoms for paediatric SARS-CoV-2 infections from an Ottawa COVID-19 assessment centre from October 2020 through April 2021.\n\nOverall, 46.3% (n=10,688) of pediatric encounters were for single symptoms, and 2.7% of these tested positive. The most common presenting single symptoms were rhinorrhea (31.8%), cough (17.4%) and fever (14.0%). Among children with high-risk exposures children in each age group, the following single symptoms had a higher proportion of positive SARS-CoV-2 cases compared to no symptoms; fever and fatigue (0-4 years); fever, cough, headache, and rhinorrhea (5-12 years); fever, loss of taste or smell, headache, rhinorrhea, sore throat, and cough (13-17 years). There was no evidence that the single symptom of either rhinorrhea or cough predicted SARS-CoV-2 infections among 0-4 year olds, despite accounting for a large volume (61.1%) of single symptom presentations in the absence of high-risk exposures.\n\nSymptom-based screening needs to be responsive to changes in evidence and local factors, including the expected resurgence of other respiratory viruses following relaxation of social distancing/masking, to reduce infection-related risks in schools and daycare settings.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Richard J Webster",
+        "author_inst": "CHEO Research Institute"
+      },
+      {
+        "author_name": "Deepti Reddy",
+        "author_inst": "CHEO Research Institute"
+      },
+      {
+        "author_name": "Mary-Ann Harrison",
+        "author_inst": "CHEO Research Institute"
+      },
+      {
+        "author_name": "Ken J Farion",
+        "author_inst": "CHEO"
+      },
+      {
+        "author_name": "Jacqueline Willmore",
+        "author_inst": "Ottawa Public Health"
+      },
+      {
+        "author_name": "Michelle Foote",
+        "author_inst": "Ottawa Public Health"
+      },
+      {
+        "author_name": "Nisha Thampi",
+        "author_inst": "CHEO"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.08.18.21262258",
     "rel_title": "Immunological Insights Into the Therapeutic Roles of CD24Fc Against Severe COVID-19",
@@ -604364,105 +603042,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "nephrology"
   },
-  {
-    "rel_doi": "10.1101/2021.08.20.21262328",
-    "rel_title": "Reduced serum neutralization capacity against SARS-CoV-2 variants in a multiplex ACE2 RBD competition assay",
-    "rel_date": "2021-08-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.20.21262328",
-    "rel_abs": "As global vaccination campaigns against SARS-CoV-2 proceed, there is particular interest in the longevity of immune protection, especially with regard to increasingly infectious virus variants. Neutralizing antibodies (Nabs) targeting the receptor binding domain (RBD) of SARS-CoV-2 are promising correlates of protective immunity and have been successfully used for prevention and therapy. As SARS-CoV-2 variants of concern (VOCs) are known to affect binding to the ACE2 receptor and by extension neutralizing activity, we developed a bead-based multiplex ACE2-RBD inhibition assay (RBDCoV-ACE2) as a highly scalable, time-, cost-, and material-saving alternative to infectious live-virus neutralization tests. By mimicking the interaction between ACE2 and the RBD, this serological multiplex assay allows the simultaneous analysis of ACE2 binding inhibition to the RBDs of all SARS-CoV-2 VOCs and variants of interest (VOIs) in a single well. Following validation against a classical virus neutralization test and comparison of performance against a commercially available assay, we analyzed 266 serum samples from 168 COVID-19 patients of varying severity. ACE2 binding inhibition was reduced for ten out of eleven variants examined compared to wild-type, especially for those displaying the E484K mutation such as VOCs beta and gamma. ACE2 binding inhibition, while highly individualistic, positively correlated with IgG levels. ACE2 binding inhibition also correlated with disease severity up to WHO grade 7, after which it reduced.",
-    "rel_num_authors": 21,
-    "rel_authors": [
-      {
-        "author_name": "Daniel Junker",
-        "author_inst": "NMI"
-      },
-      {
-        "author_name": "Alex Dulovic",
-        "author_inst": "NMI"
-      },
-      {
-        "author_name": "Matthias Becker",
-        "author_inst": "NMI"
-      },
-      {
-        "author_name": "Teresa R Wagner",
-        "author_inst": "NMI"
-      },
-      {
-        "author_name": "Philipp D Kaiser",
-        "author_inst": "NMI"
-      },
-      {
-        "author_name": "Bjoern Traenkle",
-        "author_inst": "NMI"
-      },
-      {
-        "author_name": "Katharina Kienzle",
-        "author_inst": "Department Internal Medicine I, Eberhard Karls University Tuebingen"
-      },
-      {
-        "author_name": "Stefanie Bunk",
-        "author_inst": "Department Internal Medicine I, Eberhard Karls University Tuebingen"
-      },
-      {
-        "author_name": "Carlotta Str\u00fcmper",
-        "author_inst": "Department Internal Medicine I, Eberhard Karls University Tuebingen"
-      },
-      {
-        "author_name": "Helene H\u00e4berle",
-        "author_inst": "Department Internal Medicine I, Eberhard Karls University Tuebingen"
-      },
-      {
-        "author_name": "Kristina Schmauder",
-        "author_inst": "Institute for Medical Microbiology and Hygiene, University Hospital Tuebingen"
-      },
-      {
-        "author_name": "Natalia Ruetalo",
-        "author_inst": "Institute for Medical Virology and Epidemiology, University Hospital Tuebingen"
-      },
-      {
-        "author_name": "Nisar Malek",
-        "author_inst": "Department Internal Medicine I, Eberhard Karls University Tuebingen"
-      },
-      {
-        "author_name": "Karina Althaus",
-        "author_inst": "Institute for Clinical and Experimental Transfusion Medicine, University Hospital Tuebingen"
-      },
-      {
-        "author_name": "Michael Koeppen",
-        "author_inst": "Department of Anaesthesiology and Intensive Care Medicine, University Hospital Tuebingen"
-      },
-      {
-        "author_name": "Ulrich Rothbauer",
-        "author_inst": "NMI"
-      },
-      {
-        "author_name": "Juliane Walz",
-        "author_inst": "Institute for Cell Biology, University of Tuebingen"
-      },
-      {
-        "author_name": "Michael Schindler",
-        "author_inst": "University Hospital Tuebingen"
-      },
-      {
-        "author_name": "Michael Bitzer",
-        "author_inst": "Department Internal Medicine I, Eberhard Karls University Tuebingen"
-      },
-      {
-        "author_name": "Siri G\u00f6pel",
-        "author_inst": "Department Internal Medicine I, Eberhard Karls University Tuebingen"
-      },
-      {
-        "author_name": "Nicole Schneiderhan-Marra",
-        "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.08.19.21262278",
     "rel_title": "A prospective study of the protective effect of SARS-CoV-2-specific antibodies and T cells in Moscow residents",
@@ -604989,6 +603568,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.08.17.21262165",
+    "rel_title": "Interpreting Wastewater SARS-CoV-2 Results using Bayesian Analysis",
+    "rel_date": "2021-08-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.17.21262165",
+    "rel_abs": "Wastewater surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has proven a practical complement to clinical data for assessing community-scale infection trends. Clinical assays, such as the CDC-promulgated N1, N2, and N3 have been used to detect and quantify viral RNA in wastewater but, to date, have not included estimates of reliability of true positive or true negative. Bayes Theorem was applied to estimate Type I and Type II error rates for detections of the virus in wastewater. Conditional probabilities of true positive or true negative were investigated when one assay was used, or multiple assays were run concurrently. Cumulative probability analysis was used to assess the likelihood of true SARS-CoV-2 detection using multiple samples. Results demonstrate highly reliable positive (>0.86 for priors >0.25) and negative (>0.80 for priors = 0.50) results using a single assay. Using N1 and N2 concurrently caused greater reliability (>0.99 for priors <0.05) when results concurred but generated potentially counterintuitive interpretations when results were discordant. Regional wastewater surveillance data was investigated as a means of setting prior probabilities. Probability of true detection with a single marker was investigated using cumulative probability across all combinations of positive and negative results for a set of three samples. Findings using a low (0.11) and uniformed (0.50) initial prior resulted in high probabilities of detection (>0.95) even when a set of samples included one or two negative results, demonstrating the influence of high sensitivity and specificity values. Analyses presented here provide a practical framework for understanding analytical results generated by wastewater surveillance programs.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Kyle Curtis",
+        "author_inst": "Hampton Roads Sanitation District"
+      },
+      {
+        "author_name": "Raul Alexander Gonzalez",
+        "author_inst": "Hampton Roads Sanitation District"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.08.17.21262196",
     "rel_title": "Controlled evaLuation of Angiotensin Receptor Blockers for COVID-19 respIraTorY disease (CLARITY): Statistical analysis plan for a randomised controlled Bayesian adaptive sample size trial",
@@ -606202,37 +604804,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "nephrology"
   },
-  {
-    "rel_doi": "10.1101/2021.08.16.21262109",
-    "rel_title": "COVID-19 ASSOCIATED MUCORMYCOSIS: A CASE-CONTROL STUDY",
-    "rel_date": "2021-08-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.16.21262109",
-    "rel_abs": "BackgroundIndia has seen a surge in COVID-19 associated mucormycosis (CAM) cases during the second wave of the pandemic. We conducted a study to determine independent risk factors for CAM.\n\nMethodsWe performed a retrospective case control study in a tertiary care private hospital in Pune, India. Fifty-two cases of CAM were compared with 166 concurrent controls randomly selected from the COVID-19 admissions during the same time period. Association of demographic factors, comorbidities, cumulative steroid dose used (calculated as dexamethasone equivalent), maximum respiratory support required, use of injectable/oral anticoagulation, and use of aspirin with CAM was assessed by univariate and multivariate logistic regression.\n\nResultsA total of 218 subjects (52 cases; 166 controls) were studied. Any diabetes (pre-existing diabetes and new onset diabetes during COVID-19) was noted in a significantly higher proportion of cases (73{middle dot}1%, 45{middle dot}8% P<0.001) and cumulative dexamethasone dose used in cases was significantly greater (97{middle dot}72 mg vs 60 mg; P=0{middle dot}016). In a multivariate regression analysis cumulate dexamethasone dose >120 mg (OR 9{middle dot}03, confidence interval 1{middle dot}75-46{middle dot}59, P=0{middle dot}009) and any diabetes (OR 4{middle dot}78, confidence interval 1{middle dot}46-15{middle dot}65, P=0{middle dot}01) were found to be risk factors for CAM. While use of anticoagulation (OR 0{middle dot}01, confidence interval 0{middle dot}00-0{middle dot}09, P<0{middle dot}001) and use of aspirin (OR 0{middle dot}02, confidence interval 0{middle dot}01-0{middle dot}07, P<0{middle dot}001) were found to be protective against CAM.\n\nConclusionDiabetes mellitus and cumulative dose of dexamethasone greater than 120 mg (or equivalent dose of other corticosteroid) were associated with an increased risk of CAM while use of aspirin and anticoagulation were associated with a lower risk.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Dulari Gupta",
-        "author_inst": "Deenanath Mangeshkar Hospital and Research center"
-      },
-      {
-        "author_name": "Rahul Kulkarni",
-        "author_inst": "Deenanath Mangeshkar Hospital and Research Center"
-      },
-      {
-        "author_name": "Shripad Pujari",
-        "author_inst": "Deenanath Mangeshkar Hospital and Research Center"
-      },
-      {
-        "author_name": "Atul Mulay",
-        "author_inst": "Deenanath Mangeshkar Hospital and Research Center"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.08.15.21262097",
     "rel_title": "Association of COVID-19 vaccination with risks of hospitalization and mortality due to cardiovascular and other diseases: A study of the UK Biobank",
@@ -606551,6 +605122,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.08.17.21262183",
+    "rel_title": "The association between immunosuppressants use and COVID-19 adverse outcome: National COVID-19 cohort in South Korea",
+    "rel_date": "2021-08-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.17.21262183",
+    "rel_abs": "PurposeThere is uncertainty of the effect of immunosuppression, including corticosteroids, before COVID-19 infection on COVID-19 outcomes. The aim of this study was to investigate the relationship between prehospitalization immunosuppressants use (exposure), and COVID-19 patient outcomes.\n\nMethodsWe conducted a population-based retrospective cohort study using a nationwide healthcare claims database of South Korea as of May 15, 2020. Confirmed COVID-19 infection in hospitalized individuals aged 40 years or older were included for analysis. We defined exposure variable by using inpatient and outpatient prescription records of immunosuppressants from the database. Our primary outcome was a composite endpoint of all-cause death, intensive care unit (ICU) admission, and mechanical ventilation use. Inverse probability of treatment weighting (IPTW)-adjusted logistic regression analyses were used, to estimate odds ratio (OR) and 95% confidence intervals, comparing immunosuppressants users and non-users.\n\nResultsWe identified 4,349 patients, for which 1,356 were immunosuppressants users and 2,903 were non-users. Patients who used immunosuppressants were at increased odds of the primary outcome of all-cause death, ICU admission and mechanical ventilation use (IPTW OR 1.32; 95% CI: 1.06 - 1.63). Patients who used corticosteroids were at increased odds of the primary outcome (IPTW OR 1.33; 95% CI: 1.07 - 1.64).\n\nConclusionWe support the latest guidelines from the CDC, that people on immunosuppressants are at high risk of severe COVID-19 and immunocompromised people may need booster COVID-19 vaccinations.\n\nFundingYGCs work was partially supported by 2020R1G1A1A01006229 awarded by the National Research Foundation of Korea.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Hyun Joon Shin",
+        "author_inst": "Lemuel Shattuck Hospital, Massachusetts Department of Public Health"
+      },
+      {
+        "author_name": "Ronald Chow",
+        "author_inst": "Hanyang Impact Science Research Center, Seoul, South Korea"
+      },
+      {
+        "author_name": "Hyerim Noh",
+        "author_inst": "Department of Statistics, Sookmyung Women's University, Seoul, South Korea"
+      },
+      {
+        "author_name": "Jongseong Lee",
+        "author_inst": "School of Social Work, Columbia University, New York, NY, USA"
+      },
+      {
+        "author_name": "Jihui Lee",
+        "author_inst": "Department of Healthcare Policy & Research, Weill Cornell Medicine, New York, NY, USA"
+      },
+      {
+        "author_name": "Young-Geun Choi",
+        "author_inst": "Department of Statistics, Sookmyung Women's University, Seoul, South Korea"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.08.17.21262195",
     "rel_title": "COVID-19 Incidence and Hospitalization Rates are Inversely Related to Vaccination Coverage Among the 112 Most Populous Counties in the United States",
@@ -608060,81 +606670,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.08.15.21261478",
-    "rel_title": "Household transmission of SARS-CoV-2 in Norway; a prospective, longitudinal study showing increased transmissibility of the Alpha variant (B.1.1.7) compared with other variants",
-    "rel_date": "2021-08-18",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.15.21261478",
-    "rel_abs": "ObjectivesWe studied the secondary attack rate (SAR), risk factors, and precautionary practices of household transmission in a prospective, longitudinal study. We further compared transmission between the Alpha (B.1.1.7) variant and non-Variant of Concern (non-VOC) viruses.\n\nMethodsWe recruited households of 70 confirmed COVID-19 cases with 146 household contacts from May 2020 to May 2021. Participants donated biological samples 8 times over 6 weeks and answered questionnaires. Whole genome sequencing and droplet digital PCR were used to establish the SARS-CoV-2 variant and viral load.\n\nResultsSARS-CoV-2 transmission occurred in 60% of the households, and the overall SAR for household contacts was 50%. The SAR was significantly higher for the Alpha variant (78%) compared with non-VOC viruses (43%) and was associated with a higher viral load. SAR was higher in household contacts aged [&ge;]40 years (69%) than in younger contacts (40-47%), and for contacts of cases with loss of taste/smell. Children had lower viral loads and were more often asymptomatic than adults. Sleeping separately from the primary case reduced the risk of transmission.\n\nConclusionsWe found substantial household transmission, particularly for the Alpha variant. Precautionary practices seem to reduce SAR, but preventing household transmission may become difficult with more contagious variants.",
-    "rel_num_authors": 15,
-    "rel_authors": [
-      {
-        "author_name": "Cathinka Halle Julin",
-        "author_inst": "Norwegian Institute of Public Health"
-      },
-      {
-        "author_name": "Anna Hayman Robertson",
-        "author_inst": "Norwegian Institute of Public Health"
-      },
-      {
-        "author_name": "Olav Hungnes",
-        "author_inst": "Norwegian Institute of Public Health"
-      },
-      {
-        "author_name": "Gro Tunheim",
-        "author_inst": "Norwegian Institute of Public Health"
-      },
-      {
-        "author_name": "Terese Bekkevold",
-        "author_inst": "Norwegian Institute of Public Health"
-      },
-      {
-        "author_name": "Ida Laake",
-        "author_inst": "Norwegian Institute of Public Health"
-      },
-      {
-        "author_name": "Idunn Forland Aune",
-        "author_inst": "Norwegian Institute of Public Health"
-      },
-      {
-        "author_name": "Rikard Rykkvin",
-        "author_inst": "Norwegian Institute of Public Health"
-      },
-      {
-        "author_name": "Dagny Haug Dorenberg",
-        "author_inst": "Norwegian Institute of Public Health"
-      },
-      {
-        "author_name": "Kathrine Stene-Johansen",
-        "author_inst": "Norwegian Institute of Public Health"
-      },
-      {
-        "author_name": "Einar Sverre Berg",
-        "author_inst": "Norwegian Institute of Public Health"
-      },
-      {
-        "author_name": "Johanna Eva Bodin",
-        "author_inst": "Norwegian Institute of Public Health"
-      },
-      {
-        "author_name": "Fredrik Oftung",
-        "author_inst": "Norwegian Institute of Public Health"
-      },
-      {
-        "author_name": "Anneke Steens",
-        "author_inst": "Norwegian Institute of Public Health"
-      },
-      {
-        "author_name": "Lisbeth Meyer N\u00e6ss",
-        "author_inst": "Norwegian Institute of Public Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.08.13.21262052",
     "rel_title": "Lessons Learned From the Implementation of a Participant-Collected, Mail-Based SARS-CoV-2 Serological Survey in Massachusetts, USA",
@@ -608453,6 +606988,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.08.16.21262036",
+    "rel_title": "Comparison of Antibody Levels in Response to SARS-CoV-2 Infection and Vaccination Type in a Midwestern Cohort",
+    "rel_date": "2021-08-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.16.21262036",
+    "rel_abs": "We present preliminary data in an ongoing observational study reporting SARS-CoV-2 spike protein reactive antibody levels from a convenience cohort of over 250 individuals in Kansas City. We observe stable antibody levels over one year in individuals who recovered from COVID19 infection caused by SARS-CoV-2. By comparison, our data reveals even higher antibody levels from naive individuals vaccinated with Pfizer or Moderna vaccines and slightly lower levels from Johnson & Johnson (J&J) recipients. For all vaccines, inoculation after recovery resulted in higher antibody levels than vaccination alone. Responses to Pfizer and Moderna vaccines decreased over time from high initial levels but at the time of publication remain higher than those for recovered or J&J recipients. Within our limited cohort we only see slight demographic trends including higher antibody levels in recovered female vs. male individuals. Booster doses and breakthrough infections both result in rapid increases in antibody levels.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Laura Remy",
+        "author_inst": "Stowers Institute for Medical Research"
+      },
+      {
+        "author_name": "Chieri Tomomori-Sato",
+        "author_inst": "Stowers Institute for Medical Research"
+      },
+      {
+        "author_name": "Juliana Conkright-Fincham",
+        "author_inst": "Stowers Institute for Medical Research"
+      },
+      {
+        "author_name": "Leanne M Wiedemann",
+        "author_inst": "Stowers Institute for Medical Research"
+      },
+      {
+        "author_name": "Joan W Conaway",
+        "author_inst": "University of Texas Southwestern"
+      },
+      {
+        "author_name": "Jay R Unruh",
+        "author_inst": "Stowers Institute for Medical Research"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "allergy and immunology"
+  },
   {
     "rel_doi": "10.1101/2021.08.16.21262149",
     "rel_title": "Effectiveness of COVID-19 Vaccines among Incarcerated People in California State Prisons: A Retrospective Cohort Study",
@@ -609758,61 +608332,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2021.08.17.456689",
-    "rel_title": "Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant",
-    "rel_date": "2021-08-17",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.17.456689",
-    "rel_abs": "The Delta variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has outcompeted previously prevalent variants and become a dominant strain worldwide. We report here structure, function and antigenicity of its full-length spike (S) trimer in comparison with those of other variants, including Gamma, Kappa, and previously characterized Alpha and Beta. Delta S can fuse membranes more efficiently at low levels of cellular receptor ACE2 and its pseudotyped viruses infect target cells substantially faster than all other variants tested, possibly accounting for its heightened transmissibility. Mutations of each variant rearrange the antigenic surface of the N-terminal domain of the S protein in a unique way, but only cause local changes in the receptor-binding domain, consistent with greater resistance particular to neutralizing antibodies. These results advance our molecular understanding of distinct properties of these viruses and may guide intervention strategies.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Christy L. Lavine",
-        "author_inst": "Beth Israel Deaconess Medical Center"
-      },
-      {
-        "author_name": "Haisun Zhu",
-        "author_inst": "Institute for Protein Innovation/Harvard Institutes of Medicine"
-      },
-      {
-        "author_name": "Krishna Anand",
-        "author_inst": "Institute for Protein Innovation/Harvard Institutes of Medicine"
-      },
-      {
-        "author_name": "Pei Tong",
-        "author_inst": "Brigham and Womens Hospital"
-      },
-      {
-        "author_name": "Avneesh Gautam",
-        "author_inst": "Brigham and Womens Hospital"
-      },
-      {
-        "author_name": "Megan L. Mayer",
-        "author_inst": "The Harvard Cryo-EM Center for Structural Biology/Harvard Medical School"
-      },
-      {
-        "author_name": "Richard M. Walsh Jr.",
-        "author_inst": "The Harvard Cryo-EM Center for Structural Biology/Harvard Medical School"
-      },
-      {
-        "author_name": "Wei Yang",
-        "author_inst": "Institute for Protein Innovation/Harvard Institutes of Medicine"
-      },
-      {
-        "author_name": "Michael S. Seaman",
-        "author_inst": "Beth Israel Deaconess Medical Center/Harvard Medical School"
-      },
-      {
-        "author_name": "Jianming Lu",
-        "author_inst": "Codex BioSolutions, Inc."
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "biochemistry"
-  },
   {
     "rel_doi": "10.1101/2021.08.17.456606",
     "rel_title": "Pseudotyped Bat Coronavirus RaTG13 is efficiently neutralised by convalescent sera from SARS-CoV-2 infected Patients",
@@ -610295,6 +608814,97 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2021.08.15.456341",
+    "rel_title": "Infection and transmission of SARS-CoV-2 and its alpha variant in pregnant white-tailed deer",
+    "rel_date": "2021-08-16",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.15.456341",
+    "rel_abs": "SARS-CoV-2, a novel Betacoronavirus, was first reported circulating in human populations in December 2019 and has since become a global pandemic. Recent history involving SARS-like coronavirus outbreaks (SARS-CoV and MERS-CoV) have demonstrated the significant role of intermediate and reservoir hosts in viral maintenance and transmission cycles. Evidence of SARS-CoV-2 natural infection and experimental infections of a wide variety of animal species has been demonstrated, and in silico and in vitro studies have indicated that deer are susceptible to SARS-CoV-2 infection. White-tailed deer (Odocoileus virginianus) are amongst the most abundant, densely populated, and geographically widespread wild ruminant species in the United States. Human interaction with white-tailed deer has resulted in the occurrence of disease in human populations in the past. Recently, white-tailed deer fawns were shown to be susceptible to SARS-CoV-2. In the present study, we investigated the susceptibility and transmission of SARS-CoV-2 in adult white-tailed deer. In addition, we examined the competition of two SARS-CoV-2 isolates, representatives of the ancestral lineage A (SARS-CoV-2/human/USA/WA1/2020) and the alpha variant of concern (VOC) B.1.1.7 (SARS-CoV-2/human/USA/CA_CDC_5574/2020), through co-infection of white-tailed deer. Next-generation sequencing was used to determine the presence and transmission of each strain in the co-infected and contact sentinel animals. Our results demonstrate that adult white-tailed deer are highly susceptible to SARS-CoV-2 infection and can transmit the virus through direct contact as well as vertically from doe to fetus. Additionally, we determined that the alpha VOC B.1.1.7 isolate of SARS-CoV-2 outcompetes the ancestral lineage A isolate in white-tailed deer, as demonstrated by the genome of the virus shed from nasal and oral cavities from principal infected and contact animals, and from virus present in tissues of principal infected deer, fetuses and contact animals.",
+    "rel_num_authors": 19,
+    "rel_authors": [
+      {
+        "author_name": "Konner Cool",
+        "author_inst": "Kansas State University"
+      },
+      {
+        "author_name": "Natasha N. Gaudreault",
+        "author_inst": "Kansas State University"
+      },
+      {
+        "author_name": "Igor Morozov",
+        "author_inst": "Kansas State University"
+      },
+      {
+        "author_name": "Jessie D. Trujillo",
+        "author_inst": "Kansas State University"
+      },
+      {
+        "author_name": "David A. Meekins",
+        "author_inst": "Kansas State University"
+      },
+      {
+        "author_name": "Chester McDowell",
+        "author_inst": "Kansas State University"
+      },
+      {
+        "author_name": "Mariano Carossino",
+        "author_inst": "Louisiana State University"
+      },
+      {
+        "author_name": "Dashzeveg Bold",
+        "author_inst": "Kansas State University"
+      },
+      {
+        "author_name": "Taeyong Kwon",
+        "author_inst": "Kansas State University"
+      },
+      {
+        "author_name": "Velmurugan Balaraman",
+        "author_inst": "Kansas State University"
+      },
+      {
+        "author_name": "Daniel W. Madden",
+        "author_inst": "Kansas State University"
+      },
+      {
+        "author_name": "Bianca Libanori Artiaga",
+        "author_inst": "Kansas State University"
+      },
+      {
+        "author_name": "Roman M. Pogranichniy",
+        "author_inst": "Kansas State University"
+      },
+      {
+        "author_name": "Gleyder Roman Sosa",
+        "author_inst": "Kansas State University"
+      },
+      {
+        "author_name": "Jaimie Henningson",
+        "author_inst": "Kansas State University"
+      },
+      {
+        "author_name": "William C. Wilson",
+        "author_inst": "Kansas State University"
+      },
+      {
+        "author_name": "Udeni B. R. Balasuriya",
+        "author_inst": "Louisiana State University"
+      },
+      {
+        "author_name": "Adolfo Garcia-Sastre",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Juergen A Richt",
+        "author_inst": "Kansas State University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2021.08.16.456444",
     "rel_title": "A time irreversible model of nucleotide substitution for the coronavirus evolution",
@@ -611392,81 +610002,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.08.12.21261875",
-    "rel_title": "Harmony COVID-19: a ready-to-use kit, low-cost detector, and smartphone app for point-of-care SARS-CoV-2 RNA detection",
-    "rel_date": "2021-08-13",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.12.21261875",
-    "rel_abs": "RNA amplification tests allow sensitive detection of SARS-CoV-2 infection, but their complexity and cost are prohibitive for expanding COVID-19 testing. We developed \"Harmony COVID-19\", a point-of-care test using inexpensive consumables, ready-to-use reagents, and a simple device that processes up to 4 samples simultaneously. Our lyophilized reverse-transcription, loop-mediated isothermal amplification (RT-LAMP) can detect as little as 15 SARS-CoV-2 RNA copies per reaction, and it can report as early as 17 min for samples with high viral load (2 x 105 RNA copies per reaction). Analysis of RNA extracted from clinical nasal specimens (n = 101) showed 95% concordance with RT-PCR, including 100% specificity in specimens positive for other viruses and bacteria. Analysis of contrived samples in the nasal matrix showed detection of 92% or 100% in samples with [&ge;]20 or [&ge;]100 particles per reaction, respectively. Usability testing showed 95% accuracy by healthcare workers operating the test for the first time.\n\nONE SENTENCE SUMMARYHarmony COVID-19: point-of-care SARS-CoV-2 RNA detection",
-    "rel_num_authors": 15,
-    "rel_authors": [
-      {
-        "author_name": "Nuttada Panpradist",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Robert G Atkinson",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Michael Roller",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Enos Kline",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Qin Wang",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Ian T Hull",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Jack H Kotnik",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Amy Oreskovic",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Crissa Bennett",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Daniel Leon",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Victoria Lyon",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Peter D Han",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Lea M Starita",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Matthew J Thompson",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Barry R Lutz",
-        "author_inst": "University of Washington"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.08.13.21261989",
     "rel_title": "Infectious SARS-CoV-2 in Exhaled Aerosols and Efficacy of Masks During Early Mild Infection",
@@ -611833,6 +610368,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.08.11.21261732",
+    "rel_title": "COVID-19 in Connecticut institutions of higher education during the 2020-2021 academic year",
+    "rel_date": "2021-08-13",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.11.21261732",
+    "rel_abs": "BackgroundDuring the 2020-2021 academic year, many institutions of higher education reopened to residential students while pursuing strategies to mitigate the risk of SARS-CoV-2 transmission on campus. Reopening guidance emphasized PCR or antigen testing for residential students and social distancing measures to reduce the frequency of close interpersonal contact. Connecticut colleges and universities employed a variety of approaches to reopening campuses to residential students.\n\nMethodsWe used data on testing, cases, and social contact in 18 residential college and university campuses in Connecticut to characterize institutional reopening strategies and COVID-19 outcomes. We compared institutions fall 2020 COVID-19 plans, submitted to the Connecticut Department of Public Health, and analyzed contact rates and COVID-19 outcomes throughout the academic year.\n\nResultsIn census block groups containing residence halls, fall student move-in resulted in a 475% (95% CI 373%-606%) increase in average contact, and spring move-in resulted in a 561% (441%-713%) increase in average contact. The relationship between test frequency and case rate per residential student was complex: institutions that tested students infrequently detected few cases but failed to blunt transmission, while institutions that tested students more frequently detected more cases and prevented further spread. In fall 2020, each additional test per student per week was associated with a reduction of 0.0014 cases per student per week (95% CI: -0.0028, -0.000012). Residential student case rates were associated with higher case rates in the town where the school was located, but it is not possible to determine whether on-campus infections were transmitted to the broader community or vice versa.\n\nConclusionsCampus outbreaks among residential students might be avoided or mitigated by frequent testing, social distancing, and mandatory vaccination. Vaccination rates among residential students and surrounding communities may determine the necessary scale of residential testing programs and social distancing measures during the 2021-2022 academic year.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Olivia Schultes",
+        "author_inst": "Yale School of Public Health"
+      },
+      {
+        "author_name": "Victoria Clarke",
+        "author_inst": "Yale School of Public Health"
+      },
+      {
+        "author_name": "A David Paltiel",
+        "author_inst": "Yale School of Public Health"
+      },
+      {
+        "author_name": "Matthew Cartter",
+        "author_inst": "Connecticut Department of Public Health"
+      },
+      {
+        "author_name": "Lynn Sosa",
+        "author_inst": "Connecticut Department of Public Health"
+      },
+      {
+        "author_name": "Forrest W. Crawford",
+        "author_inst": "Yale School of Public Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.08.10.21261777",
     "rel_title": "Testing Denmark: A Danish nationwide surveillance study of COVID-19",
@@ -613254,57 +611828,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2021.08.12.456182",
-    "rel_title": "Conserved T-cell epitopes predicted by bioinformatics in SARS-COV-2 variants",
-    "rel_date": "2021-08-13",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.12.456182",
-    "rel_abs": "BackgroundFinding conservative T cell epitopes in the proteome of numerous variants of SARS-COV-2 is required to develop T cell activating SARS-COV-2 capable of inducing T cell responses against SARS-COV-2 variants.\n\nMethodsA computational workflow was performed to find HLA restricted CD8+ and CD4+ T cell epitopes among conserved amino acid sequences across the proteome of 474727 SARS-CoV-2 strains.\n\nResultsA batch of covserved regions in the amino acid sequences were found in the proteome of the SARS-COV-2 strains. 2852 and 847 peptides were predicted to have high binding affinity to distint HLA class I and class II molecules. Among them, 1456 and 484 peptides are antigenic. 392 and 111 of the antigenic peptides were found in the conseved amino acid sequences. Among the antigenic-conserved peptides, 6 CD8+ T cell epitopes and 7 CD4+ T cell epitopes were identifed. The T cell epitopes could be presented to T cells by high-affinity HLA molecules which are encoded by the HLA alleles with high population coverage.\n\nConclusionsThe T cell epitopes are conservative, antigenic and HLA presentable, and could be constructed into SARS-COV-2 vaccines for inducing protective T cell immunity against SARS-COV-2 and their variants.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Feiyu Lu",
-        "author_inst": "Jilin University"
-      },
-      {
-        "author_name": "Shengnan Wang",
-        "author_inst": "Jilin University"
-      },
-      {
-        "author_name": "Ying Wang",
-        "author_inst": "Jilin University"
-      },
-      {
-        "author_name": "Yunpeng Yao",
-        "author_inst": "Jilin University"
-      },
-      {
-        "author_name": "Yangeng Wang",
-        "author_inst": "Jilin University"
-      },
-      {
-        "author_name": "Shujun Liu",
-        "author_inst": "Jilin University"
-      },
-      {
-        "author_name": "Yangyang Wang",
-        "author_inst": "College of Basic Medical Sciences, Norman Bethune Health Science Center, Jilin University"
-      },
-      {
-        "author_name": "Yongli Yu",
-        "author_inst": "Jilin University"
-      },
-      {
-        "author_name": "Liying Wang",
-        "author_inst": "Jilin University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2021.08.13.456266",
     "rel_title": "Secreted SARS-CoV-2 ORF8 modulates the cytokine expression profile of human macrophages",
@@ -613855,6 +612378,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.08.12.21261970",
+    "rel_title": "A highly efficient T-cell immunoassay provides assessment of B cell help function of SARS-CoV-2 specific memory CD4+ T cells",
+    "rel_date": "2021-08-12",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.12.21261970",
+    "rel_abs": "The B cell help function of CD4+ T cells may serve as an immunologic correlate of protective adaptive immunity. The quantitative assessment of the B cell help potential of CD4+ T cells is limited by the lack of suitable antigen-specific functional assays. Here, we describe a highly efficient antigen-specific T-B co-cultures for quantitative measurement of T-dependent B cell responses. Using Mycobacterium tuberculosis specific setup, we show that early priming and activation of CD4+ T cells is important for the mutualistic collaboration between antigen-specific T and B cells, which could be achieved by supplementing the co-cultures with autologous monocytes. We further show that monocyte-derived growth factors provide the impetus for productive T-B collaboration by conferring optimal survivability in the cultured cells. This study provides first evidence of C-type lectin domain family 11 member A (CLEC11A/SCGF) as an essential growth factor for B cell survival. Importantly, we demonstrate the successful translation of monocyte supplemented T-B co-cultures in qualitative assessment of SARS-CoV-2 specific memory CD4+ T cells by quantifying several correlates of productive T-B cross-talk like plasma cell output, secreted antibody, antibody secreting cells and IL21 secreting T cells. Thus, the method described here can provides qualitative assessment of SARS-CoV-2 spike CD4+ T cells after natural infection and can be applied to assess the B cell help function of memory CD4+ T cells generated in response to COVID-19 vaccine.\n\nOne sentence summaryQualitative assessment of antigen-specific CD4+ T cells for T-dependent B cell responses.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Asgar Ansari",
+        "author_inst": "Vaccine Immunology Laboratory, National Institute of Immunology, New Delhi, 110067, India"
+      },
+      {
+        "author_name": "Shilpa Sachan",
+        "author_inst": "Vaccine Immunology Laboratory, National Institute of Immunology, New Delhi, 110067, India"
+      },
+      {
+        "author_name": "Bimal Prasad Jit",
+        "author_inst": "Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India"
+      },
+      {
+        "author_name": "Ashok Sharma",
+        "author_inst": "Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India"
+      },
+      {
+        "author_name": "Poonam Coshic",
+        "author_inst": "Department of Transfusion Medicine, All India Institute of Medical Sciences, New Delhi, 110029, India"
+      },
+      {
+        "author_name": "Alessandro Sette",
+        "author_inst": "La Jolla Institute for Immunology, La Jolla, CA, 92037, USA"
+      },
+      {
+        "author_name": "Daniela Weiskopf",
+        "author_inst": "La Jolla Institute For Allergy & Immunology"
+      },
+      {
+        "author_name": "Nimesh Gupta",
+        "author_inst": "Vaccine Immunology Laboratory, National Institute of Immunology, New Delhi, 110067, India"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "allergy and immunology"
+  },
   {
     "rel_doi": "10.1101/2021.08.12.21261974",
     "rel_title": "Data analysis of COVID-19 wave peaks in relation to latitude and temperature for multiple nations",
@@ -615648,117 +614218,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
-  {
-    "rel_doi": "10.1101/2021.08.11.21261885",
-    "rel_title": "BNT162b2 and mRNA-1273 COVID-19 vaccine effectiveness against the Delta (B.1.617.2) variant in Qatar",
-    "rel_date": "2021-08-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.11.21261885",
-    "rel_abs": "The SARS-CoV-2 Delta (B.1.617.2) variant of concern is expanding globally. Here, we assess real-world effectiveness of the BNT162b2 (Pfizer-BioNTech) and mRNA-1273 (Moderna) vaccines against this variant in the population of Qatar, using a matched test-negative, case- control study design. BNT162b2 effectiveness against any Delta infection, symptomatic or asymptomatic, was 64.2% (95% CI: 38.1-80.1%) [&ge;]14 days after the first dose and before the second dose, but was only 53.5% (95% CI: 43.9-61.4%) [&ge;]14 days after the second dose, in a population in which a large proportion of fully vaccinated persons received their second dose several months earlier. Corresponding effectiveness measures for mRNA-1273 were 79.0% (95% CI: 58.9-90.1%) and 84.8% (95% CI: 75.9-90.8%), respectively. Effectiveness against any severe, critical, or fatal COVID-19 disease due to Delta was 89.7% (95% CI: 61.0-98.1%) for BNT162b2 and 100.0% (95% CI: 41.2-100.0%) for mRNA-1273, [&ge;]14 days after the second dose. Both BNT162b2 and mRNA-1273 are highly effective in preventing Delta hospitalization and death, but less so in preventing infection, particularly for BNT162b2.",
-    "rel_num_authors": 24,
-    "rel_authors": [
-      {
-        "author_name": "Patrick Tang",
-        "author_inst": "Sidra Medicine"
-      },
-      {
-        "author_name": "Mohammad Rubayet Hasan",
-        "author_inst": "Sidra Medicine"
-      },
-      {
-        "author_name": "Hiam Chemaitelly",
-        "author_inst": "Weill Cornell Medicine-Qatar"
-      },
-      {
-        "author_name": "HADI M. YASSINE",
-        "author_inst": "Qatar University"
-      },
-      {
-        "author_name": "Fatiha Benslimane",
-        "author_inst": "Qatar University"
-      },
-      {
-        "author_name": "Hebah A. Al Khatib",
-        "author_inst": "Qatar University"
-      },
-      {
-        "author_name": "Sawsan AlMukdad",
-        "author_inst": "Weill Cornell Medicine-Qatar,"
-      },
-      {
-        "author_name": "Peter Coyle",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Houssein H. Ayoub",
-        "author_inst": "Qatar University"
-      },
-      {
-        "author_name": "Zaina Al Kanaani",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Einas Al Kuwari",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Andrew Jeremijenko",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Anvar Hassan Kaleeckal",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Ali Nizar Latif",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Riyazuddin Mohammad Shaik",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Hanan F. Abdul Rahim",
-        "author_inst": "Qatar University"
-      },
-      {
-        "author_name": "Gheyath Nasrallah",
-        "author_inst": "Qatar University"
-      },
-      {
-        "author_name": "Mohamed Ghaith Al Kuwari",
-        "author_inst": "Primary Health Care Corporation"
-      },
-      {
-        "author_name": "Hamad Eid Al Romaihi",
-        "author_inst": "Ministry of Public Health"
-      },
-      {
-        "author_name": "Adeel A Butt",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Mohamed H. Al-Thani",
-        "author_inst": "Ministry of Public Health"
-      },
-      {
-        "author_name": "Abdullatif Al Khal",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Roberto Bertollini",
-        "author_inst": "Ministry of Public Health"
-      },
-      {
-        "author_name": "Laith J Abu-Raddad",
-        "author_inst": "Weill Cornell Medicine-Qatar"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.08.10.455874",
     "rel_title": "CytokineLink: a cytokine communication map to analyse immune responses in inflammatory and infectious diseases",
@@ -616197,6 +614656,65 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2021.08.10.455737",
+    "rel_title": "Molecular mimicry between Spike and human thrombopoietin may induce thrombocytopenia in COVID-19",
+    "rel_date": "2021-08-11",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.10.455737",
+    "rel_abs": "SARS-CoV-2 causes COVID-19, a disease curiously resulting in varied symptoms and outcomes, ranging from asymptomatic to fatal. Autoimmunity due to cross-reacting antibodies resulting from molecular mimicry between viral antigens and host proteins may provide an explanation. We computationally investigated molecular mimicry between SARS-CoV-2 Spike and known epitopes. We discovered molecular mimicry hotspots in Spike and highlight two examples with tentative autoimmune potential and implications for understanding COVID-19 complications. We show that a TQLPP motif in Spike and thrombopoietin shares similar antibody binding properties. Antibodies cross-reacting with thrombopoietin may induce thrombocytopenia, a condition observed in COVID-19 patients. Another motif, ELDKY, is shared in multiple human proteins such as PRKG1 and tropomyosin. Antibodies cross-reacting with PRKG1 and tropomyosin may cause known COVID-19 complications such as blood-clotting disorders and cardiac disease, respectively. Our findings illuminate COVID-19 pathogenesis and highlight the importance of considering autoimmune potential when developing therapeutic interventions to reduce adverse reactions.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Janelle Nunez-Castilla",
+        "author_inst": "Florida International University"
+      },
+      {
+        "author_name": "Vitalii Stebliankin",
+        "author_inst": "Florida International University"
+      },
+      {
+        "author_name": "Prabin Baral",
+        "author_inst": "Florida International University"
+      },
+      {
+        "author_name": "Christian A Balbin",
+        "author_inst": "Florida International University"
+      },
+      {
+        "author_name": "Masrur Sobhan",
+        "author_inst": "Florida International University"
+      },
+      {
+        "author_name": "Trevor Cickovski",
+        "author_inst": "Florida International University"
+      },
+      {
+        "author_name": "Ananda M Mondal",
+        "author_inst": "Florida International University"
+      },
+      {
+        "author_name": "Giri Narasimhan",
+        "author_inst": "Florida International University"
+      },
+      {
+        "author_name": "Prem Chapagain",
+        "author_inst": "Florida International University"
+      },
+      {
+        "author_name": "Kalai Mathee",
+        "author_inst": "Florida International University"
+      },
+      {
+        "author_name": "Jessica Siltberg-Liberles",
+        "author_inst": "Florida International University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "bioinformatics"
+  },
   {
     "rel_doi": "10.1101/2021.08.11.455903",
     "rel_title": "Structural Differences In 3C-like protease (Mpro) From SARS-CoV and SARS-CoV-2: Molecular Insights For Drug Repurposing Against COVID-19 Revealed by Molecular Dynamics Simulations.",
@@ -617397,49 +615915,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.08.09.21261669",
-    "rel_title": "Use of compressed sensing to expedite high-throughput diagnostic testing for COVID-19 and beyond",
-    "rel_date": "2021-08-10",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.09.21261669",
-    "rel_abs": "The rapid spread of SARS-CoV-2 has placed a significant burden on public health systems to provide rapid and accurate diagnostic testing highlighting the critical need for innovative testing approaches for future pandemics. In this study, we present a novel sample pooling procedure based on compressed sensing theory to accurately identify virally infected patients at high prevalence rates utilizing an innovative viral RNA extraction process to minimize sample dilution. At prevalence rates ranging from 0-14.3%, the number of tests required to identify the infection status of all patients was reduced by 75.6% as compared to conventional testing in primary human SARS-CoV-2 nasopharyngeal swabs and a coronavirus model system. Additionally, our modified pooling and RNA extraction process minimized sample dilution which remained constant as pool sizes increased. Our use of compressed sensing can be adapted to a wide variety of diagnostic testing applications to increase throughput for routine laboratory testing as well as a means to increase testing throughput to combat future pandemics.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC=\"FIGDIR/small/21261669v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (37K):\norg.highwire.dtl.DTLVardef@473e40org.highwire.dtl.DTLVardef@1480d21org.highwire.dtl.DTLVardef@1562579org.highwire.dtl.DTLVardef@b65ace_HPS_FORMAT_FIGEXP  M_FIG C_FIG",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Kody A. Waldstein",
-        "author_inst": "University of iowa"
-      },
-      {
-        "author_name": "Jirong Yi",
-        "author_inst": "University of Iowa"
-      },
-      {
-        "author_name": "Michael Myung Cho",
-        "author_inst": "Penn State Behrend"
-      },
-      {
-        "author_name": "Raghuraman Mudumbai",
-        "author_inst": "University of Iowa"
-      },
-      {
-        "author_name": "Xiaodong Wu",
-        "author_inst": "University of Iowa"
-      },
-      {
-        "author_name": "Steven M. Varga",
-        "author_inst": "University of Iowa"
-      },
-      {
-        "author_name": "Weiyu Xu",
-        "author_inst": "University of Iowa"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.08.09.21261729",
     "rel_title": "Symptoms that predict positive COVID-19 testing and hospitalization: an analysis of 9,000 patients",
@@ -617722,6 +616197,117 @@
     "type": "new results",
     "category": "genomics"
   },
+  {
+    "rel_doi": "10.1101/2021.08.10.455627",
+    "rel_title": "An ultrapotent neutralizing bispecific antibody with broad spectrum against SARS-CoV-2 variants",
+    "rel_date": "2021-08-10",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.10.455627",
+    "rel_abs": "In spite of the successful development of effective countermeasures against Covid-19, variants have and will continue to emerge that could compromise the efficacy of currently approved neutralizing antibodies and vaccines. Consequently, novel and more efficacious agents are urgently needed. We have developed a bispecific antibody, 2022, consisting of two antibodies, 2F8 and VHH18. 2F8 was isolated from our proprietary fully synthetic human IDEAL (Intelligently Designed and Engineered Antibody Library)-VH/VL library and VHH18 is a single domain antibody isolated from IDEAL-nanobody library. 2022 was constructed by attaching VHH18 to the C-terminal of Fc of 2F8. 2022 binds two non-overlapping epitopes simultaneously on the RBD of the SARS-CoV-2 spike protein and blocks the binding of RBD to human angiotensin-converting enzyme 2 (ACE2). 2022 potently neutralizes SARS-CoV-2 and all of the variants tested in both pseudovirus and live virus assays, including variants carrying mutations known to resist neutralizing antibodies approved under EUA and that reduce the protection efficiency of current effective vaccines. The half-maximum inhibitory concentration (IC50) of 2022 is 270 pM, 30 pM, 20 pM, and 1 pM, for wild-type, alpha, beta, and delta pseudovirus, respectively. In the live virus assay, 2022 has an IC50 of 26.4 pM, 13.3 pM, and 88.6 pM, for wild-type, beta, and delta live virus, respectively. In a mouse model of SARS-CoV-2, 2022 showed strong prophylactic and therapeutic effects. A single administration of 2022 intranasal (i.n.) or intraperitoneal (i.p.) 24 hours before virus challenge completely protected all mice from bodyweight loss, as compared with up to 20% loss of bodyweight in placebo treated mice. In addition, the lung viral titers were undetectable (FRNT assay) in all mice treated with 2022 either prophylactically or therapeutically, as compared with around 1x105 pfu/g lung tissue in placebo treated mice. In summary, bispecific antibody 2022 showed potent binding and neutralizing activity across a variety of SARS-CoV-2 variants and could be an attractive weapon to combat the ongoing waves of the COVID-19 pandemic propagated mainly by variants, especially, the much more contagious delta variant.",
+    "rel_num_authors": 24,
+    "rel_authors": [
+      {
+        "author_name": "Hui Zhang",
+        "author_inst": "Bio-Thera Solutions, Guangzhou, Guangdong, China 510530"
+      },
+      {
+        "author_name": "Haohui Huang",
+        "author_inst": "Bio-Thera Solutions, Guangzhou, Guangdong, China 510530"
+      },
+      {
+        "author_name": "Rong Li",
+        "author_inst": "Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China 510080"
+      },
+      {
+        "author_name": "Lu Zhang",
+        "author_inst": "Guangzhou Customs District Technology Center, Guangzhou,Guangdong, China 510700"
+      },
+      {
+        "author_name": "Zhiwei Wang",
+        "author_inst": "Bio-Thera Solutions, Guangzhou, Guangdong, China 510530"
+      },
+      {
+        "author_name": "Jiaping Li",
+        "author_inst": "Bio-Thera Solutions, Guangzhou, Guangdong, China 510530"
+      },
+      {
+        "author_name": "Junyou Chen",
+        "author_inst": "Bio-Thera Solutions, Guangzhou, Guangdong, China 510530"
+      },
+      {
+        "author_name": "Huafei Su",
+        "author_inst": "Bio-Thera Solutions, Guangzhou, Guangdong, China 510530"
+      },
+      {
+        "author_name": "Dandan Zheng",
+        "author_inst": "Bio-Thera Solutions, Guangzhou, Guangdong, China 510530"
+      },
+      {
+        "author_name": "Ziqi Su",
+        "author_inst": "Bio-Thera Solutions, Guangzhou, Guangdong, China 510530"
+      },
+      {
+        "author_name": "Li Wang",
+        "author_inst": "Bio-Thera Solutions, Guangzhou, Guangdong, China 510530"
+      },
+      {
+        "author_name": "Chunping Deng",
+        "author_inst": "Bio-Thera Solutions, Guangzhou, Guangdong, China 510530"
+      },
+      {
+        "author_name": "shujun Pei",
+        "author_inst": "Bio-Thera Solutions, Guangzhou, Guangdong, China 510530"
+      },
+      {
+        "author_name": "Shenghua Zhu",
+        "author_inst": "Bio-Thera Solutions, Guangzhou, Guangdong, China 510530"
+      },
+      {
+        "author_name": "Chan Li",
+        "author_inst": "Bio-Thera Solutions, Guangzhou, Guangdong, China 510530"
+      },
+      {
+        "author_name": "Yaochang Yuan",
+        "author_inst": "Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China 510080"
+      },
+      {
+        "author_name": "Haitao Yue",
+        "author_inst": "Bio-Thera Solutions, Guangzhou, Guangdong, China 510530"
+      },
+      {
+        "author_name": "Yanqun Wang",
+        "author_inst": "Guangzhou Institute of Respiratory Health"
+      },
+      {
+        "author_name": "Xiaobo Li",
+        "author_inst": "Guangzhou Customs District Technology Center, Guangzhou,Guangdong, China 510700"
+      },
+      {
+        "author_name": "Cuihua Liu",
+        "author_inst": "Bio-Thera Solutions, Guangzhou, Guangdong, China 510530"
+      },
+      {
+        "author_name": "Jinchen Yu",
+        "author_inst": "Bio-Thera Solutions, Guangzhou, Guangdong, China 510530"
+      },
+      {
+        "author_name": "Hui Zhang",
+        "author_inst": "Sun Yat-sen University"
+      },
+      {
+        "author_name": "Shengfeng Li",
+        "author_inst": "Bio-Thera Solutions, Guangzhou, Guangdong, China 510530"
+      },
+      {
+        "author_name": "Xianming Huang",
+        "author_inst": "Bio-Thera Solutions, Guangzhou, Guangdong, China 510530"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2021.08.08.21257737",
     "rel_title": "Did Low Risk Perception Mediate the COVID-19 Second Wave in Bangladesh? A Cross-sectional Study on Risk Perception and Preventive Practice",
@@ -619323,53 +617909,6 @@
     "type": "new results",
     "category": "biochemistry"
   },
-  {
-    "rel_doi": "10.1101/2021.08.09.455609",
-    "rel_title": "A Systematic Comparison of Differential Analysis Methods for CyTOF Data",
-    "rel_date": "2021-08-09",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.09.455609",
-    "rel_abs": "Cytometry techniques are widely used to discover cellular characteristics at single-cell resolution. Many data analysis methods for cytometry data focus solely on identifying subpopulations via clustering and testing for differential cell abundance. For differential expression analysis of markers between conditions, only few tools exist. These tools either reduce the data distribution to medians, discarding valuable information, or have underlying assumptions that may not hold for all expression patterns.\n\nHere, we systematically evaluated existing and novel approaches for differential expression analysis on real and simulated CyTOF data. We found that methods using median marker expressions compute fast and reliable results when the data is not strongly zero-inflated. Methods using all data detect changes in strongly zero-inflated markers, but partially suffer from overprediction or cannot handle big datasets. We present a new method, CyEMD, based on calculating the Earth Movers Distance between expression distributions that can handle strong zero-inflation without being too sensitive.\n\nAdditionally, we developed CYANUS, a user-friendly R Shiny App allowing the user to analyze cytometry data with state-of-the-art tools, including well-performing methods from our comparison. A public web interface is available at https://exbio.wzw.tum.de/cyanus/.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Lis Arend",
-        "author_inst": "Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany"
-      },
-      {
-        "author_name": "Judith Bernett",
-        "author_inst": "Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany"
-      },
-      {
-        "author_name": "Quirin Manz",
-        "author_inst": "Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany"
-      },
-      {
-        "author_name": "Melissa Klug",
-        "author_inst": "Department of Internal Medicine I, School of Medicine, University hospital rechts der Isar, Technical University of Munich, Munich, Germany"
-      },
-      {
-        "author_name": "Olga Lazareva",
-        "author_inst": "Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany"
-      },
-      {
-        "author_name": "Jan Baumbach",
-        "author_inst": "Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany"
-      },
-      {
-        "author_name": "Dario Bongiovanni",
-        "author_inst": "Department of Internal Medicine I, School of Medicine, University hospital rechts der Isar, Technical University of Munich, Munich, Germany"
-      },
-      {
-        "author_name": "Markus List",
-        "author_inst": "Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "bioinformatics"
-  },
   {
     "rel_doi": "10.1101/2021.08.08.21261770",
     "rel_title": "The effect of eye protection on SARS-CoV-2 transmission: a systematic review",
@@ -619780,6 +618319,77 @@
     "type": "new results",
     "category": "pharmacology and toxicology"
   },
+  {
+    "rel_doi": "10.1101/2021.08.06.455491",
+    "rel_title": "High genetic barrier to escape from human polyclonal SARS-CoV-2 neutralizing antibodies",
+    "rel_date": "2021-08-08",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.06.455491",
+    "rel_abs": "The number and variability of the neutralizing epitopes targeted by polyclonal antibodies in SARS-CoV-2 convalescent and vaccinated individuals are key determinants of neutralization breadth and, consequently, the genetic barrier to viral escape. Using chimeric viruses and antibody-selected viral mutants, we show that multiple neutralizing epitopes, within and outside the viral receptor binding domain (RBD), are variably targeted by polyclonal plasma antibodies and coincide with sequences that are enriched for diversity in natural SARS-CoV-2 populations. By combining plasma-selected spike substitutions, we generated synthetic  polymutant spike proteins that resisted polyclonal antibody neutralization to a similar degree as currently circulating variants of concern (VOC). Importantly, by aggregating VOC-associated and plasma-selected spike substitutions into a single polymutant spike protein, we show that 20 naturally occurring mutations in SARS-CoV-2 spike are sufficient to confer near-complete resistance to the polyclonal neutralizing antibodies generated by convalescents and mRNA vaccine recipients. Strikingly however, plasma from individuals who had been infected and subsequently received mRNA vaccination, neutralized this highly resistant SARS-CoV-2 polymutant, and also neutralized diverse sarbecoviruses. Thus, optimally elicited human polyclonal antibodies against SARS-CoV-2 should be resilient to substantial future SARS-CoV-2 variation and may confer protection against future sarbecovirus pandemics.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Fabian Schmidt",
+        "author_inst": "Rockefeller University"
+      },
+      {
+        "author_name": "Yiska Weisblum",
+        "author_inst": "Rockefeller University"
+      },
+      {
+        "author_name": "Magdalena Rutkowska",
+        "author_inst": "Rockefeller University"
+      },
+      {
+        "author_name": "Daniel Poston",
+        "author_inst": "Rockefeller University"
+      },
+      {
+        "author_name": "Justin Da Silva",
+        "author_inst": "Rockefeller University"
+      },
+      {
+        "author_name": "Fengwen Zhang",
+        "author_inst": "Rockefeller University"
+      },
+      {
+        "author_name": "Eva Bednarski",
+        "author_inst": "Rockefeller University"
+      },
+      {
+        "author_name": "Alice Cho",
+        "author_inst": "Rockefeller University"
+      },
+      {
+        "author_name": "Dennis Schaefer-Babajew",
+        "author_inst": "Rockefeller University"
+      },
+      {
+        "author_name": "Christian Gaebler",
+        "author_inst": "Rockefeller University"
+      },
+      {
+        "author_name": "Marina Caskey",
+        "author_inst": "Rockefeller University"
+      },
+      {
+        "author_name": "Michel C. Nussenzweig",
+        "author_inst": "Rockefeller University"
+      },
+      {
+        "author_name": "Theodora Hatziioannou",
+        "author_inst": "Rockefeller University"
+      },
+      {
+        "author_name": "Paul D. Bieniasz",
+        "author_inst": "Rockefeller University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2021.08.04.21261547",
     "rel_title": "Deconvoluting complex correlates of COVID19 severity with local ancestry inference and viral phylodynamics: Results of a multiomic pandemic tracking strategy",
@@ -621353,33 +619963,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.08.04.21261604",
-    "rel_title": "Preliminary Analysis of Excess Mortality in India During the Covid-19 Pandemic (Update August 4, 2021).",
-    "rel_date": "2021-08-07",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.04.21261604",
-    "rel_abs": "As both testing for SARS Cov-2 and death registrations are incomplete or not yet available in many countries, the full impact of the Covid-19 pandemic is currently unknown in many world regions.\n\nWe studied the Covid-19 and all-cause mortality in 19 Indian states (combined population of 1.27 billion) with available all-cause mortality data during the pandemic for the entire state or for large cities. Excess mortality was calculated by comparison with available data from years 2015-2019. The known Covid-19 deaths reported by the Johns Hopkins University Center for Systems Science and Engineering for a state were assumed to be accurate, unless excess mortality data suggested a higher toll during the pandemic. Data from one state were not included in the final model due to anomalies.\n\nIn several regions, fewer deaths were reported in 2020 than expected. The excess mortality in Mumbai (in Maharashtra) in 2020 was 137.0 / 100K. Areas in Andhra Pradesh, Delhi, Haryana, Karnataka, Madhya Pradesh, Tamil Nadu, and Kolkata (in West Bengal), saw spikes in mortality in the spring of 2021.\n\nThe pandemic-related mortality through August 31, 2021 in 18 Indian states was estimated to be 198.7 per 100,000 population (range 146.1 to 263.8 per 100K). If these rates apply to India as a whole, then 2.69 million people (range 1.98 to 3.57 million) may have perished in India as a result of the Covid-19 pandemic by August 31, 2021.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Christopher T Leffler",
-        "author_inst": "Virginia Commonwealth University"
-      },
-      {
-        "author_name": "Joseph D. Lykins V",
-        "author_inst": "Virginia Commonwealth University"
-      },
-      {
-        "author_name": "Edward Yang",
-        "author_inst": "Virginia Commonwealth University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.08.04.21261600",
     "rel_title": "On the persistence of mental health deterioration during the COVID-19 pandemic by sex and ethnicity in the UK: evidence from Understanding Society",
@@ -621590,6 +620173,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.08.05.21261642",
+    "rel_title": "The unique evolutionary dynamics of the SARS-CoV-2 Delta variant",
+    "rel_date": "2021-08-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.05.21261642",
+    "rel_abs": "The SARS-Coronavirus-2 (SARS-CoV-2) driven pandemic was first recognized in late 2019, and the first few months of its evolution were relatively clock-like, dominated mostly by neutral substitutions. In contrast, the second year of the pandemic was punctuated by the emergence of several variants that bore evidence of dramatic evolution. Here, we compare and contrast evolutionary patterns of various variants, with a focus on the recent Delta variant. Most variants are characterized by long branches leading to their emergence, with an excess of non-synonymous substitutions occurring particularly in the Spike and Nucleocapsid proteins. In contrast, the Delta variant that is now becoming globally dominant, lacks the signature long branch, and is characterized by a step-wise evolutionary process that is ongoing. Contrary to the \"star-like\" topologies of other variants, we note the formation of several distinct clades within Delta that we denote as clades A-E. We find that sequences from the Delta D clade are dramatically increasing in frequency across different regions of the globe. Delta D is characterized by an excess of non-synonymous mutations, mostly occurring in ORF1a/b, some of which occurred in parallel in other notable variants. We conclude that the Delta surge these days is composed almost exclusively of Delta D, and discuss whether selection or random genetic drift has driven the emergence of Delta D.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Adi Stern",
+        "author_inst": "Tel-Aviv University"
+      },
+      {
+        "author_name": "Shay Fleishon",
+        "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center"
+      },
+      {
+        "author_name": "Talia Kustin",
+        "author_inst": "Tel Aviv University"
+      },
+      {
+        "author_name": "Edo Dotan",
+        "author_inst": "Tel Aviv University"
+      },
+      {
+        "author_name": "Michal Mandelboim",
+        "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center"
+      },
+      {
+        "author_name": "Oran Erster",
+        "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center"
+      },
+      {
+        "author_name": "- Israel Consortium of SARS-CoV-2 sequencing",
+        "author_inst": ""
+      },
+      {
+        "author_name": "Ella Mendelson",
+        "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center"
+      },
+      {
+        "author_name": "Orna Mor",
+        "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center"
+      },
+      {
+        "author_name": "Neta Zuckerman",
+        "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health and Sheba Medical Center"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.08.05.21259465",
     "rel_title": "Distinct age-specific SARS-CoV-2 IgG decay kinetics following natural infection",
@@ -623243,37 +621881,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2021.08.06.455406",
-    "rel_title": "Learning torus PCA based classification for multiscale RNA backbone structure correction with application to SARS-CoV-2",
-    "rel_date": "2021-08-06",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.06.455406",
-    "rel_abs": "MotivationReconstructions of structure of biomolecules, for instance via X-ray crystallography or cryo-EM frequently contain clashes of atomic centers. Correction methods are usually based on simulations approximating biophysical chemistry, making them computationally expensive and often not correcting all clashes.\n\nResultsWe propose a computationally fast data-driven statistical method yielding suites free from within-suite clashes: From such a clash free training data set, devising mode hunting after torus PCA on adaptive cutting average linkage tree clustering (MINTAGE), we learn RNA suite shapes. With classification based on multiscale structure enhancement (CLEAN), for a given clash suite we determine its neighborhood on a mesoscopic scale involving several suites. As corrected suite we propose the Frechet mean on a torus of the largest classes in this neighborhood. We validate CLEAN MINTAGE on a benchmark data set, compare it to a state of the art correction method and apply it, as proof of concept, to two exemplary suites adjacent to helical pieces of the frameshift stimulation element of SARS-CoV-2 which are difficult to reconstruct. In contrast to a recent reconstruction proposing several different structure models, CLEAN MINTAGE unanimously proposes structure corrections within the same clash free class for all suites.\n\nCode Availabilityhttps://gitlab.gwdg.de/henrik.wiechers1/clean-mintage-code",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Henrik Wiechers",
-        "author_inst": "Georg August University Goettingen"
-      },
-      {
-        "author_name": "Benjamin Eltzner",
-        "author_inst": "Max Planck Institute for Biophysical Chemistry, Goettingen"
-      },
-      {
-        "author_name": "Kanti V. Mardia",
-        "author_inst": "School of Mathematics, University of Leeds"
-      },
-      {
-        "author_name": "Stephan F. Huckemann",
-        "author_inst": "Georgia-Augusta-University, Goettingen"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "bioinformatics"
-  },
   {
     "rel_doi": "10.1101/2021.08.06.455382",
     "rel_title": "Controlled administration of aerosolized SARS-CoV-2 to K18-hACE2 transgenic mice uncouples respiratory infection and anosmia from fatal neuroinvasion",
@@ -623656,6 +622263,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.08.03.21261365",
+    "rel_title": "Population normalisation in wastewater-based epidemiology for improved understanding of SARS-CoV-2 prevalence: A multi-site study",
+    "rel_date": "2021-08-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.03.21261365",
+    "rel_abs": "This paper aims to determine whether population normalisation significantly alters the SARS-CoV-2 trends revealed by wastewater-based epidemiology, and whether it is beneficial and/or necessary to provide an understanding of prevalence from wastewater SARS-CoV-2 concentrations. It uses wastewater SARS-CoV-2 data collected from 394 sampling sites, and implements normalisation based on concentrations of a) ammoniacal nitrogen, and b) orthophosphate. Wastewater SARS-CoV-2 metrics are evaluated at a site and aggregated level against three indicators prevalence, based on positivity rates from the Office for National Statistics Coronavirus Infection Survey and test results reported by NHS Test and Trace. Normalisation is shown to have little impact on the overall trends in the wastewater SARS-CoV-2 data on average. However, significant variability between the impact of population normalisation at different sites, which is not evident from previous WBE studies focussed on a single site, is also revealed. Critically, it is demonstrated that while the impact of normalisation on SARS-CoV-2 trends is small on average, it is not reasonable to conclude that it is always insignificant. When averaged across many sites, normalisation strengthens the correlation between wastewater SARS-CoV-2 data and indicators of prevalence; however, confidence in the improvement is low. Lastly, it is noted that most data were collected during periods of national lockdown and/or local restrictions, and thus the impacts and benefits of population normalisation are expected to be higher when normal travel habits resume.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Chris Sweetapple",
+        "author_inst": "University of Exeter"
+      },
+      {
+        "author_name": "Matthew John Wade",
+        "author_inst": "Department of Health and Social Care"
+      },
+      {
+        "author_name": "Jasmine M. S. Grimsley",
+        "author_inst": "Department of Health and Social Care"
+      },
+      {
+        "author_name": "Joshua T. Bunce",
+        "author_inst": "Department of Health and Social Care"
+      },
+      {
+        "author_name": "Peter Melville-Shreeve",
+        "author_inst": "University of Exeter"
+      },
+      {
+        "author_name": "Albert Chen",
+        "author_inst": "University of Exeter"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.08.04.21261360",
     "rel_title": "Quantifying the ongoing epidemic of disability after covid-19 in the UK population aged under 35 years; secondary analysis of the ONS Infection Survey",
@@ -625605,65 +624251,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2021.08.05.455082",
-    "rel_title": "Rapid assessment of SARS-CoV-2 evolved variants using virus-like particles",
-    "rel_date": "2021-08-05",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.05.455082",
-    "rel_abs": "Newly evolved SARS-CoV-2 variants are driving ongoing outbreaks of COVID-19 around the world. Efforts to determine why these viral variants have improved fitness are limited to mutations in the viral spike (S) protein and viral entry steps using non-SARS-CoV-2 viral particles engineered to display S. Here we show that SARS-CoV-2 virus-like particles can package and deliver exogenous transcripts, enabling analysis of mutations within all structural proteins and rapid dissection of multiple steps in the viral life cycle. Identification of an RNA packaging sequence was critical for engineered transcripts to assemble together with SARS-CoV-2 structural proteins S, nucleocapsid (N), membrane (M) and envelope (E) into non-replicative SARS-CoV-2 virus-like particles (SC2-VLPs) that deliver these transcripts to ACE2- and TMPRSS2-expressing cells. Using SC2-VLPs, we tested the effect of 30 individual mutations within the S and N proteins on particle assembly and entry. While S mutations unexpectedly did not affect these steps, SC2-VLPs bearing any one of four N mutations found universally in more-transmissible viral variants (P199L, S202R, R203M and R203K) showed increased particle production and up to 10-fold more reporter transcript expression in receiver cells. Our study provides a platform for rapid testing of viral variants outside a biosafety level 3 setting and identifies viral N mutations and viral particle assembly as mechanisms to explain the increased spread of current viral variants, including Delta (N:R203M).\n\nOne-Sentence SummaryR203M substitution within SARS-CoV-2 N, found in delta variant, improves RNA packaging into virus-like particles by 10-fold.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Abdullah M. Syed",
-        "author_inst": "Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, CA, USA"
-      },
-      {
-        "author_name": "Taha Y. Taha",
-        "author_inst": "Gladstone Institute of Virology, San Francisco, CA, USA"
-      },
-      {
-        "author_name": "Mir M. Khalid",
-        "author_inst": "Gladstone Institute of Virology, San Francisco, CA, USA"
-      },
-      {
-        "author_name": "Takako Tabata",
-        "author_inst": "Gladstone Institute of Virology, San Francisco, CA, USA"
-      },
-      {
-        "author_name": "Irene P. Chen",
-        "author_inst": "Gladstone Institute of Virology, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA"
-      },
-      {
-        "author_name": "Bharath Sreekumar",
-        "author_inst": "Gladstone Institute of Virology, San Francisco, CA, USA"
-      },
-      {
-        "author_name": "Pei-Yi Chen",
-        "author_inst": "Gladstone Institute of Virology, San Francisco, CA, USA"
-      },
-      {
-        "author_name": "Jennifer M. Hayashi",
-        "author_inst": "Gladstone Institute of Virology, San Francisco, CA, USA"
-      },
-      {
-        "author_name": "Katarzyna M. Soczek",
-        "author_inst": "Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, CA, US"
-      },
-      {
-        "author_name": "Melanie Ott",
-        "author_inst": "Gladstone Institute of Virology, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, CA, USA; Department of Medicine, Uni"
-      },
-      {
-        "author_name": "Jennifer A. Doudna",
-        "author_inst": "Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA;Innovative Genomics Institute, University of California, Berkeley, CA, USA;Molecul"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2021.08.05.455040",
     "rel_title": "Virucidal activity of CPC-containing oral rinses against SARS-CoV-2 variants and are active in the presence of human saliva",
@@ -625970,6 +624557,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.08.03.21261438",
+    "rel_title": "COVID-19 impact on stroke admissions during France's first epidemic peak: an exhaustive, nationwide, observational study",
+    "rel_date": "2021-08-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.03.21261438",
+    "rel_abs": "Background and PurposeThe COVID-19 pandemic continues to have great impacts on the care of non-COVID-19 patients. This was especially true during the first epidemic peak in France, which coincided with the national lockdown (17 March 2020 to 10 May 2020). Patients with serious and urgent disease like stroke may have experienced a degradation of care, or may have been hesitant to seek healthcare during this period. The aim of this study was to identify, on a national level, whether a decrease in stroke admissions occurred in spring 2020, by analyzing the evolution of all stroke admissions in France from January 2019 to June 2020.\n\nMethodsWe conducted a nationwide cohort study using the French national database of hospital admissions (PMSI) to extract exhaustive data on all hospitalizations in France with at least one stroke diagnosis between 1 January 2019 and 30 June 2020. The primary endpoint was the difference in the slope gradients of stroke hospitalizations between pre-epidemic, epidemic peak and post-epidemic periods. Modeling was carried out using Bayesian techniques.\n\nResultsStroke hospitalizations dropped from 10 March 2020 (slope gradient: -11.70), and began to rise again from 22 March (slope gradient: 2.090) to 7 May. In total, there were 23 873 stroke admissions during the period March-April 2020, compared to 29 263 at the same period in 2019, representing a decrease of 18.42%. The percentage change was -15.63%, - 25.19%, -18.62% for ischemic strokes, transient ischemic attacks, and hemorrhagic strokes, respectively. In spatial models of French departments, the incidence of COVID-19 explained the ratio of stroke hospitalizations.\n\nConclusionsStroke hospitalizations in France experienced a decline during the first lockdown period, which cannot be explained by a sudden change in stroke incidence. This decline is therefore likely to be a direct, or indirect, result of the COVID-19 pandemic.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Cl\u00e9mence Risser",
+        "author_inst": "H\u00f4pitaux Universitaires de Strasbourg"
+      },
+      {
+        "author_name": "Pierre Tran Ba Loc",
+        "author_inst": "H\u00f4pitaux Universitaires de Strasbourg"
+      },
+      {
+        "author_name": "Florence Binder-Foucard",
+        "author_inst": "H\u00f4pitaux Universitaires de Strasbourg"
+      },
+      {
+        "author_name": "Thibaut Fabacher",
+        "author_inst": "H\u00f4pitaux Universitaires de Strasbourg"
+      },
+      {
+        "author_name": "Hassina Lefevre",
+        "author_inst": "H\u00f4pitaux Universitaires de Strasbourg"
+      },
+      {
+        "author_name": "Claire Sauvage",
+        "author_inst": "H\u00f4pitaux Universitaires de Strasbourg"
+      },
+      {
+        "author_name": "Erik Sauleau",
+        "author_inst": "H\u00f4pitaux Universitaires de Strasbourg"
+      },
+      {
+        "author_name": "Val\u00e9rie Wolff",
+        "author_inst": "H\u00f4pitaux Universitaires de Strasbourg"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "neurology"
+  },
   {
     "rel_doi": "10.1101/2021.08.02.21261509",
     "rel_title": "Sensitive and multiplexed RNA detection with Cas13 droplets and kinetic barcoding",
@@ -627271,117 +625905,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "anesthesia"
   },
-  {
-    "rel_doi": "10.1101/2021.08.02.21261465",
-    "rel_title": "Severity, criticality, and fatality of the SARS-CoV-2 Beta variant",
-    "rel_date": "2021-08-04",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.02.21261465",
-    "rel_abs": "Severity (acute-care hospitalization), criticality (ICU hospitalization), and fatality of SARS-CoV-2 Beta (B.1.351) variant was investigated through case-control studies applied to complete national cohorts of infection, disease, and death cases in Qatar. Compared to Alpha (B.1.1.7) variant, odds of progressing to severe disease were 1.24-fold (95% CI: 1.11-1.39) higher for Beta. Odds of progressing to critical disease were 1.49-fold (95% CI: 1.13-1.97) higher. Odds of COVID-19 death were 1.57-fold (95% CI: 1.03-2.43) higher. Findings highlight risks to healthcare systems, particularly to intensive care facilities and resources, with increased circulation of Beta.",
-    "rel_num_authors": 24,
-    "rel_authors": [
-      {
-        "author_name": "Laith J Abu-Raddad",
-        "author_inst": "Weill Cornell Medicine-Qatar"
-      },
-      {
-        "author_name": "Hiam Chemaitelly",
-        "author_inst": "Weill Cornell Medicine-Qatar"
-      },
-      {
-        "author_name": "Houssein H. Ayoub",
-        "author_inst": "Qatar University"
-      },
-      {
-        "author_name": "HADI M. YASSINE",
-        "author_inst": "Qatar University"
-      },
-      {
-        "author_name": "Fatiha Benslimane",
-        "author_inst": "Qatar University"
-      },
-      {
-        "author_name": "Hebah A. Al Khatib",
-        "author_inst": "Qatar University"
-      },
-      {
-        "author_name": "Patrick Tang",
-        "author_inst": "Sidra Medicine"
-      },
-      {
-        "author_name": "Mohammad Rubayet Hasan",
-        "author_inst": "Sidra Medicine"
-      },
-      {
-        "author_name": "Peter Coyle",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Sawsan AlMukdad",
-        "author_inst": "Weill Cornell Medicine-Qatar"
-      },
-      {
-        "author_name": "Zaina Al Kanaani",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Einas Al Kuwari",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Andrew Jeremijenko",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Anvar Hassan Kaleeckal",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Ali Nizar Latif",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Riyazuddin Mohammad Shaik",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Hanan F. Abdul Rahim",
-        "author_inst": "Qatar University"
-      },
-      {
-        "author_name": "Gheyath Nasrallah",
-        "author_inst": "Qatar University"
-      },
-      {
-        "author_name": "Mohamed Ghaith Al Kuwari",
-        "author_inst": "Primary Health Care Corporation"
-      },
-      {
-        "author_name": "Adeel A Butt",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Hamad Eid Al Romaihi",
-        "author_inst": "Ministry of Public Health"
-      },
-      {
-        "author_name": "Mohamed H. Al-Thani",
-        "author_inst": "Ministry of Public Health"
-      },
-      {
-        "author_name": "Abdullatif Al Khal",
-        "author_inst": "Hamad Medical Corporation"
-      },
-      {
-        "author_name": "Roberto Bertollini",
-        "author_inst": "Ministry of Public Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.08.02.21261469",
     "rel_title": "Association of chronic kidney disease, ethnicity and socioeconomic status with COVID-19 hospitalisation and mortality: a UK Biobank study",
@@ -627800,6 +626323,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.08.02.21260750",
+    "rel_title": "Hydroxychloroquine Prophylaxis against Coronavirus Disease-19: Practice Outcomes among Health-Care Workers",
+    "rel_date": "2021-08-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.02.21260750",
+    "rel_abs": "BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a rapidly emerging virus responsible for the ongoing Covid-19 pandemic with no known effective prophylaxis. We investigated whether hydroxychloroquine(HCQ) could prevent SARS CoV-2 in healthcare workers(HCW) at high-risk of exposure.\n\nMethodThis voluntary observational study for the prevention and treatment of COVID-19 was conducted at a tertiary care center, from 12th June to 12th October 2020(total 16 weeks). All consented asymptomatic HCWs of CIMS hospital were administered 400 mg HCQ twice a day on day one followed by 400 mg once weekly to be taken with meals up to 16 weeks. Data collected included OPD registration, risk assessment, medical and family history (related to COVID), physical examination and vitals, pulse oximetry, ECG (pre and post HCQ), drug adherence, side effects, adverse drug reactions.\n\nResultThe study enrolled 927 full-time, hospital-based HCWs ((including doctors, nurses, paramedical, lab technicians, sanitary workers and others), of whom 731(78.85%) initially started HCQ while 196 (21.14%) did not volunteer. The median age and weight of the study population was 27.5 years and 69.5 kg respectively. No major associated co-morbidities were present in these HCWs. There was an increased trend towards non adherence to HCQ with each proceeding week more so after week 11. Of the 731 HCWs taking HCQ a total of 167(22.8%) tested COVID positive at different intervals of time as against 30 HCW (15.3%) out of 196 not taking HCQ. The rate of COVID-19 positive was statistically significantly higher in the HCWs taking HCQ (p=0.0220; 95% CI: 1.14% to 12.94%), as compared to those not on HCQ. Thus HCQ was not prophylactically effective against COVID 19 infection. No participants in this study experienced grade 3 or 4 adverse events. No significant difference in the median of ECG changes in QTc between pre and post HCQ administration of 46 HCWs was observed.\n\nConclusionsThis clinical study did not detect a reduction in SARS CoV-2 transmission with prophylactic administration of 400 mg/HCQ in HCWs. All participants who did contract SARSCoV-2 were either asymptomatic or had mild disease courses with full recoveries. All adverse events were self-limiting and no serious cardiovascular events were reported with use of HCQ. In the absence of robust data, it seems premature to recommend HCQ as a prophylactic panacea for COVID-19.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Parloop Bhatt",
+        "author_inst": "Care Institute of Medical Sciences"
+      },
+      {
+        "author_name": "Vishva Patel",
+        "author_inst": "Care Institute of Medical Sciences"
+      },
+      {
+        "author_name": "Prachi Shah",
+        "author_inst": "Care Institute of Medical Sciences"
+      },
+      {
+        "author_name": "Keyur Parikh",
+        "author_inst": "Care Institute of Medical Sciences"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.07.30.21261274",
     "rel_title": "High parental vaccine motivation at a neighborhood-based vaccine and testing site serving a predominantly Latinx community",
@@ -629465,81 +628019,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.07.29.21261321",
-    "rel_title": "Comparison of reported main COVID-19 information sources in national and culturally and linguistically diverse communities in Australia",
-    "rel_date": "2021-08-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.29.21261321",
-    "rel_abs": "BackgroundTo manage the COVID-19 pandemic effectively, governments need clear and effective communication. This is a challenge for culturally diverse communities as groups may have different informational needs and information-seeking behaviours. In this paper we present the frequency of information sources for COVID-19 in a culturally diverse area of Sydney, Australia.\n\nMethodsThis study reports findings from two surveys. The first recruited participants across 10 languages between March 21 and July 9, 2021. The second provides a point of reference, and was an Australian, nationally-representative sample of English-speaking participants between November 4 - 18, 2020.\n\nResultsFor the survey in culturally and linguistically diverse communities, of 708 participants, mean age was 45.4 years (SE 0.78), and 51% of respondents were female. Across all language groups, 54.7% of participants used Australian official or public broadcasters to find out about COVID-19 (n=421). Australian commercial information sources (54.1%, n=417), social media (51.6%, n=397), and family and friends in Australia (32.7%, n=252) were common sources. Patterns varied substantially across language groups. In the nationally representative survey (n=2313), 67% of participants (n=1540) used Australian official or public broadcasters, with lower proportions for social media (31.9%, n=738) and friends, family or other personal sources (23.1%; n=533).\n\nConclusionAlmost 50% of participants from culturally and linguistically diverse communities did not report using Australian official or public broadcaster as main sources of information. Instead Australian commercial information sources, friends and family, overseas sources and social media were common. Though a crude comparison of the two datasets, this data can guide policy decisions for communication to different community groups. Further analysis is needed to interpret this data. Better understanding of how diverse communities seek and receive COVID-19 health information is imperative as we manage the current COVID-19 outbreak in the Sydney region.",
-    "rel_num_authors": 15,
-    "rel_authors": [
-      {
-        "author_name": "Julie Ayre",
-        "author_inst": "The University of Sydney"
-      },
-      {
-        "author_name": "Danielle M Muscat",
-        "author_inst": "The University of Sydney"
-      },
-      {
-        "author_name": "Olivia A Mac",
-        "author_inst": "The University of Sydney"
-      },
-      {
-        "author_name": "Carys Batcup",
-        "author_inst": "The University of Sydney"
-      },
-      {
-        "author_name": "Erin Cvejic",
-        "author_inst": "The University of Sydney"
-      },
-      {
-        "author_name": "Kristen Pickles",
-        "author_inst": "The University of Sydney"
-      },
-      {
-        "author_name": "Hankiz Dolan",
-        "author_inst": "The University of Sydney"
-      },
-      {
-        "author_name": "Carissa Bonner",
-        "author_inst": "The University of Sydney"
-      },
-      {
-        "author_name": "Dana Mouwad",
-        "author_inst": "Western Sydney Local Health District"
-      },
-      {
-        "author_name": "Dipti Zachariah",
-        "author_inst": "Western Sydney Local Health District"
-      },
-      {
-        "author_name": "Una Turalic",
-        "author_inst": "Nepean Blue Mountains Local Health District"
-      },
-      {
-        "author_name": "Yvonne Santalucia",
-        "author_inst": "South Western Sydney Local Health District"
-      },
-      {
-        "author_name": "Tingting Chen",
-        "author_inst": "Western Sydney Local Health District"
-      },
-      {
-        "author_name": "Gordana Vasic",
-        "author_inst": "Western Sydney Local Health District"
-      },
-      {
-        "author_name": "Kirsten J McCaffery",
-        "author_inst": "The University of Sydney"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.07.30.21261378",
     "rel_title": "Knowledge, Attitude, and Practice among the Healthcare Professionals regarding the myths on COVID-19 vaccination - Demystified.",
@@ -629858,6 +628337,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.07.29.21261314",
+    "rel_title": "Rapid comparative evaluation of SARS-CoV-2 rapid point-of-care antigen tests",
+    "rel_date": "2021-08-01",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.29.21261314",
+    "rel_abs": "BackgroundCurrently, more than 500 different AgPOCTs for SARS-CoV-2 diagnostics are on sale (July 2021), for many of which no data about sensitivity other than self-acclaimed values by the manufacturers are available. In many cases these do not reflect real-life diagnostic sensitivities. Therefore, manufacturer-independent quality checks of available AgPOCTs are needed, given the potential implications of false-negative results.\n\nObjectiveThe objective of this study was to develop a scalable approach for direct comparison of the analytical sensitivities of commercially available SARS-CoV-2 antigen point-of-care tests (AgPOCTs) in order to rapidly identify poor performing products.\n\nMethodsWe present a methodology for quick assessment of the sensitivity of SARS-CoV-2 lateral flow test stripes suitable for quality evaluation of many different products. We established reference samples with high, medium and low SARS-CoV-2 viral loads along with a SARS-CoV-2 negative control sample. Test samples were used to semi-quantitatively assess the analytical sensitivities of 32 different commercial AgPOCTs in a head-to-head comparison.\n\nResultsAmong 32 SARS-CoV-2 AgPOCTs tested, we observe sensitivity differences across a broad range of viral loads ([~]7.0*108 to [~]1.7*105 SARS-CoV-2 genome copies per ml). 23 AgPOCTs detected the Ct25 test sample ([~]1.4*106 copies/ ml), while only five tests detected the Ct28 test sample ([~]1.7*105 copies/ ml). In the low range of analytical sensitivity we found three saliva spit tests only delivering positive results for the Ct21 sample ([~]2.2*107 copies/ ml). Comparison with published data support our AgPOCT ranking. Importantly, we identified an AgPOCT offered in many local drugstores and supermarkets, which did not reliably recognize the sample with highest viral load (Ct16 test sample with [~]7.0*108 copies/ ml) leading to serious doubts in its usefulness in SARS-CoV-2 diagnostics.\n\nConclusionThe rapid sensitivity assessment procedure presented here provides useful estimations on the analytical sensitivities of 32 AgPOCTs and identified a widely-spread AgPOCT with concerningly low sensitivity.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Anna Denzler",
+        "author_inst": "Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany"
+      },
+      {
+        "author_name": "Max L. Jacobs",
+        "author_inst": "Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany"
+      },
+      {
+        "author_name": "Viktoria Witte",
+        "author_inst": "Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany"
+      },
+      {
+        "author_name": "Paul Schnitzler",
+        "author_inst": "Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany"
+      },
+      {
+        "author_name": "Claudia M. Denkinger",
+        "author_inst": "Department of Infectious Diseases, Division of Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany"
+      },
+      {
+        "author_name": "Michael Knop",
+        "author_inst": "Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.07.30.21261347",
     "rel_title": "Wastewater based surveillance system to detect SARS-CoV-2 genetic material for countries with on-site sanitation facilities: an experience from Bangladesh",
@@ -631507,97 +630025,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.07.28.21261295",
-    "rel_title": "Virological and serological kinetics of SARS-CoV-2 Delta variant vaccine-breakthrough infections: a multi-center cohort study",
-    "rel_date": "2021-07-31",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.28.21261295",
-    "rel_abs": "ObjectivesHighly effective vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been developed but variants of concerns (VOCs) with mutations in the spike protein are worrisome, especially B.1.617.2 (Delta) which has rapidly spread across the world. We aim to study if vaccination alters virological and serological kinetics in breakthrough infections.\n\nMethodsWe conducted a multi-centre retrospective cohort study of patients in Singapore who had received a licensed mRNA vaccine and been admitted to hospital with B.1.617.2 SARS-CoV-2 infection. We compared the clinical features, virological and serological kinetics (anti-nucleocapsid, anti-spike and surrogate virus neutralization titres) between fully vaccinated and unvaccinated individuals.\n\nResultsOf 218 individuals with B.1.617.2 infection, 84 had received a mRNA vaccine of which 71 were fully vaccinated, 130 were unvaccinated and 4 received a non-mRNA. Despite significantly older age in the vaccine breakthrough group, the odds of severe COVID-19 requiring oxygen supplementation was significantly lower following vaccination (adjusted odds ratio 0.07 95%CI: 0.015-0.335, p=0.001). PCR cycle threshold (Ct) values were similar between both vaccinated and unvaccinated groups at diagnosis, but viral loads decreased faster in vaccinated individuals. Early, robust boosting of anti-spike protein antibodies was observed in vaccinated patients, however, these titers were significantly lower against B.1.617.2 as compared with the wildtype vaccine strain.\n\nConclusionThe mRNA vaccines are highly effective at preventing symptomatic and severe COVID-19 associated with B.1.617.2 infection. Vaccination is associated with faster decline in viral RNA load and a robust serological response. Vaccination remains a key strategy for control of COVID-19 pandemic.",
-    "rel_num_authors": 19,
-    "rel_authors": [
-      {
-        "author_name": "Po Ying Chia",
-        "author_inst": "National Centre for Infectious Diseases, Singapore"
-      },
-      {
-        "author_name": "Sean Ong",
-        "author_inst": "National Centre for Infectious Diseases, Singapore"
-      },
-      {
-        "author_name": "Calvin J Chiew",
-        "author_inst": "Ministry of Health, Singapore"
-      },
-      {
-        "author_name": "Li Wei Ang",
-        "author_inst": "National Centre for Infectious Diseases, Singapore"
-      },
-      {
-        "author_name": "Jean-marc Gilbert Chavatte",
-        "author_inst": "National Centre for Infectious Diseases, Singapore"
-      },
-      {
-        "author_name": "Tze Minn Mak",
-        "author_inst": "National Centre for Infectious Diseases, Singapore"
-      },
-      {
-        "author_name": "Lin Cui",
-        "author_inst": "National Centre for Infectious Diseases, Singapore"
-      },
-      {
-        "author_name": "Shirin Kalimuddin",
-        "author_inst": "Singapore General Hospital, Singapore"
-      },
-      {
-        "author_name": "Wan Ni Chia",
-        "author_inst": "Duke-NUS Medical School, National University of Singapore, Singapore"
-      },
-      {
-        "author_name": "Chee Wah Tan",
-        "author_inst": "Duke-NUS Medical School, National University of Singapore, Singapore"
-      },
-      {
-        "author_name": "Louis Yi Ann Chai",
-        "author_inst": "National University Health System, Singapore"
-      },
-      {
-        "author_name": "Seow Yen Tan",
-        "author_inst": "Changi General Hospital, Singapore"
-      },
-      {
-        "author_name": "Shuwei Zheng",
-        "author_inst": "Sengkang General Hospital, Singapore"
-      },
-      {
-        "author_name": "Raymong Tzer Pin Lin",
-        "author_inst": "National Centre for Infectious Diseases, Singapore"
-      },
-      {
-        "author_name": "Linfa Wang",
-        "author_inst": "Duke-NUS Medical School, National University of Singapore, Singapore"
-      },
-      {
-        "author_name": "Yee-Sin Leo",
-        "author_inst": "National Centre for Infectious Diseases, Singapore"
-      },
-      {
-        "author_name": "Vernon J Lee",
-        "author_inst": "Ministry of Health, Singapore"
-      },
-      {
-        "author_name": "David .Chien Lye",
-        "author_inst": "National Centre for Infectious Diseases, Singapore"
-      },
-      {
-        "author_name": "Barnaby Edward Young",
-        "author_inst": "National Centre for Infectious Diseases, Singapore"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.07.28.21261276",
     "rel_title": "Emerging and Continuing Trends in Opioid Overdose Decedent Characteristics during COVID-19",
@@ -632048,6 +630475,81 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.07.29.21261156",
+    "rel_title": "Performance of Immunoglobulin G Serology on Finger Prick Capillary Dried Blood Spot Samples to Measure SARS-CoV-2 Humoral Immunogenicity",
+    "rel_date": "2021-07-31",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.29.21261156",
+    "rel_abs": "ImportanceMeasuring humoral immunogenicity of Severe Acute Respiratory Syndrome Coronavirus 2 vaccines and finding population-level correlates of protection against coronavirus disease presents an immediate challenge to public health practitioners.\n\nObjectiveTo study the diagnostic accuracy and predictive value of finger prick capillary dried blood spot samples tested using an anti-immunoglobulin G (IgG) serology assay to measure SARS-CoV-2 seropositivity and the humoral immunogenicity of COVID-19 vaccination.\n\nDesign, Setting and ParticipantsThis cross-sectional study enrolled participants (n= 644) who had paired DBS and serum samples collected by finger prick and venipuncture, respectively, in British Columbia, Canada between January 12th, 2020 and May 21st, 2021. Samples were tested by a multiplex electrochemiluminescence assay for SARS-CoV-2 anti-Spike (S), -Nucleocapsid (N) and -receptor binding domain (RBD) IgG reactivity using a Meso Scale Discovery (MSD) platform. Additionally, unpaired DBS samples (n= 6,706) that were collected in the province during the same time period were included for analysis of SARS-CoV-2 anti-N IgG reactivity.\n\nExposureCollection of a capillary dried blood spot by finger prick alone or paired with serum by venipuncture.\n\nOutcomeHumoral immune response to SARS-CoV-2 measured by detection of anti-S, -N or - RBD IgG.\n\nResultsIn comparison to a paired-serum reference, dried blood spot samples possess a sensitivity of 80% (95% CI: 61%-91%) and specificity of 97% (95% CI: 95%-98%). Receiver operator characteristic curve analysis (ROC) found that participant DBS samples tested for anti-SARS-CoV-2 IgG by MSD V-PLEX COVID-19 Coronavirus Panel 2 assay accurately classify SARS-CoV-2 seroconversion at an 88% percent rate, AUC= 88% (95% CI: 81%-96%). Modelling found that a dried blood spot-based testing approach has a high positive predictive value (98% [95% CI: 98%-99%]) in a theoretical population with seventy-five percent COVID-19 vaccine coverage. At lower vaccine coverages of fifteen and forty-five percent, the tests positive predictive value decreased, and the negative predictive value increased.\n\nConclusionWe demonstrate that dried blood spot collected samples, when tested using an electrochemiluminescence assay, provide a valid alternative to traditional venipuncture and should be considered to reliably detect SARS-CoV-2 seropositivity.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhat is the diagnostic accuracy and predictive value of immunoglobulin G serology on finger prick capillary dried blood spot samples to measure SARS-CoV-2 humoral immunogenicity?\n\nFindingsIn comparison to a paired-serum reference, dried blood spot samples tested for anti-SARS-CoV-2 IgG possess a sensitivity of 80% (95% CI: 61%-91%) and specificity of 97% (95% CI: 95%-98%). Dried blood spot testing has a positive predictive value of 98% (95% CI: 98%-99%) when modelled in a theoretical population with COVID-19 vaccine coverage of seventy-five percent.\n\nMeaningDried blood spot samples have equal diagnostic accuracy to serum collected by venipuncture when tested by electrochemiluminescence assay and should be considered to reliably detect SARS-CoV-2 seropositivity.",
+    "rel_num_authors": 15,
+    "rel_authors": [
+      {
+        "author_name": "Aidan M Nikiforuk",
+        "author_inst": "The University of British Columbia"
+      },
+      {
+        "author_name": "Brynn McMillan",
+        "author_inst": "The University of British Columbia"
+      },
+      {
+        "author_name": "Sofia R Bartlett",
+        "author_inst": "The University of British Columbia"
+      },
+      {
+        "author_name": "Ana Citlali Marquez",
+        "author_inst": "The University of British Columbia"
+      },
+      {
+        "author_name": "Tamara Pidduck",
+        "author_inst": "BCCDC"
+      },
+      {
+        "author_name": "Jesse Kustra",
+        "author_inst": "BCCDC"
+      },
+      {
+        "author_name": "David M Goldfarb",
+        "author_inst": "Children's and Women's Health Centre of British Columbia"
+      },
+      {
+        "author_name": "Vilte Barakauskas",
+        "author_inst": "The University of British Columbia"
+      },
+      {
+        "author_name": "Graham Sinclair",
+        "author_inst": "The University of British Columbia"
+      },
+      {
+        "author_name": "David M Patrick",
+        "author_inst": "The University of British Columbia"
+      },
+      {
+        "author_name": "Manish Sadarangani",
+        "author_inst": "The University of British Columbia"
+      },
+      {
+        "author_name": "Gina S Ogilvie",
+        "author_inst": "University of British Columbia"
+      },
+      {
+        "author_name": "Muhammad Morshed",
+        "author_inst": "The University of British Columbia"
+      },
+      {
+        "author_name": "Inna Sekirov",
+        "author_inst": "The University of British Columbia"
+      },
+      {
+        "author_name": "Agatha N Jassem",
+        "author_inst": "The Univeristy of British Columbia"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.07.29.21261196",
     "rel_title": "Prospective examination of mental health in university students during the COVID-19 pandemic",
@@ -633269,61 +631771,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.07.26.21261107",
-    "rel_title": "Association between COVID-19 infection rates by region and implementation of non-pharmaceutical interventions: A cross-sectional study in Japan",
-    "rel_date": "2021-07-30",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.26.21261107",
-    "rel_abs": "BackgroundDuring a pandemic, non-pharmaceutical interventions (NPIs) play an important role in protecting oneself from infection and preventing the spread of infection to others. There are large regional differences in COVID-19 infection rates in Japan. We hypothesized that the local infection incidence may affect adherence to individual NPIs.\n\nMethodsThis cross-sectional study was conducted online among full-time workers in Japan in December 2020. Data from a total of 27,036 participants were analyzed. The questionnaire asked the respondents to identify their habits regarding seven well-known NPIs.\n\nResultsCompared to the region with the lowest infection rate, the odds ratios for the region with the highest infection rate were 1.24 (p<0.001) for wearing a mask in public, 1.08 (p=0.157) for washing hands after using the bathroom, 1.17 (p=0.031) for disinfecting hands with alcohol sanitizers when entering indoors, 1.54 (p<0.001) for gargling when returning home, 1.45 (p<0.001) for ventilating the room, 1.33 (p<0.001) for disinfecting or washing hands after touching frequently touched surfaces, and 1.32 (p<0.001) for carrying alcohol sanitizers when outdoors. Five of the seven NPIs showed statistically significant trends across regional infection levels, the two exceptions being wearing a mask in public and washing hands after using the bathroom. Multivariate adjustment did not change these trends.\n\nConclusionsThis study found that NPIs were more prevalent in regions with higher incidence rates of COVID-19 in Japanese workers. The findings suggest that the implementation of NPIs was influenced not only by personal attributes but also by contextual effects of the local infection level.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Tomomi Anan",
-        "author_inst": "University of Occupational and Environmental Health, Japan"
-      },
-      {
-        "author_name": "Tomohiro Ishimaru",
-        "author_inst": "University of Occupational and Environmental Health, Japan"
-      },
-      {
-        "author_name": "Ayako Hino",
-        "author_inst": "University of Occupational and Environmental Health, Japan"
-      },
-      {
-        "author_name": "Tomohisa Nagata",
-        "author_inst": "University of Occupational and Environmental Health, Japan"
-      },
-      {
-        "author_name": "Seiichiro Tateishi",
-        "author_inst": "University of Occupational and Environmental Health, Japan"
-      },
-      {
-        "author_name": "Mayumi Tsuji",
-        "author_inst": "University of Occupational and Environmental Health, Japan"
-      },
-      {
-        "author_name": "Akira Ogami",
-        "author_inst": "University of Occupational and Environmental Health, Japan"
-      },
-      {
-        "author_name": "Shinya Matsuda",
-        "author_inst": "University of Occupational and Environmental Health, Japan"
-      },
-      {
-        "author_name": "Yoshihisa Fujino",
-        "author_inst": "University of Occupational and Environmental Health, Japan"
-      },
-      {
-        "author_name": "- for the CORoNaWork project",
-        "author_inst": ""
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.07.27.21261237",
     "rel_title": "Correlates of Neutralizing/SARS-CoV-2-S1-binding Antibody Response with Adverse Effects and Immune Kinetics in BNT162b2-Vaccinated Individuals",
@@ -633630,6 +632077,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
+  {
+    "rel_doi": "10.1101/2021.07.26.21261162",
+    "rel_title": "Diagnostic performance of a novel digital immunoassay (RapidTesta SARS-CoV-2): a prospective observational study with 1,127 nasopharyngeal samples",
+    "rel_date": "2021-07-30",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.26.21261162",
+    "rel_abs": "IntroductionDigital immunoassays are generally regarded as superior tests for the detection of infectious disease pathogens, but there have been insufficient data concerning SARS-CoV-2 immunoassays.\n\nMethodsWe prospectively evaluated a novel digital immunoassay (RapidTesta SARS-CoV-2). Two nasopharyngeal samples were simultaneously collected for antigen tests and RT-PCR. Real-time RT-PCR for SARS-CoV-2, using a method developed by the National Institute of Infectious Diseases, Japan, served as the reference RT-PCR method.\n\nResultsDuring the study period, 1,127 nasopharyngeal samples (symptomatic patients: 802, asymptomatic patients: 325) were evaluated. For digital immunoassay antigen tests, the sensitivity was 78.3% (95% CI: 67.3%-87.1%) and the specificity was 97.6% (95% CI: 96.5%-98.5%). When technicians visually analyzed the antigen test results, the sensitivity was 71.6% (95% CI: 59.9%-81.5%) and the specificity was 99.2% (95% CI: 98.5%-99.7%). Among symptomatic patients, the sensitivity was 89.4% (95% CI; 76.9%-96.5%) with digital immunoassay antigen tests, and 85.1% (95% CI; 71.7%-93.8%) with visually analyzed the antigen test, respectively.\n\nConclusionsThe findings indicated that RapidTesta SARS-CoV-2 analysis with the DIA device had sufficient analytical performance for the detection of SARS-CoV-2 in nasopharyngeal samples. When positive DIA results are recorded without a visually recognizable red line at the positive line location on the test cassette, additional RT-PCR evaluation should be performed.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Hiromichi Suzuki",
+        "author_inst": "Department of Infectious Diseases, Faculty of Medicine, University of Tsukuba"
+      },
+      {
+        "author_name": "Yusaku Akashi",
+        "author_inst": "Division of Infectious Diseases, Department of Medicine, Tsukuba Medical Center Hospital"
+      },
+      {
+        "author_name": "Atsuo Ueda",
+        "author_inst": "Department of Clinical Laboratory, Tsukuba Medical Center Hospital"
+      },
+      {
+        "author_name": "Yoshihiko Kiyasu",
+        "author_inst": "Department of Infectious Diseases, University of Tsukuba Hospital"
+      },
+      {
+        "author_name": "Yuto Takeuchi",
+        "author_inst": "Department of Infectious Diseases, University of Tsukuba Hospital"
+      },
+      {
+        "author_name": "Yuta Maehara",
+        "author_inst": "Sekisui Medical Co., Ltd. Research & Development Division"
+      },
+      {
+        "author_name": "Yasushi Ochiai",
+        "author_inst": "Sekisui Medical Co., Ltd. Research & Development Division"
+      },
+      {
+        "author_name": "Shinya Okuyama",
+        "author_inst": "Sekisui Medical Co., Ltd. Research & Development Division"
+      },
+      {
+        "author_name": "Shigeyuki Notake",
+        "author_inst": "Department of Clinical Laboratory, Tsukuba Medical Center Hospital"
+      },
+      {
+        "author_name": "Koji Nakamura",
+        "author_inst": "Department of Clinical Laboratory, Tsukuba Medical Center Hospital"
+      },
+      {
+        "author_name": "Hiroichi Ishikawa",
+        "author_inst": "Department of Respiratory Medicine, Tsukuba Medical Center Hospital"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.07.29.454385",
     "rel_title": "3D printed cobalt-chromium-molybdenum porous superalloy with superior antiviral activity",
@@ -635083,77 +633589,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.07.27.21261116",
-    "rel_title": "Tolerability, safety and immunogenicity of intradermal delivery of a fractional dose mRNA -1273 SARS-CoV-2 vaccine in healthy adults as a dose sparing strategy",
-    "rel_date": "2021-07-28",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.27.21261116",
-    "rel_abs": "BackgroundThere is an urgent need for fair and equitable access to safe and effective vaccines to end the COVID-19 pandemic. Shortages in reagents and vaccines are a major challenge, as well as limited knowledge on dose response relationship with mRNA COVID-19 vaccines. We explored intradermal fractional dose administration of a mRNA SARS-CoV-2/COVID-19 vaccine as a potential dose-sparing strategy.\n\nMethodsWe conducted a proof-of-concept, dose-escalation, open-label, randomised-controlled vaccine trial (IDSCOVA) in healthy adults aged 18-30 years. To test initial safety, ten participants received 10 {micro}g mRNA-1273 vaccine through intradermal injection at day 1 and 29. Following a favourable safety review, thirty participants were 1:1 randomised to receive 20 {micro}g mRNA-1273 either intradermally or intramuscularly. The primary endpoint was tolerability and safety. The secondary endpoint was seroconversion and specific IgG concentration against SARS-CoV-2 spike S1 and Receptor Binding Domain (RBD) after the second dose at day 43. We compared results to two historical cohorts of non-hospitalised COVID-19 patients and vaccinated individuals.\n\nFindingsThirty-eight of forty included participants (median age 25 years) completed the study. There were no serious adverse events. Self-reported local adverse reactions after intradermal delivery were mild, both in the 10 {micro}g and the 20 {micro}g group. In the higher dose group, systemic adverse reactions were more common, but still well tolerated. All 38 participants mounted substantially higher IgG-anti-S1 and IgG-anti-RBD concentrations at day 43 than COVID-19 controls. At day 43, anti-S1 (95% CI) was 1,696 (1,309-2,198) BAU/mL for the 10 {micro}g intradermal group, 1,406 (953{middle dot}5-2,074) BAU/mL for the 20 {micro}g intramuscular group and 2,057 (1,421-2,975) BAU/mL for the 20 {micro}g intradermal group. Anti-S1 was 107{middle dot}2 (63-182{middle dot}2) BAU/mL for the convalescent plasma control group and 1,558 (547{middle dot}8-4,433) BAU/mL for the individuals vaccinated with 100 {micro}g mRNA-1273.\n\nInterpretationIntradermal administration of 10 {micro}g and 20 {micro}g mRNA-1273 vaccine was well tolerated and safe, and resulted in a robust antibody response. Intradermal vaccination has the potential to be deployed for vaccine dose-sparing.\n\nFundingThe trial was supported by crowdfunding (Wake Up to Corona).",
-    "rel_num_authors": 14,
-    "rel_authors": [
-      {
-        "author_name": "Geert V.T. Roozen",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Manon Prins",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Rob van Binnendijk",
-        "author_inst": "Rijksinstituut voor Volksgezondheid en Milieu"
-      },
-      {
-        "author_name": "Gerco den",
-        "author_inst": "National Institute for Public Health and the Environment"
-      },
-      {
-        "author_name": "Vincent Kuiper",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Corine Prins",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Jacqueline J Janse",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Annelieke C Kruithof",
-        "author_inst": "Centre for Human Drug Research"
-      },
-      {
-        "author_name": "Mariet C.W. Feltkamp",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Marjan Kuijer",
-        "author_inst": "National Institute for Public Health and the Environment"
-      },
-      {
-        "author_name": "Frits R Roosendaal",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Meta Roestenberg",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Leo G Visser",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Anna H.E. Roukens",
-        "author_inst": "Leiden University Medical Center"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.07.25.21261066",
     "rel_title": "SARS-CoV-2 Antibody Response in Patients Undergoing Kidney Transplantation",
@@ -635784,6 +634219,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.07.26.21261130",
+    "rel_title": "Vaccine effectiveness when combining the ChAdOx1 vaccine as the first dose with an mRNA COVID-19 vaccine as the second dose",
+    "rel_date": "2021-07-28",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.26.21261130",
+    "rel_abs": "BackgroundThe recommendations in several countries to stop using the ChAdOx1 vaccine has led to vaccine programs combining different vaccine types, which necessitates new knowledge on vaccine effectiveness (VE). In this study, we aimed to estimate the VE when combining the ChAdOx1 vaccine as the first dose and an mRNA vaccine as the second dose.\n\nMethodsThis nationwide population-based cohort study estimated VE against SARS-CoV-2 infection, all-cause and COVID-19 related hospitalization and death after receiving the ChAdOx1 vaccine as the first dose followed by an mRNA vaccine as the second dose. VE estimates were obtained using a Cox regression with calendar time as underlying time and adjusted for sex, age, comorbidity, heritage and hospital admission. Information on all individuals was extracted and linked from high-quality national registries.\n\nResultsA total of 5,542,079 individuals were included in the analyses (97.6% of the total Danish population). A total of 144,360 were vaccinated with the ChAdOx1 vaccine as the first dose and of these 136,551 individuals received an mRNA vaccine as the second dose. A total of 1,691,464 person-years and 83,034 cases of SARS-CoV-2 infection were included. The VE against SARS-CoV-2 infection when combining the ChAdOx1 and an mRNA vaccine was 88% (95% confidence interval (CI): 83; 92) 14 days after the second dose and onwards. There were no COVID-19 related hospitalizations and deaths among the individuals vaccinated with the combination of the ChAdOx1 and an mRNA vaccine during the study period.\n\nConclusionIn conclusion, this study found a reduction in the risk of SARS-CoV-2 infection when combining the ChAdOx1 and an mRNA vaccine, compared with unvaccinated individuals. This is similar to the VE of two doses of an mRNA vaccine. Longer follow-up time is needed to confirm vaccine induced protection against severe events, such as COVID-19 related hospitalization and death.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Mie Agermose Gram",
+        "author_inst": "Statens Serum Institut"
+      },
+      {
+        "author_name": "Hanne-Dorthe Emborg",
+        "author_inst": "Statens Serum Institut"
+      },
+      {
+        "author_name": "Ida Rask Moustsen-Helms",
+        "author_inst": "Statens Serum Institut"
+      },
+      {
+        "author_name": "Jens Nielsen",
+        "author_inst": "Statens Serum Institut"
+      },
+      {
+        "author_name": "Anne Katrine Bj\u00f8rkholt S\u00f8rensen",
+        "author_inst": "Statens Serum Institut"
+      },
+      {
+        "author_name": "Palle Valentiner-Branth",
+        "author_inst": "Statens Serum Institut"
+      },
+      {
+        "author_name": "Astrid Blicher Schelde",
+        "author_inst": "Statens Serum Institut"
+      },
+      {
+        "author_name": "Katrine Finderup Nielsen",
+        "author_inst": "Statens Serum Institut"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.07.22.21260837",
     "rel_title": "Streptococcus pneumoniae colonisation associates with impaired adaptive immune responses against SARS-CoV-2",
@@ -637193,45 +635675,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.07.23.21261041",
-    "rel_title": "The impact of large mobile air purifiers on aerosol concentration in classrooms and the reduction of airborne transmission of SARS-CoV-2",
-    "rel_date": "2021-07-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.23.21261041",
-    "rel_abs": "In the wake of the SARS-CoV-2 pandemic, an increased risk of infection by virus-containing aerosols indoors is assumed. Especially in schools, the duration of stay is long and the number of people in the rooms is large, increasing the risk of infection. This problem particularly affects schools without pre-installed ventilation systems that are equipped with filters and/or operate with fresh air. Here, the aerosol concentration is reduced by natural ventilation. In this context, we are investigating the effect of large mobile air purifiers (AP) with HEPA filters on particle concentration and their suitability for classroom use in a primary school in Germany. The three tested APs differ significantly in their air outlet characteristics. Measurements of the number of particles, the particle size distribution, and the CO2 concentration were carried out in the classroom with students (April/May 2021) and with an aerosol generator without students. In this regard, the use of APs leads to a substantial reduction in aerosol particles. At the same time, the three APs are found to have differences in their particle decay rate, noise level, and flow velocity. In addition to the measurements, the effect of various influencing parameters on the potential inhaled particle dose was investigated using a calculation model. The parameters considered include the duration of stay, particle concentration in exhaled air, respiratory flow rate, virus lifetime, ventilation interval, ventilation efficiency, AP volumetric flow, as well as room size. Based on the resulting effect diagrams, significant recommendations can be derived for reducing the risk of infection from virus-laden aerosols. Finally, the measurements were compared to computational fluid dynamics (CFD) modeling, as such tools can aid the optimal placement and configuration of APs and can be used to study the effect of the spread of aerosols from a source in the classroom.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Finn F. Duill",
-        "author_inst": "Otto-von-Guericke-Universitaet Magdeburg, Germany"
-      },
-      {
-        "author_name": "Florian Schulz",
-        "author_inst": "Otto-von-Guericke-Universitaet Magdeburg, Germany"
-      },
-      {
-        "author_name": "Aman Jain",
-        "author_inst": "Otto-von-Guericke-Universitaet Magdeburg, Germany"
-      },
-      {
-        "author_name": "Leve Krieger",
-        "author_inst": "Otto-von-Guericke-Universitaet Magdeburg, Germany"
-      },
-      {
-        "author_name": "Berend van Wachem",
-        "author_inst": "Otto-von-Guericke-Universitaet Magdeburg, Germany"
-      },
-      {
-        "author_name": "Frank Beyrau",
-        "author_inst": "Otto-von-Guericke-Universitaet Magdeburg, Germany"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.07.23.21261042",
     "rel_title": "Robust antibody levels in both diabetic and non-diabetic individuals after BNT162b2 mRNA COVID-19 vaccination",
@@ -637650,6 +636093,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.07.24.21261065",
+    "rel_title": "COVID-Q: validation of the first COVID-19 questionnaire based on patient-rated symptom gravity",
+    "rel_date": "2021-07-26",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.24.21261065",
+    "rel_abs": "ObjectivesThe aim of the present study was to develop and validate the CoronaVirus Disease - 2019 (COVID-19) Questionnaire (COVID-Q), a novel symptom questionnaire specific for COVID-19 patients, to provide a comprehensive evaluation which may be helpful for physicians.. A secondary goal of the present study was to evaluate the performance of the COVID-Q in identifying subjects at higher risk of being tested positive for COVID-19.\n\nMaterial and methodsConsecutive non-hospitalized adults who underwent nasopharyngeal and throat swab for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection at Treviso Hospital in March 2020, were enrolled. Subjects were divided into positive (cases) and negative (controls) in equal number. All of them gave consent and answered the COVID-Q. Patients not able to answer the COVID-Q due to clinical conditions were excluded.\n\nParallel Analysis and Principal Component Analysis were used to identify clusters of items measuring the same dimension. The Item Response Theory (IRT)-based analyses evaluated the functioning of item categories, the presence of clusters of local dependence among items, item fit within the model and model fit to the data.\n\nResultsAnswers obtained from 230 COVID-19 cases (113 males, and 117 females; mean age 55 years, range 20-99 years) and 230 controls (61 males, and 169 females; mean age 46 years, range 21-89) were analyzed. Parallel analysis led to the extraction of six components, which corresponded to as many clinical presentation patterns: asthenia, influenza-like symptoms, ear and nose symptoms, breathing issues, throat symptoms, and anosmia/ageusia. The final IRT models retained 27 items as significant for symptom assessment. The total score on the questionnaire was significantly associated with positivity to the molecular SARS-CoV-2 test: subjects with multiple symptoms were significantly more likely to be affected by COVID-19 (p < .001). Older age and male gender also represented risk factors. Presence of breathing issues and anosmia/ageusia were significantly related to positivity to SARS-CoV-2 (p < 0.001). None of the examined comorbidities had a significant association with COVID-19 diagnosis.\n\nConclusionAccording to the analyses, COVID-Q could be validated since the aspects it evaluated were overall significantly related to SARS-CoV-2 infection. The application of the novel COVID-Q to everyday clinical practice may help identifying subjects who are likely to be affected by COVID-19 and address them to a nasopharyngeal swab in order to achieve an early diagnosis.\n\nWhat is already known about this topic?COVID-19 symptoms are widely known. Lots of studies have been published regarding self-administered questionnaires in order to characterize and know as much as possible regarding this disease. By the way, no specific questionnaires have been validated, yet, and there is no consensus regarding this topic.\n\nWhat does this article add?This paper shows the COVID-Q, a novel symptom questionnaire specific for COVID-19 patients. The aim is to provide a comprehensive evaluation that may be helpful to clinicians in order to suspect SARS-CoV-2 infection or not.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Giacomo Spinato",
+        "author_inst": "Department of Neurosciences, University of Padova"
+      },
+      {
+        "author_name": "Cristoforo Fabbris",
+        "author_inst": "University Hospital of Treviso"
+      },
+      {
+        "author_name": "Federica Conte",
+        "author_inst": "Department of Psychology, University of Milano Bicocca"
+      },
+      {
+        "author_name": "Anna Menegaldo",
+        "author_inst": "University Hospital of Treviso, Treviso"
+      },
+      {
+        "author_name": "Leonardo Franz",
+        "author_inst": "Department of Neurosciences, University of Padova"
+      },
+      {
+        "author_name": "Piergiorgio Gaudioso",
+        "author_inst": "Department of Neurosciences, University of Padova"
+      },
+      {
+        "author_name": "Francesco Cinetto",
+        "author_inst": "Department of Medicine, Clinical Immunology and Hematology, University of Padova"
+      },
+      {
+        "author_name": "Carlo Agostini",
+        "author_inst": "Department of Medicine, Clinical Immunology and Hematology, University of Padova"
+      },
+      {
+        "author_name": "Giulio Costantini",
+        "author_inst": "Department of Psychology, University of Milano Bicocca"
+      },
+      {
+        "author_name": "Paolo Boscolo Rizzo",
+        "author_inst": "University of Trieste"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.07.24.21261040",
     "rel_title": "Novel risk factors for Coronavirus disease-associated mucormycosis (CAM): a case control study during the outbreak in India",
@@ -639159,37 +637657,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.07.23.21261020",
-    "rel_title": "Challenges to self-isolation among contacts of cases of COVID-19: a national telephone survey in Wales",
-    "rel_date": "2021-07-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.23.21261020",
-    "rel_abs": "ObjectivesTo identify the specific challenges of self-isolation experienced by population sub-groups to better target and tailor support.\n\nDesignThe Contact Adherence Behavioural Insights Study (CABINS) was a 15-minute telephone survey of confirmed contacts of cases of COVID-19 identified through the national NHS Wales Test Trace Protect (TTP) database.\n\nMethodsConfirmed contacts of cases of COVID-19 reached by TTP completed a 15-minute telephone survey (N = 2,027). Binary logistic regression models adjusted for age, gender, living alone, survey round, deprivation quintile (defined by the Welsh Index of Multiple Deprivation) and income precarity (financial security) determined which population sub-groups were more likely to experience challenges during self-isolation.\n\nResultsYounger people (aged 18-29 years) were 3 times more likely to report mental health concerns (Adjusted Odds Ratio [aOR]: 3.16, 95% Confidence Interval [CI]: 2.05-4.86) and 2 times more likely to report loneliness (aOR: 1.96, CI: 1.37-2.81) compared to people aged over 60 years. Women were 1.5 times more likely to experience mental health concerns (aOR: 1.51, 95% CI: 1.20-1.92) compared to men. People with high/very high levels of income precarity were 8 times more likely to report financial challenges (aOR: 7.73, CI: 5.10-11.74) and 3 times more likely to report mental health concerns than their more financially secure counterparts (aOR: 3.08, CI: 2.22-4.28).\n\nConclusionsSelf-isolation is particularly challenging for those with younger people, women and precarious incomes. Providing enhanced emotional, financial and social support and signposting to these groups is required to minimise the harms of self-isolation.\n\nWhat is already known on this subject?O_LISelf-isolation after notification as a contact of a positive case of COVID-19 is essential to prevent the spread of the disease. However, self-isolation can be challenging and adherence is dependent upon a range of psychological, social and economic factors.\nC_LIO_LIEmerging data suggests that the COVID-19 pandemic is having disproportionate impact on those on lower incomes and those of lower socio-economic status.\nC_LI\n\nWhat does this study add?O_LIThe most common challenges faced to self-isolation were wanting to see family and friends, followed by a lack of exercise.\nC_LIO_LIIndividuals with some income precarity were more than 7 times more likely to report financial concerns and 3 times more likely to report mental health concerns as a challenge to self-isolation than those who were financially secure.\nC_LIO_LIInterventions to support individuals to self-isolate needs to be targeted at groups most susceptible to experiencing challenges to self-isolation for infectious diseases. Our research suggests that the use of income precarity questions as a screening tool is important to direct financial and practical support through contact tracing systems.\nC_LI",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Kate Rebecca Isherwood",
-        "author_inst": "Research and Evaluation Division, Public Health Wales"
-      },
-      {
-        "author_name": "Richard G Kyle",
-        "author_inst": "Research and Evaluation Division, Public Health Wales"
-      },
-      {
-        "author_name": "Benjamin R Gray",
-        "author_inst": "Research and Evaluation Division, Public Health Wales"
-      },
-      {
-        "author_name": "Alisha R Davies",
-        "author_inst": "Research and Evaluation Division, Public Health Wales"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.07.23.21260740",
     "rel_title": "Antiviral metabolite 3'-Deoxy-3',4'-didehydro-cytidine is detectable in serum and identifies acute viral infections including COVID-19",
@@ -639840,6 +638307,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.07.24.21261007",
+    "rel_title": "Use of Indomethacin for mild and moderate Covid -19 patients. A Randomized Control Trial",
+    "rel_date": "2021-07-25",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.24.21261007",
+    "rel_abs": "IntroductionIndomethacin, a non-steroidal anti-inflammatory drug (NSAID), has been presented as a broad-spectrum antiviral agent. This randomised clinical trial in a hospital setting evaluated the efficacy and safety of this drug in RT-PCR-positive coronavirus disease 2019 (COVID-19) patients.\n\nMaterials & MethodsA total of 210 RT-PCR-positive COVID-19 patients, who provided consent were allotted, to control or case arm, based on block randomisation. The control arm received standard of care comprising paracetamol, ivermectin, and other adjuvant therapies. The patients in the case arm received indomethacin instead of paracetamol, with other medications retained. The primary endpoint was the development of hypoxia/desaturation with SpO2 [&le;] 93, while time to become afebrile and time for cough and myalgia resolution were the secondary endpoints.\n\nResultsThe results of 210 patients were available, with 103 and 107 patients in the indomethacin and paracetamol arms, respectively. We monitored patient profiles along with everyday clinical parameters. Blood chemistry at the time of admission and discharge was assessed.\n\nAs no one in either of the arms required high-flow oxygen, desaturation with SpO2 level of 93 and below was an important goal. In the indomethacin group, none of the 103 patients developed desaturation. On the other hand, 20 of the 107 patients in the paracetamol arm developed desaturation. Patients who received indomethacin also experienced more rapid symptomatic relief than those in the paracetamol arm, with most symptoms disappearing in half the time. 56 patients out of 107 in the paracetamol arm had fever on the seventh day, while no patient in the indomethacin group had fever. Neither arm reported any adverse event. The fourteenth-day follow-up revealed that the paracetamol arm patients had faced several discomforts, including myalgia, joint pain, and tiredness; indomethacin arm patients mostly complained only of tiredness.\n\nConclusionIndomethacin is a safe and effective drug for treating patients with mild and moderate covid-19.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "ravichandran rajan",
+        "author_inst": "miot hospitals, Chennai, India"
+      },
+      {
+        "author_name": "Krishna Mohan Surapaneni",
+        "author_inst": "Panimalar Medical College Hospital & Research Institute"
+      },
+      {
+        "author_name": "Suresh Kumar Sukumaran",
+        "author_inst": "Panimalar Medical College Hospital & Research Institute, Chennai, India"
+      },
+      {
+        "author_name": "Devakumar Kamaraj",
+        "author_inst": "Panimalar Medical College Hospital & Research Institute"
+      },
+      {
+        "author_name": "Sumetha Suga Devisuga",
+        "author_inst": "Panimalar Medical College Hospital & Research Institute"
+      },
+      {
+        "author_name": "Samson Oliver Ravi",
+        "author_inst": "Molbio Diagnostics, Chennai, India"
+      },
+      {
+        "author_name": "Sivakumar Vijayaraghavalu",
+        "author_inst": "Narayana Translational Research Centre, Narayana Medical College, Nellore, Andhra Pradesh, India"
+      },
+      {
+        "author_name": "Krishna Kumar Ramarathnam",
+        "author_inst": "Indian Institute of Technology Madras"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.07.22.21260942",
     "rel_title": "Safety and Immunogenicity of Nanocovax, a SARS-CoV-2 Recombinant Spike Protein Vaccine",
@@ -642481,81 +640995,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.07.21.21260921",
-    "rel_title": "Cell-Mediated and Humoral Immune Response to 2-Dose SARS-CoV2 mRNA vaccination in Immunocompromised patient population",
-    "rel_date": "2021-07-23",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.21.21260921",
-    "rel_abs": "Characterization of cell-mediated and humoral immune responses to SARS-CoV2 mRNA vaccine has implications for protective immunity in immunocompromised patients. However, studies have demonstrated poor humoral response to SARS-CoV2 mRNA vaccine in immunocompromised patients and data on cellular immune response are currently lacking. Here we compared immune response after 2-dose vaccination in 100 immunocompromised patients (solid organ transplant recipients, hematologic malignancy, autoimmune condition, and primary immunodeficiency) and 16 immunocompetent healthy healthcare workers. We find that 100% (CI=80.6-100%) of immunocompetent individuals show positive cell-mediated and humoral immune response post vaccination while only 50% (CI=40.4-59.6%) of immunocompromised patients show humoral immune response and 69% (CI=59.4-77.2%) have a positive cell-mediated immune response. 21% of immunocompromised patients have no humoral immune response or cell-mediated immune response and thus are likely vulnerable to SARS-CoV2 infection. Monitoring of immune response in immunocompromised populations, particularly in high-risk immunocompromised patients (solid organ transplant recipients, patients with severe autoimmunity, and those [&ge;]50 years), with clinical IGRA and serological assay after vaccination may identify patients who may benefit from revaccination or prophylactic monoclonal antibody therapy to prevent COVID-19 in this patient population",
-    "rel_num_authors": 15,
-    "rel_authors": [
-      {
-        "author_name": "Muthukumar Ramanathan",
-        "author_inst": "Stanford University School of Medicine"
-      },
-      {
-        "author_name": "Kanagavel Murugesan",
-        "author_inst": "Stanford University School of Medicine"
-      },
-      {
-        "author_name": "Lu M Yang",
-        "author_inst": "Stanford University School of Medicine"
-      },
-      {
-        "author_name": "Cristina Costales",
-        "author_inst": "Stanford University School of Medicine"
-      },
-      {
-        "author_name": "Philip L Bulterys",
-        "author_inst": "Stanford University School of Medicine"
-      },
-      {
-        "author_name": "Joseph Schroers-Martin",
-        "author_inst": "Stanford University School of Medicine"
-      },
-      {
-        "author_name": "Ash A Alizadeh",
-        "author_inst": "Stanford University School of Medicine"
-      },
-      {
-        "author_name": "Scott D Boyd",
-        "author_inst": "Stanford University School of Medicine"
-      },
-      {
-        "author_name": "Janice M Brown",
-        "author_inst": "Stanford University School of Medicine"
-      },
-      {
-        "author_name": "Kari C Nadeau",
-        "author_inst": "Stanford University School of Medicine"
-      },
-      {
-        "author_name": "Sruti S Nadimpalli",
-        "author_inst": "Stanford University School of Medicine"
-      },
-      {
-        "author_name": "Aileen X Wang",
-        "author_inst": "Stanford University School of Medicine"
-      },
-      {
-        "author_name": "Stephan Busque",
-        "author_inst": "Stanford University School of Medicine"
-      },
-      {
-        "author_name": "Benjamin A Pinsky",
-        "author_inst": "Stanford University School of Medicine"
-      },
-      {
-        "author_name": "Niaz Banaei",
-        "author_inst": "Stanford University School of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.07.18.21260711",
     "rel_title": "On dynamics of fractional incommensurate model of Covid-19 with nonlinear saturated incidence rate",
@@ -642854,6 +641293,69 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.07.21.21260964",
+    "rel_title": "Phase 1 safety and pharmacokinetics studies of BRII-196 and BRII-198, SARS-CoV-2 spike-targeting monoclonal antibodies",
+    "rel_date": "2021-07-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.21.21260964",
+    "rel_abs": "BackgroundBRII-196 and BRII-198 are two anti-SARS-CoV-2 monoclonal neutralizing antibodies with modified Fc region that extends half-life and are being developed as cocktail therapy for the treatment of COVID-19. Safety, tolerability, pharmacokinetics, and immunogenicity of BRII-196 and BRII-198 were investigated in healthy adults.\n\nMethodsSingle ascending doses of BRII-196 and BRII-198 were evaluated in parallel in the first-in-human, placebo-controlled phase 1 studies. A total of 32 healthy adults were randomized and received a single intravenous infusion of 750, 1500, and 3000 mg of BRII-196 (n=12), BRII-198 (n=12), or placebo (n=8) and were followed for 180 days.\n\nResultsAll infusions were well tolerated at infusion rates between 0.5 mL/min to 4 mL/min with no dose-limiting adverse events, deaths, serious adverse events, or any systemic or local infusion reactions. Most treatment-emergent adverse events were isolated asymptomatic laboratory abnormalities of Grade 1-2 in severity. Each mAb displayed pharmacokinetics expected of Fc-engineered human IgG1 with mean terminal half-lives of approximately 46 days and 76 days, respectively, with no evidence of significant anti-drug antibody development.\n\nConclusionsBRII-196 and BRII-198 were well-tolerated. Clinical results support further development as therapeutic or prophylactic options for SARS-CoV-2 infection.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Yao Zhang",
+        "author_inst": "TSB Therapeutics"
+      },
+      {
+        "author_name": "Xiaohua Hao",
+        "author_inst": "Beijing Ditan Hospital, Capital Medical University"
+      },
+      {
+        "author_name": "Ji Ma",
+        "author_inst": "Brii Biosciences"
+      },
+      {
+        "author_name": "Mingming Wang",
+        "author_inst": "Brii Biosciences"
+      },
+      {
+        "author_name": "Yanyan Li",
+        "author_inst": "Brii Biosciences"
+      },
+      {
+        "author_name": "Yang Liu",
+        "author_inst": "Brii Biosciences"
+      },
+      {
+        "author_name": "Dong Zhao",
+        "author_inst": "Beijing Ditan Hospital, Capital Medical University"
+      },
+      {
+        "author_name": "Wen Zhang",
+        "author_inst": "Beijing Ditan Hospital, Capital Medical University"
+      },
+      {
+        "author_name": "Chunming Li",
+        "author_inst": "Brii Biosciences"
+      },
+      {
+        "author_name": "Li Yan",
+        "author_inst": "Brii Biosciences"
+      },
+      {
+        "author_name": "Qing Zhu",
+        "author_inst": "TSB Therapeutics"
+      },
+      {
+        "author_name": "Fujie Zhang",
+        "author_inst": "Beijing Ditan Hospital, Capital Medical University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.07.20.21260872",
     "rel_title": "Excess mortality in India from June 2020 to June 2021 during the COVID pandemic: death registration, health facility deaths, and survey data",
@@ -644179,73 +642681,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
-  {
-    "rel_doi": "10.1101/2021.07.16.21260618",
-    "rel_title": "Antibody titers measured by commercial assays are correlated with neutralizing antibody titers calibrated by international standards",
-    "rel_date": "2021-07-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.16.21260618",
-    "rel_abs": "The World Health Organization (WHO) has highlighted the importance of an international standard (IS) for SARS-CoV-2 neutralizing antibody titer detection, with the aim of calibrating different diagnostic techniques. In this study, IS was applied to calibrate neutralizing antibody titers (IU/mL) and binding antibody titers (BAU/mL) in response to SARS-CoV-2 vaccines. Serum samples were collected from participants receiving the Moderna (n = 20) and Pfizer (n = 20) vaccines at three time points: pre-vaccination, after one dose, and after two doses. We obtained geometric mean titers of 1404.16 and 928.75 IU/mL for neutralizing antibodies after two doses of the Moderna and Pfizer vaccines, respectively. These values provide an important baseline for vaccine development and the implementation of non-inferiority trials. We also compared three commercially available kits from Roche, Abbott, and MeDiPro for the detection of COVID-19 antibodies based on binding affinity to S1 and/or RBD. Our results demonstrated that antibody titers measured by commercial assays are highly correlated with neutralizing antibody titers calibrated by IS.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Yu-An Kung",
-        "author_inst": "Chang Gung University"
-      },
-      {
-        "author_name": "Chung-Guei Huang",
-        "author_inst": "Linkou Chang Gung Memorial Hospital"
-      },
-      {
-        "author_name": "Sheng-Yu Huang",
-        "author_inst": "Chang Gung University"
-      },
-      {
-        "author_name": "Kuan-Ting Liu",
-        "author_inst": "Chang Gung University"
-      },
-      {
-        "author_name": "Peng-Nien Huang",
-        "author_inst": "Chang Gung University"
-      },
-      {
-        "author_name": "Kar-Yee Yu",
-        "author_inst": "Chang Gung University"
-      },
-      {
-        "author_name": "Shu-Li Yang",
-        "author_inst": "Linkou Chang Gung Memorial Hospital"
-      },
-      {
-        "author_name": "Chia-Pei Chen",
-        "author_inst": "Linkou Chang Gung Memorial Hospital"
-      },
-      {
-        "author_name": "Ching-Yun Cheng",
-        "author_inst": "Linkou Chang Gung Memorial Hospital"
-      },
-      {
-        "author_name": "Yueh-Te Lin",
-        "author_inst": "Chang Gung University"
-      },
-      {
-        "author_name": "Yen-Chin Liu",
-        "author_inst": "Chang Gung University"
-      },
-      {
-        "author_name": "Guang-Wu Chen",
-        "author_inst": "Chang Gung University"
-      },
-      {
-        "author_name": "Shin-Ru Shih",
-        "author_inst": "Chang Gung University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.07.19.21260776",
     "rel_title": "Integrative Metabolomic and Proteomic Signatures Define Clinical Outcomes in Severe COVID-19",
@@ -644744,6 +643179,85 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "intensive care and critical care medicine"
   },
+  {
+    "rel_doi": "10.1101/2021.07.18.21260718",
+    "rel_title": "Real-Time SARS-CoV-2 Genotyping by High-Throughput Multiplex PCR Reveals the Epidemiology of the Variants of Concern in Qatar",
+    "rel_date": "2021-07-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.18.21260718",
+    "rel_abs": "Complementing whole genome sequencing strategies with high-throughput multiplex RT-qPCR genotyping allows for more comprehensive and real-time tracking of SARS-CoV-2 variants of concern. During the second and third waves of COVID-19 in Qatar, PCR genotyping, combined with Sanger sequencing of un-typeable samples, was employed to describe the epidemiology of the Alpha, Beta and Delta variants. A total of 9792 nasopharyngeal PCR-positive samples collected between April-June 2021 were successfully genotyped, revealing the importation and transmission dynamics of these three variants in Qatar.",
+    "rel_num_authors": 16,
+    "rel_authors": [
+      {
+        "author_name": "Mohammad R. Hasan",
+        "author_inst": "Sidra Medicine, Doha, Qatar"
+      },
+      {
+        "author_name": "Mahesh K. R. Kalikiri",
+        "author_inst": "Sidra Medicine, Doha, Qatar"
+      },
+      {
+        "author_name": "Faheem Mirza",
+        "author_inst": "Sidra Medicine, Doha, Qatar"
+      },
+      {
+        "author_name": "Sathyavathi Sundararaju",
+        "author_inst": "Sidra Medicine, Doha, Qatar"
+      },
+      {
+        "author_name": "Anju Sharma",
+        "author_inst": "Sidra Medicine, Doha, Qatar"
+      },
+      {
+        "author_name": "Stephan Lorenz",
+        "author_inst": "Sidra Medicine, Doha, Qatar"
+      },
+      {
+        "author_name": "Hiam Chemaitelly",
+        "author_inst": "Weill Cornell Medicine-Qatar"
+      },
+      {
+        "author_name": "Reham A. El-Kahlout",
+        "author_inst": "Hamad Medical Corporation, Doha, Qatar"
+      },
+      {
+        "author_name": "Kin Ming Tsui",
+        "author_inst": "Sidra Medicine, Doha, Qatar"
+      },
+      {
+        "author_name": "Hadi M. Yassine",
+        "author_inst": "Qatar University, Doha, Qatar"
+      },
+      {
+        "author_name": "Peter V. Coyle",
+        "author_inst": "Hamad Medical Corporation, Doha, Qatar"
+      },
+      {
+        "author_name": "Abdullatif Al Khal",
+        "author_inst": "Hamad Medical Corporation, Doha, Qatar"
+      },
+      {
+        "author_name": "Roberto Bertollini",
+        "author_inst": "Ministry of Public Health, Doha, Qatar"
+      },
+      {
+        "author_name": "Mohamed H. Al Thani",
+        "author_inst": "Ministry of Public Health, Doha, Qatar"
+      },
+      {
+        "author_name": "Laith J. Abu-Raddad",
+        "author_inst": "Weill Cornell Medicine-Qatar"
+      },
+      {
+        "author_name": "Patrick Tang",
+        "author_inst": "Sidra Medicine, Doha, Qatar"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.07.16.21260464",
     "rel_title": "K-12 School Teaching Posture Correlates with COVID-19 Disease Outcomes in Ohio",
@@ -646489,29 +645003,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.07.19.21260522",
-    "rel_title": "Assessing COVID prevention strategies to permit the safe opening of college campuses in fall 2021",
-    "rel_date": "2021-07-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260522",
-    "rel_abs": "BackgroundEffective vaccines, improved testing technologies, and declines in COVID-19 incidence prompt an examination of the choices available to college administrators to safely resume in-person campus activities in fall 2021.\n\nObjectiveTo develop a decision support tool that assists college administrators in designing and evaluating customized COVID vaccination, screening, and prevention plans.\n\nDesignDecision analysis linked to a compartmental epidemic model, quantifying the interaction of policy instruments (e.g., vaccination promotion, asymptomatic testing, physical distancing, and other non-pharmaceutical interventions), institutional priorities (e.g., risk tolerance, desire to resume activities), and assumptions about vaccine performance and background epidemic severity.\n\nParticipantsHypothetical cohort of 5000 individuals (students, faculty, and staff) living and working in the close environs of a residential college campus.\n\nMain Outcome(s) and Measure(s)Cumulative infections over a 120-day semester.\n\nResultsUnder Base Case assumptions, if 90% coverage with an 85%-effective vaccine can be attained, the model finds that campus activities can be fully resumed while holding cumulative cases below 5% of the population without the need for routine, asymptomatic testing. With 50% population coverage using such a vaccine, a similar \"return to normalcy\" would require daily asymptomatic testing of unvaccinated individuals. The effectiveness of vaccination in reducing susceptibility to infection is a critical uncertainty.\n\nConclusions & RelevanceVaccination coverage is the most powerful tool available to college administrators to achieve a safe return to pre-pandemic operations this fall. Given the breadth of potential outcomes in the face of uncontrollable and uncertain factors, even colleges that achieve high vaccination coverage should be prepared to reinstitute testing and distancing policies on short notice.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "A David Paltiel",
-        "author_inst": "Yale School of Public Health"
-      },
-      {
-        "author_name": "Jason L Schwartz",
-        "author_inst": "Yale School of Public Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.07.19.21260815",
     "rel_title": "RNA viromics of Southern California wastewater and detection of SARS-CoV-2 single nucleotide variants.",
@@ -646938,6 +645429,109 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.07.20.21260855",
+    "rel_title": "SARS-CoV-2 incidence, transmission and reinfection in a rural and an urban setting: results of the PHIRST-C cohort study, South Africa, 2020-2021",
+    "rel_date": "2021-07-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.20.21260855",
+    "rel_abs": "BackgroundBy August 2021, South Africa experienced three SARS-CoV-2 waves; the second and third associated with emergence of Beta and Delta variants respectively.\n\nMethodsWe conducted a prospective cohort study during July 2020-August 2021 in one rural and one urban community. Mid-turbinate nasal swabs were collected twice-weekly from household members irrespective of symptoms and tested for SARS-CoV-2 using real-time reverse transcription polymerase chain reaction (rRT-PCR). Serum was collected every two months and tested for anti-SARS-CoV-2 antibodies.\n\nResultsAmong 115,759 nasal specimens from 1,200 members (follow-up rate 93%), 1976 (2%) were SARS-CoV-2-positive. By rRT-PCR and serology combined, 62% (749/1200) of individuals experienced [&ge;]1 SARS-CoV-2 infection episode, and 12% (87/749) experienced reinfection. Of 662 PCR-confirmed episodes with available data, 15% (n=97) were associated with [&ge;]1 symptom. Among 222 households, 200 (90%) had [&ge;]1 SARS-CoV-2-positive individual. Household cumulative infection risk (HCIR) was 25% (213/856). On multivariable analysis, accounting for age and sex, index case lower cycle threshold value (OR 3.9, 95%CI 1.7-8.8), urban community (OR 2.0,95%CI 1.1-3.9), Beta (OR 4.2, 95%CI 1.7-10.1) and Delta (OR 14.6, 95%CI 5.7-37.5) variant infection were associated with increased HCIR. HCIR was similar for symptomatic (21/110, 19%) and asymptomatic (195/775, 25%) index cases (p=0.165). Attack rates were highest in individuals aged 13-18 years and individuals in this age group were more likely to experience repeat infections and to acquire SARS-CoV-2 infection. People living with HIV who were not virally supressed were more likely to develop symptomatic illness, and shed SARS-CoV-2 for longer compared to HIV-uninfected individuals.\n\nConclusionsIn this study, 85% of SARS-CoV-2 infections were asymptomatic and index case symptom status did not affect HCIR, suggesting a limited role for control measures targeting symptomatic individuals. Increased household transmission of Beta and Delta variants, likely contributed to successive waves, with >60% of individuals infected by the end of follow-up.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSPrevious studies have generated wide-ranging estimates of the proportion of SARS-CoV-2 infections which are asymptomatic. A recent systematic review found that 20% (95% CI 3%-67%) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections remained asymptomatic throughout infection and that transmission from asymptomatic individuals was reduced. A systematic review and meta-analysis of 87 household transmission studies of SARS-CoV-2 found an estimated secondary attack rate of 19% (95% CI 16-22). The review also found that household secondary attack rates were increased from symptomatic index cases and that adults were more likely to acquire infection. As of December 2021, South Africa experienced three waves of SARS-CoV-2 infections; the second and third waves were associated with circulation of Beta and Delta variants respectively. SARS-CoV-2 vaccines became available in February 2021, but uptake was low in study sites reaching 5% fully vaccinated at the end of follow up. Studies to quantify the burden of asymptomatic infections, symptomatic fraction, reinfection frequency, duration of shedding and household transmission of SARS-CoV-2 from asymptomatically infected individuals have mostly been conducted as part of outbreak investigations or in specific settings. Comprehensive systematic community studies of SARS-CoV-2 burden and transmission including for the Beta and Delta variants are lacking, especially in low vaccination settings.\n\nAdded value of this studyWe conducted a unique detailed COVID-19 household cohort study over a 13 month period in South Africa, with real time reverse transcriptase polymerase chain reaction (rRT-PCR) testing twice a week irrespective of symptoms and bimonthly serology. By the end of the study in August 2021, 749 (62%) of 1200 individuals from 222 randomly sampled households in a rural and an urban community in South Africa had at least one confirmed SARS-CoV-2 infection, detected on rRT-PCR and/or serology, and 12% (87/749) experienced reinfection. Symptom data were analysed for 662 rRT-PCR-confirmed infection episodes that occurred >14 days after the start of follow-up (of a total of 718 rRT-PCR-confirmed episodes), of these, 15% (n=97) were associated with one or more symptoms. Among symptomatic indvidiausl, 9% (n=9) were hospitalised and 2% (n=2) died. Ninety percent (200/222) of included households, had one or more individual infected with SARS-CoV-2 on rRT-PCR and/or serology within the household. SARS-CoV-2 infected index cases transmitted the infection to 25% (213/856) of susceptible household contacts. Index case ribonucleic acid (RNA) viral load proxied by rRT-PCR cycle threshold value was strongly predictive of household transmission. Presence of symptoms in the index case was not associated with household transmission. Household transmission was four times greater from index cases infected with Beta variant and fifteen times greater from index cases infected with Delta variant compared to wild-type infection. Attack rates were highest in individuals aged 13-18 years and individuals in this age group were more likely to experience repeat infections and to acquire SARS-CoV-2 infection within households. People living with HIV (PLHIV) who were not virally supressed were more likely to develop symptomatic illness when infected with SARS-CoV-2, and shed SARS-CoV-2 for longer when compared to HIV-uninfected individuals.\n\nImplications of all the available evidenceWe found a high rate of SARS-CoV-2 infection in households in a rural community and an urban community in South Africa, with the majority of infections being asymptomatic in individuals of all ages. Asymptomatic individuals transmitted SARS-CoV-2 at similar levels to symptomatic individuals suggesting that interventions targeting symptomatic individuals such as symptom-based testing and contact tracing of individuals tested because they report symptoms may have a limited impact as control measures. Increased household transmission of Beta and Delta variants, likely contributed to recurrent waves of COVID-19, with >60% of individuals infected by the end of follow-up. Higher attack rates, reinfection and acquisition in adolescents and prolonged SARS-CoV-2 shedding in PLHIV who were not virally suppressed suggests that prioritised vaccination of individuals in these groups could impact community transmission.",
+    "rel_num_authors": 22,
+    "rel_authors": [
+      {
+        "author_name": "Cheryl Cohen",
+        "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri"
+      },
+      {
+        "author_name": "Jackie Kleynhans",
+        "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri"
+      },
+      {
+        "author_name": "Anne von Gottberg",
+        "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri"
+      },
+      {
+        "author_name": "Meredith McMorrow",
+        "author_inst": "Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America"
+      },
+      {
+        "author_name": "Nicole Wolter",
+        "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri"
+      },
+      {
+        "author_name": "Jinal Bhiman",
+        "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri"
+      },
+      {
+        "author_name": "Jocelyn Moyes",
+        "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri"
+      },
+      {
+        "author_name": "Mignon du Plessis",
+        "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri"
+      },
+      {
+        "author_name": "Maimuna Carrim",
+        "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri"
+      },
+      {
+        "author_name": "Amelia Buys",
+        "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri"
+      },
+      {
+        "author_name": "Neil A Martinson",
+        "author_inst": "Perinatal HIV Research Unit, Medical Research Council (MRC) Soweto Matlosana Collaborating Centre for HIV/AIDS and Tuberculosis, South Africa"
+      },
+      {
+        "author_name": "Kathleen Kahn",
+        "author_inst": "MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersr"
+      },
+      {
+        "author_name": "Stephen Tollman",
+        "author_inst": "MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersr"
+      },
+      {
+        "author_name": "Limakatso Lebina",
+        "author_inst": "Perinatal HIV Research Unit, Medical Research Council (MRC) Soweto Matlosana Collaborating Centre for HIV/AIDS and Tuberculosis, South Africa"
+      },
+      {
+        "author_name": "Floidy Wafawanaka",
+        "author_inst": "MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersr"
+      },
+      {
+        "author_name": "Jacques du Toit",
+        "author_inst": "MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersr"
+      },
+      {
+        "author_name": "Francesc Xavier Gomez-Olive",
+        "author_inst": "MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersr"
+      },
+      {
+        "author_name": "Fatima Dawood",
+        "author_inst": "Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America"
+      },
+      {
+        "author_name": "Thulisa Mkhencele",
+        "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri"
+      },
+      {
+        "author_name": "Kaiyuan Sun",
+        "author_inst": "Fogarty International Center, National Institutes of Health"
+      },
+      {
+        "author_name": "Cecile Viboud",
+        "author_inst": "Fogarty International Center, National Institutes of Health"
+      },
+      {
+        "author_name": "Stefano Tempia",
+        "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.07.19.21260707",
     "rel_title": "Increased transmissibility of emerging SARS-CoV-2 variants is driven either by viral load or probability of infection rather than environmental stability",
@@ -648179,41 +646773,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.07.20.21260889",
-    "rel_title": "Optimal vaccine allocation for COVID-19 in the Netherlands: a data-driven prioritization",
-    "rel_date": "2021-07-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.20.21260889",
-    "rel_abs": "For the control of COVID-19, vaccination programmes provide a long-term solution. The amount of available vaccines is often limited, and thus it is crucial to determine the allocation strategy. While mathematical modelling approaches have been used to find an optimal distribution of vaccines, there is an excessively large number of possible schemes to be simulated.\n\nHere, we propose an algorithm to find a near-optimal allocation scheme given an intervention objective such as minimization of new infections, hospitalizations, or deaths, where multiple vaccines are available. The proposed principle for allocating vaccines is to target subgroups with the largest reduction in the outcome of interest, such as new infections, due to vaccination that fully immunizes a single individual. We express the expected impact of vaccinating each subgroup in terms of the observed incidence of infection and force of infection. The proposed approach is firstly evaluated with a simulated epidemic and then applied to the epidemiological data on COVID-19 in the Netherlands.\n\nOur results reveal how the optimal allocation depends on the objective of infection control. In the case of COVID-19, if we wish to minimize deaths, the optimal allocation strategy is not efficient for minimizing other outcomes, such as infections. In simulated epidemics, an allocation strategy optimized for an outcome outperforms other strategies such as the allocation from young to old, from old to young, and at random. Our simulations clarify that the current policy in the Netherlands (i.e., allocation from old to young) was concordant with the allocation scheme that minimizes deaths.\n\nThe proposed method provides an optimal allocation scheme, given routine surveillance data that reflect ongoing transmissions. The principle of allocation is useful for providing plausible simulation scenarios for complex models, which give a more robust basis to determine intervention strategies.\n\nAuthor summaryVaccination is the key to controlling the ongoing COVID-19 pandemic. In the early stages of an epidemic, there is shortage of vaccine stocks. Here, we propose an algorithm that computes an optimal vaccine distribution among groups for each intervention objective (e.g., minimizing new infections, hospitalizations, or deaths). Unlike existing approaches that use detailed information on at-risk contacts between and among groups, the proposed algorithm requires only routine surveillance data on the number of cases. This method is applicable even when multiple vaccines are available. Simulation results show that the allocation scheme optimized by our algorithm performed the best compared with other strategies such as allocating vaccines at random and in the order of age. Our results also reveal that an allocation scheme optimized for one specific objective is not necessarily efficient for another, indicating the importance of the decision-making at the early phase of distributions.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Fuminari Miura",
-        "author_inst": "National Institute for Public Health and the Environment"
-      },
-      {
-        "author_name": "Ka Yin Leung",
-        "author_inst": "National Institute for Public Health and the Environment"
-      },
-      {
-        "author_name": "Don Klinkenberg",
-        "author_inst": "National Institute for Public Health and the Environment"
-      },
-      {
-        "author_name": "Kylie E.C. Ainslie",
-        "author_inst": "National Institute for Public Health and the Environment"
-      },
-      {
-        "author_name": "Jacco Wallinga",
-        "author_inst": "National Institute for Public Health and the Environment"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.07.20.21260840",
     "rel_title": "Will a natural collective immunity of Ukrainians restrain new COVID-19 waves?",
@@ -648512,6 +647071,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.07.18.21260567",
+    "rel_title": "Predicting Managers' Mental Health Across Countries Using Country-Level COVID-19 Statistics",
+    "rel_date": "2021-07-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.18.21260567",
+    "rel_abs": "BackgroundThere is limited research focusing on publicly available statistics on the Coronavirus disease 2019 (COVID-19) pandemic as predictors of mental health across countries. Managers are at risk of suffering from mental disorders during the pandemic because they face particular hardship.\n\nObjectiveWe aim to predict mental disorder (anxiety and depression) symptoms of managers across countries using country-level COVID-19 statistics.\n\nMethodsA two-wave online survey of 406 managers from 26 countries was finished in May and July 2020. We used logistic panel regression models for our main analyses and performed robustness checks using ordinary least squares regressions. In the sample of 406 managers from 26 countries, 26.5% of managers reached the cut-off levels for anxiety (General Anxiety Disorder-7; GAD-7) and 43.5% did so for depression (Patient Health Questionnaire-9; PHQ-9) symptoms.\n\nFindingsWe found that cumulative COVID-19 statistics (e.g., cumulative cases, cumulative cases per million, cumulative deaths, and cumulative deaths per million) predicted managers anxiety and depression symptoms positively, whereas daily COVID-19 statistics (daily new cases, smoothed daily new cases, daily new deaths, smoothed daily new deaths, daily new cases per million, and smoothed daily new cases per million) predicted anxiety and depression symptoms negatively. In addition, the reproduction rate was a positive predictor, while stringency of governmental lockdown measures was a negative predictor. Individually, we found that the cumulative count of deaths is the best single predictor of both anxiety and depression symptoms.\n\nConclusionsCumulative COVID-19 statistics predicted managers anxiety and depression symptoms positively, while non-cumulative daily COVID-19 statistics predicted anxiety and depression symptoms negatively. Cumulative count of deaths is the best single predictor of both anxiety and depression symptoms. Reproduction rate was a positive predictor, while stringency of governmental lockdown measures was a negative predictor.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Lun Li",
+        "author_inst": "School of Economics and Management, Tsinghua University"
+      },
+      {
+        "author_name": "Stephen X. Zhang",
+        "author_inst": "University of Adelaide"
+      },
+      {
+        "author_name": "Lorenz Graf-Vlachy",
+        "author_inst": "TU Dortmund University, Dortmund, Germany & ESCP Business School, Berlin, Germany"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.07.21.21260881",
     "rel_title": "Understanding COVID-19 Vaccine Early Skepticism and Misinformation",
@@ -649905,85 +648491,6 @@
     "type": "new results",
     "category": "biochemistry"
   },
-  {
-    "rel_doi": "10.1101/2021.07.20.453127",
-    "rel_title": "An Orally Available Cathepsin L Inhibitor Protects Lungs Against SARS-CoV-2-Induced Diffuse Alveolar Damage in African Green Monkeys",
-    "rel_date": "2021-07-21",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.20.453127",
-    "rel_abs": "The COVID-19 pandemic resulted from global infection by the SARS-CoV-2 coronavirus and rapidly emerged as an urgent health issue requiring effective treatments. To initiate infection, the Spike protein of SARS-CoV-2 requires proteolytic processing mediated by host proteases. Among the host proteases proposed to carry out this activation is the cysteine protease cathepsin L. Inhibiting cathepsin L has been proposed as a therapeutic strategy for treating COVID-19. SLV213 (K777) is an orally administered small molecule protease inhibitor that exhibits in vitro activity against a range of viruses, including SARS-CoV-2. To confirm efficacy in vivo, K777 was evaluated in an African green monkey (AGM) model of COVID-19. A pilot experiment was designed to test K777 in a prophylactic setting, animals were pre-treated with 100mg/kg K777 (N=4) or vehicle (N=2) before inoculation with SARS-CoV-2. Initial data demonstrated that K777 treatment reduced pulmonary pathology compared to vehicle-treated animals. A second study was designed to test activity in a therapeutic setting, with K777 treatment (33 mg/kg or 100 mg/kg) initiated 8 hours after exposure to the virus. In both experiments, animals received K777 daily via oral gavage for 7 days. Vehicle-treated animals exhibited higher lung weights, pleuritis, and diffuse alveolar damage. In contrast, lung pathology was reduced in K777-treated monkeys, and histopathological analyses confirmed the lack of diffuse alveolar damage. Antiviral effects were further demonstrated by quantitative reductions in viral load of samples collected from upper and lower airways. These preclinical data support the potential for early SLV213 treatment in COVID-19 patients to prevent severe lung pathology and disease progression.",
-    "rel_num_authors": 16,
-    "rel_authors": [
-      {
-        "author_name": "Felix W Frueh",
-        "author_inst": "Selva Therapeutics, Inc."
-      },
-      {
-        "author_name": "Daniel C Maneval",
-        "author_inst": "Selva Therapeutics, Inc."
-      },
-      {
-        "author_name": "Rudolph P Bohm",
-        "author_inst": "Tulane National Primate Research Center"
-      },
-      {
-        "author_name": "Jason P Dufour",
-        "author_inst": "Tulane National Primate Research Center"
-      },
-      {
-        "author_name": "Robert  V Blair",
-        "author_inst": "Tulane National Primate Research Center"
-      },
-      {
-        "author_name": "Sierra Simpson",
-        "author_inst": "Selva Therapeutics, Inc."
-      },
-      {
-        "author_name": "Kathy Powell",
-        "author_inst": "Selva Therapeutics, Inc."
-      },
-      {
-        "author_name": "Pyone P Aye",
-        "author_inst": "Tulane National Primate Research Center"
-      },
-      {
-        "author_name": "Nadia A Golden",
-        "author_inst": "Tulane National Primate Research Center"
-      },
-      {
-        "author_name": "CHAD J ROY",
-        "author_inst": "Tulane National Primate Research Center"
-      },
-      {
-        "author_name": "Sky Spencer",
-        "author_inst": "Tulane National Primate Research Center"
-      },
-      {
-        "author_name": "Kasi Russell-Lodrigue",
-        "author_inst": "Tulane National Primate Research Center"
-      },
-      {
-        "author_name": "Kenneth S Plante",
-        "author_inst": "University of Texas Medical Branch"
-      },
-      {
-        "author_name": "Jessica A Plante",
-        "author_inst": "University of Texas Medical Branch"
-      },
-      {
-        "author_name": "James H McKerrow",
-        "author_inst": "University of California, San Diego"
-      },
-      {
-        "author_name": "Jay Rappaport",
-        "author_inst": "Tulane National Primate Research Center"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2021.07.20.452858",
     "rel_title": "Cornering an Ever-Evolving Coronavirus: TATX-03, a fully human synergistic multi-antibody cocktail targeting the SARS-CoV-2 Spike Protein with in vivo efficacy",
@@ -650398,6 +648905,193 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2021.07.16.452756",
+    "rel_title": "Comparison of heat-inactivated and infectious SARS-CoV-2 across indoor surface materials shows comparable RT-qPCR viral signal intensity and persistence",
+    "rel_date": "2021-07-20",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.16.452756",
+    "rel_abs": "Environmental monitoring in public spaces can be used to identify surfaces contaminated by persons with COVID-19 and inform appropriate infection mitigation responses. Research groups have reported detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on surfaces days or weeks after the virus has been deposited, making it difficult to estimate when an infected individual may have shed virus onto a SARS-CoV-2 positive surface, which in turn complicates the process of establishing effective quarantine measures. In this study, we determined that reverse transcription-quantitative polymerase chain reaction (RT-qPCR) detection of viral RNA from heat-inactivated particles experiences minimal decay over seven days of monitoring on eight out of nine surfaces tested. The properties of the studied surfaces result in RT-qPCR signatures that can be segregated into two material categories, rough and smooth, where smooth surfaces have a lower limit of detection. RT-qPCR signal intensity (average quantification cycle (Cq)) can be correlated to surface viral load using only one linear regression model per material category. The same experiment was performed with infectious viral particles on one surface from each category, with essentially identical results. The stability of RT-qPCR viral signal demonstrates the need to clean monitored surfaces after sampling to establish temporal resolution. Additionally, these findings can be used to minimize the number of materials and time points tested and allow for the use of heat-inactivated viral particles when optimizing environmental monitoring methods.\n\nImportanceEnvironmental monitoring is an important tool for public health surveillance, particularly in settings with low rates of diagnostic testing. Time between sampling public environments, such as hospitals or schools, and notifying stakeholders of the results should be minimal, allowing decisions to be made towards containing outbreaks of coronavirus disease 2019 (COVID-19). The Safer At School Early Alert program (SASEA) [1], a large-scale environmental monitoring effort in elementary school and child care settings, has processed > 13,000 surface samples for SARS-CoV-2, detecting viral signals from 574 samples. However, consecutive detection events necessitated the present study to establish appropriate response practices around persistent viral signals on classroom surfaces. Other research groups and clinical labs developing environmental monitoring methods may need to establish their own correlation between RT - qPCR results and viral load, but this work provides evidence justifying simplified experimental designs, like reduced testing materials and the use of heat-inactivated viral particles.",
+    "rel_num_authors": 43,
+    "rel_authors": [
+      {
+        "author_name": "Rodolfo A. Salido",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Victor J. Cant\u00fa",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Alex E Clark",
+        "author_inst": "University of California San Diego"
+      },
+      {
+        "author_name": "Sandra L. Leibel",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Anahid Foroughishafiei",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Anushka Saha",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Abbas Hakim",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Alhakam Nouri",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Alma L. Lastrella",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Anelizze Castro-Mart\u00ednez",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Ashley Plascencia",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Bhavika Kapadia",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Bing Xia",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Christopher Ruiz",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Clarisse (Lisa) Marotz",
+        "author_inst": "UC San Diego"
+      },
+      {
+        "author_name": "Daniel Maunder",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Elijah S. Lawrence",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Elizabeth W. Smoot",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Emily Eisner",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Evelyn S. Crescini",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Laura Kohn",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Lizbeth Franco Vargas",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Marisol Chac\u00f3n",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Maryan Betty",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Michal Machnicki",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Min Yi Wu",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Nathan A. Baer",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Pedro Belda-Ferre",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Peter DeHoff",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Phoebe Saever",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "R. Tyler Ostrander",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Rebecca Tsai",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Shashank Sathe",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Stefan Aigner",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Sydney C Morgan",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Toan T. Ngo",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Tom Barber",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Willi Cheung",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Aaron F Carlin",
+        "author_inst": "University of California San Diego"
+      },
+      {
+        "author_name": "Gene W. Yeo",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Louise Laurent",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Rebecca Fielding-Miller",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Rob Knight",
+        "author_inst": "UCSD School of Medicine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2021.07.16.21260627",
     "rel_title": "High frequency, high throughput quantification of SARS-CoV-2 RNA in wastewater settled solids at eight publicly owned treatment works in Northern California shows strong association with COVID-19 incidence",
@@ -651575,65 +650269,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.07.19.21260410",
-    "rel_title": "Applying mixture model methods to SARS-CoV-2 serosurvey data from the SEROCoV-POP study",
-    "rel_date": "2021-07-19",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260410",
-    "rel_abs": "Serosurveys are an important tool to estimate the true extent of the current SARS-CoV-2 pandemic. So far, most serosurvey data have been analysed with cut-off based methods, which dichotomize individual measurements into sero-positives or negatives based on a predefined cutoff. However, mixture model methods can gain additional information from the same serosurvey data. Such methods refrain from dichotomizing individual values and instead use the full distribution of the serological measurements from pre-pandemic and COVID-19 controls to estimate the cumulative incidence. This study presents an application of mixture model methods to SARS-CoV-2 serosurvey data from the SEROCoV-POP study from April and May 2020 in Geneva (2766 individuals). Besides estimating the total cumulative incidence in these data (8.1% (95% CI: 6.8% - 9.8%)), we applied extended mixture model methods to estimate an indirect indicator of disease severity, which is the fraction of cases with a distribution of antibody levels similar to hospitalised COVID-19 patients. This fraction is 51.2% (95% CI: 15.2% - 79.5%) across the full serosurvey, but differs between three age classes: 21.4% (95% CI: 0% - 59.6%) for individuals between 5 and 40 years old, 60.2% (95% CI: 21.5% - 100%) for individuals between 41 and 65 years old and 100% (95% CI: 20.1% - 100%) for individuals between 66 and 90 years old. Additionally, we find a mismatch between the inferred negative distribution of the serosurvey and the validation data of pre-pandemic controls. Overall, this study illustrates that mixture model methods can provide additional insights from serosurvey data.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Judith A Bouman",
-        "author_inst": "ETH zurich"
-      },
-      {
-        "author_name": "Sarah Kadelka",
-        "author_inst": "ETH Zurich"
-      },
-      {
-        "author_name": "Silvia Stringhini",
-        "author_inst": "Geneva University Hospitals"
-      },
-      {
-        "author_name": "Francesco Pennacchio",
-        "author_inst": "Geneva University Hospitals"
-      },
-      {
-        "author_name": "Benjamin Meyer",
-        "author_inst": "University of Geneva"
-      },
-      {
-        "author_name": "Sabine Yerly",
-        "author_inst": "Geneva University Hospitals"
-      },
-      {
-        "author_name": "Laurent Kaiser",
-        "author_inst": "University of Geneva Hospitals"
-      },
-      {
-        "author_name": "Idris Guessous",
-        "author_inst": "Geneva University Hospitals"
-      },
-      {
-        "author_name": "Andrew S Azman",
-        "author_inst": "Johns Hopkins University"
-      },
-      {
-        "author_name": "Sebastian Bonhoeffer",
-        "author_inst": "ETH Zurich"
-      },
-      {
-        "author_name": "Roland R Regoes",
-        "author_inst": "ETH Zurich"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.07.15.21260595",
     "rel_title": "Identifying and alleviating bias due to differential depletion of susceptible people in post-marketing evaluations of COVID-19 vaccines",
@@ -652096,6 +650731,81 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.07.15.21260561",
+    "rel_title": "Viral Load of SARS-CoV-2 in Respiratory Aerosols Emitted by COVID-19 Patients while Breathing, Talking, and Singing",
+    "rel_date": "2021-07-19",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.15.21260561",
+    "rel_abs": "BackgroundMultiple SARS-CoV-2 superspreading events suggest that aerosols play an important role in driving the COVID-19 pandemic. However, the detailed roles of coarse (>5m) and fine ([&le;]5m) respiratory aerosols produced when breathing, talking, and singing are not well-understood.\n\nMethodsUsing a G-II exhaled breath collector, we measured viral RNA in coarse and fine respiratory aerosols emitted by COVID-19 patients during 30 minutes of breathing, 15 minutes of talking, and 15 minutes of singing.\n\nResultsAmong the 22 study participants, 13 (59%) emitted detectable levels of SARS-CoV-2 RNA in respiratory aerosols, including 3 asymptomatic patients and 1 presymptomatic patient. Viral loads ranged from 63-5,821 N gene copies per expiratory activity per patient. Patients earlier in illness were more likely to emit detectable RNA, and loads differed significantly between breathing, talking, and singing. The largest proportion of SARS-CoV-2 RNA copies was emitted by singing (53%), followed by talking (41%) and breathing (6%). Overall, fine aerosols constituted 85% of the viral load detected in our study. Virus cultures were negative.\n\nConclusionsFine aerosols produced by talking and singing contain more SARS-CoV-2 copies than coarse aerosols and may play a significant role in the transmission of SARS-CoV-2. Exposure to fine aerosols should be mitigated, especially in indoor environments where airborne transmission of SARS-CoV-2 is likely to occur. Isolating viable SARS-CoV-2 from respiratory aerosol samples remains challenging, and whether this can be more easily accomplished for emerging SARS-CoV-2 variants is an important enquiry for future studies.\n\nKey PointsWe sampled respiratory aerosols emitted by COVID-19 patients and discovered that fine aerosols ([&le;]5m) generated during talking and singing contain more SARS-CoV-2 copies than coarse aerosols (>5m) and may play a significant role in the transmission of SARS-CoV-2.",
+    "rel_num_authors": 15,
+    "rel_authors": [
+      {
+        "author_name": "Kristen K. Coleman",
+        "author_inst": "Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore"
+      },
+      {
+        "author_name": "Douglas Jie Wen Tay",
+        "author_inst": "Department of the Built Environment, National University of Singapore, Singapore"
+      },
+      {
+        "author_name": "Kai Sen Tan",
+        "author_inst": "Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore"
+      },
+      {
+        "author_name": "Sean Wei Xiang Ong",
+        "author_inst": "National Centre for Infectious Diseases, Singapore"
+      },
+      {
+        "author_name": "Than The Son",
+        "author_inst": "Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore"
+      },
+      {
+        "author_name": "Ming Hui Koh",
+        "author_inst": "Department of the Built Environment, National University of Singapore, Singapore"
+      },
+      {
+        "author_name": "Yi Qing Chin",
+        "author_inst": "National Centre for Infectious Diseases, Singapore"
+      },
+      {
+        "author_name": "Haziq Nasir",
+        "author_inst": "Division of Infectious Diseases, Department of Medicine, National University Health System, National University of Singapore, Singapore"
+      },
+      {
+        "author_name": "Tze Minn Mak",
+        "author_inst": "National Centre for Infectious Diseases, Singapore"
+      },
+      {
+        "author_name": "Justin Jang Hann Chu",
+        "author_inst": "Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore"
+      },
+      {
+        "author_name": "Donald K. Milton",
+        "author_inst": "Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health, USA"
+      },
+      {
+        "author_name": "Vincent T.K. Chow",
+        "author_inst": "Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singap"
+      },
+      {
+        "author_name": "Paul Anantharajah Tambyah",
+        "author_inst": "Division of Infectious Diseases, Department of Medicine, National University Health System, National University of Singapore, Singapore"
+      },
+      {
+        "author_name": "Mark Chen",
+        "author_inst": "National Centre for Infectious Diseases, Singapore"
+      },
+      {
+        "author_name": "Tham Kwok Wai",
+        "author_inst": "Department of the Built Environment, National University of Singapore, Singapore"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.07.15.21260537",
     "rel_title": "Characterising within-hospital SARS-CoV-2 transmission events: a retrospective analysis integrating epidemiological and viral genomic data from a UK tertiary care setting across two pandemic waves",
@@ -653609,93 +652319,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2021.07.18.452826",
-    "rel_title": "Susceptibilities of human ACE2 genetic variants in coronavirus infection",
-    "rel_date": "2021-07-19",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.18.452826",
-    "rel_abs": "The COVID-19 pandemic, caused by SARS-CoV-2, has resulted in more than 1603 million cases worldwide and 3.4 million deaths (as of May 2021), with varying incidences and death rates among regions/ethnicities. Human genetic variation can affect disease progression and outcome, but little is known about genetic risk factors for SARS-CoV-2 infection. The coronaviruses SARS-CoV, SARS-CoV-2 and HCoV-NL63 all utilize the human protein angiotensin-converting enzyme 2 (ACE2) as the receptor to enter cells. We hypothesized that the genetic variability in ACE2 may contribute to the variable clinical outcomes of COVID-19. To test this hypothesis, we first conducted an in silico investigation of single-nucleotide polymorphisms (SNPs) in the coding region of ACE2 gene. We then applied an integrated approach of genetics, biochemistry and virology to explore the capacity of select ACE2 variants to bind coronavirus spike protein and mediate viral entry. We identified the ACE2 D355N variant that restricts the spike protein-ACE2 interaction and consequently limits infection both in vitro and in vivo. In conclusion, ACE2 polymorphisms could modulate susceptibility to SARS-CoV-2, which may lead to variable disease severity.",
-    "rel_num_authors": 18,
-    "rel_authors": [
-      {
-        "author_name": "Wenlin Ren",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Yunkai Zhu",
-        "author_inst": "Fudan University"
-      },
-      {
-        "author_name": "Jun Lan",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Hedi Chen",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Yuyan Wang",
-        "author_inst": "Fudan University"
-      },
-      {
-        "author_name": "Hongyang Shi",
-        "author_inst": "Institut Pasteur of Shangha"
-      },
-      {
-        "author_name": "Fei Feng",
-        "author_inst": "Fudan University"
-      },
-      {
-        "author_name": "Da-Yuan Chen",
-        "author_inst": "Boston University School of Medicine"
-      },
-      {
-        "author_name": "Brianna Close",
-        "author_inst": "Boston University School of Medicine"
-      },
-      {
-        "author_name": "Xiaomin Zhao",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Jianping Wu",
-        "author_inst": "Westlake University"
-      },
-      {
-        "author_name": "Boxue Tian",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Zhenghong Yuan",
-        "author_inst": "Fudan University"
-      },
-      {
-        "author_name": "Dongming Zhou",
-        "author_inst": "Tianjin Medical University"
-      },
-      {
-        "author_name": "Mohsan Saeed",
-        "author_inst": "Boston University"
-      },
-      {
-        "author_name": "Xinquan Wang",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Rong Zhang",
-        "author_inst": "Fudan University"
-      },
-      {
-        "author_name": "Qiang Ding",
-        "author_inst": "Tsinghua University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2021.07.19.452910",
     "rel_title": "Integrative multi-omics landscape of non-structural protein 3 of severe acute respiratory syndrome coronaviruses",
@@ -654062,6 +652685,53 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2021.07.16.452748",
+    "rel_title": "Key substitutions in the spike protein of SARS-CoV-2 variants can predict resistance to monoclonal antibodies, but other substitutions can modify the effects",
+    "rel_date": "2021-07-19",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.16.452748",
+    "rel_abs": "Mutations in the spike protein of SARS-CoV-2 variants can compromise the effectiveness of therapeutic antibodies. Most clinical-stage therapeutic antibodies target the spike receptor binding domain (RBD), but variants often have multiple mutations in several spike regions. To help predict antibody potency against emerging variants, we evaluated 25 clinical-stage therapeutic antibodies for neutralization activity against 60 pseudoviruses bearing spikes with single or multiple substitutions in several spike domains, including the full set of substitutions in B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), B.1.429 (Epsilon), B.1.526 (Iota), A.23.1 and R.1 variants. We found that 14 of 15 single antibodies were vulnerable to at least one RBD substitution, but most combination and polyclonal therapeutic antibodies remained potent. Key substitutions in variants with multiple spike substitutions predicted resistance, but the degree of resistance could be modified in unpredictable ways by other spike substitutions that may reside outside of the RBD. These findings highlight the importance of assessing antibody potency in the context of all substitutions in a variant and show that epistatic interactions in spike can modify virus susceptibility to therapeutic antibodies.\n\nImportanceTherapeutic antibodies are effective in preventing severe disease from SARS-CoV-2 infection (COVID-19), but their effectiveness may be reduced by virus variants with mutations affecting the spike protein. To help predict resistance to therapeutic antibodies in emerging variants, we profiled resistance patterns of 25 antibody products in late stages of clinical development against a large panel of variants that include single and multiple substitutions found in the spike protein. We found that the presence of a key substitution in variants with multiple spike substitutions can predict resistance against a variant, but that other substitutions can affect the degree of resistance in unpredictable ways. These finding highlight complex interactions among substitutions in the spike protein affecting virus neutralization and potentially virus entry into cells.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Sabrina Lusvarghi",
+        "author_inst": "US Food and Drug Administration"
+      },
+      {
+        "author_name": "Wei Wang",
+        "author_inst": "US Food and Drug Administration"
+      },
+      {
+        "author_name": "Rachel Herrup",
+        "author_inst": "US Food and Drug Administration"
+      },
+      {
+        "author_name": "Sabari Nath Neerukonda",
+        "author_inst": "US Food and Drug Administration"
+      },
+      {
+        "author_name": "Russell Vassell",
+        "author_inst": "US Food and Drug Administration"
+      },
+      {
+        "author_name": "Lisa Bentley",
+        "author_inst": "Office of the Assistance Secretary for Preparedness and Response, US Department of Human Health and Services"
+      },
+      {
+        "author_name": "Ann E. Eakin",
+        "author_inst": "US National Institutes of Health"
+      },
+      {
+        "author_name": "Carol D. Weiss",
+        "author_inst": "US Food and Drug Administration"
+      }
+    ],
+    "version": "1",
+    "license": "cc0",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2021.07.19.21258787",
     "rel_title": "Dique Filipeia: A rehabilitation protocol for non-intubated COVID-19 in-hospital patients",
@@ -655575,57 +654245,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.07.13.21260467",
-    "rel_title": "Combined Anticoagulant and antiplatelet therapy is associated with an improved outcome in hospitalized COVID-19 patients: a propensity matched cohort study",
-    "rel_date": "2021-07-16",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.13.21260467",
-    "rel_abs": "BackgroundCOVID-19 is a respiratory disease that results in a prothrombotic state manifesting as thrombotic, microthrombotic and thromboembolic events. As a result, several antithrombotic modalities have been implicated in the treatment of this disease. This study aimed to identify if therapeutic anticoagulation or concurrent use of antiplatelet and anticoagulants was associated with an improved outcome in this patient population.\n\nMethodsA retrospective observational cohort study of adult patients admitted to a single university hospital for COVID-19 infection was performed. The primary outcome was a composite of in-hospital mortality, ICU admission, or the need for mechanical ventilation. The secondary outcomes were each of the components of the primary outcome, in-hospital mortality, ICU admission, or the need for mechanical ventilation.\n\nResults242 patients were included in the study and divided into 4 subgroups: therapeutic anticoagulation (TAC), prophylactic anticoagulation + antiplatelet (PACAP), therapeutic anticoagulation + antiplatelet (TACAP), and prophylactic anticoagulation (PAC) which was the reference for comparison. Multivariable cox regression analysis and propensity matching were done and showed when compared to PAC, TACAP and TAC were associated with less in-hospital all cause mortality with an adjusted hazard ratio (aHR) of 0.113 (95% confidence interval (CI) 0.028-0.449) and 0.126 (95% CI, 0.028-0.528) respectively. The number needed to treat (NNT) in both subgroups was 11. Furthermore, PACAP was associated with a reduced risk of invasive mechanical ventilation with an aHR of 0.07 (95% CI, 0.014-0.351). However, the was no statistically significant difference in the occurrence of major or minor bleeds, ICU admission, or the composite outcome of in-hospital mortality, ICU admission or the need for mechanical ventilation.\n\nConclusionThe use of combined anticoagulant and antiplatelet agents or therapeutic anticoagulation alone in hospitalized COVID-19 patients was associated with a better outcome in comparison to prophylactic anticoagulation alone without an increase in the risk of major and minor bleeds. Sufficiently powered randomized controlled trials are needed to further evaluate the safety and efficacy of combining antiplatelet and anticoagulants agents or using therapeutic anticoagulation in the management of patients with COVID-19 infection.\n\nWhat is already known about this subject ?Covid-19 infection is associated with several complex coagulation disorders resulting in thrombotic, microthrombotic and thromboembolic events. Currently, prophylactic dose anticoagulation is considered the standard of care antithrombotic regimen in hospitalized COVID-19 patients. However, high-quality data about the subject is unavailable.\n\nWhat does this study add?This is the first adequately sized study in the literature to dwell on the antithrombotic strategy consisting of combination anticoagulant and antiplatelet therapy in the treatment of COVID-19 induced hypercoagulable state. Furthermore, it also challenges the currently recommended prophylactic dosing of anticoagulation used in the treatment of those patients.\n\nHow might this impact on clinical practice?Our data suggests for the first time that concurrent use of anticoagulant and antiplatelet therapy is associated with a superior clinical outcome as compared to prophylactic anticoagulation used alone. Furthermore, it solidifies the emerging evidence that therapeutic anticoagulation is linked to better clinical results than prophylactic anticoagulation.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Kamal Matli",
-        "author_inst": "Lebanese American University Medical Center Rizk Hospital"
-      },
-      {
-        "author_name": "Nibal Chamoun",
-        "author_inst": "Lebanese American University- School of Pharmacy"
-      },
-      {
-        "author_name": "Aya Fares",
-        "author_inst": "Lebanese American University Medical Center Rizk Hospital"
-      },
-      {
-        "author_name": "Victor Zibara",
-        "author_inst": "Lebanese American University Medial Center Rizk Hospital"
-      },
-      {
-        "author_name": "Soad Al-Osta",
-        "author_inst": "Lebanese American University Medical Center Rizk Hospital"
-      },
-      {
-        "author_name": "Rabih Nasrallah",
-        "author_inst": "Lebanese American University Medical Center Rizk Hospital"
-      },
-      {
-        "author_name": "Pascale Salameh",
-        "author_inst": "Lebanese University-School of Pharmacy"
-      },
-      {
-        "author_name": "Jacques Mokhbat",
-        "author_inst": "Lebanese American University Medical Center Rizk Hospital"
-      },
-      {
-        "author_name": "Georges Ghanem",
-        "author_inst": "Lebanese American University Medical Center Rizk Hospital"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "cardiovascular medicine"
-  },
   {
     "rel_doi": "10.1101/2021.07.13.21260428",
     "rel_title": "Epidemiology and Clinical Characteristics in Individuals with Confirmed SARS-CoV-2 Infection During the Early COVID-19 Pandemic in Saudi Arabia",
@@ -656048,6 +654667,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.07.13.21260442",
+    "rel_title": "Rapid and Quantitative Detection of Human Antibodies Against the 2019 Novel Coronavirus SARS CoV2 and its Variants as a Result of Vaccination and Infection",
+    "rel_date": "2021-07-16",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.13.21260442",
+    "rel_abs": "Measuring the antibody response to 2019 SARS CoV2 is critical for diagnostic purposes, monitoring the prevalence of infection, and for gauging the efficacy of the worldwide vaccination effort COVID-19. In this study, a microchip-based grating coupled fluorescent plasmonic (GC-FP) assay was used to measure antibody levels that resulted from COVID-19 infection and vaccination. In addition, we measured the relative antibody binding towards antigens from variants CoV2 virus variants, strains B.1.1.7 (UK) and B.1.351 (S. African). Antibody levels against multiple antigens within the SARS CoV2 spike protein were significantly elevated for both vaccinated and infected individuals, while those against the nucleocapsid (N) protein were only elevated for infected individuals. GC-FP was effective for monitoring the IgG-based serological response to vaccination throughout the vaccination sequence, and could also resolve acute (within hours) increases in antibody levels. A significant decrease in antibody binding to antigens from the B.1.351 variant, but not B.1.1.7, was observed for all vaccinated subjects when measured by GC-FP as compared to the 2019 SARS CoV2 antigens. These results were corroborated by competitive ELISA assay. Collectively, the findings suggest that GC-FP is a viable, rapid, and accurate method for measuring both overall antibody levels to CoV2 and relative antibody binding to viral variants during infection or vaccination.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Benjamin Taubner",
+        "author_inst": "SUNY Polytechnic Institute"
+      },
+      {
+        "author_name": "Ruben Peredo-Wende",
+        "author_inst": "Albany Medical Center"
+      },
+      {
+        "author_name": "Ananthakrishnan Ramani",
+        "author_inst": "Albany Medical Center"
+      },
+      {
+        "author_name": "Gurpreet Singh",
+        "author_inst": "Albany Medical Center"
+      },
+      {
+        "author_name": "Klemen Strle",
+        "author_inst": "Wadsworth Center"
+      },
+      {
+        "author_name": "Nathaniel Cady",
+        "author_inst": "SUNY Polytechnic Institute"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.07.13.21260426",
     "rel_title": "Persistence of neutralizing antibodies a year after SARS-CoV-2 infection",
@@ -657165,25 +655823,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "emergency medicine"
   },
-  {
-    "rel_doi": "10.1101/2021.07.12.21260326",
-    "rel_title": "COVID-19 Pandemic Analysis",
-    "rel_date": "2021-07-15",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.12.21260326",
-    "rel_abs": "The development of coronavirus disease (COVID-19) deaths in selected nations and states is compared to the result of calculations using a conventional SEIR model of pandemic development. The model is based on the infection multiplier, R0, defined as the number of people infected by each infectious person. The infection rate increases exponentially when R0 >1.0; it remains constant at R0 = 1.0 and decreases for R0 < 1.0. R0 is determined by population behavior (frequency and proximity of interactions) and the ease by which a victim is infected by an infectious person (virulence of the virus). It is reduced by herd immunity when a large fraction of the population acquires immunity by vaccination or by recovering from infection.\n\nThe daily death rates in the U.S. and northern Europe exhibited peaks in April/May 2020 and Dec. 2020/Jan. 2021 with more a modest rate during the summer of 2020 and a gradually decreasing rate since Jan. 2021. The model produces this type of oscillatory response if it assumes that the populations R0 responds to information reported about the pandemic, but with a delay between infections and resulting behavioral adjustments. Oscillatory behavior is typical of a control loop with delay in its feedback.\n\nThe analysis concludes thatO_QDGiven the history of R0 the model predicts the development of pandemic deaths. However, since R0 is determined by the populations behavior, control of the pandemic in democracies depends primarily on preparation and the persuasive power of political and scientific authorities. Data for S. Korea and New Zealand demonstrate the effectiveness of such methods.\n\nFor each death in the U.S. about 169 persons were infected, but fewer than half of them were identified as cases.\n\nThe pandemic was prolonged in the U.S. because the population chose to keep R0 near 1.0 by relaxing restrictions once the death rate subsided.\n\nInitial values of R0 as high as 5.0 were observed, leading to infections doubling about every 2 days. If unabated, the resulting exponential growth increases the infected population by a factor of about 5000 before the death from the first infections is recorded.\n\nArrival from Italy probably initiated the pandemic in the eastern U.S., but, by the time the first death was recorded the number of domestic infections exceeded by far those that were imported. Import restrictions beyond this point are ineffective except in delaying the arrival of more virulent mutations.\n\nIf no social restrictions had been adopted, approximately 1.6 million deaths would have resulted in the U.S. The vaccine, although developed and deployed at record speed, was too late to ameliorate this result.\n\nA third peak in death rate in Sept. 2021 may be prevented if more than 80% of the population is vaccinated.\n\nC_QD",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Victor A.J. van Lint",
-        "author_inst": "retired"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.07.12.21260216",
     "rel_title": "Quantifying social contact patterns in Minnesota during Stay-at-Home social distancing order",
@@ -657578,6 +656217,161 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2021.07.12.21260360",
+    "rel_title": "The impact of hypoxia on B cells in COVID-19",
+    "rel_date": "2021-07-15",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.12.21260360",
+    "rel_abs": "Prominent early features of COVID-19 include severe, often clinically silent, hypoxia and a pronounced reduction in B cells, the latter important in defence against SARS-CoV-2. This brought to mind the phenotype of mice with VHL-deficient B cells, in which Hypoxia-Inducible Factors are constitutively active, suggesting hypoxia might drive B cell abnormalities in COVID-19. We demonstrated the breadth of early and persistent defects in B cell subsets in moderate/severe COVID-19, including reduced marginal zone-like, memory and transitional B cells, changes we also observed in B cell VHL-deficient mice. This was corroborated by hypoxia-related transcriptional changes in COVID-19 patients, and by similar B cell abnormalities in mice kept in hypoxic conditions, including reduced marginal zone and germinal center B cells. Thus hypoxia might contribute to B cell pathology in COVID-19, and in other hypoxic states. Through this mechanism it may impact on COVID-19 outcome, and be remediable through early oxygen therapy.",
+    "rel_num_authors": 35,
+    "rel_authors": [
+      {
+        "author_name": "Prasanti Kotagiri",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Federica Mescia",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Aimee Hanson",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Lorinda Turner",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Laura Bergamaschi",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Ana Penalver",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Nathan Richoz",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Stephen Moore",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Brian Ortmann",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Benjamin Dunmore",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Helene Ruffieux",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Michael Morgan",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Zewen Kelvin Tuong",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Rachael Bashford Rogers",
+        "author_inst": "Oxford University"
+      },
+      {
+        "author_name": "Myra Hosmillo",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Stephen Baker",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Anne Elmer",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Ian Goodfellow",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Ravindra Gupta",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Nathalie Kingston",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Paul Lehner",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Nicholas Matheson",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Sylvia Richardson",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Caroline Saunders",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Michael Weekes",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Berthold Gottgens",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Mark Toshner",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Christoph Hess",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Patrick Maxwell",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Menna Clatworthy",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "James A Nathan",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "John Bradley",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Paul Lyons",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Natalie Burrows",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Kenneth G C Smith",
+        "author_inst": "Cambridge University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.07.15.452246",
     "rel_title": "Gut microbiome dysbiosis during COVID-19 is associated with increased risk for bacteremia and microbial translocation.",
@@ -659074,49 +657868,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.07.09.21260259",
-    "rel_title": "Using population based Kalman estimator to model COVID-19 epidemics in France: estimating the burden of SARS-CoV-2 and the effects of NPI.",
-    "rel_date": "2021-07-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.09.21260259",
-    "rel_abs": "SummaryIn response to the COVID-19 pandemic caused by SARS-CoV-2, governments have adopted a wide range of non-pharmaceutical interventions (NPI). These include stringent measures such as strict lockdowns, closing schools, bars and restaurants, curfews, and barrier gestures such as mask-wearing and social distancing. Deciphering the effectiveness of each NPI is critical to responding to future waves and outbreaks. To this end, we first develop a dynamic model of the French COVID-19 epidemics over a one-year period. We rely on a global extended Susceptible-Infectious-Recovered (SIR) mechanistic model of infection that includes a dynamic transmission rate over time. Multilevel data across French regions are integrated using random effects on the parameters of the mechanistic model, boosting statistical power by multiplying integrated observation series. We estimate the parameters using a new population-based statistical approach based on a Kalman filter, used for the first time in analysing real-world data. We then fit the estimated time-varying transmission rate using a regression model that depends on the NPIs while accounting for vaccination coverage, the occurrence of variants of concern (VoC), and seasonal weather conditions. We show that all NPIs considered have an independent significant association with transmission rates. In addition, we show a strong association between weather conditions that reduces transmission in summer, and we also estimate increased transmissibility of VoC.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Annabelle Collin",
-        "author_inst": "Universite de Bordeaux, INP, IMB, Inria MONC"
-      },
-      {
-        "author_name": "Boris Hejblum",
-        "author_inst": "Universite de Bordeaux,  Inserm U1219, Inria SISTM"
-      },
-      {
-        "author_name": "Carole Vignals",
-        "author_inst": "Universite de Bordeaux, Inserm U1219, Inria SISTM, CHU Bordeaux"
-      },
-      {
-        "author_name": "Laurent Lehot",
-        "author_inst": "Universite de Bordeaux, Inserm U1219, inria SISTM"
-      },
-      {
-        "author_name": "Rodolphe Thiebaut",
-        "author_inst": "Universite de Bordeaux, Inserm U1219, Inria, CHU Bordeaux"
-      },
-      {
-        "author_name": "Philippe Moireau",
-        "author_inst": "Inria, LMS, CNRS 7707, Ecole polytechnique"
-      },
-      {
-        "author_name": "Melanie Prague",
-        "author_inst": "Universite de Bordeaux, Inserm U1219, Inria,  SISTM"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.07.12.21258824",
     "rel_title": "STUDY OF BLOOD GROUP ANALYSIS AND ITS CORRELATION WITH LYMPHOPENIA IN COVID 19 INFECTED CASES OUR EXPERIENCE IN TERITARY CARE HOSPITAL.",
@@ -659491,6 +658242,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "cardiovascular medicine"
   },
+  {
+    "rel_doi": "10.1101/2021.07.13.452256",
+    "rel_title": "Tissue Specific Age Dependence of the Cell Receptors Involved in the SARS-CoV-2 Infection",
+    "rel_date": "2021-07-14",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.13.452256",
+    "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic has affected tens of millions of individuals and caused hundreds of thousands of deaths worldwide. Due to its rapid surge, there is a shortage of information on viral behavior and host response after SARS-CoV-2 infection. Here we present a comprehensive, multiscale network analysis of the transcriptional response to the virus. We particularly focus on key-regulators, cell-receptors, and host-processes that are hijacked by the virus for its advantage. ACE2-controlled processes involve a key-regulator CD300e (a TYROBP receptor) and the activation of IL-2 pro-inflammatory cytokine signaling. We further investigate the age-dependency of such receptors and identify the adipose and the brain as potentially contributing tissues for the diseases severity in old patients. In contrast, several other tissues in the young population are more susceptible to SARS-CoV-2 infection. In summary, this present study provides novel insights into the gene regulatory organization during the SARS-CoV-2 infection and the tissue-specific age dependence of the cell receptors involved in COVID-19.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Christian V Forst",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Lu Zeng",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Qian Wang",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Xianxiao Zhou",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Sezen Vatansever",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Zhidong Tu",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Bin Zhang",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "systems biology"
+  },
   {
     "rel_doi": "10.1101/2021.07.13.452160",
     "rel_title": "Adaptation, spread and transmission of SARS-CoV-2 in farmed minks and related humans in the Netherlands",
@@ -660944,29 +659738,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.07.08.21260210",
-    "rel_title": "Infection fatality rate of COVID-19 in community-dwelling populations with emphasis on the elderly: An overview",
-    "rel_date": "2021-07-13",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.08.21260210",
-    "rel_abs": "ObjectiveThis mixed design synthesis aimed to estimate the infection fatality rate (IFR) of Coronavirus Disease 2019 (COVID-19) in community-dwelling elderly populations and other age groups from seroprevalence studies. Protocol: https://osf.io/47cgb.\n\nMethods and analysesEligible were seroprevalence studies done in 2020 and identified by any of four existing systematic reviews; with [&ge;]1000 participants aged [&ge;]70 years that presented seroprevalence in elderly people; that aimed to generate samples reflecting the general population; and whose location had available data on cumulative COVID-19 deaths in elderly (primary cutoff [&ge;]70 years; [&ge;]65 or [&ge;]60 also eligible). We extracted the most fully adjusted (if unavailable, unadjusted) seroprevalence estimates. We also extracted age- and residence-stratified cumulative COVID-19 deaths (until 1 week after the seroprevalence sampling midpoint) from official reports, and population statistics, to calculate IFRs corrected for unmeasured antibody types. Sample size-weighted IFRs were estimated for countries with multiple estimates. Secondary analyses examined data on younger age strata from the same studies.\n\nResultsTwenty-five seroprevalence surveys representing 14 countries were included. Across all countries, the median IFR in community-dwelling elderly and elderly overall was 2.9% (range 0.2%-6.9%) and 4.9% (range 0.2%-16.8%) without accounting for seroreversion (2.4% and 4.0%, respectively, accounting for 5% monthly seroreversion). Multiple sensitivity analyses yielded similar results. IFR was higher with larger proportions of people >85 years. Younger age strata had low IFR values (median 0.0013%, 0.0088%, 0.021%, 0.042%, 0.14%, and 0.65%, at 0-19, 20-29, 30-39, 40-49, 50-59, and 60-69 years even without accounting for seroreversion).\n\nConclusionsThe IFR of COVID-19 in community-dwelling elderly people is lower than previously reported. Very low IFRs were confirmed in the youngest populations.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Cathrine Axfors",
-        "author_inst": "Stanford University"
-      },
-      {
-        "author_name": "John P.A. Ioannidis",
-        "author_inst": "Stanford University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.07.11.21260317",
     "rel_title": "COVID-19 vaccine uptake, predictors of vaccination, and self-reported barriers to vaccination among primary school teachers in Poland",
@@ -661377,6 +660148,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.07.07.21260167",
+    "rel_title": "Indications that Stockholm has reached herd immunity, given limited restrictions, against several variants of SARS-CoV-2",
+    "rel_date": "2021-07-13",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.07.21260167",
+    "rel_abs": "\"When COVID-19 cases go up, public compliance with restrictions is poor, when cases go down, public compliance is good.\" In this article, we question this explanation and show that relatively low levels of sero-prevalence helps to keep cases down. In other words, the herd-immunity threshold appears to be much lower than previously thought. We construct a mathematical model taking pre-immunity, antibody waning and more infectious variants of concern into consideration, thereby providing a theoretical framework in which the cases in Stockholm county can be fully predicted without relying on neither oscillations in restrictions (and public compliance thereof) nor vaccination roll-out. We also show that it is very difficult to match the data from Stockholm without including pre-immunity, or, which turns out to be equivalent, great variations in susceptibility.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Marcus Carlsson",
+        "author_inst": "Lund University"
+      },
+      {
+        "author_name": "Cecilia Soderberg-Naucler",
+        "author_inst": "Department of Medicine, Karolinska Institute"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.07.12.452071",
     "rel_title": "TNF-\u03b1 levels in respiratory samples are associated with SARS-CoV-2 infection.",
@@ -662814,89 +661608,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.07.06.21260085",
-    "rel_title": "Effectiveness of Rosuvastatin plus Colchicine, Emtricitabine/Tenofovir and a combination of them in Hospitalized Patients with SARS Covid-19",
-    "rel_date": "2021-07-10",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.06.21260085",
-    "rel_abs": "BACKGROUNDThe effectiveness of rosuvastatin plus colchicine, emtricitabine/tenofovir, and of their combined use in hospitalized patients with coronavirus disease 2019 (Covid-19) pneumonia is unclear.\n\nMETHODSIn each hospital, hospitalized adults with Covid-19 pneumonia, were randomly assigned, in a 1:1 ratio, to receive: a) standard of care; or b) emtricitabine/tenofovir; or c) colchicine + rosuvastatin; or d) emtricitabine/tenofovir + colchicine + rosuvastatin. The primary outcome was all-cause mortality within the first 28 days after randomization. Severe adverse events (SAE) were those with a high probability of being treatment-related.\n\nRESULTS633 patients were randomized in 6 hospitals in Bogota, Colombia. Overall, 98% of the patients received glucocorticoids during hospitalization. The cumulative incidence of death through day 28 was 10.7% in the emtricitabine/tenofovir + colchicine + rosuvastatin arm, 14.4% in the colchicine + rosuvastatin arm, 13.8% in the emtricitabine/tenofovir arm, and 17.4% in the standard of care arm, with adjusted risk differences (aRD) against the standard treatment of -0.07 (95% confidence interval [CI], -0.17 to 0.04), aRD -0.03 (95%CI: -0.11 to 0.05) and aRD: -0.05 (95%CI: -0.15 to 0.05), respectively. Need for invasive mechanical ventilation was lower in the emtricitabine/tenofovir + colchicine + rosuvastatin arm compared to the standard treatment arm, aRD: -0.06 (95%CI: -0.11 to -0,01), but no differences were found between the other comparisons. SAE occurred in 3 patients distributed in the 3 treatment arms.\n\nCONCLUSIONSAmong patients hospitalized with moderate and severe SARS Covid-19, the use of the emtricitabine/tenofovir + colchicine + rosuvastatin combination emerges as a treatment alternative.\n\nClinicalTrials.gov number: NCT04359095",
-    "rel_num_authors": 17,
-    "rel_authors": [
-      {
-        "author_name": "Hernando Guillermo Gaitan-Duarte",
-        "author_inst": "Clinical Research Institute. Universidad Nacional de Colombia. Hospital Universitario Nacional de Colombia"
-      },
-      {
-        "author_name": "Carlos alvarez-Moreno",
-        "author_inst": "Internal Medicine Department. Universidad Nacional de Colombia. Clinica Universitaria Colombia. Clinica Colsanitas."
-      },
-      {
-        "author_name": "Carlos Javier Rincon-Rodriguez",
-        "author_inst": "Department of Clinical Epidemiology and Biostatistics. Pontificia Universidad Javeriana."
-      },
-      {
-        "author_name": "Nancy Yomayusa-Gonzalez",
-        "author_inst": "Global Institute of Clinical Excellence-Translational Research Group, Fundacion Universitaria Sanitas, Clinica Reina Sofia. Clinica Colsanitas."
-      },
-      {
-        "author_name": "Jorge Alberto Cortes",
-        "author_inst": "Internal Medicine Department. Universidad Nacional de Colombia. Infectious Diseases Service. Hospital Universitario Nacional de Colombia."
-      },
-      {
-        "author_name": "Juan Carlos Villar",
-        "author_inst": "Departamento de Investigaciones. Fundacion Cardioinfantil. Instituto de Cardiologia."
-      },
-      {
-        "author_name": "Juan Sebastian Sebastian Bravo-Ojeda",
-        "author_inst": "Clinica Santa Maria del Lago. Colsanitas."
-      },
-      {
-        "author_name": "Angel Garcia-Pena.",
-        "author_inst": "Internal Medicine Department. Hospital Universitario San Ignacio. Pontificia Universidad Javeriana."
-      },
-      {
-        "author_name": "Wilson Adarme-Jaimes.",
-        "author_inst": "SEPRO Group. Facultad de Ingenieria. Universidad Nacional de Colombia."
-      },
-      {
-        "author_name": "Viviana Alejandra Rodriguez-Romero",
-        "author_inst": "Department of Clinical Epidemiology and Biostatistics. Pontificia Universidad Javeriana."
-      },
-      {
-        "author_name": "Steffany Lorena Villate-Soto",
-        "author_inst": "Clinical Research Institute. Universidad Nacional de Colombia"
-      },
-      {
-        "author_name": "Giancarlo Buitrago",
-        "author_inst": "Clinical Research Institute, Universidad Nacional de Colombia. Hospital Universitario Nacional de Colombia."
-      },
-      {
-        "author_name": "Julio Chacon-Sarmiento",
-        "author_inst": "Clinica Reina Sofia. Clinica Colsanitas. Fundacion Universitaria Sanitas."
-      },
-      {
-        "author_name": "Martin Macias-Quintero",
-        "author_inst": "Universidad Nacional de Colombia."
-      },
-      {
-        "author_name": "Claudia Patricia Vaca",
-        "author_inst": "Departamento de Farmacia. Universidad Nacional de Colombia."
-      },
-      {
-        "author_name": "Carlos Gomez-Restrepo",
-        "author_inst": "Department of Clinical Epidemiology and Biostatistics. Pontificia Universidad Javeriana."
-      },
-      {
-        "author_name": "Nelcy Rodriguez-Malagon.",
-        "author_inst": "Department of Clinical Epidemiology and Biostatistics. Pontificia Universidad Javeriana."
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.07.08.21260188",
     "rel_title": "COVID-19 and Black Fungus: Analysis of the Public Perception through Machine Learning",
@@ -663199,6 +661910,41 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2021.07.07.21260153",
+    "rel_title": "Transient infection with SARS-CoV-2 without induction of systemic immunity",
+    "rel_date": "2021-07-10",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.07.21260153",
+    "rel_abs": "SARS-CoV-2 testing using PCR is currently used as screening test to guide isolation and contact tracing. Among 1,700 players and staff of the German Bundesliga and Bundesliga 2 who were regularly tested twice weekly, 98 individuals had a positive PCR. Among those, 11 asymptomatic cases were identified who only had a transient single positive PCR of low viral load. As only one out of 11 individuals developed SARS-CoV-2 specific cellular and humoral immunity, this indicates that transient colonization with SARS-CoV-2 may frequently occur without systemic induction of specific adaptive immunity. This knowledge may have implications for management of isolation and contact tracing, which may not be justified in these cases.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Barbara C Gaertner",
+        "author_inst": "Saarland University, Institute for Medical Microbiology and Hygiene"
+      },
+      {
+        "author_name": "Verena Klemis",
+        "author_inst": "Saarland University, Department of Transplant and Infection Immunology"
+      },
+      {
+        "author_name": "Tina Schmidt",
+        "author_inst": "Saarland University, Department of Transplant and Infection Immunology"
+      },
+      {
+        "author_name": "Martina Sester",
+        "author_inst": "Saarland University, Department of Transplant and Infection Immunology"
+      },
+      {
+        "author_name": "Tim Meyer",
+        "author_inst": "Saarland University, Institute of Sports and Preventive Medicine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.07.08.21260201",
     "rel_title": "High prevalence of previous infection with SARS-CoV-2 and persistent symptoms at a large university",
@@ -664536,53 +663282,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.07.07.21259499",
-    "rel_title": "Antibody response to SARS-CoV-2 infection and BNT162b2 vaccine in Israel",
-    "rel_date": "2021-07-08",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.07.21259499",
-    "rel_abs": "Neutralizing antibodies targeting the Spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) block viral entry to host cells, preventing disease and further spread of the pathogen. The presence of SARS-CoV-2 antibodies in serum is a reliable indicator of infection, used epidemiologically to estimate the prevalence of infection and clinically as a measurement of an antigen-specific immune response. In this study, we analyzed serum Spike protein-specific IgG antibodies from 26,170 samples, including convalescent individuals who had coronavirus disease 2019 (COVID-19) and recipients of the BNT162b2 vaccine. We find distinct serological patterns in COVID-19 convalescent and vaccinated individuals, correlated with age and gender and the presence symptoms.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Guy Shapira",
-        "author_inst": "Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel"
-      },
-      {
-        "author_name": "Ramzia Abu Hamad",
-        "author_inst": "Shamir Medical Center, Be'er Yaacov, Israel"
-      },
-      {
-        "author_name": "Chen Weiner",
-        "author_inst": "Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Shamir Medical Center, Be'er Yaacov, Israel"
-      },
-      {
-        "author_name": "Nir Rainy",
-        "author_inst": "Shamir Medical Center, Be'er Yaacov, Israel"
-      },
-      {
-        "author_name": "Reut Sorek-Abramovich",
-        "author_inst": "Shamir Medical Center, Be'er Yaacov, Israel"
-      },
-      {
-        "author_name": "Patricia Benveniste-Levkovitz",
-        "author_inst": "Shamir Medical Center, Be'er Yaacov, Israel"
-      },
-      {
-        "author_name": "Adina Bar Chaim",
-        "author_inst": "Shamir Medical Center, Be'er Yaacov, Israel"
-      },
-      {
-        "author_name": "Noam Shomron",
-        "author_inst": "Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.07.07.21253295",
     "rel_title": "Mortality among Care Home Residents in England during the first and second waves of the COVID-19 pandemic: an analysis of 4.3 million adults over the age of 65",
@@ -665177,6 +663876,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.07.08.451640",
+    "rel_title": "Insights into the mutation T1117I in the spike and the lineage B.1.1.389 of SARS-CoV-2 circulating in Costa Rica",
+    "rel_date": "2021-07-08",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.08.451640",
+    "rel_abs": "Emerging mutations and genotypes of the SARS-CoV-2 virus, responsible for the COVID-19 pandemic, have been reported globally. In Costa Rica during the year 2020, a predominant genotype carrying the mutation T1117I in the spike (S:T1117I) was previously identified. To investigate the possible effects of this mutation on the function of the spike, i.e. the biology of the virus, different bioinformatic pipelines based on phylogeny, natural selection and co-evolutionary models, molecular docking and epitopes prediction were implemented.\n\nResults of the phylogeny of sequences carrying the S:T1117I worldwide showed a polyphyletic group, with the emergency of local lineages. In Costa Rica, the mutation is found in the lineage B.1.1.389 and it is suggested to be a product of positive/adaptive selection. Different changes in the function of the spike protein and more stable interaction with a ligand (nelfinavir drug) were found. Only one epitope out 742 in the spike was affected by the mutation, with some different properties, but suggesting scarce changes in the immune response and no influence on the vaccine effectiveness.\n\nJointly, these results suggest a partial benefit of the mutation for the spread of the virus with this genotype during the year 2020 in Costa Rica, although possibly not strong enough with the introduction of new lineages during early 2021 which became predominant later. In addition, the bioinformatics pipeline offers an integrative and exhaustive in silico strategy to eventually study other mutations of interest for the SARS-CoV-2 virus and other pathogens.\n\nHighlightsO_LIIn Costa Rica during the year 2020, a predominant SARS-CoV-2 genotype carrying the mutation T1117I in the spike (S:T1117I) was identified.\nC_LIO_LIThe S:T1117I was assessed for possible effects of this mutation on the function of the spike with a in silico approach.\nC_LIO_LIPhylogeny revealed that sequences carrying the S:T1117I worldwide define a polyphyletic group, with the emergency of local lineages, including the lineage B.1.1.389 in Costa Rica.\nC_LIO_LIA positive/adaptive selection was identified for S:T1117I, with different changes in the function of the spike protein, more stable interaction with ligands and scarce changes in the immune response.\nC_LIO_LIThe bioinformatics pipeline can be eventually used to study other mutations of the SARS-CoV-2 virus and other pathogens.\nC_LI",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Jose Arturo Molina-Mora",
+        "author_inst": "Centro de Investigacion en Enfermedades Tropicales (CIET) & Facultad de Microbiologia, Universidad de Costa Rica, San Jose, Costa Rica"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "bioinformatics"
+  },
   {
     "rel_doi": "10.1101/2021.07.08.451649",
     "rel_title": "Structure of a germline-like human antibody defines a neutralizing epitope on the SARS-CoV-2 spike NTD",
@@ -666682,41 +665400,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.07.06.21260109",
-    "rel_title": "AI-DRIVEN QUANTIFICATION OF GROUND GLASS OPACITIES IN LUNGS OF COVID-19 PATIENTS USING 3D COMPUTED TOMOGRAPHY IMAGING",
-    "rel_date": "2021-07-08",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.06.21260109",
-    "rel_abs": "ObjectivesGround-glass opacity (GGO) -- a hazy, gray appearing density on computed tomography (CT) of lungs -- is one of the hallmark features of SARS-CoV-2 in COVID-19 patients. This AI-driven study is focused on segmentation, morphology, and distribution patterns of GGOs.\n\nMethodWe use an AI-driven unsupervised machine learning approach called PointNet++ to detect and quantify GGOs in CT scans of COVID-19 patients and to assess the severity of the disease. We have conducted our study on the \"MosMedData\", which contains CT lung scans of 1110 patients with or without COVID-19 infections. We quantify the morphologies of GGOs using Minkowski tensors and compute the abnormality score of individual regions of segmented lung and GGOs.\n\nResultsPointNet++ detects GGOs with the highest evaluation accuracy (98%), average class accuracy (95%), and intersection over union (92%) using only a fraction of 3D data. On average, the shapes of GGOs in the COVID-19 datasets deviate from sphericity by 15% and anisotropies in GGOs are dominated by dipole and hexapole components. These anisotropies may help to quantitatively delineate GGOs of COVID-19 from other lung diseases.\n\nConclusionThe PointNet++ and the Minkowski tensor based morphological approach together with abnormality analysis will provide radiologists and clinicians with a valuable set of tools when interpreting CT lung scans of COVID-19 patients. Implementation would be particularly useful in countries severely devastated by COVID-19 such as India, where the number of cases has outstripped available resources creating delays or even breakdowns in patient care. This AI-driven approach synthesizes both the unique GGO distribution pattern and severity of the disease to allow for more efficient diagnosis, triaging and conservation of limited resources.\n\nKey PointsOur approach to GGO analysis has four distinguishing features:\n\nO_LIWe combine an unsupervised computer vision approach with convex hull and convex points algorithms to segment and preserve the actual structure of the lung.\nC_LIO_LITo the best of our knowledge, we are the first group to use PointNet++ architecture for 3D visualization, segmentation, classification, and pattern analysis of GGOs.\nC_LIO_LIWe make abnormality predictions using a deep network and Cox proportional hazards model using lung CT images of COVID-19 patients.\nC_LIO_LIWe quantify the shapes and sizes of GGOs using Minkowski tensors to understand the morphological variations of GGOs within the COVID-19 cohort.\nC_LI",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Rajiv K. Kalia",
-        "author_inst": "University of Southern California"
-      },
-      {
-        "author_name": "Ashish Sharma",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Sagar B. Amin",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Monjoy Saha",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Satish Kumar Thittamaranahalli",
-        "author_inst": "University of Southern California"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.07.06.21260105",
     "rel_title": "Excess mortality analysis for Germany for all three COVID-19 waves in 2020 - 2021",
@@ -666987,6 +665670,125 @@
     "type": "new results",
     "category": "bioinformatics"
   },
+  {
+    "rel_doi": "10.1101/2021.07.06.451119",
+    "rel_title": "Nonclinical Safety and Immunogenicity of an rVSV-\u0394G-SARS-CoV-2-S vaccine in mice, hamsters, rabbits and pigs",
+    "rel_date": "2021-07-07",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.06.451119",
+    "rel_abs": "rVSV-{Delta}G-SARS-CoV-2-S is a clinical stage (Phase 2) replication competent recombinant vaccine against SARS-CoV-2. Nonclinical safety, immunogenicity and efficacy studies were conducted in 4 animal species, using multiple dose levels (up to 108 PFU/animal) and various dosing regimens. There were no treatment related mortalities in any study, or any noticeable clinical signs. Compared to unvaccinated controls, hematology and biochemistry parameters were unremarkable and no adverse histopathological findings gave cause for safety concern in any of the studies. There was no viral shedding in urine, nor viral RNA detected in whole blood or serum samples 7 days post vaccination. The rVSV-{Delta}G-SARS-CoV-2-S vaccine immune response gave rise to neutralizing antibodies, cellular immune response, and increased lymphocytic cellularity in the spleen germinal centers and regional lymph node. No evidence for neurovirulence was found in C57BL/6 immune competent mice or in highly sensitive IFNAR KO mice. Vaccine virus replication and distribution in K18 hACE2 transgenic mice showed a gradual clearance from the vaccination site with no vaccine virus recovered from the lungs. The rVSV-{Delta}G-SARS-CoV-2-S vaccine was well tolerated locally and systemically and elicited an effective immunogenic response up to the highest dose tested, supporting further clinical development.",
+    "rel_num_authors": 26,
+    "rel_authors": [
+      {
+        "author_name": "Noa Madar-Balakirski",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Amir Rosner",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Sharon Melamed",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Boaz Politi",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Michal Steiner",
+        "author_inst": "GSAP"
+      },
+      {
+        "author_name": "Hadas Tamir",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Yfat Yahalom Ronen",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Elad Bar-David",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Amir Ben-Shmuel",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Assa Sittner",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Itai Glinert",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Shay Weiss",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Erez Bar-Haim",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Hila Cohen",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Uri Elia",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Hagit Achdout",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Noam Erez",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Shahar Rotem",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Shlomi Lazar",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Abraham Nyska",
+        "author_inst": "Tel Aviv University"
+      },
+      {
+        "author_name": "Shmuel Yitzhaki",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Adi Beth-Din",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Haim Levy",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Nir Paran",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Tomer Israely",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Hadar Marcus",
+        "author_inst": "Israel Institute for Biological Research"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "pharmacology and toxicology"
+  },
   {
     "rel_doi": "10.1101/2021.07.06.451301",
     "rel_title": "A Newcastle disease virus-vector expressing a prefusion-stabilized spike protein of SARS-CoV-2 induces protective immune responses against prototype virus and variants of concern in mice and hamsters",
@@ -668464,53 +667266,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.07.03.21259616",
-    "rel_title": "Anaesthetic Higher Specialty Training Recruitment in the United Kingdom During the COVID-19 Pandemic: A National Survey",
-    "rel_date": "2021-07-07",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.03.21259616",
-    "rel_abs": "The most recent ST3 Anaesthetic recruitment for posts commencing in August 2021 saw larger numbers of applicants (n = 1,056) compared to previous years, with approximately 700 applicants failing to secure an ST3 post. We surveyed 536 anaesthetic junior doctors who applied for ST3 posts during this application round with the aim of investigating their experience of the recruitment process this year (response rate 536/1,056 = 51%). Approximately 61% were not offered ST3 posts (n = 326), a similar proportion to that previously reported. We asked all respondents what their potential career plans were for the next 12 to 24 months. The majority expressed intentions to take up either CT3 top-up posts or non-training fellow posts from August 2021 (79%). Other options considered by respondents included: pursuing work abroad (17%), embarking on a career break (16%), taking up an ST3 post in intensive care medicine instead of anaesthetics (15%) and permanently leaving the medical profession (9%). A number of respondents expressed a desire to pursue training in a different medical specialty (9%). Some respondents expressed an intention to pursue further education or research (10%). A large proportion of respondents (42%) expressed a lack of confidence in being able to achieve the necessary training requirements to later apply for ST4 in August 2023. The majority of respondents reported not feeling confident in achieving GMC Specialty Registration in Anaesthesia in the future without a training number (75%), and that their wider life plans have been disrupted due to the impending time out of training (78%). We received a total of 384 free-text responses to a question asking about general concerns regarding the ST3 applications process. Sentiment analysis of these free-text responses indicated that respondents felt generally negatively about the ST3 recruitment process. Some themes that were elicited from the responses included: respondents feeling the recruitment process lacked fairness, respondents suffering burnout and negative impacts on their wellbeing, difficulties in making plans for their personal lives, and feeling undervalued and abandoned despite having made personal sacrifices to support the health service during the COVID-19 pandemic. These results suggest that junior anaesthetic doctors in the UK currently have a negative perception towards postgraduate training structures, which has been exacerbated by the COVID-19 pandemic, changes to the postgraduate training curriculum and difficulties in securing higher training posts.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Fionnuala Durrant",
-        "author_inst": "Department of Anaesthesia, Guy's and St Thomas' NHS Foundation Trust, London, UK"
-      },
-      {
-        "author_name": "Stuart Edwardson",
-        "author_inst": "South East Scotland School of Anaesthesia"
-      },
-      {
-        "author_name": "Sally El-Ghazali",
-        "author_inst": "Department of Anaesthesia, Guy's and St Thomas' NHS Foundation Trust, London, UK"
-      },
-      {
-        "author_name": "Christopher Holt",
-        "author_inst": "Department of Anaesthesia, Guy's and St Thomas' NHS Foundation Trust, London, UK"
-      },
-      {
-        "author_name": "Roopa McCrossan",
-        "author_inst": "Freeman Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle-upon-Tyne, UK"
-      },
-      {
-        "author_name": "Ileena Pramanik",
-        "author_inst": "Department of Anaesthesia, Guy's and St Thomas' NHS Foundation Trust, London, UK"
-      },
-      {
-        "author_name": "Jeevakan Subramaniam",
-        "author_inst": "Department of Anaesthesia, Guy's and St Thomas' NHS Foundation Trust, London, UK"
-      },
-      {
-        "author_name": "Danny Jon Nian Wong",
-        "author_inst": "Department of Anaesthesia, Guy's and St Thomas' NHS Foundation Trust, London, UK"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "anesthesia"
-  },
   {
     "rel_doi": "10.1101/2021.07.03.21259973",
     "rel_title": "Critical Role of the Subways in the Initial Spread of SARS-CoV-2 in New York City",
@@ -668793,6 +667548,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
+  {
+    "rel_doi": "10.1101/2021.07.05.21259790",
+    "rel_title": "What We Learned From COVID 19? Trying to find best approach from pathophysiology to treatment.",
+    "rel_date": "2021-07-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.05.21259790",
+    "rel_abs": "ObjectiveCOVID-19 may yield a variety of clinical pictures, differing from pneumonitis to Acute Respiratory Distress Syndrome (ARDS) along with vascular damage in the lung tissue, named as endotheliitis. To date, no specific treatment strategy was approved by any authority for the prevention or treatment of COVID-19 in terms of endotheliitis-related comorbidities. Here, we present our experience of COVID-19 by evaluating 11,190 COVID-19 patients with the manifestations of endotheliitis in skin, lung, and brain tissues according to the different phases of COVID-19.\n\nMethodsAfter a retrospective examination, patients were divided into three groups according to their repercussions of vascular distress, which were represented by radiological, histopathological, and clinical findings. (Group A: no or mild pulmonary involvement, Group B: moderate pulmonary involvement with clinical risk of deterioration, Group C: severe pulmonary involvement and respiratory failure). We presented the characteristics and disease course of seven representative and complicated cases which represents the different phases of the disease, and discussed the treatment strategies in each group. The current pathophysiological mechanisms responsible from SARS-CoV-2 infection, COVID-19 related respiratory failure and current treatment strategies were reviewed and discussed in detail.\n\nResultsAmong 11.190 patients, 9294 patients met the criteria for Group A, and 1376 patients were presented to our clinics with Group B characteristics. Among these patients, 1896 individuals(Group B and Group C) were hospitalized. While 1220 inpatients were hospitalized within the first 10 days after the diagnosis, 676 of them were worsened and hospitalized 10 days after their diagnosis. Among hospitalized patients, 520 of them did not respond to group A and B treatments and developed hypoxemic respiratory failure (Group C) and 146 individuals needed ventilator support and were followed in the intensive care unit, and 43 (2.2%) patients died.\n\nConclusionDistinctive manifestations in each COVID-19 patient, including non-respiratory conditions in the acute phase and the emerging risk of long-lasting complications, suggest that COVID-19 has an endotheliitis-centred thrombo-inflammatory pathophysiology. Endotheliitis can also explain the mechanism behind the respiratory failure in COVID-19, and the difference of COVID-19 related ARDS from ARDS seen in other critical conditions. In addition, use of early corticosteroid in patients with early symptoms and early tocilizumab in ICU helps to reduce mortality and progression of the disease. Endotheliitis-based pathophysiological mechanisms are known to be momentarily changing and difficut to manage due to their risk of sudden aggrevation. Hence, daily evaluation of clinical, laboratory and radiological findings of patients and deciding appropriate pathophysiological treatment would help to reduce the mortality rate of COVID-19.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Adem Dirican",
+        "author_inst": "VM Samsun Medicalpark Hospital, Department of Pulmonary Medicine, Samsun, Turkey"
+      },
+      {
+        "author_name": "Selin Ildir",
+        "author_inst": "Bahcesehir University School of Medicine"
+      },
+      {
+        "author_name": "Tugce Uzar",
+        "author_inst": "Bahcesehir University School of Medicine, Istanbul, Turkey"
+      },
+      {
+        "author_name": "Irem Karaman",
+        "author_inst": "Bahcesehir University School of Medicine, Istanbul, Turkey"
+      },
+      {
+        "author_name": "Sevket OZKAYA",
+        "author_inst": "Bahcesehir University Faculty of Medicine, Department of Pulmonary Medicine, Istanbul, Turkey"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "respiratory medicine"
+  },
   {
     "rel_doi": "10.1101/2021.07.06.21260058",
     "rel_title": "Examining Medical Student Volunteering During The COVID-19 Pandemic As A Prosocial Behavior During An Emergency",
@@ -670098,125 +668888,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.07.06.21259226",
-    "rel_title": "Next-generation Serology by Mass Spectrometry: Readout of the SARS-CoV-2 Antibody Repertoire",
-    "rel_date": "2021-07-07",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.06.21259226",
-    "rel_abs": "Methods of antibody detection are used to assess exposure or immunity to a pathogen. Here, we present Ig-MS, a novel serological readout that captures the immunoglobulin (Ig) repertoire at molecular resolution, including entire variable regions in Ig light and heavy chains. Ig-MS uses recent advances in protein mass spectrometry (MS) for multi-parametric readout of antibodies, with new metrics like Ion Titer (IT) and Degree of Clonality (DoC) capturing the heterogeneity and relative abundance of individual clones without sequencing of B cells. We apply Ig-MS to plasma from subjects with severe & mild COVID-19, using the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 as the bait for antibody capture. Importantly, we report a new data type for human serology, with compatibility to any recombinant antigen to gauge our immune responses to vaccination, pathogens, or autoimmune disorders.",
-    "rel_num_authors": 26,
-    "rel_authors": [
-      {
-        "author_name": "Rafael D Melani",
-        "author_inst": "Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and the Feinberg School of Medicine, Northwestern University, Evanston, IL"
-      },
-      {
-        "author_name": "Benjamin J Des Soye",
-        "author_inst": "Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and the Feinberg School of Medicine, Northwestern University, Evanston, IL"
-      },
-      {
-        "author_name": "Jared O Kafader",
-        "author_inst": "Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and the Feinberg School of Medicine, Northwestern University, Evanston, IL"
-      },
-      {
-        "author_name": "Eleonora Forte",
-        "author_inst": "Proteomics Center of Excellence, Evanston, IL, USA; Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA"
-      },
-      {
-        "author_name": "Michael Hollas",
-        "author_inst": "Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and the Feinberg School of Medicine, Northwestern University, Evanston, IL"
-      },
-      {
-        "author_name": "Voislav Blagovich",
-        "author_inst": "Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and the Feinberg School of Medicine, Northwestern University, Evanston, IL"
-      },
-      {
-        "author_name": "Fernanda Negrao",
-        "author_inst": "Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and the Feinberg School of Medicine, Northwestern University, Evanston, IL"
-      },
-      {
-        "author_name": "John P McGee",
-        "author_inst": "Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and the Feinberg School of Medicine, Northwestern University, Evanston, IL"
-      },
-      {
-        "author_name": "Bryon Drown",
-        "author_inst": "Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and the Feinberg School of Medicine, Northwestern University, Evanston, IL"
-      },
-      {
-        "author_name": "Cameron Lloyd-Jones",
-        "author_inst": "Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and the Feinberg School of Medicine, Northwestern University, Evanston, IL"
-      },
-      {
-        "author_name": "Henrique S Seckler",
-        "author_inst": "Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and the Feinberg School of Medicine, Northwestern University, Evanston, IL"
-      },
-      {
-        "author_name": "Jeannie M Camarillo",
-        "author_inst": "Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and the Feinberg School of Medicine, Northwestern University, Evanston, IL"
-      },
-      {
-        "author_name": "Philip D Compton",
-        "author_inst": "Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and the Feinberg School of Medicine, Northwestern University, Evanston, IL"
-      },
-      {
-        "author_name": "Richard D LeDuc",
-        "author_inst": "Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and the Feinberg School of Medicine, Northwestern University, Evanston, IL"
-      },
-      {
-        "author_name": "Bryan Early",
-        "author_inst": "Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and the Feinberg School of Medicine, Northwestern University, Evanston, IL"
-      },
-      {
-        "author_name": "Ryan T Fellers",
-        "author_inst": "Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and the Feinberg School of Medicine, Northwestern University, Evanston, IL"
-      },
-      {
-        "author_name": "Byoung-Kyu Cho",
-        "author_inst": "Proteomics Center of Excellence, Evanston, IL, USA"
-      },
-      {
-        "author_name": "Basil Baby Mattamana",
-        "author_inst": "Proteomics Center of Excellence, Evanston, IL, USA"
-      },
-      {
-        "author_name": "Young Ah Goo",
-        "author_inst": "Proteomics Center of Excellence, Evanston, IL, USA"
-      },
-      {
-        "author_name": "Paul M Thomas",
-        "author_inst": "Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and the Feinberg School of Medicine, Northwestern University, Evanston, IL"
-      },
-      {
-        "author_name": "Michelle K Ash",
-        "author_inst": "Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA"
-      },
-      {
-        "author_name": "Pavan P Bhimalli",
-        "author_inst": "Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA"
-      },
-      {
-        "author_name": "Lena Al-Harthi",
-        "author_inst": "Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA"
-      },
-      {
-        "author_name": "Beverly E Sha",
-        "author_inst": "Division of Infectious Diseases, Rush University Medical Center, Chicago, IL, USA"
-      },
-      {
-        "author_name": "Jeffrey R Schneider",
-        "author_inst": "Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, USA"
-      },
-      {
-        "author_name": "Neil L Kelleher",
-        "author_inst": "Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and the Feinberg School of Medicine, Northwestern University, Evanston, IL"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "allergy and immunology"
-  },
   {
     "rel_doi": "10.1101/2021.07.06.21260080",
     "rel_title": "Untargeted saliva metabolomics reveals COVID-19 severity: Saliva Metabolomics for SARS-COV-2 Prognosis",
@@ -670627,6 +669298,109 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2021.07.06.451353",
+    "rel_title": "Receptor-binding domain recombinant protein RBD219-N1C1 on alum-CpG induces broad protection against SARS-CoV-2 variants of concern",
+    "rel_date": "2021-07-07",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.06.451353",
+    "rel_abs": "We conducted preclinical studies in mice using a yeast-produced SARS-CoV-2 RBD subunit vaccine candidate formulated with aluminum hydroxide (alum) and CpG deoxynucleotides. This formulation is equivalent to the Corbevax vaccine that recently received emergency use authorization by the Drugs Controller General of India. We compared the immune response of mice vaccinated with RBD/alum to mice vaccinated with RBD/alum+CpG. We also evaluated mice immunized with RBD/alum+CpG and boosted with RBD/alum. Mice were immunized twice intramuscularly at a 21-day interval. Compared to two doses of the /alum formulation, the RBD/alum+CpG vaccine induced a stronger and more balanced Th1/Th2 cellular immune response, with high levels of neutralizing antibodies against the original Wuhan isolate of SARS-CoV-2 as well as the B.1.1.7 (Alpha), B. 1.351 (Beta), B. 1.617.2 and (Delta) variants. Neutralizing antibody titers against the B.1.1.529 (BA.1, Omicron) variant exceeded those in human convalescent plasma after Wuhan infection but were lower than against the other variants. Interestingly, the second dose did not benefit from the addition of CpG, possibly allowing dose-sparing of the adjuvant in the future. The data reported here reinforces that the RBD/alum+CpG vaccine formulation is suitable for inducing broadly neutralizing antibodies against SARS-CoV-2 including variants of concern.",
+    "rel_num_authors": 22,
+    "rel_authors": [
+      {
+        "author_name": "Jeroen Pollet",
+        "author_inst": "Baylor College of Medicine"
+      },
+      {
+        "author_name": "Ulrich Strych",
+        "author_inst": "Baylor College of Medicine"
+      },
+      {
+        "author_name": "Wen-Hsiang Chen",
+        "author_inst": "Baylor College of Medicine"
+      },
+      {
+        "author_name": "Leroy Versteeg",
+        "author_inst": "Baylor College of Medicine"
+      },
+      {
+        "author_name": "Brian Keegan",
+        "author_inst": "Baylor College of Medicine"
+      },
+      {
+        "author_name": "Bin Zhan",
+        "author_inst": "Baylor College of Medicine"
+      },
+      {
+        "author_name": "Junfei Wei",
+        "author_inst": "Baylor College of Medicine"
+      },
+      {
+        "author_name": "Zhuyun Liu",
+        "author_inst": "Baylor College of Medicine"
+      },
+      {
+        "author_name": "Jungsoon Lee",
+        "author_inst": "Baylor College of Medicine"
+      },
+      {
+        "author_name": "Rakhi Kundu",
+        "author_inst": "Baylor College of Medicine"
+      },
+      {
+        "author_name": "Rakesh Adhikari",
+        "author_inst": "Baylor College of Medicine"
+      },
+      {
+        "author_name": "Cristina Poveda",
+        "author_inst": "Baylor College of Medicine"
+      },
+      {
+        "author_name": "Maria Jose Villar",
+        "author_inst": "Baylor College of Medicine"
+      },
+      {
+        "author_name": "Syamala Rani Thimmiraju",
+        "author_inst": "Baylor College of Medicine"
+      },
+      {
+        "author_name": "Brianna Lopez",
+        "author_inst": "Baylor College of Medicine"
+      },
+      {
+        "author_name": "Portia M. Gillespie",
+        "author_inst": "Baylor College of Medicine"
+      },
+      {
+        "author_name": "Shannon Ronca",
+        "author_inst": "Baylor College of Medicine"
+      },
+      {
+        "author_name": "Jason T. Kimata",
+        "author_inst": "Baylor College of Medicine"
+      },
+      {
+        "author_name": "Martin Reers",
+        "author_inst": "Biological E. Limited"
+      },
+      {
+        "author_name": "Vikram Paradkar",
+        "author_inst": "Biological E. Limited"
+      },
+      {
+        "author_name": "Peter Hotez",
+        "author_inst": "Baylor College of Medicine"
+      },
+      {
+        "author_name": "Maria Elena Bottazzi",
+        "author_inst": "Baylor College of Medicine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "molecular biology"
+  },
   {
     "rel_doi": "10.1101/2021.07.07.451411",
     "rel_title": "CAT, AGTR2, L-SIGN and DC-SIGN are potential receptors for the entry of SARS-CoV-2 into human cells",
@@ -672132,33 +670906,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "obstetrics and gynecology"
   },
-  {
-    "rel_doi": "10.1101/2021.07.04.21259983",
-    "rel_title": "Real time scalable data acquisition of COVID-19 in six continents through PySpark - a big data tool",
-    "rel_date": "2021-07-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.04.21259983",
-    "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was declared as a global emergency in January 2020 due to its pandemic outbreak. To examine this Coronavirus disease 2019 (COVID-19) effects various data are being generated through different platforms. This study was focused on the clinical data of COVID-19 which relied on python programming. Here, we proposed a machine learning approach to provide a insights into the COVID-19 information. PySpark is a machine learning approach which also known as Apache spark an accurate tool for the searching of results with minimum time intervals as compare to Hadoop and other tools. World Health Organization (WHO) started gathering corona patients data from last week of the February 2020. On March 11, 2020, the WHO declared COVID-19 a global pandemic. The cases became more evident and common after mid-March. This paper used the live owid (our world in data) dataset and will analyse and find out the following details on the live COVID-19 dataset. (1) The daily Corona virus scenario on various continents using PySpark in microseconds of Processor time. (2) After the various antibodies have been implemented, how they impact new cases on a regular basis utilizing various graphs. (3) Tabular representation of COVID-19 new cases in all the continents.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Tanvi S Patel",
-        "author_inst": "Computer Science & Engineering, Gujarat Technological University, Ahmedabad, Gujarat 382424, India."
-      },
-      {
-        "author_name": "Daxesh P Patel",
-        "author_inst": "Department of Chemistry, School of Sciences, Gujarat University, Ahmedabad, 380009, India."
-      },
-      {
-        "author_name": "Chirag N Patel",
-        "author_inst": "Department of Botany, Bioinformatics, and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, India."
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health informatics"
-  },
   {
     "rel_doi": "10.1101/2021.07.05.21260014",
     "rel_title": "Mild SARS-CoV-2 infection modifies DNA methylation of peripheral blood mononuclear cells from COVID-19 convalescents",
@@ -672437,6 +671184,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.07.04.21259992",
+    "rel_title": "Late surges in COVID-19 cases and varying transmission potential partially due to public health policy changes in 5 Western states, March 10, 2020-January 10, 2021",
+    "rel_date": "2021-07-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.04.21259992",
+    "rel_abs": "ObjectiveThis study investigates how the SARS-CoV-2 transmission potential varied in North Dakota, South Dakota, Montana, Wyoming, and Idaho from March 2020 through January 2021.\n\nMethodsTime-varying reproduction numbers, Rt, of a 7-day-sliding-window and of non-overlapping-windows between policy changes were estimated utilizing the instantaneous reproduction number method. Linear regression was performed to evaluate if per-capita cumulative case-count varied across counties with different population size.\n\nResultsThe median 7-day-sliding-window Rt estimates across the studied region varied between 1 and 1.25 during September through November 2020. Between November 13 and 18, Rt was reduced by 14.71% (95% credible interval, CrI, [14.41%, 14.99%]) in North Dakota following a mask mandate; Idaho saw a 1.93% (95% CrI [1.87%, 1.99%]) reduction and Montana saw a 9.63% (95% CrI [9.26%, 9.98%]) reduction following the tightening of restrictions. High-population counties had higher per-capita cumulative case-count in North Dakota at four time points (June 30, August 31, October 31, and December 31, 2020). In Idaho, North Dakota, and South Dakota, there was a positive correlation between population size and per-capita weekly incident case-count, adjusted for calendar time and social vulnerability index variables.\n\nConclusionsRt decreased after mask mandate during the regions case-count spike suggested reduction in SARS-CoV-2 transmission.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Xinyi Hua",
+        "author_inst": "Georgia Southern University Jiann-Ping Hsu College of Public Health"
+      },
+      {
+        "author_name": "Aubrey R. D. Kehoe",
+        "author_inst": "Georgia Southern University Jiann-Ping Hsu College of Public Health"
+      },
+      {
+        "author_name": "Joana Tome",
+        "author_inst": "Georgia Southern University Jiann-Ping Hsu College of Public Health"
+      },
+      {
+        "author_name": "Mina Motaghi",
+        "author_inst": "Georgia Southern University Jiann-Ping Hsu College of Public Health"
+      },
+      {
+        "author_name": "Sylvia K. Ofori",
+        "author_inst": "Georgia Southern University Jiann-Ping Hsu College of Public Health"
+      },
+      {
+        "author_name": "Po-Ying Lai",
+        "author_inst": "Boston University School of Public Health"
+      },
+      {
+        "author_name": "Sheikh Taslim Ali",
+        "author_inst": "The University of Hong Kong School of Public Health"
+      },
+      {
+        "author_name": "Gerardo Chowell",
+        "author_inst": "Georgia State University School of Public Health"
+      },
+      {
+        "author_name": "Anne C. Spaulding",
+        "author_inst": "Emory University Rollins School of Public Health"
+      },
+      {
+        "author_name": "Isaac Chun-Hai Fung",
+        "author_inst": "Georgia Southern University Jiann-Ping Hsu College of Public Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.07.04.21259980",
     "rel_title": "The impact of demographic factors on the accumulated number of COVID-19 cases per capita in Europe and the regions of Ukraine in the summer of 2021",
@@ -673902,85 +672704,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pediatrics"
   },
-  {
-    "rel_doi": "10.1101/2021.07.02.21259802",
-    "rel_title": "Survey of SARS-CoV-2 genetic diversity in two major Brazilian cities using a fast and affordable Sanger sequencing strategy.",
-    "rel_date": "2021-07-05",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.02.21259802",
-    "rel_abs": "Genetic variants of SARS-CoV-2 have been emerging and circulating in many places across the world. Rapid detection of these variants is essential since their dissemination can impact transmission rates, diagnostic procedures, disease severity, response to vaccines or patient management. Sanger sequencing has been used as the preferred approach for variant detection among circulating human immunodeficiency and measles virus genotypes. Using primers to amplify a fragment of the SARS-CoV-2 genome encoding part of the Spike protein, we showed that Sanger sequencing allowed us to rapidly detect the introduction and spread of three distinct SARS-CoV-2 variants in two major Brazilian cities. In both cities, after the predominance of variants closely related to the virus first identified in China, the emergence of the P.2 variant was quickly followed by the identification of the P1 variant, which became dominant in less than one month after it was first detected.",
-    "rel_num_authors": 16,
-    "rel_authors": [
-      {
-        "author_name": "Erick Gustavo Dorlass",
-        "author_inst": "University of Sao Paulo"
-      },
-      {
-        "author_name": "Karine Lima Lourenco",
-        "author_inst": "Federal University of Minas Gerais"
-      },
-      {
-        "author_name": "Rubens Daniel Miserani Magalhaes",
-        "author_inst": "Federal University of Minas Gerais"
-      },
-      {
-        "author_name": "Hugo Sato",
-        "author_inst": "Federal University of Minas Gerais"
-      },
-      {
-        "author_name": "Alex Fiorini",
-        "author_inst": "Federal University of Minas Gerais"
-      },
-      {
-        "author_name": "Renata Peixoto",
-        "author_inst": "Federal University of Minas Gerais"
-      },
-      {
-        "author_name": "Helena Perez Coelho",
-        "author_inst": "Federal University of Minas Gerais"
-      },
-      {
-        "author_name": "Bruna Larotonda Telezynski",
-        "author_inst": "University of Sao Paulo"
-      },
-      {
-        "author_name": "Guilherme Pereira Scagion",
-        "author_inst": "University of Sao Paulo"
-      },
-      {
-        "author_name": "Tatiana Ometto",
-        "author_inst": "University of Sao Paulo"
-      },
-      {
-        "author_name": "Luciano Matsumiya Thomazelli",
-        "author_inst": "University of Sao Paulo"
-      },
-      {
-        "author_name": "Danielle Bruna Leal Oliveira",
-        "author_inst": "Hospital Israelita Albert Einstein"
-      },
-      {
-        "author_name": "Ana Paula Fernandes",
-        "author_inst": "Federal University of Minas Gerais"
-      },
-      {
-        "author_name": "Edison Luiz Durigon",
-        "author_inst": "University of Sao Paulo"
-      },
-      {
-        "author_name": "Flavio Guimaraes da Fonseca",
-        "author_inst": "Federal University of Minas Gerais"
-      },
-      {
-        "author_name": "Santuza Maria Ribeiro Teixeira",
-        "author_inst": "Federal University of Minas Gerais"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "genetic and genomic medicine"
-  },
   {
     "rel_doi": "10.1101/2021.07.02.21259929",
     "rel_title": "Analysis of Feature Influence on Covid-19 Death Rate Per Country Using a Novel Orthogonalization Technique",
@@ -674211,6 +672934,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.06.30.21259491",
+    "rel_title": "Reduced COVID-19 Hospitalizations among New York City Residents Following Age-Based SARS-CoV-2 Vaccine Eligibility: Evidence from a Regression Discontinuity Design",
+    "rel_date": "2021-07-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.30.21259491",
+    "rel_abs": "BackgroundIn clinical trials, several SARS-CoV-2 vaccines were shown to reduce risk of severe COVID-19 illness. Local, population-level, real-world evidence of vaccine effectiveness is accumulating. We assessed vaccine effectiveness for community-dwelling New York City (NYC) residents using a quasi-experimental, regression discontinuity design, leveraging a period (January 12-March 9, 2021) when [&ge;]65-year-olds were vaccine-eligible but younger persons, excluding essential workers, were not.\n\nMethodsWe constructed segmented, negative binomial regression models of age-specific COVID-19 hospitalization rates among 45-84-year-old NYC residents during a post-vaccination program implementation period (February 21-April 17, 2021), with a discontinuity at age 65 years. The relationship between age and hospitalization rates in an unvaccinated population was incorporated using a pre-implementation period (December 20, 2020-February 13, 2021). We calculated the rate ratio (RR) and 95% confidence interval (CI) for the interaction between implementation period (pre or post) and age-based eligibility (45-64 or 65-84 years). Analyses were stratified by race/ethnicity and borough of residence. Similar analyses were conducted for COVID-19 deaths.\n\nResultsHospitalization rates among 65-84-year-olds decreased from pre- to post-implementation periods (RR 0.85, 95% CI: 0.74-0.97), controlling for trends among 45-64-year-olds. Accordingly, an estimated 721 (95% CI: 126-1,241) hospitalizations were averted. Residents just above the eligibility threshold (65-66-year-olds) had lower hospitalization rates than those below (63-64-year-olds). Racial/ethnic groups and boroughs with higher vaccine coverage generally experienced greater reductions in RR point estimates. Uncertainty was greater for the decrease in COVID-19 death rates (RR 0.85, 95% CI: 0.66-1.10).\n\nConclusionThe vaccination program in NYC reduced COVID-19 hospitalizations among the initially age-eligible [&ge;]65-year-old population by approximately 15%. The real-world evidence of vaccine effectiveness makes it more imperative to improve vaccine access and uptake to reduce inequities in COVID-19 outcomes.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Sharon K. Greene",
+        "author_inst": "New York City Department of Health and Mental Hygiene"
+      },
+      {
+        "author_name": "Alison Levin-Rector",
+        "author_inst": "New York City Department of Health and Mental Hygiene"
+      },
+      {
+        "author_name": "Emily McGibbon",
+        "author_inst": "New York City Department of Health and Mental Hygiene"
+      },
+      {
+        "author_name": "Jennifer Baumgartner",
+        "author_inst": "New York City Department of Health and Mental Hygiene"
+      },
+      {
+        "author_name": "Katelynn Devinney",
+        "author_inst": "New York City Department of Health and Mental Hygiene"
+      },
+      {
+        "author_name": "Alexandra Ternier",
+        "author_inst": "New York City Department of Health and Mental Hygiene"
+      },
+      {
+        "author_name": "Jessica Sell",
+        "author_inst": "New York City Department of Health and Mental Hygiene"
+      },
+      {
+        "author_name": "Rebecca Kahn",
+        "author_inst": "Harvard T.H. Chan School of Public Health"
+      },
+      {
+        "author_name": "Nishant Kishore",
+        "author_inst": "Harvard T.H. Chan School of Public Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc0",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.06.30.21259787",
     "rel_title": "Low dose mRNA-1273 COVID-19 vaccine generates durable T cell memory and antibodies enhanced by pre-existing crossreactive T cell memory",
@@ -675472,41 +674246,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.07.02.21259891",
-    "rel_title": "Heart Rate Variability as a Prospective Predictor of Early COVID-19 Symptoms",
-    "rel_date": "2021-07-05",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.02.21259891",
-    "rel_abs": "Heart rate variability (HRV) is the fluctuation in the time interval between consecutive heartbeats, the measurement of which is a non-invasive method for assessing the autonomic status. The autonomic nervous system plays an important role in physiological situations, and in various pathological processes such as in cardiovascular diseases and viral infections. This study examined the cardiac autonomic responses, as measured by HRV before, after, and during coronavirus disease. In this study, we used beat interval data extracted from the Welltory app from 14 eligible subjects (9 men and 5 women) with a mean age (SD) of 44 (8.7) years. HRV analysis was performed through an assessment of time-domain indices (SDNN and RMSSD). Group analysis did not reveal any statistical difference between HRV metrics before, during, and after COVID-19. However, HRV at the individual level showed a statistically significant individual change during COVID-19 in some users. These data further support the usefulness of using individual-level HRV tracking for the detection of early diseases inclusive of COVID-19.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Alexey Ponomarev",
-        "author_inst": "Welltory Inc."
-      },
-      {
-        "author_name": "Konstantin Tyapochkin",
-        "author_inst": "Welltory Inc."
-      },
-      {
-        "author_name": "Ekaterina Surkova",
-        "author_inst": "Welltory Inc."
-      },
-      {
-        "author_name": "Evgeniya Smorodnikova",
-        "author_inst": "Welltory Inc"
-      },
-      {
-        "author_name": "Pavel Pravdin",
-        "author_inst": "Welltory Inc."
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "cardiovascular medicine"
-  },
   {
     "rel_doi": "10.1101/2021.06.30.21259761",
     "rel_title": "Post-vaccination SARS-COV-2 among healthcare workers in New Jersey: a genomic epidemiological study",
@@ -675845,6 +674584,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.07.02.450964",
+    "rel_title": "SARS-CoV-2 Nsp14 mediates the effects of viral infection on the host cell transcriptome",
+    "rel_date": "2021-07-04",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.02.450964",
+    "rel_abs": "Viral infection involves complex set of events orchestrated by multiple viral proteins. To identify functions of SARS-CoV-2 proteins, we performed transcriptomic analyses of cells expressing individual viral proteins. Expression of Nsp14, a protein involved in viral RNA replication, provoked a dramatic remodeling of the transcriptome that strongly resembled that observed following SARS-CoV-2 infection. Moreover, Nsp14 expression altered the splicing of more than 1,000 genes and resulted in a dramatic increase in the number of circRNAs, which are linked to innate immunity. These effects were independent of the Nsp14 exonuclease activity and required the N7-guanine-methyltransferase domain of the protein. Activation of the NFkB pathway and increased expression of CXCL8 occurred early upon Nsp14 expression. We identified IMPDH2, which catalyzes the rate-limiting step of guanine nucleotides biosynthesis, as a key mediator of these effects. Nsp14 expression caused an increase in GTP cellular levels, and the effect of Nsp14 was strongly decreased in presence of IMPDH2 inhibitors. Together, our data demonstrate an unknown role for Nsp14 with implications for therapy.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Michela Zaffagni",
+        "author_inst": "Brandeis University"
+      },
+      {
+        "author_name": "Jenna M Harris",
+        "author_inst": "Brandeis University"
+      },
+      {
+        "author_name": "Ines L Patop",
+        "author_inst": "Brandeis University"
+      },
+      {
+        "author_name": "Nagarjuna Reddy Pamudurti",
+        "author_inst": "Brandeis University"
+      },
+      {
+        "author_name": "Sinead Nguyen",
+        "author_inst": "Brandeis University"
+      },
+      {
+        "author_name": "Sebastian Kadener",
+        "author_inst": "Brandeis University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "molecular biology"
+  },
   {
     "rel_doi": "10.1101/2021.07.03.450989",
     "rel_title": "Allotypic variation in antigen processing controls antigenic peptide generation from SARS-CoV-2 S1 Spike Glycoprotein",
@@ -677254,33 +676032,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.06.29.21259511",
-    "rel_title": "An increased ratio of SARS-CoV-2 positive to negative sense genomic and subgenomic RNAs within routine diagnostic upper respiratory tract swabs may be a marker of virion shedding",
-    "rel_date": "2021-07-03",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.29.21259511",
-    "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread rapidly in the global population since its emergence in humans in late 2019. Replication of SARS-CoV-2 is characterised by transcription and replication of genomic length RNA and shorter subgenomic RNAs to produce virus proteins and ultimately progeny virions. Here we explore the pattern of both genome-length and subgenomic RNAs and positive and negative strand SARS-CoV-2 RNAs in diagnostic nasopharyngeal swabs using sensitive probe based PCR assays as well as Ampliseq panels designed to target subgenomic RNAs. We successfully developed a multiplex PCR assay to simultaneously measure the relative amount of SARS-CoV-2 full length genomic RNA as well as subgenomic N gene and subgenomic ORF7a RNA. We found that subgenomic RNAs and both positive and negative strand RNA can be readily detected in swab samples taken up to 19 and 17 days post symptom onset respectively, and are strongly correlated with the amount of genomic length RNA present within a sample. Their detection and measurement is therefore unlikely to provide anymore insight into the stage of infection and potential infectivity of an individual beyond what can already be inferred from the total viral RNA load measured by routine diagnostic SARS-CoV-2 PCRs. Using both an original commercial and two custom SARS-CoV-2 Ampliseq mini-panels, we identified that both ORF7a and N gene subgenomic RNAs were consistently the most abundant subgenomic RNAs. We were also able to identify several non-canonical subgenomic RNAs, including one which could potentially be used to translate the ORF7b protein and others which could be used to translate ORF9b and the ORF N* which has arisen from a new transcription regulatory sequence recently created by mutations after SARS-CoV-2 jumped into people. SARS-CoV-2 genomic length and subgenomic length RNAs were present in samples even if cellular RNA was degraded, further indicating that these molecules are likely protected from degradation by the membrane structures seen in SARS-CoV-2 infected cells.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Anthony Chamings",
-        "author_inst": "Deakin University"
-      },
-      {
-        "author_name": "Tarka Raj Bhatta",
-        "author_inst": "Deakin University"
-      },
-      {
-        "author_name": "Soren Alexandersen",
-        "author_inst": "Deakin University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.06.28.21259657",
     "rel_title": "PERFORMANCE AND UTILITY OF AN ORAL FLUID-BASED RAPID POINT-OF-CARE TEST FOR SARS-COV-2 ANTIBODY RESPONSE FOLLOWING COVID-19 INFECTION OR VACCINATION",
@@ -677735,6 +676486,89 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.06.23.21259414",
+    "rel_title": "The COVID-related mental health load of neonatal healthcare professionals: a multicentre study in Italy.",
+    "rel_date": "2021-07-02",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.23.21259414",
+    "rel_abs": "BackgroundThe COVID-19 pandemic has dramatically affected healthcare professionals lives. We investigated the potential mental health risk faced by healthcare professionals working in neonatal units in a multicentre cross-sectional observational study.\n\nMethodsWe included all healthcare personnel of 7 level-3 and 6 level-2 neonatal units in Tuscany, Italy. We measured the level of physical exposure to COVID-19 risk, self-reported COVID-related stress, and mental health load outcomes (anxiety, depression, burnout, psychosomatic, and post-traumatic symptoms) via validated, self-administered, on-line questionnaires.\n\nResultsWe analysed 314 complete answers. Scores above the clinical cutoff were reported by 91% of participants for anxious symptoms, 29% for post-traumatic symptoms, 13% for burnout, and 3% for depressive symptoms. Moreover, 50% of the participants reported at least one psychosomatic symptom. COVID-related stress (but not actual physical exposure) was significantly associated with all the measured mental health load outcomes, with a Risk Ratio of 3.33 (95% Confidence interval: 1.89, 5.85) for clinically relevant anxiety, 2.39 (1.69, 3.38) for post-traumatic symptoms, 1.79 (1.16, 2.75) for emotional exhaustion, and 2.51 (0.98, 6.44) for depression.\n\nConclusionsDespite a low clinical impact of COVID-19 in neonatology, neonatal professionals are a specific population at risk for psychological consequences during the pandemic.\n\nKeynotesO_LIWe studied the mental health load (anxiety, post-traumatic, psychosomatic symptoms, burnout, depression) of healthcare professionals working in 13 neonatal units in Tuscany during the COVID-19 pandemic.\nC_LIO_LIWe found very high levels of anxiety and psychosomatic symptoms, and moderate-high post-traumatic and burnout symptoms.\nC_LIO_LIMental health load was higher in neonatal intensive (vs non-intensive) settings and in nurses (vs physicians). Mental health load outcomes were associated with COVID-related stress (rather than actual physical exposure to the virus).\nC_LI",
+    "rel_num_authors": 17,
+    "rel_authors": [
+      {
+        "author_name": "Luigi Gagliardi",
+        "author_inst": "AUSL Toscana Nord Ovest"
+      },
+      {
+        "author_name": "Serena Grumi",
+        "author_inst": "IRCCS Fondazione Mondino, Pavia, Italy"
+      },
+      {
+        "author_name": "Marzia Gentile",
+        "author_inst": "Division of Neonatology, Azienza Ospedaliero-Universitaria di Pisa, Italy"
+      },
+      {
+        "author_name": "Roberta Cacciavellani",
+        "author_inst": "Division of Neonatology and Pediatrics, Ospedale Versilia, Viareggio, AUSL Toscana Nord Ovest, Pisa, Italy"
+      },
+      {
+        "author_name": "Giulia Placidi",
+        "author_inst": "Division of Neonatology and Pediatrics, Ospedale Versilia, Viareggio, AUSL Toscana Nord Ovest, Pisa, Italy"
+      },
+      {
+        "author_name": "Angelina Vaccaro",
+        "author_inst": "Division of Neonatology and Pediatrics, Ospedale San Luca, Lucca, AUSL Toscana NordOvest, Pisa Italy"
+      },
+      {
+        "author_name": "Claudia Maggi",
+        "author_inst": "Division of Neonatology and Pediatrics, Ospedale Lotti, Pontedera, AUSL Toscana NordOvest, Pisa Italy"
+      },
+      {
+        "author_name": "Beatrice Gambi",
+        "author_inst": "Division of Neonatology, Ospedale San Giovanni di Dio, AUSL Toscana Centro, Firenze, Italy"
+      },
+      {
+        "author_name": "Letizia Magi",
+        "author_inst": "Division of Neonatology and Pediatrics, Ospedale San Donato, Arezzo, AUSL Toscana Sud Est, Arezzo, Italy"
+      },
+      {
+        "author_name": "Laura Crespin",
+        "author_inst": "Division of Neonatology and Pediatrics, Ospedale di Barga, AUSL Toscana Nord Ovest, Pisa Italy"
+      },
+      {
+        "author_name": "Graziano Memmini",
+        "author_inst": "Division of Neonatology and Pediatrics, Nuovo Ospedale Apuano, Massa, AUSL Toscana NordOvest, Pisa Italy"
+      },
+      {
+        "author_name": "Marcello De Filippo",
+        "author_inst": "Division of Neonatology and Pediatrics, Ospedale di Grosseto, AUSL Toscana Sud Est, Italy"
+      },
+      {
+        "author_name": "Elena Verucci",
+        "author_inst": "Division of Neonatology and Pediatrics, Ospedale di Livorno, AUSL Toscana Nord Ovest, Pisa, Italy"
+      },
+      {
+        "author_name": "Liliana Malandra",
+        "author_inst": "Division of Neonatology and Pediatrics, Ospedale di Cecina, AUSL Toscana Nord Ovest, Pisa Italy"
+      },
+      {
+        "author_name": "Laura Mele",
+        "author_inst": "Division of Neonatology and Pediatrics, Ospedale di Prato, AUSL Toscana Centro, Firenze, Italy"
+      },
+      {
+        "author_name": "Angelo Azzar\u00e0",
+        "author_inst": "Division of Neonatology, Azienda Ospedaliero-Universitaria Meyer, Firenze, Italy"
+      },
+      {
+        "author_name": "Livio Provenzi",
+        "author_inst": "IRCCS Fondazione Mondino, Pavia, Italy"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "pediatrics"
+  },
   {
     "rel_doi": "10.1101/2021.06.28.21259570",
     "rel_title": "Coping under stress: Prefrontal control predicts stress burden during the COVID-19 crisis",
@@ -679320,37 +678154,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.06.28.21259320",
-    "rel_title": "The acceptance of covid-19 vaccines in Sub-Saharan Africa: Evidence from 6 national phone surveys",
-    "rel_date": "2021-07-02",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259320",
-    "rel_abs": "IntroductionRecent debates surrounding the lagging covid-19 vaccination campaigns in low-income countries center around vaccine supply and financing. Yet, relatively little is known about attitudes towards covid-19 vaccines in these countries and in Africa in particular. In this paper, we provide cross-country comparable estimates of the willingness to accept a covid-19 vaccine in six Sub-Saharan African countries.\n\nMethodsWe use data from six national high-frequency phone surveys from countries representing 38% of the Sub-Saharan African population (Burkina Faso, Ethiopia, Malawi, Mali, Nigeria, and Uganda). Samples are drawn from large, nationally representative sampling frames providing a rich set of demographic and socio-economic characteristics by which we disaggregate our analysis. Using a set of re-calibrated survey weights, our analysis adjusts for the selection biases common in remote surveys.\n\nResultsAcceptance rates in the six Sub-Saharan African countries studied are generally high, with at least four in five people willing to be vaccinated in all but one country. Vaccine acceptance ranges from nearly universal in Ethiopia (97.9%, 97.2% to 98.6%) to below what would likely be required for herd immunity in Mali (64.5%, 61.3% to 67.8%). We find little evidence for systematic differences in vaccine hesitancy by sex or age but some clusters of hesitancy in urban areas, among the better educated, and in richer households. Safety concerns about the vaccine in general and its side effects emerge as the primary reservations toward a covid-19 vaccine across countries.\n\nConclusionsOur findings suggest that limited supply, not inadequate demand, likely presents the key bottleneck to reaching high covid-19 vaccine coverage in Sub-Saharan Africa. To turn intent into effective demand, targeted communication campaigns bolstering confidence in the safety of approved vaccines and reducing concerns about side effects will be crucial to safeguard the swift progression of vaccine rollout in one of the worlds poorest regions.\n\nO_TEXTBOXWhat is already known?O_LIEstimates of vaccine acceptance in high- and middle-income countries have found rates to cluster around 70% with considerable cross-country variation.\nC_LIO_LIAs vaccine rollout is severely lagging, low-income countries and particularly Sub-Saharan Africa (SSA) with almost two thirds of the global poor population remain exposed to covid-19 and its impacts on lives and livelihoods.\nC_LIO_LIMuch of the current debate on vaccination campaigns in SSA focuses on supply-chain and financial factors, yet there is a dearth of robust, comparable evidence on covid-19 vaccine hesitancy in these countries.\nC_LI\n\nWhat are the key findings?O_LICovid-19 vaccine acceptance is high in six Sub-Saharan African countries with an estimated four in five people or more in all but one study country willing to take an approved, free vaccine.\nC_LIO_LIClusters of hesitancy vary by country but generally comprise urban areas, richer households, and those with more education.\nC_LI\n\nWhat do the new findings imply?O_LILimited supply, rather than inadequate demand, likely presents the key bottleneck to achieving high covid-19 vaccine coverage in Sub-Saharan Africa.\nC_LIO_LITo reach mass coverage, information campaigns should bolster confidence in vaccine safety and alleviate concerns about side effects.\nC_LI\n\nC_TEXTBOX",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Shelton Kanyanda",
-        "author_inst": "World Bank"
-      },
-      {
-        "author_name": "Yannick Markhof",
-        "author_inst": "World Bank"
-      },
-      {
-        "author_name": "Philip Wollburg",
-        "author_inst": "World Bank"
-      },
-      {
-        "author_name": "Alberto Zezza",
-        "author_inst": "World Bank"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health policy"
-  },
   {
     "rel_doi": "10.1101/2021.06.29.21255526",
     "rel_title": "Transmissibility of COVID-19 among Vaccinated Individuals: A Rapid Literature Review",
@@ -679725,6 +678528,93 @@
     "type": "new results",
     "category": "genomics"
   },
+  {
+    "rel_doi": "10.1101/2021.07.02.450896",
+    "rel_title": "Implications of Spike-glycoprotein processing at S1/S2 by Furin, at S2' by Furin and/or TMPRSS2 and shedding of ACE2: cell-to-cell fusion, cell entry and infectivity of SARS-CoV-2",
+    "rel_date": "2021-07-02",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.02.450896",
+    "rel_abs": "Disclaimer StatementThe author has withdrawn this manuscript due to a duplicate posting of manuscript number 423106. Therefore, the author does not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author (Nabil G. Seidah at seidahn@ircm.qc.ca.",
+    "rel_num_authors": 18,
+    "rel_authors": [
+      {
+        "author_name": "Rachid Essalmani",
+        "author_inst": "Montreal Clinical Research Institute"
+      },
+      {
+        "author_name": "Jaspreet Jain",
+        "author_inst": "Montreal Clinical Research Institute"
+      },
+      {
+        "author_name": "Delia Susan-Resiga",
+        "author_inst": "Montreal Clinical Research Institute"
+      },
+      {
+        "author_name": "Ursula Andreo",
+        "author_inst": "Montreal Clinical Research Institute"
+      },
+      {
+        "author_name": "Alexandra Evagelidis",
+        "author_inst": "Montreal Clinical Research Institute"
+      },
+      {
+        "author_name": "Mouna Derbali",
+        "author_inst": "Montreal Clinical Research Institute"
+      },
+      {
+        "author_name": "David Huynh",
+        "author_inst": "Montreal Clinical Research Institute"
+      },
+      {
+        "author_name": "Frederic Dallaire",
+        "author_inst": "Montreal Clinical Research Institute"
+      },
+      {
+        "author_name": "Melanie Laporte",
+        "author_inst": "Montreal Clinical Research Institute"
+      },
+      {
+        "author_name": "Adrien Delpal",
+        "author_inst": "Universite de Marseille"
+      },
+      {
+        "author_name": "Priscila Sutto-Ortiz",
+        "author_inst": "Universite de Marseille"
+      },
+      {
+        "author_name": "Bruno Coutard",
+        "author_inst": "Aix Marseille Universite"
+      },
+      {
+        "author_name": "Claudine Mapa",
+        "author_inst": "Boston Pharmaceuticals"
+      },
+      {
+        "author_name": "Keith Wilcoxen",
+        "author_inst": "Boston Pharmaceuticals"
+      },
+      {
+        "author_name": "Etienne Decroly",
+        "author_inst": "Universite de Marseille"
+      },
+      {
+        "author_name": "Tram NQ Pham",
+        "author_inst": "Montreal Clinical Research Institute"
+      },
+      {
+        "author_name": "Eric A. Cohen",
+        "author_inst": "Montreal Clinical Research Institute"
+      },
+      {
+        "author_name": "Nabil G Seidah",
+        "author_inst": "Montreal Clinical Research Institute"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "biochemistry"
+  },
   {
     "rel_doi": "10.1101/2021.07.01.450756",
     "rel_title": "Flavonols and dihydroflavonols inhibit the main protease activity of SARS-CoV-2 and the replication of human coronavirus 229E",
@@ -681434,137 +680324,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "occupational and environmental health"
   },
-  {
-    "rel_doi": "10.1101/2021.06.28.21259529",
-    "rel_title": "Global patterns of genetic variation and association with clinical phenotypes at genes involved in SARS-CoV-2 infection",
-    "rel_date": "2021-07-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259529",
-    "rel_abs": "We investigated global patterns of genetic variation and signatures of natural selection at host genes relevant to SARS-CoV-2 infection (ACE2, TMPRSS2, DPP4, and LY6E). We analyzed novel data from 2,012 ethnically diverse Africans and 15,997 individuals of European and African ancestry with electronic health records, and integrated with global data from the 1000GP. At ACE2, we identified 41 non-synonymous variants that were rare in most populations, several of which impact protein function. However, three non-synonymous variants were common among Central African hunter-gatherers from Cameroon and are on haplotypes that exhibit signatures of positive selection. We identify strong signatures of selection impacting variation at regulatory regions influencing ACE2 expression in multiple African populations. At TMPRSS2, we identified 13 amino acid changes that are adaptive and specific to the human lineage. Genetic variants that are targets of natural selection are associated with clinical phenotypes common in patients with COVID-19.",
-    "rel_num_authors": 29,
-    "rel_authors": [
-      {
-        "author_name": "Chao Zhang",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Anurag Verma",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Yuanqing Feng",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Marcelo C. R. Melo",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Michael McQuillan",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Matthew Hansen",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Anastasia Lucas",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Joseph Park",
-        "author_inst": "Perelman School of Medicine at the University of Pennsylvania"
-      },
-      {
-        "author_name": "Alessia Ranciaro",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Simon Thompson",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Meghan A. Rubel",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Michael C. Campbell",
-        "author_inst": "University of Howard"
-      },
-      {
-        "author_name": "William Beggs",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "JIBRIL HIRBO",
-        "author_inst": "Vanderbilt University Medical Center"
-      },
-      {
-        "author_name": "Sununguko Wata Mpoloka",
-        "author_inst": "University of Botswana, Biological Sciences, Gaborone, Botswana"
-      },
-      {
-        "author_name": "Gaonyadiwe George Mokone",
-        "author_inst": "University of Botswana, Faculty of Medicine, Gaborone, Botswana"
-      },
-      {
-        "author_name": "- Regeneron Genetic Center",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Thomas Nyambo",
-        "author_inst": "Department of Biochemistry, Kampala International University in Tanzania, Dar es Salaam, Tanzania"
-      },
-      {
-        "author_name": "Dawit Wolde Meskel",
-        "author_inst": "Addis Ababa University Department of Microbial Cellular and Molecular Biology, Addis Ababa, Ethiopia"
-      },
-      {
-        "author_name": "Gurja Belay",
-        "author_inst": "Addis Ababa University Department of Microbial Cellular and Molecular Biology, Addis Ababa, Ethiopia"
-      },
-      {
-        "author_name": "Charles Fokunang",
-        "author_inst": "Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaounde I, Yaounde, Cameroon"
-      },
-      {
-        "author_name": "Alfred K. Njamnshi",
-        "author_inst": "Department of Neurology, Central Hospital Yaounde; Brain Research Africa Initiative (BRAIN), Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The "
-      },
-      {
-        "author_name": "Sabah A. Omar",
-        "author_inst": "Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya"
-      },
-      {
-        "author_name": "Scott Williams",
-        "author_inst": "Case Western Reserve University"
-      },
-      {
-        "author_name": "Daniel Rader",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Marylyn D Ritchie",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Cesar de la Fuente Nunez",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Giorgio Sirugo",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Sarah Tishkoff",
-        "author_inst": "University of Pennsylvania"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "genetic and genomic medicine"
-  },
   {
     "rel_doi": "10.1101/2021.06.28.21259631",
     "rel_title": "Correlation between the environmental parameters with outbreak pattern of COVID-19: A district level investigation based on yearlong period in India",
@@ -682075,6 +680834,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.06.21.21258023",
+    "rel_title": "ASSESSMENT OF POTENTIAL SARS-CoV-2 VIRUS N GENE INTEGRATION INTO HUMAN GENOME REVEALS NO SIGNIFICANT IMPACT ON RT-qPCR COVID-19 DIAGNOSTIC TESTING",
+    "rel_date": "2021-06-30",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.21.21258023",
+    "rel_abs": "The SARS Coronavirus 2 (SARS-CoV-2) pandemic presents new scientific and scale-up challenges for diagnostic capabilities worldwide. The gold standard diagnostic for SARS-CoV-2 infection is a reverse transcription/quantitative PCR (RT-qPCR) which targets the viral genome, an assay that has now been performed on millions of patient specimens worldwide regardless of symptomatic status. Recently Zhang et al. suggested the possibility that the SARS-CoV-2 N gene could integrate into host cell DNA through the action of the LINE-1 retrotransposon, a mobile element that is potentially active in human somatic cells, thereby calling into question the veracity of N-gene based RT-qPCR for detection of SARS-CoV-2 infection. Accordingly, we assessed the potential impact of these purported integration events on nasal swab specimens tested at our clinical laboratory. Using an N-gene based RT-qPCR assay, we tested 768 arbitrarily selected specimens and identified 2 samples which resulted in a positive detection of viral sequence in the absence of reverse transcriptase, a necessary but not sufficient signal consistent with possible integration of the SARS-CoV-2 N gene into the host genome. Regardless of possible viral N gene integration into the genome, in this small subset of samples, all patients were still positive for SARS-CoV-2 infection, as indicated by a much lower Ct value for reactions performed in the presence of reverse transcriptase (RT) versus reactions performed without RT. Moreover, one of the two positives observed in the absence of RT also tested positive when using primers targeting ORF1ab, a gene closer to the 5 end of the genome. These data are inconsistent with the N gene integration hypothesis suggested by the studies by Zhang et al., and importantly, our results suggest little to no practical impact of possible SARS-CoV-2 genome integration events on RT-qPCR testing.\n\nCOMPETING INTEREST STATEMENTThe authors of this study are employees of the Pandemic Response Lab (PRL)/ReOpen Diagnostics, a private company performing SARS-CoV-2 RT-qPCR based testing, an area of interest of this study.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Erica Briggs",
+        "author_inst": "Pandemic Response Lab (PRL) Research and Development Department, 30-02 48th Avenue, Long Island City, New York, 11101, USA"
+      },
+      {
+        "author_name": "William Ward",
+        "author_inst": "Pandemic Response Lab (PRL) Research and Development Department, 30-02 48th Avenue, Long Island City, New York, 11101, USA"
+      },
+      {
+        "author_name": "Sol Rey",
+        "author_inst": "Pandemic Response Lab (PRL) Research and Development Department, 30-02 48th Avenue, Long Island City, New York, 11101, USA"
+      },
+      {
+        "author_name": "Dylan Law",
+        "author_inst": "Pandemic Response Lab (PRL) Research and Development Department, 30-02 48th Avenue, Long Island City, New York, 11101, USA"
+      },
+      {
+        "author_name": "Katherine Nelson",
+        "author_inst": "Pandemic Response Lab (PRL) Research and Development Department, 30-02 48th Avenue, Long Island City, New York, 11101, USA"
+      },
+      {
+        "author_name": "Michael Bois",
+        "author_inst": "Pandemic Response Lab (PRL) Research and Development Department, 30-02 48th Avenue, Long Island City, New York, 11101, USA"
+      },
+      {
+        "author_name": "Nili Ostrov",
+        "author_inst": "Pandemic Response Lab (PRL) Research and Development Department, 30-02 48th Avenue, Long Island City, New York, 11101, USA; Department of Genetics, Harvard Medi"
+      },
+      {
+        "author_name": "Henry H. Lee",
+        "author_inst": "Pandemic Response Lab (PRL) Research and Development Department, 30-02 48th Avenue, Long Island City, New York, 11101, USA; Department of Genetics, Harvard Medi"
+      },
+      {
+        "author_name": "Jon M. Laurent",
+        "author_inst": "Pandemic Response Lab (PRL) Research and Development Department, 30-02 48th Avenue, Long Island City, New York, 11101, USA"
+      },
+      {
+        "author_name": "Paolo Mita",
+        "author_inst": "Pandemic Response Lab (PRL) Research and Development Department, 30-02 48th Avenue, Long Island City, New York, 11101, USA"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.06.25.21259565",
     "rel_title": "Comparative evaluation of the transmissibility of SARS-CoV-2 variants of concern",
@@ -683148,53 +681962,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2021.06.21.21259289",
-    "rel_title": "Sequencing SARS-CoV-2 Genomes from Saliva",
-    "rel_date": "2021-06-29",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.21.21259289",
-    "rel_abs": "Genomic sequencing is crucial to understanding the epidemiology and evolution of SARS-CoV-2. Often, genomic studies rely on remnant diagnostic material, typically nasopharyngeal swabs, as input into whole genome SARS-CoV-2 next-generation sequencing pipelines. Saliva has proven to be a safe and stable specimen for the detection of SARS-CoV-2 RNA via traditional diagnostic assays, however saliva is not commonly used for SARS-CoV-2 sequencing. Using the ARTIC Network amplicon-generation approach with sequencing on the Oxford Nanopore MinION, we demonstrate that sequencing SARS-CoV-2 from saliva produces genomes comparable to those from nasopharyngeal swabs, and that RNA extraction is necessary to generate complete genomes from saliva. In this study, we show that saliva is a useful specimen type for genomic studies of SARS-CoV-2.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Tara Alpert",
-        "author_inst": "Yale School of Public Health"
-      },
-      {
-        "author_name": "Chantal B.F. Vogels",
-        "author_inst": "Yale School of Public Health"
-      },
-      {
-        "author_name": "Mallery I Breban",
-        "author_inst": "Yale School of Public Health"
-      },
-      {
-        "author_name": "Mary Petrone",
-        "author_inst": "Yale School of Public Health"
-      },
-      {
-        "author_name": "- Yale IMPACT Research Team",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Anne L Wyllie",
-        "author_inst": "Yale School of Public Health"
-      },
-      {
-        "author_name": "Nathan Grubaugh",
-        "author_inst": "Yale School of Public Health"
-      },
-      {
-        "author_name": "Joseph R Fauver",
-        "author_inst": "Yale School of Public Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.06.23.21259416",
     "rel_title": "Characterizing Long COVID: Deep Phenotype of a Complex Condition",
@@ -683805,6 +682572,125 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.06.28.450244",
+    "rel_title": "Systematic genome-scale identification of host factors for SARS-CoV-2 infection across models yields a core single gene dependency; ACE2",
+    "rel_date": "2021-06-29",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.28.450244",
+    "rel_abs": "SARS-CoV-2, depends on host cell components for replication, therefore the identification of virus-host dependencies offers an effective way to elucidate mechanisms involved in viral infection. Such host factors may be necessary for infection and replication of SARS-CoV-2 and, if druggable, presents an attractive strategy for anti-viral therapy. We performed genome wide CRISPR knockout screens in Vero E6 cells and 4 human cell lines including Calu-3, Caco-2, Hek293 and Huh7 to identify genetic regulators of SARS-CoV-2 infection. Our findings identified only ACE2, the cognate SARS-CoV-2 entry receptor, as a common host dependency factor across all cell lines, while all other host genes identified were cell line specific including known factors TMPRSS2 and CTSL. Several of the discovered host-dependency factors converged on pathways involved in cell signalling, lipid metabolism, immune pathways and chromatin modulation. Notably, chromatin modulator genes KMT2C and KDM6A in Calu-3 cells had the strongest impact in preventing SARS-CoV-2 infection when perturbed. Overall, the network of host factors that have been identified will be broadly applicable to understanding the impact of SARS-CoV-2 on human cells and facilitate the development of host-directed therapies.\n\nIN BRIEFSARS-CoV-2, depends on host cell components for infection and replication. Genome-wide CRISPR screens were performed in multiple human cell lines to elucidate common host dependencies required for SARS-CoV-2 infection. Only ACE2, the cognate SARS-CoV-2 entry receptor, was common amongst cell lines, while all other host genes identified were cell line specific, several of which converged on pathways involved in cell signalling, lipid metabolism, immune pathways, and chromatin modulation. Overall, a network of host factors was identified that will be broadly applicable to understanding the impact of SARS-CoV-2 on human cells and facilitate productive targeting of host genes and pathways.\n\nHIGHLIGHTS- Genome-wide CRISPR screens for SARS-CoV-2 in multiple human cell lines\n- Identification of wide-ranging cell-type dependent genetic dependencies for SARS-CoV-2 infection\n- ACE2 is the only common host factor identified across different cell types",
+    "rel_num_authors": 26,
+    "rel_authors": [
+      {
+        "author_name": "Katherine Chan",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Adrian Granda Farias",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Hunsang Lee",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Furkan Guvenc",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Patricia Mero",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Kamaldeep Aulakh",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Kevin R Brown",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Shahan Haider",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Edyta Marcon",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Ulrich Braunschweig",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Amy Hin Yan Tong",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Shuye Pu",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Andrea Habsid",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Natasha Christie-Holmes",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Patrick Budylowski",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Audrey Astori",
+        "author_inst": "Princess Margaret Cancer Centre"
+      },
+      {
+        "author_name": "Ayoob Ghalami",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Samira Mubareka",
+        "author_inst": "Sunnybrook Research Institute"
+      },
+      {
+        "author_name": "Arinjay Banerjee",
+        "author_inst": "University of Saskatchewan"
+      },
+      {
+        "author_name": "Karen L Mossman",
+        "author_inst": "McMaster University"
+      },
+      {
+        "author_name": "Jack Greenblatt",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Scott D Gray-Owen",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Brian Raught",
+        "author_inst": "Princess Margaret Cancer Centre"
+      },
+      {
+        "author_name": "Benjamin Blencowe",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Mikko Taiplale",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Jason Moffat",
+        "author_inst": "University of Toronto"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "systems biology"
+  },
   {
     "rel_doi": "10.1101/2021.06.29.450293",
     "rel_title": "Rapid determination of the wide dynamic range of SARS-CoV-2 Spike T cell responses in whole blood of vaccinated and naturally infected",
@@ -685490,465 +684376,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.06.25.21257885",
-    "rel_title": "Automated, miniaturized, and scalable screening of healthcare workers, first responders, and students for SARS-CoV-2 in San Diego County",
-    "rel_date": "2021-06-28",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.25.21257885",
-    "rel_abs": "BackgroundSuccessful containment strategies for SARS-CoV-2, the causative virus of the COVID-19 pandemic, have involved widespread population testing that identifies infections early and enables rapid contact tracing. In this study, we developed a rapid and inexpensive RT- qPCR testing pipeline for population-level SARS-CoV-2 detection, and used this pipeline to establish a clinical laboratory dedicated to COVID-19 testing at the University of California San Diego (UCSD) with a processing capacity of 6,000 samples per day and next-day result turnaround times.\n\nMethods and findingsUsing this pipeline, we screened 6,786 healthcare workers and first responders, and 21,220 students, faculty, and staff from UCSD. Additionally, we screened 6,031 preschool-grade 12 students and staff from public and private schools across San Diego County that remained fully or partially open for in-person teaching during the pandemic. Between April 17, 2020 and February 5, 2021, participants provided 161,582 nasal swabs that were tested for the presence of SARS-CoV-2. Overall, 752 positive tests were obtained, yielding a test positivity rate of 0.47%. While the presence of symptoms was significantly correlated with higher viral load, most of the COVID-19 positive participants who participated in symptom surveys were asymptomatic at the time of testing. The positivity rate among preschool-grade 12 schools that remained open for in-person teaching was similar to the positivity rate at UCSD and lower than that of San Diego County, with the children in private schools being less likely to test positive than the adults at these schools.\n\nConclusionsMost schools across the United States have been closed for in-person learning for much of the 2020-2021 school year, and their safe reopening is a national priority. However, as there are no vaccines against SARS-CoV-2 currently available to the majority of school-aged children, the traditional strategies of mandatory masking, physical distancing, and repeated viral testing of students and staff remain key components of risk mitigation in these settings. The data presented here suggest that the safety measures and repeated testing actions taken by participating healthcare and educational facilities were effective in preventing outbreaks, and that a similar combination of risk-mitigation strategies and repeated testing may be successfully adopted by other healthcare and educational systems.",
-    "rel_num_authors": 111,
-    "rel_authors": [
-      {
-        "author_name": "Sydney C Morgan",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Stefan Aigner",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Catelyn Anderson",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "Pedro Belda-Ferre",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Peter De Hoff",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Clarisse A Marotz",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Shashank Sathe",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Mark Zeller",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "Noorsher Ahmed",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Xaver Audhya",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Nathan A Baer",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Tom Barber",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Bethany Barrick",
-        "author_inst": "Scripps Clinic"
-      },
-      {
-        "author_name": "Lakshmi Batachari",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Maryann Betty",
-        "author_inst": "University of California San Diego/Rady Children's Hospital San Diego"
-      },
-      {
-        "author_name": "Steven M Blue",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Brent Brainard",
-        "author_inst": "San Diego Fire-Rescue Department"
-      },
-      {
-        "author_name": "Tyler Buckley",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "Jamie Case",
-        "author_inst": "Scripps Clinic"
-      },
-      {
-        "author_name": "Anelizze Castro-Martinez",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Marisol Chacon",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Willi Cheung",
-        "author_inst": "University of California San Diego/ San Diego State University"
-      },
-      {
-        "author_name": "LaVonnye Chong",
-        "author_inst": "Rady Children's Hospital San Diego"
-      },
-      {
-        "author_name": "Nicole G Coufal",
-        "author_inst": "University of California San Diego/ Rady Children's Hospital San Diego/ Rady Children's Institute for Genomic Medicine"
-      },
-      {
-        "author_name": "Evelyn S Crescini",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Scott DeGrand",
-        "author_inst": "Rady Children's Hospital San Diego"
-      },
-      {
-        "author_name": "David P Dimmock",
-        "author_inst": "Rady Children's Institute for Genomic Medicine"
-      },
-      {
-        "author_name": "J Joelle Donofrio-Odmann",
-        "author_inst": "Rady Children's Hospital San Diego / University of California San Diego / San Diego Fire-Rescue Department"
-      },
-      {
-        "author_name": "Emily R Eisner",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Mehrbod Estaki",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Lizbeth Franco Vargas",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Michele Freddock",
-        "author_inst": "Rady Children's Institute for Genomic Medicine"
-      },
-      {
-        "author_name": "Robert M Gallant",
-        "author_inst": "University of California San Diego / Salk Institute for Biological Studies"
-      },
-      {
-        "author_name": "Andrea Galmozzi",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "Nina J Gao",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Sheldon Gilmer",
-        "author_inst": "Rady Children's Hospital San Diego"
-      },
-      {
-        "author_name": "Edyta M Grzelak",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "Abbas Hakim",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Jonathan Hart",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "Charlotte Hobbs",
-        "author_inst": "Rady Children's Institute for Genomic Medicine"
-      },
-      {
-        "author_name": "Greg Humphrey",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Nadja Ilkenhans",
-        "author_inst": "Salk Institute for Biological Studies/ Ruperto Carola University"
-      },
-      {
-        "author_name": "Marni Jacobs",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Christopher A Kahn",
-        "author_inst": "University of California San Diego/ San Diego Fire-Rescue Department"
-      },
-      {
-        "author_name": "Bhavika K Kapadia",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Matthew Kim",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Sunil Kurian",
-        "author_inst": "Scripps Clinic"
-      },
-      {
-        "author_name": "Alma L Lastrella",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Elijah S Lawrence",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Kari Lee",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Qishan Liang",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Hanna Liliom",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "Valentina Lo Sardo",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "Robert Logan",
-        "author_inst": "San Diego Fire-Rescue Department"
-      },
-      {
-        "author_name": "Michal Machnicki",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Celestine G Magallanes",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Clarence K Mah",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Denise Malacki",
-        "author_inst": "Rady Children's Hospital San Diego"
-      },
-      {
-        "author_name": "Ryan J Marina",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Christopher Marsh",
-        "author_inst": "Scripps Clinic"
-      },
-      {
-        "author_name": "Natasha K Martin",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Nathaniel L Matteson",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "Daniel J Maunder",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Kyle McBride",
-        "author_inst": "Rady Children's Hospital San Diego"
-      },
-      {
-        "author_name": "Bryan McDonald",
-        "author_inst": "Salk Institute for Biological Studies"
-      },
-      {
-        "author_name": "Daniel McDonald",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Michelle McGraw",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "Audra R Meadows",
-        "author_inst": "March of Dimes Foundation"
-      },
-      {
-        "author_name": "Michelle Meyer",
-        "author_inst": "Scripps Clinic"
-      },
-      {
-        "author_name": "Amber L Morey",
-        "author_inst": "University of California San Diego/ San Diego State University"
-      },
-      {
-        "author_name": "Jasmine R Mueller",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Toan T Ngo",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Julie Nguyen",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "Viet Nguyen",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "Laura J Nicholson",
-        "author_inst": "The Scripps Research Institute/ Scripps Clinic"
-      },
-      {
-        "author_name": "Alhakam Nouri",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Victoria Nudell",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "Eugenio Nunez",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Kyle O'Neill",
-        "author_inst": "San Diego Fire-Rescue Department"
-      },
-      {
-        "author_name": "R Tyler Ostrander",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Priyadarshini Pantham",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Samuel S Park",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "David Picone",
-        "author_inst": "San Diego Fire-Rescue Department"
-      },
-      {
-        "author_name": "Ashley Plascencia",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Isaraphorn Pratumchai",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "Michael Quigley",
-        "author_inst": "Scripps Clinic"
-      },
-      {
-        "author_name": "Michelle Franc Ragsac",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Andrew C Richardson",
-        "author_inst": "Rady Children's Hospital San Diego"
-      },
-      {
-        "author_name": "Refugio Robles-Sikisaka",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "Christopher A Ruiz",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Justin Ryan",
-        "author_inst": "Rady Children's Hospital San Diego"
-      },
-      {
-        "author_name": "Lisa Sacco",
-        "author_inst": "Rady Children's Hospital San Diego"
-      },
-      {
-        "author_name": "Sharada Saraf",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "Phoebe Seaver",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Leigh Sewall",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "Elizabeth W Smoot",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Kathleen M Sweeney",
-        "author_inst": "Rady Children's Hospital San Diego"
-      },
-      {
-        "author_name": "Chandana Tekkatte",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Rebecca Tsai",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Holly Valentine",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Shawn Walsh",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "August Williams",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Min Yi Wu",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Bing Xia",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Brian Yee",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Jason Z Zhang",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Kristian G Andersen",
-        "author_inst": "The Scripps Research Institute"
-      },
-      {
-        "author_name": "Lauge Farnaes",
-        "author_inst": "University of California San Diego / Rady Children's Institute of Genomic Medicine"
-      },
-      {
-        "author_name": "Rob Knight",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Gene W Yeo",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Louise C Laurent",
-        "author_inst": "University of California San Diego"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.06.23.21259422",
     "rel_title": "Overcoming COVID-19 vaccine preferential bias in Europe: Is the end of the pandemic still foreseeable?",
@@ -686311,6 +684738,37 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2021.06.25.449831",
+    "rel_title": "Solar simulated ultraviolet radiation inactivates HCoV-NL63 and SARS-CoV-2 coronaviruses at environmentally relevant doses",
+    "rel_date": "2021-06-28",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.25.449831",
+    "rel_abs": "The germicidal properties of short wavelength ultraviolet C (UVC) light are well established and used to inactivate many viruses and other microbes. However, much less is known about germicidal effects of terrestrial solar UV light, confined exclusively to wavelengths in the UVA and UVB regions. Here, we have explored the sensitivity of the human coronaviruses HCoV-NL63 and SARS-CoV-2 to solar-simulated full spectrum ultraviolet light (sUV) delivered at environmentally relevant doses. First, HCoV-NL63 coronavirus inactivation by sUV-exposure was confirmed employing (i) viral plaque assays, (ii) RT-qPCR detection of viral genome replication, and (iii) infection-induced stress response gene expression array analysis. Next, a detailed dose-response relationship of SARS-CoV-2 coronavirus inactivation by sUV was elucidated, suggesting a half maximal suppression of viral infectivity at low sUV doses. Likewise, extended sUV exposure of SARS-CoV-2 blocked cellular infection as revealed by plaque assay and stress response gene expression array analysis. Moreover, comparative (HCoV-NL63 versus SARS-CoV-2) single gene expression analysis by RT-qPCR confirmed that sUV exposure blocks coronavirus-induced redox, inflammatory, and proteotoxic stress responses. Based on our findings, we estimate that solar ground level full spectrum UV light impairs coronavirus infectivity at environmentally relevant doses. Given the urgency and global scale of the unfolding SARS-CoV-2 pandemic, these prototype data suggest feasibility of solar UV-induced viral inactivation, an observation deserving further molecular exploration in more relevant exposure models.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Georg T. Wondrak",
+        "author_inst": "Department of Pharmacology and Toxicology, College of Pharmacy and UA Cancer Center, University of Arizona, Tucson, Arizona"
+      },
+      {
+        "author_name": "Jana Jandova",
+        "author_inst": "Department of Pharmacology and Toxicology, College of Pharmacy and UA Cancer Center, University of Arizona, Tucson, Arizona"
+      },
+      {
+        "author_name": "Spencer J. Williams",
+        "author_inst": "Department of Immunobiology, College of Medicine, University of Arizona, Tucson, Arizona"
+      },
+      {
+        "author_name": "Dominik Schenten",
+        "author_inst": "Department of Immunobiology, College of Medicine, University of Arizona, Tucson, Arizona"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2021.06.28.450163",
     "rel_title": "N4-hydroxycytidine and inhibitors of dihydroorotate dehydrogenase synergistically suppress SARS-CoV-2 replication",
@@ -688148,93 +686606,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.06.17.21258858",
-    "rel_title": "The serological diversity of serum IgG/IgA/IgM against the SARS-CoV-2 nucleoprotein, spike, and receptor-binding domain and neutralizing antibodies in patients with COVID-19 in Japan",
-    "rel_date": "2021-06-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.17.21258858",
-    "rel_abs": "ObjectivesTo compare the temporal changes of IgM, IgG, and IgA antibodies against the SARS-CoV-2 nucleoprotein, S1 subunit, and receptor binding domain and neutralizing antibodies (NAbs) against SARS-CoV-2 in patients with COVID-19.\n\nMethodsA total of five patients in Nissan Tamagawa Hospital, Tokyo, Japan confirmed COVID-19 from August 8, 2020 to August 14, 2020 were investigated. Serum samples were acquired multiple times from 0 to 76 days after symptom onset. Using a fully automated CLIA analyzer, we measured the levels of IgG, IgA, and IgM against the SARS-CoV-2 N, S1, and RBD and NAbs against SARS-CoV-2.\n\nResultsThe levels of IgG antibodies against SARS-CoV-2 structural proteins increased over time in all cases but IgM and IgA levels against SARS-CoV-2 showed different increasing trends among individuals in the early stage. In particular, we observed IgA antibodies increasing before IgG and IgM in 3/5 cases. The NAb levels against SARS-CoV-2 increased and kept above 10 AU/mL more than around 70 days after symptom onset in all cases. Furthermore, in the early stage, NAb levels were more than cut off value in 4/5 COVID-19 patients some of whose antibodies against RBD didnt exceed 10 AU/mL.\n\nConclusionsOur findings indicate that patients with COVID-19 should be examined for IgG, IgA and IgM antibodies against SARS-CoV-2 structural proteins and NAbs against SARS-CoV-2 in addition to conventional antibody testing methods for SARS-CoV-2 (IgG and IgM kits) to analyze the diversity of patients immune mechanisms.",
-    "rel_num_authors": 18,
-    "rel_authors": [
-      {
-        "author_name": "Yudai Kaneko",
-        "author_inst": "The University of Tokyo"
-      },
-      {
-        "author_name": "Akira Sugiyama",
-        "author_inst": "The University of Tokyo"
-      },
-      {
-        "author_name": "Toshiya Tanaka",
-        "author_inst": "The University of Tokyo"
-      },
-      {
-        "author_name": "Kazushige Fukui",
-        "author_inst": "Medical & Biological Laboratories Co., Ltd"
-      },
-      {
-        "author_name": "Akashi Taguchi",
-        "author_inst": "The University of Tokyo"
-      },
-      {
-        "author_name": "Aya Nakayama",
-        "author_inst": "The University of Tokyo"
-      },
-      {
-        "author_name": "Kazumasa Koga",
-        "author_inst": "Nissan Tamagawa Hospital"
-      },
-      {
-        "author_name": "Yoshiro Kishi",
-        "author_inst": "Medical & Biological Laboratories Co., Ltd"
-      },
-      {
-        "author_name": "Wang Daming",
-        "author_inst": "Suzhou Institute of Biomedical Engineering and Technology Chinese Academy of Sciences"
-      },
-      {
-        "author_name": "Chungen Qian",
-        "author_inst": "Huazhong University of Science and Technology"
-      },
-      {
-        "author_name": "Fuzhen Xia",
-        "author_inst": "Shenzhen YHLO Biotech Co., Ltd"
-      },
-      {
-        "author_name": "Fan He",
-        "author_inst": "Shenzhen YHLO Biotech Co., Ltd"
-      },
-      {
-        "author_name": "Liang Zheng",
-        "author_inst": "Shenzhen YHLO Biotech Co., Ltd"
-      },
-      {
-        "author_name": "Yi Yu",
-        "author_inst": "Shenzhen YHLO Biotech Co., Ltd"
-      },
-      {
-        "author_name": "Yuichiro Wada",
-        "author_inst": "The University of Tokyo"
-      },
-      {
-        "author_name": "Yoshiaki Wada",
-        "author_inst": "Nissan Tamagawa Hospital"
-      },
-      {
-        "author_name": "Tatsuhiko Kodama",
-        "author_inst": "The University of Tokyo"
-      },
-      {
-        "author_name": "Takeshi Kawamura",
-        "author_inst": "The University of Tokyo"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.06.08.21258599",
     "rel_title": "Susceptibility of zero community transmission regimes to new variants of SARS-CoV-2: a modelling study of Queensland",
@@ -688529,6 +686900,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.06.22.21259345",
+    "rel_title": "Multi-centre post-implementation evaluation of SARS-CoV-2 antigen-based point of care tests used for asymptomatic screening of continuing care healthcare workers",
+    "rel_date": "2021-06-25",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.22.21259345",
+    "rel_abs": "OBJECTIVESFrequent screening of SARS-CoV-2 among asymptomatic populations using antigen-based point of care tests (APOCT) is occurring globally with limited clinical performance data. The positive predictive value (PPV) of two APOCT used in the asymptomatic screening of SARS-CoV-2 among healthcare workers (HCW) at continuing care (CC) sites across Alberta, Canada was evaluated.\n\nMETHODSBetween February 22 and May 2, 2021, CC sites implemented SARS-CoV-2 voluntary screening of their asymptomatic HCW. Onsite testing with Abbott Panbio or BD Veritor occurred on a weekly or twice weekly basis. Positive APOCT were confirmed with a real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) reference method.\n\nRESULTSA total of 71,847 APOCT (17,689 Veritor and 54,158 Panbio) were performed among 369 CC sites. Eighty-seven (0.12%) APOCT were positive, of which 39 (0.05%) confirmed as true positives using rRT-PCR. Use of the Veritor and Panbio resulted in a 76.6% and 30.0% false positive detection, respectively (p<0.001). This corresponded to a 23.4% and 70.0% PPV for the Veritor and Panbio, respectively.\n\nCONCLUSIONSFrequent screening of SARS-CoV-2 among asymptomatic HCW in CC, using APOCT, resulted in a very low detection rate and a high detection of false positives. Careful assessment between the risks vs benefits of APOCT programs in this population needs to be thoroughly considered before implementation.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Jamil N Kanji",
+        "author_inst": "University of Calgary; Alberta Precision Laboratories"
+      },
+      {
+        "author_name": "Dustin Proctor",
+        "author_inst": "University of Calgary"
+      },
+      {
+        "author_name": "William Stokes",
+        "author_inst": "University of Alberta; Alberta Precision Laboratories"
+      },
+      {
+        "author_name": "Byron M Berenger",
+        "author_inst": "University of Calgary; Alberta Precision Laboratories"
+      },
+      {
+        "author_name": "James Silvius",
+        "author_inst": "University of Calgary"
+      },
+      {
+        "author_name": "Graham Tipples",
+        "author_inst": "University of Alberta; Li Ka Shing Institute for Virology; Alberta Precision Laboratories"
+      },
+      {
+        "author_name": "A Mark Joffe",
+        "author_inst": "University of Alberta; Alberta Health Services"
+      },
+      {
+        "author_name": "Allison A Venner",
+        "author_inst": "University of Calgary; Alberta Precision Laboratories"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.06.22.21259349",
     "rel_title": "Inflection in prevalence of SARS-CoV-2 infections missing the N501Y mutation as a marker of rapid Delta (B.1.617.2) lineage expansion in Ontario, Canada",
@@ -689846,53 +688264,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.06.21.21259225",
-    "rel_title": "The burden of COVID-19 and Case Fatality Rate in Pune India: An Analysis of First and Second Wave of the Pandemic",
-    "rel_date": "2021-06-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.21.21259225",
-    "rel_abs": "BackgroundThe recent second wave in India in April-May 2021 placed an unprecedented burden on the Indian health systems. However, limited data exist on the epidemiology of the COVID-19 pandemic from the first wave through the second wave in India. With detailed epidemiologic data, we aimed to assess trends in incident cases and case fatality, its risk between pandemic waves in Pune, an epicenter of COVID-19 cases in India, a country with the second-largest absolute burden worldwide.\n\nMethodsProgrammatic COVID-19 data from Pune city between the first wave (March 09th 2020-October 31st, 2020), maintenance phase (November 01st 2020-February 14th, 2021), the second wave (February 15th, 2021-May 31st, 2021) were assessed for trends of incident cases, time-to-death, and case fatality rate (CFR). In addition, Poisson regression models adjusted for age and gender were used to determine the independent effect of pandemic waves on mortality.\n\nResultsOf 465,192 COVID-19 cases, 162,182 (35%) were reported in the first wave, and 4,146 (2.5%) died among them; Maintenance period registered 27,517 (6%) cases with 590 (2.1%) deaths; Second wave reported 275,493 (59%) cases and 3184 (1.1%) deaths (p<0.01). The overall CFR was 1.16 per 1000 person-days (PD), which declined from 1.80 per 1000 PD during the first wave to 0.77 per 1000 PD in the second wave. The risk of death was 1.49 times higher during the first wave (adjusted case fatality rate ratio-aCFRR,1.49; 95% CI: 1.37-1.62) and 35% lower in the second wave (aCFRR, 0.65; 95% CI: 0.59 - 0.70), compared to the maintenance phase.\n\nInterpretationThe absolute burden of COVID-19 cases and deaths were more significant in the second wave in Pune, India; however, the CFR declined as the pandemic progressed. Nevertheless, investigating newer therapies and implementing mass vaccinations against COVID-19 are urgently needed.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Prasad Bogam",
-        "author_inst": "Johns Hopkins India, Pune, India"
-      },
-      {
-        "author_name": "Aparna Joshi",
-        "author_inst": "Indian Institute of Science Education and Research, Pune, India"
-      },
-      {
-        "author_name": "Sanket Nagarkar",
-        "author_inst": "Indian Institute of Science Education and Research, Pune, India"
-      },
-      {
-        "author_name": "Divyashri Jain",
-        "author_inst": "BJ Government Medical College-Johns Hopkins University Clinical Research Site (CRS), Pune, India"
-      },
-      {
-        "author_name": "Nikhil Gupte",
-        "author_inst": "Johns Hopkins India, Pune, India"
-      },
-      {
-        "author_name": "L S Shashidhara",
-        "author_inst": "Pune Knowledge Cluster, Pune, India"
-      },
-      {
-        "author_name": "Joy Merwin Monteiro",
-        "author_inst": "Indian Institute of Science Education and Research, Pune, India"
-      },
-      {
-        "author_name": "Vidya Mave",
-        "author_inst": "BJ Government Medical College-Johns Hopkins University Clinical Research Site (CRS), Pune, India"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.06.21.21257586",
     "rel_title": "Data-Driven Prediction of COVID-19 Cases in Germany for Decision Making",
@@ -690255,6 +688626,45 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2021.06.25.449750",
+    "rel_title": "A random priming amplification method for whole genome sequencing of SARS-CoV-2 and H1N1 influenza A virus.",
+    "rel_date": "2021-06-25",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.25.449750",
+    "rel_abs": "BackgroundNon-targeted whole genome sequencing is a powerful tool to comprehensively identify constituents of microbial communities in a sample. There is no need to direct the analysis to any identification before sequencing which can decrease the introduction of bias and false negatives results. It also allows the assessment of genetic aberrations in the genome (e.g., single nucleotide variants, deletions, insertions and copy number variants) including in noncoding protein regions.\n\nMethodsThe performance of four different random priming amplification methods to recover RNA viral genetic material of SARS-CoV-2 were compared in this study. In method 1 (H-P) the reverse transcriptase (RT) step was performed with random hexamers whereas in methods 2-4 RT incorporating an octamer primer with a known tag. In methods 1 and 2 (K-P) sequencing was applied on material derived from the RT-PCR step, whereas in methods 3 (SISPA) and 4 (S-P) an additional amplification was incorporated before sequencing.\n\nResultsThe SISPA method was the most effective and efficient method for non-targeted/random priming whole genome sequencing of COVID that we tested. The SISPA method described in this study allowed for whole genome assembly of SARS-CoV-2 and influenza A(H1N1)pdm09 in mixed samples. We determined the limit of detection and characterization of SARS-CoV-2 virus which was 103 pfu/ml (Ct, 22.4) for whole genome assembly and 101 pfu/ml (Ct, 30) for metagenomics detection.\n\nConclusionsThe SISPA method is predominantly useful for obtaining genome sequences from RNA viruses or investigating complex clinical samples as no prior sequence information is needed. It might be applied to monitor genomic virus changes, virus evolution and can be used for fast metagenomics detection or to assess the general picture of different pathogens within the sample.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Klaudia Chrzastek",
+        "author_inst": "The Pirbright Institute"
+      },
+      {
+        "author_name": "Chandana Tennakoon",
+        "author_inst": "The Pirbright Institute"
+      },
+      {
+        "author_name": "Dagmara Bialy",
+        "author_inst": "The Pirbright Institute"
+      },
+      {
+        "author_name": "Graham L Freimanis",
+        "author_inst": "The Pirbright Institute"
+      },
+      {
+        "author_name": "John Flannery",
+        "author_inst": "The Pirbright Institute"
+      },
+      {
+        "author_name": "Holly Shelton",
+        "author_inst": "The Pirbright institute"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2021.06.25.449871",
     "rel_title": "Engineered chimeric T cell receptor fusion construct (TRuC)-expressing T cells prevent translational shutdown in SARS-CoV-2-infected cells",
@@ -691612,37 +690022,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2021.06.22.21259331",
-    "rel_title": "Validation of the 4C Deterioration Model for COVID-19 in a UK teaching hospital during Wave 2",
-    "rel_date": "2021-06-24",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.22.21259331",
-    "rel_abs": "The 4C Deterioration model was developed and validated on data collected in UK hospitals until August 26, 2020, but has not yet been validated in the presence of SARS-CoV-2 variants and novel treatment regimens that have emerged subsequently. In this first validation study of the 4C Deterioration model on patients admitted between August 27, 2020 and April 16, 2021 we found, despite a slightly overestimation of risk, that the discrimination (area under the curve 0.75, 95% CI 0.71-0.78) and calibration of the model remained consistent with the development study, strengthening the evidence for adopting this model into clinical practice.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Sarah L Cowan",
-        "author_inst": "Addenbrookes Hospital, Cambridge Biomedical Campus"
-      },
-      {
-        "author_name": "Martin Wiegand",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Jacobus Preller",
-        "author_inst": "Addenbrookes Hospital, Cambridge Biomedical Campus"
-      },
-      {
-        "author_name": "Robert J B Goudie",
-        "author_inst": "University of Cambridge"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health informatics"
-  },
   {
     "rel_doi": "10.1101/2021.06.22.21259354",
     "rel_title": "Selective tweeting of COVID-19 articles: Does title or abstract positivity influence dissemination?",
@@ -691985,6 +690364,41 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2021.06.14.21258907",
+    "rel_title": "Hybrid-Quantum approach for the optimal lockdown to stop the SARS-CoV-2 community spread subject to maximizing nation economy globally",
+    "rel_date": "2021-06-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.14.21258907",
+    "rel_abs": "Owing to the SARS-CoV-2 epidemic (severe acute respiratory coronavirus 2 syndromes), the global situation has changed drastically. Several countries, including India, Europe, U.S.A., introduced a full state/nation lockdown to minimize the disease transmission through human interaction after the virus entered the population and to minimize the loss of human life. Millions of people have gone unemployed due to lockdown implementation, resulting in business and industry closure and leading to a national economic slowdown. Therefore, preventing the spread of the COVID-19 virus in the world while also preserving the global economy is an essential problem requiring an effective and immediate solution. Using the compartmental epidemiology S, E, I, R or D (Susceptible, Exposed, Infectious, Recovery or Death) model extended to multiple population regions we predict the evolution of the SARS-CoV-2 disease and construct an optimally scheduled lockdown calendar to execute lockdown over phases, using the well-known Knapsack problem. A comparative analysis of both classical and quantum models shows that our model decreases SARS-CoV-2 active cases while retaining the average global economic factor, GDP, in contrast to the scenario with no lockdown.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Sahil Zaman",
+        "author_inst": "Acharya Prafulla Chandra College, New Barrackpur"
+      },
+      {
+        "author_name": "Alex Khan",
+        "author_inst": "Aligned IT, LLC, USA"
+      },
+      {
+        "author_name": "Arindam Sadhu",
+        "author_inst": "Narula Institute of Technology, India"
+      },
+      {
+        "author_name": "Dr Kunal Das Sr.",
+        "author_inst": "Acharya Prafulla Chandra College"
+      },
+      {
+        "author_name": "Faisal Shah Khan",
+        "author_inst": "Khalifa University, UAE"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.06.18.21259062",
     "rel_title": "Temporal changes in mental response and prevention patterns, and their impact from uncertainty stress during the transition in China from the COVID-19 epidemic to sporadic infection",
@@ -693446,29 +691860,6 @@
     "type": "new results",
     "category": "genomics"
   },
-  {
-    "rel_doi": "10.1101/2021.06.18.21259133",
-    "rel_title": "Effectiveness of Tocilizumab, Sarilumab, and Anakinra for critically ill patients with COVID-19 The REMAP-CAP COVID-19 Immune Modulation Therapy Domain Randomized Clinical Trial",
-    "rel_date": "2021-06-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.18.21259133",
-    "rel_abs": "BACKGROUNDThe interleukin-6 receptor antagonist tocilizumab improves outcomes in critically ill patients with coronavirus disease 2019 (COVID-19). However, the effectiveness of other immune modulating agents is unclear.\n\nMETHODSWe evaluated four immunomodulatory agents in an ongoing international, multifactorial, adaptive platform trial. Adult participants with COVID-19 were randomized to receive tocilizumab, sarilumab, anakinra, or standard care (control). In addition, a small group (n=21) of participants were randomized to interferon-{beta}1a. The primary outcome was an ordinal scale combining in-hospital mortality (assigned -1) and days free of organ support to day 21. The trial used a Bayesian statistical model with pre-defined triggers for superiority, equivalence or futility.\n\nRESULTSStatistical triggers for equivalence between tocilizumab and sarilumab; and for inferiority of anakinra to the other active interventions were met at a planned adaptive analysis. Of the 2274 critically ill participants enrolled, 972 were assigned to tocilizumab, 485 to sarilumab, 378 to anakinra and 418 to control. Median organ support-free days were 7 (interquartile range [IQR] -1, 16), 9 (IQR -1, 17), 0 (IQR -1, 15) and 0 (IQR -1, 15) for tocilizumab, sarilumab, anakinra and control, respectively. Median adjusted odds ratios were 1.46 (95%CrI 1.13, 1.87), 1.50 (95%CrI 1.13, 2.00), and 0.99 (95%CrI 0.74, 1.35) for tocilizumab, sarilumab and anakinra, yielding 99.8%, 99.8% and 46.6% posterior probabilities of superiority, respectively, compared to control. Median adjusted odds ratios for hospital survival were 1.42 (95%CrI 1.05,1.93), 1.51 (95%CrI 1.06, 2.20) and 0.97 (95%CrI 0.66, 1.40) for tocilizumab, sarilumab and anakinra respectively, compared to control, yielding 98.8%, 98.8% and 43.6% posterior probabilities of superiority, respectively, compared to control. All treatments appeared safe.\n\nCONCLUSIONSIn patients with severe COVID-19 receiving organ support, tocilizumab and sarilumab are similarly effective at improving survival and reducing duration of organ support. Anakinra is not effective in this population. (ClinicalTrials.gov number: NCT02735707)",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "- The REMAP-CAP Investigators",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Lennie P.G. Derde",
-        "author_inst": "University Medical Center Utrecht"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "intensive care and critical care medicine"
-  },
   {
     "rel_doi": "10.1101/2021.06.22.21259318",
     "rel_title": "Efficacy of Proxalutamide in Hospitalized COVID-19 Patients: A Randomized, Double-Blind, Placebo-Controlled, Parallel-Design Clinical Trial",
@@ -693815,6 +692206,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.06.18.21259156",
+    "rel_title": "Factors affecting the transmission of SARS-CoV-2 in school settings",
+    "rel_date": "2021-06-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.18.21259156",
+    "rel_abs": "BackgroundSeveral studies have reported SARS-CoV-2 outbreaks in schools, with a wide range of secondary attack rate (SAR; range: 0-100%). We aimed to examine key risk factors to better understand SARS-CoV-2 transmission in schools.\n\nMethodsWe collected records of 39 SARS-CoV-2 school outbreaks globally published through July 2021 and compiled information on hypothesized risk factors. We utilized the directed acyclic graph (DAG) to conceptualize risk mechanisms, used logistic regression to examine each risk-factor group, and further built multi-risk models.\n\nResultsThe best-fit model showed that the intensity of concurrent community transmission (adjusted odds ratio [aOR]: 1.2, 95% CI: 1.17 - 1.24, for each increase of 1 case per 10,000 persons per week), individualism (aOR: 1.72, 95% CI: 1.19 - 2.5, above vs. below the median) were associated higher risk, whereas preventive measures (aOR: 0.22, 95% CI: 0.17 - 0.29, distancing and masking vs. none) and higher population immunity (aOR: 0.28, 95% CI: 0.22 - 0.35) were associated with lower risk of SARS-CoV-2 transmission in schools. Compared to students in pre-schools, the aOR was 0.35 (95% CI: 0.23 - 0.54) for students in primary schools and 1.3 (95% CI: 0.9 - 1.88) for students in high schools.\n\nConclusionsPreventive measures in schools (e.g. social distancing and mask-wearing) and communal efforts to lower transmission and increase vaccination uptake (i.e. vaccine-induced population immunity) in the community should be taken to collectively reduce transmission and protect children in schools. Flexible reopening policies may be considered for different levels of schools given their risk differences.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Haokun Yuan",
+        "author_inst": "Columbia University"
+      },
+      {
+        "author_name": "Connor Reynolds",
+        "author_inst": "Columbia University"
+      },
+      {
+        "author_name": "Sydney Ng",
+        "author_inst": "Columbia University"
+      },
+      {
+        "author_name": "Wan Yang",
+        "author_inst": "Columbia University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.06.14.21258886",
     "rel_title": "The majority of the variation in COVID-19 rates between nations is explained by median age, obesity rate, and island status",
@@ -694672,53 +693094,6 @@
     "type": "new results",
     "category": "molecular biology"
   },
-  {
-    "rel_doi": "10.1101/2021.06.15.21258948",
-    "rel_title": "The Knowledge and Attitude of Physicians Regarding Vaccinations in Yerevan, Armenia: Challenges for COVID-19",
-    "rel_date": "2021-06-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.15.21258948",
-    "rel_abs": "BackgroundThis primary-data analysis investigates the current level of awareness and medical knowledge of physicians in 20 health facilities in Yerevan, Armenia regarding vaccination - specifically with regard to HPV infection and the recently-introduced Gardasil vaccine used against HPV infection - that may have implications for successful roll-outs of national programmes for new vaccines, including those for COVID-19.\n\nMethodsA questionnaire-based cross-sectional study was completed by 348 physicians who met the study inclusion criteria, from 20 out of 36 randomly selected healthcare facilities in Yerevan, Armenia, between Dec 2017 to Sep 2018. The aim of the questionnaire was to identify physicians awareness of and attitudes to HPV-related cervical cancer and the Gardasil vaccine. Responses were analysed using SPSS software (Version 16).\n\nResultsThe responding physicians displayed a respectable level of knowledge and awareness regarding vaccination with regard to some characteristics (e.g. more than 81% knew that HPV infection was commonly asymptomatic, 87% were knew that HPV infection was implicated in most cervical cancers and 87% knew that cervical cancer is the most prevalent cancer amongst women) but low knowledge in others and poor understanding of key issues such as the age at which women were most likely to develop cervical cancer (only 15% answered correctly); whether or not the vaccine should be administered to people who had already been affected (27% answered correctly) and whether sexually active young people should be treated for infection before vaccination (26%). Lack of confidence within the surveyed groups regarding the value of vaccination and, in particular concerns over the reasons for administering it to certain age cohorts, was driven by misconceptions.\n\nConclusionsArmenian physicians awareness of vaccine characteristics, the reasons for their inclusion in the national vaccination programme and the characteristics of the diseases they treat can be poor. The study further suggests that drivers of vaccine hesitancy are complex, may not be consistent from vaccine to vaccine, and may vary from generation to generation. The Armenian healthcare sector may need to provide additional training, awareness-raising and educational activities to improve understanding of and trust in vaccination programmes. Further studies are warranted to better understand knowledge, attitudes and practices (KAP) regarding immunization and vaccination programmes amongst Armenian healthcare workers.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Arman R Badalyan",
-        "author_inst": "Yerevan State Medical University after M. Heratsi"
-      },
-      {
-        "author_name": "Marine Hovhannisyan",
-        "author_inst": "Yerevan State Medical University after M. Heratsi"
-      },
-      {
-        "author_name": "Gayane Ghavalyan",
-        "author_inst": "Yerevan State Medical University after M. Heratsi"
-      },
-      {
-        "author_name": "Mary M Ter-Stepanyan",
-        "author_inst": "Yerevan State Medical University after M. Heratsi"
-      },
-      {
-        "author_name": "Rory Cave",
-        "author_inst": "University of West London"
-      },
-      {
-        "author_name": "Jennifer Cole",
-        "author_inst": "Royal Holloway University of London"
-      },
-      {
-        "author_name": "Andrew W.K. Farlow",
-        "author_inst": "University of Oxford, Oxford Martin School"
-      },
-      {
-        "author_name": "Hermine Mkrtchyan",
-        "author_inst": "University of West London"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.06.21.449058",
     "rel_title": "I will teach you here or there, I will try to teach you anywhere: perceived supports and barriers for emergency remote teaching during COVID-19 pandemic",
@@ -694993,6 +693368,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.06.18.21259072",
+    "rel_title": "Evaluation of the effectiveness of remdesivir in treating severe COVID-19 using data from the ISARIC WHO Clinical Characterisation Protocol UK: a prospective, national cohort study.",
+    "rel_date": "2021-06-21",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.18.21259072",
+    "rel_abs": "BackgroundRemdesivir has been evaluated in clinical trial populations, but there is a sparsity of evidence evaluating effectiveness in general populations.\n\nMethodsAdults eligible to be treated with remdesivir, requiring oxygen but not ventilated, were identified from UK patients hospitalised with COVID-19. Patients treated with remdesivir within 24h of hospitalisation were compared with propensity-score matched controls; estimates of effectiveness were calculated for short-term outcomes (14-day mortality, 28-day mortality, time-to-recovery among others) using multivariable modelling.\n\nResults9,278 out of 39,330 patients satisfied eligibility criteria. 1,549 patients were identified as  treated and matched with 4,964 controls. Patients were 62% male, mean (SD) age 63.1 (15.6) years, 80%  White ethnicity, and symptomatic for a median of 6 days prior to baseline. There was no statistically significant benefit of remdesivir at 14 days in terms of mortality or clinical status; there were signals of effectiveness in time-to-recovery after day 9, and a reduction in 28-day mortality.\n\nConclusionIn a real-world setting, initiation of remdesivir within 24h of hospitalisation in conjunction with standard of care was not associated with a benefit at 14 days but supports clinical trial evidence of a potential reduction in 28-day mortality.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Barbara N Arch",
+        "author_inst": "University of Liverpool"
+      },
+      {
+        "author_name": "Dorottya Kovacs",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Janet T Scott",
+        "author_inst": "MRC-University of Glasgow Center for Virus research"
+      },
+      {
+        "author_name": "Ashley P Jones",
+        "author_inst": "University of Liverpool"
+      },
+      {
+        "author_name": "Ewen M Harrison",
+        "author_inst": "University of Edinburgh"
+      },
+      {
+        "author_name": "Anna Rosala-Hallas",
+        "author_inst": "University of Liverpool"
+      },
+      {
+        "author_name": "Carrol G Gamble",
+        "author_inst": "University of Liverpool"
+      },
+      {
+        "author_name": "Peter JM Openshaw",
+        "author_inst": "Imperial College London"
+      },
+      {
+        "author_name": "J Kenneth Baillie",
+        "author_inst": "Roslin Institute, University of Edinburgh"
+      },
+      {
+        "author_name": "Malcolm Gracie Semple",
+        "author_inst": "University of Liverpool"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.06.15.21258966",
     "rel_title": "Tocilizumab in COVID-19 - A Bayesian reanalysis of RECOVERY",
@@ -696346,117 +694776,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.06.17.21259103",
-    "rel_title": "REACT-1 round 12 report: resurgence of SARS-CoV-2 infections in England associated with increased frequency of the Delta variant",
-    "rel_date": "2021-06-21",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.17.21259103",
-    "rel_abs": "BackgroundEngland entered a third national lockdown from 6 January 2021 due to the COVID-19 pandemic. Despite a successful vaccine rollout during the first half of 2021, cases and hospitalisations have started to increase since the end of May as the SARS-CoV-2 Delta (B.1.617.2) variant increases in frequency. The final step of relaxation of COVID-19 restrictions in England has been delayed from 21 June to 19 July 2021.\n\nMethodsThe REal-time Assessment of Community Transmision-1 (REACT-1) study measures the prevalence of swab-positivity among random samples of the population of England. Round 12 of REACT-1 obtained self-administered swab collections from participants from 20 May 2021 to 7 June 2021; results are compared with those for round 11, in which swabs were collected from 15 April to 3 May 2021.\n\nResultsBetween rounds 11 and 12, national prevalence increased from 0.10% (0.08%, 0.13%) to 0.15% (0.12%, 0.18%). During round 12, we detected exponential growth with a doubling time of 11 (7.1, 23) days and an R number of 1.44 (1.20, 1.73). The highest prevalence was found in the North West at 0.26% (0.16%, 0.41%) compared to 0.05% (0.02%, 0.12%) in the South West. In the North West, the locations of positive samples suggested a cluster in Greater Manchester and the east Lancashire area. Prevalence in those aged 5-49 was 2.5 times higher at 0.20% (0.16%, 0.26%) compared with those aged 50 years and above at 0.08% (0.06%, 0.11%). At the beginning of February 2021, the link between infection rates and hospitalisations and deaths started to weaken, although in late April 2021, infection rates and hospital admissions started to reconverge. When split by age, the weakened link between infection rates and hospitalisations at ages 65 years and above was maintained, while the trends converged below the age of 65 years. The majority of the infections in the younger group occurred in the unvaccinated population or those without a stated vaccine history. We observed the rapid replacement of the Alpha (B.1.1.7) variant of SARS-CoV-2 with the Delta variant during the period covered by rounds 11 and 12 of the study.\n\nDiscussionThe extent to which exponential growth continues, or slows down as a consequence of the continued rapid roll-out of the vaccination programme, including to young adults, requires close monitoring. Data on community prevalence are vital to track the course of the epidemic and inform ongoing decisions about the timing of further lifting of restrictions in England.",
-    "rel_num_authors": 24,
-    "rel_authors": [
-      {
-        "author_name": "Steven Riley",
-        "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc"
-      },
-      {
-        "author_name": "Caroline E. Walters",
-        "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc"
-      },
-      {
-        "author_name": "Haowei Wang",
-        "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc"
-      },
-      {
-        "author_name": "Oliver Eales",
-        "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc"
-      },
-      {
-        "author_name": "David Haw",
-        "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc"
-      },
-      {
-        "author_name": "Kylie E. C. Ainslie",
-        "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc"
-      },
-      {
-        "author_name": "Christina Atchinson",
-        "author_inst": "School of Public Health, Imperial College London, UK"
-      },
-      {
-        "author_name": "Claudio Fronterre",
-        "author_inst": "CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK"
-      },
-      {
-        "author_name": "Peter J. Diggle",
-        "author_inst": "CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK"
-      },
-      {
-        "author_name": "Andrew J. Page",
-        "author_inst": "Quadram Institute, Norwich, UK"
-      },
-      {
-        "author_name": "Sophie J. Prosolek",
-        "author_inst": "Quadram Institute, Norwich, UK"
-      },
-      {
-        "author_name": "Alexander J. Trotter",
-        "author_inst": "Quadram Institute, Norwich, UK"
-      },
-      {
-        "author_name": "Le Viet Thanh",
-        "author_inst": "Quadram Institute, Norwich, UK"
-      },
-      {
-        "author_name": "Nabil-Fareed Alikhan",
-        "author_inst": "Quadram Institute, Norwich, UK"
-      },
-      {
-        "author_name": "Leigh M Jackson",
-        "author_inst": "Medical School, University of Exeter, UK"
-      },
-      {
-        "author_name": "Catherine Ludden",
-        "author_inst": "Department of Medicine, University of Cambridge, UK"
-      },
-      {
-        "author_name": "- The COVID-19 Genomics UK (COG-UK) Consortium",
-        "author_inst": "-"
-      },
-      {
-        "author_name": "Deborah Ashby",
-        "author_inst": "School of Public Health, Imperial College London, UK"
-      },
-      {
-        "author_name": "Christl A Donnelly",
-        "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc"
-      },
-      {
-        "author_name": "Graham Cooke",
-        "author_inst": "Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic"
-      },
-      {
-        "author_name": "Wendy Barclay",
-        "author_inst": "Department of Infectious Disease, Imperial College London, UK"
-      },
-      {
-        "author_name": "Helen Ward",
-        "author_inst": "School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear"
-      },
-      {
-        "author_name": "Ara Darzi",
-        "author_inst": "Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a"
-      },
-      {
-        "author_name": "Paul Elliott",
-        "author_inst": "School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.06.18.21258699",
     "rel_title": "Screening for the alpha variant of SARS-CoV-2 (B.1.1.7) and the impact of this variant on circulating biomarkers in hospitalised patients",
@@ -696871,6 +695190,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.06.20.21258949",
+    "rel_title": "Role of physiotherapy team in critically ill COVID-19 patients pronation: can a multidisciplinary management reduce the complications rate?",
+    "rel_date": "2021-06-21",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.20.21258949",
+    "rel_abs": "ObjectivesDuring the pandemic, critically ill COVID-19 patients management presented an increased workload for Intensive Care Unit (ICU) nursing staff, particularly during pronation maneuvers, with high risk of complications. In this scenario, a support during pronation by the ICU Physiotherapy Team was introduced.\n\nResearch methodologyRetrospective analysis. Consecutive critically ill COVID-19 patients.\n\nSettingA COVID-19 Center in southern Switzerland, between March 16th and April 30th, 2020.\n\nMain Outcome MeasuresRates and characteristics of pronation-related complications.\n\nResultsForty-two patients on mechanical ventilation (MV) were treated; 296 standard prone/supine positioning were performed, with 3.52 cycles/patient. One (0.3%) major complication was observed, while fourteen (33.3%) patients developed minor complications, e.g. pressure injuries. The incidence of pressure sores was related to ICU length-of-stay (LOS) (p = 0.029) and MV days (p = 0.015), while their number (n = 27) further correlated with ICU LOS (p = 0.001) and MV days (p = 0.001). The propensity matching score analysis did not show any protective factor of pronation regarding pressure injuries (p = 0.448). No other significant correlation was found.\n\nConclusionThe specific pronation team determined a low rate of major complications in critically ill COVID19 patients. The high rate of minor complications appeared to be related to disease severity, rather than from pronation.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Andrea Glotta",
+        "author_inst": "Clinica Luganese Moncucco"
+      },
+      {
+        "author_name": "Nicola Faldarini",
+        "author_inst": "Clinica Luganese Moncucco"
+      },
+      {
+        "author_name": "Maira Biggiogero",
+        "author_inst": "Clinica Luganese Moncucco"
+      },
+      {
+        "author_name": "Andrea Saporito",
+        "author_inst": "Ospedale Regionale di Bellinzona e Valli"
+      },
+      {
+        "author_name": "Diana Olivieri",
+        "author_inst": "Clinica Luganese Moncucco"
+      },
+      {
+        "author_name": "Claudia Molteni",
+        "author_inst": "Clinica Luganese Moncucco"
+      },
+      {
+        "author_name": "Stefano Petazzi",
+        "author_inst": "Clinica Luganese Moncucco"
+      },
+      {
+        "author_name": "Romano Mauri",
+        "author_inst": "Clinica Luganese Moncucco"
+      },
+      {
+        "author_name": "Xavier Capdevila",
+        "author_inst": "University of Montpellier"
+      },
+      {
+        "author_name": "Samuele Ceruti",
+        "author_inst": "Clinica Luganese Moncucco"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "intensive care and critical care medicine"
+  },
   {
     "rel_doi": "10.1101/2021.06.21.449284",
     "rel_title": "SARS-CoV-2 activates ER stress and Unfolded protein response",
@@ -698695,33 +697069,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2021.06.19.449095",
-    "rel_title": "Mutations within the Open Reading Frame (ORF) including Ochre stop codon of the Surface Glycoprotein gene of SARS-CoV-2 virus erase potential seed location motifs of human non-coding microRNAs.",
-    "rel_date": "2021-06-19",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.19.449095",
-    "rel_abs": "MicroRNA are short and non-coding RNA, 18-25 nucleotides in length. They are produced at the early stage of viral infection. The roles played by cellular miRNAs and miRNA-mediated gene-silencing in the COVID-19 epidemic period is critical in order to develop novel therapeutics. We analysed SARS-CoV-2 Surface Glycoprotein (S) nucleotide sequence originating from India as well as Iran, Australia, Germany, Italy, Russia, China, Japan and Turkey and identified mutation in potential seed location of several human miRNA. Seventy single nucleotide polymorphisms (SNP) were detected in the S gene out of which, 36, 32 and 2 were cases of transitions, transversions and deletions respectively. Eleven human miRNA targets were identified on the reference S gene sequence with a score >80 in the miRDB database. Mutation A845S erased a common binding site of 7 human miRNA (miR-195-5p, miR-16-5p, miR-15b-5p, miR-15a-5p, miR-497-5p, miR-424-5p and miR-6838-5p). A synonymous mutation altered the wild type Ochre stop codon within the S gene sequence (Italy) to Opal thereby changing the seed sequence of miR-511-3p. Similar (synonymous) mutations were detected at amino acid position 659 and 1116 of the S gene where amino acids serine and threonine were retained, abolishing potential seed location for miR-219a-1-3p and miR-20b-3p respectively. The significance of this finding in reference to the strategy to use synthetic miRNA combinations as a novel therapeutic tool is discussed.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Krishna Himmatbhai Goyani",
-        "author_inst": "Shri Jagdishprasad Jhabarmal Tibrewala University"
-      },
-      {
-        "author_name": "Shalin Vaniawala",
-        "author_inst": "Government Medical College, Surat"
-      },
-      {
-        "author_name": "Pratap Narayan Mukhopadhyaya",
-        "author_inst": "Wobble Base Bioresearch Private Limited"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "molecular biology"
-  },
   {
     "rel_doi": "10.1101/2021.06.10.21258611",
     "rel_title": "Working in a care home during the COVID-19 pandemic: How has the pandemic changed working practices?",
@@ -698980,6 +697327,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.06.14.21258855",
+    "rel_title": "The Clinical Utility of Serial Procalcitonin and Procalcitonin Clearance in Predicting the Outcome of COVID-19 Patients",
+    "rel_date": "2021-06-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.14.21258855",
+    "rel_abs": "BackgroundThe pandemic of coronavirus disease 2019 (COVID-19) represents a significant threat to global health. Sensitive tests that effectively predict the disease outcome are essentially required to guide proper intervention.\n\nObjectivesTo evaluate the predictive ability of serial procalcitonin (PCT) measurement to predict the outcome of COVID-19 patients, using PCT clearance (PCT-c) as a tool to reflect its dynamic changes.\n\nMethodsA prospective observational study of inpatients diagnosed with COVID-19 at the Quarantine Hospitals of Ain-Shams University, Cairo, Egypt. During the first five days of hospitalization, serial PCT and PCT-c values were obtained and compared between survivors and non-survivors. Patients were followed up to hospital discharge or in-hospital mortality.\n\nResultsCompared to survivors, serial PCT levels of non-survivors were significantly higher (p [&le;] 0.001) and progressively increased during follow-up. In contrast, PCT-c values were significantly lower (p < 0.01) and progressively decreased. Receiver operating characteristic (ROC) curve analysis showed that using the initial PCT value alone, at a cut-off value of 0.80 ng/ml, the area under the curve for predicting in-hospital mortality was 0.81 with 61.1% sensitivity and 87.3% accuracy. Serial measurements showed better predictive performance, and the combined prediction value was better than the single prediction by the initial PCT alone.\n\nConclusionsSerial PCT measurement could be a helpful laboratory tool to predict the prognosis and outcome of COVID-19 patients. Moreover, PCT-c could be a reliable tool to assess PCT progressive kinetics.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Sara I. Taha",
+        "author_inst": "Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt."
+      },
+      {
+        "author_name": "Aalaa K. Shata",
+        "author_inst": "Department of Pulmonary Medicine, Faculty of Medicine, Ain Shams university, Cairo, Egypt."
+      },
+      {
+        "author_name": "Shereen A. Baioumy",
+        "author_inst": "Department of Microbiology and Immunology, Faculty of Medicine, Zagazig University, Zagazig, Egypt"
+      },
+      {
+        "author_name": "Shaimaa H. Fouad",
+        "author_inst": "Department of Internal Medicine / Allergy and Clinical Immunology, Ain Shams University, Cairo, Egypt."
+      },
+      {
+        "author_name": "Aya H. Moussa",
+        "author_inst": "Department of Anesthesia, Intensive Care and Pain Management, Faculty of Medicine, Ain Shams University, Cairo, Egypt."
+      },
+      {
+        "author_name": "Mariam K. Youssef",
+        "author_inst": "Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt."
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.06.14.21258919",
     "rel_title": "Age-Based Disparities in Hospitalizations and Mortality for Coronavirus Disease 2019 (COVID-19)",
@@ -700361,25 +698747,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.06.16.21259009",
-    "rel_title": "Analysis of the Second COVID-19 Wave in India and the United Kingdom Using a Birth-Death Model",
-    "rel_date": "2021-06-18",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.16.21259009",
-    "rel_abs": "Several countries have witnessed multiple waves of the COVID-19 pandemic between 2020 and 21. The method in [8] is applied here to analyze the COVID-19 waves in India and the UK. For this, a birth-death model is fitted to the active and total cases data for 30 days periods called windows starting from 16th March 2020 up to 10th May 2021. Peculiarities of the parameters suggested a classification of the above windows into three categories: (i) whose fitted parameters predicted a rise in the number of active cases before a fall to zero, (ii) which predicted a decrease, without rising, in the active cases to zero and (iii) which predicted an increase in the active cases until the entire susceptible population gets infected. It follows that some of the type (iii) windows are of the same or lesser concern when compared to some type (i) windows. Further analysis of the type (iii) windows leads to the identification of those which could be indicators of the start of a new wave of the pandemic. The study thus proposes a method for using the present data for identifying pandemic waves in the near future.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Narayanan C Viswanath",
-        "author_inst": "Government Engineering College, Thrissur"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.06.12.21258345",
     "rel_title": "Coadministration of AYUSH 64 as an adjunct to Standard of Care in mild and moderate COVID-19: A randomised, controlled, multicentric clinical trial",
@@ -700686,6 +699053,141 @@
     "type": "new results",
     "category": "synthetic biology"
   },
+  {
+    "rel_doi": "10.1101/2021.06.17.448459",
+    "rel_title": "Memory B cells control SARS-CoV-2 variants upon mRNA vaccination of naive and COVID-19 recovered individuals.",
+    "rel_date": "2021-06-17",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.17.448459",
+    "rel_abs": "How a previous SARS-CoV-2 infection may amplify and model the memory B cell (MBC) response elicited by mRNA vaccines was addressed by a comparative longitudinal study of two cohorts, naive individuals and disease-recovered patients, up to 2 months after vaccination. The quality of the memory response was assessed by analysis of the VDJ repertoire, affinity and neutralization against variants of concerns (VOC), using unbiased cultures of 2452 MBCs. Upon boost, the MBC pool of recovered patients selectively expanded, further matured and harbored potent neutralizers against VOC. Maturation of the MBC response in naive individuals was much less pronounced. Nevertheless, and as opposed to their weaker neutralizing serum response, half of their RBD-specific MBCs displayed high affinity towards multiple VOC and one-third retained neutralizing potency against B.1.351. Thus, repeated vaccine challenges could reduce these differences by recall of affinity-matured MBCs and allow naive vaccinees to cope efficiently with VOC.",
+    "rel_num_authors": 30,
+    "rel_authors": [
+      {
+        "author_name": "Aurelien Sokal",
+        "author_inst": "Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMS 8253, Universite de Paris, Paris, France."
+      },
+      {
+        "author_name": "Giovanna Barba-Spaeth",
+        "author_inst": "Institut Pasteur, Unite de Virologie Structurale, Paris, France."
+      },
+      {
+        "author_name": "Ignacio Fernandez",
+        "author_inst": "Institut Pasteur, Unite de Virologie Structurale, Paris, France."
+      },
+      {
+        "author_name": "Matteo Broketa",
+        "author_inst": "Institut Pasteur, Anticorps en therapie et en pathologie, UMR 1222 INSERM, France"
+      },
+      {
+        "author_name": "Imane Azzaoui",
+        "author_inst": "INSERM U955, equipe 2. Institut Mondor de Recherche Biomedicale (IMRB), Universite Paris-Est Creteil (UPEC), Creteil, France."
+      },
+      {
+        "author_name": "Andrea de La Selle",
+        "author_inst": "Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMS 8253, Universite de Paris, Paris, France."
+      },
+      {
+        "author_name": "Alexis Vandenberghe",
+        "author_inst": "INSERM U955, equipe 2. Institut Mondor de Recherche Biomedicale (IMRB), Universite Paris-Est Creteil (UPEC), Creteil, France."
+      },
+      {
+        "author_name": "Slim Fourati",
+        "author_inst": "Departement de Virologie, Bacteriologie, Hygiene et Mycologie-Parasitologie, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hopitaux de Pari"
+      },
+      {
+        "author_name": "Anais Roeser",
+        "author_inst": "Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMS 8253, Universite de Paris, Paris, France."
+      },
+      {
+        "author_name": "Annalisa Meola",
+        "author_inst": "Institut Pasteur, Unite de Virologie Structurale, Paris, France."
+      },
+      {
+        "author_name": "Magali Bouvier-Alias",
+        "author_inst": "Departement de Virologie, Bacteriologie, Hygiene et Mycologie-Parasitologie, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hopitaux de Pari"
+      },
+      {
+        "author_name": "Etienne Crickx",
+        "author_inst": "Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMS 8253, Universite de Paris, Paris, France."
+      },
+      {
+        "author_name": "Laetitia Languille",
+        "author_inst": "Service de Medecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hopitaux de Paris (AP-HP), Universite Paris-Est Creteil (UPEC), "
+      },
+      {
+        "author_name": "Marc Michel",
+        "author_inst": "Service de Medecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hopitaux de Paris (AP-HP), Universite Paris-Est Creteil (UPEC), "
+      },
+      {
+        "author_name": "Bertrand Godeau",
+        "author_inst": "Service de Medecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hopitaux de Paris (AP-HP), Universite Paris-Est Creteil (UPEC), "
+      },
+      {
+        "author_name": "Sebastien Gallien",
+        "author_inst": "Service des Maladies infectieuses, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hopitaux de Paris (AP-HP), Universite Paris-Est Creteil (U"
+      },
+      {
+        "author_name": "Giovanna Melica",
+        "author_inst": "Service des Maladies infectieuses, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hopitaux de Paris (AP-HP), Universite Paris-Est Creteil (U"
+      },
+      {
+        "author_name": "Yann Nguyen",
+        "author_inst": "Service de Medecine Interne, Hopital Beaujon, Assistance Publique des Hopitaux de Paris, Universite de Paris, Clichy, France"
+      },
+      {
+        "author_name": "Virginie Zarrouk",
+        "author_inst": "Service de Medecine Interne, Hopital Beaujon, Assistance Publique des Hopitaux de Paris, Universite de Paris, Clichy, France"
+      },
+      {
+        "author_name": "Florence Canoui-Poitrine",
+        "author_inst": "Departement de Sante Publique, Unite de Recherche Clinique (URC), CEpiA (Clinical Epidemiology and Ageing), EA 7376- Institut Mondor de Recherche Biomedicale (I"
+      },
+      {
+        "author_name": "France Noizat-Pirenne",
+        "author_inst": "Etablissement Francais du Sang, INSERM U955, Universite Paris-Est Creteil (UPEC), Creteil, France"
+      },
+      {
+        "author_name": "Jerome Megret",
+        "author_inst": "Plateforme de Cytometrie en Flux, Structure Federative de Recherche Necker, INSERM US24-CNRS UMS3633, Paris, France."
+      },
+      {
+        "author_name": "Jean-Michel Pawlotsky",
+        "author_inst": "Departement de Virologie, Bacteriologie, Hygiene et Mycologie-Parasitologie, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hopitaux de Pari"
+      },
+      {
+        "author_name": "Simon Fillatreau",
+        "author_inst": "Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMS 8253, Universite de Paris, Paris, France."
+      },
+      {
+        "author_name": "Pierre Brunhs",
+        "author_inst": "Institut Pasteur, Anticorps en therapie et en pathologie, UMR 1222 INSERM, France"
+      },
+      {
+        "author_name": "Felix A. Rey",
+        "author_inst": "Institut Pasteur, Unite de Virologie Structurale, Paris, France."
+      },
+      {
+        "author_name": "Jean-Claude Weill",
+        "author_inst": "Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMS 8253, Universite de Paris, Paris, France."
+      },
+      {
+        "author_name": "Claude-Agnes Reynaud",
+        "author_inst": "Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMS 8253, Universite de Paris, Paris, France."
+      },
+      {
+        "author_name": "Pascal Chappert",
+        "author_inst": "Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMS 8253, Universite de Paris, Paris, France."
+      },
+      {
+        "author_name": "Matthieu Mahevas",
+        "author_inst": "Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMS 8253, Universite de Paris, Paris, France."
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2021.06.17.448820",
     "rel_title": "SARS-CoV-2 spike P681R mutation enhances and accelerates viral fusion",
@@ -702723,245 +701225,6 @@
     "type": "new results",
     "category": "pathology"
   },
-  {
-    "rel_doi": "10.1101/2021.06.16.448525",
-    "rel_title": "A SARS-CoV-2 spike ferritin nanoparticle vaccine protects against heterologous challenge with B.1.1.7 and B.1.351 virus variants in Syrian golden hamsters",
-    "rel_date": "2021-06-16",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.16.448525",
-    "rel_abs": "The emergence of SARS-CoV-2 variants of concern (VOC) requires adequate coverage of vaccine protection. We evaluated whether a spike ferritin nanoparticle vaccine (SpFN), adjuvanted with the Army Liposomal Formulation QS21 (ALFQ), conferred protection against the B.1.1.7 and B.1.351 VOCs in Syrian golden hamsters. SpFN-ALFQ was administered as either single or double-vaccination (0 and 4 week) regimens, using a high (10 g) or low (0.2 g) immunogen dose. Animals were intranasally challenged at week 11. Binding antibody responses were comparable between high- and low-dose groups. Neutralizing antibody titers were equivalent against WA1, B.1.1.7, and B.1.351 variants following two high dose two vaccinations. SpFN-ALFQ vaccination protected against SARS-CoV-2-induced disease and viral replication following intranasal B.1.1.7 or B.1.351 challenge, as evidenced by reduced weight loss, lung pathology, and lung and nasal turbinate viral burden. These data support the development of SpFN-ALFQ as a broadly protective, next-generation SARS-CoV-2 vaccine.",
-    "rel_num_authors": 56,
-    "rel_authors": [
-      {
-        "author_name": "Kathryn McGuckin Wuertz",
-        "author_inst": "U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA"
-      },
-      {
-        "author_name": "Erica Barkei",
-        "author_inst": "Veterinary Pathology Division, Walter Reed Army Institute of Research, Silver Spring, Maryland USA"
-      },
-      {
-        "author_name": "Wei-hung Chen",
-        "author_inst": "Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA; Henry M. Jack"
-      },
-      {
-        "author_name": "Elizabeth J. Martinez",
-        "author_inst": "Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA; Henry M. Jack"
-      },
-      {
-        "author_name": "Ines Elakhal Naouar",
-        "author_inst": "Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA; Diagnostics Countermeasures Branch, Center for Infectious Diseases"
-      },
-      {
-        "author_name": "Linda Jagodzinski",
-        "author_inst": "Diagnostics Countermeasures Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA"
-      },
-      {
-        "author_name": "Dominic Paquin-Proulx",
-        "author_inst": "U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA; Henry M. Jacks"
-      },
-      {
-        "author_name": "Gregory D. Gromowski",
-        "author_inst": "Virus Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA"
-      },
-      {
-        "author_name": "Isabella Swafford",
-        "author_inst": "U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA; Henry M. Jacks"
-      },
-      {
-        "author_name": "Akshaya Ganesh",
-        "author_inst": "U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA; Oak Ridge Inst"
-      },
-      {
-        "author_name": "Ming Dong",
-        "author_inst": "U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA; Henry M. Jacks"
-      },
-      {
-        "author_name": "Xiankun Zeng",
-        "author_inst": "Pathology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland USA"
-      },
-      {
-        "author_name": "Paul V. Thomas",
-        "author_inst": "Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA; Henry M. Jack"
-      },
-      {
-        "author_name": "Rajeshwer S. Sankhala",
-        "author_inst": "Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA; Henry M. Jack"
-      },
-      {
-        "author_name": "Agnes Hajduczki",
-        "author_inst": "Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA; Henry M. Jack"
-      },
-      {
-        "author_name": "Caroline E. Peterson",
-        "author_inst": "Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA; Henry M. Jack"
-      },
-      {
-        "author_name": "Caitlin H. Kuklis",
-        "author_inst": "Virus Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA"
-      },
-      {
-        "author_name": "Sandrine Soman",
-        "author_inst": "Virus Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA"
-      },
-      {
-        "author_name": "Lindsey Wieczorek",
-        "author_inst": "U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA; Henry M. Jacks"
-      },
-      {
-        "author_name": "Michelle Zemil",
-        "author_inst": "U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA; Henry M. Jacks"
-      },
-      {
-        "author_name": "Alexander Anderson",
-        "author_inst": "Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA; Oak Ridge Ins"
-      },
-      {
-        "author_name": "Janice Darden",
-        "author_inst": "Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA; Diagnostics Countermeasures Branch, Center for Infectious Diseases"
-      },
-      {
-        "author_name": "Heather Hernandez",
-        "author_inst": "Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA; Diagnostics Countermeasures Branch, Center for Infectious Diseases"
-      },
-      {
-        "author_name": "Hannah Grove",
-        "author_inst": "Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA; Diagnostics Countermeasures Branch, Center for Infectious Diseases"
-      },
-      {
-        "author_name": "Vincent Dussupt",
-        "author_inst": "Walter Reed Army Institute of Research"
-      },
-      {
-        "author_name": "Holly Hack",
-        "author_inst": "Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA; Diagnostics Countermeasures Branch, Center for Infectious Diseases"
-      },
-      {
-        "author_name": "Rafael A. de la Barrera",
-        "author_inst": "Pilot Bioproduction Facility, Walter Reed Army Institute of Research, Silver Spring, Maryland USA"
-      },
-      {
-        "author_name": "Stasya N. Zarling",
-        "author_inst": "Pilot Bioproduction Facility, Walter Reed Army Institute of Research, Silver Spring, Maryland USA"
-      },
-      {
-        "author_name": "James F. Wood",
-        "author_inst": "Pilot Bioproduction Facility, Walter Reed Army Institute of Research, Silver Spring, Maryland USA"
-      },
-      {
-        "author_name": "Jeffrey W. Froude",
-        "author_inst": "Pilot Bioproduction Facility, Walter Reed Army Institute of Research, Silver Spring, Maryland USA"
-      },
-      {
-        "author_name": "Matthew J. Gagne",
-        "author_inst": "Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland USA"
-      },
-      {
-        "author_name": "Amy R. Henry",
-        "author_inst": "Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland USA"
-      },
-      {
-        "author_name": "Elyham Bayat Mokhtari",
-        "author_inst": "Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda,"
-      },
-      {
-        "author_name": "Prakriti Mudvari",
-        "author_inst": "Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda,"
-      },
-      {
-        "author_name": "Shelly  J Krebs",
-        "author_inst": "U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA; Henry M. Jacks"
-      },
-      {
-        "author_name": "Andrew S. Pekosz",
-        "author_inst": "W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland USA"
-      },
-      {
-        "author_name": "Jeffrey R. Currier",
-        "author_inst": "Virus Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA"
-      },
-      {
-        "author_name": "Swagata Kar",
-        "author_inst": "BioQual, Inc., Rockville, Maryland USA"
-      },
-      {
-        "author_name": "Marciel Porto",
-        "author_inst": "BioQual, Inc., Rockville, Maryland USA"
-      },
-      {
-        "author_name": "Adrienne Winn",
-        "author_inst": "BioQual, Inc., Rockville, Maryland USA"
-      },
-      {
-        "author_name": "Kamil Radzyminski",
-        "author_inst": "BioQual, Inc., Rockville, Maryland USA"
-      },
-      {
-        "author_name": "Mark G. Lewis",
-        "author_inst": "BioQual Inc, Rockville, Maryland USA"
-      },
-      {
-        "author_name": "Sandhya Vasan",
-        "author_inst": "Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA"
-      },
-      {
-        "author_name": "Mehul Suthar",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Victoria Polonis",
-        "author_inst": "U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA"
-      },
-      {
-        "author_name": "Gary Matyas",
-        "author_inst": "U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA"
-      },
-      {
-        "author_name": "Eli A. Boritz",
-        "author_inst": "Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda,"
-      },
-      {
-        "author_name": "Daniel C. Douek",
-        "author_inst": "Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland USA"
-      },
-      {
-        "author_name": "Robert Seder",
-        "author_inst": "Cellular Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland U"
-      },
-      {
-        "author_name": "Sharon Daye",
-        "author_inst": "One Health Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland USA"
-      },
-      {
-        "author_name": "Mangala Rao",
-        "author_inst": "U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA"
-      },
-      {
-        "author_name": "Sheila Peel",
-        "author_inst": "Diagnostics Countermeasures Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA"
-      },
-      {
-        "author_name": "M. Gordon Joyce",
-        "author_inst": "Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA; Henry M. Jack"
-      },
-      {
-        "author_name": "Diane L. Bolton",
-        "author_inst": "U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA; Henry M. Jacks"
-      },
-      {
-        "author_name": "Nelson L. Michael",
-        "author_inst": "Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA"
-      },
-      {
-        "author_name": "Kayvon Modjarrad",
-        "author_inst": "Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA"
-      }
-    ],
-    "version": "1",
-    "license": "cc0",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2021.06.16.448653",
     "rel_title": "Nafamostat-interferon-alpha combination suppresses SARS-CoV-2 infection in vitro and in vivo",
@@ -703368,6 +701631,85 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2021.06.14.448461",
+    "rel_title": "Protective efficacy of rhesus adenovirus COVID-19 vaccines against mouse-adapted SARS-CoV-2",
+    "rel_date": "2021-06-15",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.14.448461",
+    "rel_abs": "The global COVID-19 pandemic has sparked intense interest in the rapid development of vaccines as well as animal models to evaluate vaccine candidates and to define immune correlates of protection. We recently reported a mouse-adapted SARS-CoV-2 virus strain (MA10) with the potential to infect wild-type laboratory mice, driving high levels of viral replication in respiratory tract tissues as well as severe clinical and respiratory symptoms, aspects of COVID-19 disease in humans that are important to capture in model systems. We evaluated the immunogenicity and protective efficacy of novel rhesus adenovirus serotype 52 (RhAd52) vaccines against MA10 challenge in mice. Baseline seroprevalence is lower for rhesus adenovirus vectors than for human or chimpanzee adenovirus vectors, making these vectors attractive candidates for vaccine development. We observed that RhAd52 vaccines elicited robust binding and neutralizing antibody titers, which inversely correlated with viral replication after challenge. These data support the development of RhAd52 vaccines and the use of the MA10 challenge virus to screen novel vaccine candidates and to study the immunologic mechanisms that underscore protection from SARS-CoV-2 challenge in wild-type mice.\n\nImportanceWe have developed a series of SARS-CoV-2 vaccines using rhesus adenovirus serotype 52 (RhAd52) vectors, which exhibits a lower seroprevalence than human and chimpanzee vectors, supporting their development as novel vaccine vectors or as an alternative Ad vector for boosting. We sought to test these vaccines using a recently reported mouse-adapted SARS-CoV-2 (MA10) virus to i) evaluate the protective efficacy of RhAd52 vaccines and ii) further characterize this mouse-adapted challenge model and probe immune correlates of protection. We demonstrate RhAd52 vaccines elicit robust SARS-CoV-2-specific antibody responses and protect against clinical disease and viral replication in the lungs. Further, binding and neutralizing antibody titers correlated with protective efficacy. These data validate the MA10 mouse model as a useful tool to screen and study novel vaccine candidates, as well as the development of RhAd52 vaccines for COVID-19.",
+    "rel_num_authors": 16,
+    "rel_authors": [
+      {
+        "author_name": "Lisa Tostanoski",
+        "author_inst": "Beth Israel Deaconess Medical Center"
+      },
+      {
+        "author_name": "Lisa Gralinski",
+        "author_inst": "University of North Carolina at Chapel Hill"
+      },
+      {
+        "author_name": "David Martinez",
+        "author_inst": "University of North Carolina at Chapel Hill"
+      },
+      {
+        "author_name": "Alexandra Schaefer",
+        "author_inst": "UNC-CH, School of Public Health"
+      },
+      {
+        "author_name": "Shant Mahrokhian",
+        "author_inst": "Beth Israel Deaconess Medical Center"
+      },
+      {
+        "author_name": "Zhenfeng Li",
+        "author_inst": "Beth Israel Deaconess Medical Center"
+      },
+      {
+        "author_name": "Felix Nampanya",
+        "author_inst": "Beth Israel Deaconess Medical Center"
+      },
+      {
+        "author_name": "Huahua Wan",
+        "author_inst": "Beth Israel Deaconess Medical Center"
+      },
+      {
+        "author_name": "Jingyou Yu",
+        "author_inst": "Beth Israel Deaconess Medical Center"
+      },
+      {
+        "author_name": "Aiquan Chang",
+        "author_inst": "Beth Israel Deaconess Medical Center"
+      },
+      {
+        "author_name": "Jinyan Liu",
+        "author_inst": "Beth Israel Deaconess Medical Center"
+      },
+      {
+        "author_name": "Katherine McMahan",
+        "author_inst": "Beth Israel Deaconess Medical Center"
+      },
+      {
+        "author_name": "Kenneth Dinnon III",
+        "author_inst": "University of North Carolina at Chapel Hill"
+      },
+      {
+        "author_name": "Sarah R. Leist",
+        "author_inst": "University of North Carolina"
+      },
+      {
+        "author_name": "Ralph S. Baric",
+        "author_inst": "University of North Carolina at Chapel Hill"
+      },
+      {
+        "author_name": "Dan H. Barouch",
+        "author_inst": "Beth Israel Deaconess Medical Center"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2021.06.15.448497",
     "rel_title": "The SARS-CoV-2 nucleocapsid protein associates with the replication organelles before viral assembly at the Golgi/ERGIC and lysosome-mediated egress",
@@ -704536,25 +702878,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.06.15.448568",
-    "rel_title": "Deep Mutational Scanning of Dynamic Interaction Networks in the SARS-CoV-2 Spike Protein Complexes: Allosteric Hotspots Control Functional Mimicry and Resilience to Mutational Escape",
-    "rel_date": "2021-06-15",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.15.448568",
-    "rel_abs": "We develop a computational approach for deep mutational scanning of residue interaction networks in the SARS-CoV-2 spike protein complexes to characterize mechanisms of functional mimicry and resilience to mutational escape by miniprotein inhibitors. Using a dynamic mutational profiling and sensitivity analysis of protein stability, binding interactions and global network parameters describing allosteric signaling, we identify regulatory hotspots in the SARS-CoV-2 S complexes with the ACE2 host receptor and ultra-potent miniproteins. The results revealed that global circulating variants are associated with allosteric control points that are dynamically coupled to structural stability hotspots. In this mechanism, variant-induced perturbations of flexible allosteric sites can result in global network changes and elicit specific protein responses. The binding affinity fingerprints and allosteric signatures of the SARS-CoV-2 complexes with miniproteins are determined by a dynamic cross-talk between regulatory control points and conformationally adaptable allosteric hotspots that collectively control structure-functional mimicry, signal transmission and resilience to mutational escape.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Gennady Verkhivker",
-        "author_inst": "Chapman University School of Pharmacy"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "biophysics"
-  },
   {
     "rel_doi": "10.1101/2021.06.13.21258857",
     "rel_title": "Estimating decay curves of neutralising antibodies to SARS-CoV-2 infection",
@@ -704765,6 +703088,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.06.14.21258236",
+    "rel_title": "Survey of COVID-19 associated symptoms and reported deaths in an urban community in Kano, Nigeria.",
+    "rel_date": "2021-06-15",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.14.21258236",
+    "rel_abs": "BackgroundNigeria reported the first case of COVID-19 on February 27, 2020. By June of 2020, many people reported experiencing mild COVID-19 associated symptoms, yet did not get tested due to inaccessible testing and insufficient knowledge of the disease. There were media stories quoting grave diggers in Kano who reported high burial rates during this time.\n\nMethodsIn order to draw more data on COVID-19 cases during this time period, we conducted a cross-sectional symptom survey in Kano, surveying 291 adults. Participants were asked to report demographic characteristics, past COVID-19 testing and symptoms, and community deaths. To assess associations between COVID-19 associated symptoms and socio-demographic characteristics, bivariate analyses using Chi-square tests were performed. A logistic regression assessing the association between any reported symptoms and the kind of work (indoor/outdoor) was done while adjusting for age, gender and education level.\n\nResultsHalf of the respondents reported at least one symptom associated with COVID-19; the three most common symptoms were loss of appetite, cough, and fever. There was a statistically significant relationship between age group of the respondent and presence of COVID-19 associated symptoms. Gender or level of education did not have statistically significant association with COVID-19 associated symptoms among the respondents. People with outdoor occupations such as trading and hawking were more than twice as likely to report COVID-19 associated symptoms compared to those who were unemployed. Just under half of the respondents reported knowing someone who died in their community, with unexplained causes attributed to two-thirds of these cases. Our study found evidence of COVID-19 associated symptoms especially among the older population and unexplained deaths in Kano. Lack of confirmatory laboratory tests and absence of baseline vital statistics precluded us from finding definitive evidence for or against COVID-19 infection and associated mortality.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Disha Shahani",
+        "author_inst": "eHealth Africa"
+      },
+      {
+        "author_name": "Zayyad Sani Farouq",
+        "author_inst": "EHA Clinics"
+      },
+      {
+        "author_name": "Hadiza Galadima",
+        "author_inst": "Old Dominion University"
+      },
+      {
+        "author_name": "Ashna Khare",
+        "author_inst": "eHealth Africa"
+      },
+      {
+        "author_name": "Nirmal Ravi",
+        "author_inst": "eHealth Africa"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.06.10.21258685",
     "rel_title": "A Meta-Analysis of Influenza Vaccination Following Correspondence: Considerations for COVID-19",
@@ -705783,73 +704141,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "rehabilitation medicine and physical therapy"
   },
-  {
-    "rel_doi": "10.1101/2021.06.10.21258638",
-    "rel_title": "Urine test predicts kidney injury and death in COVID-19",
-    "rel_date": "2021-06-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.10.21258638",
-    "rel_abs": "BackgroundKidney injury is common in COVID-19 infection, but serum creatinine (SCr) is not a sensitive or specific marker of kidney injury. We hypothesized that molecular markers of tubular injury could diagnose COVID-19 associated kidney damage and predict its clinical course.\n\nMethodsThis is a prospective cohort study of 444 consecutive COVID-19 patients (43.9% females, 20.5% African American, 54.1% Latinx) in Columbia Universitys Emergency Department at the peak of the New York pandemic (March-April 2020). Urine and blood were collected simultaneously at admission (median time of day 0, IQR 0-2 days) and within 1 day of a positive SARS-CoV-2 test in 70% of patients. Biomarker assays were blinded to clinical data.\n\nResultsUrinary NGAL (uNGAL) was strongly associated with AKI diagnosis (267{+/-}301 vs. 96{+/-}139 ng/mL, P=1.6x10-10). uNGAL >150ng/mL had 80% specificity and 75% sensitivity to diagnose AKIN stage 2 or higher. uNGAL quantitatively predicted the duration of AKI and outcomes, including death, dialysis, shock, and longer hospital stay. The risk of death increased 73% per standard deviation of uNGAL [OR (95%CI): 1.73 (1.29-2.33), P=2.8x10-4] and was independent of baseline SCr, co-morbidities, and proteinuria [adjusted OR (95%CI): 1.51 (1.10-2.11), P=1.2x10-2]. Proteinuria and uKIM-1 also indicated tubular injury but were not diagnostic of AKI. Typically, distal nephron segments transcribe NGAL, but in COVID-19 biopsies with widespread acute tubular injury (ATI), NGAL expression overlapped KIM-1 in proximal tubules.\n\nConclusionuNGAL predicted diagnosis, duration, and severity of AKI and ATI, as well as hospital stay, dialysis, shock, and death in patients with acute COVID-19.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Katherine Xu",
-        "author_inst": "Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Ning Shang",
-        "author_inst": "Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Abraham Levitman",
-        "author_inst": "Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Alexa Corker",
-        "author_inst": "Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Satoru Kudose",
-        "author_inst": "Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Andrew Yaeh",
-        "author_inst": "Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Uddhav Neupane",
-        "author_inst": "Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Jacob Stevens",
-        "author_inst": "Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Sumit Mohan",
-        "author_inst": "Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Rosemary Sampogna",
-        "author_inst": "Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Vivette D'Agati",
-        "author_inst": "Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Krzysztof Kiryluk",
-        "author_inst": "Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Jonathan Barasch",
-        "author_inst": "Columbia University Irving Medical Center"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "nephrology"
-  },
   {
     "rel_doi": "10.1101/2021.06.11.21258735",
     "rel_title": "Quarantine and testing strategies to reduce transmission risk from imported SARS-CoV-2 infections: a global modelling study",
@@ -706180,6 +704471,237 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.06.14.448343",
+    "rel_title": "COVID-eVax, an electroporated plasmid DNA vaccine candidate encoding the SARS-CoV-2 Receptor Binding Domain, elicits protective immune responses in animal models of COVID-19",
+    "rel_date": "2021-06-14",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.14.448343",
+    "rel_abs": "The COVID-19 pandemic caused by the {beta}-coronavirus SARS-CoV-2 has made the development of safe and effective vaccines a critical global priority. To date, four vaccines have already been approved by European and American authorities for preventing COVID-19 but the development of additional vaccine platforms with improved supply and logistics profiles remains a pressing need. Here we report the preclinical evaluation of a novel COVID-19 vaccine candidate based on the electroporation of engineered, synthetic cDNA encoding a viral antigen in the skeletal muscle, a technology previously utilized for cancer vaccines. We constructed a set of prototype DNA vaccines expressing various forms of the SARS-CoV-2 Spike (S) protein and assessed their immunogenicity in animal models. Among them, COVID-eVax - a DNA plasmid encoding a secreted monomeric form of SARS-CoV-2 S protein RBD - induced the most potent anti-SARS-CoV-2 neutralizing antibody responses (including against the current most common variants of concern) and a robust T cell response. Upon challenge with SARS-CoV-2, immunized K18-hACE2 transgenic mice showed reduced weight loss, improved pulmonary function and significantly lower viral replication in the lungs and brain. COVID-eVax conferred significant protection to ferrets upon SARS-CoV-2 challenge. In summary, this study identifies COVID-eVax as an ideal COVID-19 vaccine candidate suitable for clinical development. Accordingly, a combined phase I-II trial has recently started in Italy.",
+    "rel_num_authors": 54,
+    "rel_authors": [
+      {
+        "author_name": "Antonella Conforti",
+        "author_inst": "Evvivax"
+      },
+      {
+        "author_name": "Emanuele Marra",
+        "author_inst": "Takis Biotech"
+      },
+      {
+        "author_name": "Fabio Palombo",
+        "author_inst": "Takis Biotech"
+      },
+      {
+        "author_name": "Giuseppe Roscilli",
+        "author_inst": "Takis Biotech"
+      },
+      {
+        "author_name": "Micol Rava",
+        "author_inst": "San Raffaele Scientific Institute"
+      },
+      {
+        "author_name": "Valeria Fumagalli",
+        "author_inst": "San Raffaele Scientific Institute"
+      },
+      {
+        "author_name": "Alessia Muzi",
+        "author_inst": "Takis Biotech"
+      },
+      {
+        "author_name": "Mariano Maffei",
+        "author_inst": "San Raffaele Scientific Institute"
+      },
+      {
+        "author_name": "Laura Luberto",
+        "author_inst": "Takis Biotech"
+      },
+      {
+        "author_name": "Lucia Lione",
+        "author_inst": "Takis Biotech"
+      },
+      {
+        "author_name": "Erika Salvatori",
+        "author_inst": "Takis Biotech"
+      },
+      {
+        "author_name": "Mirco Compagnone",
+        "author_inst": "Takis Biotech"
+      },
+      {
+        "author_name": "Eleonora Pinto",
+        "author_inst": "Takis Biotech"
+      },
+      {
+        "author_name": "Emiliano Pavoni",
+        "author_inst": "Takis Biotech"
+      },
+      {
+        "author_name": "Federica Bucci",
+        "author_inst": "Takis Biotech"
+      },
+      {
+        "author_name": "Grazia Vitagliano",
+        "author_inst": "Takis Biotech"
+      },
+      {
+        "author_name": "Daniela Stoppoloni",
+        "author_inst": "Takis Biotech"
+      },
+      {
+        "author_name": "Maria Lucrezia Pacello",
+        "author_inst": "Takis Biotech"
+      },
+      {
+        "author_name": "Manuela Cappelletti",
+        "author_inst": "Takis Biotech"
+      },
+      {
+        "author_name": "Fabiana Fosca Ferrara",
+        "author_inst": "Takis Biotech"
+      },
+      {
+        "author_name": "Valerio Chiarini",
+        "author_inst": "Takis Biotech"
+      },
+      {
+        "author_name": "Roberto Arriga",
+        "author_inst": "Takis Biotech"
+      },
+      {
+        "author_name": "Abraham Nyska",
+        "author_inst": "Tel Aviv University"
+      },
+      {
+        "author_name": "Pietro Di Lucia",
+        "author_inst": "San Raffaele Scientific Institute"
+      },
+      {
+        "author_name": "Davide Marotta",
+        "author_inst": "San Raffaele Scientific Institute"
+      },
+      {
+        "author_name": "Elisa Bono",
+        "author_inst": "San Raffaele Scientific Institute"
+      },
+      {
+        "author_name": "Leonardo Giustini",
+        "author_inst": "San Raffaele Scientific Institute"
+      },
+      {
+        "author_name": "Eleonora Sala",
+        "author_inst": "San Raffaele Scientific Institute"
+      },
+      {
+        "author_name": "Chiara Perucchini",
+        "author_inst": "San Raffaele Scientific Institute"
+      },
+      {
+        "author_name": "Jemma Paterson",
+        "author_inst": "PHE"
+      },
+      {
+        "author_name": "Kathryn A Ryan",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Amy Challis",
+        "author_inst": "PHE"
+      },
+      {
+        "author_name": "Giulia Matusali",
+        "author_inst": "Inmi"
+      },
+      {
+        "author_name": "Francesca Colavita",
+        "author_inst": "INMI"
+      },
+      {
+        "author_name": "Gianfranco Caselli",
+        "author_inst": "Rottapharm"
+      },
+      {
+        "author_name": "Elena Criscuolo",
+        "author_inst": "HSR"
+      },
+      {
+        "author_name": "Nicola A Clementi",
+        "author_inst": "Vita-Salute San Raffaele University"
+      },
+      {
+        "author_name": "Nicasio Mancini",
+        "author_inst": "Universita Vita-Salute San Raffaele"
+      },
+      {
+        "author_name": "Rudiger Gross",
+        "author_inst": "Ulm university"
+      },
+      {
+        "author_name": "Alina Siedel",
+        "author_inst": "Ulm University"
+      },
+      {
+        "author_name": "Lukas Wettstein",
+        "author_inst": "Ulm University"
+      },
+      {
+        "author_name": "Jan Munch",
+        "author_inst": "Ulm University"
+      },
+      {
+        "author_name": "Lorena Donnici",
+        "author_inst": "INGM"
+      },
+      {
+        "author_name": "Matteo Conti",
+        "author_inst": "INGM"
+      },
+      {
+        "author_name": "Raffaele De Francesco",
+        "author_inst": "INGM"
+      },
+      {
+        "author_name": "Mirela Kuka",
+        "author_inst": "HSR"
+      },
+      {
+        "author_name": "Gennaro Ciliberto",
+        "author_inst": "IFO"
+      },
+      {
+        "author_name": "Concetta Castilletti",
+        "author_inst": "INMI"
+      },
+      {
+        "author_name": "Maria R. Capobianchi",
+        "author_inst": "National Institute for Infectious Diseases"
+      },
+      {
+        "author_name": "Giuseppe Ippolito",
+        "author_inst": "National Institute Infectious Diseaseas"
+      },
+      {
+        "author_name": "Luca Guidotti",
+        "author_inst": "HSR"
+      },
+      {
+        "author_name": "Lucio Rovati",
+        "author_inst": "Rottapharm"
+      },
+      {
+        "author_name": "Matteo Iannacone",
+        "author_inst": "San Raffaele Scientific Institute"
+      },
+      {
+        "author_name": "Luigi Aurisicchio",
+        "author_inst": "Takis Biotech"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2021.06.12.448149",
     "rel_title": "Regulatory dissection of the severe COVID-19 risk locus introgressed by Neanderthals",
@@ -707417,49 +705939,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.06.09.21258232",
-    "rel_title": "COVID-19 antibody detection and assay performance using red cell agglutination",
-    "rel_date": "2021-06-12",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.09.21258232",
-    "rel_abs": "Red cells can be labelled with peptides from the SARS-CoV-2 spike protein and used for serologic screening of SARS-CoV-2 antibodies. We evaluated 140 convalescent COVID-19 patients and 275 healthy controls using this C19-kodecyte assay. The analytical performance of the new assay was compared with a virus neutralizing assay and 2 commercial chemiluminescent antibody tests (Total assay and IgG assay, Ortho). The C19-kodecyte assay detected SARS-CoV-2 antibodies with a sensitivity of 92.8% and specificity of 96.3%, well within the minimum performance range required by FDA for EUA authorization of serologic tests. The Cohens kappa coefficient was 0.90 indicating an almost perfect agreement with the Total assay. The Pearson correlation coefficient was 0.20 with the neutralizing assay (0.49 with IgG, and 0.41 with Total assays). The limited correlation in assay reaction strengths suggested that the assays may detect different antibody specificities. Our easily scalable C19-kodecyte assay may vastly improve test capacity in blood typing laboratories using their routine setups for column agglutination technique.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Kshitij Srivastava",
-        "author_inst": "NIH Clinical Center"
-      },
-      {
-        "author_name": "Kamille A West",
-        "author_inst": "NIH Clinical Center"
-      },
-      {
-        "author_name": "Valeria De Giorgi",
-        "author_inst": "NIH Clinical Center"
-      },
-      {
-        "author_name": "Michael R Holbrook",
-        "author_inst": "NIH-IRF"
-      },
-      {
-        "author_name": "Nicolai V Bovin",
-        "author_inst": "Bioorganic Chemistry"
-      },
-      {
-        "author_name": "Stephen M Henry",
-        "author_inst": "AUT University"
-      },
-      {
-        "author_name": "Willy A Flegel",
-        "author_inst": "National Institutes of Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc0",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.06.09.21258422",
     "rel_title": "Impact of baseline SARS-CoV-2 antibody status on syndromic surveillance and the risk of subsequent Covid-19 -- a prospective multicentre cohort study",
@@ -707790,6 +706269,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.06.08.21258525",
+    "rel_title": "COVID19, Consumption and Inequality: A Systematic Analysis of Rural Population of India",
+    "rel_date": "2021-06-12",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258525",
+    "rel_abs": "BackgroundCOVID19 pandemic has had major impact on consumption levels and inequality within India. Government policy interventions have targeted poor households for cash and food transfers. It is important, however, to study the impact of the pandemic on consumption levels of non-poor in India, and in particular the middle class. In this paper, we aim to quantify the changes in consumption levels and inequality over time, across all groups of rural households in India.\n\nMethodsWe analyze three rounds of COVID 19-related shock surveys between May and September 2020. These surveys cover rural households of six large states in India and are representative of more than 442 million (52% of Indias rural population).\n\nFindingsIn the early phase of the pandemic, it was the bottom 40% of households that experienced the most severe decline in consumption. But as the pandemic deepened, consumption declined across all classes of households. Besides the poorest, it was particularly severe for the middle class (defined as 40%-80%). We also measure consumption inequality over time and find that the Gini coefficient of consumption distribution increased significantly.\n\nInterpretationIn addition to focusing on poor households, policy responses to alleviate peoples sufferings would have to consider a more comprehensive boost to consumption and compensate for the reduced consumption among middle class families as well.\n\nFundingNone.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Mudit Kapoor",
+        "author_inst": "Indian Statistical Institution, Delhi"
+      },
+      {
+        "author_name": "Shamika Ravi",
+        "author_inst": "Brookings Institution"
+      },
+      {
+        "author_name": "A.K.Shiva Kumar",
+        "author_inst": "Development Economist and Policy Advisor"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health economics"
+  },
   {
     "rel_doi": "10.1101/2021.06.08.21258561",
     "rel_title": "The impact of Covid-19 vaccination on the Italian healthcare system: a scenario analysis",
@@ -709359,61 +707865,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2021.06.09.447754",
-    "rel_title": "An outbreak of SARS-CoV-2 with high mortality in mink (Neovison vison) on multiple Utah farms",
-    "rel_date": "2021-06-10",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.09.447754",
-    "rel_abs": "The breadth of animal hosts that are susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and may serve as reservoirs for continued viral transmission are not known entirely. In August 2020, an outbreak of SARS-CoV-2 occurred in multiple mink farms in Utah and was associated with high mink mortality and rapid viral transmission between animals. The outbreaks epidemiology, pathology, molecular characterization, and tissue distribution of virus within infected mink is provided. Infection of mink was likely by reverse zoonosis. Once established, infection spread rapidly between independently housed animals and farms, and caused severe respiratory disease and death. Clinical signs were most notably sudden death, anorexia, and increased respiratory effort. Gross pathology examination revealed severe pulmonary congestion and edema. Microscopically there was pulmonary edema with moderate vasculitis, perivasculitis, and fibrinous interstitial pneumonia. Reverse transcriptase polymerase chain reaction (RT-PCR) of tissues collected at necropsy demonstrated the presence of SARS-CoV-2 viral RNA in multiple organs including nasal turbinates, lung, tracheobronchial lymph node, epithelial surfaces, and others. Whole genome sequencing from multiple mink was consistent with published SARS-CoV-2 genomes with few polymorphisms. The Utah mink SARS-CoV-2 strain fell into Clade GH, which is unique among mink and other animal strains sequenced to date and did not share other spike RBD mutations Y453F and F486L found in mink. Localization of viral RNA by in situ hybridization revealed a more localized infection, particularly of the upper respiratory tract. Mink in the outbreak reported herein had high levels of virus in the upper respiratory tract associated with mink-to-mink transmission in a confined housing environment and were particularly susceptible to disease and death due to SARS-CoV-2 infection.\n\nAuthor SummaryThe recent emergence and worldwide spread of the novel coronavirus has resulted in worldwide disease and economic hardship. The virus, known as SARS-CoV-2 is believed to have originated in bats and has spread worldwide through human-to-human virus transmission. It remains unclear which animal species, other than humans, may also be susceptible to viral infection and could naturally transmit the virus to susceptible hosts. In this study, we describe an outbreak of disease and death due to SARS-CoV-2 infection in farmed mink in Utah, United States. The investigation reveals that mink can spread the virus rapidly between animals and that the disease in mink is due to the viral infection and damage to tissues of the upper and lower respiratory system. The determination that mink are susceptible to SARS-CoV-2 indicates the need for strict biosecurity measures on mink farms to remediate mink-to-mink and human-to-mink transmission for the protection of mink, as well as prevent potential transmission from mink to humans.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Chrissy Eckstrand",
-        "author_inst": "Washington Animal Disease Diagnostic Laboratory, Washington State University, Pullman, WA 99163"
-      },
-      {
-        "author_name": "Tom Baldwin",
-        "author_inst": "Utah Veterinary Diagnostic Laboratory, Utah State University, Logan, UT 84341"
-      },
-      {
-        "author_name": "Mia Kim Torchetti",
-        "author_inst": "National Veterinary Services Laboratories, Ames, IA 50010"
-      },
-      {
-        "author_name": "Mary Lea Killian",
-        "author_inst": "National Veterinary Services Laboratories, Ames, IA 50010"
-      },
-      {
-        "author_name": "Kerry A Rood",
-        "author_inst": "Utah State University, Animal, Dairy, and Veterinary Sciences, Logan, UT 84341"
-      },
-      {
-        "author_name": "Michael Clayton",
-        "author_inst": "Utah Veterinary Diagnostic Laboratory, Utah State University, Logan, UT 84341"
-      },
-      {
-        "author_name": "Jason A Lott",
-        "author_inst": "Fur Breeders Agricultural Cooperative, Logan, UT 84321"
-      },
-      {
-        "author_name": "Rebecca M Wolking",
-        "author_inst": "Washington Animal Disease Diagnostic Laboratory, Washington State University, Pullman, WA 99163"
-      },
-      {
-        "author_name": "Daniel S Bradway",
-        "author_inst": "Washington Animal Disease Diagnostic Laboratory, Washington State University, Pullman, WA 99163"
-      },
-      {
-        "author_name": "Timothy Baszler",
-        "author_inst": "Washington Animal Disease Diagnostic Laboratory, Washington State University, Pullman, WA 99163"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2021.06.08.21258471",
     "rel_title": "BNT162b2 mRNA vaccinations in Israel: understanding the impact and improving the vaccination policies by redefining the immunized population",
@@ -709772,6 +708223,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.06.08.21258434",
+    "rel_title": "The impact of COVID-19 pandemic on influenza transmission: molecular and epidemiological evidence",
+    "rel_date": "2021-06-10",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258434",
+    "rel_abs": "To quantify the impact of COVID-19-related control measures on the spread of human influenza virus, we analyzed case numbers, viral molecular sequences, personal behavior data, and policy stringency data from various countries, and found consistent evidence of decrease in influenza incidence after the emergence of COVID-19.\n\nArticle SummaryWe quantify a noticeable decrease in H1N1 and H3N2 cases and genetic diversity in selected countries since the onset of the COVID-19 pandemic.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Leon K Tran",
+        "author_inst": "Department of Statistics, Stanford University, CA, USA"
+      },
+      {
+        "author_name": "Dai-Wei Huang",
+        "author_inst": "College of Life Science, National Tsing Hua University, Hsinchu, Taiwan"
+      },
+      {
+        "author_name": "Nien-Kung Li",
+        "author_inst": "College of Life Science, National Tsing Hua University, Hsinchu, Taiwan"
+      },
+      {
+        "author_name": "Julia Palacios",
+        "author_inst": "Department of Statistics, Stanford University, CA, USA"
+      },
+      {
+        "author_name": "Hsiao-Han Chang",
+        "author_inst": "Department of Life Science & Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan"
+      },
+      {
+        "author_name": "Lucy M Li",
+        "author_inst": "The Public Health Company, Goleta, CA, USA"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.06.07.21258476",
     "rel_title": "Possible future waves of SARS-CoV-2 infection generated by variants of concern with a range of characteristics",
@@ -711141,73 +709631,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.06.08.21258572",
-    "rel_title": "The influence of sex, gender, age, and ethnicity on psychosocial factors and substance use throughout phases of the COVID-19 pandemic",
-    "rel_date": "2021-06-09",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258572",
-    "rel_abs": "The SARS-CoV-2 (COVID-19) pandemic has had profound physical and mental health effects on populations around the world. Limited empirical research has used a gender-based lens to evaluate the mental health impacts of the pandemic, overlooking the impact of public health measures on marginalized groups, such as women, and the gender diverse community. This study used a gender-based analysis to determine the prevalence of psychosocial symptoms and substance use by age, ethnicity, income, rurality, education level, Indigenous status, and sexual orientation.\n\nParticipants in the study were recruited from previously established cohorts as a part of the COVID-19 Rapid Evidence Study of a Provincial Population-Based Cohort for Gender and Sex (RESPPONSE) study. Those who agreed to participate were asked to self-report symptoms of depression, anxiety, pandemic stress, loneliness, alcohol use, and cannabis use across five phases of the pandemic as well as retrospectively before the pandemic.\n\nFor all psychosocial outcomes, there was a significant effect of time with all five phases of the pandemic being associated with more psychosocial symptoms relative to pre-COVID levels (p < .0001). Gender was significantly associated with all outcomes (p < .0001) with men exhibiting lower scores (i.e., less symptoms) than women and gender diverse participants, and women exhibiting lower scores than the gender diverse group. Other significant predictors were age (younger populations experiencing more symptoms, p < .0001), ethnicity (Chinese/Taiwanese individuals experiencing less symptoms, p = .005), and Indigenous status (Indigenous individuals experiencing more symptoms, p < .0001). Alcohol use and cannabis use increased relative to pre-pandemic levels, and women reported a greater increase in cannabis use than men (p < .0001). Our findings highlight the need for policy makers and leaders to proactively consider gender when tailoring public health measures for future pandemics.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Lori A. Brotto",
-        "author_inst": "Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, Canada"
-      },
-      {
-        "author_name": "Kyle Chankasingh",
-        "author_inst": "Faculty of Health Sciences, Simon Fraser University"
-      },
-      {
-        "author_name": "Alexandra Baaske",
-        "author_inst": "Women's Health Research Institute"
-      },
-      {
-        "author_name": "Arianne Albert",
-        "author_inst": "Women's Health Research Institute"
-      },
-      {
-        "author_name": "Amy Booth",
-        "author_inst": "Women's Health Research Institute"
-      },
-      {
-        "author_name": "Angela Kaida",
-        "author_inst": "Faculty of Health Sciences, Simon Fraser University"
-      },
-      {
-        "author_name": "Laurie W. Smith",
-        "author_inst": "Women's Health Research Institute"
-      },
-      {
-        "author_name": "Sarai Racey",
-        "author_inst": "Women's Health Research Institute"
-      },
-      {
-        "author_name": "Anna Gottschlich",
-        "author_inst": "Women's Health Research Institute"
-      },
-      {
-        "author_name": "Melanie C.M. Murray",
-        "author_inst": "Department of Medicine, University of British Columbia"
-      },
-      {
-        "author_name": "Manish Sadarangani",
-        "author_inst": "Department of Pediatrics, University of British Columbia"
-      },
-      {
-        "author_name": "Gina S. Ogilvie",
-        "author_inst": "School of Population and Public Health, University of British Columbia"
-      },
-      {
-        "author_name": "Liisa A.M Galea",
-        "author_inst": "Department of Psychology, University of British Columbia"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.06.07.21258447",
     "rel_title": "Breakthrough infection with SARS-CoV-2 and its predictors among healthcare workers in a medical college and hospital complex in Delhi, India",
@@ -711742,6 +710165,161 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.06.08.21258284",
+    "rel_title": "Highly-specific memory B cells generation after the 2nd dose of BNT162b2 vaccine compensate for the decline of serum antibodies and absence of mucosal IgA",
+    "rel_date": "2021-06-09",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258284",
+    "rel_abs": "Specific memory B cells and antibodies are reliable read-out of vaccine efficacy. We analyzed these biomarkers after one and two doses of BNT162b2 vaccine. The second dose significantly increases the level of highly-specific memory B cells and antibodies. Two months after the second dose, specific antibody levels decline, but highly specific memory B cells continue to increase thus predicting a sustained protection from COVID-19.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC=\"FIGDIR/small/21258284v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (28K):\norg.highwire.dtl.DTLVardef@1700325org.highwire.dtl.DTLVardef@deb172org.highwire.dtl.DTLVardef@53f056org.highwire.dtl.DTLVardef@c7a98d_HPS_FORMAT_FIGEXP  M_FIG Graphical Abstract\n\nC_FIG",
+    "rel_num_authors": 35,
+    "rel_authors": [
+      {
+        "author_name": "Eva Piano Mortari",
+        "author_inst": "Ospedale Pediatrico Bambino Gesu"
+      },
+      {
+        "author_name": "Cristina Russo",
+        "author_inst": "Bambino Gesu Children Hospital"
+      },
+      {
+        "author_name": "Maria Rosaria Vinci",
+        "author_inst": "Bambino Gesu Children Hospital"
+      },
+      {
+        "author_name": "Sara Terreri",
+        "author_inst": "Bambino Gesu Children Hospital"
+      },
+      {
+        "author_name": "Ane Fernandez Salinas",
+        "author_inst": "Bambino Gesu Children Hospital"
+      },
+      {
+        "author_name": "Livia Piccioni",
+        "author_inst": "Bambino Gesu Children Hospital"
+      },
+      {
+        "author_name": "Claudia Alteri",
+        "author_inst": "University of Milano"
+      },
+      {
+        "author_name": "luna Colagrossi",
+        "author_inst": "Bambino Gesu Children Hospital"
+      },
+      {
+        "author_name": "Luana Coltella",
+        "author_inst": "Bambino gesu Children Hospital"
+      },
+      {
+        "author_name": "Stefania Ranno",
+        "author_inst": "Bambino Gesu Children Hospital"
+      },
+      {
+        "author_name": "Giulia Linardos",
+        "author_inst": "Bambino Gesu Children hospital"
+      },
+      {
+        "author_name": "Marilena Agosta",
+        "author_inst": "Bambino Gesu children hospital"
+      },
+      {
+        "author_name": "Christian Albano",
+        "author_inst": "bambino gesu children hospita"
+      },
+      {
+        "author_name": "Chiara Agrati",
+        "author_inst": "Spallanzani Roma"
+      },
+      {
+        "author_name": "Concetta Castilletti",
+        "author_inst": "Spallanzani Roma"
+      },
+      {
+        "author_name": "Silvia Meschi",
+        "author_inst": "National institute of infectious diseases l spallanzani"
+      },
+      {
+        "author_name": "Paolo Romania",
+        "author_inst": "La Sapienza Roma"
+      },
+      {
+        "author_name": "Giuseppe Roscilli",
+        "author_inst": "Takis"
+      },
+      {
+        "author_name": "Emiliano Pavoni",
+        "author_inst": "Takis"
+      },
+      {
+        "author_name": "Vincenzo Camisa",
+        "author_inst": "Bambino Gesu Children Hospital"
+      },
+      {
+        "author_name": "Annapaola Santoro",
+        "author_inst": "Bambino gesu children hospital"
+      },
+      {
+        "author_name": "Rita Brugaletta",
+        "author_inst": "Bambino gesu children hospital"
+      },
+      {
+        "author_name": "Nicola Magnavita",
+        "author_inst": "Policlinico Gemelli Roma"
+      },
+      {
+        "author_name": "Alessandra Ruggiero",
+        "author_inst": "Bambino gesu children hospital"
+      },
+      {
+        "author_name": "Nicola Cotugno",
+        "author_inst": "Bambino Gesu children hospital"
+      },
+      {
+        "author_name": "Donato Amodio",
+        "author_inst": "Bambino gesu children hospital"
+      },
+      {
+        "author_name": "Marta Luisa Cioffi Degli Atti",
+        "author_inst": "Bambino gesu children hospital"
+      },
+      {
+        "author_name": "Daniela Giorgio",
+        "author_inst": "Bambino gesu children hospital"
+      },
+      {
+        "author_name": "Nicoletta Russo",
+        "author_inst": "Bambino gesu children hospital"
+      },
+      {
+        "author_name": "Guglielmo Salvatori",
+        "author_inst": "Bambino gesu children hospital"
+      },
+      {
+        "author_name": "tiziana corsetti",
+        "author_inst": "bambino gesu children hospital"
+      },
+      {
+        "author_name": "Franco Locatelli",
+        "author_inst": "Bambino gesu children hospital"
+      },
+      {
+        "author_name": "Carlo Federico Perno",
+        "author_inst": "Bambino gesu children hospital"
+      },
+      {
+        "author_name": "Salvatore Zaffina",
+        "author_inst": "Bambino gesu children hospital"
+      },
+      {
+        "author_name": "Rita Carsetti",
+        "author_inst": "Bambino Gesu Children Hospital"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "allergy and immunology"
+  },
   {
     "rel_doi": "10.1101/2021.06.08.21258558",
     "rel_title": "Response of Unvaccinated US Adults to Official Information About the Pause in Use of the Johnson & Johnson-Janssen COVID-19 Vaccine",
@@ -713171,29 +711749,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.06.06.21258091",
-    "rel_title": "Safety and efficacy of antiviral therapy alone or in combination in COVID-19 - a randomized controlled trial (SEV COVID Trial)",
-    "rel_date": "2021-06-08",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.06.21258091",
-    "rel_abs": "BackgroundDefinitive antiviral treatment is not available for COVID-19 infection except remdesivir that even with many doubts. Various combination antivirals have been tried.\n\nMethodsA single-center, open-label, parallel-arm, stratified randomized controlled trial evaluated the therapeutic potential of hydroxychloroquine and lopinavir-ritonavir in combination with ribavirin in COVID-19. Enrolled patients in severe category were randomized into three groups: A: standard treatment, B: hydroxychloroquine+ribavirin+standard treatment, or C: lopinavir+ritonavir+ribavirin+standard treatment; while non-severe category into two groups: A: standard treatment or B: hydroxychloroquine+ribavirin. Combination antivirals was given for 10 days and followed for 28 days. The primary endpoints were safety, symptomatic and laboratory recovery of organ dysfunctions, and time to SARS-CoV-2 RT-PCR negative report.\n\nResultsTotal 111 patients randomized: 24, 23, and 24 in severe category A, B, and C respectively, and 20 in each non-severe group. Two patients receiving ribavirin experienced drug induced liver injury and another developed QT prolongation after hydroxychloroquine. In the severe category, 47.6%, 55%, and 30.09% in A, B, and C groups respectively showed symptomatic recovery compared to 93.3% and 86.7% in A and B groups respectively in the non-severe category at 72hrs (P>0.05).\n\nConclusionsThe results failed to show statistical superiority of the antiviral combination therapies to that of the standard therapy in both the severe and non-severe categories in symptomatic adult patients of COVID-19. However, results do indicate the benefit of non-standard interventional combination therapy in severe disease. Furthermore, the dose of ribavirin needs to be reconsidered in the Indian population.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "- SEV COVID trial group",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Prasan Kumar Panda",
-        "author_inst": "AIIMS Rishikesh"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.06.07.21258351",
     "rel_title": "Antibody longevity and cross-neutralizing activity following SARS-CoV-2 wave 1 and B.1.1.7 infections",
@@ -713684,6 +712239,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.06.07.446560",
+    "rel_title": "Mapping Potential Antigenic Drift Sites (PADS) on SARS-CoV-2 Spike in Continuous Epitope-Paratope Space",
+    "rel_date": "2021-06-08",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.07.446560",
+    "rel_abs": "SARS-CoV-2 mutations with antigenic effects pose a risk to immunity developed through vaccination and natural infection. While vaccine updates for current variants of concern (VOCs) are underway, it is likewise important to prepare for further antigenic mutations as the virus navigates the heterogeneous global landscape of host immunity. Toward this end, a wealth of data and tools exist that can augment existing genetic surveillance of VOC evolution. In this study, we integrate published datasets describing genetic, structural, and functional constraints on mutation along with computational analyses of antibody-spike co-crystal structures to identify a set of potential antigenic drift sites (PADS) within the receptor binding domain (RBD) and N-terminal domain (NTD) of SARS-CoV-2 spike protein. Further, we project the PADS set into a continuous epitope-paratope space to facilitate interpretation of the degree to which newly observed mutations might be antigenically synergistic with existing VOC mutations, and this representation suggests that functionally convergent and synergistic antigenic mutations are accruing across VOC NTDs. The PADS set and synergy visualization serve as a reference as new mutations are detected on VOCs, enable proactive investigation of potentially synergistic mutations, and offer guidance to antibody and vaccine design efforts.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC=\"FIGDIR/small/446560v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (27K):\norg.highwire.dtl.DTLVardef@13b884forg.highwire.dtl.DTLVardef@171fe3eorg.highwire.dtl.DTLVardef@eac445org.highwire.dtl.DTLVardef@fba613_HPS_FORMAT_FIGEXP  M_FIG C_FIG",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Nathaniel Loren Miller",
+        "author_inst": "Massachusetts Institute of Technology"
+      },
+      {
+        "author_name": "Thomas Clark",
+        "author_inst": "Massachusetts Institute of Technology"
+      },
+      {
+        "author_name": "Rahul Raman",
+        "author_inst": "Massachusetts Institute of Technology"
+      },
+      {
+        "author_name": "Ram Sasisekharan",
+        "author_inst": "Massachusetts Institute of Technology"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2021.06.07.447437",
     "rel_title": "FXa cleaves the SARS-CoV-2 spike protein and blocks cell entry to protect against infection with inferior effects in B.1.1.7 variant",
@@ -715137,41 +713723,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "rheumatology"
   },
-  {
-    "rel_doi": "10.1101/2021.06.05.21258401",
-    "rel_title": "Self-reported adaptability among postgraduate dental learners and their instructors: accelerated change induced by COVID-19",
-    "rel_date": "2021-06-07",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.05.21258401",
-    "rel_abs": "It is forecasted that the skills and competencies necessary for post-pandemic success in higher education need to be founded upon adaptability, coping, and Self-regulated Learning (SRL). It is worth investigating how stakeholders perceived their adaptability and coping with the accelerated change accompanying COVID-19. Accordingly, the purpose of this study was to assess the self-reported adaptability of postgraduate dental learners and their instructors in the context of abrupt transition to distance learning induced by the pandemic.\n\nThis study utilized a convergent mixed methods study design. The qualitative and quantitative data were concurrently collected from instructors and learners. The datasets were analyzed independently, and the generated information was integrated using a joint model analysis.\n\nThe percentage of average of self-reported adaptability of both groups was 81.15%. The instructors, with a mean of satisfaction of 17.94 ({+/-}1.76), rated their adaptability significantly higher than the learners, with a mean of satisfaction of 15.66 ({+/-}2.77) (p=0.002). The thematic analysis resulted in two interrelated themes: Self and Environment. Within the Self theme, three subthemes surfaced: Cognitions, Emotions, Behaviors. As for the Environment theme, it encapsulated two subthemes: Enablers and Impediments.\n\nThe stakeholders perceived themselves to have adapted well to the transition, and SRL appeared as a cornerstone in the adaptation to the accelerated change (accompanying COVID-19). There appeared to be an interplay between the cognitions, emotions, and behaviors on the level of the self as part of the adaptation process. Also, building upon existent models of SRL, this study uncovered that the stakeholders considered the environment to play a crucial role in their adaptation process. This highlights the importance of developing a climate that remains, despite external pressures, conducive to attaining learning and teaching goals. It is also crucial for university-level mental health promotion activities to proactively foster, among learners and instructors, adaptability, building  academic resilience.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Farah Otaki",
-        "author_inst": "MBRU"
-      },
-      {
-        "author_name": "Fatemeh Amir-Rad",
-        "author_inst": "MBRU"
-      },
-      {
-        "author_name": "Manal Al-Halabi",
-        "author_inst": "Mohammed Bin Rashed University of Medicine and Health Sciences"
-      },
-      {
-        "author_name": "Zaid Baqain",
-        "author_inst": "MBRU"
-      },
-      {
-        "author_name": "Nabil Zary",
-        "author_inst": "Mohammed Bin Rashid University of Medicine and Health Sciences"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "medical education"
-  },
   {
     "rel_doi": "10.1101/2021.06.06.21258414",
     "rel_title": "Effects of immunosuppressive therapy reduction and early post-infection graft function in kidney transplant recipients with COVID-19",
@@ -715534,6 +714085,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "gastroenterology"
   },
+  {
+    "rel_doi": "10.1101/2021.06.07.447287",
+    "rel_title": "A Web Portal and Workbench for Biological Dissection of Single Cell COVID-19 Host Responses",
+    "rel_date": "2021-06-07",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.07.447287",
+    "rel_abs": "Numerous studies have provided single-cell transcriptome profiles of host responses to SARS-CoV-2 infection. Critically lacking however is a datamine that allows users to compare and explore cell profiles to gain insights and develop new hypotheses. To accomplish this, we harmonized datasets from COVID-19 and other control condition blood, bronchoalveolar lavage, and tissue samples, and derived a compendium of gene signature modules per cell type, subtype, clinical condition, and compartment. We demonstrate approaches to probe these via a new interactive web portal (http://toppcell.cchmc.org/ COVID-19). As examples, we develop three hypotheses: (1) a multicellular signaling cascade among alternatively differentiated monocyte-derived macrophages whose tasks include T cell recruitment and activation; (2) novel platelet subtypes with drastically modulated expression of genes responsible for adhesion, coagulation and thrombosis; and (3) a multilineage cell activator network able to drive extrafollicular B maturation via an ensemble of genes strongly associated with risk for developing post-viral autoimmunity.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Daniel P Krummel",
+        "author_inst": "University of Cincinnati"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2021.06.05.447177",
     "rel_title": "Neutralization against B.1.351 and B.1.617.2 with sera of COVID-19 recovered cases and vaccinees of BBV152",
@@ -716847,77 +715417,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.06.03.21258317",
-    "rel_title": "Prevalence of long-term effects in individuals diagnosed with COVID-19: a living systematic review",
-    "rel_date": "2021-06-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.03.21258317",
-    "rel_abs": "ObjectivePost COVID-19 condition refers to persisting or recurring symptoms weeks after acute COVID-19 illness which can significantly impact quality of life and health systems. It is important to understand the manifestation and magnitude of this condition. The objective of this living systematic review is to summarize the prevalence of symptoms and sequelae reported by people [&ge;]4 weeks after COVID-19 diagnosis.\n\nDesignSystematic review, meta-analysis and narrative synthesis.\n\nData sourcesEmbase, Medline, PsychInfo, Cochrane Central and select grey literature up to April 14, 2021.\n\nMethodsWe adapted a previous search strategy used by the U.K. National Institute for Health and Care Excellence and updated it to search for new literature. Two reviewers screened references independently; one extracted data and assessed risk of bias and certainty of the evidence while another verified them. Prevalence data from laboratory-confirmed populations were meta-analyzed using a random effects model and synthesized separately in the short-term (4-12 weeks) and long-term (>12 weeks) periods after diagnosis. Data from clinically-diagnosed populations were synthesized narratively.\n\nResultsOf the 4444 unique citations, 84 observational studies met our inclusion criteria. Over 100 post COVID-19 symptoms and sequelae were reported. Sixty-one percent (95% CI: 44-76%, low certainty) and 53% (95% CI: 41-65%, low certainty) of laboratory-confirmed individuals reported persistence or presence of one or more symptoms in the short- and long-term periods, respectively. The most prevalent symptoms in both periods included: fatigue, general pain or discomfort, shortness of breath, cognitive impairment and mental health symptoms.\n\nConclusionsA substantial proportion of individuals reported a variety of symptoms [&ge;]4 weeks after COVID-19 diagnosis. Due to gaps in the research base, and the low certainty of the evidence currently available, further research is needed to determine the true burden of post COVID-19 condition in the general population and in specific subgroups.\n\nPROSPERO registration numberCRD42021231476.",
-    "rel_num_authors": 14,
-    "rel_authors": [
-      {
-        "author_name": "Francesca Reyes Domingo",
-        "author_inst": "Public Health Agency of Canada"
-      },
-      {
-        "author_name": "Lisa A Waddell",
-        "author_inst": "Public Health Agency of Canada"
-      },
-      {
-        "author_name": "Angela M Cheung",
-        "author_inst": "University Health Network and University of Toronto"
-      },
-      {
-        "author_name": "Curtis L Cooper",
-        "author_inst": "University of Ottawa and Ottawa Hospital Research Institute"
-      },
-      {
-        "author_name": "Veronica J Belcourt",
-        "author_inst": "Public Health Agency of Canada"
-      },
-      {
-        "author_name": "Alexandra M. E. Zuckermann",
-        "author_inst": "Public Health Agency of Canada"
-      },
-      {
-        "author_name": "Tricia Corrin",
-        "author_inst": "Public Health Agency of Canada"
-      },
-      {
-        "author_name": "Rukshanda Ahmad",
-        "author_inst": "Public Health Agency of Canada"
-      },
-      {
-        "author_name": "Laura Boland",
-        "author_inst": "Public Health Agency of Canada"
-      },
-      {
-        "author_name": "Claudie Laprise",
-        "author_inst": "Public Health Agency of Canada"
-      },
-      {
-        "author_name": "Leanne Idzerda",
-        "author_inst": "Public Health Agency of Canada"
-      },
-      {
-        "author_name": "Anam Khan",
-        "author_inst": "Public Health Agency of Canada"
-      },
-      {
-        "author_name": "Kate Morissette",
-        "author_inst": "Public Health Agency of Canada"
-      },
-      {
-        "author_name": "Alejandra Jaramillo Garcia",
-        "author_inst": "Public Health Agency of Canada"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.06.03.21258300",
     "rel_title": "Field evaluation of specificity and sensitivity of a standard SARS-CoV-2 antigen rapid diagnostic test: A prospective study at a teaching hospital in Northern Ghana",
@@ -717292,6 +715791,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.06.02.21258257",
+    "rel_title": "Efficacy of clarithromycin on COVID-19 pneumonia without oxygen administration; protocol for multicenter, open-label, randomized-controlled, 3-armed parallel group comparison, exploratory trial (CAME COVID study)",
+    "rel_date": "2021-06-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.02.21258257",
+    "rel_abs": "IntroductionThe coronavirus disease 2019 (COVID-19) epidemic has been emerged worldwide. Although several medications have been approved for treating moderate-to-severe COVID-19, no treatment strategy has been established for mild COVID-19 patients who do not require oxygen administration. The spread of SARS -CoV-2 has been mostly through patients with mild COVID-19; therefore, treating patients with mild COVID-19 is critical in society. Clarithromycin is a macrolide antimicrobial agent that has been widely used for bacterial respiratory infectious diseases. Clarithromycin also acts an immunomodulating drug and suppresses cytokine storms in viral respiratory diseases, including influenza infection. In this study, we aimed to evaluate the efficacy of clarithromycin in patients with mild COVID-19.\n\nMethods and analysisThis is a multicenter, open-label, randomized controlled, 3-armed parallel group comparison, exploratory trial. Subjects with mild COVID-19 pneumonia who did not require oxygen administration were enrolled and randomly assigned in a 1:1:1 ratio to Group A (administration of clarithromycin 800 mg/day), Group B (administration of clarithromycin 400 mg/day), or Group C (standard treatment without clarithromycin). The primary endpoint was the number of days required to improve clinical symptoms as measured by the severity score. Secondary endpoints included days to recover the body temperature, proportion of subjects with oxygen administration, inflammatory cytokines, viral load, serum immunoglobulins, peripheral blood lymphocytes, blood biomarkers, and pneumonia infiltrations.\n\nEthics and disseminationThe study protocol was approved by the Clinical Research Review Board of Nagasaki University in accordance with the Clinical Trials Act in Japan. The study will be conducted in accordance with the Declaration of Helsinki, the Clinical Trials Act, and other current legal regulations in Japan. Written informed consent will be obtained from all participants. The results of this study will be reported as journal publications.\n\nRegistrationThis study was registered at the Japan Registry of Clinical Trials (registration number: jRCTs071210011).\n\nStrengths and limitations of this studyO_LIThis is the first randomized controlled trial to evaluate the efficacy of clarithromycin against COVID-19 pneumonia, especially in patients with mild COVID-19 pneumonia who do not require oxygen administration.\nC_LIO_LITo date, no treatment strategy has been established for mild COVID-19 pneumonia.\nC_LIO_LIThe major limitations of this study are its exploratory nature and relatively small sample size.\nC_LIO_LIAnother limitation is the open-label study design and generalizability because this study was conducted only in Japan with Japanese patients.\nC_LI",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Kazuko Yamamoto",
+        "author_inst": "Nagasaki University Hospital"
+      },
+      {
+        "author_name": "Naoki Hosogaya",
+        "author_inst": "Nagasaki University Hospital"
+      },
+      {
+        "author_name": "Noriho Sakamoto",
+        "author_inst": "Nagasaki University Hospital"
+      },
+      {
+        "author_name": "Haruo Yoshida",
+        "author_inst": "Nagasaki University Graduate School of Biomedical Sciences"
+      },
+      {
+        "author_name": "Hiroshi Ishii",
+        "author_inst": "Fukuoka University Hospital"
+      },
+      {
+        "author_name": "Kazuhiro Yatera",
+        "author_inst": "University of Occupational and Environmental Health"
+      },
+      {
+        "author_name": "Koichi Izumikawa",
+        "author_inst": "Nagasaki University Hospital"
+      },
+      {
+        "author_name": "Katsunori Yanagihara",
+        "author_inst": "Nagasaki University Hospital"
+      },
+      {
+        "author_name": "Hiroshi Mukae",
+        "author_inst": "Nagasaki University Hospital"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "respiratory medicine"
+  },
   {
     "rel_doi": "10.1101/2021.06.02.21258243",
     "rel_title": "A Cluster-based Model of COVID-19 Transmission Dynamics",
@@ -718501,61 +717051,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2021.06.01.21258175",
-    "rel_title": "Antibody profiling reveals gender differences in response to SARS-COVID-2 infection",
-    "rel_date": "2021-06-04",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.01.21258175",
-    "rel_abs": "The recent emergence of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to an ongoing global COVID-19 pandemic and public health crisis. Detailed study of human immune response to SARS-COVIS-2 infection is the important topic for a successful treatment of this disease. Our study was aimed to characterize immune response on the level of antibody profiling in convalescent plasma of patients in Georgia. Antibodies against the following SARS-COV-2 proteins were studied: nucleocapsid and various regions of Spike (S) protein: S1, S2 and Receptor binding domain (RBD). Convalescent plasma of patients 6-8 weeks after initial confirmation of SARS-COV-2 infection were tested. Nearly 80% out of 154 patients studied showed presence of antibodies against nucleocapsid protein. The antibody response to three fragments of S protein was significantly less and varied in the range of 20-30%. Significantly more females as compared to males were producing antibodies against S1 fragment, whereas the difference between genders by the antibodies against nucleocapsid protein and RBD was statistically significant only by one-tailed Fisher exact test. There were no differences between the males and females by antibodies against S2 fragment. Thus, immune response against some viral antigens are stronger in females and we suggest that it could be one of the factors of less female fatality after SARS-COVID-2 infection.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Lia Tsverava",
-        "author_inst": "Institute of Chemical Biology, Ilia State University, Tbilisi, Georgia  and I.Beritashvili Center of Experimental Biomedicine, Tbilisi, Georgia"
-      },
-      {
-        "author_name": "Nazibrola Chitadze",
-        "author_inst": "National Center for Disease Control, Tbilisi, Georgia"
-      },
-      {
-        "author_name": "Gvantsa Chanturia",
-        "author_inst": "National Center for Disease Control, Tbilisi, Georgia"
-      },
-      {
-        "author_name": "Merab Kekelidze",
-        "author_inst": "National Center for Disease Control, Tbilisi, Georgia"
-      },
-      {
-        "author_name": "David Dzneladze",
-        "author_inst": "I.Beritashvili Center of Experimental Biomedicine, Tbilisi, Georgia"
-      },
-      {
-        "author_name": "Paata Imnadze",
-        "author_inst": "National Center for Disease Control, Tbilisi, Georgia"
-      },
-      {
-        "author_name": "Amiran Gamkrelidze",
-        "author_inst": "National Center for Disease Control, Tbilisi, Georgia"
-      },
-      {
-        "author_name": "Vincenzo Lagani",
-        "author_inst": "Institute of Chemical Biology, Ilia State University"
-      },
-      {
-        "author_name": "Zaza Khuchua",
-        "author_inst": "Institute of Chemical Biology, Ilia State University and Sechenov University, Department of Biochemistry, Moscow, Russia"
-      },
-      {
-        "author_name": "Revaz Solomonia",
-        "author_inst": "Ilia State University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.06.03.21258009",
     "rel_title": "Comparing India's second COVID wave with the first wave, a single center experience",
@@ -718826,6 +717321,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "respiratory medicine"
   },
+  {
+    "rel_doi": "10.1101/2021.06.03.21258240",
+    "rel_title": "Aggregating probabilistic predictions of the safety, efficacy, and timing of a COVID-19 vaccine",
+    "rel_date": "2021-06-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.03.21258240",
+    "rel_abs": "Safe, efficacious vaccines were developed to reduce the transmission of SARS-CoV-2 during the COVID-19 pandemic. But in the middle of 2020, vaccine effectiveness, safety, and the timeline for when a vaccine would be approved and distributed to the public was uncertain. To support public health decision making, we solicited trained forecasters and experts in vaccinology and infectious disease to provide monthly probabilistic predictions from July to September of 2020 of the efficacy, safety, timing, and delivery of a COVID-19 vaccine. We found, that despite sparse historical data, a consensus--a combination of human judgment probabilistic predictions--can quantify the uncertainty in clinical significance and timing of a potential vaccine. The consensus underestimated how fast a therapy would show a survival benefit and the high efficacy of approved COVID-19 vaccines. However, the consensus did make an accurate prediction for when a vaccine would be approved by the FDA. Compared to individual forecasters, the consensus was consistently above the 50th percentile of the most accurate forecasts. A consensus is a fast and versatile method to build probabilistic predictions of a developing vaccine that is robust to poor individual predictions. Though experts and trained forecasters did underestimate the speed of development and the high efficacy of a SARS-CoV-2 vaccine, consensus predictions can improve situational awareness for public health officials and for the public make clearer the risks, rewards, and timing of a vaccine.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Thomas Charles McAndrew",
+        "author_inst": "Lehigh University"
+      },
+      {
+        "author_name": "Juan Cambeiro",
+        "author_inst": "Metaculus"
+      },
+      {
+        "author_name": "Tamay Besiroglu",
+        "author_inst": "Metaculus"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.06.01.21258187",
     "rel_title": "The Impact of COVID-19 Vaccination on California's Return to Normalcy",
@@ -720555,45 +719077,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.06.02.21257869",
-    "rel_title": "Variant-of-concern-attributable health and health system-related outcomes: a population-level propensity-score matched cohort study",
-    "rel_date": "2021-06-03",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.02.21257869",
-    "rel_abs": "BackgroundAs the transmission of SARS-CoV-2 variants intensifies globally, the burden of COVID-19 on the already strained health systems is becoming increasingly concerning. While there is growing literature on the effects of various variants-of-concern (VOC) on increased transmission, the extent to which VOCs may lead to more severe disease remains debated.\n\nMethodsIn the current analysis, we use a population-based propensity-score matched cohort study of all incident laboratory-confirmed COVID-19 cases with VOC testing in Ontario, Canada to estimate healthcare resource use and health outcomes attributable to VOCs introduced to Ontario between January 1 and April 9, 2021, relative to the previously circulating wild-type strain.\n\nResultsWe find that VOCs are associated with a higher odds of hospitalisation (odds ratio [OR], 2.25; 95% confidence interval [CI], 2.10-2.40) and ICU admission (OR, 3.31; 95%CI, 2.84-3.86); as well as with a higher odds of mortality for both the general COVID-19 population (OR 1.75; 1.47-2.09) and hospitalised cases (OR, 1.62; 95%CI, 1.23-2.15).\n\nConclusionTaken together, these findings suggest that health systems may face increased demand for healthcare resources as VOCs predominate worldwide in view of low global vaccination coverage.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Aysegul Erman",
-        "author_inst": "University Health Network"
-      },
-      {
-        "author_name": "Sharmistha Mishra",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Kali Barrett",
-        "author_inst": "University Health Network"
-      },
-      {
-        "author_name": "Stephen Mac",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "David MJ Naimark",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Beate Sander",
-        "author_inst": "University Health Network"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.06.02.21258073",
     "rel_title": "Affinity tag coating enables reliable detection of antigen-specific B cells in ImmunoSpot assays",
@@ -720876,6 +719359,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.06.01.21258147",
+    "rel_title": "Minimum manufacturing costs, national prices and estimated global availability of new repurposed therapies for COVID-19.",
+    "rel_date": "2021-06-03",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.01.21258147",
+    "rel_abs": "BackgroundCurrently, only dexamethasone, tocilizumab and sarilumab have conclusively been shown to reduce mortality of COVID-19. Safe and effective treatments will need to be both affordable and widely available globally to be used alongside vaccination programmes. This analysis will estimate and compare potential generic minimum costs of a selection of approved COVID-19 drug candidates with available international list prices.\n\nMethodsWe searched for repurposed drugs that have been approved by at least one of the WHO, FDA or NICE, or at least given emergency use authorisation or recommended for off-label prescription. Drug prices were searched for, for dexamethasone, budesonide, baricitinib, tocilizumab, casirivimab and imdevimab, and sarilumab using active pharmaceutical ingredients (API) data extracted from global shipping records. This was compared with national pricing data from a range of low, medium, and high-income countries. Annual API export volumes from India were used to estimate the current availability of each drug.\n\nResultsRepurposed therapies can be generically manufactured for some treatments at very low per-course costs, ranging from $2.58 for IV dexamethasone (or $0.19 orally) and $4.34 for inhaled budesonide. No export price data was available for baricitinib, tocilizumab, casirivimab and imdevimab or sarilumab, but courses of these treatments are priced highly, ranging from $6.67 for baricitinib to $875.5 for sarilumab. When comparing international list prices, we found wide variations between countries.\n\nConclusionsSuccessful management of COVID-19 will require equitable access to treatment for all populations, not just those able to pay high prices. Dexamethasone and budesonide are widely available and affordable, whilst monoclonal antibodies and IV treatment courses are more expensive.\n\nKey PointsO_LIRe-purposed drugs must be affordable worldwide to compliment COVID-19 vaccine programmes.\nC_LIO_LIEstimated costs/course were: dexamethasone (Oral $0.22, IV $2.58), budesonide ($4.34), baricitnib ($6.67), tocilizumab ($410.59), sarilumab ($875.70). Casirivimab and imdevimab = no data available.\nC_LIO_LIHigh drug prices will limit access.\nC_LI",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Junzheng Wang",
+        "author_inst": "Imperial College London"
+      },
+      {
+        "author_name": "Jacob Levi",
+        "author_inst": "University College London Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "Leah Ellis",
+        "author_inst": "Imperial College London"
+      },
+      {
+        "author_name": "Andrew Hill",
+        "author_inst": "University of Liverpool"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health economics"
+  },
   {
     "rel_doi": "10.1101/2021.05.30.21258086",
     "rel_title": "Virologic features of SARS-CoV-2 infection in children",
@@ -722529,33 +721043,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.05.26.21257743",
-    "rel_title": "COVID-19 patient accounts of illness severity, treatments and lasting symptoms",
-    "rel_date": "2021-06-02",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.26.21257743",
-    "rel_abs": "First-person accounts of COVID-19 illness and treatment complement and enrich data derived from electronic medical or public health records. With patient-reported data, it is uniquely possible to ascertain in-depth contextual information as well as behavioral and emotional responses to illness. The Novel Coronavirus Illness Patient Report (NCIPR) dataset includes complete survey responses from 1,592 confirmed COVID-19 patients ages 18 to 98. NCIPR survey questions address symptoms, medical complications, home and hospital treatments, lasting effects, anxiety about illness, employment impacts, quarantine behaviors, vaccine-related behaviors and effects, and illness of other family/household members. Additional questions address financial security, perceived discrimination, pandemic impacts (relationship, social, stress, sleep), health history, and coping strategies. Detailed patient reports of illness, environment, and psychosocial impact, proximal to timing of infection and considerate of demographic variation, is meaningful for understanding pandemic-related public health from the perspective of those that contracted the disease.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Moriah Thomason",
-        "author_inst": "New York University Langone"
-      },
-      {
-        "author_name": "Denise Werchan",
-        "author_inst": "New York University Langone"
-      },
-      {
-        "author_name": "Cassandra Hendrix",
-        "author_inst": "New York University Langone"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.05.27.21257583",
     "rel_title": "Vaccine effectiveness of the BNT162b2 mRNA COVID-19 vaccine against RT-PCR confirmed SARS-CoV-2 infections, hospitalisations and mortality in prioritised risk groups",
@@ -722946,6 +721433,85 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.06.01.21258124",
+    "rel_title": "Regular testing of asymptomatic healthcare workers identifies cost-efficient SARS-CoV-2 preventive measures",
+    "rel_date": "2021-06-02",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.01.21258124",
+    "rel_abs": "Protecting healthcare professionals is crucial in maintaining a functioning health-care system. The risk of infection and optimal preventive strategies for health-care workers during the COVID-19 pandemic remain poorly understood. Here we report the results of a weekly testing regime that has been performed since the beginning of the COVID-19 pandemic to identify pre- and asymptomatic healthcare workers. Based on these observations we have developed a mathematical model of SARS-CoV-2 transmission that integrates the sources of infection from inside and outside the hospital. The data were used to study how regular testing and a desynchronisation protocol are effective in preventing transmission of COVID-19 infection at work, and compared both strategies in terms of workforce availability and cost-effectiveness. We showed that case incidence among healthcare workers is higher than would be explained solely by community infection. Furthermore, while testing and desynchronisation protocols are both effective in preventing nosocomial transmission, regular testing maintains work productivity with implementation costs.",
+    "rel_num_authors": 16,
+    "rel_authors": [
+      {
+        "author_name": "DANIEL SANCHEZ-TALTAVULL",
+        "author_inst": "UNIVERSITY OF BERN"
+      },
+      {
+        "author_name": "Violeta Castelo-Szekely",
+        "author_inst": "University of Bern"
+      },
+      {
+        "author_name": "Shaira Murugan",
+        "author_inst": "University of Bern"
+      },
+      {
+        "author_name": "Tim Rollenske",
+        "author_inst": "University of Bern"
+      },
+      {
+        "author_name": "Stephanie C. Ganal-Vonarburg",
+        "author_inst": "University of Bern"
+      },
+      {
+        "author_name": "Isabel Buchi",
+        "author_inst": "University of Bern"
+      },
+      {
+        "author_name": "Adrian Keogh",
+        "author_inst": "University of Bern"
+      },
+      {
+        "author_name": "Hai Li",
+        "author_inst": "University of Bern"
+      },
+      {
+        "author_name": "Lilian Salm",
+        "author_inst": "University of Bern"
+      },
+      {
+        "author_name": "Daniel Spari",
+        "author_inst": "University of Bern"
+      },
+      {
+        "author_name": "Bahtiyar Yilmaz",
+        "author_inst": "University of Bern"
+      },
+      {
+        "author_name": "Jakob Zimmermann",
+        "author_inst": "University of Bern"
+      },
+      {
+        "author_name": "- UVCM-COVID researchers",
+        "author_inst": ""
+      },
+      {
+        "author_name": "Michael Gerfin",
+        "author_inst": "University of Bern"
+      },
+      {
+        "author_name": "Edgar Roldan",
+        "author_inst": "ICTP - The Abdus Salam International Centre for Theoretical Physics"
+      },
+      {
+        "author_name": "Guido Beldi",
+        "author_inst": "University of Bern"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.05.29.21257950",
     "rel_title": "Performance evaluation of virus concentration methods for implementing SARS-CoV-2 Wastewater-based epidemiology emphasizing quick data turnaround.",
@@ -724219,89 +722785,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.05.30.21257971",
-    "rel_title": "Heterologous ChAdOx1 nCoV-19 and BNT162b2 prime-boost vaccination elicits potent neutralizing antibody responses and T cell reactivity",
-    "rel_date": "2021-06-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.30.21257971",
-    "rel_abs": "Heterologous COVID-19 vaccination regimens combining vector- and mRNA-based vaccines are already administered, but data on solicited adverse reactions, immunological responses and elicited protection are limited. We aimed to evaluate the reactogenicity, humoral and cellular immune responses towards different SARS-CoV-2 variants after a heterologous ChAdOx1 nCoV-19 BNT162b2 prime-boost vaccination and analyzed a cohort of 26 individuals aged 25-46 (median 30.5) years that received a ChAdOx1 nCoV-19 prime followed by a BNT162b2 boost after an 8- week interval. Self-reported solicited symptoms after ChAdOx1 nCoV-19 prime were in line with previous reports and less severe after the BNT162b2 boost. Antibody titers increased significantly over time resulting in strong neutralization titers two weeks after the BNT162b2 boost. Neutralizing activity against the prevalent strain B.1.1.7 (Alpha) and immune-evading VOC B.1.351 (Beta) was [~]4-fold higher than in individuals receiving homologous BNT162b2 vaccination. No difference was seen in neutralization of VOI B.1.617 (Kappa). In addition, the heterologous vaccination induced CD4+ and CD8+ T cells reactive to SARS-CoV-2 spike peptides of all analyzed variants; Wuhan-Hu-1, B.1.1.7, B.1.351, and P.1 (Gamma). In conclusion, heterologous ChAdOx1 nCoV-19 / BNT162b2 prime-boost vaccination regimen is not associated with serious adverse events and results in a potent humoral immune response and elicits T cell reactivity. Variants B.1.1.7, B.1.351 and B.1.617.1 are potently neutralized by sera of all participants and reactive T cells recognize spike peptides of all tested variants. These results suggest that this heterologous vaccination regimen is at least as immunogenic and protective as homologous vaccinations.",
-    "rel_num_authors": 17,
-    "rel_authors": [
-      {
-        "author_name": "Ruediger Gross",
-        "author_inst": "Ulm University Medical Center"
-      },
-      {
-        "author_name": "Michelle Zanoni",
-        "author_inst": "Ulm University Medical Center"
-      },
-      {
-        "author_name": "Alina Seidel",
-        "author_inst": "Ulm University Medical Center"
-      },
-      {
-        "author_name": "Carina Conzelmann",
-        "author_inst": "Ulm University Medical Center"
-      },
-      {
-        "author_name": "Andrea Gilg",
-        "author_inst": "Ulm University Medical Center"
-      },
-      {
-        "author_name": "Daniela Krnavek",
-        "author_inst": "Ulm University Medical Center"
-      },
-      {
-        "author_name": "Suemeyye Erdemci-evin",
-        "author_inst": "Ulm University Medical Center"
-      },
-      {
-        "author_name": "Benjamin Mayer",
-        "author_inst": "Ulm University"
-      },
-      {
-        "author_name": "Markus Hoffmann",
-        "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung"
-      },
-      {
-        "author_name": "Stefan Poehlmann",
-        "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung"
-      },
-      {
-        "author_name": "Alexandra Beil",
-        "author_inst": "University Hospital Ulm"
-      },
-      {
-        "author_name": "Joris Kroschel",
-        "author_inst": "University Hospital Ulm"
-      },
-      {
-        "author_name": "Bernd Jahrsdoerfer",
-        "author_inst": "Ulm University"
-      },
-      {
-        "author_name": "Hubert Schrezenmeier",
-        "author_inst": "Ulm University"
-      },
-      {
-        "author_name": "Frank Kirchhoff",
-        "author_inst": "Ulm University Medical Center"
-      },
-      {
-        "author_name": "Jan Muench",
-        "author_inst": "Ulm University Medical Center"
-      },
-      {
-        "author_name": "Janis A Mueller",
-        "author_inst": "Ulm University Medical Center"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.06.01.21257665",
     "rel_title": "Self-resetting Molecular Probes for Nucleic Acids Enabled by Fuel Dissipative Systems",
@@ -724588,6 +723071,97 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.05.31.21255594",
+    "rel_title": "Signatures of mast cell activation are associated with severe COVID-19",
+    "rel_date": "2021-06-01",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.31.21255594",
+    "rel_abs": "Lung inflammation is a hallmark of Coronavirus disease 2019 (COVID-19) in severely ill patients and the pathophysiology of disease is thought to be immune-mediated. Mast cells (MCs) are polyfunctional immune cells present in the airways, where they respond to certain viruses and allergens, often promoting inflammation. We observed widespread degranulation of MCs during acute and unresolved airway inflammation in SARS-CoV-2-infected mice and non-human primates. In humans, transcriptional changes in patients requiring oxygen supplementation also implicated cells with a MC phenotype. MC activation in humans was confirmed, through detection of the MC-specific protease, chymase, levels of which were significantly correlated with disease severity. These results support the association of MC activation with severe COVID-19, suggesting potential strategies for intervention.",
+    "rel_num_authors": 19,
+    "rel_authors": [
+      {
+        "author_name": "Janessa Tan",
+        "author_inst": "Duke-NUS Medical School"
+      },
+      {
+        "author_name": "Danielle Anderson",
+        "author_inst": "Duke-NUS Medical School"
+      },
+      {
+        "author_name": "Abhay P.S. Rathore",
+        "author_inst": "Duke University"
+      },
+      {
+        "author_name": "Aled O'Neill",
+        "author_inst": "Duke-NUS Medical School"
+      },
+      {
+        "author_name": "Chinmay Kumar Mantri",
+        "author_inst": "Duke-NUS Medical School"
+      },
+      {
+        "author_name": "Wilfried A.A. Saron",
+        "author_inst": "Duke-NUS Medical School"
+      },
+      {
+        "author_name": "Cheryl Lee",
+        "author_inst": "Duke-NUS Medical School"
+      },
+      {
+        "author_name": "Wern Chui Chu",
+        "author_inst": "Duke-NUS Medical School"
+      },
+      {
+        "author_name": "Adrian Kang",
+        "author_inst": "Duke-NUS Medical School"
+      },
+      {
+        "author_name": "Randy Foo",
+        "author_inst": "Duke-NUS Medical School"
+      },
+      {
+        "author_name": "Shirin Kalimuddin",
+        "author_inst": "Singapore General Hospital"
+      },
+      {
+        "author_name": "Jenny Low",
+        "author_inst": "Singapore General Hospital"
+      },
+      {
+        "author_name": "Lena Ho",
+        "author_inst": "Duke-NUS Medical School"
+      },
+      {
+        "author_name": "Paul Tambyah",
+        "author_inst": "National University of Singapore"
+      },
+      {
+        "author_name": "Thomas W. Burke",
+        "author_inst": "Duke University"
+      },
+      {
+        "author_name": "Christopher W. Woods",
+        "author_inst": "Duke University School of Medicine"
+      },
+      {
+        "author_name": "Kuan Rong Chan",
+        "author_inst": "Duke-NUS Medical School"
+      },
+      {
+        "author_name": "Joern Karhausen",
+        "author_inst": "Duke University"
+      },
+      {
+        "author_name": "Ashley L. St John",
+        "author_inst": "Duke-NUS Medical School"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.05.30.21258040",
     "rel_title": "Effect of 2021 Assembly Election in India on Covid-19 Transmission",
@@ -725569,77 +724143,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.05.30.446322",
-    "rel_title": "SARS-CoV-2-specific memory B cells can persist in the elderly despite loss of neutralising antibodies",
-    "rel_date": "2021-05-31",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.30.446322",
-    "rel_abs": "Memory B cells (MBC) can provide a recall response able to supplement waning antibodies with an affinity-matured response better able to neutralise variant viruses. We studied a cohort of vulnerable elderly care home residents and younger staff, a high proportion of whom had lost neutralising antibodies (nAb), to investigate their reserve immunity from SARS-CoV-2-specific MBC. Class-switched spike and RBD-tetramer-binding MBC with a classical phenotype persisted five months post-mild/asymptomatic SARS-CoV-2 infection, irrespective of age. Spike/RBD-specific MBC remained detectable in the majority who had lost nAb, although at lower frequencies and with a reduced IgG/IgA isotype ratio. Functional spike/S1/RBD-specific recall was also detectable by ELISpot in some who had lost nAb, but was significantly impaired in the elderly, particularly to RBD. Our findings demonstrate persistence of SARS-CoV-2-specific MBC beyond loss of nAb, but highlight the need for careful monitoring of functional defects in RBD-specific B cell immunity in the elderly.\n\nOne sentence summaryCirculating class-switched spike and RBD-specific memory B cells can outlast detectable neutralising antibodies but are functionally constrained in the elderly.",
-    "rel_num_authors": 14,
-    "rel_authors": [
-      {
-        "author_name": "Anna Jeffery-Smith",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Alice R Burton",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Sabela Lens",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Chloe Rees-Spear",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Monika Patel",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Robin Gopal",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Luke Muir",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Felicity Aiano",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Katie J Doores",
-        "author_inst": "Kings College London"
-      },
-      {
-        "author_name": "J. Yimmy Chow",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Shamez N Ladhani",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Maria Zambon",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Laura E McCoy",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Mala K Maini",
-        "author_inst": "University College London"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2021.05.29.445137",
     "rel_title": "Functional characterization of SARS-CoV-2 vaccine elicited antibodies in immunologically naive and pre-immune humans",
@@ -725974,6 +724477,77 @@
     "type": "new results",
     "category": "bioinformatics"
   },
+  {
+    "rel_doi": "10.1101/2021.05.31.446421",
+    "rel_title": "Accelerated Antibody Discovery Targeting the SARS-CoV-2 Spike Protein for COVID-19 Therapeutic Potential",
+    "rel_date": "2021-05-31",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.31.446421",
+    "rel_abs": "Rapid deployment of technologies capable of high-throughput and high-resolution screening is imperative for timely response to viral outbreaks. Risk mitigation in the form of leveraging multiple advanced technologies further increases the likelihood of identifying efficacious treatments in an aggressive timeline. In this study, we describe two parallel, yet distinct, in vivo approaches for accelerated discovery of antibodies targeting the SARS-CoV-2 spike protein. Working with human transgenic Alloy-GK mice, we detail a single B-cell discovery workflow to directly interrogate antibodies secreted from plasma cells for binding specificity and ACE2 receptor blocking activity. Additionally, we describe a concurrent accelerated hybridoma-based workflow utilizing a DiversimAb mouse model for increased diversity. The panel of antibodies isolated from both workflows revealed binding to distinct epitopes with both blocking and non-blocking profiles. Sequence analysis of the resulting lead candidates uncovered additional diversity with the opportunity for straightforward engineering and affinity maturation. By combining in vivo models with advanced integration of screening and selection platforms, lead antibody candidates can be sequenced and fully characterized within one to three months.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Tracey E Mullen",
+        "author_inst": "Abveris Inc."
+      },
+      {
+        "author_name": "Rashed Abdullah",
+        "author_inst": "Abveris Inc."
+      },
+      {
+        "author_name": "Jacqueline Boucher",
+        "author_inst": "Abveris Inc."
+      },
+      {
+        "author_name": "Anna Susi Brousseau",
+        "author_inst": "Abveris Inc."
+      },
+      {
+        "author_name": "Narayan K Dasuri",
+        "author_inst": "Abveris Inc."
+      },
+      {
+        "author_name": "Noah T Ditto",
+        "author_inst": "Carterra"
+      },
+      {
+        "author_name": "Andrew M Doucette",
+        "author_inst": "Abveris Inc."
+      },
+      {
+        "author_name": "Chloe Emery",
+        "author_inst": "Abveris Inc."
+      },
+      {
+        "author_name": "Justin Gabriel",
+        "author_inst": "Abveris Inc."
+      },
+      {
+        "author_name": "Brendan Greamo",
+        "author_inst": "Abveris Inc."
+      },
+      {
+        "author_name": "Ketan S Patil",
+        "author_inst": "Abveris Inc."
+      },
+      {
+        "author_name": "Kelly Rothenberger",
+        "author_inst": "Abveris Inc."
+      },
+      {
+        "author_name": "Justin Stolte",
+        "author_inst": "Abveris Inc."
+      },
+      {
+        "author_name": "Colby A Souders",
+        "author_inst": "Abveris Inc."
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2021.05.31.446386",
     "rel_title": "Spike mutation T403R allows bat coronavirus RaTG13 to use human ACE2",
@@ -727290,33 +725864,6 @@
     "type": "confirmatory results",
     "category": "biophysics"
   },
-  {
-    "rel_doi": "10.1101/2021.05.28.446250",
-    "rel_title": "Computational genomic analysis of the lung tissue microenvironment in COVID-19 patients",
-    "rel_date": "2021-05-30",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.28.446250",
-    "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 virus has affected over 170 million people, and caused over 3.5 million deaths throughout the world as of May 2021. Although over 150 million people around the world have recovered from this disease, the long term effects of the disease are still under study. A year after the start of the pandemic, data from COVID-19 recovered patients shows multiple organs affected with a broad spectrum of manifestations. Long term effects of SARS-CoV-2 infection includes fatigue, chest pain, cellular damage, and robust innate immune response with inflammatory cytokine production. More clinical studies and clinical trials are needed to not only document, but also to understand and determine the factors that predispose certain people to the long term side effects of his infection.\n\nIn this manuscript, our goal was to explore the multidimensional landscape of infected lung tissue microenvironment to better understand complex interactions between SARS-CoV-2 viral infection, immune response and the lungs microbiome of COVID-19 patients. Each sample was analyzed with several machine learning tools allowing simultaneous detection and quantification of viral RNA amount at genome and gene level; human gene expression and fractions of major types of immune cells, as well as metagenomic analysis of bacterial and viral abundance. To contrast and compare specific viral response to SARS-COV-2 we have analyzed deep sequencing data from additional cohort of patients infected with NL63 strain of corona virus.\n\nOur correlation analysis of three types of measurements in patients i.e. fraction of viral RNA (at genome and gene level), Human RNA (transcripts and gene level) and bacterial RNA (metagenomic analysis), showed significant correlation between viral load as well as level of specific viral gene expression with the fractions of immune cells present in lung lavage as well as with abundance of major fractions of lung microbiome in COVID-19 patients.\n\nOur exploratory study has provided novel insights into complex regulatory signaling interactions and correlative patterns between the viral infection, inhibition of innate and adaptive immune response as well as microbiome landscape of the lung tissue. These initial findings could provide better understanding of the diverse dynamics of immune response and the side effects of the SARS-CoV-2 infection.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Krithika Bhuvaneshwar",
-        "author_inst": "Georgetown University"
-      },
-      {
-        "author_name": "Subha Madhavan",
-        "author_inst": "GEORGETOWN UNIVERSITY"
-      },
-      {
-        "author_name": "Yuriy Gusev",
-        "author_inst": "Georgetown University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "genomics"
-  },
   {
     "rel_doi": "10.1101/2021.05.28.446065",
     "rel_title": "Human genome integration of SARS-CoV-2 contradicted by long-read sequencing",
@@ -727583,6 +726130,105 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.05.26.21257834",
+    "rel_title": "Development and external validation of a diagnostic multivariable prediction model for a prompt identification of cases at high risk for SARS-COV-2 infection among patients admitted to the emergency department",
+    "rel_date": "2021-05-29",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.26.21257834",
+    "rel_abs": "BackgroundAn urgent need exists for an early detection of cases with a high-risk of SARS-CoV-2 infection, particularly in high-flow and -risk settings, such as emergency departments (EDs). The aim of this work is to develop and validate a predictive model for the evaluation of SARS-CoV-2 infection risk, with the rationale of using this tool to manage ED patients.\n\nMethodsA retrospective study was performed by cross-sectionally reviewing the electronical case records of patients admitted to Niguarda Hospital or referred to its ED in the period 15 March to 24 April 2020.\n\nDerivation sample was composed of non-random inpatients hospitalized on 24 April and admitted before 22 April 2020. Validation sample was composed of consecutive patients who visited the ED between 15 and 25 March 2020. The association between the dichotomic outcome and each predictor was explored by univariate analysis with logistic regression models.\n\nResultsA total of 113 patients in the derivation sample and 419 in the validation sample were analyzed. History of fever, elder age and low oxygen saturation showed to be significant predictors of SARS-CoV-2 infection. The neutrophil count improves the discriminative ability of the model, even if its calibration and usefulness in terms of diagnosis is unclear.\n\nConclusionThe discriminatory ability of the identified models makes the overall performance suboptimal; their implementation to calculate the individual risk of infection should not be used without additional investigations. However, they could be useful to evaluate the spatial allocation of patients while awaiting the result of the nasopharyngeal swab.\n\nKey Messages boxO_ST_ABSWhat is already known on this topicC_ST_ABS1 year after the onset of the coronavirus disease 2019 (COVID-19) pandemic, the trend of its spread has not shown a substantial global reduction. An urgent need exists for efficient early detection of cases with a high risk of SARS-CoV-2 infection and a number of diagnostic prediction models have been developed, but a few models were externally validated in high-flow and -risk settings, such as emergency departments (EDs).\n\nWhat this study addsThis study develops and validate predictive models for the evaluation of SARS-CoV-2 infection risk, with the rationale of using these tools to promptly manage patients who are afferent to the ED, allocating them accordingly to the risk of infection while awaiting swab result. History of fever, older age and low oxygen saturation showed to be significant predictors of the presence of SARS-CoV-2 infection. The use of laboratory findings, such as neutrophil count, showed to improve the discriminative ability of the model, even if its calibration and usefulness in terms of diagnosis is unclear.",
+    "rel_num_authors": 21,
+    "rel_authors": [
+      {
+        "author_name": "Nicola Ughi",
+        "author_inst": "ASST Grande Ospedale Metropolitano Niguarda"
+      },
+      {
+        "author_name": "Antonella ADINOLFI",
+        "author_inst": "ASST Grande Ospedale Metropolitano Niguarda"
+      },
+      {
+        "author_name": "Michel CHEVALLARD",
+        "author_inst": "ASST Grande Ospedale Metropolitano Niguarda"
+      },
+      {
+        "author_name": "Laura BELLOLI",
+        "author_inst": "ASST Grande Ospedale Metropolitano Niguarda"
+      },
+      {
+        "author_name": "Michele SENATORE",
+        "author_inst": "ASST Grande Ospedale Metropolitano Niguarda"
+      },
+      {
+        "author_name": "Alessandro TOSCANO",
+        "author_inst": "ASST Grande Ospedale Metropolitano Niguarda"
+      },
+      {
+        "author_name": "Andrea BELLONE",
+        "author_inst": "ASST Grande Ospedale Metropolitano Niguarda"
+      },
+      {
+        "author_name": "Cristina GIANNATTASIO",
+        "author_inst": "ASST Grande Ospedale Metropolitano Niguarda"
+      },
+      {
+        "author_name": "Paolo TARSIA",
+        "author_inst": "ASST Grande Ospedale Metropolitano Niguarda"
+      },
+      {
+        "author_name": "Massimo Puoti",
+        "author_inst": "ASST Grande Ospedale Metropolitano Niguarda"
+      },
+      {
+        "author_name": "Francesco SCAGLIONE",
+        "author_inst": "ASST Grande Ospedale Metropolitano Niguarda"
+      },
+      {
+        "author_name": "Fabrizio COLOMBO",
+        "author_inst": "ASST Grande Ospedale Metropolitano Niguarda"
+      },
+      {
+        "author_name": "Michaela BERTUZZI",
+        "author_inst": "ASST Grande Ospedale Metropolitano Niguarda"
+      },
+      {
+        "author_name": "Giuseppe BETTONI",
+        "author_inst": "ASST Grande Ospedale Metropolitano Niguarda"
+      },
+      {
+        "author_name": "Davide FERRAZZI",
+        "author_inst": "ASST Grande Ospedale Metropolitano Niguarda"
+      },
+      {
+        "author_name": "Alessandro MALOBERTI",
+        "author_inst": "ASST Grande Ospedale Metropolitano Niguarda"
+      },
+      {
+        "author_name": "Armanda DICUONZO",
+        "author_inst": "ASST Grande Ospedale Metropolitano Niguarda"
+      },
+      {
+        "author_name": "Francesca DEL GAUDIO",
+        "author_inst": "ASST Grande Ospedale Metropolitano Niguarda"
+      },
+      {
+        "author_name": "Claudio ROSSETTI",
+        "author_inst": "ASST Grande Ospedale Metropolitano Niguarda"
+      },
+      {
+        "author_name": "Oscar Massimiliano EPIS",
+        "author_inst": "ASST Grande Ospedale Metropolitano Niguarda"
+      },
+      {
+        "author_name": "- Niguarda COVID group",
+        "author_inst": ""
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "emergency medicine"
+  },
   {
     "rel_doi": "10.1101/2021.05.26.21257835",
     "rel_title": "Inferring SARS-CoV-2 variant within-host kinetics",
@@ -728948,49 +727594,6 @@
     "type": "new results",
     "category": "biophysics"
   },
-  {
-    "rel_doi": "10.1101/2021.05.28.446204",
-    "rel_title": "The N-terminal and central domains of CoV-2 nsp1 play key functional roles in suppression of cellular gene expression and preservation of viral gene expression",
-    "rel_date": "2021-05-28",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.28.446204",
-    "rel_abs": "Nonstructural protein 1 (nsp1) is the first viral protein synthesized during coronavirus (CoV) infection and is a key virulence factor that dampens the innate immune response. It restricts cellular gene expression through a combination of inhibiting translation by blocking the mRNA entry channel of the 40S ribosomal subunit and by promoting mRNA degradation. We performed a detailed structure-guided mutational analysis of CoV-2 nsp1 coupled with in vitro and cell-based functional assays, revealing insight into how it coordinates these activities against host but not viral mRNA. We found that residues in the N-terminal and central regions of nsp1 not involved in docking into the 40S mRNA entry channel nonetheless stabilize its association with the ribosome and mRNA, thereby enhancing its restriction of host gene expression. These residues are also critical for the ability of mRNA containing the CoV-2 leader sequence to escape translational repression. Notably, we identify CoV-2 nsp1 mutants that gain the ability to repress translation of viral leader-containing transcripts. These data support a model in which viral mRNA binding functionally alters the association of nsp1 with the ribosome, which has implications for drug targeting and understanding how engineered or emerging mutations in CoV-2 nsp1 could attenuate the virus.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Aaron Stephen Mendez",
-        "author_inst": "University of California, Berkeley"
-      },
-      {
-        "author_name": "Michael Ly",
-        "author_inst": "University of California, Berkeley"
-      },
-      {
-        "author_name": "Ang\u00e9lica M. Gonz\u00e1lez-S\u00e1nchez",
-        "author_inst": "University of California, Berkeley"
-      },
-      {
-        "author_name": "Ella Hartenian",
-        "author_inst": "University of California, Berkeley"
-      },
-      {
-        "author_name": "Nicholas Ingolia",
-        "author_inst": "University of California, Berkeley"
-      },
-      {
-        "author_name": "Jamie H Cate",
-        "author_inst": "University of California, Berkeley"
-      },
-      {
-        "author_name": "Britt Glaunsinger",
-        "author_inst": "University of California Berkeley"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "molecular biology"
-  },
   {
     "rel_doi": "10.1101/2021.05.28.446155",
     "rel_title": "Digital PCR to quantify ChAdOx1 nCoV-19 copies in blood and tissues",
@@ -729212,6 +727815,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.05.28.21258006",
+    "rel_title": "Fear, Anxiety, Stress, and Depression of novel coronavirus (COVID-19) pandemic among patients and their healthcare workers",
+    "rel_date": "2021-05-28",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.28.21258006",
+    "rel_abs": "BackgroundDisease pandemics are known to cause psychological distress. The ensuing mental health issues are not only restricted to the patients and their relatives/friends but affect the healthcare workers (HCWs) as well. Our study aims to assess these psychological trends during the COVID-19 pandemic between the two most affected population groups, that is, patients and frontline healthcare workers.\n\nMethodsA survey questionnaire including scales to assess fear, anxiety, stress, depression - PSS 10, and DASS 21 was distributed and sent to all COVID-19 suspected/confirmed individuals and healthcare workers at a tertiary care center along with a second visit after 14 days of answering the first questionnaire and this continued as follow up. Data were analyzed with the SPSS Version 23 using various tests of significance.\n\nResultsIn the community, COVID-19 patients in the age group 41-50 with respiratory tract symptoms and those who were home isolated/quarantined experienced a greater tendency of mental health problems. Healthcare workers posted in COVID-19 designated areas of the hospital displayed higher levels of stress, anxiety, and depression.\n\nConclusionThe high degree of uncertainty associated with novel pathogens has a profound effect on the psychological state of suspected/confirmed cases as well as healthcare workers. Within the community, individuals suspected of having COVID-19 display a significant mental health burden, while HCWs also experience an unprecedented amount of stress during such enduring situations.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSWhat is the psychological impact among patients and their healthcare workers during the COVID-19 pandemic?\n\nFindingsIn this observational study based on PSS 10 and DASS 21 questionnaire that included 156 patients and 226 health care workers, the patients in the age group 41-50 with respiratory tract symptoms and those who were home isolated/quarantined experienced a greater tendency of mental health problems. Similar burden was observed among health care workers.\n\nMeaningIn a COVID-19 pandemic both population groups displayed higher levels of fear, anxiety, stress, and depression.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Ashwin Parchani",
+        "author_inst": "AIIMS Rishikesh"
+      },
+      {
+        "author_name": "K Vidhya",
+        "author_inst": "AIIMS Rishikesh"
+      },
+      {
+        "author_name": "Prasan Kumar Panda",
+        "author_inst": "AIIMS Rishikesh"
+      },
+      {
+        "author_name": "Vikram Singh Rawat",
+        "author_inst": "AIIMS Rishikesh"
+      },
+      {
+        "author_name": "Yogesh Arvind Bahurupi",
+        "author_inst": "AIIMS Rishikesh"
+      },
+      {
+        "author_name": "Deepjyoti Kalita",
+        "author_inst": "AIIMS Rishikesh"
+      },
+      {
+        "author_name": "Harsh Kumar",
+        "author_inst": "AIIMS Rishikesh"
+      },
+      {
+        "author_name": "Naveen Dr",
+        "author_inst": "AIIMS Rishikesh"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.05.28.21257954",
     "rel_title": "Age- and gender-dependent differences in attitudes towards COVID-19 vaccination and underlying psychological processes",
@@ -730533,181 +729183,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.05.24.21257632",
-    "rel_title": "High-resolution within-sewer SARS-CoV-2 surveillance facilitates informed intervention",
-    "rel_date": "2021-05-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.24.21257632",
-    "rel_abs": "To assist in the COVID-19 public health guidance on a college campus, daily composite wastewater samples were withdrawn at 20 manhole locations across the University of Colorado Boulder campus. Low-cost autosamplers were fabricated in-house to enable an economical approach to this distributed study. These sample stations operated from August 25th until November 23rd during the fall 2020 semester, with 1,512 samples collected. The concentration of SARS-CoV-2 in each sample was quantified through two comparative reverse transcription quantitative polymerase chain reactions (RT-qPCRs). These methods were distinct in the utilization of technical replicates and normalization to an endogenous control. (1) Higher temporal resolution compensates for supply chain or other constraints that prevent technical or biological replicates. (2) The endogenous control normalized data agreed with the raw concentration data, minimizing the utility of normalization. The raw wastewater concentration values reflected SARS-CoV-2 prevalence on campus as detected by clinical services. Overall, combining the low-cost composite sampler with a method that quantifies the SARS-CoV-2 signal within six hours enabled actionable and time-responsive data delivered to key stakeholders. With daily reporting of the findings, wastewater surveillance assisted in decision making during critical phases of the pandemic on campus, from detecting individual cases within populations ranging from 109 to 2,048 individuals to monitoring the success of on-campus interventions.\n\nSynopsisTracking SARS-CoV-2 in on-campus wastewater informs and monitors public health decisions and actions.\n\nTOC/Abstract Art\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=86 SRC=\"FIGDIR/small/21257632v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (25K):\norg.highwire.dtl.DTLVardef@628b4corg.highwire.dtl.DTLVardef@1a74157org.highwire.dtl.DTLVardef@1b2f526org.highwire.dtl.DTLVardef@1fcbcb8_HPS_FORMAT_FIGEXP  M_FIG C_FIG",
-    "rel_num_authors": 40,
-    "rel_authors": [
-      {
-        "author_name": "Katelyn Reeves",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Jennifer N. Liebig",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Anontio Dimitri Feula",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Tassa Saldi",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Erika Lasda",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "William James Johnson",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Jacob Lilienfeld",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "John Robert Maggi",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Kevin Pulley",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Paul J. Wilkerson",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Breanna Real",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Gordon Zak",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Jack C. Davis",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Morgan R. Fink",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Patrick Gonzalez",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Cole R. Hager",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Christopher Ozeroff",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Kimgan L. Tat",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Michaela L. Alkire",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Claire E. Butler",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Elle Coe",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Jessica Darby",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Nicholas Freeman",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Heidi Heuer",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Jeffery R. Jones",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Madeline Karr",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Sara Key",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Kiersten Maxwell",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Lauren Nelson",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Emily Marie Saldana",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Lewis Salveson",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Rachel Shea",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Kate Tomlinson",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Jorge Vargas-Barriga",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Bailey Vigil",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Gloria Brisson",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Roy Parker",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Leslie A. Leinwand",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Kristen K. Bjorkman",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Cresten B. Mansfeldt",
-        "author_inst": "University of Colorado Boulder"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.05.25.21257716",
     "rel_title": "Behaviour of smokers and their influencers in the UK during COVID-19 pandemic",
@@ -731158,6 +729633,97 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.05.24.21257703",
+    "rel_title": "COVID-19 mass testing: harnessing the power of wastewater epidemiology",
+    "rel_date": "2021-05-26",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.24.21257703",
+    "rel_abs": "BackgroundCOVID-19 patients shed SARS-CoV-2 RNA in their faeces. We hypothesised that detection of SARS-CoV-2 RNA in wastewater treatment plant (WWTP) influent could be a valuable tool to assist in public health decision making. We aimed to rapidly develop and validate a scalable methodology for the detection of SARS-CoV-2 RNA in wastewater that could be implemented at a national level and to determine the relationship between the wastewater signal and COVID-19 cases in the community.\n\nMethodsWe developed a filtration-based methodology for the concentration of SARS-CoV-2 from WWTP influent and subsequent detection and quantification by RT-qPCR. This methodology was used to monitor 28 WWTPs across Scotland, serving 50% of the population. For each WWTP catchment area, we collected data describing COVID-19 cases and deaths. We quantified spatial and temporal relationships between SARS-CoV-2 RNA in wastewater and COVID-19 cases.\n\nFindingsDaily WWTP SARS-CoV-2 influent viral RNA load, calculated using daily influent flow rates, had the strongest correlation ({rho}>0.9) with COVID-19 cases within a catchment. As the incidence of COVID-19 cases within a community increased, a linear relationship emerged between cases and influent viral RNA load. There were significant differences between WWTPs in their capacity to predict case numbers based on influent viral RNA load, with the limit of detection ranging from twenty-five cases for larger plants to a single case in smaller plants.\n\nInterpretationThe levels of SARS-CoV-2 RNA in WWTP influent provide a cost-effective and unbiased measure of COVID-19 incidence within a community, indicating that national scale wastewater-based epidemiology can play a role in COVID-19 surveillance. In Scotland, wastewater testing has been expanded to cover 75% of the population, with sub-catchment sampling being used to focus surge testing. SARS-CoV-2 variant detection, assessment of vaccination on community transmission and surveillance for other infectious diseases represent promising future applications.\n\nFundingThis study was funded by project grants from the Scottish Government via the Centre of Expertise for Waters (CD2019/06) and The Natural Environment Research Councils COVID-19 Rapid Response grants (NE/V010441/1). The Roslin Institute receives strategic funding from the Biotechnology and Biological Sciences Research Council (BB/P013740/1, BBS/E/D/20002173). Sample collection and supplementary analysis was funded and undertaken by Scottish Water and the majority of the sample analysis was funded and undertaken by the Scottish Environment Protection Agency.",
+    "rel_num_authors": 19,
+    "rel_authors": [
+      {
+        "author_name": "Stephen F Fitzgerald",
+        "author_inst": "The Roslin Institute, UNiversity of Edinburgh"
+      },
+      {
+        "author_name": "Gianluigi Rossi",
+        "author_inst": "The Roslin Institute, University of Edinburgh"
+      },
+      {
+        "author_name": "Alison S Low",
+        "author_inst": "The Roslin Institute, University of Edinburgh"
+      },
+      {
+        "author_name": "Sean P MacAteer",
+        "author_inst": "The Roslin, Institute, University of Edinburgh"
+      },
+      {
+        "author_name": "Brian O'Keefe",
+        "author_inst": "Scottish Environment Protection Agency"
+      },
+      {
+        "author_name": "David Findlay",
+        "author_inst": "Scottish Environment Protection Agency"
+      },
+      {
+        "author_name": "Greame J Cameron",
+        "author_inst": "Scottish Environment Protection Agency"
+      },
+      {
+        "author_name": "Peter Pollard",
+        "author_inst": "Scottish Environment Protection Agency"
+      },
+      {
+        "author_name": "Peter T. R. Singleton",
+        "author_inst": "Scottish Environment Protection Agency"
+      },
+      {
+        "author_name": "George Ponton",
+        "author_inst": "Scottish Water"
+      },
+      {
+        "author_name": "Andrew C Singer",
+        "author_inst": "UK Centre for Ecology & Hydrology"
+      },
+      {
+        "author_name": "Kata Farkas",
+        "author_inst": "School of Natural Sciences, Bangor University"
+      },
+      {
+        "author_name": "David L Jones",
+        "author_inst": "School of Natural Sciences, Bangor University"
+      },
+      {
+        "author_name": "Davd W. Graham",
+        "author_inst": "School of Engineering, Newcastle University"
+      },
+      {
+        "author_name": "Marcos Quintela-Baluja",
+        "author_inst": "School of Engineering, Newcastle University"
+      },
+      {
+        "author_name": "Christine Tait-Burkard",
+        "author_inst": "The Roslin, Institute, University of Edinburgh"
+      },
+      {
+        "author_name": "David L Gally",
+        "author_inst": "The Roslin, Institute, University of Edinburgh"
+      },
+      {
+        "author_name": "Rowland Raymond Kao",
+        "author_inst": "The Roslin, Institute, University of Edinburgh"
+      },
+      {
+        "author_name": "Alexander Corbishley",
+        "author_inst": "The Roslin, Institute, University of Edinburgh"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.05.24.21257738",
     "rel_title": "Post-vaccination SARS-CoV-2 infection: risk factors and illness profile in a prospective, observational community-based case-control study",
@@ -732575,25 +731141,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.05.24.21257594",
-    "rel_title": "A comparative study of SIR Model, Linear Regression, Logistic Function and ARIMA Model for forecasting COVID-19 cases",
-    "rel_date": "2021-05-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.24.21257594",
-    "rel_abs": "Starting February 2020, COVID-19 was confirmed in 11,946 people worldwide, with a mortality rate of almost 2%. A significant number of epidemic diseases including human Coronavirus display patterns. In this study with the benefit of data analytic, we develop regression models and a Susceptible-Infected-Recovered (SIR) model for the contagion to compare the performance of models to predict number of cases. first, we implement a good understanding of data and perform Exploratory Data Analysis (EDA). Then, we derive the parameters of the model from the available data corresponding to the top 4 regions based on the history of infections and the most infected people as of the end of August 2020. Then models are compared and further research are introduced.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Saina Abolmaali",
-        "author_inst": "Auburn University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.05.24.21257365",
     "rel_title": "Monitoring of SARS-CoV-2 B.1.1.7 variant early-phase spreading in South-Moravian Region in the Czech Republic and evaluation of its pathogenicity",
@@ -732920,6 +731467,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.05.21.21257631",
+    "rel_title": "Detecting COVID-19 Related Pneumonia on CT Scans using Hyperdimensional Computing",
+    "rel_date": "2021-05-25",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.21.21257631",
+    "rel_abs": "Pneumonia is a common complication associated with COVID-19 infections. Unlike common versions of pneumonia spread quickly through large lung regions, COVID-19 related pneumonia starts in small localized pockets before spreading over the course of several days. This makes the infection more resilient and with a high probability of developing acute respiratory distress syndrome. Because of the peculiar spread pattern, the use of pulmonary computerized tomography (CT) scans was key in identifying COVID-19 infections. Identifying uncommon pulmonary diseases could be a strong line of defense in early detection of new respiratory infection-causing viruses. In this paper we describe a classification algorithm based on hyperdimensional computing for the detection of COVID-19 pneumonia in CT scans. We test our algorithm using three different datasets. The highest reported accuracy is 95.2% with an F1 score of 0.90, and all three models had a precision of 1 (0 false positives).",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Neftali D Watkinson",
+        "author_inst": "University of California, Irvine"
+      },
+      {
+        "author_name": "Victor Joe",
+        "author_inst": "UCI Medical Center"
+      },
+      {
+        "author_name": "Tony Givargis",
+        "author_inst": "University of California, Irvine"
+      },
+      {
+        "author_name": "Alexandru Nicolau",
+        "author_inst": "University of California, Irvine"
+      },
+      {
+        "author_name": "Alexander Veidenbaum",
+        "author_inst": "University of California, Irvine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health informatics"
+  },
   {
     "rel_doi": "10.1101/2021.05.23.21257692",
     "rel_title": "COVID-19 gender difference pattern in Iranian population, compared to the global pattern; a systematic review and meta-analysis",
@@ -734357,125 +732939,6 @@
     "type": "new results",
     "category": "pathology"
   },
-  {
-    "rel_doi": "10.1101/2021.05.25.445649",
-    "rel_title": "Divergent early antibody responses define COVID-19 disease trajectories",
-    "rel_date": "2021-05-25",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.25.445649",
-    "rel_abs": "A damaging inflammatory response is strongly implicated in the pathogenesis of severe COVID-19 but mechanisms contributing to this response are unclear. In two prospective cohorts, early non-neutralizing, afucosylated, anti-SARS-CoV-2 IgG predicted progression from mild, to more severe COVID-19. In contrast to the antibody structures that predicted disease progression, antibodies that were elicited by mRNA SARS-CoV-2 vaccines were low in Fc afucosylation and enriched in sialylation, both modifications that reduce the inflammatory potential of IgG. To study the biology afucosylated IgG immune complexes, we developed an in vivo model which revealed that human IgG-Fc{gamma}R interactions can regulate inflammation in the lung. Afucosylated IgG immune complexes induced inflammatory cytokine production and robust infiltration of the lung by immune cells. By contrast, vaccine elicited IgG did not promote an inflammatory lung response. Here, we show that IgG-Fc{gamma}R interactions can regulate inflammation in the lung and define distinct lung activities associated with the IgG that predict severe COVID-19 and protection against SARS-CoV-2.\n\nOne Sentence SummaryDivergent early antibody responses predict COVID-19 disease trajectory and mRNA vaccine response and are functionally distinct in vivo.",
-    "rel_num_authors": 26,
-    "rel_authors": [
-      {
-        "author_name": "Saborni Chakraborty",
-        "author_inst": "Stanford University"
-      },
-      {
-        "author_name": "Joseph C. Gonzalez",
-        "author_inst": "Stanford University"
-      },
-      {
-        "author_name": "Benjamin L. Sievers",
-        "author_inst": "J. Craig Venter Institute"
-      },
-      {
-        "author_name": "Vamsee Mallajosyula",
-        "author_inst": "Stanford University"
-      },
-      {
-        "author_name": "Megha Dubey",
-        "author_inst": "Stanford University"
-      },
-      {
-        "author_name": "Yik-Ling Bowie Cheng",
-        "author_inst": "Stanford University"
-      },
-      {
-        "author_name": "Kim Quyen Thi Tran",
-        "author_inst": "Stanford University"
-      },
-      {
-        "author_name": "Srijoni Chakraborty",
-        "author_inst": "San Jose State University"
-      },
-      {
-        "author_name": "Arianna Cassidy",
-        "author_inst": "University of California, San Francisco"
-      },
-      {
-        "author_name": "Steven T. Chen",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Aanika Sinnott",
-        "author_inst": "J. Craig Venter Institute"
-      },
-      {
-        "author_name": "Terri Gelbart",
-        "author_inst": "J. Craig Venter Institute"
-      },
-      {
-        "author_name": "Yarden Golan",
-        "author_inst": "University of California, San Francisco"
-      },
-      {
-        "author_name": "Mary Prahl",
-        "author_inst": "University of California, San Francisco"
-      },
-      {
-        "author_name": "Upinder Singh",
-        "author_inst": "Stanford University"
-      },
-      {
-        "author_name": "Seunghee Kim-Schulze",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Robert Sherwood",
-        "author_inst": "Cornell University"
-      },
-      {
-        "author_name": "Sheng Zhang",
-        "author_inst": "Cornell University"
-      },
-      {
-        "author_name": "Thomas U. Marron",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Sacha Gnjatic",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Stephanie L. Gaw",
-        "author_inst": "University of California, San Francisco"
-      },
-      {
-        "author_name": "Kari C. Nadeau",
-        "author_inst": "Stanford University"
-      },
-      {
-        "author_name": "Miriam Merad",
-        "author_inst": "Icahn School of medicine"
-      },
-      {
-        "author_name": "Prasanna Jagannathan",
-        "author_inst": "Stanford University"
-      },
-      {
-        "author_name": "Gene S Tan",
-        "author_inst": "J. Craig Venter Institute"
-      },
-      {
-        "author_name": "Taia T. Wang",
-        "author_inst": "Stanford University School of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2021.05.24.445534",
     "rel_title": "SARS-CoV-2 convergent evolution as a guide to explore adaptive advantage",
@@ -734790,6 +733253,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.05.22.21257649",
+    "rel_title": "The COVID in the Context of Pregnancy, Infancy and Parenting (CoCoPIP) Study: protocol for a longitudinal study of parental mental health, social interactions, physical growth, and cognitive development of infants during the pandemic.",
+    "rel_date": "2021-05-24",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.22.21257649",
+    "rel_abs": "IntroductionWhile the secondary impact of the COVID pandemic on the psychological wellbeing of pregnant women and parents has become apparent over the past year, the impact of these changes on early social interactions, physical growth and cognitive development of their infants is unknown, as is the way in which a range of COVID related changes have mediated this impact. This study (CoCoPIP) will investigate: i) how parents experiences of the social, medical, and financial changes during the pandemic have impacted pre and postnatal parental mental health and parent-infant social interaction; and (ii) the extent to which these COVID-related changes in parental pre and postnatal mental health and social interaction are associated with fetal and infant development.\n\nMethods and analysisThe CoCoPIP study is a national online survey initiated in July 2020. This ongoing study (n = 1700 families currently enrolled as of 6th May 2021) involves both quantitative and qualitative data being collected across pregnancy and infancy. It is designed to identify the longitudinal impact of the pandemic from pregnancy to two years of age, with the aim of identifying if stress-associated moderators (i.e., loss of income, COVID-19 illness, access to ante/postnatal support) impact parental mental health, and in turn, infant development. In addition, we aim to document individual differences in social and cognitive development in toddlers who were born during restrictions intended to mitigate COVID-19 spread (e.g., social distancing, national lockdowns).\n\nEthics and disseminationEthical approval was given by the University of Cambridge, Psychology Research Ethics Committee (PREC) (PRE.2020.077). Findings will be made available via community engagement, public forums (e.g., social media,) and to national (e.g., NHS England) and local (Cambridge Universities Hospitals NHS Foundation Trust) healthcare partners. Results will be submitted for publication in peer-reviews journals.\n\nStrengths and Limitations of this study- This is a new cohort of families being followed from prenatal to postnatal (up to 18 months) during the COVID-19 pandemic.\n- The study involves the collection of quantifiable data to identify the short- and long-term influences of the pandemic on key aspects of infant development.\n- The study also has a range of open-ended questions for qualitative analysis aimed at exploring familial experiences in more detail.\n- The data is being collected online and is therefore limited to self- and parent-report measures, with no direct assessment of child development and parental mental health.\n- Although the sample of families being recruited are diverse in their indices of multiple deprivation (IMD) and geographic location, they may not be fully representative of the wider population.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Ezra Aydin",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Staci M Weiss",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Kevin A Glasgow",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Jane Barlow",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Topun Austin",
+        "author_inst": "Cambridge University Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "Mark H Johnson",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Sarah Lloyd-Fox",
+        "author_inst": "University of Cambridge"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health policy"
+  },
   {
     "rel_doi": "10.1101/2021.05.23.445371",
     "rel_title": "Unsupervised explainable AI for the collective analysis of a massive number of genome sequences: various examples from the small genome of pandemic SARS-CoV-2 to the human genome",
@@ -736295,73 +734801,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.05.24.21257402",
-    "rel_title": "Retrospective screening for SARS-CoV-2 among 5,800 hospitalizations related to influenza-like illness during the 2018-19 pre-pandemic and 2019-2020 pandemic influenza seasons in the VAHNSI network, Spain.",
-    "rel_date": "2021-05-24",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.24.21257402",
-    "rel_abs": "On March 9 2020 the WHO Global Influenza Program (GIP) asked participant sites on the Global Influenza Hospital Surveillance Network (GIHSN) to contribute to data collection concerning severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We re-analysed 5,833 viral RNA archived samples collected prospectively from hospital admissions for influenza-like illness (ILI) in the Valencia Region of Spain by the VAHNSI network (4 hospitals, catchment area population 1,118,732) during the prepandemic 2018/2019 (n=4,010) and pandemic 2019/2020 (n=1,823) influenza seasons, for the presence of SARS-CoV-2. We did not find evidence for community-acquired SARS-CoV-2 infection in hospital admissions for ILI in our region before early March 2020.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Ainara Mira Iglesias",
-        "author_inst": "FISABIO-Public Health"
-      },
-      {
-        "author_name": "Beatriz Mengual-Chulia",
-        "author_inst": "FISABIO- Public Health"
-      },
-      {
-        "author_name": "Laura Cano-Perez",
-        "author_inst": "FISABIO-Public Health"
-      },
-      {
-        "author_name": "Javier Garcia Rubio",
-        "author_inst": "FISABIO-Public Health"
-      },
-      {
-        "author_name": "Miguel Tortajada-Girbes",
-        "author_inst": "Hospital Doctor Peset, Valencia, Spain"
-      },
-      {
-        "author_name": "Mario Carballido-Fernandez",
-        "author_inst": "Hospital General Universitario de Castellon, Castellon, Spain and Universidad CEU Cardenal Herrera, Castellon, Spain"
-      },
-      {
-        "author_name": "Juan Mollar-Maseres",
-        "author_inst": "Hospital Universitario y Politecnico La Fe, Valencia, Spain"
-      },
-      {
-        "author_name": "German Schwarz-Chavarri",
-        "author_inst": "Hospital General de Alicante, Alicante, Spain"
-      },
-      {
-        "author_name": "Sandra Garcia Esteban",
-        "author_inst": "FISABIO-Public Health"
-      },
-      {
-        "author_name": "Joan Puig Barbera",
-        "author_inst": "FISABIO-Public Health"
-      },
-      {
-        "author_name": "Javier Diez-Domingo",
-        "author_inst": "FISABIO-Public Health"
-      },
-      {
-        "author_name": "F. Xavier Lopez-Labrador",
-        "author_inst": "FISABIO-Public Health and CIBERESP"
-      },
-      {
-        "author_name": "- Valencia Hospital Network for the Study of Influenza and Respiratory Viruses Disease",
-        "author_inst": ""
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.05.22.21256870",
     "rel_title": "Smartwatch Facilitated Remote Health Care for Patients Undergoing Transcatheter Aortic Valve Replacement Amid COVID-19 Pandemic",
@@ -736760,6 +735199,105 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "genetic and genomic medicine"
   },
+  {
+    "rel_doi": "10.1101/2021.05.17.21257134",
+    "rel_title": "Heterologous vaccination strategy for containing COVID-19 pandemic",
+    "rel_date": "2021-05-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.17.21257134",
+    "rel_abs": "An unequitable vaccine allocation and continuously emerging SARS-CoV-2 variants pose challenges to contain the pandemic, which underscores the need for licensing more vaccine candidates, increasing manufacturing capacity and implementing better immunization strategy. Here, we report data from a proof-of-concept investigation in two healthy individuals who received two doses of inactivated whole-virus COVID-19 vaccines, followed by a single heterologous boost vaccination after 7 months with an mRNA vaccine candidate (LPP-Spike-mRNA) developed by Stemirna Therapeutics. Following the boost, Spike-specific antibody (Ab), memory B cell and T cell responses were significantly increased. These findings indicate that a heterologous immunization strategy combining inactivated and mRNA vaccines can generate robust vaccine responses and therefore provide a rational and effective vaccination regimen.",
+    "rel_num_authors": 21,
+    "rel_authors": [
+      {
+        "author_name": "Ang Lin",
+        "author_inst": "Stemirna Therapeutics"
+      },
+      {
+        "author_name": "Jingjing Liu",
+        "author_inst": "National Institutes for Food and Drug Control (NIFDC), Beijing, China."
+      },
+      {
+        "author_name": "Xiaopin Ma",
+        "author_inst": "Stemirna Therapeutics"
+      },
+      {
+        "author_name": "Fanfan Zhao",
+        "author_inst": "Stemirna Therapeutics"
+      },
+      {
+        "author_name": "Bo Yu",
+        "author_inst": "Stemirna Therapeutics"
+      },
+      {
+        "author_name": "Jiaxin He",
+        "author_inst": "Stemirna Therapeutics"
+      },
+      {
+        "author_name": "Mingyun Shen",
+        "author_inst": "Stemirna Therapeutics"
+      },
+      {
+        "author_name": "Lei Huang",
+        "author_inst": "Stemirna Therapeutics"
+      },
+      {
+        "author_name": "Hongming Tang",
+        "author_inst": "Shanghai East Hospital, Tongji University"
+      },
+      {
+        "author_name": "Erpeng Jiang",
+        "author_inst": "Shanghai East Hospital, Tongji University"
+      },
+      {
+        "author_name": "Yue Wang",
+        "author_inst": "Shanghai East Hospital, Tongji University"
+      },
+      {
+        "author_name": "Pingfang Cui",
+        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences"
+      },
+      {
+        "author_name": "Yujiang Zhang",
+        "author_inst": "Stemirna Therapeutics"
+      },
+      {
+        "author_name": "Weiguo Yao",
+        "author_inst": "Stemirna Therapeutics"
+      },
+      {
+        "author_name": "Aihua Zhang",
+        "author_inst": "Stemirna Therapeutics"
+      },
+      {
+        "author_name": "Youchun Wang",
+        "author_inst": "Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC)"
+      },
+      {
+        "author_name": "Yuhua Li",
+        "author_inst": "National Institutes for Food and Drug Control (NIFDC), Beijing, China."
+      },
+      {
+        "author_name": "Weijin Huang",
+        "author_inst": "Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC)"
+      },
+      {
+        "author_name": "Qihan Li",
+        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences"
+      },
+      {
+        "author_name": "Zhongmin Liu",
+        "author_inst": "Shanghai East Hospital, Tongji University"
+      },
+      {
+        "author_name": "Hangwen Li",
+        "author_inst": "Stemirna Therapeutics; Shanghai East Hospital, Tongji University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.05.21.21257572",
     "rel_title": "Towards Internationally standardised humoral Immune Correlates of Protection from SARS CoV 2 infection and COVID-19 disease",
@@ -738365,37 +736903,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.05.19.21257217",
-    "rel_title": "Detection of SARS-CoV-2 in saliva using tailed amplicon sequencing",
-    "rel_date": "2021-05-21",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.19.21257217",
-    "rel_abs": "The most recent virus from the Coronaviridae family infecting humans, SARS-CoV-2, has resulted in a global pandemic. As part of the surveillance efforts, SARS-CoV-2 genomes are increasingly being made publicly available. Methods that include both short- and long-read sequencing have been used to elucidate SARS-CoV-2 genomes; however, many of these untargeted approaches may require deeper sequencing for greater genome coverage. For this reason, sequence capture or amplicon-based approaches for SARS-CoV-2 genome sequencing have been developed. The present study evaluated a modified sequence capture approach, namely, tailed amplicon sequencing, to determine SARS-CoV-2 near complete genome sequences from the saliva of infected individuals. Particularly, the suitability of saliva samples stored at room temperature using OMNIgene(R)*ORAL OME-505 was evaluated. The tailed amplicon sequencing approach poses the additional advantage of being a cost-effective method for library preparation. Different known SARS-CoV-2 variants were identified across the infected subjects, with an average of > 99.4% genome coverage. This methodology also enabled robust genomic surveillance using phylogenetic analyses. The present study supports the suitability of saliva stored at room temperature using collection devices for SARS-CoV-2 variant detection. Importantly, the present study supports the use of tailed amplicon sequencing approaches as an alternative, cost-effective method for SARS-CoV-2 detection in saliva for genomic surveillance.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Aaron Garoutte",
-        "author_inst": "Diversigen, Inc."
-      },
-      {
-        "author_name": "Tasha Marie Santiago-Rodriguez",
-        "author_inst": "Diversigen, Inc."
-      },
-      {
-        "author_name": "Heather L Fehling",
-        "author_inst": "Clinical Reference Laboratory, Inc"
-      },
-      {
-        "author_name": "Rafal Iwasiow",
-        "author_inst": "DNA Genotek"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health informatics"
-  },
   {
     "rel_doi": "10.1101/2021.05.19.21257467",
     "rel_title": "COVID-19 Mitigation Practices and COVID-19 Rates in Schools: Report on Data from Florida, New York and Massachusetts",
@@ -738810,6 +737317,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.05.19.21257470",
+    "rel_title": "RT-qPCR half reaction optimization for the detection of SARS-CoV-2",
+    "rel_date": "2021-05-21",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.19.21257470",
+    "rel_abs": "BACKGROUNDThe main laboratory test for the diagnosis of COVID-19 is the reverse transcription real-time polymerase chain reaction (RT-qPCR). However, the RT-qPCR is an expensive method due to the number of tests required.\n\nOBJECTIVESTo evaluate an alternative RT-qPCR approach for the detection of SARS-CoV-2 sing half of the total volume currently recommended by the US Centers for Disease Control and Prevention.\n\nMETHODSThe analytical limit of detection (LoD) and the reaction efficiency using half volumes of RT-qPCR assay were evaluated for both the N1 and N2 regions by using a synthetic control RNA. A panel of 76 SARS-CoV-2-positive and 26 SARS-CoV-2-negative clinical samples were evaluated to establish the clinical sensitivity and specificity.\n\nFINDINGSThe RT-qPCR assay efficiency was 105% for both the half and standard reactions considering the N2 target and 84% (standard) and 101% (half) for N1. The RT-qPCR half reaction LoD for N1 and N2 were 20 and 80 copies/{micro}L, respectively. Clinical sensitivity and specificity were 100%. The half reaction presented a decrease of up to 5.5 cycle thresholds when compared with the standard RT-qPCR.\n\nCONCLUSIONSThe use of RT-qPCR half reaction proved to be a feasible and economic strategy for detection of SARS-CoV-2 RNA.\n\nSponsorshipThis work was supported by FAPERGS (20/2551-0000265-9) and by Fundo de Incentivo a Pesquisa e Eventos do Hospital de Clinicas de Porto Alegre (FIPE/HCPA) (Project no. 2020-0163).",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Priscila Lamb Wink",
+        "author_inst": "Hospital de Clinicas de Porto Alegre"
+      },
+      {
+        "author_name": "Fabiana Volpato",
+        "author_inst": "Hospital de Clinicas de Porto Alegre"
+      },
+      {
+        "author_name": "Daiana Lima-Morales",
+        "author_inst": "Hospital de Clinicas de Porto Alegre"
+      },
+      {
+        "author_name": "Rodrigo Minuto Paiva",
+        "author_inst": "Hospital de Clinicas de Porto Alegre"
+      },
+      {
+        "author_name": "Julia Biz Willig",
+        "author_inst": "Hospital de Clinicas de Porto Alegre"
+      },
+      {
+        "author_name": "Hugo Bock",
+        "author_inst": "Hospital de Clinicas de Porto Alegre"
+      },
+      {
+        "author_name": "Fernanda de-Paris",
+        "author_inst": "Hospital de Clinicas de Porto Alegre"
+      },
+      {
+        "author_name": "Afonso Luis Barth",
+        "author_inst": "Hospital de Clinicas de Porto Alegre"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.05.19.21257485",
     "rel_title": "Dysbiosis and structural disruption of the respiratory microbiota in COVID-19 patients with severe and fatal outcomes",
@@ -740047,45 +738601,6 @@
     "type": "new results",
     "category": "biophysics"
   },
-  {
-    "rel_doi": "10.1101/2021.05.21.445118",
-    "rel_title": "Missense variants in human ACE2 modify binding to SARS-CoV-2 Spike",
-    "rel_date": "2021-05-21",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.21.445118",
-    "rel_abs": "SARS-CoV-2 infection begins with the interaction of the SARS-CoV-2 Spike (Spike) and human angiotensin-converting enzyme 2 (ACE2). To explore whether population variants in ACE2 might influence Spike binding and hence infection, we selected 10 ACE2 variants based on affinity predictions and prevalence in gnomAD and measured their affinities for Spike receptor binding domain through surface plasmon resonance (SPR). We discovered variants that enhance and reduce binding, including two variants with distinct population distributions that enhanced affinity for Spike. ACE2 p.Ser19Pro ({Delta}{Delta}G = {+/-} 0.59 0.08 kcal mol-1) is often seen in the gnomAD African cohort (AF = 0.003) whilst p.Lys26Arg ({Delta}{Delta}G = 0.26 0.09 kcal mol-1) is predominant in the Ashkenazi Jewish (AF = 0.01) and European non-Finnish (AF = 0.006) cohorts. Carriers of these alleles may be more susceptible to infection or severe disease and these variants may influence the global epidemiology of Covid-19. We also identified three rare ACE2 variants that strongly inhibited (p.Glu37Lys, {Delta}{Delta}G = -1.33 {+/-} 0.15 kcal mol-1 and p.Gly352Val, predicted {Delta}{Delta}G = -1.17 kcal mol-1) or abolished (p.Asp355Asn) Spike binding. These variants may confer resistance to infection. Finally, we calibrated the mCSM-PPI2 {Delta}{Delta}G prediction algorithm against our SPR data, give new predictions for all possible ACE2 missense variants at the Spike interface and estimate the overall burden of ACE2 variants on Covid-19 phenotypes.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Stuart A MacGowan",
-        "author_inst": "University of Dundee"
-      },
-      {
-        "author_name": "Michael I Barton",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Mikhail Kutuzov",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Omer Dushek",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Philip Anton van der Merwe",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Geoffrey J Barton",
-        "author_inst": "University of Dundee"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "genetics"
-  },
   {
     "rel_doi": "10.1101/2021.05.21.21256124",
     "rel_title": "Rapid identification of Sars-CoV-2 variants of concern using the portable peakPCR platform",
@@ -740436,6 +738951,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "occupational and environmental health"
   },
+  {
+    "rel_doi": "10.1101/2021.05.18.21257426",
+    "rel_title": "Modeling waning and boosting of COVID-19 in Canada with vaccination",
+    "rel_date": "2021-05-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.18.21257426",
+    "rel_abs": "SARS-CoV-2, the causative agent of COVID-19, has caused devastating health and economic impacts around the globe since its appearance in late 2019. The advent of effective vaccines leads to open questions on how best to vaccinate the population. To address such questions, we developed a model of COVID-19 infection by age that includes the waning and boosting of immunity against SARS-CoV-2 in the context of infection and vaccination. The model also accounts for changes to infectivity of the virus, such as public health mitigation protocols over time, increases in the transmissibility of variants of concern, changes in compliance to mask wearing and social distancing, and changes in testing rates. The model is employed to study public health mitigation and vaccination of the COVID-19 epidemic in Canada, including different vaccination programs (rollout by age), and delays between doses in a two-dose vaccine. We find that the decision to delay the second dose of vaccine is appropriate in the Canadian context. We also find that the benefits of a COVID-19 vaccination program in terms of reductions in infections is increased if vaccination of 15-19 year olds are included in the vaccine rollout.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Lauren Childs",
+        "author_inst": "Virginia Tech"
+      },
+      {
+        "author_name": "David W Dick",
+        "author_inst": "York University"
+      },
+      {
+        "author_name": "Zhilan Feng",
+        "author_inst": "Purdue University"
+      },
+      {
+        "author_name": "Jane M Heffernan",
+        "author_inst": "York University"
+      },
+      {
+        "author_name": "Jing Li",
+        "author_inst": "California State University"
+      },
+      {
+        "author_name": "Gergely R\u00f6st",
+        "author_inst": "University of Szeged"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.05.18.21257386",
     "rel_title": "FOCUS: Forecasting COVID-19 in the United States",
@@ -742145,57 +740699,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.05.18.21257372",
-    "rel_title": "Potential contributors to increased pulmonary embolism hospitalizations during the Covid-19 pandemic",
-    "rel_date": "2021-05-19",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.18.21257372",
-    "rel_abs": "BackgroundAfter the first Covid-19 infection wave, a constant increase of pulmonary embolism (PE) hospitalizations not linked with active PCR-confirmed Covid-19 has been observed but potential contributors to this observation are unclear. Therefore, we analyzed associations between changes in PE hospitalizations and (1) the incidence of non-Covid-19 pneumonia, (2) the use of computed tomography pulmonary angiography (CTPA), (3) volume depletion and (4) preceding Covid-19 infection numbers in Germany.\n\nMethodsClaims data of Helios hospitals in Germany were used and consecutive cases with a hospital admission between May 6 and December 15, 2020 (PE surplus period) were analyzed and compared to corresponding periods covering the same weeks in 2016-2019 (control period). We analyzed the number of PE cases in the target period with multivariable Poisson general linear mixed models (GLMM) including (a) cohorts of 2020 versus 2016- 2019, (b) the number of cases with pneumonia, (c) CTPA, and (d) volume depletion and adjusted for age and sex. In order to associate the daily number of PE cases in 2020 with the number of preceding SARS-CoV-2 infections in Germany, we calculated the average number of daily infections (divided by 10,000) occurring 14 up to 90 days with increasing window sizes before PE cases and modelled the data with Poisson regression.\n\nResultsThere were 2,404 PE hospitalizations between May 6 and December 15, 2020 as opposed to 2,112 - 2,236 (total 8,717) in the corresponding 2016 - 2019 control periods. (crude rate ratio [CRR] 1.10, 95% CI 1.05 - 1.15, P<0.01). Using multivariable Poisson GLMM adjusted for age, sex and volume depletion, PE cases were significantly associated with the number of cases with pneumonia (CRR 1.09, 95 % CI 1.07-1.10, P<0.01), and with CTPA (CRR 1.10, 95 % CI 1.09-1.10, P<0.01). The increase of PE cases in 2020 compared with the control period remained significant (CRR 1.07, 95 % CI 1.02-1.12, P<0.01) when controlling for those factors. In the 2020 cohort, number of preceding average daily Covid-19 infections were associated with increased PE case incidence in all investigated windows, i.e. including preceding infections from 14 to 90 days. The best model (log likelihood -576) was with a window size of 4 days, i.e. average Covid-19 infections 14 - 17 days before PE hospitalization had a risk of 1.20 (95 % CI 1.12- 1.29, P<0.01).\n\nConclusionsThere is an increase in PE cases since early May 2020 compared to corresponding periods in 2016 - 2019. This surplus was significant even when controlling for changes in potential modulators such as demographics, volume depletion, non-Covid-19 pneumonia, CTPA use and preceding Covid-19 infections. Future studies are needed (1) to investigate a potential causal link for increased risk of delayed PE with preceding SARS-CoV-2 infection, and (2) to define optimal screening for SARS-CoV-2 in patients presenting with pneumonia and PE.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Daniela Husser",
-        "author_inst": "Heart Center Leipzig"
-      },
-      {
-        "author_name": "Sven Hohenstein",
-        "author_inst": "Leipzig Heart Institute"
-      },
-      {
-        "author_name": "Vincent Pellissier",
-        "author_inst": "Leipzig Heart Institute"
-      },
-      {
-        "author_name": "Laura Ueberham",
-        "author_inst": "Heart Center Leipzig"
-      },
-      {
-        "author_name": "Sebastian Koenig",
-        "author_inst": "Heart Center Leipzig"
-      },
-      {
-        "author_name": "Gerhard Hindricks",
-        "author_inst": "Heart Center Leipzig"
-      },
-      {
-        "author_name": "Andreas Meier-Hellmann",
-        "author_inst": "Helios Kliniken"
-      },
-      {
-        "author_name": "Ralf Kuhlen",
-        "author_inst": "Helios Health"
-      },
-      {
-        "author_name": "ANDREAS BOLLMANN",
-        "author_inst": "Heart Center Leipzig"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "cardiovascular medicine"
-  },
   {
     "rel_doi": "10.1101/2021.05.17.21257358",
     "rel_title": "Economic Impact Payment, Human Mobility and the COVID-19 Mitigation in the United States",
@@ -742498,6 +741001,65 @@
     "type": "new results",
     "category": "biophysics"
   },
+  {
+    "rel_doi": "10.1101/2021.05.19.444569",
+    "rel_title": "Spatially distributed infection increases viral load in a computational model of SARS-CoV-2 lung infection",
+    "rel_date": "2021-05-19",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.19.444569",
+    "rel_abs": "A key question in SARS-CoV-2 infection is why viral loads and patient outcomes vary dramatically across individuals. Because spatial-temporal dynamics of viral spread and immune response are challenging to study in vivo, we developed Spatial Immune Model of Coronavirus (SIMCoV), a scalable computational model that simulates hundreds of millions of lung cells, including respiratory epithelial cells and T cells. SIMCoV replicates viral growth dynamics observed in patients and shows how spatially dispersed infections can lead to increased viral loads. The model also shows how the timing and strength of the T cell response can affect viral persistence, oscillations, and control. By incorporating spatial interactions, SIMCoV provides a parsimonious explanation for the dramatically different viral load trajectories among patients by varying only the number of initial sites of infection, and the magnitude and timing of the T cell immune response. When the branching airway structure of the lung is explicitly represented, we find that virus spreads faster than in a 2D layer of epithelial cells, but much more slowly than in an undifferentiated 3D grid or in a well-mixed ODE model. These results illustrate how realistic spatially explicit computational models can improve understanding of within-host dynamics of SARS-CoV-2 infection.\n\nSummaryA key question in SARS-CoV-2 infection is why viral loads and patient outcomes are so different across individuals. Because its difficult to see how the virus spreads in the lungs of infected people, we developed Spatial Immune Model of Coronavirus (SIMCoV), a computational model that simulates hundreds of millions of cells, including lung cells and immune cells. SIMCoV simulates how virus grows and then declines, and the simulations match data observed in patients. SIMCoV shows that when there are more initial infection sites, the virus grows to a higher peak. The model also shows how the timing of the immune response, particularly the T cell response, can affect how long the virus persists and whether it is ultimately cleared from the lungs. SIMCoV shows that the different viral loads in different patients can be explained by how many different places the virus is initially seeded inside their lungs. We explicitly add the branching airway structure of the lung into the model and show that virus spreads slightly faster than it would in a two-dimensional layer of lung cells, but much slower than traditional mathematical models based on differential equations. These results illustrate how realistic spatial computational models can improve understanding of how SARS-CoV-2 infection spreads in the lung.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Melanie E. Moses",
+        "author_inst": "University of New Mexico"
+      },
+      {
+        "author_name": "Steve Hofmeyr",
+        "author_inst": "Lawrence Berkeley National Laboratory"
+      },
+      {
+        "author_name": "Judy L Cannon",
+        "author_inst": "University of New Mexico"
+      },
+      {
+        "author_name": "Akil Andrews",
+        "author_inst": "University of New Mexico"
+      },
+      {
+        "author_name": "Rebekah Gridley",
+        "author_inst": "University of New Mexico"
+      },
+      {
+        "author_name": "Monica Hinga",
+        "author_inst": "University of New Mexico"
+      },
+      {
+        "author_name": "Kirtus Leyba",
+        "author_inst": "Arizona State University"
+      },
+      {
+        "author_name": "Abigail Pribisova",
+        "author_inst": "University of New Mexico"
+      },
+      {
+        "author_name": "Vanessa Surjadidjaja",
+        "author_inst": "University of New Mexico"
+      },
+      {
+        "author_name": "Humayra Tasnim",
+        "author_inst": "University of New Mexico"
+      },
+      {
+        "author_name": "Stephanie Forrest",
+        "author_inst": "Arizona State University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2021.05.19.444825",
     "rel_title": "Adaptive immune determinants of viral clearance and protection in mouse models of SARS-CoV-2",
@@ -743635,97 +742197,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.05.15.21257261",
-    "rel_title": "Systematic Review and Meta-analysis on COVID-19 Vaccine Hesitancy",
-    "rel_date": "2021-05-18",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.15.21257261",
-    "rel_abs": "BackgroundThe presented meta-analysis was developed in response to the publication of several studies addressing COVID-19 vaccines hesitancy. We aimed to identify the proportion of vaccine acceptance and rejection, and factors affecting vaccine hesitancy worldwide especially with the fast emergency approval of vaccines.\n\nMethodsOnline database search was performed, and relevant studies were included with no language restriction. A meta-analysis was conducted using R software to obtain the random effect model of the pooled prevalence of vaccine acceptance and rejection. Eggers regression test was performed to assess publication bias. Quality assessment was assessed using Newcastle-Ottawa Scale quality assessment tool.\n\nResultsThirty-nine out of 12246 articles met the predefined inclusion criteria. All studies were cross-sectional designs. The pooled proportion of COVID-19 vaccine hesitancy was 17% (95% CI: 14-20) while the pooled proportion of COVID-19 vaccine acceptance was 75% (95% CI: 71-79). The vaccine hesitancy and the vaccine acceptance showed high heterogeneity (I2=100%). Case fatality ratio and the number of reported cases had significant effect on the vaccine acceptance as the pooled proportion of vaccine acceptance increased by 39.95% (95% CI: 20.1-59.8) for each 1% increase in case fatality (P<0.0001) and decreased by 0.1% (95% CI: -0.2-0.01) for each 1000 reported case of COVID-19, P= 0.0183).\n\nConclusionTransparency in reporting the number of newly diagnosed COVID-19 cases and deaths is mandatory as these factors are the main determinants of COVID-19 vaccine acceptance.",
-    "rel_num_authors": 19,
-    "rel_authors": [
-      {
-        "author_name": "Shaimaa Abdulaziz Abdulmoneim",
-        "author_inst": "Egyptian Ministry of Health and Population"
-      },
-      {
-        "author_name": "Iman Ahmed Fathalla Aboelsaad",
-        "author_inst": "Egyptian Ministry of Health and Population"
-      },
-      {
-        "author_name": "Dina Mohamed Hanaa Hafez",
-        "author_inst": "Alexandria University Students Hospital, Egypt"
-      },
-      {
-        "author_name": "Abdallah Almaghraby",
-        "author_inst": "Cardiology and Angiology department, Alexandria University, Egypt"
-      },
-      {
-        "author_name": "samar ossama el-ganainy",
-        "author_inst": "pharos university in alexandria"
-      },
-      {
-        "author_name": "Amr Alnagar",
-        "author_inst": "Department of General Surgery-Faculty of Medicine-Alexandria University"
-      },
-      {
-        "author_name": "Ramy Shaaban",
-        "author_inst": "Department of Instructional Technology and Learning Sciences, Utah State University, USA"
-      },
-      {
-        "author_name": "Yasir Ahmed Mohammed Elhadi",
-        "author_inst": "Department of Public Health, Medical Research office, Sudanese Medical Research Association, Khartoum, Sudan"
-      },
-      {
-        "author_name": "Ehsan Akram Deghidy",
-        "author_inst": "Department of Biomedical Informatics and Medical Statistics, Medical Research Institute, Alexandria University, Alexandria,"
-      },
-      {
-        "author_name": "Ahmed El-Sayed Nour El-Deen",
-        "author_inst": "Department of physiology, Faculty of Medicine, Al-Azhar University, Assuit, Egypt."
-      },
-      {
-        "author_name": "Karem Mohamed Salem",
-        "author_inst": "Departement of internal medicine , Faculty of medicine , Fayoum University , Egypt"
-      },
-      {
-        "author_name": "Noha Alaa Hamdy",
-        "author_inst": "Pharmacy Practice department, Faculty of Pharmacy, Alexandria University"
-      },
-      {
-        "author_name": "Samar Galal kabeel",
-        "author_inst": "Egyptian Ministry of Health and population"
-      },
-      {
-        "author_name": "Eman Ahmad Fadel Elsherbeny",
-        "author_inst": "Department of Woman's Health and Midwifery Nursing, Faculty of Nursing, Mansoura University, Egypt"
-      },
-      {
-        "author_name": "Mohamed Moustafa Tahoun",
-        "author_inst": "\" World Health Organization, Regional Office for The Eastern Mediterranean - WHO Health Emergencies Programme Department of Epidemiology, High Institute of Publ"
-      },
-      {
-        "author_name": "Ramy Mohamed Ghazy",
-        "author_inst": "Tropical Health, High Institute of Public Health, Alexandria University, Egypt"
-      },
-      {
-        "author_name": "Nagwa Ibrahim Elfeshawy",
-        "author_inst": "Department of Woman's Health and Midwifery Nursing, Faculty of Nursing, Mansoura University, Egypt"
-      },
-      {
-        "author_name": "Ehab Elrewany",
-        "author_inst": "Tropical  Health department,High Institute of Public Health, Alexandria university"
-      },
-      {
-        "author_name": "Alaa khalil",
-        "author_inst": "Cairo University Medical school"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.05.14.21257244",
     "rel_title": "Controlling risk of SARS-CoV-2 infection in essential workers of enclosed food manufacturing facilities",
@@ -745796,6 +744267,109 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.05.15.21257254",
+    "rel_title": "Inhibitor screening of Spike variants reveals the heterogeneity of neutralizing antibodies to COVID-19 infection and vaccination",
+    "rel_date": "2021-05-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.15.21257254",
+    "rel_abs": "Mutations of the coronavirus responsible for coronavirus disease 2019 (COVID-19) could impede drug development and reduce the efficacy of COVID-19 vaccines. Here, we developed a multiplexed Spike-ACE2 Inhibitor Screening (mSAIS) assay that can measure the neutralizing effect of antibodies across numerous variants of the coronaviruss Spike (S) protein simultaneously. By screening purified antibodies and serum from convalescent COVID-19 patients and vaccinees against 72 S variants with the mSAIS assay, we identified new S mutations that are sensitive and resistant to neutralization. Serum from both infected and vaccinated groups with a high titer of neutralizing antibodies (NAbs) displayed a broader capacity to neutralize S variants than serum with low titer NAbs. These data were validated using serum from a large vaccinated cohort (n=104) with a tiled S peptide microarray. In addition, similar results were obtained using a SARS-CoV-2 pseudovirus neutralization assay specific for wild-type S and four prevalent S variants (D614G, B.1.1.7, B.1.351, P.1), thus demonstrating that high antibody diversity is associated with high NAb titers. Our results demonstrate the utility of the mSAIS platform in screening NAbs. Moreover, we show that heterogeneous antibody populations provide a more protective effect against S variants, which may help direct COVID-19 vaccine and drug development.\n\nHighlightsO_LIDeveloped a high throughput assay to screen the neutralizing effect of antibodies across multiple SARS-CoV-2 Spike variants simultaneously.\nC_LIO_LICharacterized the heterogeneity of neutralizing antibodies produced in response to COVID-19 infection and vaccination.\nC_LIO_LIDemonstrated the capacity of Spike variants neutralization is associated with the diversity of anti-Spike antibodies.\nC_LI",
+    "rel_num_authors": 22,
+    "rel_authors": [
+      {
+        "author_name": "Xiaomei Zhang",
+        "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom"
+      },
+      {
+        "author_name": "Mei Zheng",
+        "author_inst": "Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China."
+      },
+      {
+        "author_name": "Te Liang",
+        "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom"
+      },
+      {
+        "author_name": "Haijian Zhou",
+        "author_inst": "State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Diseas"
+      },
+      {
+        "author_name": "Hongye Wang",
+        "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom"
+      },
+      {
+        "author_name": "Jiahui Zhang",
+        "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom"
+      },
+      {
+        "author_name": "Jing Ren",
+        "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom"
+      },
+      {
+        "author_name": "Huoying Peng",
+        "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom"
+      },
+      {
+        "author_name": "Siping Li",
+        "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom"
+      },
+      {
+        "author_name": "Haodong Bian",
+        "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom"
+      },
+      {
+        "author_name": "Chundi Wei",
+        "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom"
+      },
+      {
+        "author_name": "Shangqi Yin",
+        "author_inst": "Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China."
+      },
+      {
+        "author_name": "Chaonan He",
+        "author_inst": "Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China"
+      },
+      {
+        "author_name": "Ying Han",
+        "author_inst": "Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China."
+      },
+      {
+        "author_name": "Minghui Li",
+        "author_inst": "State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Diseas"
+      },
+      {
+        "author_name": "Xuexin Hou",
+        "author_inst": "State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Diseas"
+      },
+      {
+        "author_name": "Jie Zhang",
+        "author_inst": "Beijing Key Laboratory of Monoclonal Antibody Research and Development, Sino Biological, Inc., Beijing, 100176, China"
+      },
+      {
+        "author_name": "Liangzhi Xie",
+        "author_inst": "Beijing Key Laboratory of Monoclonal Antibody Research and Development, Sino Biological, Inc., Beijing, 100176, China"
+      },
+      {
+        "author_name": "Jing Lv",
+        "author_inst": "Gobond Testing Technology (Beijing) Co., Ltd., Beijing, 102629, China."
+      },
+      {
+        "author_name": "Biao Kan",
+        "author_inst": "State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Diseas"
+      },
+      {
+        "author_name": "Yajie Wang",
+        "author_inst": "Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China."
+      },
+      {
+        "author_name": "xiaobo yu",
+        "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.05.14.21257231",
     "rel_title": "Patient Characteristics in Cases of Reinfection or Prolonged viral shedding in SARS-CoV-2",
@@ -747129,41 +745703,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.05.18.444605",
-    "rel_title": "In Silico Molecular-Based Rationale for SARS-CoV-2 Spike Circulating Mutations Able to Escape Bamlanivimab and Etesevimab Monoclonal Antibodies",
-    "rel_date": "2021-05-18",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.18.444605",
-    "rel_abs": "The purpose of this work was to provide an in silico molecular rationale of the role eventually played by currently circulating S-RBDCoV-2 mutations in evading the immune surveillance effects elicited by the two Eli Lilly LY-CoV555/bamlanivimab and LY-CoV016/etesevimab monoclonal antibodies. The main findings from this study and shows that, compared to the wild-type SARS-CoV-2 spike protein, mutations E484A/G/K/Q/R/V, Q493K/L/R, S494A/P/R, L452R and F490S are predicted to be markedly resistant to neutralization by LY-CoV555, while mutations K417E/N/T, D420A/G/N, N460I/K/S/T, T415P, and Y489C/S are predicted to confer LY-CoV016 escaping advantage to the viral protein. A challenge of our global in silico results against the relevant experimental data resulted in an overall 90% agreement. This achievement not only constitutes a further, robust validation of our computer-based approach but also yields a molecular-based rationale for all relative experimental findings, and leads us to conclude that the current circulating SARS-CoV-2 and all possible emergent variants carrying these mutations in the spike protein can present new challenges for mAb-based therapies and ultimately threaten the fully-protective efficacy of currently available vaccines.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Erik Laurini",
-        "author_inst": "University of Trieste"
-      },
-      {
-        "author_name": "Domenico Marson",
-        "author_inst": "University of Trieste"
-      },
-      {
-        "author_name": "Suzana Aulic",
-        "author_inst": "University of Trieste"
-      },
-      {
-        "author_name": "Alice Fermeglia",
-        "author_inst": "University of Trieste"
-      },
-      {
-        "author_name": "Sabrina PRICL",
-        "author_inst": "University of Trieste"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "biophysics"
-  },
   {
     "rel_doi": "10.1101/2021.05.18.444622",
     "rel_title": "Single-dose immunisation with a multimerised SARS-CoV-2 receptor binding domain (RBD) induces an enhanced and protective response in mice",
@@ -747602,6 +746141,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "genetic and genomic medicine"
   },
+  {
+    "rel_doi": "10.1101/2021.05.18.21257259",
+    "rel_title": "SARS-CoV-2 Vaccine-Induced Antibody Response and Reinfection in Persons with Past Natural Infection",
+    "rel_date": "2021-05-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.18.21257259",
+    "rel_abs": "Several studies have shown that subjects with a history of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection had significantly higher antibody titers than previously uninfected vaccinees after vaccination with mRNA vaccine. Yet no information is available for other vaccines.\n\nIn the current observational cohort study, 105 health care workers who had received Covishield an Adeno associated viral vector-based DNA vaccine were enrolled at Sarojini Nadu Medical College Agra, India. The study included 40 (23 men and 17 women) subjects with a previous history of SARS-CoV-2 infection and 65 participants (39 men and 26 women) who were not infected previously. Both the groups received the adenovirus vector vaccine ChAdOx1-S recombinant vaccines (Covishield, Astra Zeneca). The levels of SARS-CoV-2-anti-spike-IgG-antibodies titer were measured using Electrochemiluminescence immunoassay on Roche platform as arbitrary units per milliliter (AU/ml).\n\nAfter 28 days of the second dose, subjects with no previous SARSCoV-2 infection showed a significantly lower level of circulating anti-spike-IgG-antibody titers compared to previously infected participants. After the second dose, we also observed a significant increase in SARS-CoV-2 infection in subjects with no prior history of SARS-CoV-2 infection compared to subjects with a previous history of natural infection.\n\nThe most important observation of the study is a low percentage of infection in previously infected subjects. The finding of the study also indicates the presence of robust humoral memory response in previously infected patients.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Nitu Chauhan",
+        "author_inst": "Department of Transfusion Medicine, Sarojini Naidu Medical College Agra, Uttar Pradesh, India"
+      },
+      {
+        "author_name": "Ajeet Singh Chahar",
+        "author_inst": "Department of Transfusion Medicine, Sarojini Naidu Medical College Agra, Uttar Pradesh, India"
+      },
+      {
+        "author_name": "Prem Singh",
+        "author_inst": "Department of Transfusion Medicine, Sarojini Naidu Medical College Agra, Uttar Pradesh, India"
+      },
+      {
+        "author_name": "Neel Sarovar Bhavesh",
+        "author_inst": "International Centre for Genetic Engineering and Biotechnology, New Delhi, India"
+      },
+      {
+        "author_name": "Ravi Tandon",
+        "author_inst": "School of Biotechnology and Special Center for Systems Medicine, Jawaharlal Nehru University, New Delhi, India"
+      },
+      {
+        "author_name": "Rupesh Chaturvedi",
+        "author_inst": "School of Biotechnology and Special Center for Systems Medicine, Jawaharlal Nehru University, New Delhi, India"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.05.16.21257155",
     "rel_title": "Evaluation of High Flow Local Extraction on control of the aerosol plume in an operating theatre",
@@ -748991,37 +747569,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.05.04.21256574",
-    "rel_title": "Predictors of Social Distancing and Mask-Wearing Behavior: Panel Survey in Seven U.S. States",
-    "rel_date": "2021-05-17",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256574",
-    "rel_abs": "This paper presents preliminary summary results from a longitudinal study of participants in seven U.S. states during the COVID-19 pandemic. In addition to standard socio-economic characteristics, we collect data on various economic preference parameters: time, risk, and social preferences, and risk perception biases. We pay special attention to predictors that are both important drivers of social distancing and are potentially malleable and susceptible to policy levers. We note three important findings: (1) demographic characteristics exert the largest influence on social distancing measures and mask-wearing, (2) we show that individual risk perception and cognitive biases exert a critical role in influencing the decision to adopt social distancing measures, (3) we identify important demographic groups that are most susceptible to changing their social distancing behaviors. These findings can help inform the design of policy interventions regarding targeting specific demographic groups, which can help reduce the transmission speed of the COVID-19 virus. (JEL I11, I12, I18, D81, D91, D62, D64)",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Plamen Nikolov",
-        "author_inst": "State University of New York (at Binghamton)"
-      },
-      {
-        "author_name": "Andreas Pape",
-        "author_inst": "State University of New York (at Binghamton)"
-      },
-      {
-        "author_name": "Ozlem Tonguc",
-        "author_inst": "State University of New York (at Binghamton)"
-      },
-      {
-        "author_name": "Charlotte Williams",
-        "author_inst": "State University of New York (at Binghamton)"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health economics"
-  },
   {
     "rel_doi": "10.1101/2021.05.16.444324",
     "rel_title": "Verification of SARS-CoV-2-Encoded small RNAs and contribution to Infection-Associated lung inflammation",
@@ -749324,6 +747871,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.05.13.21257146",
+    "rel_title": "Sociodemographic inequality in COVID-19 vaccination coverage amongst elderly adults in England: a national linked data study",
+    "rel_date": "2021-05-17",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.13.21257146",
+    "rel_abs": "ObjectiveTo examine inequalities in COVID-19 vaccination rates amongst elderly adults in England\n\nDesignCohort study\n\nSettingPeople living in private households and communal establishments in England\n\nParticipants6,829,643 adults aged [&ge;] 70 years (mean 78.7 years, 55.2% female) who were alive on 15 March 2021.\n\nMain outcome measuresHaving received the first dose of a vaccine against COVID-19 by 15 March 2021. We calculated vaccination rates and estimated unadjusted and adjusted odds ratios using logistic regression models.\n\nResultsBy 15 March 2021, 93.2% of people living in England aged 70 years and over had received at least one dose of a COVID-19 vaccine. While vaccination rates differed across all factors considered apart from sex, the greatest disparities were seen between ethnic and religious groups. The lowest rates were in people of Black African and Black Caribbean ethnic backgrounds, where only 67.2% and 73.9% had received a vaccine, with adjusted odds of not being vaccinated at 5.01 (95% CI 4.86 - 5.16) and 4.85 (4.75 - 4.96) times greater than the White British group. The proportion of individuals self-identifying as Muslim and Buddhist who had received a vaccine was 79.1% and 84.1%, respectively. Older age, greater area deprivation, less advantaged socio-economic position (proxied by living in a rented home), being disabled and living either alone or in a multi-generational household were also associated with higher odds of not having received the vaccine.\n\nConclusionPeople disproportionately affected seem most hesitant to COVID-19 vaccinations. Policy Interventions to improve these disparities are urgently needed.\n\nSummary BoxO_ST_ABSWhat is already known on this subject?C_ST_ABSThe UK began an ambitious vaccination programme to combat the COVID-19 pandemic on 8th December 2020. Existing evidence suggests that COVID-19 vaccination rates differ by level of area deprivation, ethnicity and certain underlying health conditions, such as learning disability and mental health problems.\n\nWhat does this study add?Our study shows that first dose vaccination rates in adults aged 70 or over differed markedly by ethnic group and self-reported religious affiliation, even after adjusting for geography, socio-demographic factors and underlying health conditions. Our study also highlights differences in vaccination rates by deprivation, household composition, and disability status, factors disproportionately associated with SARS-CoV-2 infection. Public health policy and community engagement aimed at promoting vaccination uptake is these groups are urgently needed.\n\nStrengths and limitations of this studyO_LIUsing nationwide linked population-level data from clinical records and the 2011 Census, we examined a wide range of socio-demographic characteristics not available n electronic health records\nC_LIO_LIMost demographic and socio-economic characteristics are derived from the 2011 Census and therefore are 10 years old. However, we focus primarily on characteristics that are unlikely to change over time, such as ethnicity or religion, or likely to be stable for our population\nC_LIO_LIBecause the data are based on the 2011 Census, it excluded people living in England in 2011 but not taking part in the 2011 Census; respondents who could not be linked to the 2011-2013 NHS patients register; recent migrants. Consequently, we excluded 5.4% of vaccinated people who could not be linked\nC_LI",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Vahe Nafilyan",
+        "author_inst": "Office for National Statistics"
+      },
+      {
+        "author_name": "Ted Dolby",
+        "author_inst": "Office for National Statistics"
+      },
+      {
+        "author_name": "Cameron Razieh",
+        "author_inst": "Diabetes Research Centre, University of Leicester"
+      },
+      {
+        "author_name": "Charlotte Gaughan",
+        "author_inst": "Office for National Statistics"
+      },
+      {
+        "author_name": "Jasper Morgan",
+        "author_inst": "Office for National Statistics"
+      },
+      {
+        "author_name": "Daniel Ayoubkhani",
+        "author_inst": "Office for National Statistics"
+      },
+      {
+        "author_name": "Ann Sarah Walker",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Kamlesh Khunti",
+        "author_inst": "Diabetes Research Centre, University of Leicester"
+      },
+      {
+        "author_name": "Myer Glickman",
+        "author_inst": "Office for National Statistics"
+      },
+      {
+        "author_name": "Thomas Yates",
+        "author_inst": "Diabetes Research Centre, University of Leicester"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.05.17.21257012",
     "rel_title": "Pre-Exposure Prophylaxis with Various Doses of Hdroxychloroquine among high-risk COVID 19 Healthcare Personnel: CHEER randomized controlled trial",
@@ -750916,129 +749518,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2021.05.15.444222",
-    "rel_title": "Stabilization of the SARS-CoV-2 Spike receptor-binding domain using deep mutational scanning and structure-based design",
-    "rel_date": "2021-05-16",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.15.444222",
-    "rel_abs": "The unprecedented global demand for SARS-CoV-2 vaccines has demonstrated the need for highly effective vaccine candidates that are thermostable and amenable to large-scale manufacturing. Nanoparticle immunogens presenting the receptor-binding domain (RBD) of the SARS-CoV-2 Spike protein (S) in repetitive arrays are being advanced as second-generation vaccine candidates, as they feature robust manufacturing characteristics and have shown promising immunogenicity in preclinical models. Here, we used previously reported deep mutational scanning (DMS) data to guide the design of stabilized variants of the RBD. The selected mutations fill a cavity in the RBD that has been identified as a linoleic acid binding pocket. Screening of several designs led to the selection of two lead candidates that expressed at higher yields than the wild-type RBD. These stabilized RBDs possess enhanced thermal stability and resistance to aggregation, particularly when incorporated into an icosahedral nanoparticle immunogen that maintained its integrity and antigenicity for 28 days at 35-40{degrees}C, while corresponding immunogens displaying the wild-type RBD experienced aggregation and loss of antigenicity. The stabilized immunogens preserved the potent immunogenicity of the original nanoparticle immunogen, which is currently being evaluated in a Phase I/II clinical trial. Our findings may improve the scalability and stability of RBD-based coronavirus vaccines in any format and more generally highlight the utility of comprehensive DMS data in guiding vaccine design.",
-    "rel_num_authors": 27,
-    "rel_authors": [
-      {
-        "author_name": "Daniel Ellis",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Natalie Brunette",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Katherine H. D. Crawford",
-        "author_inst": "Fred Hutchinson Cancer Research Center"
-      },
-      {
-        "author_name": "Alexandra C. Walls",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Minh N. Pham",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Chengbo Chen",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Karla-Luise Herpoldt",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Brooke Fiala",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Michael Murphy",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Deleah Pettie",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "John C. Kraft",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Keara D. Malone",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Mary Jane Navarro",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Cassie Ogohara",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Elizabeth Kepl",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Rashmi Ravichandran",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Claire Sydeman",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Maggie Ahlrichs",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Max Johnson",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Alyssa Blackstone",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Lauren Carter",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Tyler N Starr",
-        "author_inst": "Fred Hutchinson Cancer Research Center"
-      },
-      {
-        "author_name": "Allison J. Greaney",
-        "author_inst": "Fred Hutchinson Cancer Research Center"
-      },
-      {
-        "author_name": "Kelly K. Lee",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "David Veesler",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Jesse D Bloom",
-        "author_inst": "Fred Hutchinson Cancer Research Center"
-      },
-      {
-        "author_name": "Neil P. King",
-        "author_inst": "University of Washington"
-      }
-    ],
-    "version": "1",
-    "license": "cc0_ng",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2021.05.15.444128",
     "rel_title": "Pan-ErbB inhibition protects from SARS-CoV-2 replication, inflammation, and injury",
@@ -751593,6 +750072,69 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.05.12.21257117",
+    "rel_title": "Seven-day COVID-19 quarantine may be too short: assessing post-quarantine transmission risk in four university cohorts",
+    "rel_date": "2021-05-15",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.12.21257117",
+    "rel_abs": "BackgroundDespite rising rates of vaccination, quarantine remains critical to control SARS-CoV-2 transmission. COVID-19 quarantine length around the world varies in part due to the limited amount of empirical data.\n\nObjectiveTo assess post-quarantine transmission risk for various quarantine lengths.\n\nDesignCohort study.\n\nSettingFour US universities, September 2020 to February 2021.\n\nParticipants3,641 students and staff were identified as close contacts to SARS-CoV-2-positive individuals. They entered strict or non-strict quarantine and were tested on average twice per week for SARS-CoV-2. Strict quarantine included designated housing with a private room, private bathroom and meal delivery. Non-strict quarantine potentially included interactions with household members.\n\nMeasurementsDates of exposure and last negative and first positive tests during quarantine.\n\nResultsOf the 418 quarantined individuals who eventually converted to positive, 11%, 4.2%, and 1.2% were negative and asymptomatic on days 7, 10 and 14, respectively. The US CDC recently shortened its quarantine guidance from 14 to 7 days based on estimates of 2.3-8.6% post-quarantine transmission risk at day 7, significantly below the 11% risk we report here. Notably, 6% of individuals tested positive after day 7 in strict quarantine, versus 14% in non-strict quarantine. Ongoing exposure during quarantine likely explains the higher rate of COVID-19 in non-strict quarantine.\n\nLimitationsQuarantine should be longer for individuals using antigen testing, given antigen testings lower sensitivity than qPCR. Results apply in settings in which SAR-CoV-2 variants do not affect latent period.\n\nConclusionsTo maintain the 5% transmission risk that the CDC used in its guidance, our data suggest that quarantine with qPCR testing 1 day before intended release should extend to 10 days for non-strict quarantine.\n\nFunding SourceNone.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Andrew Bo Liu",
+        "author_inst": "Harvard Medical School"
+      },
+      {
+        "author_name": "Dan Davidi",
+        "author_inst": "Harvard Medical School"
+      },
+      {
+        "author_name": "Hannah Emily Landsberg",
+        "author_inst": "Boston University"
+      },
+      {
+        "author_name": "Maria Francesconi",
+        "author_inst": "Harvard University Health Services"
+      },
+      {
+        "author_name": "Judy T Platt",
+        "author_inst": "Boston University"
+      },
+      {
+        "author_name": "Giang T Nguyen",
+        "author_inst": "Harvard Medical School"
+      },
+      {
+        "author_name": "Sehyo Yune",
+        "author_inst": "Northeastern University"
+      },
+      {
+        "author_name": "Anastasia Deckard",
+        "author_inst": "Duke University"
+      },
+      {
+        "author_name": "Jamie Puglin",
+        "author_inst": "Duke University"
+      },
+      {
+        "author_name": "Steven B Haase",
+        "author_inst": "Duke University School of Medicine"
+      },
+      {
+        "author_name": "Davidson H Hamer",
+        "author_inst": "Boston University School of Public Health"
+      },
+      {
+        "author_name": "Michael Springer",
+        "author_inst": "Harvard Medical School"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.05.13.21257141",
     "rel_title": "Risk of COVID-19 variant importation - How useful are travel control measures?",
@@ -753210,25 +751752,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.05.13.21257193",
-    "rel_title": "Different approaches to quantify years of life lost from COVID-19",
-    "rel_date": "2021-05-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.13.21257193",
-    "rel_abs": "The burden of an epidemic is often characterized by death counts, but this can be misleading as it fails to acknowledge the age of the deceased patients. Years of life lost is therefore widely used as a more relevant metric, however, such calculations in the context of COVID-19 are all biased upwards: patients dying from COVID-19 are typically multimorbid, having far worse life expectation than the general population. These questions are quantitatively investigated using a unique Hungarian dataset that contains individual patient level data on comorbidities for all COVID-19 deaths in the country. To account for the comorbidities of the patients, a parametric survival model using 11 important long-term conditions was used to estimate a more realistic years of life lost. As of 12 May, 2021, Hungary reported a total of 27,837 deaths from COVID-19 in patients above 50 years of age. The usual calculation indicates 10.5 years of life lost for each death, which decreases to 9.2 years per death after adjusting for 11 comorbidities. The expected number of years lost implied by the life table, reflecting the mortality of a developed country just before the pandemic is 11.1 years. The years of life lost due to COVID-19x in Hungary is therefore 12% or 1.3 years per death lower when accounting for the comorbidities and is below its expected value, but how this should be interpreted is still a matter of debate. Further research is warranted on how to optimally integrate this information into epidemiologic risk assessments during a pandemic.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Tamas Ferenci",
-        "author_inst": "Obuda University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.05.08.21256726",
     "rel_title": "Acute biliary pancreatitis management during the COVID-19 pandemic",
@@ -753555,6 +752078,125 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.05.07.21256823",
+    "rel_title": "Evolution of human antibody responses up to one year after SARS-CoV-2 infection",
+    "rel_date": "2021-05-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.07.21256823",
+    "rel_abs": "Assessment of the kinetics of SARS-CoV-2 antibodies is essential to predict protection against reinfection and durability of vaccine protection. Here, we longitudinally measured Spike (S) and Nucleocapsid (N)-specific antibodies in 1,309 healthcare workers (HCW) including 393 convalescent COVID-19 and 916 COVID-19 negative HCW up to 405 days. From M1 to M7-9 after infection, SARS-CoV-2 antibodies decreased moderately in convalescent HCW in a biphasic model, with men showing a slower decay of anti-N (p=0.02), and a faster decay of anti-S (p=0.0008) than women. At M11-13, anti-N antibodies dramatically decreased (half-life: 210 days) while anti-S stabilized (half-life: 630 days) at a median of 2.41 log Arbitrary Units (AU)/mL (Interquartile Range (IQR): 2.11 -2.75). One case of reinfection was recorded in convalescent HCW (0.47 per 100 person-years) versus 50 in COVID-19 negative HCW (10.11 per 100 person-years). Correlation with live-virus neutralization assay revealed that variants D614G and B.1.1.7, but not B.1.351, were sensitive to anti-S antibodies at 2.3 log AU/mL, while IgG [&ge;] 3 log AU/mL neutralized all three variants. After SARS-CoV-2 vaccination, anti-S levels reached 4 logs regardless of pre-vaccination IgG levels, type of vaccine, and number of doses. Our study demonstrates a long-term persistence of anti-S IgG antibodies that may protect against reinfection. By significantly increasing cross-neutralizing antibody titers, a single-dose vaccination strengthens protection against escape mutants.",
+    "rel_num_authors": 26,
+    "rel_authors": [
+      {
+        "author_name": "Floriane Gallais",
+        "author_inst": "Virology Laboratory, Strasbourg University Hospital, Strasbourg, France;  Strasbourg University, INSERM, IRM UMR-S 1109, F-67000 Strasbourg, France"
+      },
+      {
+        "author_name": "Pierre Gantner",
+        "author_inst": "Virology Laboratory, Strasbourg University Hospital, Strasbourg, France;  Strasbourg University, INSERM, IRM UMR-S 1109, F-67000 Strasbourg, France"
+      },
+      {
+        "author_name": "Timothee Bruel",
+        "author_inst": "Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France.  CNRS UMR 3569, Paris, France.  5Vaccine Research Institute, Creteil, France."
+      },
+      {
+        "author_name": "Aurelie Velay",
+        "author_inst": "Virology Laboratory, Strasbourg University Hospital, Strasbourg, France;  Strasbourg University, INSERM, IRM UMR-S 1109, F-67000 Strasbourg, France"
+      },
+      {
+        "author_name": "Delphine Planas",
+        "author_inst": "Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France.  CNRS UMR 3569, Paris, France.  5Vaccine Research Institute, Creteil, France."
+      },
+      {
+        "author_name": "Marie-Josee Wendling",
+        "author_inst": "Virology Laboratory, Strasbourg University Hospital, Strasbourg, France;"
+      },
+      {
+        "author_name": "Sophie Bayer",
+        "author_inst": "CHU de Strasbourg, Laboratoire de Biochimie Clinique et Biologie Moleculaire, F-67091 Strasbourg, France"
+      },
+      {
+        "author_name": "Morgane Solis",
+        "author_inst": "Virology Laboratory, Strasbourg University Hospital, Strasbourg, France;  Strasbourg University, INSERM, IRM UMR-S 1109, F-67000 Strasbourg, France;"
+      },
+      {
+        "author_name": "Elodie Laugel",
+        "author_inst": "Virology Laboratory, Strasbourg University Hospital, Strasbourg, France;  Strasbourg University, INSERM, IRM UMR-S 1109, F-67000 Strasbourg, France"
+      },
+      {
+        "author_name": "Nathalie Reix",
+        "author_inst": "CHU de Strasbourg, Laboratoire de Biochimie Clinique et Biologie Moleculaire, F-67091 Strasbourg, France"
+      },
+      {
+        "author_name": "Anne Schneider",
+        "author_inst": "CHU de Strasbourg, Departement de Genetique Moleculaire du cancer, F-67091 Strasbourg, France."
+      },
+      {
+        "author_name": "Ludovic Glady",
+        "author_inst": "CHU de Strasbourg, Laboratoire de Biochimie Clinique et Biologie Moleculaire, F-67091 Strasbourg, France"
+      },
+      {
+        "author_name": "Baptiste Panaget",
+        "author_inst": "Virology Laboratory, Strasbourg University Hospital, Strasbourg, France;  Strasbourg University, INSERM, IRM UMR-S 1109, F-67000 Strasbourg, France"
+      },
+      {
+        "author_name": "Nicolas Collongues",
+        "author_inst": "Centre d'investigation Clinique INSERM 1434, CHU Strasbourg, France."
+      },
+      {
+        "author_name": "Marialuisa Partisani",
+        "author_inst": "CHU de Strasbourg, Trait d Union, F-67091 Strasbourg, France."
+      },
+      {
+        "author_name": "Jean-Marc Lessinger",
+        "author_inst": "CHU de Strasbourg, Laboratoire de Biochimie Clinique et Biologie Moleculaire, F-67091 Strasbourg, France"
+      },
+      {
+        "author_name": "Arnaud Fontanet",
+        "author_inst": "Emerging Diseases Epidemiology Unit, Department of Global Health, Institut Pasteur, Paris, France"
+      },
+      {
+        "author_name": "David Rey",
+        "author_inst": "CHU de Strasbourg, Trait d Union, F-67091 Strasbourg, France."
+      },
+      {
+        "author_name": "Yves Hansmann",
+        "author_inst": "CHU de Strasbourg, Service des infectieuses et tropicales, F-67091 Strasbourg, France."
+      },
+      {
+        "author_name": "Laurence Kling-Pillitteri",
+        "author_inst": "CHU de Strasbourg, Service de Pathologies Professionnelles, F-67091 Strasbourg, France."
+      },
+      {
+        "author_name": "Olivier Schwartz",
+        "author_inst": "Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris, France.  CNRS UMR 3569, Paris, France.  5Vaccine Research Institute, Creteil, France."
+      },
+      {
+        "author_name": "Jerome De Seze",
+        "author_inst": "Centre d'investigation Clinique INSERM 1434, CHU Strasbourg, France."
+      },
+      {
+        "author_name": "Nicolas Meyer",
+        "author_inst": "CHU de Strasbourg, Service de sante Publique, GMRC, F-67091 Strasbourg, France."
+      },
+      {
+        "author_name": "Maria Gonzalez",
+        "author_inst": "CHU de Strasbourg, Service de Pathologies Professionnelles, F-67091 Strasbourg, France."
+      },
+      {
+        "author_name": "Catherine Schmidt-Mutter",
+        "author_inst": "Centre d'investigation Clinique INSERM 1434, CHU Strasbourg, France."
+      },
+      {
+        "author_name": "Samira Fafi-Kremer",
+        "author_inst": "Virology Laboratory, Strasbourg University Hospital, Strasbourg, France;  Strasbourg University, INSERM, IRM UMR-S 1109, F-67000 Strasbourg, France"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.05.08.21256885",
     "rel_title": "In hospital cardiac arrest in Intensive Care Unit versus non Intensive Care Unit patients with COVID 19. A systematic review and meta analysis",
@@ -755664,193 +754306,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pediatrics"
   },
-  {
-    "rel_doi": "10.1101/2021.05.06.21256755",
-    "rel_title": "Clinical coding of long COVID in English primary care: a federated analysis of 58 million patient records in situ using OpenSAFELY",
-    "rel_date": "2021-05-13",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.06.21256755",
-    "rel_abs": "BackgroundLong COVID is a term to describe new or persistent symptoms at least four weeks after onset of acute COVID-19. Clinical codes to describe this phenomenon were released in November 2020 in the UK, but it is not known how these codes have been used in practice.\n\nMethodsWorking on behalf of NHS England, we used OpenSAFELY data encompassing 96% of the English population. We measured the proportion of people with a recorded code for long COVID, overall and by demographic factors, electronic health record software system, and week. We also measured variation in recording amongst practices.\n\nResultsLong COVID was recorded for 23,273 people. Coding was unevenly distributed amongst practices, with 26.7% of practices having not used the codes at all. Regional variation was high, ranging between 20.3 per 100,000 people for East of England (95% confidence interval 19.3-21.4) and 55.6 in London (95% CI 54.1-57.1). The rate was higher amongst women (52.1, 95% CI 51.3-52.9) compared to men (28.1, 95% CI 27.5-28.7), and higher amongst practices using EMIS software (53.7, 95% CI 52.9-54.4) compared to TPP software (20.9, 95% CI 20.3-21.4).\n\nConclusionsLong COVID coding in primary care is low compared with early reports of long COVID prevalence. This may reflect under-coding, sub-optimal communication of clinical terms, under-diagnosis, a true low prevalence of long COVID diagnosed by clinicians, or a combination of factors. We recommend increased awareness of diagnostic codes, to facilitate research and planning of services; and surveys of clinicians experiences, to complement ongoing patient surveys.",
-    "rel_num_authors": 43,
-    "rel_authors": [
-      {
-        "author_name": "- The OpenSAFELY Collaborative",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Alex J Walker",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Brian MacKenna",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Peter Inglesby",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Christopher T Rentsch",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Helen J Curtis",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Caroline E Morton",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Jessica Morley",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Amir Mehrkar",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Sebastian CJ Bacon",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "George Hickman",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Christopher Bates",
-        "author_inst": "TPP"
-      },
-      {
-        "author_name": "Richard Croker",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "David Evans",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Tom Ward",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Jonathan Cockburn",
-        "author_inst": "TPP"
-      },
-      {
-        "author_name": "Simon Davy",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Krishnan Bhaskaran",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Anna Schultze",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Elizabeth J Williamson",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "William J Hulme",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Helen I McDonald",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Laurie Tomlinson",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Rohini Mathur",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Rosalind M Eggo",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Kevin Wing",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Angel YS Wong",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Harriet Forbes",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "John Tazare",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "John Parry",
-        "author_inst": "TPP"
-      },
-      {
-        "author_name": "Frank Hester",
-        "author_inst": "TPP"
-      },
-      {
-        "author_name": "Sam Harper",
-        "author_inst": "TPP"
-      },
-      {
-        "author_name": "Shaun O'Hanlon",
-        "author_inst": "EMIS"
-      },
-      {
-        "author_name": "Alex Eavis",
-        "author_inst": "EMIS"
-      },
-      {
-        "author_name": "Richard Jarvis",
-        "author_inst": "EMIS"
-      },
-      {
-        "author_name": "Dima Avramov",
-        "author_inst": "EMIS"
-      },
-      {
-        "author_name": "Paul Griffiths",
-        "author_inst": "EMIS"
-      },
-      {
-        "author_name": "Aaron Fowles",
-        "author_inst": "EMIS"
-      },
-      {
-        "author_name": "Nasreen Parkes",
-        "author_inst": "EMIS"
-      },
-      {
-        "author_name": "Ian J Douglas",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Stephen JW Evans",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Liam Smeeth",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Ben Goldacre",
-        "author_inst": "University of Oxford"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.05.06.21256766",
     "rel_title": "SARS-CoV-2 RNA and antibody detection in human milk from a prospective multicenter study in Spain",
@@ -756189,6 +754644,33 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2021.02.09.21250610",
+    "rel_title": "Pooling of samples for SARS-CoV-2 detection using rapid antigen tests",
+    "rel_date": "2021-05-13",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.09.21250610",
+    "rel_abs": "While molecular assays, such as RT-PCR, have been widely used throughout the COVID-19 pandemic, the technique is costly and resource intensive. As a means to reduce costs and increase diagnostic efficiency, pooled testing for RT-PCR has been implemented. However, pooling samples for antigen testing has not been evaluated. We propose a pooling strategy for antigen testing that would significantly expand SARS-CoV-2 surveillance, especially for low-to-middle income countries, schools, and workplaces. Our data demonstrate that combining of up to 20 nasal swab specimens per pool can expand surveillance with antigen tests, even if a pool contains only one positive sample.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Nol Salcedo",
+        "author_inst": "E25Bio, Inc."
+      },
+      {
+        "author_name": "Alexander Harmon",
+        "author_inst": "E25Bio, Inc."
+      },
+      {
+        "author_name": "Bobby Brooke Herrera",
+        "author_inst": "E25Bio, Inc."
+      }
+    ],
+    "version": "2",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.05.08.21256892",
     "rel_title": "Impact of vaccination on the COVID-19 pandemic: Evidence from U.S. states",
@@ -757514,37 +755996,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.05.11.21257008",
-    "rel_title": "Characteristics of SARS-CoV-2 Positive Individuals in California From Two Periods During Notable Decline in Incident Infection",
-    "rel_date": "2021-05-12",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.11.21257008",
-    "rel_abs": "Despite declining SARS-CoV-2 incidence, continued epidemic monitoring is warranted. We collected SARS-CoV-2 test results from 150 drive-through testing centers across California from two observation periods: February 23rd-March 3rd 2021 and April 15th-April 30th 2021. We assessed SARS-CoV-2 positivity, stratified by Hispanic heritage among sociodemographic characteristics and potential exposures. We analyzed 114,789 test results (5.1% and 2.6% positive during the respective observation periods). Nearly half of all positive tests were among testers reporting a recent exposure (48.8% and 45.3% during the respective observation periods). Those findings may provide insight into evolving local transmission dynamics and support targeted public health strategies.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Lao-Tzu Allan-Blitz",
-        "author_inst": "Brigham and Women's Hospital"
-      },
-      {
-        "author_name": "Isaac Turner",
-        "author_inst": "Curative Inc."
-      },
-      {
-        "author_name": "Fred Hertlein",
-        "author_inst": "Curative Inc."
-      },
-      {
-        "author_name": "Jeffrey D. Klausner",
-        "author_inst": "Department of Preventive Medicine, Keck School of Medicine, University of Southern California"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.05.11.21256917",
     "rel_title": "Methotrexate Hampers Immunogenicity to BNT162b2 mRNA COVID-19 Vaccine in Immune-Mediated Inflammatory Disease",
@@ -758051,6 +756502,117 @@
     "type": "new results",
     "category": "biochemistry"
   },
+  {
+    "rel_doi": "10.1101/2021.05.12.443228",
+    "rel_title": "Interferon-armed RBD dimer enhances the immunogenicity of RBD for sterilizing immunity against SARS-CoV-2",
+    "rel_date": "2021-05-12",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.12.443228",
+    "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global crisis, urgently necessitating the development of safe, efficacious, convenient-to-store, and low-cost vaccine options. A major challenge is that the receptor-binding domain (RBD)-only vaccine fails to trigger long-lasting protective immunity if used solely for vaccination. To enhance antigen processing and cross-presentation in draining lymph nodes (DLNs), we developed an interferon (IFN)-armed RBD dimerized by immunoglobulin fragment (I-R-F). I-R-F efficiently directs immunity against RBD to DLN. A low dose of I-R-F induces not only high titer long-lasting neutralizing antibodies but also comprehensive T cell responses than RBD, and even provides comprehensive protection in one dose without adjuvant. This study shows that the I-R-F vaccine provides rapid and complete protection throughout upper and lower respiratory tracts against high dose SARS-CoV-2 challenge in rhesus macaques. Due to its potency and safety, this engineered vaccine may become one of the next-generation vaccine candidates in the global race to defeat COVID-19.",
+    "rel_num_authors": 24,
+    "rel_authors": [
+      {
+        "author_name": "Shiyu Sun",
+        "author_inst": "Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China   University of Chinese Academy of Science"
+      },
+      {
+        "author_name": "Yueqi Cai",
+        "author_inst": "Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China   University of Chinese Academy of Science"
+      },
+      {
+        "author_name": "Tian-Zhang Song",
+        "author_inst": "Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunm"
+      },
+      {
+        "author_name": "Yang Pu",
+        "author_inst": "Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, 100005, China"
+      },
+      {
+        "author_name": "Lin Cheng",
+        "author_inst": "Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third Peoples Hospital, Shenzhen, 518112, Guangdong Province, China"
+      },
+      {
+        "author_name": "Hairong Xu",
+        "author_inst": "Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China"
+      },
+      {
+        "author_name": "Chaoyang Meng",
+        "author_inst": "Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China"
+      },
+      {
+        "author_name": "Yifan Lin",
+        "author_inst": "Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China   University of Chinese Academy of Science"
+      },
+      {
+        "author_name": "Jin Sun",
+        "author_inst": "State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou"
+      },
+      {
+        "author_name": "Silin Zhang",
+        "author_inst": "School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China."
+      },
+      {
+        "author_name": "Yu Gao",
+        "author_inst": "Key Laboratory of Protein and Peptide Pharmaceuticals, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Bei"
+      },
+      {
+        "author_name": "Jian-Bao Han",
+        "author_inst": "Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy o"
+      },
+      {
+        "author_name": "Xiao-Li Feng",
+        "author_inst": "Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy o"
+      },
+      {
+        "author_name": "Dan-Dan Yu",
+        "author_inst": "Kunming National High-level Biosafety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy o"
+      },
+      {
+        "author_name": "Yalan Zhu",
+        "author_inst": "Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China"
+      },
+      {
+        "author_name": "Pu Gao",
+        "author_inst": "Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China"
+      },
+      {
+        "author_name": "Haidong Tang",
+        "author_inst": "School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China."
+      },
+      {
+        "author_name": "Jincun Zhao",
+        "author_inst": "State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou"
+      },
+      {
+        "author_name": "Jiaming Yang",
+        "author_inst": "Livzon Mabpharm Inc., Zhuhai, Guangdong 519045, China"
+      },
+      {
+        "author_name": "Zenxiang Hu",
+        "author_inst": "Livzon Mabpharm Inc., Zhuhai, Guangdong 519045, China"
+      },
+      {
+        "author_name": "Zheng Zhang",
+        "author_inst": "Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third Peoples Hospital, Shenzhen, 518112, Guangdong Province, China"
+      },
+      {
+        "author_name": "Yang-Xin Fu",
+        "author_inst": "UT southwestern medical center"
+      },
+      {
+        "author_name": "Yong-Tang Zheng",
+        "author_inst": "Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunm"
+      },
+      {
+        "author_name": "Hua Peng",
+        "author_inst": "Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2021.05.12.443645",
     "rel_title": "Neutralization potential of Covishield vaccinated individuals against B.1.617.1",
@@ -760372,89 +758934,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.05.11.21256578",
-    "rel_title": "Live virus neutralization testing in convalescent and vaccinated subjects against 19A, 20B, 20I/501Y.V1 and 20H/501.V2 isolates of SARS-CoV-2",
-    "rel_date": "2021-05-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.11.21256578",
-    "rel_abs": "BackgroundSARS-CoV-2 mutations appeared recently and can lead to conformational changes in the spike protein and probably induce modifications in antigenicity. In this study, we wanted to assess the neutralizing capacity of antibodies to prevent cell infection, using a live virus neutralisation test.\n\nMethodsSera samples were collected from different populations: two-dose vaccinated COVID-19-naive healthcare workers (HCWs; Pfizer-BioNTech BNT161b2), 6-months post mild COVID-19 HCWs, and critical COVID-19 patients. We tested various clades such as 19A (initial one), 20B (B.1.1.241 lineage), 20I/501Y.V1 (B.1.1.7 lineage), and 20H/501Y.V2 (B.1.351 lineage).\n\nResultsNo significant difference was observed between the 20B and 19A isolates for HCWs with mild COVID-19 and critical patients. However, a significant decrease in neutralisation ability was found for 20I/501Y.V1 in comparison with 19A isolate for critical patients and HCWs 6-months post infection. Concerning 20H/501Y.V2, all populations had a significant reduction in neutralising antibody titres in comparison with the 19A isolate. Interestingly, a significant difference in neutralisation capacity was observed for vaccinated HCWs between the two variants whereas it was not significant for the convalescent groups.\n\nConclusionNeutralisation capacity was slightly reduced for critical patients and HCWs 6-months post infection. No neutralisation escape could be feared concerning the two variants of concern in both populations. The reduced neutralising response observed towards the 20H/501Y.V2 in comparison with the 19A and 20I/501Y.V1 isolates in fully immunized subjects with the BNT162b2 vaccine is a striking finding of the study.",
-    "rel_num_authors": 17,
-    "rel_authors": [
-      {
-        "author_name": "Claudia Gonzalez",
-        "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associ\u00e9 au Centre National de R\u00e9f\u00e9rence des virus des infections respiratoires, Hospices C"
-      },
-      {
-        "author_name": "Carla Saade",
-        "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associ\u00e9 au Centre National de R\u00e9f\u00e9rence des virus des infections respiratoires, Hospices C"
-      },
-      {
-        "author_name": "Antonin Bal",
-        "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associ\u00e9 au Centre National de R\u00e9f\u00e9rence des virus des infections respiratoires, Hospices C"
-      },
-      {
-        "author_name": "Martine Valette",
-        "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associ\u00e9 au Centre National de R\u00e9f\u00e9rence des virus des infections respiratoires, Hospices C"
-      },
-      {
-        "author_name": "Kahina Saker",
-        "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associ\u00e9 au Centre National de R\u00e9f\u00e9rence des virus des infections respiratoires, Hospices C"
-      },
-      {
-        "author_name": "Bruno Lina",
-        "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associ\u00e9 au Centre National de R\u00e9f\u00e9rence des virus des infections respiratoires, Hospices C"
-      },
-      {
-        "author_name": "Laurence Josset",
-        "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associ\u00e9 au Centre National de R\u00e9f\u00e9rence des virus des infections respiratoires, Hospices C"
-      },
-      {
-        "author_name": "Mary-Anne Trabaud",
-        "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associ\u00e9 au Centre National de R\u00e9f\u00e9rence des virus des infections respiratoires, Hospices C"
-      },
-      {
-        "author_name": "Guillaume Thiery",
-        "author_inst": "Centre Hospitalier Universitaire de Saint-Etienne, Unit\u00e9 des soins intensifs, Saint-Etienne, France ;"
-      },
-      {
-        "author_name": "Elisabeth Botelho-Nevers",
-        "author_inst": "CIRI, \u00e9quipe GIMAP, Universit\u00e9 de Lyon, Universit\u00e9 de Saint-Etienne, INSERM U1111, CNRS UMR 5308, ENS de Lyon, UCBL1, Saint Etienne, France ; D\u00e9partement des ma"
-      },
-      {
-        "author_name": "St\u00e9phane Paul",
-        "author_inst": "CIRI, \u00e9quipe GIMAP, Universit\u00e9 de Lyon, Universit\u00e9 de Saint-Etienne, INSERM U1111, CNRS UMR5308, ENS de Lyon, UCBL1, Saint-Etienne, France ; D\u00e9partement d'immun"
-      },
-      {
-        "author_name": "Paul Verhoeven",
-        "author_inst": "CIRI, \u00e9quipe GIMAP, Universit\u00e9 de Lyon, Universit\u00e9 de Saint-Etienne, INSERM U1111, CNRS UMR5308, ENS de Lyon, UCBL1, Saint Etienne, France ; D\u00e9partement des age"
-      },
-      {
-        "author_name": "Thomas Bourlet",
-        "author_inst": "CIRI, \u00e9quipe GIMAP, Universit\u00e9 de Lyon, Universit\u00e9 de Saint-Etienne, INSERM U1111, CNRS UMR5308, ENS de Lyon, UCBL1, Saint Etienne, France ; D\u00e9partement des age"
-      },
-      {
-        "author_name": "Sylvie Pillet",
-        "author_inst": "CIRI, \u00e9quipe GIMAP, Universit\u00e9 de Lyon, Universit\u00e9 de Saint-Etienne, INSERM U1111, CNRS UMR5308, ENS de Lyon, UCBL1, Saint Etienne, France ; D\u00e9partement des age"
-      },
-      {
-        "author_name": "Florence Morfin",
-        "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associ\u00e9 au Centre National de R\u00e9f\u00e9rence des virus des infections respiratoires, Hospices C"
-      },
-      {
-        "author_name": "Sophie Trouillet-Assant",
-        "author_inst": "Laboratoire de Virologie, Institut des Agents Infectieux, Laboratoire associ\u00e9 au Centre National de R\u00e9f\u00e9rence des virus des infections respiratoires, Hospices C"
-      },
-      {
-        "author_name": "Bruno Pozzetto",
-        "author_inst": "CIRI, \u00e9quipe GIMAP, Universit\u00e9 de Lyon, Universit\u00e9 de Saint-Etienne, INSERM U1111, CNRS UMR5308, ENS de Lyon, UCBL1, Saint-Etienne, France; D\u00e9partement des agen"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.05.05.21256710",
     "rel_title": "Evolution of COVID-19 symptoms during the first 9 months after illness onset",
@@ -760733,6 +759212,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.05.10.21256995",
+    "rel_title": "Magnetofluidic platform for rapid multiplexed screening of SARS-CoV-2 variants and respiratory pathogens",
+    "rel_date": "2021-05-11",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.10.21256995",
+    "rel_abs": "The rise of highly transmissible SARS-CoV-2 variants brings new challenges and concerns with vaccine efficacy, diagnostic sensitivity, and public health responses in the fight to end the pandemic. Widespread detection of variant strains will be critical to inform policy decisions to mitigate further spread, and post-pandemic multiplexed screening of respiratory viruses will be necessary to properly manage patients presenting with similar respiratory symptoms. In this work, we have developed a portable, magnetofluidic cartridge platform for automated PCR testing in <30 min. Cartridges were designed for multiplexed detection of SARS-CoV-2 with either distinctive variant mutations or with Influenza A and B. The platform demonstrated a limit of detection down to 2 copies/{micro}L SARS-CoV-2 RNA with successful identification of B.1.1.7 and B.1.351 variants. The multiplexed SARS-CoV-2/Flu assay was validated using archived clinical nasopharyngeal swab eluates (n = 116) with an overall sensitivity/specificity of 98.1%/95.2%, 85.7%/100%, 100%/98.2%, respectively, for SARS-CoV-2, Influenza A, and Influenza B. Further testing with saliva (n = 14) demonstrated successful detection of all SARS-CoV-2 positive samples with no false-positives.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Alexander Y Trick",
+        "author_inst": "Johns Hopkins University"
+      },
+      {
+        "author_name": "Fan-En Chen",
+        "author_inst": "Johns Hopkins University"
+      },
+      {
+        "author_name": "Liben Chen",
+        "author_inst": "Johns Hopkins University"
+      },
+      {
+        "author_name": "Pei-Wei Lee",
+        "author_inst": "Johns Hopkins University"
+      },
+      {
+        "author_name": "Alexander C Hasnain",
+        "author_inst": "Johns Hopkins University"
+      },
+      {
+        "author_name": "Heba H Mostafa",
+        "author_inst": "Johns Hopkins University School of Medicine"
+      },
+      {
+        "author_name": "Karen C Carroll",
+        "author_inst": "Johns Hopkins University School of Medicine"
+      },
+      {
+        "author_name": "Tza-Huei Wang",
+        "author_inst": "Johns Hopkins University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.05.11.21257011",
     "rel_title": "COVID-19 in patients hospitalized and healthcare workers: what have changed after the first wave in a university hospital",
@@ -762206,37 +760732,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "obstetrics and gynecology"
   },
-  {
-    "rel_doi": "10.1101/2021.05.07.21256742",
-    "rel_title": "INDIA'S PRAGMATIC VACCINATION STRATEGY AGAINST COVID-19: A MATHEMATICAL MODELLING BASED ANALYSIS",
-    "rel_date": "2021-05-10",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.07.21256742",
-    "rel_abs": "ObjectivesTo investigate the impact of targeted vaccination strategies on morbidity and mortality due to COVID-19, as well as on the incidence of SARS-CoV-2, in India.\n\nDesignMathematical modelling.\n\nSettingsIndian epidemic of COVID-19 and vulnerable population.\n\nData sourcesCountry specific and age-segregated pattern of social contact, case fatality rate and demographic data obtained from peer-reviewed literature and public domain.\n\nModelAn age-structured dynamical model describing SARS-CoV-2 transmission in India incorporating uncertainty in natural history parameters was constructed.\n\nInterventionsComparison of different vaccine strategies by targeting priority groups such as key workers including health care professionals, individuals with comorbidities (24 - 60 year), and all above 60.\n\nMain outcome measuresIncidence reduction and averted deaths in different scenarios, assuming that the current restrictions are fully lifted as vaccination is implemented.\n\nResultsThe priority groups together account for about 18% of Indias population. An infection preventing vaccine with 60% efficacy covering all these groups would reduce peak symptomatic incidence by 20.6% (95% uncertainty intervals (CrI) 16.7 - 25.4), and cumulative mortality by 29.7% (95% CrI 25.8-33.8). A similar vaccine with ability to prevent symptoms (but not infection) will reduce peak incidence of symptomatic cases by 10.4% (95% CrI 8.4 - 13.0), and cumulative mortality by 32.9% (95% CrI 28.6 - 37.3). In the event of insufficient vaccine supply to cover all priority groups, model projections suggest that after keyworkers, vaccine strategy should prioritise all who are > 60, and subsequently individuals with comorbidities. In settings with weakest transmission, such as sparsely-populated rural areas, those with comorbidities should be prioritised after keyworkers.\n\nConclusionsAn appropriately targeted vaccination strategy would witness substantial mitigation of impact of COVID-19 in a country like India with wide heterogenity.  Smart vaccination, based on public health considerations, rather than mass vaccination, appears prudent.\n\nO_TEXTBOXStrengths and limitation of this study\n\nO_LIThe model in this study is informed by age-dependent risk factors for SARS-CoV-2 infection among contacts, and is stratified by co-morbidities (diabetes and/or hypertension), and vaccination status.\nC_LIO_LIData on mortality and large-scale contact tracing from within India, and the recent national sero-survey results were used, which constituted a major strength of this investigation.\nC_LIO_LIDistinguishing between  infection and  symptomatic disease   preventing vaccines, the model was simulated under a range of scenarios for the basic reproduction number (R0).\nC_LIO_LIShould they have been available, real life country-specific data on excess risks of deaths due to comorbidities would have added strength to the presented model.\nC_LIO_LIKey priority group-specific data on social mixing and potential associated transmission was not available, and remained as a limitation.\nC_LI\n\nC_TEXTBOX",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Sandip Mandal",
-        "author_inst": "Indian Council of Medical Research, New Delhi"
-      },
-      {
-        "author_name": "Nimalan Arinaminpathy",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Balram Bhargava",
-        "author_inst": "Indian Council of Medical Research, New Delhi"
-      },
-      {
-        "author_name": "Samiran Panda",
-        "author_inst": "Indian Council of Medical Research, New Delhi"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health policy"
-  },
   {
     "rel_doi": "10.1101/2021.05.06.21256705",
     "rel_title": "Estimated Spike Evolution and Impact of Emerging SARS-CoV-2 Variants",
@@ -762795,6 +761290,77 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "neurology"
   },
+  {
+    "rel_doi": "10.1101/2021.05.08.21256775",
+    "rel_title": "Intra-host evolution provides for continuous emergence of SARS-CoV-2 variants",
+    "rel_date": "2021-05-10",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.08.21256775",
+    "rel_abs": "Variants of concern (VOC) in SARS-CoV-2 refer to viral genomes that differ significantly from the ancestor virus and that show the potential for higher transmissibility and/or worse clinical progression. VOC have the potential to disrupt ongoing public health measures and vaccine efforts. Yet, little is known regarding how frequently different viral variants emerge and under what circumstances. We report a longitudinal study to determine the degree of SARS-CoV-2 sequence evolution in 94 COVID-19 cases and to estimate the frequency at which highly diverse variants emerge. 2 cases accumulated [&ge;]9 single-nucleotide variants (SNVs) over a two-week period and 1 case accumulated 23 SNVs over a three-week period, including three non-synonymous mutations in the Spike protein (D138H, E554D, D614G). We estimate that in 2% of COVID cases, viral variants with multiple mutations, including in the Spike glycoprotein, can become the dominant strains in as little as one month of persistent in patient virus replication. This suggests the continued local emergence of VOC independent of travel patterns. Surveillance by sequencing for (i) viremic COVID-19 patients, (ii) patients suspected of re-infection, and (iii) patients with diminished immune function may offer broad public health benefits.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Justin Landis",
+        "author_inst": "Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine"
+      },
+      {
+        "author_name": "Razia Moorad",
+        "author_inst": "Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine"
+      },
+      {
+        "author_name": "Linda J. Pluta",
+        "author_inst": "Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine"
+      },
+      {
+        "author_name": "Carolina Caro-Vegas",
+        "author_inst": "Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine"
+      },
+      {
+        "author_name": "Ryan P. McNamara",
+        "author_inst": "Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine"
+      },
+      {
+        "author_name": "Anthony B Eason",
+        "author_inst": "Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine"
+      },
+      {
+        "author_name": "Aubrey Bailey",
+        "author_inst": "Kuopio Center for Gene and Cell Therapy"
+      },
+      {
+        "author_name": "Femi Cleola S. Villamor",
+        "author_inst": "Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine"
+      },
+      {
+        "author_name": "Angelic Juarez",
+        "author_inst": "Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine"
+      },
+      {
+        "author_name": "Jason P Wong",
+        "author_inst": "Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine"
+      },
+      {
+        "author_name": "Brian Yang",
+        "author_inst": "Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine"
+      },
+      {
+        "author_name": "Grant S. Broussard",
+        "author_inst": "Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine"
+      },
+      {
+        "author_name": "Blossom Damania",
+        "author_inst": "Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine"
+      },
+      {
+        "author_name": "Dirk Dittmer",
+        "author_inst": "University of North Carolina at Chapel Hill"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.05.08.21256619",
     "rel_title": "Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2",
@@ -764452,41 +763018,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "sexual and reproductive health"
   },
-  {
-    "rel_doi": "10.1101/2021.05.05.21256675",
-    "rel_title": "Relative role of border restrictions, case finding and contact tracing in controlling SARS-CoV-2 in the presence of undetected transmission",
-    "rel_date": "2021-05-09",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.05.21256675",
-    "rel_abs": "BackgroundSeveral countries have controlled the spread of COVID-19 through varying combinations of border restrictions, case finding, contact tracing and careful calibration on the resumption of domestic activities. However, evaluating the effectiveness of these measures based on observed cases alone is challenging as it does not reflect the transmission dynamics of missed infections.\n\nMethodsCombining data on notified local COVID-19 cases with known and unknown sources of infections (i.e. linked and unlinked cases) in Singapore in 2020 with a transmission model, we reconstructed the incidence of missed infections and estimated the relative effectiveness of different types of outbreak control. We also examined implications for estimation of key real-time metrics -- the reproduction number and ratio of unlinked to linked cases, using observed data only as compared to accounting for missed infections.\n\nFindingsPrior to the partial lockdown in Singapore, initiated in April 2020, we estimated 89% (95%CI 75-99%) of the infections caused by notified cases were contact traced, but only 12.5% (95%CI 2-69%) of the infections caused by missed infectors were identified. We estimated that the reproduction number was 1.23 (95%CI 0.98-1.54) after accounting for missed infections but was 0.90 (95%CI 0.79-1.1) based on notified cases alone. At the height of the outbreak, the ratio of missed to notified infections was 34.1 (95%CI 26.0-46.6) but the ratio of unlinked to linked infections was 0.81 (95%CI 0.59-1.36). Our results suggest that when case finding and contact tracing identifies at least 50% and 20% of the infections caused by missed and notified cases respectively, the reproduction number could be reduced by more than 14%, rising to 20% when contact tracing is 80% effective.\n\nInterpretationDepending on the relative effectiveness of border restrictions, case finding and contact tracing, unobserved outbreak dynamics can vary greatly. Commonly used metrics to evaluate outbreak control -- typically based on notified data -- could therefore misrepresent the true underlying outbreak.\n\nFundingMinistry of Health, Singapore.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed, BioRxiv and MedRxiv for articles published in English up to Mar 20, 2021 using the terms: (2019-nCoV OR \"novel coronavirus\" OR COVID-19 OR SARS-CoV-2) AND (border OR travel OR restrict* OR import*) AND (\"case finding\" OR surveillance OR test*) AND (contact trac*) AND (model*). The majority of modelling studies evaluated the effectiveness of various combinations of interventions in the absence of outbreak data. For studies that reconstructed the initial spread of COVID-19 with outbreak data, they further simulated counterfactual scenarios in the presence or absence of these interventions to quantify the impact to the outbreak trajectory. None of the studies disentangled the effects of case finding, contact tracing, introduction of imported cases and the reproduction number, in order to reproduce an observed SARS-CoV-2 outbreak trajectory.\n\nAdded value of this studyNotified COVID-19 cases with unknown and known sources of infection are identified through case finding and contact tracing respectively. Their respective daily incidence and the growth rate over time may differ. By capitalising on these differences in the outbreak data and the use of a mathematical model, we could identify the key drivers behind the growth and decline of both notified and missed COVID-19 infections in different time periods -- e.g. domestic transmission vs external introductions, relative role of case finding and contact tracing in domestic transmission. Estimating the incidence of missed cases also allows us to evaluate the usefulness of common surveillance metrics that rely on observed cases.\n\nImplications of all the available evidenceComprehensive outbreak investigation data integrated with mathematical modelling helps to quantify the strengths and weaknesses of each outbreak control intervention during different stages of the pandemic. This would allow countries to better allocate limited resources to strengthen outbreak control. Furthermore, the data and modelling approach allows us to estimate the extent of missed infections in the absence of population wide seroprevalence surveys. This allows us to compare the growth dynamics of notified and missed infections as reliance on the observed data alone may create the illusion of a controlled outbreak.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Rachael Pung",
-        "author_inst": "Ministry of Health, Singapore"
-      },
-      {
-        "author_name": "Hannah E. Clapham",
-        "author_inst": "Saw Swee Hock School of Public Health, National University of Singapore, Singapore"
-      },
-      {
-        "author_name": "Vernon J. Lee",
-        "author_inst": "Ministry of Health, Singapore"
-      },
-      {
-        "author_name": "Adam J Kucharski",
-        "author_inst": "London School of Hygiene & Tropical Medicine"
-      },
-      {
-        "author_name": "- CMMID COVID-19 working group",
-        "author_inst": ""
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.05.05.21256396",
     "rel_title": "A prospective diagnostic study to measure the accuracy of detection of SARS-CoV-2 Variants Of Concern (VOC) utilising a novel RT-PCR GENotyping algorithm in an In silico Evaluation (VOC-GENIE)",
@@ -765273,6 +763804,49 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2021.05.08.443275",
+    "rel_title": "In-vivo Protection from SARS-CoV-2 infection by ATN-161 in k18-hACE2 transgenic mice",
+    "rel_date": "2021-05-09",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.08.443275",
+    "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an infectious disease that has spread worldwide. Current treatments are limited in both availability and efficacy, such that improving our understanding of the factors that facilitate infection is urgently needed to more effectively treat infected individuals and to curb the pandemic. We and others have previously demonstrated the significance of interactions between the SARS-CoV-2 spike protein, integrin 5{beta}1, and human ACE2 to facilitate viral entry into host cells in vitro. We previously found that inhibition of integrin 5{beta}1 by the clinically validated small peptide ATN-161 inhibits these spike protein interactions and cell infection in vitro. In continuation with our previous findings, here we have further evaluated the therapeutic potential of ATN-161 on SARS-CoV-2 infection in k18-hACE2 transgenic (SARS-CoV-2 susceptible) mice in vivo. We discovered that treatment with single- or repeated intravenous doses of ATN-161 (1 mg/kg) within 48 hours after intranasal inoculation with SARS-CoV-2 lead to a reduction of lung viral load, viral immunofluorescence and improved lung histology in a majority of mice 72 hours post-infection. Furthermore, ATN-161 reduced SARS-CoV-2-induced increased expression of lung integrin 5 and v (an 5-related integrin that has also been implicated in SARS-CoV-2 interactions) as well as the C-X-C motif chemokine ligand 10 (Cxcl10), further supporting the potential involvement of these integrins, and the anti-inflammatory potential of ATN-161, respectively, in SARS-CoV-2 infection. To the best of our knowledge, this is the first study demonstrating the potential therapeutic efficacy of targeting integrin 5{beta}1 in SARS-CoV-2 infection in vivo and supports the development of ATN-161 as a novel SARS-CoV-2 therapy.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Amruta Narayanappa",
+        "author_inst": "Tulane School of Medicine"
+      },
+      {
+        "author_name": "Elizabeth B Engler-Chiurazzi",
+        "author_inst": "Tulane University"
+      },
+      {
+        "author_name": "Isabel C Murray-Brown",
+        "author_inst": "Tulane University"
+      },
+      {
+        "author_name": "Timothy E Gressett",
+        "author_inst": "Tulane University"
+      },
+      {
+        "author_name": "Ifechukwude J Biose",
+        "author_inst": "Tulane University"
+      },
+      {
+        "author_name": "Wesley H Chastain",
+        "author_inst": "Tulane University"
+      },
+      {
+        "author_name": "Gregory Bix",
+        "author_inst": "Tulane University"
+      }
+    ],
+    "version": "1",
+    "license": "",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2021.05.07.442971",
     "rel_title": "Expansion of tissue-resident CD8+ T cells and CD4+ Th17 cells in the nasal mucosa following mRNA COVID-19 vaccination",
@@ -766574,29 +765148,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pediatrics"
   },
-  {
-    "rel_doi": "10.1101/2021.05.04.21256588",
-    "rel_title": "Computing a Lower Bound for the Total Size of the COVID-19 Infected Population Iceberg Using the General Age-Group Distribution",
-    "rel_date": "2021-05-07",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256588",
-    "rel_abs": "Epidemics and Pandemics such as COVID-19 require estimating total infection prevalence. Accurate estimates support better monitoring, evaluation of proximity to herd immunity, estimation of infection fatality rates (IFRs), and assessment of risks due to infection by asymptomatic individuals, especially in developing countries, which lack population-wide serological testing.\n\nWe suggest a method for estimating the infection prevalence by finding the Pivot group, the population sub-group with the highest susceptibility for being confirmed as positively infected. We differentiate susceptibility to infection, assumed to be uniform across all population sub-groups (a key assumption), from susceptibility to developing symptoms and complications, which differs between sub-groups (e.g., by age). We compute the minimal infection-prevalence factor by which the number of positively confirmed patients should be multiplied that allows for a sufficient number of Pivot-group infections that explains the number of Pivot group confirmations.\n\nWe applied the method to the COVID-19 pandemic, using UK and Spain serological surveys. Our key assumption held, and actual infection-prevalence factors were consistent with our predictions. We computed minimal infection-prevalence factors, and when possible, assessed IFRs and serology-based IFRs, for the COVID-19 pandemic in eight countries.\n\nEstimating a lower bound for an epidemics infection prevalence using our methodology is feasible, and the assumptions underlying it are valid. The use of our methodology is often necessary for developing countries, especially in the early phases of an epidemic when serological data are not yet available or when new mutations of a known virus appear.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Yuval Shahar",
-        "author_inst": "Ben Gurion University"
-      },
-      {
-        "author_name": "Osnat Mokryn",
-        "author_inst": "University of Haifa"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.05.05.21256712",
     "rel_title": "Unified real-time environmental-epidemiological data for multiscale modeling of the COVID-19 pandemic",
@@ -766907,6 +765458,85 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.05.05.21256475",
+    "rel_title": "Extracorporeal membrane oxygenation in COVID-19 patients and in-hospital mortality: results from the Brazilian Registry using a propensity score matched analysis",
+    "rel_date": "2021-05-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.05.21256475",
+    "rel_abs": "Around 5% of coronavirus disease 2019 (COVID-19) patients develop critical disease, with severe pneumonia and acute respiratory distress syndrome (ARDS). In these cases, extracorporeal membrane oxygenation (ECMO) may be considered when conventional therapy fails. This study aimed to assess the clinical characteristics and in-hospital outcomes of COVID-19 patients with ARDS refractory to standard lung-protective ventilation and pronation treated with ECMO support and to compare them to patients who did not receive ECMO. Patients were selected from the Brazilian COVID-19 Registry. At the moment of the analysis, 7,646 patients were introduced in the registry, eight of those received ECMO support (0.1%). The convenience sample of patients submitted to ECMO was compared to control patients selected by genetic matching for gender, age, comorbidities, pronation, ARDS and hospital, in a 5:1 ratio. From the 48 patients included in the study, eight received ECMO and 40 were matched controls. There were no significant differences in demographic, clinical and laboratory characteristics. Mortality was higher in the ECMO group (n = 7; 87.5%) when compared with controls (n = 17; 42.5%), (p=0.048). In conclusion, COVID 19 patients with ARDS refractory to conventional therapy who received ECMO support had worse outcomes to patients who did not receive ECMO. Our findings are not different from previous studies including a small number of patients, however there is a huge difference from Extracorporeal Life Support Organization results, which encourages us to keep looking for our best excellence.",
+    "rel_num_authors": 16,
+    "rel_authors": [
+      {
+        "author_name": "Daniela Ponce",
+        "author_inst": "Faculdade de Medicina de Botucatu. Universidade Estadual Paulista Julio de Mesquita Filho"
+      },
+      {
+        "author_name": "Milena Soriano Marcolino",
+        "author_inst": "Hospital Universitario, Universidade Federal de Minas Gerais"
+      },
+      {
+        "author_name": "Magda Carvalho Pires",
+        "author_inst": "Departamento de Estatistica, Universidade Federal de Minas Gerais."
+      },
+      {
+        "author_name": "Rafael Lima Rodrigues de Carvalho",
+        "author_inst": "Instituto de Avaliacaoo de Tecnologia em Saude"
+      },
+      {
+        "author_name": "Heloisa Reniers Vianna",
+        "author_inst": "Hospital Universitario Ciencias Medicas"
+      },
+      {
+        "author_name": "Matheus Carvalho Alves Nogueira",
+        "author_inst": "Hospitais da Rede Mater Dei"
+      },
+      {
+        "author_name": "Fernando Antonio Botoni",
+        "author_inst": "Hospital Julia Kubitschek"
+      },
+      {
+        "author_name": "Fernando Graca Aranha",
+        "author_inst": "Hospital SOS Cardio"
+      },
+      {
+        "author_name": "Andre Soares de Moura Costa",
+        "author_inst": "Hospitais da Rede Mater Dei"
+      },
+      {
+        "author_name": "Giovanna Grunewald Vietta",
+        "author_inst": "Hospital SOS Cardio"
+      },
+      {
+        "author_name": "Felipe Ferraz Martins Graca Aranha",
+        "author_inst": "Hospital SOS Cardio"
+      },
+      {
+        "author_name": "Maria Clara Pontello Barbosa Lima",
+        "author_inst": "Universidade Federal de Ouro Preto. Hospitais da Rede Mater Dei."
+      },
+      {
+        "author_name": "Ana Paula Beck da Silva Etges",
+        "author_inst": "Universidade Federal do Rio Grande do Sul, Instituto de Avaliacao de Tecnologia em Saude"
+      },
+      {
+        "author_name": "Antonio Tolentino Nogueira de Sa",
+        "author_inst": "Faculty of Medicine, Universidade Federal de Minas Gerais"
+      },
+      {
+        "author_name": "Luana Martins Oliveira",
+        "author_inst": "CEPEAD, Universidade Federal de Minas Gerais"
+      },
+      {
+        "author_name": "Carisi Anne Polanczyk",
+        "author_inst": "Universidade Federal do Rio Grande do Sul, Instituto de Avaliacao de Tecnologia em Saude"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.05.06.21253948",
     "rel_title": "The first GAEN-based COVID-19 contact tracing app in Norway identifies 80% of close contacts in \"real life\" scenarios.",
@@ -768696,169 +767326,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.05.04.21256507",
-    "rel_title": "Describing the burden of the COVID-19 pandemic in people with psoriasis: findings from a global cross-sectional study",
-    "rel_date": "2021-05-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256507",
-    "rel_abs": "BackgroundIndirect excess morbidity has emerged as a major concern in the COVID-19 pandemic. People with psoriasis may be particularly vulnerable to this because of prevalent anxiety and depression, multimorbidity and therapeutic use of immunosuppression.\n\nObjectiveCharacterise the factors associated with worsening psoriasis in the COVID-19 pandemic, using mental health status (anxiety and depression) as the main exposure of interest.\n\nMethodsGlobal cross-sectional study using a primary outcome of self-reported worsening of psoriasis. Individuals with psoriasis completed an online self-report questionnaire (PsoProtectMe; Psoriasis Patient Registry for Outcomes, Therapy and Epidemiology of COVID-19 Infection Me) between May 2020 and January 2021. Each individual completed a validated screen for anxiety (Generalized Anxiety Disorder-2) and depression (Patient Health Questionnaire-2). Odds ratios (OR) and 95% confidence intervals (CI) were estimated using multivariable logistic regression.\n\nResults4,043 people with psoriasis (without COVID-19) from 86 countries self-reported to PsoProtectMe (mean age 47.2 years [SD 15.1]; mean BMI 27.6kg/m2 [SD 6.0], 2,684 [66.4%] female and 3,016 [74.6%] of white European ethnicity). 1,728 (42.7%) participants (1322 [77%] female) reported worsening of their psoriasis in the pandemic. A positive screen for anxiety or depression associated with worsening psoriasis in age and gender adjusted (OR 2.04, 95% CI 1.77-2.36), and fully adjusted (OR 2.01, 95% CI 1.72-2.34) logistic regression models. Female sex, obesity, shielding behaviour and systemic immunosuppressant non-adherence also associated with worsening psoriasis. The commonest reason for non-adherence was concern regarding complications related to COVID-19.\n\nConclusionsThese data indicate an association between poor mental health and worsening psoriasis in the pandemic. Access to holistic care including psychological support may mitigate potentially long-lasting effects of the pandemic on health outcomes in psoriasis. The study also highlights an urgent need to address patient concerns about immunosuppressant-related risks, which may be contributing to non-adherence.",
-    "rel_num_authors": 37,
-    "rel_authors": [
-      {
-        "author_name": "Satveer K Mahil",
-        "author_inst": "St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK"
-      },
-      {
-        "author_name": "Mark Yates",
-        "author_inst": "Centre for Rheumatic Diseases, King's College London"
-      },
-      {
-        "author_name": "Zenas Z Yiu",
-        "author_inst": "Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese"
-      },
-      {
-        "author_name": "Sinead M Langan",
-        "author_inst": "Faculty of Epidemiology, and Population Health, London School of Hygiene and Tropical Medicine, London, UK"
-      },
-      {
-        "author_name": "Teresa Tsakok",
-        "author_inst": "St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK"
-      },
-      {
-        "author_name": "Nick Dand",
-        "author_inst": "Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King's College London, London, UK"
-      },
-      {
-        "author_name": "Kayleigh J Mason",
-        "author_inst": "Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese"
-      },
-      {
-        "author_name": "Helen McAteer",
-        "author_inst": "The Psoriasis Association, Northampton, UK"
-      },
-      {
-        "author_name": "Freya Meynall",
-        "author_inst": "St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK"
-      },
-      {
-        "author_name": "Bolaji Coker",
-        "author_inst": "NIHR Biomedical Research Centre at Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK"
-      },
-      {
-        "author_name": "Alexandra Vincent",
-        "author_inst": "NIHR Biomedical Research Centre at Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK"
-      },
-      {
-        "author_name": "Dominic Urmston",
-        "author_inst": "The Psoriasis Association, Northampton, UK"
-      },
-      {
-        "author_name": "Amber Vesty",
-        "author_inst": "The Psoriasis Association, Northampton, UK"
-      },
-      {
-        "author_name": "Jade Kelly",
-        "author_inst": "Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese"
-      },
-      {
-        "author_name": "Camille Lancelot",
-        "author_inst": "International Federation of Psoriasis Associations"
-      },
-      {
-        "author_name": "Lucy Moorhead",
-        "author_inst": "St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK"
-      },
-      {
-        "author_name": "Herve Bachelez",
-        "author_inst": "Department of Dermatology, AP-HP Hopital Saint-Louis, Paris, France"
-      },
-      {
-        "author_name": "Francesca Capon",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Claudia R Contreras",
-        "author_inst": "Catedra de Dermatologia, Hospital de Clinicas, Facultad de Ciencias Medicas, Universidad Nacional de Asuncion, Paraguay"
-      },
-      {
-        "author_name": "Claudia De La Cruz",
-        "author_inst": "Clinica Dermacross, Santiago, Chile"
-      },
-      {
-        "author_name": "Paola Di Meglio",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Paolo Gisondi",
-        "author_inst": "Section of Dermatology and Venereology, University of Verona, Verona, Italy"
-      },
-      {
-        "author_name": "Denis Jullien",
-        "author_inst": "Department of Dermatology, Edouard Herriot Hospital, Hospices Civils de Lyon, University of Lyon, Lyon, France"
-      },
-      {
-        "author_name": "Jo Lambert",
-        "author_inst": "Department of Dermatology, Ghent University, Ghent, Belgium"
-      },
-      {
-        "author_name": "Luigi Naldi",
-        "author_inst": "Centro Studi GISED, Bergamo, Italy"
-      },
-      {
-        "author_name": "Sam Norton",
-        "author_inst": "Psychology Department, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, UK"
-      },
-      {
-        "author_name": "Luis Puig",
-        "author_inst": "Department of Dermatology, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Catalonia, Spain"
-      },
-      {
-        "author_name": "Phyllis Spuls",
-        "author_inst": "Department of Dermatology, Amsterdam Public Health/Infection and Immunology, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands"
-      },
-      {
-        "author_name": "Tiago Torres",
-        "author_inst": "Department of Dermatology, Centro Hospitalar do Porto, Portugal"
-      },
-      {
-        "author_name": "Richard B Warren",
-        "author_inst": "Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese"
-      },
-      {
-        "author_name": "Hoseah Waweru",
-        "author_inst": "International Federation of Psoriasis Associations"
-      },
-      {
-        "author_name": "John Weinman",
-        "author_inst": "School of Cancer and Pharmaceutical Sciences, Kings College London, London, UK"
-      },
-      {
-        "author_name": "Matt A Brown",
-        "author_inst": "Centre for Rheumatic Diseases, King's College London, London, UK"
-      },
-      {
-        "author_name": "James B Galloway",
-        "author_inst": "Centre for Rheumatic Diseases, King's College London, London, UK"
-      },
-      {
-        "author_name": "Christopher M Griffiths",
-        "author_inst": "3Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Res"
-      },
-      {
-        "author_name": "Jonathan N Barker",
-        "author_inst": "NIHR Biomedical Research Centre at Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK"
-      },
-      {
-        "author_name": "Catherine H Smith",
-        "author_inst": "St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "dermatology"
-  },
   {
     "rel_doi": "10.1101/2021.05.04.21256575",
     "rel_title": "SARS-CoV-2 infections and hospitalizations among immigrants in Norway: significance of occupation, household crowding, education, household income and medical risk. A nationwide register study",
@@ -769245,6 +767712,93 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "emergency medicine"
   },
+  {
+    "rel_doi": "10.1101/2021.05.04.21256609",
+    "rel_title": "SARS-CoV-2 infection and reinfection in a seroepidemiological workplace cohort in the United States",
+    "rel_date": "2021-05-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256609",
+    "rel_abs": "Identifying the extent of SARS-CoV-2 reinfection is crucial for understanding possible long-term epidemic dynamics. We analysed longitudinal PCR and serological testing data from a prospective cohort of 4411 US employees in four states between April 2020 and February 2021. We conducted a multivariable logistic regression investigating the association between baseline serological status and subsequent PCR test result in order to calculate an odds ratio for reinfection. We estimated an adjusted odds ratio of 0.09 (95% CI: 0.005 - 0.48) for reinfection, implying that the presence of SARS-CoV-2 antibodies at baseline is associated with around 91% reduced odds of a subsequent PCR positive test. This suggests that primary infection with SARS-CoV-2 provides protection against reinfection in the majority of individuals, at least over a sixth month time period. We also highlight two major sources of bias and uncertainty to be considered when estimating reinfection risk, confounders and the choice of baseline time point, and show how to account for both in our analysis.",
+    "rel_num_authors": 18,
+    "rel_authors": [
+      {
+        "author_name": "Emilie Finch",
+        "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London. WC1E 7HT UK"
+      },
+      {
+        "author_name": "Rachel Lowe",
+        "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London. WC1E 7HT UK"
+      },
+      {
+        "author_name": "Stephanie Fischinger",
+        "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA and Institut fur HIV Forschung, Universitat Duisburg-Essen, Duisburg, Germany"
+      },
+      {
+        "author_name": "Michael de St Aubin",
+        "author_inst": "Harvard Humanitarian Initiative, Cambridge, MA, USA"
+      },
+      {
+        "author_name": "Sameed M. Siddiqui",
+        "author_inst": "Computational and Systems Biology Program, Massachusetts Institute of Technology and Broad Institute of MIT and Harvard, Cambridge, MA, USA"
+      },
+      {
+        "author_name": "Diana Dayal",
+        "author_inst": "Space Exploration Technologies Corp"
+      },
+      {
+        "author_name": "Michael A. Loesche",
+        "author_inst": "Space Exploration Technologies Corp and Brigham and Women's Hospital, Boston"
+      },
+      {
+        "author_name": "Justin Rhee",
+        "author_inst": "Space Exploration Technologies Corp"
+      },
+      {
+        "author_name": "Samuel Berger",
+        "author_inst": "Space Exploration Technologies Corp"
+      },
+      {
+        "author_name": "Yiyuan Hu",
+        "author_inst": "Space Exploration Technologies Corp"
+      },
+      {
+        "author_name": "Matthew J. Gluck",
+        "author_inst": "Space Exploration Technologies Corp"
+      },
+      {
+        "author_name": "Benjamin Mormann",
+        "author_inst": "Space Exploration Technologies Corp"
+      },
+      {
+        "author_name": "Mohammad A. Hasdianda",
+        "author_inst": "Brigham and Women's Hospital, Boston"
+      },
+      {
+        "author_name": "Elon R. Musk",
+        "author_inst": "Space Exploration Technologies Corp"
+      },
+      {
+        "author_name": "Galit Alter",
+        "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA and Broad Institute of MIT and Harvard, Cambridge, MA, USA"
+      },
+      {
+        "author_name": "Anil S. Menon",
+        "author_inst": "Space Exploration Technologies Corp"
+      },
+      {
+        "author_name": "Eric J. Nilles",
+        "author_inst": "Harvard Humanitarian Initiative, Cambridge, MA, USA and Brigham and Women's Hospital, Boston"
+      },
+      {
+        "author_name": "Adam J. Kucharski",
+        "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London. WC1E 7HT UK"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.05.04.21256597",
     "rel_title": "SARS-CoV-2 seroprevalence in Germany - a population based sequential study in five regions",
@@ -770637,41 +769191,6 @@
     "type": "new results",
     "category": "molecular biology"
   },
-  {
-    "rel_doi": "10.1101/2021.05.03.21256561",
-    "rel_title": "dPQL: a lossless distributed algorithm for generalized linear mixed model with application to privacy-preserving hospital profiling",
-    "rel_date": "2021-05-05",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.03.21256561",
-    "rel_abs": "Hospital profiling provides a quantitative comparison of health care providers for their quality of care regarding certain clinical outcomes. To implement hospital profiling, the generalized linear mixed model (GLMM) is usually used to fit clinical or administrative claims data, adjusting for the effects of covariates. For better generalizability, data across multiple hospitals, databases or networks are desired. However, due to the privacy regulation and the computation complexity of GLMM, a convenient distributed algorithm for hospital profiling is needed. In this paper, we develop a novel distributed Penalized Quasi Likelihood algorithm (dPQL) to fit GLMM, when only aggregated data, rather than the individual patient data are available across hospitals. The dPQL algorithm is based on a newly-developed distributed linear mixed model (DLMM) algorithm. This proposed dPQL algorithm is lossless, i.e. it obtains identical results as if the individual patient data are pooled from all hospitals. We demonstrate the usage of the dPQL algorithms by ranking 929 hospitals for COVID-19 mortality or referral to hospice in Asch, et al. 2020.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Chongliang Luo",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Md. Nazmul Islam",
-        "author_inst": "OptumLabs at UnitedHealth Group"
-      },
-      {
-        "author_name": "Natalie E. Sheils",
-        "author_inst": "OptumLabs at UnitedHealth Group"
-      },
-      {
-        "author_name": "John Buresh",
-        "author_inst": "OptumLabs at UnitedHealth Group"
-      },
-      {
-        "author_name": "Yong Chen",
-        "author_inst": "University of Pennsylvania"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health informatics"
-  },
   {
     "rel_doi": "10.1101/2021.05.05.442779",
     "rel_title": "ProLung\u2122-budesonide Inhibits SARS-CoV-2 Replication and Reduces Lung Inflammation",
@@ -771006,6 +769525,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "occupational and environmental health"
   },
+  {
+    "rel_doi": "10.1101/2021.05.01.21256442",
+    "rel_title": "Prevalence of anxiety, depression, and stress among teachers during the COVID-19 pandemic: Systematic review",
+    "rel_date": "2021-05-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.01.21256442",
+    "rel_abs": "ObjectiveIdentifying the prevalence of anxiety, depression, and stress among teachers during the COVID-19 pandemic.\n\nMethodsSystematic review of original studies published in any language. Protocol published in PROSPERO under number CRD42021240543. The search was carried out in the Web of Science, PsycINFO, Pubmed, Embase, LILACS, and SciELO databases, using the descriptors: anxiety, depression, stress, teacher, faculty, COVID-19, and their synonyms. Narrative synthesis was carried out in line with the synthesis without meta-analysis (SWiM) in systematic reviews.\n\nResultsOf the 1,372 records identified, six studies, all cross-sectional, were included in the review. The studies were carried out in China, Brazil, the United States of America, India, and Spain. Five studies included more women than men. The participants were aged from 24 to 60 years. Three studies included only school teachers, two included schools and universities teachers, and one only university teachers. Of the five studies, all dealt with remote activities and only one included teachers who returned to face-to-face classes one to two weeks ago. The prevalence of anxiety ranged from 10% to 49.4%, and depression from 15.9% to 28.9%, being considerably higher in studies with teachers who worked in schools. The prevalence of stress ranged from 12.6% to 50.6%.\n\nConclusionsThe prevalence of anxiety, depression, and stress was high among teachers during the pandemic, with great variation between studies. Anxiety and stress were more prevalent in the Spanish study. The results show the need for measures for the care of teachers mental health, especially when returning to face-to-face classes.\n\nWhat is already known about this subject?[tpltrtarr] With remote classes during the COVID-19 pandemic, there were changes in the professional practice of teachers.\n[tpltrtarr]Sudden changes in professional practice can result in increased levels of anxiety, depression, and stress.\n[tpltrtarr]Returning to face-to-face classes can also result in increased levels of anxiety, depression, and stress.\n\n\nWhat are the new findings?[tpltrtarr] The prevalence of anxiety ranged from 10% to 49.4%, with higher rates recorded in female teachers, with comorbidities and working in schools.\n[tpltrtarr]The prevalence of depression ranged from 15.9% to 28.9%, with higher rates identified in school teachers.\n[tpltrtarr]The prevalence of stress varied from 12.6% to 50.6%, with higher rates observed among female teachers and those with chronic diseases.\n[tpltrtarr]The only study that performed data collection during the return to face-to-face classes registered a higher prevalence of anxiety and stress than the other studies, in which the research was carried out during remote classes.\n\n\nHow might this impact policy or clinical practice in the foreseeable future?[tpltrtarr] Better training of teachers to handle the remote education model can contribute to preventing work overload and mental problems. Further, pedagogical and psychological support, especially for those who work in schools, can also prove effective.\n[tpltrtarr]The return to face-to-face classes can increase stress and anxiety. Ensuring bio-safety protocols for safe return to face-to-face activities, can contribute to mitigating anxiety and stress about the risk of contracting the disease.\n[tpltrtarr]There is insufficient evidence to determine a cause and effect relationship of the COVID-19 pandemic with anxiety, depression, and stress among teachers. Prospective cohort studies with control of confounding factors are necessary to infer that the pandemic has increased mental health problems in these professionals.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "David Franciole de Oliveira Silva",
+        "author_inst": "Federal University of Rio Grande do Norte"
+      },
+      {
+        "author_name": "Ricardo Ney Oliveira Cobucci",
+        "author_inst": "Potiguar University"
+      },
+      {
+        "author_name": "Severina Carla Vieira Cunh Lima",
+        "author_inst": "Federal University of Rio Grande do Norte"
+      },
+      {
+        "author_name": "Fabia Barbosa de Andrade",
+        "author_inst": "Federal University of Rio Grande do Norte"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "occupational and environmental health"
+  },
   {
     "rel_doi": "10.1101/2021.05.01.21256470",
     "rel_title": "LENZILUMAB EFFICACY AND SAFETY IN NEWLY HOSPITALIZED COVID-19 SUBJECTS: RESULTS FROM THE LIVE-AIR PHASE 3 RANDOMIZED DOUBLE-BLIND PLACEBO-CONTROLLED TRIAL",
@@ -772643,61 +771193,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2021.04.30.442222",
-    "rel_title": "Possible role of accessory proteins in the viral replication for the 20I/501Y.V1 (B.1.1.7) SARS-CoV-2 variant",
-    "rel_date": "2021-05-04",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.30.442222",
-    "rel_abs": "The study investigates the replication cycle and transcriptional pattern of the B.1.1.7 variant. It was observed that the B.1.1.7 variant required a longer maturation time. The transcriptional response demonstrated higher expression of ORF6 and ORF8 compared to nucleocapsid transcript till the eclipse period which might influence higher viral replication. The number of infectious viruses titer is higher in the B.1.1.7, despite a lesser copy number than B.1, indicating higher infectivity.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Dimpal A Nyayanit",
-        "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India Pin-411021"
-      },
-      {
-        "author_name": "Prasad Sarkale",
-        "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India Pin-411021"
-      },
-      {
-        "author_name": "Anita Shete-Aich",
-        "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India Pin-411021"
-      },
-      {
-        "author_name": "Abhinendra Kumar",
-        "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India Pin-411021"
-      },
-      {
-        "author_name": "Savita Patil",
-        "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India Pin-411021"
-      },
-      {
-        "author_name": "Triparna Majumdar",
-        "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India Pin-411021"
-      },
-      {
-        "author_name": "Shreekant Baradkar",
-        "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India Pin-411021"
-      },
-      {
-        "author_name": "Pranita Gawande",
-        "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India Pin-411021"
-      },
-      {
-        "author_name": "Sreelekshmy Mohandas",
-        "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India Pin-411021"
-      },
-      {
-        "author_name": "Pragya Dhruv Yadav",
-        "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India Pin-411021"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2021.05.03.442392",
     "rel_title": "The method utilized to purify the SARS-CoV-2 N protein can affect its molecular properties",
@@ -773008,6 +771503,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "nephrology"
   },
+  {
+    "rel_doi": "10.1101/2021.05.01.21256452",
+    "rel_title": "A hemagglutination-based, semi-quantitative test for point-of-care determination of SARS-CoV-2 antibody levels",
+    "rel_date": "2021-05-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.01.21256452",
+    "rel_abs": "Serologic, point-of-care tests to detect antibodies against SARS-CoV-2 are an important tool in the COVID-19 pandemic. The majority of current point-of-care antibody tests developed for SARS-CoV-2 rely on lateral flow assays, but these do not offer quantitative information. To address this, we developed a new method of COVID-19 antibody testing employing hemagglutination tested on a dry card, similar to that which is already available for rapid typing of ABO blood groups. A fusion protein linking red blood cells (RBCs) to the receptor-binding domain (RBD) of SARS-CoV-2 spike protein was placed on the card. 200 COVID-19 patient and 200 control plasma samples were reconstituted with O-negative RBCs to form whole blood and added to the dried protein, followed by a stirring step and a tilting step, 3-minute incubation, and a second tilting step. The sensitivity for the hemagglutination test, Euroimmun IgG ELISA test and RBD-based CoronaChek lateral flow assay was 87.0%, 86.5%, and 84.5%, respectively, using samples obtained from recovered COVID-19 individuals. Testing pre-pandemic samples, the hemagglutination test had a specificity of 95.5%, compared to 97.3% and 98.9% for the ELISA and CoronaChek, respectively. A distribution of agglutination strengths was observed in COVID-19 convalescent plasma samples, with the highest agglutination score (4) exhibiting significantly higher neutralizing antibody titers than weak positives (2) (p<0.0001). Strong agglutinations were observed within 1 minute of testing, and this shorter assay time also increased specificity to 98.5%. In conclusion, we developed a novel rapid, point-of-care RBC agglutination test for the detection of SARS-CoV-2 antibodies that can yield semi-quantitative information on neutralizing antibody titer in patients. The five-minute test may find use in determination of serostatus prior to vaccination, post-vaccination surveillance and travel screening.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Robert Kruse",
+        "author_inst": "Department of Pathology, Johns Hopkins University School of Medicine"
+      },
+      {
+        "author_name": "Yuting Huang",
+        "author_inst": "Department of Medicine, University of Maryland Medical Center Midtown Campus"
+      },
+      {
+        "author_name": "Alyssa Lee",
+        "author_inst": "Johns Hopkins University School of Medicine"
+      },
+      {
+        "author_name": "Xianming Zhu",
+        "author_inst": "Department of Pathology, Johns Hopkins University School of Medicine"
+      },
+      {
+        "author_name": "Ruchee Shrestha",
+        "author_inst": "Department of Medicine, Johns Hopkins University School of Medicine"
+      },
+      {
+        "author_name": "Oliver Laeyendecker",
+        "author_inst": "Department of Medicine, Johns Hopkins University School of Medicine"
+      },
+      {
+        "author_name": "Kirsten Littlefield",
+        "author_inst": "Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health"
+      },
+      {
+        "author_name": "Andy Pekosz",
+        "author_inst": "Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health"
+      },
+      {
+        "author_name": "Evan M Bloch",
+        "author_inst": "Department of Pathology, Johns Hopkins University School of Medicine"
+      },
+      {
+        "author_name": "Aaron A.R. Tobian",
+        "author_inst": "Department of Pathology, Johns Hopkins University School of Medicine"
+      },
+      {
+        "author_name": "Zack Z Wang",
+        "author_inst": "Department of Medicine, Johns Hopkins University School of Medicine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.04.30.21256415",
     "rel_title": "A Meta-analysis of Mortality, Need for ICU admission, Use of Mechanical Ventilation and Adverse Effects with Ivermectin Use in COVID-19 Patients",
@@ -774090,20 +772644,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "respiratory medicine"
   },
-  {
-    "rel_doi": "10.1101/2021.05.04.21256107",
-    "rel_title": "Environmental Screening for Surface SARS-CoV-2 Contamination in Urban High-Touch Areas",
-    "rel_date": "2021-05-04",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256107",
-    "rel_abs": "The novel human coronavirus 2 (SARS-CoV-2) is responsible for the COVID-19 outbreak, which reached pandemic-level infection rates in just a few short months after being identified in late 2019. Early transmission models focused on surface contamination, but current research provides evidence for person-to-person transmission via aerosolized viral particles. As such, the CDCs guidance has recently been updated to increasingly redirect the focus of prevention methods to aerosol routes. Inhalation of SARS-CoV-2 particles presents the most significant threat of infection to individuals. A secondary route, from hand to mouth, eyes or nose, is likely after contact with a surface contaminated with particles that have settled out of aerosols or been deposited by contaminated hands. Using common molecular detection methods including endpoint and quantitative PCR, we investigated whether there is detectable contamination by SARS-CoV-2 on high-touch surfaces on public transit vehicles and on other high-touch surfaces on a college campus during normal use. Our results indicate that SARS-CoV-2 can be successfully recovered and detected on common high-touch surfaces, albeit in comparatively lower frequencies as public health guidance progressed and more rigorous sanitization procedures were implemented.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC=\"FIGDIR/small/21256107v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (27K):\norg.highwire.dtl.DTLVardef@f8604forg.highwire.dtl.DTLVardef@7b02d5org.highwire.dtl.DTLVardef@1f700a9org.highwire.dtl.DTLVardef@14c5b54_HPS_FORMAT_FIGEXP  M_FIG C_FIG Graphical abstract created with permission from BioRender.com (2021).",
-    "rel_num_authors": 0,
-    "rel_authors": null,
-    "version": "1",
-    "license": "",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "occupational and environmental health"
-  },
   {
     "rel_doi": "10.1101/2021.05.04.21256537",
     "rel_title": "Modeling and Predicting Antibody Durability for mRNA-1273 Vaccine for SARS-CoV-2 Variants",
@@ -774380,6 +772920,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.04.30.21256385",
+    "rel_title": "The immediate and longer-term impact of the COVID-19 pandemic on the mental health and wellbeing of older adults in England",
+    "rel_date": "2021-05-03",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.30.21256385",
+    "rel_abs": "ObjectiveTo evaluate changes in mental health and wellbeing before and during the initial and later phases of the COVID-19 pandemic and investigate whether patterns varied with age, sex, and socioeconomic status.\n\nDesignProspective cohort study.\n\nParticipantsEnglish Longitudinal Study of Ageing cohort of 5146 community dwelling adults aged 52 years and older (53% women, average age 66.74 years, standard deviation 10.62) who provided data before the pandemic (2018-19) and at two occasions in 2020 (June-July and November-December).\n\nMain outcome measureDepression, poor quality of life, loneliness and anxiety.\n\nResultsThe prevalence of clinically significant depressive symptoms increased from 12.5% pre-pandemic to 22.6% in June-July 2020, with a further rise to 28.5% in November-December. This was accompanied by increased loneliness and deterioration in quality of life. The prevalence of anxiety rose from 9.4% to 10.9% between June-July and November-December 2022. Women and non-partnered people experienced worse changes in mental health and wellbeing. Participants with less wealth had lowest levels of mental health before and during the pandemic. Higher socioeconomic groups had better mental health overall, but responded to the pandemic with more negative changes. Patterns of changes were similar across age groups, the only exception was for depression which showed a smaller increase in the 75+ age group than in the youngest age group (50-59 years).\n\nConclusionsThese data showed that mental health and wellbeing continued to worsen as lockdown continued, and that socioeconomic inequalities persisted. Women and non-partnered people experienced greater deterioration in all mental health outcomes. The immediate provision of diagnosis of mental health problems and targeted psychological interventions should target and support sociodemographic groups of older people at higher risk of psychological distress.\n\nWhat is already known on this topic- The COVID-19 pandemic and mitigation measures have upended the economic and social lives of many, leading to widespread psychological distress.\n- During the early months of the pandemic, levels of depression, anxiety and loneliness were high and lower levels of wellbeing were reported across the adult population, with certain higher risk groups identified.\n- However, evidence from longitudinal studies of representative samples of older adults that include pre-pandemic data is scarce, and little is known about mental health beyond the initial period of the pandemic. Repeated assessments are needed in order to understand whether mental health and wellbeing levels recovered or continued to deteriorate throughout 2020.\n\n\nWhat this study adds- These data suggest that mental health and wellbeing deteriorated significantly during June-July 2020 compared with pre-pandemic levels and continued to deteriorate during the second national lockdown in November-December 2020, showing that older individuals did not adapt to circumstances.\n- Inequalities in experiences of mental ill-health and poor wellbeing during 2020 were evident, with women, individuals living alone and those with less wealth being particularly vulnerable. Furthermore, socioeconomic inequalities in mental health have persisted during the pandemic.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Paola Zaninotto",
+        "author_inst": "UCL"
+      },
+      {
+        "author_name": "Eleonora Iob",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Panayotes Demakakos",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Andrew Steptoe",
+        "author_inst": "University College London"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.04.30.21256372",
     "rel_title": "Rehabilitation needs and mortality associated with the Covid-19 pandemic: a population-based study of all hospitalised and home-healthcare individuals in a Swedish healthcare region",
@@ -775909,49 +774480,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2021.05.03.437411",
-    "rel_title": "The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (Mpro)",
-    "rel_date": "2021-05-03",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.03.437411",
-    "rel_abs": "The COVID-19 pandemic, instigated by the SARS-CoV-2 coronavirus, continues to plague the globe. The SARS-CoV-2 main protease, or Mpro, is a promising target for development of novel antiviral therapeutics. Previous X-ray crystal structures of Mpro were obtained at cryogenic temperature or room temperature only. Here we report a series of high-resolution crystal structures of unliganded Mpro across multiple temperatures from cryogenic to physiological, and another at high humidity. We interrogate these datasets with parsimonious multiconformer models, multi-copy ensemble models, and isomorphous difference density maps. Our analysis reveals a temperature-dependent conformational landscape for Mpro, including mobile solvent interleaved between the catalytic dyad, mercurial conformational heterogeneity in a key substrate-binding loop, and a far-reaching intramolecular network bridging the active site and dimer interface. Our results may inspire new strategies for antiviral drug development to counter-punch COVID-19 and combat future coronavirus pandemics.\n\nSynopsisX-ray crystallography at variable temperature for SARS-CoV-2 Mpro reveals a complex conformational landscape, including mobile solvent at the catalytic dyad, mercurial conformational heterogeneity in a key substrate-binding loop, and an intramolecular network bridging the active site and dimer interface.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Ali Ebrahim",
-        "author_inst": "Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England"
-      },
-      {
-        "author_name": "Blake T Riley",
-        "author_inst": "Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031"
-      },
-      {
-        "author_name": "Desigan Kumaran",
-        "author_inst": "Biology Department, Brookhaven National Laboratory, Upton, NY 11973"
-      },
-      {
-        "author_name": "Babak Andi",
-        "author_inst": "National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973"
-      },
-      {
-        "author_name": "Martin R Fuchs",
-        "author_inst": "National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973"
-      },
-      {
-        "author_name": "Sean McSweeney",
-        "author_inst": "National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973"
-      },
-      {
-        "author_name": "Daniel A Keedy",
-        "author_inst": "CUNY Advanced Science Research Center"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "biophysics"
-  },
   {
     "rel_doi": "10.1101/2021.05.02.442384",
     "rel_title": "In silico and in vitro Demonstration of Homoharrintonine Antagonism of RBD-ACE2 Binding and its Anti-inflammatory and anti-thrombogenic Properties in a 3D human vascular lung model",
@@ -776266,6 +774794,137 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.04.27.21256207",
+    "rel_title": "SARS-CoV-2 antibodies remain detectable 12 months after infection and antibody magnitude is associated with age and COVID-19 severity",
+    "rel_date": "2021-05-02",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.27.21256207",
+    "rel_abs": "ImportanceThe persistence of SARS-CoV-2 antibodies may be a predictive correlate of protection for both natural infections and vaccinations. Identifying predictors of robust antibody responses is important to evaluate the risk of re-infection / vaccine failure and may be translatable to vaccine effectiveness.\n\nObjectiveTo 1) determine the durability of anti-SARS-CoV-2 IgG and neutralizing antibodies in subjects who experienced mild and moderate to severe COVID-19, and 2) to evaluate the correlation of age and IgG responses to both endemic human seasonal coronaviruses (HCoVs) and SARS-CoV-2 according to infection outcome.\n\nDesignLongitudinal serum samples were collected from PCR-confirmed SARS-CoV-2 positive participants (U.S. active duty service members, dependents and military retirees, including a range of ages and demographics) who sought medical treatment at seven U.S. military hospitals from March 2020 to March 2021 and enrolled in a prospective observational cohort study.\n\nResultsWe observed SARS-CoV-2 seropositivity in 100% of inpatients followed for six months (58/58) to one year (8/8), while we observed seroreversion in 5% (9/192) of outpatients six to ten months after symptom onset, and 18% (2/11) of outpatients followed for one year. Both outpatient and inpatient anti-SARS-CoV-2 binding-IgG responses had a half-life (T1/2) of >1000 days post-symptom onset. The magnitude of neutralizing antibodies (geometric mean titer, inpatients: 378 [246-580, 95% CI] versus outpatients: 83 [59-116, 95% CI]) and durability (inpatients: 65 [43-98, 95% CI] versus outpatients: 33 [26-40, 95% CI]) were associated with COVID-19 severity. Older age was a positive correlate with both higher IgG binding and neutralizing antibody levels when controlling for COVID-19 hospitalization status. We found no significant relationships between HCoV antibody responses and COVID-19 clinical outcomes, or the development of SARS-CoV-2 neutralizing antibodies.\n\nConclusions and RelevanceThis study demonstrates that humoral responses to SARS-CoV-2 infection are robust on longer time-scales, including those arising from milder infections.\n\nHowever, the magnitude and durability of the antibody response after natural infection was lower and more variable in younger participants who did not require hospitalization for COVID-19. These findings support vaccination against SARS-CoV-2 in all suitable populations including those individuals that have recovered from natural infection.",
+    "rel_num_authors": 29,
+    "rel_authors": [
+      {
+        "author_name": "Eric Laing",
+        "author_inst": "Uniformed Services University"
+      },
+      {
+        "author_name": "Nusrat J Epsi",
+        "author_inst": "Uniformed Services University, Henry M. Jackson Foundation"
+      },
+      {
+        "author_name": "Stephanie A Richard",
+        "author_inst": "Uniformed Services University, Henry M. Jackson Foundation"
+      },
+      {
+        "author_name": "Emily C Samuels",
+        "author_inst": "Uniformed Services University, Henry M. Jackson Foundation"
+      },
+      {
+        "author_name": "Wei Wang",
+        "author_inst": "US Food and Drug Admininstration"
+      },
+      {
+        "author_name": "Russell Vassell",
+        "author_inst": "US Food and Drug Administration"
+      },
+      {
+        "author_name": "Daniel F Ewing",
+        "author_inst": "Naval Medical Research Center-Fort Detrick"
+      },
+      {
+        "author_name": "Rachel Herrup",
+        "author_inst": "US Food and Drug Administration"
+      },
+      {
+        "author_name": "Spencer L. Sterling",
+        "author_inst": "Uniformed Services University, Henry M. Jackson Foundation"
+      },
+      {
+        "author_name": "David A Lindholm",
+        "author_inst": "Brooke Army Medical Center"
+      },
+      {
+        "author_name": "Eugene V Millar",
+        "author_inst": "Uniformed Services University, Henry M. Jackson Foundation"
+      },
+      {
+        "author_name": "Ryan C Maves",
+        "author_inst": "Naval Medical Center San Diego"
+      },
+      {
+        "author_name": "Derek T Larson",
+        "author_inst": "Fort Belvoir Community Hospital"
+      },
+      {
+        "author_name": "Rhonda E Colombo",
+        "author_inst": "Uniformed Services University, Henry M. Jackson Foundation, Madigan Army Medical Center"
+      },
+      {
+        "author_name": "Sharon Chi",
+        "author_inst": "Tripler Army Medical Center"
+      },
+      {
+        "author_name": "Cristian S Madar",
+        "author_inst": "Tripler Army Medical Center"
+      },
+      {
+        "author_name": "Tahaniyat Lalani",
+        "author_inst": "Naval Medical Center Portsmouth"
+      },
+      {
+        "author_name": "Anuradha Ganesan",
+        "author_inst": "Uniformed Services University, Henry M. Jackson Foundation, Walter Reed National Military Medical Center"
+      },
+      {
+        "author_name": "Anthony Fries",
+        "author_inst": "U.S. Air Force School of Aerospace Medicine"
+      },
+      {
+        "author_name": "Christopher J Colombo",
+        "author_inst": "Madigan Army Medical Center"
+      },
+      {
+        "author_name": "Katrin Mende",
+        "author_inst": "Uniformed Services University, Henry M. Jackson Foundation, Brooke Army Medical Center"
+      },
+      {
+        "author_name": "Mark P Simons",
+        "author_inst": "Uniformed Services University"
+      },
+      {
+        "author_name": "Kevin L Schully",
+        "author_inst": "Naval Medical Research Center-Fort Detrick"
+      },
+      {
+        "author_name": "Carol D Weiss",
+        "author_inst": "US Food and Drug Administration"
+      },
+      {
+        "author_name": "David R Tribble",
+        "author_inst": "Uniformed Services University"
+      },
+      {
+        "author_name": "Brian K Agan",
+        "author_inst": "Uniformed Services University, Henry M. Jackson Foundation"
+      },
+      {
+        "author_name": "Simon D Pollett",
+        "author_inst": "Uniformed Services University, Henry M. Jackson Foundation"
+      },
+      {
+        "author_name": "Christopher C Broder",
+        "author_inst": "Uniformed Services University"
+      },
+      {
+        "author_name": "Timothy H Burgess",
+        "author_inst": "Uniformed Services University"
+      }
+    ],
+    "version": "1",
+    "license": "cc0",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.04.28.21256261",
     "rel_title": "Aspirin and NSAID use and the risk of COVID-19",
@@ -777503,141 +776162,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.04.30.21256119",
-    "rel_title": "Association between oral anticoagulants and COVID-19 related outcomes: two cohort studies",
-    "rel_date": "2021-04-30",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.30.21256119",
-    "rel_abs": "ObjectivesWe investigated the role of routinely prescribed oral anticoagulants (OACs) in COVID-19 outcomes, comparing current OAC use versus non-use in Study 1; and warfarin versus direct oral anticoagulants (DOACs) in Study 2.\n\nDesignTwo cohort studies, on behalf of NHS England.\n\nSettingPrimary care data and pseudonymously-linked SARS-CoV-2 antigen testing data, hospital admissions, and death records from England.\n\nParticipantsStudy 1: 70,464 people with atrial fibrillation (AF) and CHA{square}DS{square}-VASc score of 2. Study 2: 372,746 people with non-valvular AF.\n\nMain outcome measuresTime to test for SARS-CoV-2, testing positive for SARS-CoV-2, COVID-19 related hospital admission, COVID-19 deaths or non-COVID-19 deaths in Cox regression.\n\nResultsIn Study 1, we included 52,416 current OAC users and 18,048 non-users. We observed no difference in risk of being tested for SARS-CoV-2 associated with current use (adjusted HR, 1.01, 95%CI, 0.96 to 1.05) versus non-use. We observed a lower risk of testing positive for SARS-CoV-2 (adjusted HR, 0.73, 95%CI, 0.60 to 0.90), and COVID-19 deaths (adjusted HR, 0.69, 95%CI, 0.49 to 0.97) associated with current use versus non-use. In Study 2, we included 92,339 warfarin users and 280,407 DOAC users. We observed a lower risk of COVID-19 deaths (adjusted HR, 0.79, 95%CI, 0.76 to 0.83) associated with warfarin versus DOACs. Similar associations were found for all other outcomes.\n\nConclusionsAmong people with AF and a CHA{square}DS{square}-VASc score of 2, those receiving OACs had a lower risk of receiving a positive COVID-19 test and severe COVID-19 outcomes than non-users; this might be explained by a causal effect of OACs in preventing severe COVID-19 outcomes or more cautious behaviours leading to reduced infection risk. There was no evidence of a higher risk of severe COVID-19 outcomes associated with warfarin versus DOACs in people with non-valvular AF regardless of CHA{square}DS{square}-VASc score.\n\nKey pointsO_ST_ABSWhat is already known on this topicC_ST_ABSO_LICurrent studies suggest that prophylactic or therapeutic anticoagulant use, particularly low molecular weight heparin, lower the risk of pulmonary embolism and mortality during hospitalisation among patients with COVID-19.\nC_LIO_LIReduced vitamin K status has been reported to be correlated with severity of COVID-19. This could mean that warfarin, as a vitamin K antagonist, is associated with more severe COVID-19 disease than non-vitamin K anticoagulants.\nC_LI\n\nWhat this study addsO_LIIn 70,464 people with atrial fibrillation, at the threshold of being treated with an OAC based on risk of stroke, we observed a lower risk of testing positive for SARS-CoV-2 and COVID-19 related deaths associated with routinely prescribed OACs, relative to non-use.\nC_LIO_LIThis might be explained by OACs preventing severe COVID-19 outcomes, or more cautious behaviours and environmental factors reducing the risk of SARS-CoV-2 infection in those taking OACs.\nC_LIO_LIIn 372,746 people with non-valvular atrial fibrillation, there was no evidence of a higher risk of severe COVID-19 outcomes associated with warfarin compared with DOACs.\nC_LI",
-    "rel_num_authors": 30,
-    "rel_authors": [
-      {
-        "author_name": "Angel YS Wong",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Laurie Tomlinson",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Jeremy P Brown",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "William Elson",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Alex J Walker",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Anna J Schultze",
-        "author_inst": "London School of Hygiene and Trop. Med."
-      },
-      {
-        "author_name": "Caroline E Morton",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "David Evans",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Peter Inglesby",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Brian MacKenna",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Krishnan Bhaskaran",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Christopher T. Rentsch",
-        "author_inst": "US Department of Veterans Affairs, London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Emma Powell",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Elizabeth T. Williamson",
-        "author_inst": "London School of Hygiene & Tropical Medicine"
-      },
-      {
-        "author_name": "Richard Croker",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Seb Bacon",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "William Hulme",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Chris Bates",
-        "author_inst": "TPP"
-      },
-      {
-        "author_name": "Helen J Curtis",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Amir Mehrkar",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Jonathan Cockburn",
-        "author_inst": "TPP"
-      },
-      {
-        "author_name": "Helen I McDonald",
-        "author_inst": "London School of Medicine and Tropical Medicine"
-      },
-      {
-        "author_name": "Rohini I Mathur",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Kevin Wing",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Harriet Forbes",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Rosalind M Eggo",
-        "author_inst": "London School of Hygiene & Tropical Medicine"
-      },
-      {
-        "author_name": "Stephen Evans",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Liam Smeeth",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Ben Goldacre",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Ian J Douglas",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.04.27.21256185",
     "rel_title": "Pre-pandemic mental and physical health as predictors of COVID-19 vaccine hesitancy: evidence from a UK-wide cohort study",
@@ -777924,6 +776448,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.04.29.21256255",
+    "rel_title": "Objective and Subjective COVID-19 Vaccine Reactogenicity by Age and Vaccine Manufacturer",
+    "rel_date": "2021-04-30",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.29.21256255",
+    "rel_abs": "Several vaccines against SARS-CoV-2 have been granted emergency use authorization from the United States Food and Drug Administration and similar regulatory bodies abroad to combat the COVID-19 pandemic. While these vaccines have been shown to be extremely safe, transient side-effects lasting 24-48 hours post-vaccination have been reported. Here we conducted a retrospective analysis of 50977 subscribers to the WHOOP platform (33119 males, 17858 females; total of 65686 unique responses) who received either the AstraZeneca (AZ, n=2093), Janssen/Johnson & Johnson (J&J&J, n=3888), Moderna (n=23776; M1, 14553 first dose; M2, 9223 second dose), or Pfizer/BioNTech (n=35929; P&B1, 22387 first dose; P&B2, 13542 second dose) vaccines using data collected through April 14, 2021. Subjective reactogenicity was assessed using self-reported surveys. Results from these surveys indicated that the odds of self-reporting an adverse event after vaccination depend on gender, age, and manufacturer. Objectively measured cardiovascular (resting heart rate, RHR; heart rate variability, HRV) and sleep (total sleep duration, % light sleep, and % restorative sleep [a combination of REM and slow wave sleep]) metrics were assessed using a wrist-worn biometric device (Whoop Inc, Boston, MA, USA) and compared to the same day of the week, one week prior. Data are presented as a percent change from baseline {+/-} 95% confidence intervals. On the night after vaccination, RHR was higher (AZ: 13.5{+/-}0.76%; J&J&J: 16.5{+/-}0.64%; M1: 2.86{+/-}0.19%; M2: 9.3{+/-}0.53%; P&B1: 1.18{+/-}0.14%; P&B2: 13.5{+/-}0.36%) and HRV (AZ: -21.8{+/-}1.47%; J&J&J: - 25.6{+/-}1.15%; M1: -4.8{+/-}055%; M2: -19.9{+/-}1.33%; P&B1: -1.7{+/-}0.45%; P&B2: 8.60{+/-}1.10%) was lower than baseline levels. As for sleep metrics, total sleep was lower after the AZ and J&J&J vaccines (AZ: -3.7{+/-}0.98%; J&J&J: -3.8{+/-}0.80%; M1: 0.94{+/-}0.32%; M2: 0.14{+/-}0.80%; P&B1: 1.10{+/-}0.25%; P&B2: 0.35{+/-}0.63%); for AZ, J&J&J and the second dose of Moderna and P&B, a greater percentage of sleep post-vaccination came from light sleep (AZ: 9.24{+/-}1.22%; J&J&J: 13.8{+/-}1.02%; M1: 1.73{+/-}0.40%; M2: 8.02{+/-}0.99%; P&B1: 0.44{+/-}0.31%; P&B2: 2.54{+/-}0.74%) and a lower percentage from restorative sleep (AZ: -9.21{+/-}1.27%; J&J&J: -12.6{+/-}1.00%; M1: 0.16{+/-}0.43%; M2: -8.31{+/-}1.05%; P&B1: 1.27{+/-}0.34%; P&B2: -1.36{+/-}0.83%) than the week prior. Across all objective metrics measured, there were general trends that indicated an attenuated response in older populations and a larger response after the second dose for the Pfizer/BioNTech and Moderna vaccines (AstraZeneca second dose not analyzed). Importantly, the effects of the vaccines on cardiovascular and sleep measures were transient and returned to baseline by the second night following vaccination (P > 0.05 or absolute Cohens d < 0.25). In summary, these results confirm the previously observed subjective symptomatology trends, and for the first time show that objectively measured cardiovascular and sleep parameters are altered the night after vaccination. Moreover, these results suggest that the response may be different between vaccine manufacturers and may be modified by age and larger after the second dose. This information can be used to inform policy makers and employers considering offering paid time off for vaccination, as well as individuals planning their commitments post-vaccination.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "David Presby",
+        "author_inst": "WHOOP Inc"
+      },
+      {
+        "author_name": "Emily Capodilupo",
+        "author_inst": "WHOOP Inc."
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "allergy and immunology"
+  },
   {
     "rel_doi": "10.1101/2021.04.27.21256214",
     "rel_title": "SARS-CoV-2 serological findings and exposure risk among employees in school and retail after first and second wave COVID-19 pandemic in Oslo, Norway: a cohort study",
@@ -779187,77 +777734,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.04.28.21256122",
-    "rel_title": "Antibody response to SARS-CoV-2 infection over six months among Nicaraguan outpatients",
-    "rel_date": "2021-04-29",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.28.21256122",
-    "rel_abs": "New information is emerging about SARS-CoV-2 epidemiology and immunity, but little of this information comes from low- and middle-income countries or from patients receiving care in the outpatient setting. The current study investigated the SARS-CoV-2 infection status and antibody responses in 157 patients seeking care for a respiratory disease suggestive of COVID-19 in private healthcare clinics during the first wave (June-October 2020) of infections in Nicaragua. We examined nasal swabs for the presence of viral RNA via RT-PCR and longitudinally collected sera for the changes in SARS-CoV-2 Spike antibody levels over six months. Among patients with confirmed SARS-CoV-2 infections, we evaluated if clinical symptoms were associated with age, hematological parameters and co-morbidities. The combination of PCR and paired serology identified 60 (38%) of the 157 outpatients as acute COVID-19. While both PCR and serology identified the majority (n = 38, 64%) of the acute infections, a notable number of outpatients were identified by RT-qPCR (n = 13, 22%) or by serology (n = 9, 14%) only. During the longitudinal study, we identified 6 new infections by serology among the 97 non-COVID-19 subjects. In conclusion, this study report that more than one third of the outpatients seeking care for acute respiratory disease during the first epidemic wave of SARS-CoV-2 in Nicaragua had an acute mild COVID-19 infection that correlate with prolonged humoral response. This immune response to the RBD antigen, more likely IgG dependent, significantly increased between the acute to convalescent and decay in the late convalescent but still remained seropositive.",
-    "rel_num_authors": 14,
-    "rel_authors": [
-      {
-        "author_name": "Filemon Bucardo",
-        "author_inst": "National Autonomous University of Leon, Nicaragua (UNAN-Leon)."
-      },
-      {
-        "author_name": "Fredman Gonzalez",
-        "author_inst": "National Autonomous University of Leon, Nicaragua (UNAN-Leon)"
-      },
-      {
-        "author_name": "Omar Zepeda",
-        "author_inst": "National Autonomous University of Leon, Nicaragua (UNAN-Leon)"
-      },
-      {
-        "author_name": "Christian T Toval Ruiz",
-        "author_inst": "National Autonomous University of Leon, Nicaragua (Leon)"
-      },
-      {
-        "author_name": "Armando J Matute",
-        "author_inst": "National Autonomous University of Leon, Nicaragua (UNAN-Leon)"
-      },
-      {
-        "author_name": "Hernan Vanegas",
-        "author_inst": "National Autonomous University of Leon, Nicaragua (UNAN-Leon)"
-      },
-      {
-        "author_name": "Nancy Munguia",
-        "author_inst": "National Autonomous University of Leon, Nicaragua (UNAN-Leon)"
-      },
-      {
-        "author_name": "Edwing Centeno",
-        "author_inst": "National Autonomous University of Leon, Nicaragua (UNAN-Leon)"
-      },
-      {
-        "author_name": "Yaoska Reyes",
-        "author_inst": "National Autonomous University of Leon, Nicaragua (UNAN-Leon)"
-      },
-      {
-        "author_name": "Johan Nordgren",
-        "author_inst": "Department of Clinical and Experimental Medicine, Linkoping University, Linkoping, Sweden"
-      },
-      {
-        "author_name": "Lennart Svensson",
-        "author_inst": "Department of Clinical and Experimental Medicine, Linkoping University, Linkoping, Sweden"
-      },
-      {
-        "author_name": "Aravinda M de Silva",
-        "author_inst": "Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA"
-      },
-      {
-        "author_name": "LAKSHMANANE PREMKUMAR",
-        "author_inst": "Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599"
-      },
-      {
-        "author_name": "Silvia Becker-Dreps",
-        "author_inst": "Departments of Family Medicine and Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.04.25.21256049",
     "rel_title": "Previously infected vaccinees broadly neutralize SARS-CoV-2 variants",
@@ -779632,6 +778108,161 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2021.04.29.441258",
+    "rel_title": "Allelic variation in Class I HLA determines pre-existing memory responses to SARS-CoV-2 that shape the CD8+ T cell repertoire upon viral exposure",
+    "rel_date": "2021-04-29",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.29.441258",
+    "rel_abs": "Effective presentation of antigens by HLA class I molecules to CD8+ T cells is required for viral elimination and generation of long-term immunological memory. In this study, we applied a single-cell, multi-omic technology to generate the first unified ex vivo characterization of the CD8+ T cell response to SARS-CoV-2 across 4 major HLA class I alleles. We found that HLA genotype conditions key features of epitope specificity, TCR /{beta} sequence diversity, and the utilization of pre-existing SARS-CoV-2 reactive memory T cell pools. Single-cell transcriptomics revealed functionally diverse T cell phenotypes of SARS-CoV-2-reactive T cells, associated with both disease stage and epitope specificity. Our results show that HLA variations influence pre-existing immunity to SARS-CoV-2 and shape the immune repertoire upon subsequent viral exposure.\n\nOne-Sentence SummaryWe perform a unified, multi-omic characterization of the CD8+ T cell response to SARS-CoV-2, revealing pre-existing immunity conditioned by HLA genotype.",
+    "rel_num_authors": 35,
+    "rel_authors": [
+      {
+        "author_name": "Joshua M Francis",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Del Leistritz-Edwards",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Augustine Dunn",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Christina Tarr",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Jesse Lehman",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Conor Dempsey",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Andrew Hamel",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Violeta Rayon",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Gang Liu",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Yuntong Wang",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Marcos Wille",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Melissa Durkin",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Kane Hadley",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Aswathy Sheen",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Benjamin Roscoe",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Mark Ng",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Graham Rockwell",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Margaret Manto",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Elizabeth Gienger",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Joshua Nickerson",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "- MGH COVID-19 Collection and Processing Team",
+        "author_inst": "-"
+      },
+      {
+        "author_name": "Amir Moarefi",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Michael Noble",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Thomas Malia",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Philip D Bardwell",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "William Gordon",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Joanna Swain",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Mojca Skoberne",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Karsten Sauer",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Tim Harris",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Ananda W Goldrath",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Alex K Shalek",
+        "author_inst": "Massachusetts Institute of Technology"
+      },
+      {
+        "author_name": "Anthony J Coyle",
+        "author_inst": "Repertoire Immune Medicines"
+      },
+      {
+        "author_name": "Christophe Benoist",
+        "author_inst": "Harvard Medical School"
+      },
+      {
+        "author_name": "Daniel C Pregibon",
+        "author_inst": "Repertoire Immune Medicines"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2021.04.28.441880",
     "rel_title": "Protracted yet coordinated differentiation of long-lived SARS-CoV-2-specific CD8+ T cells during COVID-19 convalescence",
@@ -781101,53 +779732,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.04.26.21256105",
-    "rel_title": "Reopening California: Seeking Robust, Non-Dominated COVID-19 Exit Strategies",
-    "rel_date": "2021-04-28",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.26.21256105",
-    "rel_abs": "Amid global scarcity of COVID-19 vaccines and the threat of new variant strains, California and other jurisdictions face the question of when and how to implement and relax COVID-19 Nonpharmaceutical Interventions (NPIs). While policymakers have attempted to balance the health and economic impacts of the pandemic, decentralized decision-making, deep uncertainty, and the lack of widespread use of comprehensive decision support methods can lead to the choice of fragile or inefficient strategies. This paper uses simulation models and the Robust Decision Making (RDM) approach to stress-test Californias reopening strategy and other alternatives over a wide range of futures. We find that plans which respond aggressively to initial outbreaks are required to robustly control the pandemic. Further, the best plans adapt to changing circumstances, lowering their stringent requirements to reopen over time or as more constituents are vaccinated. While we use California as an example, our results are particularly relevant for jurisdictions where vaccination roll-out has been slower.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Pedro Nascimento de Lima",
-        "author_inst": "Pardee RAND Graduate School"
-      },
-      {
-        "author_name": "Robert Lempert",
-        "author_inst": "RAND Corporation"
-      },
-      {
-        "author_name": "Raffaele Vardavas",
-        "author_inst": "RAND Corporation"
-      },
-      {
-        "author_name": "Lawrence Baker",
-        "author_inst": "RAND Corporation"
-      },
-      {
-        "author_name": "Jeanne Ringel",
-        "author_inst": "RAND Corporation"
-      },
-      {
-        "author_name": "Carolyn M Rutter",
-        "author_inst": "RAND Corporation"
-      },
-      {
-        "author_name": "Jonathan Ozik",
-        "author_inst": "Argonne National Laboratory"
-      },
-      {
-        "author_name": "Nicholson Collier",
-        "author_inst": "Argonne National Laboratory"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.04.26.21256108",
     "rel_title": "Forecasting COVID-19 disease cases using the SARIMA-NNAR hybrid model",
@@ -781406,6 +779990,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.04.26.21256154",
+    "rel_title": "Optimal use of COVID19 Ag-RDT screening at border crossings to prevent community transmission: a modeling analysis",
+    "rel_date": "2021-04-28",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.26.21256154",
+    "rel_abs": "BackgroundCountries around the world have implemented restrictions on mobility, especially cross-border travel to reduce or prevent SARS-CoV-2 community transmission. Rapid antigen testing (Ag-RDT), with on-site administration and rapid turnaround time may provide a valuable screening measure to ease cross-border travel while minimizing risk of local transmission. To maximize impact, we developed an optimal Ag-RDT screening algorithm for cross-border entry.\n\nMethodsUsing a previously developed mathematical model, we determined the daily number of imported COVID-19 cases that would generate no more than a relative 1% increase in cases over one month for different effective reproductive numbers (Rt) of the recipient country. We then developed an algorithm- for differing levels of Rt, arrivals per day, mode of travel, and SARS-CoV-2 prevalence amongst travelers-to determine the minimum proportion of people that would need Ag-RDT testing at border crossings to ensure no greater than the relative 1% community spread increase.\n\nFindingsWhen daily international arrivals and/or COVID-19 prevalence amongst arrivals increases, the proportion of arrivals required to test using Ag-RDT increases. At very high numbers of international arrivals/COVID-19 prevalence, Ag-RDT testing is not sufficient to prevent increased community spread, especially for lower levels of Rt. In these cases, Ag-RDT screening would need to be supplemented with other measures to prevent an increase in community transmission.\n\nInterpretationAn efficient Ag-RDT algorithm for SARS-CoV-2 testing depends strongly on Rt, volume of travel, proportion of land and air arrivals, test sensitivity, and COVID-19 prevalence among travelers.\n\nFundingUSAID, Government of the Netherlands",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Joshua M Chevalier",
+        "author_inst": "Department of Global Health, Boston University School of Public Health, Boston, MA, USA"
+      },
+      {
+        "author_name": "Karla Therese L. Sy",
+        "author_inst": "Department of Epidemiology, Boston University School of Public Health; Department of Global Health, Boston University School of Public Health"
+      },
+      {
+        "author_name": "Sarah J Girdwood",
+        "author_inst": "Health Economics and Epidemiology Research Office, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the W"
+      },
+      {
+        "author_name": "Shaukat Khan",
+        "author_inst": "Clinton Health Access Initiative, Boston, MA, USA"
+      },
+      {
+        "author_name": "Heidi Albert",
+        "author_inst": "FIND, Cape Town, South Africa"
+      },
+      {
+        "author_name": "Amy Toporowski",
+        "author_inst": "FIND, Geneva, Switzerland"
+      },
+      {
+        "author_name": "Emma Hannay",
+        "author_inst": "FIND, Geneva, Switzerland"
+      },
+      {
+        "author_name": "Sergio Carmona",
+        "author_inst": "FIND, Geneva, Switzerland"
+      },
+      {
+        "author_name": "Brooke E Nichols",
+        "author_inst": "Department of Global Health, Boston University School of Public Health; Health Economics and Epidemiology Research Office, Department of Internal Medicine, Scho"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.04.26.21256136",
     "rel_title": "Detecting in-school transmission of SARS-CoV-2 from case ratios and documented clusters",
@@ -782991,89 +781626,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.04.19.21255748",
-    "rel_title": "Blood transcriptomes of anti-SARS-CoV2 antibody positive healthy individuals with prior asymptomatic versus clinical infection",
-    "rel_date": "2021-04-27",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.19.21255748",
-    "rel_abs": "Despite tremendous efforts by the international research community to understand the pathophysiology of SARS-CoV-2 infection, the reasons behind the clinical variability, ranging from asymptomatic infection to lethal disease, are still unclear. Existing inter-individual variations of the immune responses, due to environmental exposures and genetic factors, may be critical to the development or not of symptomatic disease after infection with SARS-CoV-2, and transcriptomic differences marking such responses may be observed even later, after convalescence. Herein, we performed genome-wide transcriptional whole-blood profiling to test the hypothesis that immune response-related gene signatures may differ between healthy individuals with prior entirely asymptomatic versus clinical SARS-CoV-2 infection, all of which developed an equally robust antibody response. Among 12.789 protein-coding genes analyzed, there were only six and nine genes with significantly decreased or increased expression, respectively, in those with prior asymptomatic infection (n=17, mean age 34 years) relatively to those with clinical infection (n=15, mean age 37 years). All six genes with decreased expression (IFIT3, IFI44L, RSAD2, FOLR3, PI3, ALOX15), are involved in innate immune response while the first two are interferon-induced proteins. Among genes with increased expression six are involved in immune response (GZMH, CLEC1B, CLEC12A), viral mRNA translation (GCAT), energy metabolism (CACNA2D2) and oxidative stress response (ENC1). Notably, 8/15 differentially expressed genes are regulated by interferons. Our results suggest that an intrinsically weaker expression of some innate immunity-related genes may be associated with an asymptomatic disease course in SARS-CoV-2 infection. Whether a certain gene signature predicts, or not, those who will develop a more efficient immune response upon exposure to SARS-CoV-2, with implications for prioritization for vaccination, warrant further study.",
-    "rel_num_authors": 17,
-    "rel_authors": [
-      {
-        "author_name": "Petros P. Sfikakis",
-        "author_inst": "National and Kapodistrian University of Athens, Medical School"
-      },
-      {
-        "author_name": "Kleio-Maria Verrou",
-        "author_inst": "National and Kapodistrian University of Athens, Medical School"
-      },
-      {
-        "author_name": "Ourania Tsitsilonis",
-        "author_inst": "National and Kapodistrian University of Athens, Department of Biology"
-      },
-      {
-        "author_name": "Dimitris Paraskevis",
-        "author_inst": "National and Kapoditrian University of Athens, Medical School"
-      },
-      {
-        "author_name": "Efstathios Kastritis",
-        "author_inst": "National and Kapodistrian University of Athens, Medical School"
-      },
-      {
-        "author_name": "Evi Lianidou",
-        "author_inst": "National and Kapodistrian University of Athens, Department of Chemistry"
-      },
-      {
-        "author_name": "Paraskevi Moutsatsou",
-        "author_inst": "National and Kapodistrian University of Athens, Department of Clinical Biochemistry"
-      },
-      {
-        "author_name": "Evangelos Terpos",
-        "author_inst": "National and Kapodistrian University of Athens, Medical School"
-      },
-      {
-        "author_name": "Ioannis Trougakos",
-        "author_inst": "National and Kapodistrian University of Athens, Faculty of Biology"
-      },
-      {
-        "author_name": "Vasiliki Chini",
-        "author_inst": "National and Kapodistrian University of Athens, Medical School"
-      },
-      {
-        "author_name": "Menelaos Manoloukos",
-        "author_inst": "National and Kapodistrian University of Athens, Medical School"
-      },
-      {
-        "author_name": "Panagiotis Moulos",
-        "author_inst": "BSRC \"Alexander Fleming\""
-      },
-      {
-        "author_name": "Georgios A. Pavlopoulos",
-        "author_inst": "National and Kapodistrian University of Athens, Medical School"
-      },
-      {
-        "author_name": "George Kollias",
-        "author_inst": "National and Kapodistrian University of Athens, Medical School"
-      },
-      {
-        "author_name": "Giannis Ampatziadis-Michailidis",
-        "author_inst": "National and Kapodistrian University of Athens, Medical School"
-      },
-      {
-        "author_name": "Pantelis Hatzis",
-        "author_inst": "National and Kapodistrian University of Athens, Medical School"
-      },
-      {
-        "author_name": "Meletios A. Dimopoulos",
-        "author_inst": "National and Kapodistrian University of Athens, Medical School"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.04.19.21255768",
     "rel_title": "Pharmacovigilance Analysis on Cerebrovascular Accidents and Coronavirus disease 2019 Vaccines",
@@ -783296,6 +781848,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.04.21.21255782",
+    "rel_title": "Mathematical modeling suggests pre-existing immunity to SARS-CoV-2",
+    "rel_date": "2021-04-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.21.21255782",
+    "rel_abs": "Mathematical models have largely failed to predict the unfolding of the COVID-19 pandemic. We revisit several variants of the SEIR-model and investigate various adjustments to the model in order to achieve output consistent with measured data in Manaus, India and Stockholm. In particular, Stockholm is interesting due to the almost constant NPIs, which substantially simplifies the mathematical modeling. Analyzing mobility data for Stockholm, we argue that neither behavioral changes, age and activity stratification nor NPIs alone are sufficient to explain the observed pandemic progression. We find that the most plausible hypothesis is that a large portion of the population, between 40 to 60 percent, have some protection against infection with the original variant of SARS-CoV-2.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Marcus Carlsson",
+        "author_inst": "Lund University"
+      },
+      {
+        "author_name": "Gad Hatem",
+        "author_inst": "Department of clinical sciences"
+      },
+      {
+        "author_name": "Cecilia Soderberg-Naucler",
+        "author_inst": "Department of Medicine, Karolinska Institute"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.04.21.21255898",
     "rel_title": "Indicators for Risk of Airborne Transmission in Shared Indoor Environments and their application to COVID-19 Outbreaks",
@@ -784636,37 +783215,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.04.26.21254638",
-    "rel_title": "Performance Decay of Molecular Assays Near the Limit of Detection: Probabilistic Modeling using Real-World COVID-19 Data",
-    "rel_date": "2021-04-27",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.26.21254638",
-    "rel_abs": "The gold standard for diagnosis of COVID-19 is detection of SARS-CoV-2 RNA by RT-PCR. However, the effect of systematic changes in specimen viral burden on the overall assay performance is not quantitatively described. We observed decreased viral burdens in our testing population as the pandemic progressed, with median sample Ct values increasing from 22.7 to 32.8 from weeks 14 and 20, respectively. We developed a method using computer simulations to quantify the implications of variable SARS-CoV-2 viral burden on observed assay performance. We found that overall decreasing viral burden can have profound effects on assay detection rates. When real-world Ct values were used as source data in a bootstrap resampling simulation, the sensitivity of the same hypothetical assay decreased from 97.59 (95% CI 97.3-97.9) in week 12, to 74.42 (95% CI 73.9-75) in week 20. Furthermore, simulated assays with a 3-fold or 10-fold reduced sensitivity would both appear to be >95% sensitive early in the pandemic, but sensitivity would fall to 85.55 (95% CI 84.9-86.2) and 74.38 (95% CI 73.6-75.1) later in the pandemic, respectively. Our modeling approach can be used to better quantitate the impact that specimen viral burden may have on the clinical application of tests and specimens.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Thomas JS Durant",
-        "author_inst": "Yale School of Medicine: Department of Laboratory Medicine"
-      },
-      {
-        "author_name": "Chris D Koch",
-        "author_inst": "Yale School of Medicine: Department of Laboratory Medicine"
-      },
-      {
-        "author_name": "Christopher A Kerantzas",
-        "author_inst": "Yale School of Medicine: Department of Laboratory Medicine"
-      },
-      {
-        "author_name": "David R Peaper",
-        "author_inst": "Yale School of Medicine: Department of Laboratory Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "pathology"
-  },
   {
     "rel_doi": "10.1101/2021.04.25.21256024",
     "rel_title": "COVID-19 vaccine acceptance in older Syrian refugees: preliminary findings from an ongoing study",
@@ -784973,6 +783521,65 @@
     "type": "new results",
     "category": "genomics"
   },
+  {
+    "rel_doi": "10.1101/2021.04.26.21256081",
+    "rel_title": "Clinical validation of RCSMS: a rapid and sensitive CRISPR-Cas12a test for the molecular detection of SARS-CoV-2 from saliva",
+    "rel_date": "2021-04-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.26.21256081",
+    "rel_abs": "Early detection of SARS-CoV-2 using molecular techniques is paramount to the fight against COVID-19. Due to its high sensitivity and specificity, RT-qPCR is the \"gold standard\" method for this purpose. However, its technical requirements, processing time and elevated costs hamper its use towards massive and timely molecular testing for COVID-19 in rural and socioeconomically deprived areas of Latin America. The advent and rapid evolution of CRISPR-Cas technology has boosted the development of new pathogen detection methodologies. Recently, DETECTR -a combination of isothermal RT-LAMP amplification and Cas12a-mediated enzymatic detection-has been successfully validated in the Netherlands and the USA as a rapid and low-cost alternative to RT-qPCR for the detection of SARS-CoV-2 from nasopharyngeal swabs. Here, we evaluated the performance of RCSMS, a locally adapted variant of DETECTR, to ascertain the presence of SARS-CoV-2 in saliva samples from 276 patients in two hospitals in Lima, Peru (current status over a total of 350 samples). We show that a low-cost thermochemical treatment with TCEP/EDTA is sufficient to inactivate viral particles and cellular nucleases in saliva, eliminating the need to extract viral RNA with commercial kits, as well as the cumbersome nasopharyngeal swab procedure and the requirement of biosafety level 2 laboratories for molecular analyses. Our clinical validation shows that RCSMS detects up to 5 viral copies per reaction in 40 min, with sensitivity and specificity of 93.8% and 99.0% in the field, respectively, relative to RT-qPCR. Since CRISPR-Cas biosensors can be easily reprogrammed by using different guide RNA molecules, RCSMS has the potential to be quickly adapted for the detection of new SARS-CoV-2 variants. Notably, estimation of its negative and positive predictive values suggests that RCSMS can be confidently deployed in both high and low prevalence settings. Furthermore, our field study validates the use of lateral flow strips to easily visualize the presence of SARS-CoV-2, which paves the way to deploy RCSMS as a \"point of care\" test in environments with limited access to state-of-the-art diagnostic laboratories. In sum, RCSMS is a fast, efficient and inexpensive alternative to RT-qPCR for expanding COVID-19 testing capacity in low- and middle-income countries.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Joaqu\u00edn Abugatt\u00e1s N\u00fa\u00f1ez del Prado",
+        "author_inst": "Facultad de Ciencias y Filosof\u00eda, Universidad Peruana Cayetano Heredia, Lima, Per\u00fa"
+      },
+      {
+        "author_name": "Ang\u00e9lica Quintana Reyes",
+        "author_inst": "Facultad de Ciencias y Filosof\u00eda, Universidad Peruana Cayetano Heredia, Lima, Per\u00fa"
+      },
+      {
+        "author_name": "Juan Blume La Torre",
+        "author_inst": "Facultad de Ciencias y Filosof\u00eda, Universidad Peruana Cayetano Heredia, Lima, Per\u00fa"
+      },
+      {
+        "author_name": "Renzo Guti\u00e9rrez-Loli",
+        "author_inst": "Facultad de Ciencias y Filosof\u00eda, Universidad Peruana Cayetano Heredia, Lima, Per\u00fa"
+      },
+      {
+        "author_name": "Alejandro Pinz\u00f3n Olejua",
+        "author_inst": "Department of Computer Science, Christian-Albrecht University of Kiel, Germany"
+      },
+      {
+        "author_name": "Elena Chamorro Chirinos",
+        "author_inst": "Hospital Nacional Guillermo Almenara Yrigoyen, EsSalud, Lima, Per\u00fa"
+      },
+      {
+        "author_name": "F\u00e9lix Antonio Loza Mauricio",
+        "author_inst": "Hospital Nacional Edgardo Rebagliati Martins, EsSalud, Lima, Per\u00fa"
+      },
+      {
+        "author_name": "Jorge L Magui\u00f1a",
+        "author_inst": "Instituto de Evaluaci\u00f3n de Tecnolog\u00edas en Salud e Investigaci\u00f3n (IETSI), EsSalud, Lima, Per\u00fa"
+      },
+      {
+        "author_name": "Julio Leon",
+        "author_inst": "IMS RIKEN Center for Integrative Medical Sciences, Japan"
+      },
+      {
+        "author_name": "Piere Rodriguez-Aliaga",
+        "author_inst": "Department of Biology, Stanford University, California, USA"
+      },
+      {
+        "author_name": "Edward M\u00e1laga-Trillo",
+        "author_inst": "Facultad de Ciencias y Filosof\u00eda, Universidad Peruana Cayetano Heredia, Lima, Per\u00fa"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.04.24.21256040",
     "rel_title": "The dark side of SARS-CoV-2 rapid antigen testing: screening asymptomatic patients.",
@@ -786426,49 +785033,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
-  {
-    "rel_doi": "10.1101/2021.04.23.21256006",
-    "rel_title": "Fatigue symptoms associated with COVID-19 in convalescent or recovered COVID-19 patients; a systematic review and meta-analysis",
-    "rel_date": "2021-04-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.23.21256006",
-    "rel_abs": "BackgroundThe prevalence and prognosis of post-acute stage SARS-CoV-2 infection fatigue symptoms remain largely unknown.\n\nAimsWe performed a systematic review to evaluate the prevalence of fatigue in post-recovery from SARS-CoV-2 infection.\n\nMethodMedline, Embase, PsycINFO, CINAHL, Web of Science, Scopus, trial registries, Cochrane Central Register of Controlled Trials and Google Scholar were searched for studies on fatigue in samples that recovered from PCR diagnosed COVID-19. English, French and Spanish studies were included. Meta-analyses were conducted separately for each recruitment setting.\n\nResultsWe identified 41 studies with 9362 patients that recovered from COVID-19. Post-COVID-19 patients self-report of fatigue was higher compared to healthy controls (RR = 3.688, 95%CI [2.502, 5.436], p < 0.001). Over 50% of patients discharged from inpatient care reported symptoms of fatigue during the first (ER = 0.517, 95%CI [0.278, 0.749]) and second month following recovery (ER = 0.527, 95%CI [0.337, 0.709]). 10% of the community patients reported fatigue in the first-month post-recovery. Patient setting moderated the association between COVID-19 recovery and fatigue symptoms (R2 = 0.11, p < 0.001). Female patients recovering from COVID-19 had a greater self-report of fatigue (OR = 1.782, 95%CI [1.531, 2.870]). Patients recruited through social media had fatigue above 90% across multiple time points. Fatigue was highest in studies from Europe.\n\nConclusionFatigue is a symptom associated with functional challenges which could have economic and social impacts. Developing long-term planning for fatigue management amongst patients beyond the acute stages of SARS-CoV-2 infection is essential to optimizing patient care and public health outcomes. Further studies should examine the impact of sociodemographic, pandemic-related restrictions and pre-existing conditions on fatigue.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Sanjay Rao",
-        "author_inst": "University of Ottawa, Department of Psychiatry"
-      },
-      {
-        "author_name": "Tarek Benzouak",
-        "author_inst": "Carleton University"
-      },
-      {
-        "author_name": "Sasha Gunpat",
-        "author_inst": "Carleton University, Department of Psychology"
-      },
-      {
-        "author_name": "Rachel J Burns",
-        "author_inst": "Carleton University, Department of Psychology"
-      },
-      {
-        "author_name": "Tayyeb A Tahir",
-        "author_inst": "University Hospital of Wales, Department of Liaison Psychiatry"
-      },
-      {
-        "author_name": "Stephen Jolles",
-        "author_inst": "University Hospital of Wales, Department of Immunology"
-      },
-      {
-        "author_name": "Steve Kisely",
-        "author_inst": "University of Queensland, Department of Psychiatry"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "psychiatry and clinical psychology"
-  },
   {
     "rel_doi": "10.1101/2021.04.23.21255993",
     "rel_title": "Depression during the COVID-19 pandemic amongst residents of homeless shelters in France.",
@@ -786811,6 +785375,41 @@
     "type": "new results",
     "category": "biochemistry"
   },
+  {
+    "rel_doi": "10.1101/2021.04.25.441372",
+    "rel_title": "Control-theoretic immune tradeoffs explain SARS-CoV-2 virulence and transmission variation",
+    "rel_date": "2021-04-26",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.25.441372",
+    "rel_abs": "Dramatic variation in SARS-CoV-2 virulence and transmission between hosts has driven the COVID-19 pandemic. The complexity and dynamics of the immune response present a challenge to understanding variation in SARS-CoV-2 infections. To address this challenge, we apply control theory, a framework used to study complex feedback systems, to establish rigorous mathematical bounds on immune responses. Two mechanisms of SARS-CoV-2 biology are sufficient to create extreme variation between hosts: (1) a sparsely expressed host receptor and (2) potent, but not unique, suppression of interferon. The resulting model unifies disparate and unexplained features of the SARS-CoV-2 pandemic, predicts features of future viruses that threaten to cause pandemics, and identifies potential interventions.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Anish A Sarma",
+        "author_inst": "California Institute of Technology"
+      },
+      {
+        "author_name": "Aartik Sarma",
+        "author_inst": "University of California-San Francisco"
+      },
+      {
+        "author_name": "Marie Csete",
+        "author_inst": "-"
+      },
+      {
+        "author_name": "Peter P Lee",
+        "author_inst": "City of Hope Cancer Center"
+      },
+      {
+        "author_name": "John C Doyle",
+        "author_inst": "California Institute of Technology"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "new results",
+    "category": "systems biology"
+  },
   {
     "rel_doi": "10.1101/2021.04.26.440920",
     "rel_title": "A SARS CoV-2 nucleocapsid vaccine protects against distal viral dissemination",
@@ -788044,65 +786643,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.04.22.21255949",
-    "rel_title": "Optimal health and economic impact of non-pharmaceutical intervention measures prior and post vaccination in England: a mathematical modelling study",
-    "rel_date": "2021-04-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.22.21255949",
-    "rel_abs": "BackgroundEven with good progress on vaccination, SARS-CoV-2 infections in the UK may continue to impose a high burden of disease and therefore pose substantial challenges for health policy decision makers. Stringent government-mandated physical distancing measures (lockdown) have been demonstrated to be epidemiologically effective, but can have both positive and negative economic consequences. The duration and frequency of any intervention policy could, in theory, could be optimised to maximise economic benefits while achieving substantial reductions in disease.\n\nMethodsHere we use a pre-existing SARS-CoV-2 transmission model to assess the health and economic implications of different strengths of control through time in order to identify optimal approaches to non-pharmaceutical intervention stringency in the UK, considering the role of vaccination in reducing the need for future physical distancing measures. The model is calibrated to the COVID-19 epidemic in England and we carry out retrospective analysis of the optimal timing of precautionary breaks in 2020 and the optimal relaxation policy from the January 2021 lockdown, considering the willingness to pay for health improvement.\n\nResultsWe find that the precise timing and intensity of interventions is highly dependent upon the objective of control. As intervention measures are relaxed, we predict a resurgence in cases, but the optimal intervention policy can be established dependent upon the willingness to pay (WTP) per QALY loss avoided. Our results show that establishing an optimal level of control can result in a reduction in net monetary loss of billions of pounds, dependent upon the precise WTP value.\n\nConclusionsIt is vital, as the UK emerges from lockdown, but continues to face an on-going pandemic, to accurately establish the overall health and economic costs when making policy decisions. We demonstrate how some of these can be quantified, employing mechanistic infectious disease transmission models to establish optimal levels of control for the ongoing COVID-19 pandemic.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Michael Tildesley",
-        "author_inst": "University of Warwick"
-      },
-      {
-        "author_name": "Anna Vassall",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Steven Riley",
-        "author_inst": "Dept Inf Dis Epi, Imperial College"
-      },
-      {
-        "author_name": "Mark Jit",
-        "author_inst": "London School of Hygiene & Tropical Medicine"
-      },
-      {
-        "author_name": "Frank Sandmann",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Edward M Hill",
-        "author_inst": "University of Warwick"
-      },
-      {
-        "author_name": "Robin Thompson",
-        "author_inst": "University of Warwick"
-      },
-      {
-        "author_name": "Benjamin Atkins",
-        "author_inst": "University of Warwick"
-      },
-      {
-        "author_name": "John Edmunds",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Louise M Dyson",
-        "author_inst": "University of Warwick"
-      },
-      {
-        "author_name": "Matt J Keeling",
-        "author_inst": "University of Warwick"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.04.21.21255876",
     "rel_title": "Impact of national and regional lockdowns on COVID-19 epidemic waves: Application to the 2020 spring wave in France",
@@ -788361,6 +786901,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.04.21.21255880",
+    "rel_title": "Efficacy of universal masking for source control and personal protection from simulated cough and exhaled aerosols in a room",
+    "rel_date": "2021-04-25",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.21.21255880",
+    "rel_abs": "Face masks reduce the spread of infectious respiratory diseases such as COVID-19 by blocking aerosols produced during coughs and exhalations (\"source control\"). Masks also slow and deflect cough and exhalation airflows, which changes the dispersion of aerosols. Factors such as the directions in which people are facing (orientation) and separation distance also affect aerosol dispersion. However, it is not clear how masking, orientation, and distance interact. We placed a respiratory aerosol simulator (\"source\") and a breathing simulator (\"recipient\") in a 3 m x 3 m chamber and measured aerosol concentrations for different combinations of masking, orientation, and separation distance. When the simulators were front-to-front during coughing, masks reduced the 15-minute mean aerosol concentration at the recipient by 92% at 0.9 and 1.8 m separation. When the simulators were side-by-side, masks reduced the concentration by 81% at 0.9 m and 78% at 1.8 m. During breathing, masks reduced the aerosol concentration by 66% when front-to-front and 76% when side-by-side at 0.9 m. Similar results were seen at 1.8 m. When the simulators were unmasked, changing the orientations from front-to-front to side-by-side reduced the cough aerosol concentration by 59% at 0.9 m and 60% at 1.8 m. When both simulators were masked, changing the orientations did not significantly change the concentration at either distance during coughing or breathing. Increasing the distance between the simulators from 0.9 m to 1.8 m during coughing reduced the aerosol concentration by 25% when no masks were worn but had little effect when both simulators were masked. During breathing, when neither simulator was masked, increasing the separation reduced the concentration by 13%, which approached significance, while the change was not significant when both source and recipient were masked. Our results show that universal masking reduces exposure to respiratory aerosol particles regardless of the orientation and separation distance between the source and recipient.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "William G Lindsley",
+        "author_inst": "National Institute for Occupational Safety and Health"
+      },
+      {
+        "author_name": "Donald H Beezhold",
+        "author_inst": "National Institute for Occupational Safety and Health"
+      },
+      {
+        "author_name": "Raymond C Derk",
+        "author_inst": "National Institute for Occupational Safety and Health"
+      },
+      {
+        "author_name": "Jayme Coyle",
+        "author_inst": "National Institute for Occupational Safety and Health"
+      },
+      {
+        "author_name": "Francoise M Blachere",
+        "author_inst": "National Institute for Occupational Safety and Health"
+      },
+      {
+        "author_name": "Theresa Boots",
+        "author_inst": "National Institute for Occupational Safety and Health"
+      },
+      {
+        "author_name": "Jeffrey S Reynolds",
+        "author_inst": "National Institute for Occupational Safety and Health"
+      },
+      {
+        "author_name": "Walter G McKinney",
+        "author_inst": "National Institute for Occupational Safety and Health"
+      },
+      {
+        "author_name": "Erik Sinsel",
+        "author_inst": "National Institute for Occupational Safety and Health"
+      },
+      {
+        "author_name": "John D Noti",
+        "author_inst": "National Institute for Occupational Safety and Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc0",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.04.22.21255908",
     "rel_title": "Learning from the resilience of hospitals and their staff to the COVID-19 pandemic: a scoping review.",
@@ -789554,81 +788149,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.04.20.21255806",
-    "rel_title": "Cerebral venous sinus thrombosis (CVST) is not significantly linked to COVID-19 vaccines or non-COVID vaccines in a large multi-state US health system",
-    "rel_date": "2021-04-23",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.20.21255806",
-    "rel_abs": "Cerebral venous sinus thrombosis (CVST) has been reported in a small number of individuals who have received the mRNA vaccines1 or the adenoviral vector vaccines for COVID-19 in the US2 and Europe3. Continued pharmacovigilance is integral to mitigating the risk of rare adverse events that clinical trials are underpowered to detect, however, these anecdotal reports have led to the pause or withdrawal of some vaccines in many jurisdictions and exacerbated vaccine hesitancy at a critical moment in the fight against the COVID-19 pandemic. We investigated the frequencies of CVST seen among individuals who received FDA-authorized COVID-19 vaccines from Pfizer-BioNTech (n = 94,818 doses), Moderna (n = 36,350 doses) and Johnson & Johnson - J&J (n = 1,745 doses), and among individuals receiving one of 10 FDA-approved non-COVID-19 vaccines (n = 771,805 doses). Comparing the incidence rates of CVST in 30-day time windows before and after vaccination, we found no statistically significant differences for the COVID-19 vaccines or any other vaccines studied in this population. In total, we observed 3 cases of CVST within the 30 days following Pfizer-BioNTech vaccination (2 females, 1 male; Ages (years): [79, 80, 84]), including one individual with a prior history of thrombosis and another individual with recent trauma in the past 30 days. We did not observe any cases of CVST among the patients receiving Moderna or J&J vaccines in this study population. We further found the baseline CVST incidence in the study population between 2017 and 2021 to be 45 to 98 per million patient years. Overall, this real-world evidence-based study highlights that CVST is rare and is not significantly associated with COVID-19 vaccination. In addition, there is a need for a concerted international effort to monitor EHR data across diverse patient populations and to investigate the underlying biological mechanisms leading to these rare clotting events.",
-    "rel_num_authors": 15,
-    "rel_authors": [
-      {
-        "author_name": "Colin Pawlowski",
-        "author_inst": "nference"
-      },
-      {
-        "author_name": "John Rincon-Hekking",
-        "author_inst": "nference"
-      },
-      {
-        "author_name": "Samir Awasthi",
-        "author_inst": "nference"
-      },
-      {
-        "author_name": "Viral Pandey",
-        "author_inst": "nference"
-      },
-      {
-        "author_name": "Patrick Lenehan",
-        "author_inst": "nference"
-      },
-      {
-        "author_name": "AJ Venkatakrishnan",
-        "author_inst": "nference"
-      },
-      {
-        "author_name": "Sairam Bade",
-        "author_inst": "nference Labs"
-      },
-      {
-        "author_name": "John C OHoro",
-        "author_inst": "Mayo Clinic"
-      },
-      {
-        "author_name": "Abinash Virk",
-        "author_inst": "Mayo Clinic"
-      },
-      {
-        "author_name": "Melanie D Swift",
-        "author_inst": "Mayo Clinic"
-      },
-      {
-        "author_name": "Amy W Williams",
-        "author_inst": "Mayo Clinic"
-      },
-      {
-        "author_name": "Gregory J Gores",
-        "author_inst": "Mayo Clinic"
-      },
-      {
-        "author_name": "Andrew D Badley",
-        "author_inst": "Mayo Clinic"
-      },
-      {
-        "author_name": "John Halamka",
-        "author_inst": "Mayo Clinic"
-      },
-      {
-        "author_name": "Venky Soundararajan",
-        "author_inst": "nference"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.04.23.441151",
     "rel_title": "Large-scale analysis of synonymous viral variants reveals global adaptation of the SARS-CoV-2 to the human codon usage",
@@ -790059,6 +788579,141 @@
     "type": "new results",
     "category": "bioinformatics"
   },
+  {
+    "rel_doi": "10.1101/2021.04.20.440658",
+    "rel_title": "Gut microbiota diversity and C-Reactive Protein are predictors of disease severity in COVID-19 patients",
+    "rel_date": "2021-04-23",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.20.440658",
+    "rel_abs": "Risk factors for COVID-19 disease severity are still poorly understood. Considering the pivotal role of gut microbiota on host immune and inflammatory functions, we investigated the association between changes in gut microbiota composition and the clinical severity of COVID-19. We conducted a multicentre cross-sectional study prospectively enrolling 115 COVID-19 patients categorized according to: 1) WHO Clinical Progression Scale - mild 19 (16.5%), moderate 37 (32.2%) or severe 59 (51.3%); and 2) location of recovery from COVID-19 - ambulatory 14 (household isolation; 12.2%), hospitalized in ward 40 (34.8%) or intensive care unit 61 (53.0%). Gut microbiota analysis was performed through 16S rRNA gene sequencing and data obtained was further related with clinical parameters of COVID-19 patients. Risk factors for COVID-19 severity were identified by univariate and multivariable logistic regression models.\n\nIn comparison with mild COVID-19 patients, the gut microbiota of moderate and severe patients has: a) lower Firmicutes/Bacteroidetes ratio, b) higher abundance of Proteobacteria; and c) lower abundance of beneficial butyrate-producing bacteria such as Roseburia and Lachnospira genera. Multivariable regression analysis showed that Shannon index diversity (odds ratio [OR] 2.85 [95% CI 1.09-7.41]; p=0.032) and C-Reactive Protein (OR 3.45 [95% CI 1.33-8.91]; p=0.011) were risk factors for COVID-19 severe disease (a score of 6 or higher in WHO clinical progression scale).\n\nIn conclusion, our results demonstrated that hospitalised moderate and severe COVID-19 patients have microbial signatures of gut dysbiosis and for the first time, the gut microbiota diversity is pointed out as a prognostic biomarker for COVID-19 disease severity.",
+    "rel_num_authors": 30,
+    "rel_authors": [
+      {
+        "author_name": "Andre Moreira-Rosario",
+        "author_inst": "Faculdade de Ciencias Medicas|NOVA Medical School, Universidade NOVA de Lisboa"
+      },
+      {
+        "author_name": "Claudia Marques",
+        "author_inst": "Faculdade de Ciencias Medicas|NOVA Medical School, Universidade NOVA de Lisboa"
+      },
+      {
+        "author_name": "Helder Pinheiro",
+        "author_inst": "Infectious Diseases Department Hospital Curry Cabral, Centro Hospitalar Universitario Lisboa Central"
+      },
+      {
+        "author_name": "Joao Ricardo Araujo",
+        "author_inst": "Faculdade de Ciencias Medicas|NOVA Medical School, Universidade NOVA de Lisboa"
+      },
+      {
+        "author_name": "Pedro Ribeiro",
+        "author_inst": "Centro de Medicina Laboratorial Germano de Sousa, Lisboa, Portugal"
+      },
+      {
+        "author_name": "Rita Rocha",
+        "author_inst": "i3S - Instituto de Investigacao e Inovacao em Saude, Universidade do Porto, Portugal"
+      },
+      {
+        "author_name": "Ines Mota",
+        "author_inst": "Faculdade de Ciencias Medicas|NOVA Medical School, Universidade NOVA de Lisboa"
+      },
+      {
+        "author_name": "Diogo Pestana",
+        "author_inst": "Faculdade de Ciencias Medicas|NOVA Medical School, Universidade NOVA de Lisboa"
+      },
+      {
+        "author_name": "Rita Ribeiro",
+        "author_inst": "Centro de Medicina Laboratorial Germano de Sousa, Lisboa, Portugal"
+      },
+      {
+        "author_name": "Ana Pereira",
+        "author_inst": "Centro de Medicina Laboratorial Germano de Sousa, Lisboa, Portugal"
+      },
+      {
+        "author_name": "Maria Jose de Sousa",
+        "author_inst": "Faculdade de Ciencias Medicas|NOVA Medical School, Universidade NOVA de Lisboa"
+      },
+      {
+        "author_name": "Jose Pereira-Leal",
+        "author_inst": "Ophiomics Precision Medicine, Lisboa, Portugal"
+      },
+      {
+        "author_name": "Jose de Sousa",
+        "author_inst": "Centro de Medicina Laboratorial Germano de Sousa, Lisboa, Portugal"
+      },
+      {
+        "author_name": "Juliana Morais",
+        "author_inst": "Faculdade de Ciencias Medicas|NOVA Medical School, Universidade NOVA de Lisboa"
+      },
+      {
+        "author_name": "Diana Teixeira",
+        "author_inst": "Faculdade de Ciencias Medicas|NOVA Medical School, Universidade NOVA de Lisboa"
+      },
+      {
+        "author_name": "Julio Cesar Rocha",
+        "author_inst": "Faculdade de Ciencias Medicas|NOVA Medical School, Universidade NOVA de Lisboa"
+      },
+      {
+        "author_name": "Marta Silvestre",
+        "author_inst": "Faculdade de Ciencias Medicas|NOVA Medical School, Universidade NOVA de Lisboa"
+      },
+      {
+        "author_name": "Nuno Principe",
+        "author_inst": "Department of Emergency and Intensive Care Medicine, Sao Joao University Hospital Center - Porto"
+      },
+      {
+        "author_name": "Nuno Gatta",
+        "author_inst": "Department of Emergency and Intensive Care Medicine, Sao Joao University Hospital Center - Porto"
+      },
+      {
+        "author_name": "Jose Amado",
+        "author_inst": "Department of Emergency and Intensive Care Medicine, Sao Joao University Hospital Center - Porto"
+      },
+      {
+        "author_name": "Lurdes Santos",
+        "author_inst": "Infectious Diseases Service - ID Intensive Care Unit, Sao Joao University Hospital Center - Faculty of Medicine, Porto"
+      },
+      {
+        "author_name": "Fernando Maltez",
+        "author_inst": "Infectious Diseases Department Hospital Curry Cabral, Centro Hospitalar Universitario Lisboa Central, Lisboa"
+      },
+      {
+        "author_name": "Ana Boquinhas",
+        "author_inst": "Emergency Department, CUF Infante Santo Hospital, Lisboa, Portugal"
+      },
+      {
+        "author_name": "Germano de Sousa",
+        "author_inst": "Centro de Medicina Laboratorial Germano de Sousa, Lisboa, Portugal"
+      },
+      {
+        "author_name": "Nuno Germano",
+        "author_inst": "Polyvalent Intensive Care Unit, Hospital Curry Cabral, Centro Hospitalar Universitario Lisboa Central, Lisboa, Portugal"
+      },
+      {
+        "author_name": "Goncalo Sarmento",
+        "author_inst": "Internal Medicine Department, Centro Hospitalar Entre Douro e Vouga, Santa Maria da Feira, Portugal"
+      },
+      {
+        "author_name": "Cristina Granja",
+        "author_inst": "Anesthesiology Department, Centro Hospital Universitario Sao Joao, Porto, Portugal"
+      },
+      {
+        "author_name": "Pedro Povoa",
+        "author_inst": "Faculdade de Ciencias Medicas|NOVA Medical School, Universidade NOVA de Lisboa"
+      },
+      {
+        "author_name": "Ana Faria",
+        "author_inst": "Faculdade de Ciencias Medicas|NOVA Medical School, Universidade NOVA de Lisboa"
+      },
+      {
+        "author_name": "Conceicao Calhau",
+        "author_inst": "Faculdade de Ciencias Medicas|NOVA Medical School, Universidade NOVA de Lisboa"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2021.04.23.441125",
     "rel_title": "Computational investigation reveals that the mutant strains of SARS-CoV2 are highly infectious than wildtype",
@@ -791456,101 +790111,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "rehabilitation medicine and physical therapy"
   },
-  {
-    "rel_doi": "10.1101/2021.04.15.21255482",
-    "rel_title": "Single dose of BNT162b2 mRNA vaccine against SARS-CoV2 induces neutralizing antibody and polyfunctional T-cell responses in patients with CML",
-    "rel_date": "2021-04-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.15.21255482",
-    "rel_abs": "Patients receiving targeted cancer treatments such as tyrosine kinase inhibitors (TKIs) have been classified in the clinically extremely vulnerable group to develop severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), including patients with Chronic Myeloid Leukaemia (CML) taking TKIs. In addition, concerns that immunocompromised individuals with solid and haematological malignancies may not mount an adequate immune response to a single dose of SARS-CoV-2 BNT162b2 (Pfizer-BioNTech) vaccine have been raised.\n\nWe evaluated humoral and cellular immune responses after a first injection of BNT162b2 vaccine in 16 CML patients. Seroconversion and cellular immune response prior and after vaccination were assessed.\n\nBy day 21 post-vaccination, anti-Spike IgG were detected in 14/16 (87.5%) of CML patients and all developed a neutralizing antibody response (ID50>50), including medium (ID50 of 200-500) or high (501-2000) neutralising antibodies titres in 9/16 (56.25%) patients. T cell response was seen in 14/15 (93.3%) evaluable patients, with polyfunctional responses seen in 12/15 (80%) patients (polyfunctional CD4+ response 9/15, polyfunctional CD8+ T cell response 9/15).\n\nThese data demonstrate the immunogenicity of a single dose of SARS-CoV-2 BNT162b2 vaccine in most CML patients with both neutralizing antibodies and polyfunctional T-cell responses seen, in contrast to patients with solid tumour or lymphoid haematological malignancies.\n\nFundingKings Together Rapid COVID-19 Call awards to MHM, KJD; A Huo Family Foundation Award to MHM, KJD; Chronic Disease Research Foundation award CDRF-22/2020 to KJD, MHM; Wellcome Trust Investigator Award 106223/Z/14/Z to MHM; CG was supported by the MRC-KCL Doctoral Training Partnership in Biomedical Sciences (MR/N013700/1); Fondation Dormeur, Vaduz for funding equipment to KJD",
-    "rel_num_authors": 20,
-    "rel_authors": [
-      {
-        "author_name": "Patrick Harrington",
-        "author_inst": "Guy's and St Thomas' NHS Foundation Trust"
-      },
-      {
-        "author_name": "Katie Doores",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Deepti Radia",
-        "author_inst": "Guy's & St Thomas' NHS Foundation Trust"
-      },
-      {
-        "author_name": "Amy O'Reilly",
-        "author_inst": "Guy's & St Thomas' NHS Foundation Trust"
-      },
-      {
-        "author_name": "Ho Pui Jeff Lam",
-        "author_inst": "Guy's & St Thomas' NHS Foundation Trust"
-      },
-      {
-        "author_name": "Jeffrey Seow",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Carl Graham",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Thomas Lechmere",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Donal McLornan",
-        "author_inst": "Guy's & St Thomas' NHS Foundation Trust"
-      },
-      {
-        "author_name": "Richard Dillon",
-        "author_inst": "Guy's & St Thomas' NHS Foundation Trust"
-      },
-      {
-        "author_name": "Yogita Shanmugharaj",
-        "author_inst": "Guy's & St Thomas' NHS Foundation Trust"
-      },
-      {
-        "author_name": "Andreas Espehana",
-        "author_inst": "Guy's & St Thomas' NHS Foundation Trust"
-      },
-      {
-        "author_name": "Claire Woodley",
-        "author_inst": "Guy's & St Thomas' NHS Foundation Trust"
-      },
-      {
-        "author_name": "Jamie Saunders",
-        "author_inst": "Guy's & St Thomas' NHS Foundation Trust"
-      },
-      {
-        "author_name": "Natalia Curto-Garcia",
-        "author_inst": "Guy's & St Thomas' NHS Foundation Trust"
-      },
-      {
-        "author_name": "Jennifer O'Sullivan",
-        "author_inst": "Guy's & St Thomas' NHS Foundation Trust"
-      },
-      {
-        "author_name": "Shahram Kordasti",
-        "author_inst": "Guy's & St Thomas' NHS Foundation Trust"
-      },
-      {
-        "author_name": "Michael H Malim",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Claire Harrison",
-        "author_inst": "Guy's & St Thomas' NHS Foundation Trust"
-      },
-      {
-        "author_name": "Hugues de Lavallade",
-        "author_inst": "Guy's & St Thomas' NHS Foundation Trust"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "hematology"
-  },
   {
     "rel_doi": "10.1101/2021.04.20.21255596",
     "rel_title": "Comparison of SARS-CoV-2 serological assays for use in epidemiological surveillance in Scotland",
@@ -791873,6 +790433,69 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.04.14.21255443",
+    "rel_title": "Association of in-hospital use of ACE-I/ARB and COVID-19 outcomes in African American population",
+    "rel_date": "2021-04-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.14.21255443",
+    "rel_abs": "ImportanceThe ACE D allele is more prevalent among African Americans (AA) compared to other races/ethnicities and has previously been associated with severe COVID-19 pathogenesis through excessive ACE1 activity. ACE-I/ARBs may counteract this mechanism, but their association with COVID-19 outcomes has not been specifically tested in the AA population.\n\nObjectivesTo determine whether the use of ACE-I/ARBs is associated with COVID-19 in-hospital mortality in AA compared with non-AA population.\n\nDesign, Setting, and ParticipantsIn this observational, retrospective study, patient-level data were extracted from the Mount Sinai Health Systems (MSHS) electronic medical record (EMR) database, and 6,218 patients with a laboratory-confirmed COVID-19 diagnosis from February 24 to May 31, 2020 were identified as ACE-I/ARB users.\n\nExposuresPatients with an active prescription from January 1, 2019 up to the date of admission for ACE-I/ARB (outpatient use) and patients administered ACE-I/ARB during hospitalization (in-hospital use) were identified.\n\nMain Outcomes and MeasuresThe primary outcome was in-hospital mortality, assessed in the entire, AA, and non-AA population.\n\nResultsOf the 6,218 COVID-19 patients, 1,138 (18.3%) were ACE-I/ARB users. In a multivariate logistic regression model, ACE-I/ARB use was independently associated with reduced risk of in-hospital mortality in the entire population (OR, 0.655; 95% CI, 0.505-0.850; P=0.001), AA population (OR, 0.44; 95% CI, 0.249-0.779; P=0.005), and non-AA population (OR, 0.748, 95% CI, 0.553-1.012, P=0.06). In the AA population, in-hospital use of ACE-I/ARBs was associated with improved mortality (OR, 0.378; 95% CI, 0.188-0.766; P=0.006) while outpatient use was not (OR, 0.889; 95% CI, 0.375-2.158; P=0.812). When analyzing each medication class separately, ARB in-hospital use was significantly associated with reduced in-hospital mortality in the AA population (OR, 0.196; 95% CI, 0.074-0.516; P=0.001), while ACE-I use was not associated with impact on mortality in any population.\n\nConclusion and RelevanceIn-hospital use of ARBs was associated with a significant reduction in in-hospital mortality among COVID-19-positive AA patients. These results support further investigation of ARBs to improve outcomes in AA patients at high risk for COVID-19-related mortality.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Shilong Li",
+        "author_inst": "Sema4, Stamford, CT, USA"
+      },
+      {
+        "author_name": "Rangaprasad Sarangarajan",
+        "author_inst": "BERG, 500 Old Connecticut Path, Bldg B 3rd Floor, Framingham, MA, USA."
+      },
+      {
+        "author_name": "Tomi Jun",
+        "author_inst": "Division of Hematology & Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA."
+      },
+      {
+        "author_name": "Yu-Han Kao",
+        "author_inst": "Sema4, Stamford, CT, USA"
+      },
+      {
+        "author_name": "Zichen Wang",
+        "author_inst": "Sema4, Stamford, CT, USA"
+      },
+      {
+        "author_name": "Emilio Schadt",
+        "author_inst": "Sema4, Stamford, CT, USA"
+      },
+      {
+        "author_name": "Michael A. Kiebish",
+        "author_inst": "BERG, 500 Old Connecticut Path, Bldg B 3rd Floor, Framingham, MA, USA."
+      },
+      {
+        "author_name": "Elder Granger",
+        "author_inst": "BERG, 500 Old Connecticut Path, Bldg B 3rd Floor, Framingham, MA, USA."
+      },
+      {
+        "author_name": "Niven R. Narain",
+        "author_inst": "BERG, 500 Old Connecticut Path, Bldg B 3rd Floor, Framingham, MA, USA."
+      },
+      {
+        "author_name": "Rong Chen",
+        "author_inst": "Sema4, Stamford, CT, USA"
+      },
+      {
+        "author_name": "Eric E. Schadt",
+        "author_inst": "Sema4, Stamford, CT, USA"
+      },
+      {
+        "author_name": "Li Li",
+        "author_inst": "Sema4, Stamford, CT, USA"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.04.19.21252978",
     "rel_title": "Mid-Regional pro-Adrenomedullin (MR-proADM), C-Reactive Protein (CRP) and Other Biomarkers in the Early Identification of Disease Progression in COVID-19 Patients in the Acute NHS Setting",
@@ -793333,33 +791956,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.04.20.440716",
-    "rel_title": "Recognition of Divergent Viral Substrates by the SARS-CoV-2 Main Protease",
-    "rel_date": "2021-04-21",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.20.440716",
-    "rel_abs": "The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease (COVID-19), is an ideal target for pharmaceutical inhibition. It is required for infection, it cleaves the viral polyprotein at multiple sites, and it is conserved among coronaviruses and distinct from human proteases. We present crystal structures of SARS-CoV-2 Mpro bound to two viral substrate peptides. The structures show how Mpro recognizes substrates and how the peptide sequence can dictate catalytic efficiency by influencing the position of the scissile bond. One peptide, constituting the junction between viral non-structural proteins 8 and 9 (nsp8/9), has P1 and P2 residues that are unique among SARS-CoV-2 cleavage sites but conserved among nsp8/9 junctions in coronaviruses. Mpro cleaves nsp8/9 inefficiently, and amino acid substitutions at P1 or P2 can enhance catalysis. Visualization of Mpro with intact substrates provides new templates for antiviral drug design and suggests that the coronavirus lifecycle selects for finely tuned substrate-dependent catalytic parameters.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Gary Frey",
-        "author_inst": "Harvard Medical School"
-      },
-      {
-        "author_name": "Mark Namchuk",
-        "author_inst": "Harvard Medical School"
-      },
-      {
-        "author_name": "Stephen M Hinshaw",
-        "author_inst": "Harvard Medical School"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "biochemistry"
-  },
   {
     "rel_doi": "10.1101/2021.04.18.440376",
     "rel_title": "GIVE Statistic for Goodness of Fit in Instrumental Variables Models with Application to COVID Data",
@@ -793786,6 +792382,89 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2021.04.20.440676",
+    "rel_title": "Eicosanoid signaling as a therapeutic target in middle-aged mice with severe COVID-19",
+    "rel_date": "2021-04-21",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.20.440676",
+    "rel_abs": "Coronavirus disease 2019 (COVID-19) is especially severe in aged populations1. Resolution of the COVID-19 pandemic has been advanced by the recent development of SARS-CoV-2 vaccines, but vaccine efficacy is partly compromised by the recent emergence of SARS-CoV-2 variants with enhanced transmissibility2. The emergence of these variants emphasizes the need for further development of anti-SARS-CoV-2 therapies, especially in aged populations. Here, we describe the isolation of a new set of highly virulent mouse-adapted viruses and use them to test a novel therapeutic drug useful in infections of aged animals. Initially, we show that many of the mutations observed in SARS-CoV-2 during mouse adaptation (at positions 417, 484, 501 of the spike protein) also arise in humans in variants of concern (VOC)2. Their appearance during mouse adaptation indicates that immune pressure is not required for their selection. Similar to the human infection, aged mice infected with mouse-adapted SARS-CoV-2 develop more severe disease than young mice. In murine SARS, in which severity is also age-dependent, we showed that elevated levels of an eicosanoid, prostaglandin D2 (PGD2) and of a phospholipase, PLA2G2D, contributed to poor outcomes in aged mice3,4. Using our virulent mouse-adapted SARS-CoV-2, we show that infection of middle-aged mice lacking expression of DP1, a PGD2 receptor, or PLA2G2D are protected from severe disease. Further, treatment with a DP1 antagonist, asapiprant, protected aged mice from a lethal infection. DP1 antagonism is one of the first interventions in SARS-CoV-2-infected animals that specifically protects aged animals, and demonstrates that the PLA2G2D-PGD2/DP1 pathway is a useful target for therapeutic interventions. (Words: 254)",
+    "rel_num_authors": 17,
+    "rel_authors": [
+      {
+        "author_name": "Stanley Perlman",
+        "author_inst": "University of Iowa"
+      },
+      {
+        "author_name": "Lok Yin Roy Wong",
+        "author_inst": "University of Iowa"
+      },
+      {
+        "author_name": "Jian Zheng",
+        "author_inst": "University of Iowa"
+      },
+      {
+        "author_name": "Kevin Wilhelmsen",
+        "author_inst": "BIOAGE Labs"
+      },
+      {
+        "author_name": "Kun Li",
+        "author_inst": "University of Iowa"
+      },
+      {
+        "author_name": "Miguel E Ortiz Bezara",
+        "author_inst": "University of Iowa"
+      },
+      {
+        "author_name": "Nicholas J Schnicker",
+        "author_inst": "University of Iowa"
+      },
+      {
+        "author_name": "Alejandro A A Pezzulo",
+        "author_inst": "University of Iowa Roy J. and Lucille A. Carver College of Medicine"
+      },
+      {
+        "author_name": "Peter J Szachowicz",
+        "author_inst": "University of Iowa"
+      },
+      {
+        "author_name": "Klaus Klumpp",
+        "author_inst": "BIOAGE Labs"
+      },
+      {
+        "author_name": "Fred Aswad",
+        "author_inst": "BIOAGE Labs"
+      },
+      {
+        "author_name": "Justin Rebo",
+        "author_inst": "BIOAGE Labs"
+      },
+      {
+        "author_name": "Shut Narumiya",
+        "author_inst": "Kyoto University"
+      },
+      {
+        "author_name": "Makoto Murakami",
+        "author_inst": "The University of Tokyo"
+      },
+      {
+        "author_name": "David Meyerholz",
+        "author_inst": "University of Iowa"
+      },
+      {
+        "author_name": "Kristen Fortney",
+        "author_inst": "BIOAGE Labs"
+      },
+      {
+        "author_name": "Paul B McCray",
+        "author_inst": "University of Iowa"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2021.04.21.440680",
     "rel_title": "Human Taste Cells Express ACE2: A Portal for SARS-CoV-2 Infection",
@@ -795047,121 +793726,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "sports medicine"
   },
-  {
-    "rel_doi": "10.1101/2021.04.15.21255550",
-    "rel_title": "Impaired antigen-specific memory B cell and plasma cell responses including lack of specific IgG upon SARS-CoV-2 BNT162b2 vaccination among Kidney Transplant and Dialysis patients",
-    "rel_date": "2021-04-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.15.21255550",
-    "rel_abs": "Patients with kidney failure are at increased risk during the COVID-19 pandemic and effective vaccinations are needed. It is not known how efficient mRNA vaccines mount B and plasma cell responses in dialysis patients (DP) or kidney transplant recipients (KTR) compared to healthy controls (HC). We studied humoral and B cell responses of 25 HC, 44 DP and 40 KTR. Markedly impaired anti-BNT162b2 responses were identified among KTR and DP compared to 100% seroconversion in HC. In DP, the response was delayed (3-4 weeks after boost) and reduced with anti-S1 IgG positivity in 31 (70.5%) and anti-S1 IgA in 30 (68.2%) of 44, respectively. In contrast, KTR did not develop IgG response except one patient who had prior unrecognized infection and developed anti-S1 IgG. The majority of antigen-specific B cells (RBD+) were identified in the plasmablast or post-switch memory B cell compartments in HC, whereas these RBD+ B cells were enriched among pre-switch and naive B cells from DP and KTR. Single cell transcriptome and CITE-seq analyses found reduced frequencies of plasmablasts, TCF7+CD27+GZMK+ T cells and proliferating MKI67-expressing lymphocytes among KTR non-responders. Importantly, the frequency and absolute number of antigen-specific circulating plasmablasts in the whole cohort correlated with the Ig response, a characteristic not reported for other vaccinations. In conclusion, this data indicate that lack of T cell help related to immunosuppression results in impaired germinal center differentiation of B and plasma cell memory. There is an urgent need to improve vaccination protocols in patients after kidney transplantation or on chronic dialysis.\n\nOne Sentence SummaryKidney transplant recipients and dialysis patients show a markedly diminished humoral response and impaired molecular B cell memory formation upon vaccination with BNT162b2.",
-    "rel_num_authors": 25,
-    "rel_authors": [
-      {
-        "author_name": "Hector Rincon-Arevalo",
-        "author_inst": "Charite Universtitaetsmedizin Berlin"
-      },
-      {
-        "author_name": "Mira Choi",
-        "author_inst": "Charite Universitaetsmedizin Berlin"
-      },
-      {
-        "author_name": "Ana-Luisa Stefanski",
-        "author_inst": "Charite Universitaetsmedizin Berlin"
-      },
-      {
-        "author_name": "Fabian Halleck",
-        "author_inst": "Charite Universitaetsmedizin Berlin"
-      },
-      {
-        "author_name": "Ulrike Weber",
-        "author_inst": "Charite Universitaetsmedizin Berlin"
-      },
-      {
-        "author_name": "Franziska Szelinski",
-        "author_inst": "Charite Universitaetsmedizin Berlin"
-      },
-      {
-        "author_name": "Bernd Jahrsdoerfer",
-        "author_inst": "Institute of Transfusion Medicine, Ulm University"
-      },
-      {
-        "author_name": "Hubert Schrezenmeier",
-        "author_inst": "Institute of Transfusion Medicine, Ulm University"
-      },
-      {
-        "author_name": "Carolin Ludwig",
-        "author_inst": "Institute of Transfusion Medicine, Ulm University"
-      },
-      {
-        "author_name": "Arne Sattler",
-        "author_inst": "Charite Universitaetsmedizin Berlin"
-      },
-      {
-        "author_name": "Katja Kotsch",
-        "author_inst": "Charite Universitaetsmedizin Berlin"
-      },
-      {
-        "author_name": "Alexander Potekhin",
-        "author_inst": "Diaverum Neubrandenburg"
-      },
-      {
-        "author_name": "Yidan Chen",
-        "author_inst": "Charite Universitaetsmedizin Berlin"
-      },
-      {
-        "author_name": "Gerd R. Burmester",
-        "author_inst": "Charite Universitaetsmedizin Berlin"
-      },
-      {
-        "author_name": "Kai-Uwe Eckardt",
-        "author_inst": "Charite Universitaetsmedizin Berlin"
-      },
-      {
-        "author_name": "Gabriela Maria Guerra",
-        "author_inst": "Deutsches Rheumaforschungszentrum (DRFZ), Berlin, Germany"
-      },
-      {
-        "author_name": "Pawel Durek",
-        "author_inst": "Deutsches Rheumaforschungszentrum (DRFZ), Berlin, Germany"
-      },
-      {
-        "author_name": "Frederik Heinrich",
-        "author_inst": "Deutsches Rheumaforschungszentrum (DRFZ), Berlin, Germany"
-      },
-      {
-        "author_name": "Marta Ferreira-Gomes",
-        "author_inst": "Deutsches Rheumaforschungszentrum (DRFZ), Berlin, Germany"
-      },
-      {
-        "author_name": "Andreas Radbruch",
-        "author_inst": "Deutsches Rheumaforschungszentrum (DRFZ), Berlin, Germany"
-      },
-      {
-        "author_name": "Klemens Budde",
-        "author_inst": "Charite Universitaetsmedizin Berlin"
-      },
-      {
-        "author_name": "Andreia C. Lino",
-        "author_inst": "Deutsches Rheumaforschungszentrum (DRFZ), Berlin, Germany"
-      },
-      {
-        "author_name": "Mir-Farzin Mashreghi",
-        "author_inst": "Deutsches Rheumaforschungszentrum (DRFZ), Berlin, Germany"
-      },
-      {
-        "author_name": "Eva Schrezenmeier",
-        "author_inst": "Charite Universitaetsmedizin, Berlin"
-      },
-      {
-        "author_name": "Thomas Doerner",
-        "author_inst": "Charite Univeritaetsmedizin Berlin"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "nephrology"
-  },
   {
     "rel_doi": "10.1101/2021.04.19.21255730",
     "rel_title": "The impact of COVID-19 on the oncologic outcomes of 3236 patients undergoing ColoRectal Cancer surgery in Northern Italy in 2019 and 2020 (COVID-CRC): results of a multicentric comparative cohort study.",
@@ -795516,6 +794080,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.04.15.21255533",
+    "rel_title": "Evaluation of seven different rapid methods for nucleic acid detection of SARS-COV-2 virus",
+    "rel_date": "2021-04-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.15.21255533",
+    "rel_abs": "BackgroundIn the current COVID-19 pandemic there is mass screening of SARS-CoV-2 happening round the world due to the extensive spread of the infections. There is a high demand for rapid diagnostic tests to expedite identification of cases and to facilitate early isolation and control spread. Hence this study evaluates seven different rapid nucleic acid detection assays that are commercially available for SARS-CoV-2 virus detection.\n\nMethodsNasopharyngeal samples were collected from 4859 participants and were tested for SARS-CoV-2 virus by the gold standard RT-PCR method along with one of these seven rapid methods of detection. Evaluation of the rapid nucleic acid detection assays was done by comparing the results of these rapid methods with the gold standard RT-qPCR results for SARS-COV-2 detection.\n\nResultsAQ-TOP had the highest sensitivity (98%) and strong kappa value of 0.943 followed by Genechecker and Abbot ID NOW. The POCKIT (ii RT-PCR) assay had the highest test accuracy of 99.29% followed by Genechecker and Cobas Liat. Atila iAMP showed the highest percentage of invalid reports (35.5%) followed by AQ-TOP with 6% and POCKIT with 3.7% of invalid reports.\n\nConclusionGenechecker system, Abbott ID NOW and Cobas Liat, were found to have best performance and agreement when compared to the standard RT-PCR for COVID-19 detection. With further research, these rapid tests have the potential to be employed in large scale screening of COVID-19.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Sally Mahmoud",
+        "author_inst": "Biogenix Lab G42, Abu Dhabi, UAE"
+      },
+      {
+        "author_name": "Esra Ibrahim",
+        "author_inst": "Biogenix Lab G42, Abu Dhabi, UAE"
+      },
+      {
+        "author_name": "Subhashini Ganesan",
+        "author_inst": "G42 Healthcare"
+      },
+      {
+        "author_name": "Bhagyashree Thakre",
+        "author_inst": "Biogenix Lab G42, Abu Dhabi, UAE"
+      },
+      {
+        "author_name": "Juliet Teddy",
+        "author_inst": "Biogenix Lab G42, Abu Dhabi, UAE"
+      },
+      {
+        "author_name": "Preety Raheja",
+        "author_inst": "Biogenix Lab G42, Abu Dhabi, UAE"
+      },
+      {
+        "author_name": "Walid Zaher",
+        "author_inst": "G42 Healthcare Abu Dhabi, UAE"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.04.17.21255663",
     "rel_title": "Asymptomatic or mild symptomatic SARS-CoV-2 infection elicits durable neutralizing antibody responses in children and adolescents",
@@ -796821,113 +795428,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "radiology and imaging"
   },
-  {
-    "rel_doi": "10.1101/2021.04.19.21255742",
-    "rel_title": "Post-COVID-19 syndrome in outpatients: a cohort study",
-    "rel_date": "2021-04-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.19.21255742",
-    "rel_abs": "BackgroundAfter mild COVID-19, some outpatients experience persistent symptoms. However, data are scarce and prospective studies are urgently needed.\n\nObjectivesTo characterize the post-COVID-19 syndrome after mild COVID-19 and identify predictors.\n\nParticipantsOutpatients with symptoms suggestive of COVID-19 with (1) PCR-confirmed COVID-19 (COVID-positive) or (2) SARS-CoV-2 negative PCR (COVID-negative).\n\nDesignMonocentric cohort study with prospective phone interview between more than three months to ten months after initial visit to the emergency department and outpatient clinics.\n\nMain MeasuresData of the initial visits were extracted from the electronic medical file. Predefined persistent symptoms were assessed through a structured phone interview. Associations between long-term symptoms and PCR results, as well as predictors of persistent symptoms among COVID-positive, were evaluated by multivariate logistic regression adjusted for age, gender, smoking, comorbidities, and timing of the survey.\n\nKey resultsThe study population consisted of 418 COVID-positive and 89 COVID-negative patients, mostly young adults (median age of 41 versus 36 years in COVID-positive and COVID-negative, respectively; p=0.020) and health care workers (67% versus 82%; p=0.006). Median time between the initial visit and the phone survey was 150 days in COVID-positive and 242 days in COVID-negative patients. Persistent symptoms were reported by 223 (53%) COVID-positive and 33 (37%) COVID-negative patients (p=0.006). Overall, 21% COVID-positive and 15% COVID-negative patients (p=0.182) attended care for this purpose. Four surveyed symptoms were independently associated with COVID-19: fatigue (adjusted odds ratio [or] 2.14, 95%CI 1.04-4.41), smell/taste disorder (26.5, 3.46-202), dyspnea (2.81, 1.10-7.16) and memory impairment (5.71, 1.53-21.3). Among COVID-positive, female gender (1.67, 1.09-2.56) and overweight/obesity (1.67, 1.10-2.56) were predictors of persistent symptoms.\n\nConclusionsMore than half of COVID-positive outpatients report persistent symptoms up to ten months after a mild disease. Only 4 of 14 symptoms were associated with COVID-19 status. The symptoms and predictors of the post-COVID-19 syndrome need further characterization as this condition places a significant burden on society.",
-    "rel_num_authors": 23,
-    "rel_authors": [
-      {
-        "author_name": "Florian Desgranges",
-        "author_inst": "Lausanne University Hospital"
-      },
-      {
-        "author_name": "Eliana Tadini",
-        "author_inst": "Lausanne University Hospital"
-      },
-      {
-        "author_name": "Aline Munting",
-        "author_inst": "Lausanne University Hospital"
-      },
-      {
-        "author_name": "Jean Regina",
-        "author_inst": "Lausanne University Hospital"
-      },
-      {
-        "author_name": "Filippidis Paraskevas",
-        "author_inst": "Lausanne University Hospital"
-      },
-      {
-        "author_name": "Eleftherios Karachalias",
-        "author_inst": "Data Scientist, Cardiff, England"
-      },
-      {
-        "author_name": "Benjamin Viala",
-        "author_inst": "Lausanne University Hospital"
-      },
-      {
-        "author_name": "V\u00e9ronique Suttels",
-        "author_inst": "Lausanne University Hospital"
-      },
-      {
-        "author_name": "David Haefliger",
-        "author_inst": "Lausanne University Hospital"
-      },
-      {
-        "author_name": "Eleftheria Kampouri",
-        "author_inst": "Lausanne University Hospital"
-      },
-      {
-        "author_name": "Mathias Van Singer",
-        "author_inst": "Lausanne University Hospital"
-      },
-      {
-        "author_name": "Jonathan Tschopp",
-        "author_inst": "Lausanne University Hospital"
-      },
-      {
-        "author_name": "Laurence Rochat Stettler",
-        "author_inst": "Lausanne University Hospital"
-      },
-      {
-        "author_name": "Sim\u00e9on Schaad",
-        "author_inst": "Lausanne University Hospital"
-      },
-      {
-        "author_name": "Thomas Brahier",
-        "author_inst": "Lausanne University Hospital"
-      },
-      {
-        "author_name": "Olivier Hugli",
-        "author_inst": "Lausanne University Hospital"
-      },
-      {
-        "author_name": "Yolanda Mueller Chabloz",
-        "author_inst": "Lausanne University Hospital"
-      },
-      {
-        "author_name": "Alexandre Gouveia",
-        "author_inst": "Lausanne University Hospital"
-      },
-      {
-        "author_name": "Onya Opota",
-        "author_inst": "Lausanne University Hospital"
-      },
-      {
-        "author_name": "Pierre-Nicolas Carron",
-        "author_inst": "Lausanne University Hospital"
-      },
-      {
-        "author_name": "Beno\u00eet Guery",
-        "author_inst": "Lausanne University Hospital"
-      },
-      {
-        "author_name": "Matthaios Papadimitriou-Olivgeris",
-        "author_inst": "Lausanne University Hospit"
-      },
-      {
-        "author_name": "No\u00e9mie Boillat-Blanco",
-        "author_inst": "Lausanne University Hospital"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.04.18.21255699",
     "rel_title": "INTRANASAL APPLICATION OF LACTOCOCCUS LACTIS W 136 BACTERIA EARLY IN COVID 19 INFECTION MAY HAVE A BENEFICIAL IMMUNOMODULATORY EFFECT: A PROOF-OF-CONCEPT STUDY",
@@ -797390,6 +795890,97 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2021.04.20.440651",
+    "rel_title": "Comparison of Mucosal and Intramuscular Immunization against SARS-CoV-2 with Replication-Defective and Replicating Single-cycle Adenovirus Vaccines",
+    "rel_date": "2021-04-20",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.20.440651",
+    "rel_abs": "SARS-CoV-2 enters the body at mucosal surfaces, such as the nose and lungs. These events involve a small number of virions at these mucosal barriers and are therefore a strategic point to stop a COVID-19 infection before it starts. Despite this, most vaccines against COVID-19 are being injected into the muscle where they will not generate the highest levels of mucosal protection. The vaccines that are approved for use in humans are all replication-defective (RD) mRNA, DNA, or adenovirus (Ad) vaccines that do not amplify antigen transgenes. We developed single cycle adenovirus (SC-Ad) vectors that replicate antigen genes up to 10,000-fold in human cells, but that are disabled from producing infectious Ad particles. We show here that SC-Ad expressing the full-length SARS-CoV-2 spike protein produces 100-fold more spike protein than a matched RD-Ad-Spike vector. When Ad-permissive hamsters were immunized with these vaccines by intranasal (IN) or intramuscular (IM) routes, SC-Ad produced significantly stronger antibody responses as compared to RD-Ad against the spike protein that rose over 14 weeks after one immunization. Single IN or IM immunizations generated significant antibody responses in serum and in bronchoalveolar lavages (BALs). IN priming, but not IM priming, generated HLA-restricted CD8 T cell responses in BALs. SC-Ad-Spike generated antibodies that retain binding to spike receptor binding domains (RBDs) with mutations from new viral variants. These data suggest empowering the genomes of gene-based vaccines with the ability to amplify antigen genes can increase potency. This may be particularly advantageous when applying mucosal vaccines to combat mucosal pathogens like SARS-CoV-2.\n\nOne Sentence SummaryArming adenovirus vaccines with the ability to replicate vaccine antigen genes may increase potency for systemic, or more importantly, mucosal immunization against mucosal pathogens.",
+    "rel_num_authors": 19,
+    "rel_authors": [
+      {
+        "author_name": "Michael A Barry",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Haley Mudrick",
+        "author_inst": "Mayo"
+      },
+      {
+        "author_name": "Erin McGlinch",
+        "author_inst": "Mayo"
+      },
+      {
+        "author_name": "Brian Parrett",
+        "author_inst": "Mayo"
+      },
+      {
+        "author_name": "Jack Hemsath",
+        "author_inst": "Mayo"
+      },
+      {
+        "author_name": "Mary Barry",
+        "author_inst": "Mayo"
+      },
+      {
+        "author_name": "Jeffrey Rubin",
+        "author_inst": "Mayo"
+      },
+      {
+        "author_name": "Chisom Uzendu",
+        "author_inst": "Mayo"
+      },
+      {
+        "author_name": "Michael Hansen",
+        "author_inst": "Mayo"
+      },
+      {
+        "author_name": "Courtney Erskine",
+        "author_inst": "Mayo"
+      },
+      {
+        "author_name": "Virginia VanKeulen",
+        "author_inst": "Mayo"
+      },
+      {
+        "author_name": "Aleksandra Drelich",
+        "author_inst": "UTMB"
+      },
+      {
+        "author_name": "Chien-Te Kent Tseng",
+        "author_inst": "UTMB"
+      },
+      {
+        "author_name": "Christopher Shane Massey",
+        "author_inst": "UTMB"
+      },
+      {
+        "author_name": "Madiha Fida",
+        "author_inst": "Mayo"
+      },
+      {
+        "author_name": "Gina A Suh",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Tobias Peikert",
+        "author_inst": "Mayo"
+      },
+      {
+        "author_name": "Matthew Block",
+        "author_inst": "Mayo"
+      },
+      {
+        "author_name": "Gloria Olivier",
+        "author_inst": "Mayo"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2021.04.19.440446",
     "rel_title": "Inactivation of SARS-CoV-2 in chlorinated swimming pool water",
@@ -799115,69 +797706,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "primary care research"
   },
-  {
-    "rel_doi": "10.1101/2021.04.07.21255044",
-    "rel_title": "COVID transmission and contact tracing using WHO risk assement tool among frontline healthcare workers : Insights from a South Indian tertiary care centre",
-    "rel_date": "2021-04-19",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.07.21255044",
-    "rel_abs": "BackgroundThe high exposure risk to COVID among frontline heathcare workers was a major challenge to healthcare systems across the globe that warranted close monitoring through risk assessment and contact tracing strategies. The objective of our study was to characterize exposure risk factors for transmission and subsequent COVID positivity among the frontlinehealthcare workers in our institution during the pandemic period.\n\nMethodsThe retrospective observational study conducted over a period of 6 months from June 2020 to November 2020 at a 1300-bedded South Indian tertiary care centre included frontline healthcare workers who were assessed for their identified encounter with COVID positive individual using a modified WHO COVID risk assessment tool. Additional risk attributes of exposure characterized among COVID positive healthcare workers comprised of shared space, cluster related transmissions and multiple instances of exposure to COVID.\n\nResultsAmong a total of 4744 contacts with COVID positive individuals assessed for risk stratification during the study period, 942 (19.8%) were high risk and 3802 (80.2%) were low risk exposures respectively. 106 (2.2%) turned COVID positive during the surveillance period of 14 days. Frontline workers working in COVID areas had significant low COVID rates as compared to other areas (N=1, 0.9%). The average monthly COVID positivity rates being 1.66%, the attack rates among high risk and low risk contacts among the total HCWs screened were 5% (46/942) and 1.57% (60/3802) respectively. Shared space (70%) and IPC breaches (66%) were found to be highly prevalent in the COVID positive cohort, along with maskless encounters (43%) and multiple exposure (39%). The attack rate among the 6 identified COVID cluster groups (5.5%) were found to be higher than the attack rate (2.2%) noted among the total contacts screened and no significant association was observed between risk categories in the clusters.\n\nDiscussionOur study highlights higher risk of COVID positivity among high risk contacts as compared to low risk contacts. However, the high COVID positivity rate in low risk group among cluster transmissions and its lack of association with risk assessment highlight the suboptimal utility of the risk assessment strategy among cluster groups.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Merlin Moni",
-        "author_inst": "Amrita Institute of Medical Sciences"
-      },
-      {
-        "author_name": "Kiran G Kulirankal",
-        "author_inst": "Amrita Institute of Medical Sciences"
-      },
-      {
-        "author_name": "Preetha Prasanna",
-        "author_inst": "Amrita Institute of Medical Science"
-      },
-      {
-        "author_name": "Ann Mary",
-        "author_inst": "Amrita Institute of Medical Science"
-      },
-      {
-        "author_name": "Elizabeth Mary Thomas",
-        "author_inst": "Amrita Institute of Medical Science"
-      },
-      {
-        "author_name": "Rejitha P Sundaram",
-        "author_inst": "Amrita Institute of Medical Science"
-      },
-      {
-        "author_name": "Binil Babu",
-        "author_inst": "Amrita Institute of Medical Science"
-      },
-      {
-        "author_name": "Veena Bindu",
-        "author_inst": "Amrita Institute of Medical Science"
-      },
-      {
-        "author_name": "Fabia Edathadathil",
-        "author_inst": "Amrita Institute of Medical Science"
-      },
-      {
-        "author_name": "Sai Bala",
-        "author_inst": "Amrita Institute of Medical Science"
-      },
-      {
-        "author_name": "Beena K V",
-        "author_inst": "Amrita Institute of Medical Science"
-      },
-      {
-        "author_name": "Dipu T Sathyapalan",
-        "author_inst": "Amrita Institute of Medical Sciences"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.04.13.21255395",
     "rel_title": "How disease risk awareness modulates transmission: coupling infectious disease models with behavioral dynamics",
@@ -799560,6 +798088,85 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2021.04.18.440366",
+    "rel_title": "An Immune Cell Atlas Reveals Dynamic COVID-19 Specific Neutrophil Programming Amendable to Dexamethasone Therapy",
+    "rel_date": "2021-04-19",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.18.440366",
+    "rel_abs": "SARS-CoV-2 is a novel coronavirus that causes acute respiratory distress syndrome (ARDS), death and long-term sequelae. Innate immune cells are critical for host defense but are also the primary drivers of ARDS. The relationships between innate cellular responses in ARDS resulting from COVID-19 compared to other causes of ARDS, such as bacterial sepsis is unclear. Moreover, the beneficial effects of dexamethasone therapy during severe COVID-19 remain speculative, but understanding the mechanistic effects could improve evidence-based therapeutic interventions. To interrogate these relationships, we developed an scRNA-Seq and plasma proteomics atlas (biernaskielab.ca/COVID_neutrophil). We discovered that compared to bacterial ARDS, COVID-19 was associated with distinct neutrophil polarization characterized by either interferon (IFN) or prostaglandin (PG) active states. Neutrophils from bacterial ARDS had higher expression of antibacterial molecules such as PLAC8 and CD83. Dexamethasone therapy in COVID patients rapidly altered the IFNactive state, downregulated interferon responsive genes, and activated IL1R2+ve neutrophils. Dexamethasone also induced the emergence of immature neutrophils expressing immunosuppressive molecules ARG1 and ANXA1, which were not present in healthy controls. Moreover, dexamethasone remodeled global cellular interactions by changing neutrophils from information receivers into information providers. Importantly, male patients had higher proportions of IFNactive neutrophils, a greater degree of steroid-induced immature neutrophil expansion, and increased mortality benefit compared to females in the dexamethasone era. Indeed, the highest proportion of IFNactive neutrophils was associated with mortality. These results define neutrophil states unique to COVID-19 when contextualized to other life-threatening infections, thereby enhancing the relevance of our findings at the bedside. Furthermore, the molecular benefits of dexamethasone therapy are also defined, and the identified pathways and plasma proteins can now be targeted to develop improved therapeutics.",
+    "rel_num_authors": 16,
+    "rel_authors": [
+      {
+        "author_name": "Sarthak Sinha",
+        "author_inst": "University of Calgary"
+      },
+      {
+        "author_name": "Nicole Rosin",
+        "author_inst": "University of Calgary"
+      },
+      {
+        "author_name": "Rohit Arora",
+        "author_inst": "University of Calgary"
+      },
+      {
+        "author_name": "Elodie Labit",
+        "author_inst": "University of Calgary"
+      },
+      {
+        "author_name": "Arzina Jaffer",
+        "author_inst": "University of Calgary"
+      },
+      {
+        "author_name": "Leslie Cao",
+        "author_inst": "University of Calgary"
+      },
+      {
+        "author_name": "Raquel Farias",
+        "author_inst": "University of Calgary"
+      },
+      {
+        "author_name": "Angela P Nguyen",
+        "author_inst": "University of Calgary"
+      },
+      {
+        "author_name": "Luiz G. N. de Almeida",
+        "author_inst": "University of Calgary"
+      },
+      {
+        "author_name": "Antoine Dufour",
+        "author_inst": "University of Calgary"
+      },
+      {
+        "author_name": "Amy Bromley",
+        "author_inst": "University of Calgary"
+      },
+      {
+        "author_name": "Braedon McDonald",
+        "author_inst": "University of Calgary"
+      },
+      {
+        "author_name": "Mark Gillrie",
+        "author_inst": "University of Calgary"
+      },
+      {
+        "author_name": "Marvin J Fritzler",
+        "author_inst": "University of Calgary"
+      },
+      {
+        "author_name": "Bryan Yipp",
+        "author_inst": "University of Calgary"
+      },
+      {
+        "author_name": "Jeff Biernaskie",
+        "author_inst": "University of Calgary"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2021.04.17.440278",
     "rel_title": "Differential plasmacytoid dendritic cell phenotype and type I Interferon response in asymptomatic and severe COVID-19 infection",
@@ -800893,101 +799500,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.04.12.21255313",
-    "rel_title": "Strategies and action points to ensure equitable uptake of COVID-19 vaccinations: A national qualitative interview study to explore the views of undocumented migrants, asylum seekers, and refugees",
-    "rel_date": "2021-04-19",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.12.21255313",
-    "rel_abs": "IntroductionEarly evidence confirms lower COVID-19 vaccine uptake in established ethnic minority populations, yet there has been little focus on understanding vaccine hesitancy and barriers to vaccination in migrants. Growing populations of precarious migrants (including undocumented migrants, asylum seekers and refugees) in the UK and Europe are considered to be under-immunised groups and may be excluded from health systems, yet little is known about their views on COVID-19 vaccines specifically, which are essential to identify key solutions and action points to strengthen vaccine roll-out.\n\nMethodsWe did an in-depth semi-structured qualitative interview study of recently arrived migrants (foreign-born, >18 years old; <10 years in the UK) to the UK with precarious immigration status between September 2020 and March 2021, seeking their input into strategies to strengthen COVID-19 vaccine delivery and uptake. We used the  Three Cs model (confidence, complacency and convenience) to explore COVID-19 vaccine hesitancy, barriers and access. Data were analysed using a thematic framework approach. Data collection continued until data saturation was reached, and no novel concepts were arising. The study was approved by the University of London ethics committee (REC 2020.00630).\n\nResultsWe approached 20 migrant support groups nationwide, recruiting 32 migrants (mean age 37.1 years; 21 [66%] female; mean time in the UK 5.6 years [SD 3.7 years]), including refugees (n = 3), asylum seekers (n = 19), undocumented migrants (n = 8) and migrants with limited leave to remain (n = 2) from 15 different countries (5 WHO regions). 23 (72%) of 32 migrants reported being hesitant about accepting a COVID-19 vaccine and communicated concerns over vaccine content, side-effects, lack of accessible information in an appropriate language, lack of trust in the health system and low perceived need. Participants reported a range of barriers to accessing the COVID-19 vaccine and expressed concerns that their communities would be excluded from or de-prioritised in the roll-out. Undocumented migrants described fears over being charged and facing immigration checks if they present for a vaccine. All participants (n = 10) interviewed after recent government announcements that COVID-19 vaccines can be accessed without facing immigration checks remained unaware of this. Participants stated that convenience of access would be a key factor in their decision around whether to accept a vaccine and proposed alternative access points to primary care services (for example, walk-in centres in trusted places such as foodbanks, community centres and charities), alongside promoting registration with primary care for all, and working closely with communities to produce accessible information on COVID-19 vaccination.\n\nConclusionsPrecarious migrants may be hesitant about accepting a COVID-19 vaccine and face multiple and unique barriers to access, requiring simple but innovative solutions to ensure equitable access and uptake. Vaccine hesitancy and low awareness around entitlement and relevant access points could be easily addressed with clear, accessible, and tailored information campaigns, co-produced and delivered by trusted sources within marginalised migrant communities. These findings have immediate relevance to the COVID-19 vaccination initiatives in the UK and in other European and high-income countries with diverse migrant populations.\n\nFundingNIHR",
-    "rel_num_authors": 20,
-    "rel_authors": [
-      {
-        "author_name": "Anna Deal",
-        "author_inst": "St George's, UOL"
-      },
-      {
-        "author_name": "Sally E Hayward",
-        "author_inst": "St George's, University of London"
-      },
-      {
-        "author_name": "Mashal Huda",
-        "author_inst": "St George's, University of London"
-      },
-      {
-        "author_name": "Felicity Knights",
-        "author_inst": "St George's, University of London"
-      },
-      {
-        "author_name": "Alison F Crawshaw",
-        "author_inst": "St George's, University of London"
-      },
-      {
-        "author_name": "Jessica Carter",
-        "author_inst": "St George's, University of London"
-      },
-      {
-        "author_name": "Osama B Hassan",
-        "author_inst": "St George's, University of London"
-      },
-      {
-        "author_name": "Yasmin Farah",
-        "author_inst": "St George's, University of London"
-      },
-      {
-        "author_name": "Yusuf Ciftci",
-        "author_inst": "Doctors of the World UK"
-      },
-      {
-        "author_name": "May Rowland-Pomp",
-        "author_inst": "St George's, University of London"
-      },
-      {
-        "author_name": "Kieran Rustage",
-        "author_inst": "St George's, University of London"
-      },
-      {
-        "author_name": "Lucy Goldsmith",
-        "author_inst": "St George's, University of London"
-      },
-      {
-        "author_name": "Monika Hartmann",
-        "author_inst": "Doctors of the World UK"
-      },
-      {
-        "author_name": "Sandra Mounier-Jack",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Rachel Burns",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Anna Miller",
-        "author_inst": "Doctors of the World UK"
-      },
-      {
-        "author_name": "Fatima Wurie",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Ines Campos-Matos",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Azeem Majeed",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Sally Hargreaves",
-        "author_inst": "St George's University of London"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health policy"
-  },
   {
     "rel_doi": "10.1101/2021.04.16.21255647",
     "rel_title": "Prospective predictive performance comparison between Clinical Gestalt and validated COVID-19 mortality scores.",
@@ -801314,6 +799826,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
+  {
+    "rel_doi": "10.1101/2021.04.16.21255616",
+    "rel_title": "Prevalence and Transmission of SARS-CoV-2 in Childcare Facilities: A Longitudinal Study",
+    "rel_date": "2021-04-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.16.21255616",
+    "rel_abs": "ObjectivesPrevious data indicate that children might play a less crucial role in SARS-CoV-2 transmission than initially assumed. We conducted a study to gain further knowledge on prevalence, transmission and spread of SARS-CoV-2 among preschool children, their parents and caretakers.\n\nMethodsChildren, their parents and care givers in 14 childcare facilities in Dresden, Saxony/ Germany were invited to participate in the KiTaCoviDD19-study between July 2020 and January 2021. Seroprevalence of SARS-CoV-2 antibodies was assessed up to 4 times during the study period in all participating adults and personal characteristics as well as epidemiological information of personal SARS-CoV-2 history were obtained. Stool viral shedding of SARS-CoV-2 was analyzed every 2-4 weeks in all participating children.\n\nResultsIn total, 318 children, 299 parents and 233 childcare workers were enrolled. The percentage of seropositive adults and SARS-CoV-2 positive detected children rose considerably by January 2021. However, the rate of SARS-CoV-2 positive children was considerably lower than the rate of seropositive adults. Overall, we detected a maximum of three connected cases in children. About 50% of SARS-CoV-2 infections in children could not be connected to a secondary case within our study population.\n\nConclusionThe study could not provide evidence for a relevant asymptomatic (\"silent\") spread of SARS-CoV-2 in childcare facilities, neither in a low nor a high prevalence setting. This finding adds to the evidence that childcare and educational settings do not play a crucial role in driving the SARS-CoV-2 pandemic.\n\nTable of Contents SummaryThis longitudinal study among children, parents and childcare workers provides further insight on SARS-CoV-2 prevalence and transmission within childcare facilities.\n\nWhats Known on This SubjectBased on age distribution of SARS-CoV-2 infections and previous data of very limited spread of COVID-19 among primary and secondary schools there is reason to believe that children play a less crucial role in SARS-CoV-2 transmission than initially assumed.\n\nWhat This Study AddsPreviously published studies focus mainly on SARS-CoV-2 transmission in schools. This longitudinal study provides information on prevalence, transmission and spread of SARS-CoV-2 within childcare facilities during low- and high-prevalence settings.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Luise Haag",
+        "author_inst": "Department of Pediatrics, University Hospital and Medical Faculty Carl Gustav Carus, Technische Universitaet Dresden"
+      },
+      {
+        "author_name": "Judith Blankenburg",
+        "author_inst": "Department of Pediatrics, University Hospital and Medical Faculty Carl Gustav Carus, Technische Universitaet Dresden"
+      },
+      {
+        "author_name": "Manja Unrath",
+        "author_inst": "Department of Pediatrics, University Hospital and Medical Faculty Carl Gustav Carus, Technische Universitaet Dresden"
+      },
+      {
+        "author_name": "Johanna Grabietz",
+        "author_inst": "Department of Pediatrics, University Hospital and Medical Faculty Carl Gustav Carus, Technische Universitaet Dresden"
+      },
+      {
+        "author_name": "Elisabeth Kahre",
+        "author_inst": "Department of Pediatrics, University Hospital and Medical Faculty Carl Gustav Carus, Technische Universitaet Dresden"
+      },
+      {
+        "author_name": "Lukas Galow",
+        "author_inst": "Department of Pediatrics, University Hospital and Medical Faculty Carl Gustav Carus, Technische Universitaet Dresden"
+      },
+      {
+        "author_name": "Josephine Schneider",
+        "author_inst": "Department of Pediatrics, University Hospital and Medical Faculty Carl Gustav Carus, Technische Universitaet Dresden"
+      },
+      {
+        "author_name": "Alexander Dalpke",
+        "author_inst": "Institute for Medical Microbiology and Virology, Medical Faculty Carl Gustav Carus, Technische Universitaet Dresden"
+      },
+      {
+        "author_name": "Christian Lueck",
+        "author_inst": "Institute for Medical Microbiology and Virology, Medical Faculty Carl Gustav Carus, Technische Universitaet Dresden"
+      },
+      {
+        "author_name": "Leo Buettner",
+        "author_inst": "Institute for Medical Microbiology and Virology, Medical Faculty Carl Gustav Carus, Technische Universitaet Dresden"
+      },
+      {
+        "author_name": "Jakob Peter Armann",
+        "author_inst": "Department of Pediatrics, University Hospital and Medical Faculty Carl Gustav Carus, Technische Universitaet Dresden"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.04.16.21255543",
     "rel_title": "Will the Large-scale Vaccination Succeed in Containing the COVID-19 Epidemic and How Soon?",
@@ -802655,57 +801226,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.04.12.21251656",
-    "rel_title": "Evaluating the impact of keeping indoor dining closed on COVID-19 rates among large US cities: a quasi-experimental design",
-    "rel_date": "2021-04-16",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.12.21251656",
-    "rel_abs": "ObjectiveIndoor dining is one of the potential key drivers of COVID-19 transmission. We leverage the heterogeneity in state government preemption of city indoor dining closures, to estimate the impact of keeping indoor dining closed on COVID-19 incidence.\n\nMethodsWe obtained case rates and city/state re-opening dates from March to October 2020 in 11 U.S. cities. We categorized cities as (treatment) cities that were allowed by the state to reopen but kept indoor dining closed; and (comparison) cities that would have kept indoor dining closed but were preempted by their state and had to reopen indoor dining.\n\nResultsKeeping indoor dining closed was associated with a 43% (IRR=0.57, 95% CI 0.46 to 0.69) decline in COVID-19 incidence over 4-weeks compared with cities that reopened indoor dining. These results were consistent after testing alternative modeling strategies.\n\nConclusionsKeeping indoor dining closed contributes to reductions in COVID-19 spread.\n\nPolicy ImplicationsEvidence of the relationship between indoor dining and COVID-19 incidence can inform state and local decisions to restrict indoor dining as a tailored strategy to reduce COVID-19 incidence.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Alina S Schnake-Mahl",
-        "author_inst": "Urban Health Collaborative, Dornsife School of Public Health, Drexel University, Philadelphia, PA"
-      },
-      {
-        "author_name": "Gabriella O'Leary",
-        "author_inst": "Department of Health Management and Policy, Dornsife School of Public Health, Drexel University, Philadelphia, PA; Urban Health Collaborative, Dornsife School o"
-      },
-      {
-        "author_name": "Pricila Mullachery",
-        "author_inst": "Urban Health Collaborative, Dornsife School of Public Health, Drexel University, Philadelphia, PA"
-      },
-      {
-        "author_name": "Vaishnavi Vaidya",
-        "author_inst": "Urban Health Collaborative, Dornsife School of Public Health, Drexel University, Philadelphia, PA"
-      },
-      {
-        "author_name": "Gabrielle Connor",
-        "author_inst": "Department of Health Management and Policy, Dornsife School of Public Health, Drexel University, Philadelphia, PA"
-      },
-      {
-        "author_name": "Heather Rollins",
-        "author_inst": "Urban Health Collaborative, Dornsife School of Public Health, Drexel University, Philadelphia, PA"
-      },
-      {
-        "author_name": "Jennifer Kolker",
-        "author_inst": "Urban Health Collaborative, Dornsife School of Public Health, Drexel University, Philadelphia, PA; Department of Health Management and Policy, Dornsife School o"
-      },
-      {
-        "author_name": "Ana V Diez Roux",
-        "author_inst": "Urban Health Collaborative, Dornsife School of Public Health, Drexel University, Philadelphia, PA; 3.\tDepartment of Epidemiology and Biostatistics, Dornsife Sch"
-      },
-      {
-        "author_name": "Usama Bilal",
-        "author_inst": "Urban Health Collaborative, Dornsife School of Public Health, Drexel University, Philadelphia, PA; 3.\tDepartment of Epidemiology and Biostatistics, Dornsife Sch"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.04.12.21255149",
     "rel_title": "Clumpiness: Modeling the Impact of Social Dynamics on COVID-19 Spread",
@@ -803040,6 +801560,77 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.04.16.440173",
+    "rel_title": "Viral neuroinvasion and neurotropism without neuronal damage in the hACE2 mouse model of COVID-19",
+    "rel_date": "2021-04-16",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.16.440173",
+    "rel_abs": "Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) not only affects the respiratory tract but also causes neurological symptoms such as loss of smell and taste, headache, fatigue or severe cerebrovascular complications. Using transgenic mice expressing human angiotensin-converting enzyme 2 (hACE2) we investigated the spatiotemporal distribution and pathomorphological features in the CNS following intranasal infection with SARS-CoV-2 variants, also after prior influenza A virus infection. Apart from Omicron, we found all variants to frequently spread to and within the CNS. Infection was restricted to neurons and appeared to spread from the olfactory bulb mainly in basally orientated regions in the brain and into the spinal cord, independent of ACE2 expression and without evidence of neuronal cell death, axonal damage or demyelination. However, microglial activation, microgliosis and a mild macrophage and T cell dominated inflammatory response was consistently observed, accompanied by apoptotic death of endothelial, microglial and immune cells, without their apparent infection. Microgliosis and immune cell apoptosis indicate a potential role of microglia for pathogenesis and viral effect in COVID-19 and possible impairment of neurological functions, especially in long COVID. These data may also be informative for the selection of therapeutic candidates, and broadly support investigation of agents with adequate penetration into relevant regions of the CNS.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Frauke Seehusen",
+        "author_inst": "University of Zurich"
+      },
+      {
+        "author_name": "Jordan J. Clark",
+        "author_inst": "University of Liverpool"
+      },
+      {
+        "author_name": "Parul Sharma",
+        "author_inst": "University of Liverpool"
+      },
+      {
+        "author_name": "Eleanor Bentley",
+        "author_inst": "University of Liverpool"
+      },
+      {
+        "author_name": "Adam Kirby",
+        "author_inst": "University of Liverpool"
+      },
+      {
+        "author_name": "Krishanthi Subramaniam",
+        "author_inst": "University of Liverpool"
+      },
+      {
+        "author_name": "Sabina Wunderlin Giuliani",
+        "author_inst": "University of Zurich"
+      },
+      {
+        "author_name": "Grant Hughes",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Edward I Patterson",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Benedict D Michael",
+        "author_inst": "University of Liverpool"
+      },
+      {
+        "author_name": "Andrew Owen",
+        "author_inst": "University of Liverpool"
+      },
+      {
+        "author_name": "Julian Alexander Hiscox",
+        "author_inst": "University of Liverpool"
+      },
+      {
+        "author_name": "James P Stewart",
+        "author_inst": "University of Liverpool"
+      },
+      {
+        "author_name": "Anja Kipar",
+        "author_inst": "University of Zurich"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "pathology"
+  },
   {
     "rel_doi": "10.1101/2021.04.16.440101",
     "rel_title": "A pair of non-competing neutralizing human monoclonal antibodies protecting from disease in a SARS-CoV-2 infection model",
@@ -804361,113 +802952,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.04.12.21255308",
-    "rel_title": "Performance of vaccination with CoronaVac in a cohort of healthcare workers (HCW) - preliminary report",
-    "rel_date": "2021-04-15",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.12.21255308",
-    "rel_abs": "BackgroundCoronaVac, a vaccine containing inactivated SARS-CoV-2, demonstrated efficacy of 50.39% 14 days or more after the 2nd dose.\n\nThe objective of this study is to report the occurrence of symptomatic COVID-19 in a cohort of HCW vaccinated with CoronaVac and to estimate its effectiveness.\n\nMethodsCoronaVac was given to HCWs inHospital das Clinicas on 18-21 January, 2021 (epi week 3) (22,402 HCWs), and on 14-16 February, 2021 (epi week 7) (21,652 HCWs). Weekly cases of symptomatic COVID-19 were evaluated. Using the period from 2020 epi week 24 through 2021 epi week 2 (before vaccination), a Poisson regression was fit to model the HCWs with COVID-19 of the hospital, and the officially reported cases in the city of Sao Paulo. The predicted numbers of cases among HCWs for 2021 epi weeks 3-12 were then compared to the observed numbers of cases (after vaccination). Effectiveness was estimated for weeks 9-12 (2 to 5 weeks after the 2nd dose). 142 samples after vaccination were evaluated for SARS-CoV-2 variants of concern.\n\nResultsSince the 1st dose there were 380 HCW diagnosed with COVID-19. On visual analysis, the number of cases of COVID-19 in the city increased sharply in 2021. The number of cases among the HCW did not follow. The estimated effectiveness 2 and 3 weeks after 2nd dose was 50.7% and 51.8%, respectively, and increased over the next 2 weeks. 67/142 samples (47%) were variants of concern, mostly P1 (57).\n\nConclusionCoronavac is effective in preventing COVID-19.",
-    "rel_num_authors": 23,
-    "rel_authors": [
-      {
-        "author_name": "Elizabeth Faria",
-        "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil"
-      },
-      {
-        "author_name": "Ana Rubia Guedes",
-        "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil"
-      },
-      {
-        "author_name": "Maura S Oliveira",
-        "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil"
-      },
-      {
-        "author_name": "Moacyr Vergara Godoy Moreira",
-        "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil"
-      },
-      {
-        "author_name": "Fernando Liebhart Maia",
-        "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil"
-      },
-      {
-        "author_name": "Antonio Santos Barboza",
-        "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil"
-      },
-      {
-        "author_name": "Mariana Deckers Leme",
-        "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil"
-      },
-      {
-        "author_name": "Leila Suemi Harima Letaif",
-        "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil"
-      },
-      {
-        "author_name": "Anna Miethke-Morais",
-        "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil"
-      },
-      {
-        "author_name": "Eloisa Bonfa",
-        "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil"
-      },
-      {
-        "author_name": "Aluisio C Segurado",
-        "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil"
-      },
-      {
-        "author_name": "Francis M Tomazini",
-        "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil"
-      },
-      {
-        "author_name": "Alcir Alves Santos Jr.",
-        "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil"
-      },
-      {
-        "author_name": "Pedro Figueiredo",
-        "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil"
-      },
-      {
-        "author_name": "Pamela Santos Andrade",
-        "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil"
-      },
-      {
-        "author_name": "Franciane Mendes Oliveira",
-        "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil"
-      },
-      {
-        "author_name": "Raissa Heloisa de Araujo Eliodoro",
-        "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil"
-      },
-      {
-        "author_name": "Jaqueline Goes de Jesus",
-        "author_inst": "Instituto de Medicina Tropical"
-      },
-      {
-        "author_name": "Carolina Santos Lazari",
-        "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil"
-      },
-      {
-        "author_name": "Ester C Sabino",
-        "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Brazil"
-      },
-      {
-        "author_name": "Silvia F Costa",
-        "author_inst": "University of Sao Paulo"
-      },
-      {
-        "author_name": "Antonio Carlos Pedroso de Lima",
-        "author_inst": "Instituto de Matematica e Estatistica, Universidade de Sao Paulo, Brazil"
-      },
-      {
-        "author_name": "Anna S Levin",
-        "author_inst": "Universidade de Sao Paulo, Brazil"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.04.13.21255393",
     "rel_title": "Facemask usage during the COVID-19 pandemic among people with primary ciliary dyskinesia: a participatory project",
@@ -804682,6 +803166,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.04.13.21255336",
+    "rel_title": "Trajectories of compliance with COVID-19 related guidelines: longitudinal analyses of 50,000 UK adults",
+    "rel_date": "2021-04-15",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255336",
+    "rel_abs": "BackgroundGovernments have implemented a range of measure to tackle COVID-19, primarily focusing on changing citizens behaviours in order to lower transmission of the virus. Some policymakers have expressed concern that citizens would not maintain high levels of compliance with these behaviours over the pandemic and would instead exhibit so-called \"behavioural fatigue\". While the concept has been criticized, there have been few tests of behavioural fatigue using data from the COVID-19 pandemic, and none that have tracked individuals compliance trajectories.\n\nMethodsWe used longitudinal data on self-reported compliance from 50,851 adults in the COVID-19 Social Study collected across two waves of the pandemic in the UK (01 April 2020 - 22 February 2021). We modelled typical compliance trajectories using latent growth curve analysis (LGCA) and tested for behavioural fatigue by attempting to identify a set of participants whose compliance decreased substantially over the study period.\n\nResultsWe selected a four-class LGCA solution. Most individuals maintained high levels of compliance over the pandemic and reported similar levels of compliance across the first and second waves. Approximately one in seven participants had decreasing levels of compliance across the pandemic, reporting noticeably lower levels of compliance in the second wave, a pattern compatible with behavioural fatigue. Individuals with declining compliance levels differed from those with consistently high compliance on multiple characteristics, including (young) age, better physical health, lower empathy and conscientiousness and greater general willingness to take risks.\n\nConclusionWhile a minority, not all individuals have maintained high compliance across the pandemic. Decreasing compliance is related to several psychological traits. The results suggest that targeting of behaviour change messages later in the pandemic may be needed to increase compliance.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Liam Wright",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Andrew Steptoe",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Daisy Fancourt",
+        "author_inst": "University College London"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.04.12.21255344",
     "rel_title": "Seroepidemiology among Employees of New York City Health and Hospitals during the First Wave of the SARS-CoV-2 Epidemic",
@@ -806295,49 +804806,6 @@
     "type": "new results",
     "category": "biochemistry"
   },
-  {
-    "rel_doi": "10.1101/2021.04.14.439863",
-    "rel_title": "Clinicopathologic features of a feline SARS-CoV-2 infection model parallel acute COVID-19 in humans",
-    "rel_date": "2021-04-14",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.14.439863",
-    "rel_abs": "The emergence and ensuing dominance of COVID-19 on the world stage has emphasized the urgency of efficient animal models for the development of therapeutics and assessment of immune responses to SARS-CoV-2 infection. Shortcomings of current animal models for SARS-CoV-2 include limited lower respiratory disease, divergence from clinical COVID-19 disease, and requirements for host genetic modifications to permit infection. This study validates a feline model for SARS-CoV-2 infection that results in clinical disease and histopathologic lesions consistent with severe COVID-19 in humans. Intra-tracheal inoculation of concentrated SARS-CoV-2 caused infected cats to develop clinical disease consistent with that observed in the early exudative phase of COVID-19. A novel clinical scoring system for feline respiratory disease was developed and utilized, documenting a significant degree of lethargy, fever, dyspnea, and dry cough in infected cats. In addition, histopathologic pulmonary lesions such as diffuse alveolar damage, hyaline membrane formation, fibrin deposition, and proteinaceous exudates were observed due to SARS-CoV-2 infection, imitating lesions identified in people hospitalized with ARDS from COVID-19. A significant correlation exists between the degree of clinical disease identified in infected cats and pulmonary lesions. Viral loads and ACE2 expression were quantified in nasal turbinates, distal trachea, lung, and various other organs. Natural ACE2 expression, paired with clinicopathologic correlates between this feline model and human COVID-19, encourage use of this model for future translational studies.\n\nAuthor SummaryIdentifying an ideal animal model to study COVID-19 has been difficult, and current models come with challenges that restrict their potential in translational studies. Few lab animals naturally express the receptors necessary for viral infection (ACE2), and many fail to manifest clinical signs or pathology similar to that seen in humans. Other models (non-human primates, mink) are ideal for disease and transmission studies, but are restricted by cost, husbandry challenges, and scarce availability. Alternatively, cats naturally express ACE2 receptors, are naturally infected with SARS-CoV-2 and can transmit virus from cat-to-cat. Prior to this study, cats infected by oral/nasal routes have not displayed significant clinical disease or lung pathology. However, we demonstrate that direct inoculation of concentrated SARS-CoV-2 virus in the trachea of cats induces analogous clinical and pathologic features to hospitalized patients with acute COVID-19. Our results show that infected cats exhibit significant clinical signs during experimental infection (coughing, increased respiratory effort, lethargy, and fever) and exhibit extensive lung lesions that mimic severe COVID-19 pathology such as diffuse alveolar damage and hyaline membrane formation - highlighting the immeasurable potential for this feline model to address translational approaches for COVID-19 and to better understand the role of cats in transmission and disease.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Jennifer Rudd",
-        "author_inst": "Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University; Stillwater, OK, USA"
-      },
-      {
-        "author_name": "Miruthula Tamil Selvan",
-        "author_inst": "Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University; Stillwater, OK, USA"
-      },
-      {
-        "author_name": "Shannon Cowan",
-        "author_inst": "Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University; Stillwater, OK, USA"
-      },
-      {
-        "author_name": "Yun-Fan Kao",
-        "author_inst": "Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University; Stillwater, OK, USA"
-      },
-      {
-        "author_name": "Cecily Midkiff",
-        "author_inst": "Division of Comparative Pathology, National Primate Research Center, Tulane University; Covington, LA, USA"
-      },
-      {
-        "author_name": "Jerry Ritchey",
-        "author_inst": "Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University; Stillwater, OK, USA"
-      },
-      {
-        "author_name": "Craig A Miller",
-        "author_inst": "Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University; Stillwater, OK, USA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2021.04.13.439743",
     "rel_title": "Dynamic Profiling of  Binding and Allosteric Propensities  of the SARS-CoV-2 Spike Protein with Different Classes of Antibodies:  Mutational and Perturbation-Based Scanning Reveal Allosteric Duality of Functionally Adaptable Hotspots",
@@ -806672,6 +805140,85 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health systems and quality improvement"
   },
+  {
+    "rel_doi": "10.1101/2021.04.10.21255111",
+    "rel_title": "Rapid spread and high impact of the Variant of Concern P.1 in the largest city of Brazil",
+    "rel_date": "2021-04-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.10.21255111",
+    "rel_abs": "First in Manaus in the Brazilian Northern region, the Variant of Concern P.1 traveled 3800 kilometers southeast to endanger Sao Paulo contributing to the collapse of the health system. Here, we show evidence of how fast the VOC P.1 has spread in the most populated city in South America.",
+    "rel_num_authors": 16,
+    "rel_authors": [
+      {
+        "author_name": "Gabriela Barbosa",
+        "author_inst": "UNIFESP"
+      },
+      {
+        "author_name": "Luiz Vinicius Leao Moreira",
+        "author_inst": "Federal University of Sao Paulo (UNIFESP)"
+      },
+      {
+        "author_name": "Alberto Fernando Oliveira Justo",
+        "author_inst": "Federal University of Sao Paulo (UNIFESP)"
+      },
+      {
+        "author_name": "Ana Helena Perosa",
+        "author_inst": "Federal University of Sao Paulo (UNIFESP)"
+      },
+      {
+        "author_name": "Ana Paula Chaves",
+        "author_inst": "UNIFESP"
+      },
+      {
+        "author_name": "Mariana Sardinha Bueno",
+        "author_inst": "UNIFESP"
+      },
+      {
+        "author_name": "Luciano Kleber de Souza Luna",
+        "author_inst": "Universidade Federal de Sao Paulo"
+      },
+      {
+        "author_name": "Danielle Dias Conte",
+        "author_inst": "UNIFESP"
+      },
+      {
+        "author_name": "Joseane Mayara Carvalho",
+        "author_inst": "UNIFESP"
+      },
+      {
+        "author_name": "Janesly Prates",
+        "author_inst": "UNIFESP"
+      },
+      {
+        "author_name": "Patricia Sousa Dantas",
+        "author_inst": "UNIFESP"
+      },
+      {
+        "author_name": "Klinger Faico",
+        "author_inst": "UNIFESP"
+      },
+      {
+        "author_name": "Clarice Camargo",
+        "author_inst": "UNIFESP"
+      },
+      {
+        "author_name": "Paola Cristina Resende",
+        "author_inst": "Oswaldo Cruz Institute"
+      },
+      {
+        "author_name": "Marilda Siqueira",
+        "author_inst": "Oswald Cruz Intitute"
+      },
+      {
+        "author_name": "Nancy cristina junqueira Bellei",
+        "author_inst": "Federal University of Sao Paulo"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.04.13.21255142",
     "rel_title": "Effect of COVID-19 on Lipid Profile and its Correlation with Acute Phase Reactants",
@@ -807805,133 +806352,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.04.09.21255194",
-    "rel_title": "Antibody and T-cell responses to a single dose of the AZD1222/Covishield vaccine in previously SARS-CoV-2 infected and naive health care workers in Sri Lanka",
-    "rel_date": "2021-04-13",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.09.21255194",
-    "rel_abs": "BackgroundIn order to determine the immunogenicity of a single dose of the AZD1222/Covishield vaccine in a real-world situation, we assessed the immunogenicity, in a large cohort of health care workers in Sri Lanka.\n\nMethodsSARS-CoV-2 antibodies was carried out in 607 naive and 26 previously infected health care workers (HCWs) 28 to 32 days following a single dose of the vaccine. Haemagglutination test (HAT) for antibodies to the receptor binding domain (RBD) of the wild type virus, B.1.1.7, B.1.351 and the surrogate neutralization assay (sVNT) was carried out in 69 naive and 26 previously infected individuals. Spike protein (pools S1 and S2) specific T cell responses were measured by ex vivo ELISpot IFN{gamma} assays in 76 individuals.\n\nResults92.9% of previously naive HCWs seroconverted to a single dose of the vaccine, irrespective of age and gender; and ACE2 blocking antibodies were detected in 67/69 (97.1%) previously naive vaccine recipients. Although high levels of antibodies were found to the RBD of the wild type virus, the titres for B.1.1.7 and B.1.351 were lower in previously naive HCWs. Ex vivo T cell responses were observed to S1 in 63.9% HCWs and S2 in 31.9%. The ACE2 blocking titres measured by the sVNT significantly increased (p<0.0001) from a median of 54.1 to 97.9 % of inhibition, in previously infected HCWs and antibodies to the RBD for the variants B.1.1.7 and B.1.351 also significantly increased.\n\nDiscussiona single dose of the AZD1222/Covishield vaccine was shown to be highly immunogenic in previously naive individuals inducing antibody levels greater than following natural infection. In infected individuals, a single dose induced very high levels of ACE2 blocking antibodies and antibodies to RBDs of SARS-CoV-2 variants of concern.\n\nFundingWe are grateful to the World Health Organization, UK Medical Research Council and the Foreign and Commonwealth Office.",
-    "rel_num_authors": 28,
-    "rel_authors": [
-      {
-        "author_name": "Chandima Jeewandara",
-        "author_inst": "University of Sri Jayewardenepura"
-      },
-      {
-        "author_name": "Achala Kamaladasa",
-        "author_inst": "University of Sri Jayewardenepura"
-      },
-      {
-        "author_name": "Pradeep D Pushpakumara",
-        "author_inst": "University of SriJayewardenepura"
-      },
-      {
-        "author_name": "Deshni Jayathilaka",
-        "author_inst": "University of Sri Jayewardenepura"
-      },
-      {
-        "author_name": "Inoka Sepali",
-        "author_inst": "Inoka Sepali Abeyratne"
-      },
-      {
-        "author_name": "Saubhagyagya Danasekara",
-        "author_inst": "University of Sri Jayewardenepura"
-      },
-      {
-        "author_name": "Dinuka Guruge",
-        "author_inst": "Colombo Municipal Council, Colombo, Sri Lanka"
-      },
-      {
-        "author_name": "Thushali Ranasinghe",
-        "author_inst": "University of Sri Jayewardenepura"
-      },
-      {
-        "author_name": "Shashika Dayaratne",
-        "author_inst": "University of Sri Jayewardenepura"
-      },
-      {
-        "author_name": "Thilagaraj T Padmanadan",
-        "author_inst": "University of Sri Jayewardenepura"
-      },
-      {
-        "author_name": "Gayasha Somathilaka",
-        "author_inst": "University of Sri Jayewardenepura"
-      },
-      {
-        "author_name": "Deshan Madusanka",
-        "author_inst": "University of Sri Jayewardenepura"
-      },
-      {
-        "author_name": "Shyrar Tanussiya",
-        "author_inst": "University of Sri Jayewardenepura"
-      },
-      {
-        "author_name": "Tibutius Jayadas",
-        "author_inst": "University of Sri Jayewardenepura"
-      },
-      {
-        "author_name": "Heshan Kuruppu",
-        "author_inst": "University of Sri Jayewardenepura"
-      },
-      {
-        "author_name": "Ayesha Wijesinghe",
-        "author_inst": "University of Sri Jayewardenepura"
-      },
-      {
-        "author_name": "Nimasha Thashmi",
-        "author_inst": "University of Sri Jayewardenepura"
-      },
-      {
-        "author_name": "Dushantha Milroy",
-        "author_inst": "Base Hospital, Dambadeniya, Sri Lanka"
-      },
-      {
-        "author_name": "Achini Nandasena",
-        "author_inst": "University of Sri Jayewardenepura"
-      },
-      {
-        "author_name": "Nilanka Sanjeewani",
-        "author_inst": "University of Sri Jayewardenepura"
-      },
-      {
-        "author_name": "Ruwan Wijayamuni",
-        "author_inst": "Colombo Municipal Council, Colombo, Sri Lanka"
-      },
-      {
-        "author_name": "Sudath Samaraweera",
-        "author_inst": "Epidemiology Unit, Ministry of Health Sri Lanka"
-      },
-      {
-        "author_name": "Lisa Schimanski",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Tiong Tan",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Tao Dong",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Graham Ogg",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Alain Townsend",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Gathsaurie Neelika Malavige",
-        "author_inst": "University of Sri Jayewardenepura"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "allergy and immunology"
-  },
   {
     "rel_doi": "10.1101/2021.04.09.21255131",
     "rel_title": "Early and ongoing importations of SARS-CoV-2 in Canada",
@@ -808266,6 +806686,85 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.04.09.21255195",
+    "rel_title": "Ovarian follicular function is not altered by SARS-Cov-2 infection or BNT162b2 mRNA Covid-19 vaccination.",
+    "rel_date": "2021-04-13",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.09.21255195",
+    "rel_abs": "ImportanceThis is the first study to examine the impact of SARS-Cov-2 infection and COVID-19 vaccination on ovarian function.\n\nObjectiveTo characterize anti-COVID-19 antibodies in follicular fluid and compare ovarian follicle function in women following confirmed SARS-CoV-2 infection, COVID-19 vaccination, and non-infected, unvaccinated controls.\n\nDesignThis is a cohort study conducted between February 1 and March 10, 2021.\n\nSettingA single university hospital-based IVF clinic.\n\nParticipantsConsecutive sample of female patients undergoing oocyte retrieval.\n\nInterventionsConsenting patients were recruited and assigned to one of three study groups: recovering from confirmed COVID 19 (n=9); vaccinated (n=9); and uninfected, non-vaccinated controls (n=14). Serum and follicular fluid samples were taken and analyzed for anti-COVID IgG as well as estrogen, progesterone and HSPG2 concentration, as well as the number and maturity of aspirated oocytes and previous estrogen and progesterone measurements.\n\nMain outcome measuresFollicular function, including steroidogenesis, follicular response to the LH/hCG trigger, and oocyte quality biomarkers.\n\nResultsBoth natural and vaccine elicited anti-COVID IgG antibodies were detected in the follicular fluid in levels proportional to the IgG serum concentration. No differences were detected in any of the surrogate ovarian follicle quality reporting parameters.\n\nConclusions and relevanceBoth SARS-COV-2 infection and vaccination with the BNT162b2 mRNA vaccine mediate IgG immunity that crosses into the follicular fluid. No detrimental effect on follicular function was detected.\n\nTrial RegistrationCinicalTrials.gov registry number NCT04822012\n\nKey PointCOVID 19 disease and BNT162b2 mRNA vaccine induce anti-COVID IgG in follicular fluid; neither recent infection nor vaccination appear to negatively effect follicular function.",
+    "rel_num_authors": 16,
+    "rel_authors": [
+      {
+        "author_name": "Yaakov Bentov",
+        "author_inst": "Department of Obstetrics and Gynecology, Hadassah Mount Scopus-Hebrew  University medical center, Jerusalem, Israel"
+      },
+      {
+        "author_name": "Ofer Beharier",
+        "author_inst": "Department of Obstetrics and Gynecology, Hadassah Mount Scopus-Hebrew  University medical center, Jerusalem, Israel"
+      },
+      {
+        "author_name": "Arbel Moav-Zafrir",
+        "author_inst": "Department of Obstetrics and Gynecology, Hadassah Mount Scopus-Hebrew  University medical center, Jerusalem, Israel"
+      },
+      {
+        "author_name": "Maor Kabessa",
+        "author_inst": "Department of Obstetrics and Gynecology, Hadassah Mount Scopus-Hebrew  University medical center, Jerusalem, Israel"
+      },
+      {
+        "author_name": "Miri Godin",
+        "author_inst": "Department of Obstetrics and Gynecology, Hadassah Mount Scopus-Hebrew  University medical center, Jerusalem, Israel"
+      },
+      {
+        "author_name": "Caryn Greenfield",
+        "author_inst": "Department of Obstetrics and Gynecology, Hadassah Mount Scopus-Hebrew  University medical center, Jerusalem, Israel"
+      },
+      {
+        "author_name": "Mali Ketzinel-Gilad",
+        "author_inst": "MALCA@hadassah.org.ilDepartment of Obstetrics and Gynecology, Hadassah Mount Scopus-Hebrew  University medical center, Jerusalem, Israel"
+      },
+      {
+        "author_name": "Efrat Esh Broder",
+        "author_inst": "Department of Obstetrics and Gynecology, Hadassah Mount Scopus-Hebrew  University medical center, Jerusalem, Israel"
+      },
+      {
+        "author_name": "Hananel Holzer",
+        "author_inst": "Hadassah University medical center, Jerusalem, Israel"
+      },
+      {
+        "author_name": "Dana Wolf",
+        "author_inst": "Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel"
+      },
+      {
+        "author_name": "Esther Oiknine-Djian",
+        "author_inst": "Clinical Virology Unit, Hadassah Hebrew University Medical Center, Jerusalem, Israel"
+      },
+      {
+        "author_name": "Iyad Barghouti",
+        "author_inst": "Biochemistry Laboratory, Hadassah University Hospital, Mt. Scopus, Jerusalem"
+      },
+      {
+        "author_name": "Debra Goldman-Wohl",
+        "author_inst": "Division of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem"
+      },
+      {
+        "author_name": "Simcha Yagel",
+        "author_inst": "Division of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem"
+      },
+      {
+        "author_name": "Asnat Walfisch",
+        "author_inst": "Department of Obstetrics and Gynecology, Hadassah Mount Scopus-Hebrew  University medical center, Jerusalem, Israel"
+      },
+      {
+        "author_name": "Anat Hershko Klement",
+        "author_inst": "Department of Obstetrics and Gynecology, Hadassah Mount Scopus-Hebrew  University medical center, Jerusalem, Israel"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "obstetrics and gynecology"
+  },
   {
     "rel_doi": "10.1101/2021.04.12.21255304",
     "rel_title": "Survey of Behaviour Attitudes Towards Preventive Measures Following COVID-19 Vaccination",
@@ -809739,185 +808238,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.04.11.439379",
-    "rel_title": "One Health Investigation of SARS-CoV-2 Infection and Seropositivity among Pets in Households with Confirmed Human COVID-19 Cases - Utah and Wisconsin, 2020",
-    "rel_date": "2021-04-13",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.11.439379",
-    "rel_abs": "BackgroundApproximately 67% of U.S. households have pets. Limited data are available on SARS-CoV-2 in pets. We assessed SARS-CoV-2 infection in pet cohabitants as a sub-study of an ongoing COVID-19 household transmission investigation.\n\nMethodsMammalian pets from households with [&ge;]1 person with laboratory-confirmed COVID-19 were eligible for inclusion from April-May 2020. Demographic/exposure information, oropharyngeal, nasal, rectal, and fur swabs, feces, and blood were collected from enrolled pets and tested by rRT-PCR and virus neutralization assays.\n\nFindingsWe enrolled 37 dogs and 19 cats from 34 of 41 eligible households. All oropharyngeal, nasal, and rectal swabs tested negative by rRT-PCR; one dogs fur swabs (2%) tested positive by rRT-PCR at the first animal sampling. Among 47 pets with serological results from 30 households, eight (17%) pets (4 dogs, 4 cats) from 6 (20%) households had detectable SARS-CoV-2 neutralizing antibodies. In households with a seropositive pet, the proportion of people with laboratory-confirmed COVID-19 was greater (median 79%; range: 40-100%) compared to households with no seropositive pet (median 37%; range: 13-100%) (p=0.01). Thirty-three pets with serologic results had frequent daily contact ([&ge;]1 hour) with the human index patient before the persons COVID-19 diagnosis. Of these 33 pets, 14 (42%) had decreased contact with the human index patient after diagnosis and none (0%) were seropositive; of the 19 (58%) pets with continued contact, 4 (21%) were seropositive.\n\nInterpretationsSeropositive pets likely acquired infection from humans, which may occur more frequently than previously recognized. People with COVID-19 should restrict contact with animals.\n\nFundingCenters for Disease Control and Prevention, U.S. Department of Agriculture",
-    "rel_num_authors": 41,
-    "rel_authors": [
-      {
-        "author_name": "Grace W Goryoka",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Caitlin M. Cossaboom",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Radhika Gharpure",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Patrick Dawson",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Cassandra Tansey",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "John Rossow",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Victoria Mrotz",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Jane Rooney",
-        "author_inst": "United States Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services"
-      },
-      {
-        "author_name": "Mia Torchetti",
-        "author_inst": "United States Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, National Veterinary Services Laboratories"
-      },
-      {
-        "author_name": "Christina M Loiacono",
-        "author_inst": "United States Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, National Veterinary Services Laboratories"
-      },
-      {
-        "author_name": "Mary L Killian",
-        "author_inst": "United States Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, National Veterinary Services Laboratories"
-      },
-      {
-        "author_name": "Melinda Jenkins-Moore",
-        "author_inst": "United States Department of Agriculture, Animal and Plant Health Inspection Service, Veterinary Services, National Veterinary Services Laboratories"
-      },
-      {
-        "author_name": "Ailam Lim",
-        "author_inst": "Wisconsin Veterinary Diagnostic Laboratory"
-      },
-      {
-        "author_name": "Keith Poulsen",
-        "author_inst": "Wisconsin Veterinary Diagnostic Laboratory"
-      },
-      {
-        "author_name": "Dan Christensen",
-        "author_inst": "Wisconsin Veterinary Diagnostic Laboratory"
-      },
-      {
-        "author_name": "Emma Sweet",
-        "author_inst": "Wisconsin Veterinary Diagnostic Laboratory"
-      },
-      {
-        "author_name": "Dallin Peterson",
-        "author_inst": "Utah Department of Health"
-      },
-      {
-        "author_name": "Anna L Sangster",
-        "author_inst": "Utah Department of Health"
-      },
-      {
-        "author_name": "Erin L Young",
-        "author_inst": "Utah Department of Health"
-      },
-      {
-        "author_name": "Kelly F Oakeson",
-        "author_inst": "Utah Department of Health"
-      },
-      {
-        "author_name": "Dean Taylor",
-        "author_inst": "Utah Department of Agriculture and Food"
-      },
-      {
-        "author_name": "Amanda Price",
-        "author_inst": "Utah Department of Agriculture and Food"
-      },
-      {
-        "author_name": "Tair Kiphibane",
-        "author_inst": "Salt Lake County Health Department"
-      },
-      {
-        "author_name": "Rachel Klos",
-        "author_inst": "Wisconsin Department of Health Services"
-      },
-      {
-        "author_name": "Darlene Konkle",
-        "author_inst": "Wisconsin Department of Agriculture, Trade and Consumer Protection"
-      },
-      {
-        "author_name": "Sanjib Bhattacharyya",
-        "author_inst": "City of Milwaukee Health Department Milwaukee"
-      },
-      {
-        "author_name": "Trivikram Dasu",
-        "author_inst": "City of Milwaukee Health Department Milwaukee"
-      },
-      {
-        "author_name": "Victoria T Chu",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Nathaniel M Lewis",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Krista Queen",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Jing Zhang",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Anna Uehara",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Elizabeth A Dietrich",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Suxiang Tong",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Hannah L Kirking",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Jeffrey R Doty",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Laura S Murrell",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Jessica R Spengler",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Anne Straily",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Ryan Wallace",
-        "author_inst": "Centers for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Casey Barton Behravesh",
-        "author_inst": "Centers for Disease Control and Prevention"
-      }
-    ],
-    "version": "1",
-    "license": "cc0",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2021.04.08.21254779",
     "rel_title": "Immunogenicity of SARS-CoV-2 Vaccine in Dialysis",
@@ -810252,6 +808572,37 @@
     "type": "new results",
     "category": "molecular biology"
   },
+  {
+    "rel_doi": "10.1101/2021.04.12.439473",
+    "rel_title": "Revealing the threat of emerging SARS-CoV-2 mutations to antibody therapies",
+    "rel_date": "2021-04-12",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.12.439473",
+    "rel_abs": "The ongoing massive vaccination and the development of effective intervention offer the long-awaited hope to end the global rage of the COVID-19 pandemic. However, the rapidly growing SARS-CoV-2 variants might compromise existing vaccines and monoclonal antibody (mAb) therapies. Although there are valuable experimental studies about the potential threats from emerging variants, the results are limited to a handful of mutations and Eli Lilly and Regeneron mAbs. The potential threats from frequently occurring mutations on the SARS-CoV-2 spike (S) protein receptor-binding domain (RBD) to many mAbs in clinical trials are largely unknown. We fill the gap by developing a topology-based deep learning strategy that is validated with tens of thousands of experimental data points. We analyze 261,348 genome isolates from patients to identify 514 non-degenerate RBD mutations and investigate their impacts on 16 mAbs in clinical trials. Our findings, which are highly consistent with existing experimental results about variants from the UK, South Africa, Brazil, US-California, and Mexico shed light on potential threats of 95 high-frequency mutations to mAbs not only from Eli Lilly and Regeneron but also from Celltrion and Rockefeller University that are in clinical trials. We unveil, for the first time, that high-frequency mutations R346K/S, N439K, G446V, L455F, V483F/A, E484Q/V/A/G/D, F486L, F490L/V/S, Q493L, and S494P/L might compromise some of mAbs in clinical trials. Our study gives rise to a general perspective about how mutations will affect current vaccines.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Jiahui Chen",
+        "author_inst": "Michigan State University"
+      },
+      {
+        "author_name": "Kaifu Gao",
+        "author_inst": "Michigan State University"
+      },
+      {
+        "author_name": "Rui Wang",
+        "author_inst": "Michigan State University"
+      },
+      {
+        "author_name": "Guo-Wei Wei",
+        "author_inst": "Michigan State University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "biochemistry"
+  },
   {
     "rel_doi": "10.1101/2021.04.11.439322",
     "rel_title": "Prediction and evolution of the molecular fitness of SARS-CoV-2 variants: Introducing SpikePro",
@@ -811689,49 +810040,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2021.04.07.21254793",
-    "rel_title": "Covid-19 and Excess Mortality in Medicare Beneficiaries",
-    "rel_date": "2021-04-10",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.07.21254793",
-    "rel_abs": "We estimated excess mortality in Medicare recipients with probable and confirmed Covid-19 infections in the general community and amongst residents of long-term care (LTC) facilities. We considered 28,389,098 Medicare and dual-eligible recipients from one year before February 29, 2020 through September 30, 2020, with mortality followed through November 30th, 2020. Probable and confirmed Covid-19 diagnoses, presumably mostly symptomatic, were determined from ICD-10 codes. We developed a Risk Stratification Index (RSI) mortality model which was applied prospectively to establish baseline mortality risk. Excess deaths attributable to Covid-19 were estimated by comparing actual-to-expected deaths based on historical comparisons and in closely matched cohorts with and without Covid-19. 677,100 (2.4%) beneficiaries had confirmed Covid-19 and 2,917,604 (10.3%) had probable Covid-19. 472,329 confirmed cases were community living and 204,771 were in LTC. Mortality following a probable or confirmed diagnosis in the community increased from an expected incidence of about 4% to actual incidence of 7.5%. In long-term care facilities, the corresponding increase was from 20.3% to 24.6%. The absolute increase was therefore similar at 3-4% in the community and in LTC residents. The percentage increase was far greater in the community (89%) than among patients in chronic care facilities (21%) who had higher baseline risk. The LTC population without probable or confirmed Covid-19 diagnoses experienced 38,932 excess deaths (35%) compared to historical estimates. Limitations in access to Covid-19 testing and disease under-reporting in LTC patients probably were important factors, although social isolation and disruption in usual care presumably also contributed. Remarkably, there were 31,360 fewer deaths than expected in community dwellers without probable or confirmed Covid-19 diagnoses, representing a 6% reduction. Disruptions to the healthcare system and avoided medical care were thus apparently offset by other factors, representing overall benefit. The Covid-19 pandemic had marked effects on mortality, but the effects were highly context-dependent.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Scott D Greenwald",
-        "author_inst": "Health Data Analytics Institute"
-      },
-      {
-        "author_name": "Nassib G Chamoun",
-        "author_inst": "Health Data Analytics Institute"
-      },
-      {
-        "author_name": "Paul J Manberg",
-        "author_inst": "Health Data Analytics Institute"
-      },
-      {
-        "author_name": "Josh Gray",
-        "author_inst": "Health Data Analytics Institute"
-      },
-      {
-        "author_name": "David Clain",
-        "author_inst": "Health Data Analytics Institute"
-      },
-      {
-        "author_name": "Kamal Maheshwari",
-        "author_inst": "Cleveland Clinic"
-      },
-      {
-        "author_name": "Daniel I Sessler",
-        "author_inst": "Cleveland Clinic"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health informatics"
-  },
   {
     "rel_doi": "10.1101/2021.04.07.21254925",
     "rel_title": "Antibody Responses in Elderly Residential Care Persons following COVID-19 mRNA Vaccination",
@@ -811994,6 +810302,29 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2021.04.09.439203",
+    "rel_title": "A trimeric hydrophobic zipper mediates the intramembrane assembly of SARS-CoV-2 spike",
+    "rel_date": "2021-04-10",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.09.439203",
+    "rel_abs": "The S protein of the SARS-CoV-2 is a Type I membrane protein that mediates membrane fusion and viral entry. A vast amount of structural information is available for the ectodomain of S, a primary target by the host immune system, but much less is known regarding its transmembrane domain (TMD) and its membrane-proximal regions. Here, we determined the nuclear magnetic resonance (NMR) structure of the S protein TMD in bicelles that closely mimic a lipid bilayer. The TMD structure is a transmembrane -helix (TMH) trimer that assembles spontaneously in membrane. The trimer structure shows an extensive hydrophobic core along the 3-fold axis that resembles that of a trimeric leucine/isoleucine zipper, but with tetrad, not heptad, repeat. The trimeric core is strong in bicelles, resisting hydrogen-deuterium exchange for weeks. Although highly stable, structural guided mutagenesis identified single mutations that can completely dissociate the TMD trimer. Multiple studies have shown that the membrane anchor of viral fusion protein can form highly specific oligomers, but the exact function of these oligomers remain unclear. Our findings should guide future experiments to address the above question for SARS coronaviruses.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Qingshan Fu",
+        "author_inst": "Harvard Medical School"
+      },
+      {
+        "author_name": "James J Chou",
+        "author_inst": "Harvard Medical School"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "biochemistry"
+  },
   {
     "rel_doi": "10.1101/2021.04.08.438911",
     "rel_title": "Nanobody Repertoires for Exposing Vulnerabilities of SARS-CoV-2",
@@ -813575,45 +811906,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.04.07.21254703",
-    "rel_title": "Prevalence of SARS-CoV-2 antibodies in Denmark: Nationwide, population-based seroepidemiological surveys",
-    "rel_date": "2021-04-09",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.07.21254703",
-    "rel_abs": "BackgroundSeroprevalence studies have proven an important tool to monitor the progression of the coronavirus disease 2019 (COVID-19) epidemic. We present results of consecutive population-based seroprevalence surveys performed in Denmark in 2020.\n\nMethodsInvitation letters including a questionnaire covering symptoms were sent to representatively drawn samples of the population in spring, late summer and autumn/winter of 2020. Blood samples from participants taken at public test-centers were analyzed for total Ig and seroprevalence estimates per population segment calculated and compared to other surveillance parameters.\n\nResultsFrom 34,081 participating individuals (response rate 33%), we obtained seroprevalence estimates increasing from 1.1% (95%CI: 0.7%-1.7) in May to 4.0 % (95%CI: 3.4%-4.7%) in December 2020. By December 2020, 1.5% of the population 12 years and older had tested positive by PCR. Seroprevalence estimates were roughly 3 times higher in those aged 12-29 compared to 65+ and higher in metropolitan municipalities. Among seropositives, loss of taste/smell were the more specific symptoms, 32%-56% did not report any symptoms. In half of seroconverted families, we did not see evidence of transmission between generations. Infected individuals in older age groups were hospitalized several fold more often than in younger.\n\nConclusionsSeroprevalence increased during 2020; younger age groups were primarily infected in the autumn/winter surge. Approximately half were asymptomatically infected. Denmark has a high per capita test rate; roughly two undiagnosed infections of COVID-19 were estimated to occur for each diagnosed case. The epidemic appears to have progressed relatively modestly during 2020 in Denmark.\n\nsummaryWe describe population-based COVID-19 seroprevalence surveys performed in Denmark in 2020. The seroprevalence increased during the year, particularly in adolescents and young adults, but was overall low. Roughly two undiagnosed cases per PCR-confirmed case were detected by December 2020.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Laura Espenhain",
-        "author_inst": "Statens Serum Institut"
-      },
-      {
-        "author_name": "Siri Tribler",
-        "author_inst": "Statens Serum Institut"
-      },
-      {
-        "author_name": "Charlotte Svaerke Joergensen",
-        "author_inst": "Statens Serum Institut"
-      },
-      {
-        "author_name": "Christian Holm Hansen",
-        "author_inst": "Statens Serum Institut"
-      },
-      {
-        "author_name": "Ute Wolf Sonksen",
-        "author_inst": "Statens Serum Institut"
-      },
-      {
-        "author_name": "Steen Ethelberg",
-        "author_inst": "Statens Serum Institut"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.04.06.21255039",
     "rel_title": "An extended SEIARD model for COVID-19 vaccination in Mexico: analysis and forecast",
@@ -813808,6 +812100,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.04.07.21255071",
+    "rel_title": "Results Availability and Timeliness of Registered COVID-19 Clinical Trials: A Cross-Sectional Study",
+    "rel_date": "2021-04-09",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.07.21255071",
+    "rel_abs": "ObjectiveTo examine how and when the results of COVID-19 clinical trials are disseminated.\n\nDesignCross-sectional bibliographic study\n\nSettingThe COVID-19 clinical trial landscape\n\nParticipants285 registered interventional clinical trials for the treatment and prevention of COVID-19 completed by 30 June 2020\n\nMain outcome measuresOverall reporting and reporting by dissemination route (i.e., by journal article, preprint, or results on a registry); time to reporting by dissemination route.\n\nResultsFollowing automated and manual searches of the COVID-19 literature, we located 41 trials (14%) with results spread across 47 individual results publications published by 15 August 2020. The most common dissemination route was preprints (n = 25) followed by journal articles (n = 18), and results on a registry (n = 2). Of these, four trials were available as both a preprint and journal publication. The cumulative incidence of any reporting surpassed 20% at 119 days from completion. Sensitivity analyses using alternate dates available and definitions of results did not appreciably change the reporting percentage. Expanding minimum follow-up time to 3 months increased the overall reporting percentage to 19%.\n\nConclusionCOVID-19 trials completed during the first six months of the pandemic did not consistently yield rapid results in the literature or on clinical trial registries. Our findings suggest that the COVID-19 response may be seeing quicker results disclosure compared to non-emergency conditions. Issues with the reliability and timeliness of trial registration data may impact our estimates. Ensuring registry data is accurate should be a priority for the research community during a pandemic. Data collection is underway for Phase 2 of the DIRECCT study expanding our trial population to those completed anytime in 2020.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Maia Salholz-Hillel",
+        "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin"
+      },
+      {
+        "author_name": "Peter Grabitz",
+        "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin"
+      },
+      {
+        "author_name": "Molly Pugh-Jones",
+        "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin"
+      },
+      {
+        "author_name": "Daniel Strech",
+        "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin Berlin"
+      },
+      {
+        "author_name": "Nicholas J DeVito",
+        "author_inst": "University of Oxford"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "medical ethics"
+  },
   {
     "rel_doi": "10.1101/2021.04.06.21254740",
     "rel_title": "Detecting Pathogen-Associated RNA via Piecewise Isothermal Testing achieving Sample-to-Result Integration",
@@ -815261,93 +813588,6 @@
     "type": "new results",
     "category": "biochemistry"
   },
-  {
-    "rel_doi": "10.1101/2021.04.07.438808",
-    "rel_title": "Identifying SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of Nsp13 Helicase",
-    "rel_date": "2021-04-08",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.07.438808",
-    "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global public health challenge. While the efficacy of vaccines against emerging and future virus variants remains unclear, there is a need for therapeutics. Repurposing existing drugs represents a promising and potentially rapid opportunity to find novel antivirals against SARS-CoV-2. The virus encodes at least nine enzymatic activities that are potential drug targets. Here we have expressed, purified and developed enzymatic assays for SARS-CoV-2 nsp13 helicase, a viral replication protein that is essential for the coronavirus life cycle. We screened a custom chemical library of over 5000 previously characterised pharmaceuticals for nsp13 inhibitors using a FRET-based high-throughput screening (HTS) approach. From this, we have identified FPA-124 and several suramin-related compounds as novel inhibitors of nsp13 helicase activity in vitro. We describe the efficacy of these drugs using assays we developed to monitor SARS-CoV-2 growth in Vero E6 cells.",
-    "rel_num_authors": 18,
-    "rel_authors": [
-      {
-        "author_name": "Rupert Beale",
-        "author_inst": "The Francis Crick Institute"
-      },
-      {
-        "author_name": "Agustina P Bertolin",
-        "author_inst": "The Francis Crick Institute"
-      },
-      {
-        "author_name": "Annabel Borg",
-        "author_inst": "The Francis Crick Institute"
-      },
-      {
-        "author_name": "Berta Canal",
-        "author_inst": "The Francis Crick Institute"
-      },
-      {
-        "author_name": "John FX Diffley",
-        "author_inst": "The Francis Crick Institute"
-      },
-      {
-        "author_name": "Lucy S Drury",
-        "author_inst": "The Francis Crick Institute"
-      },
-      {
-        "author_name": "Ruth Harvey",
-        "author_inst": "The Francis Crick Institute"
-      },
-      {
-        "author_name": "Michael Howell",
-        "author_inst": "The Francis Crick Institute"
-      },
-      {
-        "author_name": "Saira Hussain",
-        "author_inst": "The Francis Crick Institute"
-      },
-      {
-        "author_name": "Svend Kjaer",
-        "author_inst": "The Francis Crick Institute"
-      },
-      {
-        "author_name": "John McCauley",
-        "author_inst": "The Francis Crick Institute"
-      },
-      {
-        "author_name": "Laura McCoy",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Jennifer Milligan",
-        "author_inst": "The Francis Crick Institute"
-      },
-      {
-        "author_name": "Viktor Posse",
-        "author_inst": "The Francis Crick Institute"
-      },
-      {
-        "author_name": "Rachel Ulferts",
-        "author_inst": "The Francis Crick Institute"
-      },
-      {
-        "author_name": "Florian Weissmann",
-        "author_inst": "The Francis Crick Institute"
-      },
-      {
-        "author_name": "Mary Wu",
-        "author_inst": "The Francis Crick Institute"
-      },
-      {
-        "author_name": "Jingkun Zeng",
-        "author_inst": "The Francis Crick Institute"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "biochemistry"
-  },
   {
     "rel_doi": "10.1101/2021.04.07.438804",
     "rel_title": "Identifying SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of Nsp3 Papain-like Protease",
@@ -815902,6 +814142,205 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2021.04.07.438818",
+    "rel_title": "Structural basis for broad sarbecovirus neutralization by a human monoclonal antibody",
+    "rel_date": "2021-04-08",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.07.438818",
+    "rel_abs": "The recent emergence of SARS-CoV-2 variants of concern (VOC) and the recurrent spillovers of coronaviruses in the human population highlight the need for broadly neutralizing antibodies that are not affected by the ongoing antigenic drift and that can prevent or treat future zoonotic infections. Here, we describe a human monoclonal antibody (mAb), designated S2x259, recognizing a highly conserved cryptic receptor-binding domain (RBD) epitope and cross-reacting with spikes from all sarbecovirus clades. S2x259 broadly neutralizes spike-mediated entry of SARS-CoV-2 including the B.1.1.7, B.1.351, P.1 and B.1.427/B.1.429 VOC, as well as a wide spectrum of human and zoonotic sarbecoviruses through inhibition of ACE2 binding to the RBD. Furthermore, deep-mutational scanning and in vitro escape selection experiments demonstrate that S2x259 possesses a remarkably high barrier to the emergence of resistance mutants. We show that prophylactic administration of S2x259 protects Syrian hamsters against challenges with the prototypic SARS-CoV-2 and the B.1.351 variant, suggesting this mAb is a promising candidate for the prevention and treatment of emergent VOC and zoonotic infections. Our data unveil a key antigenic site targeted by broadly-neutralizing antibodies and will guide the design of pan-sarbecovirus vaccines.",
+    "rel_num_authors": 46,
+    "rel_authors": [
+      {
+        "author_name": "M. Alejandra Tortorici",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Nadine Czudnochowski",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Tyler N Starr",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      },
+      {
+        "author_name": "Roberta Marzi",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Alexandra C. Walls",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Fabrizia Zatta",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "John E. Bowen",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Stefano Jaconi",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Julia di Iulio",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Zhaoqian Wang",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Anna De Marco",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Samantha Zepeda",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Dora Pinto",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Zhuoming Liu",
+        "author_inst": "Washington University School of Medicine"
+      },
+      {
+        "author_name": "Martina Beltramello",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Istvan Bartha",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Michael P. Housley",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Florian A Lempp",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Laura E. Rosen",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Exequiel Dellota Jr.",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Hanna Kaiser",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Martin Montiel-Ruiz",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Jiayi Zhou",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Amin Addetia",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      },
+      {
+        "author_name": "Barbara Guarino",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Katja Culap",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Nicole Sprugasci",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Christian Saliba",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Eneida Vetti",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Isabella Giacchetto-Sasselli",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Chiara Silacci Fregni",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Rana Abdelnabi",
+        "author_inst": "Rega Institute, KU Leuven"
+      },
+      {
+        "author_name": "Caroline Shi-Yan Foo",
+        "author_inst": "Katholieke Universiteit Leuven"
+      },
+      {
+        "author_name": "Colin Havenar-Daughton",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Michael A Schmid",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Fabio Benigni",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Elisabetta Cameroni",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Johan Neyts",
+        "author_inst": "Rega Institute"
+      },
+      {
+        "author_name": "Amalio Telenti",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Gyorgy Snell",
+        "author_inst": "Vir Biotechnology Inc"
+      },
+      {
+        "author_name": "Herbert W Virgin",
+        "author_inst": "Vir Biotechnology"
+      },
+      {
+        "author_name": "Sean P. J. Whelan",
+        "author_inst": "Washington University in Saint Louis"
+      },
+      {
+        "author_name": "Jesse D Bloom",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      },
+      {
+        "author_name": "Davide Corti",
+        "author_inst": "Humabs Biomed SA, subsidiary of Vir Biotechnology"
+      },
+      {
+        "author_name": "David Veesler",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Matteo Samuele Pizzuto",
+        "author_inst": "Vir Biotechnology"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2021.04.06.21254996",
     "rel_title": "Examining changes in sleep duration associated with the onset of the COVID-19 pandemic: Who is sleeping and who is not?",
@@ -817431,57 +815870,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.04.01.21254795",
-    "rel_title": "Intensity of home-based telework and work engagement during the COVID-19 pandemic",
-    "rel_date": "2021-04-07",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.01.21254795",
-    "rel_abs": "ObjectiveThe present study examined the relationship between the intensity of home-based telework and work engagement.\n\nMethodsThis cross-sectional study using a self-administrated questionnaire survey was conducted from December 22 to 25, 2020, in Japan. The subjects were asked single-item questions about the intensity of telework and three-item questions about work engagement using the Utrecht Work Engagement Scale. Coefficients were estimated using a multilevel regression model nested by prefecture of residence and adjusted for covariates.\n\nResultsHigh-intensity (four or more days per week) telework was not associated with high work engagement for men or women. In contrast, low and moderate intensity (three days per week to once per month) were associated with high work engagement. The results were consistent when stratified by sex.\n\nConclusionsReasonable-intensity telework may have beneficial effects on work engagement.\n\nClinical SignificanceThis study revealed that a reasonable intensity of telework may have beneficial effects on work engagement. A reasonable intensity is defined as low (once per week to once per month) or moderate intensity (two to three days per week) for both men and women.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Tomohisa Nagata",
-        "author_inst": "University of Occupational and Environmental Health, Japan"
-      },
-      {
-        "author_name": "Masako Nagata",
-        "author_inst": "University of Occupational and Environmental Health, Japan"
-      },
-      {
-        "author_name": "Kazunori Ikegami",
-        "author_inst": "University of Occupational and Environmental Health, Japan"
-      },
-      {
-        "author_name": "Ayako Hino",
-        "author_inst": "University of Occupational and Environmental Health, Japan"
-      },
-      {
-        "author_name": "Seiichiro Tateishi",
-        "author_inst": "University of Occupational and Environmental Health, Japan"
-      },
-      {
-        "author_name": "Mayumi Tsuji",
-        "author_inst": "University of Occupational and Environmental Health, Japan"
-      },
-      {
-        "author_name": "Shinya Matsuda",
-        "author_inst": "University of Occupational and Environmental Health, Japan"
-      },
-      {
-        "author_name": "Yoshihisa Fujino",
-        "author_inst": "University of Occupational and Environmental Health, Japan"
-      },
-      {
-        "author_name": "Koji Mori",
-        "author_inst": "University of Occupational and Environmental Health, Japan"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "occupational and environmental health"
-  },
   {
     "rel_doi": "10.1101/2021.04.04.21254903",
     "rel_title": "Monitoring carbon dioxide to quantify the risk of indoor airborne transmission of COVID-19",
@@ -817732,6 +816120,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.04.05.21254722",
+    "rel_title": "Outcomes of COVID-19 Vaccination Efforts in Florida from December 14, 2020 to March 15, 2021 on Older Individuals",
+    "rel_date": "2021-04-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.05.21254722",
+    "rel_abs": "Per-capita, Florida ranks second in those 65 years of age and older (20.5%) with more than 4,500,000 individuals in this category. COVID-19 vaccine was allocated in a phased roll-out beginning December 14, 2020. Phase 1A included health care personnel with direct patient contact, and residents and staff of nursing homes (NHs) and assisted living facilities (ALFs). Following this initial phase, individuals 65 years of age and older became eligible for vaccination, along with individuals determined by hospital providers to be extremely medically vulnerable to COVID-19. This strategy was based on the desire to most immediately reduce morbidity and mortality, as COVID-19 morbidity and mortality is age-related. Through March 15, 2021, 4,338,099 individuals received COVID-19 vaccine, including 2,431,540 individuals who completed their vaccination series. Of all those vaccinated, 70% were 65 years of age and older, and 63% of those 65 years of age and older. Beginning February 1, 2021, the decline in the number of new cases per week became greater in those 65 years of age and older than those younger. By March 15, 2021, the number of new cases, hospitalizations, and deaths per day for those 65 years of age and older relative to mid-January, were 82%, 80%, and 92% lower respectively. In comparison, the number of new cases, hospitalizations, and deaths per day for those younger than 65 years of age were 70%, 60%, and 87% lower respectively. Reductions in rates in those 65 year of age and older, were thus greater than in those who were younger (p <0.01; Wilcoxon test). These data show that vaccination efforts directed at those 65 years of age and older results in accelerated rates of overall declines in COVID-19 hospitalizations and mortality.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Scott Rivkees",
+        "author_inst": "Florida Department of Health"
+      },
+      {
+        "author_name": "Shamarial Roberson",
+        "author_inst": "Florida Department of Health"
+      },
+      {
+        "author_name": "Carina Blackmore",
+        "author_inst": "Florida Department of Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.04.06.438552",
     "rel_title": "The SARS-CoV-2 Nsp3 macrodomain reverses PARP9/DTX3L-dependent ADP-ribosylation induced by interferon signalling",
@@ -819257,65 +817672,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.04.01.21254794",
-    "rel_title": "Effect of Tocilizumab on ventilator free days composite outcome in SARS-CoV-2 patients. A retrospective competing risk analysis.",
-    "rel_date": "2021-04-07",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.01.21254794",
-    "rel_abs": "BackgroundSARS-CoV-2 infection demonstrates a wide range of severity, the more severe cases demonstrate a cytokine storm with elevated serum interleukin-6, hence IL-6 receptor antibody Tocilizumab was tried for the management of severe cases.\n\nObjectivesThe effect of Tocilizumab treatment on the composite outcome of ventilator free days, among critically ill SARS-CoV-2 patients.\n\nMethodRetrospective observational propensity score matching study, comparing mechanically ventilated patients upon ICU admission who received Tocilizumab to a control group. Utilizing competing risk analysis method, and reporting sub-distributional hazard ratio of a composite outcome of ventilator free days at day 28.\n\nResults29 patients in the intervention group were compared to 29 patients in the control group. Matched groups were similar at base line. The primary outcome of ventilator free days was higher in the intervention group (SHR 2.7, 95% CI: 1.2 - 6.3; p = 0.02), crude ICU mortality rate was not different between Tocilizumab and control groups (37.9% versus 62% respectively, p = 0.1), actual ventilator free days were significantly longer in Tocilizumab group (mean difference 4.7 days, 95% CI 1.1 - 8.3; p = 0.02). Sensitivity analysis by Cox regression showed a significantly lower hazard ratio of death in Tocilizumab group (HR 0.49, 95% CI: 0.25 - 0.97; p = 0.04). While there was no difference in grown positive cultures among groups (55.2% in Tocilizumab group versus 34.5% in the control, 95% CI of difference: -7.11% to 54.4%; p = 0.1).\n\nConclusionTocilizumab may improve the composite outcome of ventilator free days at day 28 among mechanically ventilated SARS-CoV-2 patients, it is associated with significantly longer actual ventilator free days, and insignificantly lower mortality and superinfection.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Ahmed F. Mady",
-        "author_inst": "King Saud Medical City"
-      },
-      {
-        "author_name": "Basheer Abdulrahman",
-        "author_inst": "King Saud Medical City"
-      },
-      {
-        "author_name": "Omar E. Ramadan",
-        "author_inst": "King Saud Medical City"
-      },
-      {
-        "author_name": "Shahzad A. Mumtaz",
-        "author_inst": "King Saud Medical City"
-      },
-      {
-        "author_name": "Mohammed A. Al-Odat",
-        "author_inst": "King Saud Medical City"
-      },
-      {
-        "author_name": "Ahmed Kuhail",
-        "author_inst": "King Saud Medical City"
-      },
-      {
-        "author_name": "Rehab Altoraifi",
-        "author_inst": "King Saud Medical City"
-      },
-      {
-        "author_name": "Rayan Alshae",
-        "author_inst": "King Saud Medical City"
-      },
-      {
-        "author_name": "Abdulrahman M. Alharthy",
-        "author_inst": "King Saud Medical City"
-      },
-      {
-        "author_name": "Dimitrios Karakitsos",
-        "author_inst": "King Saud Medical City"
-      },
-      {
-        "author_name": "Waleed Th. Aletreby",
-        "author_inst": "King Saud Medical City"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "intensive care and critical care medicine"
-  },
   {
     "rel_doi": "10.1101/2021.04.05.21254924",
     "rel_title": "Phylogenetic estimates of SARS-CoV-2 introductions into Washington State",
@@ -819642,6 +817998,101 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health systems and quality improvement"
   },
+  {
+    "rel_doi": "10.1101/2021.04.05.21254952",
+    "rel_title": "mRNA vaccination compared to infection elicits an IgG-predominant response with greater SARS-CoV-2 specificity and similar decrease in variant spike recognition",
+    "rel_date": "2021-04-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.05.21254952",
+    "rel_abs": "During the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, new vaccine strategies including lipid nanoparticle delivery of antigen encoding RNA have been deployed globally. The BioNTech/Pfizer mRNA vaccine BNT162b2 encoding SARS-CoV-2 spike protein shows 95% efficacy in preventing disease, but it is unclear how the antibody responses to vaccination differ from those generated by infection. Here we compare the magnitude and breadth of antibodies targeting SARS-CoV-2, SARS-CoV-2 variants of concern, and endemic coronaviruses, in vaccinees and infected patients. We find that vaccination differs from infection in the dominance of IgG over IgM and IgA responses, with IgG reaching levels similar to those of severely ill COVID-19 patients and shows decreased breadth of the antibody response targeting endemic coronaviruses. Viral variants of concern from B.1.1.7 to P.1 to B.1.351 form a remarkably consistent hierarchy of progressively decreasing antibody recognition by both vaccinees and infected patients exposed to Wuhan-Hu-1 antigens.",
+    "rel_num_authors": 20,
+    "rel_authors": [
+      {
+        "author_name": "Katharina Roeltgen",
+        "author_inst": "Stanford University School of Medicine, Stanford, CA, USA"
+      },
+      {
+        "author_name": "Sandra C.A. Nielsen",
+        "author_inst": "Stanford University School of Medicine, Stanford, CA, USA"
+      },
+      {
+        "author_name": "Prabhu S Arunachalam",
+        "author_inst": "Stanford University, Stanford, CA, USA"
+      },
+      {
+        "author_name": "Fan Yang",
+        "author_inst": "Stanford University School of Medicine, Stanford, CA, USA"
+      },
+      {
+        "author_name": "Ramona A. Hoh",
+        "author_inst": "Stanford University School of Medicine, Stanford, CA, USA"
+      },
+      {
+        "author_name": "Oliver F. Wirz",
+        "author_inst": "Stanford University School of Medicine, Stanford, CA, USA"
+      },
+      {
+        "author_name": "Alexandra S Lee",
+        "author_inst": "Sean N. Parker Center for Allergy & Asthma Research, Stanford, CA, USA"
+      },
+      {
+        "author_name": "Fei Gao",
+        "author_inst": "Stanford University, Stanford, CA, USA"
+      },
+      {
+        "author_name": "Vamsee Mallajosyula",
+        "author_inst": "Stanford University, Stanford, CA, USA"
+      },
+      {
+        "author_name": "Chunfeng Li",
+        "author_inst": "Stanford University, Stanford, CA, USA"
+      },
+      {
+        "author_name": "Emily Haraguchi",
+        "author_inst": "Stanford University School of Medicine, Stanford, CA, USA"
+      },
+      {
+        "author_name": "Massa J Shoura",
+        "author_inst": "Stanford University School of Medicine, Stanford, CA, USA"
+      },
+      {
+        "author_name": "James L Wilbur",
+        "author_inst": "Meso Scale Diagnostics LLC, Rockville, Maryland, USA."
+      },
+      {
+        "author_name": "Jacob N. Wohlstadter",
+        "author_inst": "Meso Scale Diagnostics LLC, Rockville, Maryland, USA."
+      },
+      {
+        "author_name": "Mark M. Davis",
+        "author_inst": "Stanford University, Stanford, CA, USA"
+      },
+      {
+        "author_name": "Benjamin A. Pinsky",
+        "author_inst": "Stanford University School of Medicine, Stanford, CA, USA"
+      },
+      {
+        "author_name": "George B. Sigal",
+        "author_inst": "Meso Scale Diagnostics LLC, Rockville, Maryland, USA."
+      },
+      {
+        "author_name": "Bali Pulendran",
+        "author_inst": "Stanford University, Stanford, CA, USA"
+      },
+      {
+        "author_name": "Kari C. Nadeau",
+        "author_inst": "Sean N. Parker Center for Allergy & Asthma Research, Stanford, CA, USA."
+      },
+      {
+        "author_name": "Scott D. Boyd",
+        "author_inst": "Stanford University School of Medicine, Stanford, CA, USA"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.04.05.21254940",
     "rel_title": "Single Prime hAd5 Spike (S) + Nucleocapsid (N) Dual Antigen Vaccination of Healthy Volunteers Induces a Ten-Fold Increase in Mean S- and N- T-Cell Responses Equivalent to T-Cell Responses from Patients Previously Infected with SARS-CoV-2",
@@ -820951,101 +819402,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.04.01.21254585",
-    "rel_title": "Increasing concentration of COVID-19 by socioeconomic determinants and geography in Toronto, Canada: an observational study",
-    "rel_date": "2021-04-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.01.21254585",
-    "rel_abs": "BackgroundInequities in the burden of COVID-19 observed across Canada suggest heterogeneity within community transmission.\n\nObjectivesTo quantify the magnitude of heterogeneity in the wider community (outside of long-term care homes) in Toronto, Canada and assess how the magnitude in concentration evolved over time (January 21 to November 21, 2020).\n\nDesignRetrospective, population-based observational study using surveillance data from Ontarios Case and Contact Management system.\n\nSettingToronto, Canada.\n\nParticipantsLaboratory-confirmed cases of COVID-19 (N=33,992).\n\nMeasurementsWe generated epidemic curves by SDOH and crude Lorenz curves by neighbourhoods to visualize inequities in the distribution of COVID-19 cases by social determinants of health (SDOH) and estimated the crude Gini coefficient. We examined the correlation between SDOH using Pearson correlation coefficients.\n\nResultsThe Gini coefficient of cumulative cases by population size was 0.41 (95% CI: 0.36-0.47) and were estimated for: household income (0.20, 95%CI: 0.14-0.28); visible minority (0.21, 95%CI: 0.16-0.28); recent immigration (0.12, 95%CI: 0.09-0.16); suitable housing (0.21, 95%CI: 0.14-0.30); multi-generational households (0.19, 95%CI: 0.15-0.23); and essential workers (0.28, 95% CI: 0.23-0.34). Most SDOH were highly correlated.\n\nLocally acquired cases were concentrated in higher income neighbourhoods in the early phase of the epidemic, and then concentrated in lower income neighbourhoods. Mirroring the trajectory of epidemic curves by income, the Lorenz curve shifted over time from below to above the line of equality with a similar pattern across SDOH.\n\nLimitationsStudy relied on area-based measures of the SDOH and individual case counts of COVID-19. We cannot infer concentration of cases by specific occupational exposures given limitation to broad occupational categories.\n\nConclusionCOVID-19 is increasingly concentrated by SDOH given socioeconomic inequities and structural racism.\n\nPrimary Funding SourceCanadian Institutes of Health Research.",
-    "rel_num_authors": 20,
-    "rel_authors": [
-      {
-        "author_name": "Sharmistha Mishra",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Huiting Ma",
-        "author_inst": "St. Michael's Hospital, Unity Health Toronto"
-      },
-      {
-        "author_name": "Gary Moloney",
-        "author_inst": "St. Michael's Hospital, Unity Health Toronto"
-      },
-      {
-        "author_name": "Kristy CY Yiu",
-        "author_inst": "St. Michael's Hospital, Unity Health Toronto"
-      },
-      {
-        "author_name": "Dariya Darvin",
-        "author_inst": "St. Michael's Hospital, Unity Health Toronto"
-      },
-      {
-        "author_name": "David Landsman",
-        "author_inst": "St. Michael's Hospital, Unity Health Toronto"
-      },
-      {
-        "author_name": "Jeff Kwong",
-        "author_inst": "ICES"
-      },
-      {
-        "author_name": "Andrew Calzavara",
-        "author_inst": "ICES"
-      },
-      {
-        "author_name": "Sharon Straus",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Adrienne K Chan",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Effie Gournis",
-        "author_inst": "Toronto Public Health"
-      },
-      {
-        "author_name": "Heather Rilkoff",
-        "author_inst": "Public Health Ontario"
-      },
-      {
-        "author_name": "Yiqing Xia",
-        "author_inst": "St. Michael's Hospital, Unity Health Toronto"
-      },
-      {
-        "author_name": "Alan Katz",
-        "author_inst": "University of Manitoba"
-      },
-      {
-        "author_name": "Tyler Williamson",
-        "author_inst": "University of Calgary"
-      },
-      {
-        "author_name": "Kamil Malikov",
-        "author_inst": "Ontario Ministry of Health"
-      },
-      {
-        "author_name": "Rafal Kustra",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Mathieu Maheu-Giroux",
-        "author_inst": "McGill University"
-      },
-      {
-        "author_name": "Beate Sander",
-        "author_inst": "University Health Network"
-      },
-      {
-        "author_name": "Stefan Baral",
-        "author_inst": "JHSPH"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.04.02.21252580",
     "rel_title": "Therapeutic application of alpha-1-antitrypsin in COVID-19",
@@ -821408,6 +819764,117 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "rheumatology"
   },
+  {
+    "rel_doi": "10.1101/2021.03.31.21254674",
+    "rel_title": "Efficient Maternal to Neonatal transfer of SARS-CoV-2 and BNT162b2 antibodies",
+    "rel_date": "2021-04-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.31.21254674",
+    "rel_abs": "BackgroundThe significant risks posed to mothers and fetuses by COVID-19 in pregnancy have sparked a worldwide debate surrounding the pros and cons of antenatal SARS-CoV-2 inoculation, as we lack sufficient evidence regarding vaccine effectiveness in pregnant women and their offspring. We aimed to provide substantial evidence for the effect of BNT162b2 mRNA vaccine versus native infection on maternal humoral, as well as transplacentally acquired fetal immune response, potentially providing newborn protection.\n\nMethodsA multicenter study where parturients presenting for delivery were recruited at 8 medical centers across Israel and assigned to three study groups: vaccinated (n=86); PCR confirmed SARS-CoV-2 infected during pregnancy (n=65), and unvaccinated non-infected controls (n=62). Maternal and fetal blood samples were collected from parturients prior to delivery and from the umbilical cord following delivery, respectively. Sera IgG and IgM titers were measured using Milliplex MAP SARS-CoV-2 Antigen Panel (for S1, S2, RBD and N).\n\nResultsBNT162b2 mRNA vaccine elicits strong maternal humoral IgG response (Anti-S and RBD) that crosses the placenta barrier and approaches maternal titers in the fetus within 15 days following the first dose. Maternal to neonatal anti-COVID-19 antibodies ratio did not differ when comparing sensitization (vaccine vs. infection). IgG transfer rate was significantly lower for third-trimester as compared to second trimester infection. Lastly, fetal IgM response was detected in 5 neonates, all in the infected group.\n\nConclusionsAntenatal BNT162b2 mRNA vaccination induces a robust maternal humoral response that effectively transfers to the fetus, supporting the role of vaccination during pregnancy.",
+    "rel_num_authors": 24,
+    "rel_authors": [
+      {
+        "author_name": "Ofer Beharier",
+        "author_inst": "Hadassah Hebrew University Medical Center"
+      },
+      {
+        "author_name": "Romina Plitman Mayo",
+        "author_inst": "Weizmann Institute of Science"
+      },
+      {
+        "author_name": "Tal Raz",
+        "author_inst": "Hebrew University"
+      },
+      {
+        "author_name": "Kira Nahum Sacks",
+        "author_inst": "Wolfson Medical Center"
+      },
+      {
+        "author_name": "Letizia Schreiber",
+        "author_inst": "Wolfson Medical Center"
+      },
+      {
+        "author_name": "Yael Suissa-Cohen",
+        "author_inst": "Hadassah Hebrew University Medical Center"
+      },
+      {
+        "author_name": "Rony Chen",
+        "author_inst": "Rabin Medical Center"
+      },
+      {
+        "author_name": "Rachel Gomez-Tolub",
+        "author_inst": "Rabin Medical Center"
+      },
+      {
+        "author_name": "Eran Hadar",
+        "author_inst": "Rabin Medical Center"
+      },
+      {
+        "author_name": "Rinat Gabbay-Benziv",
+        "author_inst": "Hillel Yaffe Medical Center"
+      },
+      {
+        "author_name": "Yuval Jaffe Moshkovich",
+        "author_inst": "Hillel Yaffe Medical Center"
+      },
+      {
+        "author_name": "Tal Biron-Shental",
+        "author_inst": "Meir Medical Center"
+      },
+      {
+        "author_name": "Gil Shechter-Maor",
+        "author_inst": "Meir Medical Center"
+      },
+      {
+        "author_name": "Sivan Farladansky-Gershnabel",
+        "author_inst": "Meir Medical Center"
+      },
+      {
+        "author_name": "Hen Yitzhak Sela",
+        "author_inst": "Shaare Zedek Medical Center"
+      },
+      {
+        "author_name": "Hedi Benyamini-Raischer",
+        "author_inst": "Emek Medical Center"
+      },
+      {
+        "author_name": "Nitzan D Sela",
+        "author_inst": "Emek Medical Center"
+      },
+      {
+        "author_name": "Debra Goldman-Wohl",
+        "author_inst": "Hadassah Hebrew University Medical Center"
+      },
+      {
+        "author_name": "Ziv Shulman",
+        "author_inst": "Weizmann Institute of Science"
+      },
+      {
+        "author_name": "Ariel Many",
+        "author_inst": "Sourasky Medical Center"
+      },
+      {
+        "author_name": "Haim Barr",
+        "author_inst": "Weizmann Institute of Science"
+      },
+      {
+        "author_name": "Simcha Yagel",
+        "author_inst": "Hadassah Hebrew University Medical Center"
+      },
+      {
+        "author_name": "Michal Neeman",
+        "author_inst": "Weizmann Institute of Science"
+      },
+      {
+        "author_name": "Michal Kovo",
+        "author_inst": "Wolfson Medical Center"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "obstetrics and gynecology"
+  },
   {
     "rel_doi": "10.1101/2021.03.31.21254723",
     "rel_title": "Quantifying Face Mask Comfort",
@@ -822805,101 +821272,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2021.04.05.437453",
-    "rel_title": "Ageing impairs the airway epithelium defence response to SARS-CoV-2",
-    "rel_date": "2021-04-06",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.05.437453",
-    "rel_abs": "Age-dependent differences in the clinical response to SARS-CoV-2 infection is well-documented1-3 however the underlying molecular mechanisms involved are poorly understood. We infected fully differentiated human nasal epithelium cultures derived from healthy children (1-12 years old), young adults (26-34 years old) and older adults (56-62 years old) with SARS-COV-2 to identify age-related cell-intrinsic differences that may influence viral entry, replication and host defence response. We integrated imaging, transcriptomics, proteomics and biochemical assays revealing age-related changes in transcriptional regulation that impact viral replication, effectiveness of host responses and therapeutic drug targets. Viral load was lowest in infected older adult cultures despite the highest expression of SARS-CoV-2 entry and detection factors. We showed this was likely due to lower expression of hijacked host machinery essential for viral replication. Unlike the nasal epithelium of young adults and children, global host response and induction of the interferon signalling was profoundly impaired in older adults, which preferentially expressed proinflammatory cytokines mirroring the \"cytokine storm\" seen in severe COVID-194,5. In silico screening of our virus-host-drug network identified drug classes with higher efficacy in older adults. Collectively, our data suggests that cellular alterations that occur during ageing impact the ability for the host nasal epithelium to respond to SARS-CoV-2 infection which could guide future therapeutic strategies.",
-    "rel_num_authors": 20,
-    "rel_authors": [
-      {
-        "author_name": "Alexander Capraro",
-        "author_inst": "UNSW Sydney"
-      },
-      {
-        "author_name": "Sharon L Wong",
-        "author_inst": "UNSW Sydney"
-      },
-      {
-        "author_name": "Anurag Adhikari",
-        "author_inst": "Kirby Institute"
-      },
-      {
-        "author_name": "Katelin M Allan",
-        "author_inst": "UNSW Sydney"
-      },
-      {
-        "author_name": "Hardip R Patel",
-        "author_inst": "Australian National University"
-      },
-      {
-        "author_name": "Ling Zhong",
-        "author_inst": "UNSW Sydney"
-      },
-      {
-        "author_name": "Mark Raftery",
-        "author_inst": "UNSW Sydney"
-      },
-      {
-        "author_name": "Adam Jaffe",
-        "author_inst": "UNSW Sydney"
-      },
-      {
-        "author_name": "Malinna Yeang",
-        "author_inst": "UNSW Sydney"
-      },
-      {
-        "author_name": "Anupriya Aggarwal",
-        "author_inst": "Kirby Institute"
-      },
-      {
-        "author_name": "Lindsay Wu",
-        "author_inst": "UNSW Sydney"
-      },
-      {
-        "author_name": "Elvis Pandzic",
-        "author_inst": "UNSW Sydney"
-      },
-      {
-        "author_name": "Renee M Whan",
-        "author_inst": "UNSW Sydney"
-      },
-      {
-        "author_name": "Stuart Turville",
-        "author_inst": "Kirby Institute"
-      },
-      {
-        "author_name": "Rowena A Bull",
-        "author_inst": "UNSW Sydney"
-      },
-      {
-        "author_name": "Nadeem Kaakoush",
-        "author_inst": "UNSW Sydney"
-      },
-      {
-        "author_name": "William D Rawlinson",
-        "author_inst": "UNSW Sydney"
-      },
-      {
-        "author_name": "Nicodemus Tedla",
-        "author_inst": "UNSW Sydney"
-      },
-      {
-        "author_name": "Fatemeh Vafaee",
-        "author_inst": "UNSW Sydney"
-      },
-      {
-        "author_name": "Shafagh A Waters",
-        "author_inst": "UNSW Sydney"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2021.04.06.438614",
     "rel_title": "Altered O-glycosylation Level of SARS-CoV-2 Spike Protein by Host O-glycosyltransferase Strengthens Its Trimeric Structure",
@@ -823210,6 +821582,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.04.01.21254679",
+    "rel_title": "Is convalescent plasma futile in COVID-19? A Bayesian re-analysis of the RECOVERY randomised controlled trial",
+    "rel_date": "2021-04-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.01.21254679",
+    "rel_abs": "IntroductionRandomised trials are generally performed from a frequentist perspective reporting point estimates and 95% confidence intervals. This approach can confuse \"evidence of no effect\" with \"no evidence of an effect\" and does not allow for contextual knowledge. The RECOVERY trial evaluated convalescent plasma for patients hospitalised with COVID-19, the interaction test for the primary outcome was not statistically significant, and the trial concluded no evidence of an effect. From the clinical immunology perspective, there is strong justification to expect differential responses to convalescent plasma in patients who already have their own antibodies to SARS-CoV2 (seropositive) versus those who do not (seronegative).\n\nMethodsOutcome data was extracted from the RECOVERY trial both overall and for seronegative participants. A Bayesian re-analysis with a wide variety of priors (vague, optimistic, skeptical and pessimistic) was performed calculating the posterior probability for both any benefit or a modest benefit (number needed to treat of 100).\n\nResultsAcross all patients, when analysed with a vague prior the likelihood of any benefit or a modest benefit was estimated to be 64% and 18% respectively. In contrast, in the seronegative subgroup, the likelihood of any benefit or a modest benefit was estimated to be 90% and 74%. Results were broadly consistent across all prior distributions.\n\nConclusionPerforming clinical trials during a pandemic is challenging, and RECOVERY has provided high quality evidence for numerous therapies. However, the use of frequentist hypothesis testing in this trial has led to the trialists and governing bodies to conclude a strong evidence of no effect. Based on this trial, and other prior knowledge there remains a strong probability that convalescent plasma provides at least a modest benefit in seronegative patients.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Fergus W Hamilton",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Todd Campbell Lee",
+        "author_inst": "McGill University"
+      },
+      {
+        "author_name": "David T Arnold",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Richard J Lilford",
+        "author_inst": "University of Birmingham"
+      },
+      {
+        "author_name": "Karla Hemming",
+        "author_inst": "University of Birmingham"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.03.31.21254685",
     "rel_title": "Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador",
@@ -824879,41 +823286,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.03.28.21254468",
-    "rel_title": "A Vaccination Simulator for COVID-19: Effective and Sterilizing Immunization Cases.",
-    "rel_date": "2021-04-04",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.28.21254468",
-    "rel_abs": "Accurate modeling provides a means by which a complex problem can be examined for informed decision-making. We present a particle-based SEIR epidemic simulator as a tool to assess the impact of vaccination strategies on viral propagation and to model both sterilizing and effective immunization outcomes. The simulator includes modules to support contact tracing of the interactions amongst individuals as well as epidemiological testing of the general population. The simulator particles are distinguished by age, thus enabling a more accurate representation of the rates of infection and mortality in accordance with differential demographic susceptibilities and medical outcomes. Moreover, thanks to the age differentiation of particles, the vaccination can be simulated based on the age group descending order or randomly across all age groups. The simulator can be calibrated by region of interest and variable vaccination strategies (i.e. random or prioritized by age) so as to enable locality-sensitive virus mitigation policy measures and resource allocation. The results described, based on the experience of the province of Lecco, Italy, indicate that the tool can be used to evaluate vaccination strategies in a way that incorporates local circumstances of viral propagation and demographic susceptibilities. Further, the simulator accounts for modeling the distinction between sterilizing immunization, in which immunized people are no longer contagious, and that of effective immunization, in which symptoms and mortality outcomes are diminished but individuals can still transmit the virus. The sterilizing-age-based vaccination scenario results in the least number of deaths compared to other scenarios. Furthermore, the results show that the vaccination of the most vulnerable portion of the population should be prioritized for the effective immunization case. As the vaccination rate increases, the mortality gap between the scenarios shrinks.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Aknur Karabay",
-        "author_inst": "Institute of Smart Systems and Artificial Intelligence"
-      },
-      {
-        "author_name": "Askat Kuzdeuov",
-        "author_inst": "Institute of Smart Systems and Artificial Intelligence"
-      },
-      {
-        "author_name": "Shyryn Ospanova",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Michael Lewis",
-        "author_inst": "Nazarbayev University, School of Engineering and Digital Sciences"
-      },
-      {
-        "author_name": "Atakan Huseyin Varol",
-        "author_inst": "Institute of Smart Systems and Artificial Intelligence"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.03.19.21253989",
     "rel_title": "Comprehensive assessment of humoral response after Pfizer BNT162b2 mRNA Covid-19 vaccination: a three-case series",
@@ -825180,6 +823552,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.04.02.438274",
+    "rel_title": "Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN",
+    "rel_date": "2021-04-04",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.02.438274",
+    "rel_abs": "High-fidelity replication of the large RNA genome of coronaviruses (CoVs) is mediated by a 3'-to-5' exoribonuclease (ExoN) in non-structural protein 14 (nsp14), which excises nucleotides including antiviral drugs mis-incorporated by the low-fidelity viral RNA-dependent RNA polymerase (RdRp) and has also been implicated in viral RNA recombination and resistance to innate immunity. Here we determined a 1.6-[A] resolution crystal structure of SARS-CoV-2 ExoN in complex with its essential co-factor, nsp10. The structure shows a highly basic and concave surface flanking the active site, comprising several Lys residues of nsp14 and the N-terminal amino group of nsp10. Modeling suggests that this basic patch binds to the template strand of double-stranded RNA substrates to position the 3' end of the nascent strand in the ExoN active site, which is corroborated by mutational and computational analyses. Molecular dynamics simulations further show remarkable flexibility of multi-domain nsp14 and suggest that nsp10 stabilizes ExoN for substrate RNA-binding to support its exoribonuclease activity. Our high-resolution structure of the SARS-CoV-2 ExoN-nsp10 complex serves as a platform for future development of anti-coronaviral drugs or strategies to attenuate the viral virulence.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Nicholas H Moeller",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Ke Shi",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "\u00d6zlem Demir",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Surajit Banerjee",
+        "author_inst": "Cornell University"
+      },
+      {
+        "author_name": "Lulu Yin",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Christopher Belica",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Cameron Durfee",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Rommie E Amaro",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Hideki Aihara",
+        "author_inst": "University of Minnesota"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "biochemistry"
+  },
   {
     "rel_doi": "10.1101/2021.04.02.438262",
     "rel_title": "Recovery from acute SARS-CoV-2 infection and development of anamnestic immune responses in T cell-depleted rhesus macaques",
@@ -826653,49 +825076,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2021.03.29.21253174",
-    "rel_title": "Detection of cross-reactive IgA in saliva against SARS-CoV-2 Spike1 subunit",
-    "rel_date": "2021-04-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21253174",
-    "rel_abs": "Abundant secretory IgA (sIgA) in mucus, breast milk, and saliva provides immunity that prevents infection of mucosal surfaces. sIgA in pre-pandemic breast milk samples have been reported to cross-react with SARS-CoV-2, but whether it also occurs in saliva and, if so, whether it cross-reacts with SARS-CoV-2, has remained unknown. We aimed to clarify whether sIgA in saliva cross-reacts with SARS-CoV-2 spike 1 subunit in individuals who have not been infected with this virus. The study included 137 (male, n = 101; female, n = 36; mean age, 38.7 [24-65] years) of dentists and doctors in the Kanagawa Dental University Hospital. Saliva and blood samples were analyzed by PCR and immunochromatography for IgG and IgM, respectively. We then identified patients with saliva samples that were confirmed as PCR- and IgM-negative for COVID-19. Proportions of SARS-CoV-2 cross-reactive IgA-positive individuals were determined by enzyme-linked immunosorbent assay using a biotin-labeled spike S1-mFc recombinant protein covering the receptor-binding domain of SARS-CoV-2. The proportion of SARS-CoV-2 cross-reactive IgA-positive individuals was 46.7%, and this correlated negatively with age (r = -0.218, p = 0.01). The proportion of IgA-positive individuals [&ge;] 50 y was significantly lower than that of patients aged [&le;] 49 y (p = 0.008). sIgA was purified from the saliva of all patients, and the salivary sIgA was found to suppress the binding of SARS-CoV-2 spike protein to the ACE-2 receptor. We found SARS-CoV-2 cross-reactive sIgA in the saliva of some participants who had never been infected with the virus, suggesting that sIgA helps prevent SARS-CoV-2 infection.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Keiichi Tsukinoki",
-        "author_inst": "Department of Environmental Pathology, Graduate School of Dentistry, Kanagawa Dental University"
-      },
-      {
-        "author_name": "Tatsuo Yamamoto",
-        "author_inst": "Department of Dental Sociology, Graduate School of Dentistry, Kanagawa Dental University"
-      },
-      {
-        "author_name": "Keisuke Handa",
-        "author_inst": "Department of Oral Biochemistry, Graduate School of Dentistry, Kanagawa Dental University"
-      },
-      {
-        "author_name": "Mariko Iwamiya",
-        "author_inst": "Department of Clinical Laboratory, Kanagawa Dental University Hospital"
-      },
-      {
-        "author_name": "Juri Saruta",
-        "author_inst": "Department of Environmental Pathology, Graduate School of Dentistry, Kanagawa Dental University"
-      },
-      {
-        "author_name": "Satoshi Ino",
-        "author_inst": "Department of Minimal Intervention Prosthodontics, Graduate School of Dentistry, Kanagawa Dental University"
-      },
-      {
-        "author_name": "Takashi Sakurai",
-        "author_inst": "Department of Maxillofacial Radiology, Graduate School of Dentistry, Kanagawa Dental University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "dentistry and oral medicine"
-  },
   {
     "rel_doi": "10.1101/2021.03.29.21254233",
     "rel_title": "Estimating the strength of selection for new SARS-CoV-2 variants",
@@ -827210,6 +825590,129 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2021.04.01.438035",
+    "rel_title": "The neutralization potency of anti-SARS-CoV-2 therapeutic human monoclonal antibodies is retained against novel viral variants",
+    "rel_date": "2021-04-01",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.01.438035",
+    "rel_abs": "A wide range of SARS-CoV-2 neutralizing monoclonal antibodies (mAbs) were reported to date, most of which target the spike glycoprotein and in particular its receptor binding domain (RBD) and N-terminal domain (NTD) of the S1 subunit. The therapeutic implementation of these antibodies has been recently challenged by emerging SARS-CoV-2 variants that harbor extensively mutated spike versions. Consequently, the re-assessment of mAbs, previously reported to neutralize the original early-version of the virus, is of high priority.\n\nFour previously selected mAbs targeting non-overlapping epitopes, were evaluated for their binding potency to RBD versions harboring individual mutations at spike positions 417, 439, 453, 477, 484 and 501. Mutations at these positions represent the prevailing worldwide distributed modifications of the RBD, previously reported to mediate escape from antibody neutralization. Additionally, the in vitro neutralization potencies of the four RBD-specific mAbs, as well as two NTD-specific mAbs, were evaluated against two frequent SARS-CoV-2 variants of concern (VOCs): (i) the B.1.1.7 variant, emerged in the UK and (ii) the B.1.351 variant, emerged in South Africa. Variant B.1.351 was previously suggested to escape many therapeutic mAbs, including those authorized for clinical use. The possible impact of RBD mutations on recognition by mAbs is addressed by comparative structural modelling. Finally, we demonstrate the therapeutic potential of three selected mAbs by treatment of K18-hACE2 transgenic mice two days post infection with each of the virus strains.\n\nOur results clearly indicate that despite the accumulation of spike mutations, some neutralizing mAbs preserve their potency against SARS-CoV-2. In particular, the highly potent MD65 and BL6 mAbs are shown to retain their ability to bind the prevalent novel viral mutations and to effectively protect against B.1.1.7 and B.1.351 variants of high clinical concern.",
+    "rel_num_authors": 27,
+    "rel_authors": [
+      {
+        "author_name": "Efi Makdasi",
+        "author_inst": "IIBR"
+      },
+      {
+        "author_name": "Anat Zvi",
+        "author_inst": "IIBR"
+      },
+      {
+        "author_name": "Ron Alcalay",
+        "author_inst": "IIBR"
+      },
+      {
+        "author_name": "Tal Noy-Porat",
+        "author_inst": "IIBR"
+      },
+      {
+        "author_name": "Eldar Peretz",
+        "author_inst": "IIBR"
+      },
+      {
+        "author_name": "Adva Mechaly",
+        "author_inst": "IIBR"
+      },
+      {
+        "author_name": "Yinon Levy",
+        "author_inst": "IIBR"
+      },
+      {
+        "author_name": "Eyal Epstein",
+        "author_inst": "IIBR"
+      },
+      {
+        "author_name": "Theodor Chitlaru",
+        "author_inst": "IIBR"
+      },
+      {
+        "author_name": "Ariel Tennenhouse",
+        "author_inst": "Weizmann Institute of Science"
+      },
+      {
+        "author_name": "Moshe Aftalion",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "David Gur",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Nir Paran",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Hadas Tamir",
+        "author_inst": "IIBR"
+      },
+      {
+        "author_name": "Oren Zimhony",
+        "author_inst": "Kaplan Medical Center"
+      },
+      {
+        "author_name": "Shay Weiss",
+        "author_inst": "IIBR"
+      },
+      {
+        "author_name": "Michal Mandelboim",
+        "author_inst": "Israel Ministry of Health"
+      },
+      {
+        "author_name": "Ella Mendelson",
+        "author_inst": "Israel Ministry of Health"
+      },
+      {
+        "author_name": "Neta Zuckerman",
+        "author_inst": "Israel Ministry of Health"
+      },
+      {
+        "author_name": "Ital Nemet",
+        "author_inst": "Israel Ministry of Health"
+      },
+      {
+        "author_name": "Limor Kliker",
+        "author_inst": "Israel Ministry of Health"
+      },
+      {
+        "author_name": "Shmuel Yitzhaki",
+        "author_inst": "IIBR"
+      },
+      {
+        "author_name": "Shmuel C Shapira",
+        "author_inst": "IIBR"
+      },
+      {
+        "author_name": "Tomer Israely",
+        "author_inst": "IBR"
+      },
+      {
+        "author_name": "Sarel J. Fleishman",
+        "author_inst": "Weizmann Institute of Science"
+      },
+      {
+        "author_name": "Ohad Mazor",
+        "author_inst": "Israel Institute for Biological Research"
+      },
+      {
+        "author_name": "Ronit Rosenfeld",
+        "author_inst": "IIBR"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2021.03.31.437931",
     "rel_title": "Limiting the priming dose of a SARS CoV-2 vaccine improves virus-specific immunity",
@@ -828795,65 +827298,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "oncology"
   },
-  {
-    "rel_doi": "10.1101/2021.03.30.21254459",
-    "rel_title": "Healthcare workers' perceptions and attitudes towards the UK COVID-19 vaccination programme",
-    "rel_date": "2021-03-31",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.30.21254459",
-    "rel_abs": "ObjectivesTo explore healthcare workers (HCWs) perceptions and attitudes towards the COVID-19 vaccination programme in the UK, including their expectations, concerns and views on whether to promote vaccination to others. To understand the key factors shaping HCWs attitudes towards COVID-19 vaccination in the UK.\n\nDesignThis study was designed as a rapid qualitative appraisal integrating data from a review of UK policies and guidance on COVID-19 vaccination with data from in-depth semi-structured telephone interviews with frontline HCWs in the UK. Data were analysed using framework analysis.\n\nParticipantsInterviews were carried out with a purposive sample of HCWs from two large London-based hospital Trusts (n=24) and 24 government policies and guidelines on the vaccination programme were reviewed.\n\nResultsThe level of uncertainty about the vaccines long-term safety and efficacy against mutant strains made it difficult for HCWs to balance the benefits against the risks of vaccination. HCWs felt that government decisions on vaccine rollout had not been supported by evidence-based science and this impacted their level of trust and confidence in the programme. The spread of misinformation online also impacted HCWs attitudes towards vaccination, particularly among junior level and Black, Asian and Minority Ethnic (BAME) HCWs. Most HCWs felt encouraged to promote vaccination to their patients and the majority said they would advocate vaccination or engage in conversations about vaccination with others when relevant.\n\nConclusionIn order to improve HCWs trust and confidence in the UKs COVID-19 vaccination programme, there needs to be clarity about what is known and not known about the vaccines and transparency around the evidence-base supporting government decisions on vaccine rollout. Effort is also needed to dispel the spread of vaccine-related misinformation online and to address specific concerns, particularly among BAME and junior level HCWs.\n\nStrengths and limitations of this studyO_LIThis is the first qualitative study to understand the factors influencing healthcare workers (HCWs) attitudes towards COVID-19 vaccination in the UK\nC_LIO_LIThis study integrated interview and policy data and captured HCWs perceptions and attitudes in real-time as the vaccination programme was being rolled out in the UK\nC_LIO_LIOur interview study sample was limited in its representation of junior level HCWs and areas of the UK\nC_LIO_LIThis research may have been impacted by selection bias as those with stronger views on vaccination may have been more likely to participate in the study\nC_LI",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Louisa Manby",
-        "author_inst": "UCL"
-      },
-      {
-        "author_name": "Anna Dowrick",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Amelia Karia",
-        "author_inst": "UCL"
-      },
-      {
-        "author_name": "Laura Maio",
-        "author_inst": "Dementia UK"
-      },
-      {
-        "author_name": "Caroline Buck",
-        "author_inst": "UCL"
-      },
-      {
-        "author_name": "Georgina Singleton",
-        "author_inst": "UCL"
-      },
-      {
-        "author_name": "Sasha Lewis-Jackson",
-        "author_inst": "UCL"
-      },
-      {
-        "author_name": "Inayah Uddin",
-        "author_inst": "UCL"
-      },
-      {
-        "author_name": "Samantha Vanderslott",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Sam Martin",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Cecilia Vindrola-Padros",
-        "author_inst": "University College London"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health systems and quality improvement"
-  },
   {
     "rel_doi": "10.1101/2021.03.29.21254589",
     "rel_title": "Impact of COVID-19 pandemic on rare diseases- A case study on thalassaemia patients in Bangladesh",
@@ -829172,6 +827616,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.03.29.21254334",
+    "rel_title": "Estimating the asymptomatic proportion of SARS-CoV-2 infection in the general population: Analysis of a nationwide serosurvey in the Netherlands",
+    "rel_date": "2021-03-31",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21254334",
+    "rel_abs": "BackgroundThe proportion of SARS-CoV-2 positive persons who are asymptomatic - and whether this proportion is age-dependent - are still open research questions. Because an unknown proportion of reported symptoms among SARS-CoV-2 positives will be attributable to another infection or affliction, the observed, or  crude proportion without symptoms may underestimate the proportion of persons without symptoms that are caused by SARS-CoV-2 infection.\n\nMethodsBased on a large population-based serological study comprising test results on seropositivity and self-reported symptom history conducted in April/May 2020 in the Netherlands (n=3147), we estimated the proportion of reported symptoms among those persons infected with SARS-CoV-2 that is attributable to this infection, where the set of relevant symptoms fulfills the ECDC case definition of COVID-19, using inferential methods for the attributable risk (AR). Generalised additive regression modelling was used to estimate the age-dependent relative risk (RR) of reported symptoms, and the AR and asymptomatic proportion (AP) were calculated from the fitted RR.\n\nResultsUsing age-aggregated data, the estimated AP was 70% (95% CI: 65-77%). The estimated AP decreased with age, from 80% (95% CI: 67-100%) for the <20 years age-group, to 55% (95% CI: 48-68%) for the 70+ years age-group.\n\nConclusionWhereas the  crude AP represents a lower bound for the proportion of persons infected with SARS-CoV-2 without COVID-19 symptoms, the AP as estimated via an attributable risk approach represents an upper bound. Age-specific AP estimates can inform the implementation of public health actions such as targetted virological testing and therefore enhance containment strategies.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Scott A. McDonald",
+        "author_inst": "Netherlands National Institute for Public Health and the Environment"
+      },
+      {
+        "author_name": "Fuminari Miura",
+        "author_inst": "Netherlands National Institute for Public Health and the Environment"
+      },
+      {
+        "author_name": "Eric R.A. Vos",
+        "author_inst": "Netherlands National Institute for Public Health and the Environment"
+      },
+      {
+        "author_name": "Michiel van Boven",
+        "author_inst": "Netherlands National Institute for Public Health and the Environment"
+      },
+      {
+        "author_name": "Hester E. de Melker",
+        "author_inst": "Netherlands National Institute for Public Health and the Environment"
+      },
+      {
+        "author_name": "Fiona R. M. van der Klis",
+        "author_inst": "Netherlands National Institute for Public Health and the Environment"
+      },
+      {
+        "author_name": "Rob S. van Binnendijk",
+        "author_inst": "Netherlands National Institute for Public Health and the Environment"
+      },
+      {
+        "author_name": "Gerco den Hartog",
+        "author_inst": "Netherlands National Institute for Public Health and the Environment"
+      },
+      {
+        "author_name": "Jacco Wallinga",
+        "author_inst": "Netherlands National Institute for Public Health and the Environmen"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.03.30.21254631",
     "rel_title": "Performance of early warning signals for disease emergence: a case study on COVID-19 data",
@@ -830321,41 +828816,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.03.30.21254537",
-    "rel_title": "Mitigating the identity and health threat of COVID-19: Perspectives of Middle-Class South Asians living in the UK",
-    "rel_date": "2021-03-31",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.30.21254537",
-    "rel_abs": "The recognition and representation of BAME community as \"high risk\" of Covid-19 in the UK presents both a health and an identity threat to this ethnic group. This study employed thematic analysis to explore response to these threats as related by a sample of thirteen middle class members of the South Asian community. This work advances both health and identity psychological theory by recognising the affinity between expressions of health efficacy and identity. Our findings identify South Asian intragroup stigmatisation and commonalities that have implications for the promotion of health behaviour and health communications for minority groups.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Kristin Hanson",
-        "author_inst": "Kingston University London"
-      },
-      {
-        "author_name": "Emma O'Dwyer",
-        "author_inst": "Kingston University London"
-      },
-      {
-        "author_name": "Sharmistha Chaudhura",
-        "author_inst": "Kingston University London"
-      },
-      {
-        "author_name": "Luiz Gustavo Silva Sousa",
-        "author_inst": "Fluminense Federal University"
-      },
-      {
-        "author_name": "Tushna Vandrevala",
-        "author_inst": "Kingston University London"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.03.31.437823",
     "rel_title": "Linking Diabetes mellitus to SARS-CoV-2 infection through differential targeting of the microRNAs in the Pancreas tissue",
@@ -830642,6 +829102,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.03.29.21254581",
+    "rel_title": "A new Reproduction Index Ri and its Usefulness for Germany's Covid19-Data",
+    "rel_date": "2021-03-31",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21254581",
+    "rel_abs": "In the course of a large-scale infectious disease a time-dependent Reproduction rate is an important parameter for political, economic and social decisions. In this paper we focus on that parameter and introduce a mathematical implementation in addition to the mostly used definition of Robert-Koch-Institute (RKI) in Germany.\n\nSuch value is of particular interest in order to serve as a criterion for possible Lock-Downs and \"LockUps\" in society and can provide deep insights into a pandemic event.\n\nBoth the definition of the new Reproduction index and the RKIs Reproduction number are compared analytically, applied to simple model calculations and finally on real Covid19 data. Clear advantages of the new Reproduction index become apparent and some weaknesses of the RKIs Reproduction number become clearly visible.\n\nIn addition we propose two additional ways of displaying pandemic data to have the pandemic behaviour at a glance. We find that some signatures of the pandemic appear now very well expressed - especially in conjunction with the new Reproduction index Ri.\n\nThis all could be very helpful for future political, social and economic decisions.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Robert N.J. Conradt",
+        "author_inst": "CONRADT Mess- und Regeltechnik"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.03.26.21254398",
     "rel_title": "A RANDOMIZED TRIAL - INTENSIVE TREATMENT BASED IN IVERMECTIN AND IOTA-CARRAGEENAN AS PRE-EXPOSURE PROPHYLAXIS FOR COVID- 19 IN HEALTHCARE AGENTS",
@@ -832171,41 +830650,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "palliative medicine"
   },
-  {
-    "rel_doi": "10.1101/2021.03.26.21254432",
-    "rel_title": "Analyzing the Global Impact of COVID-19 Vaccination Progress: A Result-oriented Storytelling Approach",
-    "rel_date": "2021-03-29",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.26.21254432",
-    "rel_abs": "The next big step in combating the coronavirus disease 2019 (COVID-19) pandemic will be gaining widespread acceptance of a vaccination campaign for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but achieving high uptake need proper understandings. Many health professionals, researchers, statisticians, and programmers to track the viruses spread in different parts of the world have used various methods. However, the proliferation of vaccines produced by talented scientists around the world has sparked a strong desire to extract meaningful insights from available data. Until now, several vaccines against coronavirus disease (COVID-19) have been approved and are being distributed worldwide in various regions. This study aims to report the detailed data analysis and result-oriented storytelling of the COVID-19 vaccination program of different countries across the globe. To analyze the vaccination trend globally this research utilized two different open datasets provided by ourworldindata.org and worldometers.info. An exploratory data analysis (EDA) with interactive data visualization using various python libraries was conducted, and the results are presented in this article to better understand the impact of ongoing vaccination programs around the world. Apart from the valuable insights gained from the data of various countries, this investigation also included a comparison of the number of confirmed and death cases before and after vaccination to determine the efficacy of each vaccine in each country. The results show that a large number of people are still undecided about whether or not to get a COVID-19 vaccine, despite the viruss continued devastating effects on communities. Overall, our findings contribute to ongoing research aimed at informing policy on how to persuade the unvaccinated to be vaccinated.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Samrat Kumar Dey",
-        "author_inst": "Dhaka International University (DIU)"
-      },
-      {
-        "author_name": "Dr. Md. Mahbubur Rahman",
-        "author_inst": "Military Institute of Science and Technology (MIST)"
-      },
-      {
-        "author_name": "Dr. Umme Raihan Siddiqi",
-        "author_inst": "Shaheed Suhrawardy Medical College (ShSMC),"
-      },
-      {
-        "author_name": "Arpita Howlader",
-        "author_inst": "Patuakhali Science and Technology University (PSTU)"
-      },
-      {
-        "author_name": "Arifuzzaman Tushar",
-        "author_inst": "Dhaka International University (DIU),"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.03.26.21253712",
     "rel_title": "A Novel Diagnostic Test to Screen SARS-CoV-2 Variants Containing E484K and N501Y Mutations",
@@ -832656,6 +831100,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.03.26.21254422",
+    "rel_title": "Targeting the Microbiome With KB109 in Outpatients with Mild to Moderate COVID-19 Reduced Medically Attended Acute Care Visits and Improved Symptom Duration in Patients With Comorbidities",
+    "rel_date": "2021-03-29",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.26.21254422",
+    "rel_abs": "IntroductionIn 2020, the world experienced the beginning of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also known as the coronavirus disease 2019 (COVID-19) pandemic. Mounting evidence indicates that the gut microbiome plays a role in host immune response to infections and, in turn, may have an impact on the disease trajectory of SARS-CoV2 infection. However, it remains to be established whether modulation of the microbiome can impact COVID-19-related symptomatology and patient outcomes. Therefore, we conducted a study designed to modulate the microbiome evaluating the safety and physiologic effects of KB109 combined with self-supportive care (SSC) vs SSC alone in non-hospitalized patients with mild to moderate COVID-19. KB109 is a novel synthetic glycan developed to increase the production of gut microbial metabolites that support immune system homeostasis through gut microbiome modulation. Our goal was to gain a better understanding of the safety of KB109, the natural course of COVID-19 symptomatology, and the possible role of the gut microbiome in patients with mild to moderate COVID-19.\n\nMethodsAdult patients who tested positive for COVID-19 were randomized 1:1 to receive KB109 combined with SSC or SSC alone for 14 days and were then followed for an additional 21 days (35 days in total). Patients self-assessed their COVID-19-related symptoms (8 cardinal symptoms plus 5 additional symptoms) and self-reported comorbidities. The primary and secondary objectives were to evaluate the safety of KB109 plus SSC compared with that of SSC alone and to evaluate selected measures of health, respectively.\n\nResultsBetween July 2, 2020 and December 23, 2020, 350 patients were randomized to receive KB109 and SSC (n=174) or SSC alone (n=176). Overall, the most common comorbidities reported were hypertension (18.0% [63/350 patients]) followed by chronic lung disease (8.6% 30/350 patients). KB109 was well tolerated with most treatment-emergent adverse events being mild to moderate in severity. The administration of KB109 plus SSC reduced medically-attended visits (ie, hospitalization, emergency room visits, or urgent care visits) by 50.0% in the overall population and by 61.7% in patients with [&ge;]1 comorbidity; in patients aged [&ge;]45 years or with [&ge;]1 comorbidity, medically-attended visits were reduced by 52.8%, In the SSC group, patients reporting [&ge;]1 comorbidity had a longer median time to resolution of symptoms than those who reported no comorbidities at baseline (13 overall symptoms: 30 vs 21 days, respectively; hazard ratio [HR]=1.163 [95% CI, 0.723-1.872]; 8 cardinal symptoms: 21 vs 15 days, respectively; HR=1.283 [95% CI, 0.809-2.035]). In patients reporting [&ge;]1 comorbidity, median time to resolution of symptoms was shorter in the KB109 plus SSC group compared with the SSC alone group (13 overall symptoms: 30 vs 21 days, respectively; HR=1.422 [95% CI, 0.898-2.250]; 8 cardinal symptoms: 17 vs 21 days, respectively; HR=1.574 [95% CI, 0.997-2.485]). In the KB109 plus SSC group, patients aged [&ge;]45 years or with [&ge;]1 comorbidity had a shorter median time to resolution of symptoms compared with SSC alone (overall 13 symptoms: 21 vs 31 days; HR=1.597 [95% CI, 1.064-2.398]).\n\nConclusionsResults from our study show that KB109 is well tolerated among patients with mild to moderate COVID-19. Patients with [&ge;]1 comorbidity had a longer duration of COVID-19 symptoms than those without comorbidities. Moreover, in patients reporting [&ge;]1 comorbidity or aged [&ge;]45 years (at-risk population), administration of KB109 plus SSC improved median time to resolution of COVID-19-related symptoms and reduced the rate of medically-attended visits compared with SSC alone.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "John P Haran",
+        "author_inst": "University of Massachusetts Medical School"
+      },
+      {
+        "author_name": "Yan Zheng",
+        "author_inst": "Kaleido Biosciences, Inc, Lexington, MA"
+      },
+      {
+        "author_name": "Katharine Knobil",
+        "author_inst": "Kaleido Biosciences, Inc, Lexington, MA"
+      },
+      {
+        "author_name": "Norma Alonzo-Palma",
+        "author_inst": "Kaleido Biosciences, Inc, Lexington, MA"
+      },
+      {
+        "author_name": "Jonathan Lawrence",
+        "author_inst": "Kaleido Biosciences, Inc, Lexington, MA"
+      },
+      {
+        "author_name": "Mark Wingertzahn",
+        "author_inst": "Kaleido Biosciences, Inc, Lexington, MA"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.03.28.21254477",
     "rel_title": "Changes in utilization and outcomes of mechanical ventilation of COVID-19 during the course of the pandemic in Germany in 2020: an observational study of 7,490 patients",
@@ -833961,37 +832444,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.03.26.21254435",
-    "rel_title": "Prevalence and associated factors with mental health outcomes among interns and residents physicians during COVID-19 epidemic in Panama: a cross-sectional study",
-    "rel_date": "2021-03-28",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.26.21254435",
-    "rel_abs": "BackgroundA new coronavirus SARS-CoV-2 was associated with a newly identified respiratory syndrome, COVID-19 in Wuhan, China, in early December 2019. SARS-CoV-2 rapidly spread across the globe resulting in 117 million cases and 2.59 million deaths by March 2021. Rapidly increased numbers of COVID-19 cases overwhelmed public health systems across the world, imposing increased working hours and workloads for health care workers. Here, we have evaluated the prevalence of health outcomes and associated factors of interns and resident physicians in Panama.\n\nMethodsA cross-sectional study was undertaken during July 23, 2020, to August 13, 2020, to evaluate the prevalence of health outcomes and associated factors in interns and residents across Panama. Snowball sampling was used to recruit participants. Then an electronic questionnaire with scales to evaluate anxiety disorders (GAD-7), depression (PHQ-9) and post-traumatic stress (IES-R) was evaluated. In addition, socio-demographic variables, clinical history of mental disorders and COVID-19 exposure were evaluated. Independent analyses for each mental health outcome were undertaken using a logistic regression analysis.\n\nResultsA total of 517/1205 (42.9%) interns and residents were nationwide recruited. Of these 274 (53.0%) were interns and 243 (47.0%) residents. The overall prevalence of depression symptoms was 25.3%, 13.7% anxiety and 12.2% post-traumatic stress. At least, 9.3% participants reported having suicidal ideation.\n\nThe most parsimonious model showed females had a higher prevalence of mental health disorders, in all results and the married participants were more likely to present depression (OR, 1.73; 95% CI, 1.03-2.91; P = 0.039) or at least one alteration to mental health (OR, 1.66; 95% CI, 1.03-2.68; P = 0.039). Resident physicians in surgical specialties were less likely to have post-traumatic stress (OR, 0.20; 95% CI, 0.06-0.63; P = 0.006) or at least one mental health disturbance (OR, 0.46; 95% CI, 0.26-0.83; P = 0.010). A history of psychological trauma and psychiatric pathology were risk factors for most of the disorders investigated.\n\nConclusionsA high prevalence of mental health disorders was found, showing the need to mitigate this emotional burden among healthcare workers in the current context of the COVID-19 pandemic.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Edward A. Espinosa-Guerra",
-        "author_inst": "Public Health and Preventive Medicine, Residency Program, Complejo Hospitalario Dr. Arnulfo Arias Madrid, Panama City, Panama"
-      },
-      {
-        "author_name": "Edgar R. Rodriguez-Barria",
-        "author_inst": "Department of Psychiatry, Residency Program, Complejo Hospitalario Dr. Arnulfo Arias Madrid, Panama City, Panama"
-      },
-      {
-        "author_name": "Christl A. Donnelly",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Jean Paul Carrera",
-        "author_inst": "University of Oxford"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "psychiatry and clinical psychology"
-  },
   {
     "rel_doi": "10.1101/2021.03.26.21254367",
     "rel_title": "Emergence of a SARS-CoV-2 E484K variant of interest in Arizona",
@@ -834266,6 +832718,125 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.03.25.21254335",
+    "rel_title": "Infliximab is associated with attenuated immunogenicity to BNT162b2 and ChAdOx1 nCoV-19 SARS-CoV-2 vaccines",
+    "rel_date": "2021-03-28",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.25.21254335",
+    "rel_abs": "BackgroundDelayed second-dose SARS-CoV-2 vaccination trades maximal effectiveness for a lower level of immunity across more of the population. We investigated whether patients with inflammatory bowel disease treated with infliximab have attenuated serological responses to a single-dose of a SARS-CoV-2 vaccine.\n\nMethodsAntibody responses and seroconversion rates in infliximab-treated patients (n=865) were compared to a cohort treated with vedolizumab (n=428), a gut-selective anti-integrin 4{beta}7 monoclonal antibody. Our primary outcome was anti-SARS-CoV-2 spike (S) antibody concentrations 3-10 weeks after vaccination in patients without evidence of prior infection. Secondary outcomes were seroconversion rates, and antibody responses following past infection or a second dose of the BNT162b2 vaccine.\n\nFindingsGeometric mean [SD] anti-SARS-CoV-2 antibody concentrations were lower in patients treated with infliximab than vedolizumab, following BNT162b2 (6.0 U/mL [5.9] vs 28.8 U/mL [5.4] P<0.0001) and ChAdOx1 nCoV-19 (4.7 U/mL [4.9]) vs 13.8 U/mL [5.9] P<0.0001) vaccines. In our multivariable models, antibody concentrations were lower in infliximab-compared to vedolizumab-treated patients who received the BNT162b2 (fold change [FC] 0.29 [95% CI 0.21, 0.40], p<0.0001) and ChAdOx1 nCoV-19 (FC 0.39 [95% CI 0.30, 0.51], p<0.0001) vaccines. In both models, age [&ge;] 60 years, immunomodulator use, Crohns disease, and smoking were associated with lower, whilst non-white ethnicity was associated with higher, anti-SARS-CoV-2 antibody concentrations. Seroconversion rates after a single-dose of either vaccine were higher in patients with prior SARS-CoV-2 infection and after two doses of BNT162b2 vaccine.\n\nInterpretationInfliximab is associated with attenuated immunogenicity to a single-dose of the BNT162b2 and ChAdOx1 nCoV-19 SARS-CoV-2 vaccines. Vaccination after SARS-CoV-2 infection, or a second dose of vaccine, led to seroconversion in most patients. Delayed second dosing should be avoided in patients treated with infliximab.\n\nFundingRoyal Devon and Exeter and Hull University Hospital Foundation NHS Trusts. Unrestricted educational grants: F. Hoffmann-La Roche AG (Switzerland), Biogen GmbH (Switzerland), Celltrion Healthcare (South Korea) and Galapagos NV (Belgium).\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSFaced with further surges of SARS-CoV-2 infection, a growing number of countries, including the UK, have opted to delay second vaccine doses for all people. This strategy trades maximal effectiveness against a lower level of protective immunity across more of the at-risk population.\n\nWe have previously shown that seroprevalence, seroconversion in PCR-confirmed cases, and the magnitude of anti-SARS-CoV-2 antibodies following SARS-CoV-2 infection are reduced in infliximab-compared with vedolizumab-treated patients. Whether single-doses of vaccines are effective in patients treated with anti-TNF therapies is unknown.\n\nWe searched PubMed from 25 November 2019 to 23 March 2021 with the terms \"anti-tumour necrosis factor\" or \"anti-integrin\" or \"infliximab\" or \"adalimumab\" or \"vedolizumab\" or \"biological therapy\" or \"biologic therapy\" AND \"SARS-CoV-2\" or \"coronavirus\" or \"COVID-19\" or AND \"seroprevalence\" or \"seroconversion\" or \"antibody\" or \"antibody response\" or \"magnitude\" or \"immunogenicity\" AND \"vaccine\" or \"vaccination\" or \"immunisation\" or \"immunization\" or \"ChAdOx1 nCoV-19\" or \"BNT162b2\" or \"mRNA-1273\", without restriction on language.\n\nSerological responses to SARS-CoV-2 vaccines have been reported in registration trials and small observational cohorts of healthy volunteers. Two small studies, including one unpublished preprint, found that COVID-19 vaccine immunogenicity rates were lower in transplant recipients and patients with malignancy receiving immunosuppressive therapy, and fewer patients treated with potent immunosuppressants seroconverted than healthy controls. No studies have assessed the effect of anti-TNF therapy on immunogenicity following SARS-CoV-2 vaccination.\n\nAdded value of this studyTo test if anti-TNF drugs attenuate serological responses to primary SARS-CoV-2 vaccines, we analysed anti-SARS-CoV-2 spike (S) antibody concentrations and seroconversion rates in 1293 patients with inflammatory bowel disease who received primary vaccinations with either the ChAdOx1 nCoV-19 or BNT162b2 vaccines. 865 were treated with the anti-TNF drug infliximab and outcomes were compared to a reference cohort of 428 patients treated with vedolizumab, a gut selective anti-integrin 4{beta}7 monoclonal antibody that is not associated with impaired systemic immune responses.\n\nAnti-SARS-CoV-2 antibody levels and rates of seroconversion were lower following primary vaccination with both the BNT162b2 and ChAdOx1 nCoV-19 vaccines in patients with IBD treated with infliximab compared to vedolizumab. Older age, immunomodulator use, Crohns disease (versus ulcerative colitis or inflammatory bowel disease unclassified), and current smoking were associated with lower anti-SARS-CoV-2 antibody concentrations, irrespective of vaccine type. Non-white ethnicity was associated with higher anti-SARS-CoV-2 (S) antibody concentrations following primary vaccination with both vaccines. Antibody concentrations and seroconversion rates were higher in patients with past SARS-CoV-2 infection prior to a single-dose of either vaccine, and after 2 doses of the BNT162b2 vaccine.\n\nImplications of the available evidenceOur findings have important implications for patients treated with anti-TNF therapy, particularly for those also treated with an immunomodulator. Poor antibody responses to a single-dose of vaccine exposes these patients to a potential increased risk of SARS-CoV-2 infection. However, higher rates of seroconversion in patients with two exposures to SARS-CoV-2 antigen, even in the presence of TNF blockade, suggest that all patients receiving these drugs should be prioritized for optimally timed second doses. Until patients receive a second vaccine dose, they should consider that they are not protected from SARS-CoV-2 infection and continue to practice enhanced physical distancing and shielding if appropriate. Even after two antigen exposures, a small subset of patients failed to mount an antibody response. Antibody testing and adapted vaccine schedules should be considered to protect these at-risk patients.",
+    "rel_num_authors": 26,
+    "rel_authors": [
+      {
+        "author_name": "Nicholas A Kennedy",
+        "author_inst": "Royal Devon and Exeter NHS Foundation Trust"
+      },
+      {
+        "author_name": "Simeng Lin",
+        "author_inst": "Royal Devon and Exeter NHS Foundation Trust"
+      },
+      {
+        "author_name": "James R Goodhand",
+        "author_inst": "Royal Devon and Exeter NHS Foundation Trust"
+      },
+      {
+        "author_name": "Neil Chanchlani",
+        "author_inst": "Royal Devon and Exeter NHS Foundation Trust"
+      },
+      {
+        "author_name": "Benjamin Hamilton",
+        "author_inst": "Royal Devon and Exeter NHS Foundation Trust"
+      },
+      {
+        "author_name": "Claire Bewshea",
+        "author_inst": "Exeter IBD and Pharmacogenetics Research Group"
+      },
+      {
+        "author_name": "Rachel Nice",
+        "author_inst": "Royal Devon and Exeter NHS Foundation Trust"
+      },
+      {
+        "author_name": "Desmond Chee",
+        "author_inst": "Royal Devon and Exeter NHS Foundation Trust"
+      },
+      {
+        "author_name": "JR Fraser Cummings",
+        "author_inst": "University Hospital Southampton NHS Foundation Trust"
+      },
+      {
+        "author_name": "Aileen Fraser",
+        "author_inst": "University Hospitals Bristol NHS Foundation Trust"
+      },
+      {
+        "author_name": "Peter M Irving",
+        "author_inst": "Guy's and St Thomas' NHS Foundation Trust"
+      },
+      {
+        "author_name": "Nikolaos Kamperidis",
+        "author_inst": "St Marks Hospital and Academic Institute"
+      },
+      {
+        "author_name": "Klaartje B Kok",
+        "author_inst": "Barts Health NHS Trust"
+      },
+      {
+        "author_name": "Christropher A Lamb",
+        "author_inst": "Newcastle upon Tyne Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "Jonathan MacDonald",
+        "author_inst": "Queen Elizabeth University Hospital"
+      },
+      {
+        "author_name": "Shameer J Mehta",
+        "author_inst": "University College London Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "Richard CG Pollok",
+        "author_inst": "St George's University Hospital NHS Foundation Trust"
+      },
+      {
+        "author_name": "Tim Raine",
+        "author_inst": "Cambridge University Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "Philip J Smith",
+        "author_inst": "Liverpool University Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "Ajay M Verma",
+        "author_inst": "Kettering General Hospital"
+      },
+      {
+        "author_name": "Timothy J Mcdonald",
+        "author_inst": "Royal Devon and Exeter NHS Foundation Trust"
+      },
+      {
+        "author_name": "Shaji Sebastian",
+        "author_inst": "Hull University Teaching Hospitals NHS Trust"
+      },
+      {
+        "author_name": "Charlie Lees",
+        "author_inst": "Western General Hospital"
+      },
+      {
+        "author_name": "Nick Powell",
+        "author_inst": "Imperial College Healthcare NHS Trust"
+      },
+      {
+        "author_name": "Tariq Ahmad",
+        "author_inst": "Royal Devon and Exeter NHS Foundation Trust"
+      },
+      {
+        "author_name": "- CLARITY IBD Contributors",
+        "author_inst": ""
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "gastroenterology"
+  },
   {
     "rel_doi": "10.1101/2021.03.26.437274",
     "rel_title": "Mechanism of a COVID-19 nanoparticle vaccine candidate that elicits a broadly neutralizing antibody response to SARS-CoV-2 variants",
@@ -835967,41 +834538,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.03.22.21253831",
-    "rel_title": "The vaccine-elicited immunoglobulin profile in milk after COVID-19 mRNA-based vaccination is IgG-dominant and lacks secretory antibodies",
-    "rel_date": "2021-03-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.22.21253831",
-    "rel_abs": "The Pfizer/BioNTech and Moderna mRNA-based COVID-19 vaccines are licensed under emergency use authorization, with millions of doses already administered globally [1]. No COVID-19 vaccines are yet under investigation for use in infants or young children. As such, the passive immunity of the antibodies (Abs) provided through milk from a vaccinated person may be one of the only ways to protect this population until pediatric COVID-19 vaccines are licensed. Our early work (as well as an expanded study being published concurrently with this report) examining the milk Ab response after SARS-CoV-2 infection demonstrated that Spike-specific IgA in milk after infection is dominant and highly correlated with a secretory Ab response [2]. Determining if secretory Abs are elicited in milk is critical, as this Ab class is highly stable and resistant to enzymatic degradation in all mucosae - not only in the infant oral/nasal cavity and gut, but in the airways and GI tract as well [3, 4]. Presently, we describe our analysis of the milk Ab response 14 days after completion of an mRNA-based COVID-19 vaccine regimen among 10 individuals. It was evident that unlike the post-infection milk Ab profile, IgG dominates after COVID-19 vaccination. One hundred percent of post-vaccine milk contained significant levels of Spike-specific IgG, with 8/10 samples exhibiting high IgG endpoint titers. Conversely, 6/10 (60%) of post-vaccine samples were positive for Spike specific IgA, with only 1 (10%) exhibiting high IgA endpoint titer. Furthermore, 5/10 (50%) post-vaccine milk samples contained Spike-specific secretory Ab, none of which were found to be high-titer. As our analyses of the immune response in milk to COVID-19 vaccination continues, it will provide a critical opportunity to address huge knowledge gaps, inform the field as to which COVID-19 vaccine, if any, is likely to provide the best milk Ab response, and highlight the need to design improved vaccines with protection of the breastfeeding infant in mind.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Alisa Fox",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Caroline Norris",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Fatima Amanat",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Susan Zolla-Pazner",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Rebecca L Powell",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "allergy and immunology"
-  },
   {
     "rel_doi": "10.1101/2021.03.21.21254072",
     "rel_title": "Hyperglycemia in Acute COVID-19 is Characterized by Adipose Tissue Dysfunction and Insulin Resistance",
@@ -836424,6 +834960,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.03.22.21254139",
+    "rel_title": "Acute Brain Ischemia, Infarction and Hemorrhage in Subjects Dying with or Without Autopsy-Proven Acute Pneumonia",
+    "rel_date": "2021-03-26",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.22.21254139",
+    "rel_abs": "Stroke is one of the most serious complications of Covid-19 disease but it is still unclear whether stroke is more common with Covid-19 pneumonia as compared to non-Covid-19 pneumonia. We investigated the concurrence rate of autopsy-confirmed acute brain ischemia, acute brain infarction and acute brain hemorrhage with autopsy-proven acute non-Covid pneumonia in consecutive autopsies in the Arizona Study of Aging and Neurodegenerative Disorders (AZSAND), a longitudinal clinicopathological study of normal aging and neurodegenerative diseases. Of 691 subjects with a mean age of 83.4 years, acute pneumonia was histopathologically diagnosed in 343 (49.6%); the concurrence rates for histopathologically-confirmed acute ischemia, acute infarction or subacute infarction was 14% and did not differ between pneumonia and non-pneumonia groups while the rates of acute brain hemorrhage were 1.4% and 2.0% of those with or without acute pneumonia, respectively. In comparison, in reviews of Covid-19 publications, reported clinically-determined rates of acute brain infarction range from 0.5% to 20% while rates of acute brain hemorrhage range from 0.13% to 2%. In reviews of Covid-19 autopsy studies, concurrence rates for both acute brain infarction and acute brain hemorrhage average about 10%. Covid-19 pneumonia and non-Covid-19 pneumonia may have similar risks tor concurrent acute brain infarction and acute brain hemorrhage when pneumonia is severe enough to cause death. Additionally, acute brain ischemia, infarction or hemorrhage may not be more common in subjects dying of acute pneumonia than in subjects dying without acute pneumonia.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Thomas G Beach",
+        "author_inst": "Banner Sun Health Research Institute"
+      },
+      {
+        "author_name": "Lucia I Sue",
+        "author_inst": "Banner Sun Health Research Institute"
+      },
+      {
+        "author_name": "Anthony J Intorcia",
+        "author_inst": "Banner Sun Health Research Institute"
+      },
+      {
+        "author_name": "Michael J Glass",
+        "author_inst": "Banner Sun Health Research Institute"
+      },
+      {
+        "author_name": "Jessica E Walker",
+        "author_inst": "Banner Sun Health Research Institute"
+      },
+      {
+        "author_name": "Richard Arce",
+        "author_inst": "Banner Sun Health Research Institute"
+      },
+      {
+        "author_name": "Courtney M Nelson",
+        "author_inst": "Banner Sun Health Research Institute"
+      },
+      {
+        "author_name": "Geidy E Serrano",
+        "author_inst": "Banner Sun Health Research Institute"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "neurology"
+  },
   {
     "rel_doi": "10.1101/2021.03.22.21254081",
     "rel_title": "COVID-19 reinfection: A Rapid Systematic Review of Case Reports and Case Series",
@@ -837881,45 +836464,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.03.25.21254324",
-    "rel_title": "Droplet Digital RT-PCR to detect SARS-CoV-2 variants of concern in wastewater.",
-    "rel_date": "2021-03-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.25.21254324",
-    "rel_abs": "Wastewater surveillance has shown to be a valuable and efficient tool to obtain information about the trends of COVID-19 in the community. Since the recent emergence of new variants, associated with increased transmissibility and/or antibody escape (variants of concern), there is an urgent need for methods that enable specific and timely detection and quantification of the occurrence of these variants in the community. In this study we demonstrate the use of RT-ddPCR on wastewater samples for specific detection of mutation N501Y. This assay enabled simultaneous enumeration of the concentration of variants with the 501Y mutation and Wild Type (WT, containing 501N) SARS-CoV-2 RNA. Detection of N501Y was possible in samples with mixtures of WT with low proportions of lineage B.1.351 (0.5%). The method could accurately determine the proportion of N501Y and WT in mixtures of SARS-CoV-2 RNA. The application to raw sewage samples from the cities of Amsterdam and Utrecht demonstrated that this method can be applied to determine the concentrations and the proportions of WT and N501Y containing SARS-CoV-2 RNA in wastewater samples. The emergence of N501Y in Amsterdam and Utrecht wastewater aligned with the emergence of B.1.1.7 as causative agent of COVID-19 in the Netherlands, indicating that RT-ddPCR of wastewater samples can be used to monitor the emergence of the N501Y mutation in the community. It also indicates that RT-ddPCR could be used for sensitive and accurate monitoring of current (like K417N, E484K) or future mutations present in SARS-CoV-2 variants of concern. Monitoring emergence of these mutations in the community via wastewater is rapid, efficient and valuable in supporting public health decision-making.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Leo Heijnen",
-        "author_inst": "KWR, Water Research Institute, Nieuwegein, The Netherlands"
-      },
-      {
-        "author_name": "Goffe Elsinga",
-        "author_inst": "KWR, Water Research Institute, Nieuwegein, The Netherlands"
-      },
-      {
-        "author_name": "Miranda de Graaf",
-        "author_inst": "Erasmus University Medical Center, Department of Viroscience, Rotterdam, The Netherlands"
-      },
-      {
-        "author_name": "Richard Molenkamp",
-        "author_inst": "Erasmus University Medical Center, Department of Viroscience, Rotterdam, The Netherlands"
-      },
-      {
-        "author_name": "Marion P.G. Koopmans",
-        "author_inst": "Erasmus University Medical Center, Department of Viroscience, Rotterdam, The Netherlands"
-      },
-      {
-        "author_name": "Gertjan Medema",
-        "author_inst": "KWR, Water Research Institute, Nieuwegein, The Netherlands"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.03.23.21254054",
     "rel_title": "Tocilizumab in hospitalized COVID-19 patients: A meta-analysis of randomized controlled trials",
@@ -838242,6 +836786,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "cardiovascular medicine"
   },
+  {
+    "rel_doi": "10.1101/2021.03.23.21254214",
+    "rel_title": "Mouth-rinses and SARS-CoV-2 viral load in saliva: A living systematic review",
+    "rel_date": "2021-03-26",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.23.21254214",
+    "rel_abs": "ObjectiveTo conduct a living systematic review of the clinical evidence regarding the effect of different mouth-rinses on the viral load of SARS-CoV-2 in the saliva of infected patients. The viral load in aerosols, the duration of the reduction in viral load, viral clearance, SARS-CoV-2 cellular infectivity, and salivary cytokine profiles were also evaluated.\n\nMaterials and methodsThis study was reported using the PRISMA guidelines. An electronic search was conducted in seven databases and in preprint repositories. We included human clinical trials that evaluated the effect of mouth-rinses with antiseptic substances on the viral load of SARS-CoV-2 in the saliva of children or adults that tested positive for SARS-CoV-2 using reverse transcriptase polymerase chain reaction (RT-PCR). Risk of bias was assessed using the ROBINS-I tool. PROSPERO registration number CRD42021240561.\n\nResultsFour studies matching eligibility criteria were selected for evaluation (n=32 participants). Study participants underwent oral rinses with hydrogen peroxide (H2O2) at 1 %, povidone-iodine (PI) at 0.5% or 1%, chlorhexidine gluconate (CHX) at 0.2% or 0.12% or cetylpyridinium chloride (CPC) at 0.075%. Only one study included a control group with sterile water. Three of the studies identified a significant reduction in viral load up to 3, 4, and 6 hours after the use of mouthwashes with PI, CHX, and CPC or PI vs. sterile water, respectively, while one study did not identify a significant reduction in viral load after the use of H2O2 rinses.\n\nConclusionsAccording to the present systematic review, the effect of the use of mouth-rinses on SARS-CoV-2 viral load in the saliva of COVID-19 patients remains uncertain. This is mainly due to the limited number of patients included and a high risk of bias present in the studies analyzed. Evidence from well-designed randomized clinical trials is required for further and more objective evaluation of this effect.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Akram Hern\u00e1ndez V\u00e1squez",
+        "author_inst": "Universidad San Ignacio de Loyola, Lima, Peru"
+      },
+      {
+        "author_name": "Antonio Barrenechea Pulache",
+        "author_inst": "Universidad Cient\u00edfica del Sur, Lima, Peru"
+      },
+      {
+        "author_name": "Daniel Comand\u00e9",
+        "author_inst": "Instituto de Efectividad Cl\u00ednica y Sanitaria (IECS). Buenos Aires, Argentina"
+      },
+      {
+        "author_name": "Diego Aza\u00f1edo",
+        "author_inst": "Independent Researcher. Lima, Peru"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "dentistry and oral medicine"
+  },
   {
     "rel_doi": "10.1101/2021.03.25.21254362",
     "rel_title": "Estimation of the Reproduction Number for COVID-19 Based on Latest Vaccination Results and the Timing for Herd-Immunity: Prospect for 2021",
@@ -839399,81 +837974,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
-  {
-    "rel_doi": "10.1101/2021.03.26.21254390",
-    "rel_title": "Regional performance variation in external validation of four prediction models for severity of COVID-19 at hospital admission: An observational multi-centre cohort study",
-    "rel_date": "2021-03-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.26.21254390",
-    "rel_abs": "BackgroundSeveral prediction models for coronavirus disease-19 (COVID-19) have been published. Prediction models should be externally validated to assess their performance before implementation. This observational cohort study aimed to validate published models of severity for hospitalized patients with COVID-19 using clinical and laboratory predictors.\n\nMethodsPrediction models fitting relevant inclusion criteria were chosen for validation. The outcome was either mortality or a composite outcome of mortality and ICU admission (severe disease). 1295 patients admitted with symptoms of COVID-19 at Kings Cross Hospital (KCH) in London, United Kingdom, and 307 patients at Oslo University Hospital (OUH) in Oslo, Norway were included. The performance of the models was assessed in terms of discrimination and calibration.\n\nResultsWe identified two models for prediction of mortality (referred to as Xie and Zhang1) and two models for prediction of severe disease (Allenbach and Zhang2).\n\nThe performance of the models was variable. For prediction of mortality Xie had good discrimination at OUH with an area under the receiver-operating characteristic (AUROC) 0.87 [95 % confidence interval (CI) 0.79-0.95] and acceptable discrimination at KCH, AUROC 0.79 [0.76-0.82]. In prediction of severe disease, Allenbach had acceptable discrimination (OUH AUROC 0.81 [0.74-0.88] and KCH AUROC 0.72 [0.68-0.75]). The Zhang models had moderate to poor discrimination. Initial calibration was poor for all models but improved with recalibration.\n\nConclusionsThe performance of the four prediction models was variable. The Xie model had the best discrimination for mortality, while the Allenbach model had acceptable results for prediction of severe disease.",
-    "rel_num_authors": 15,
-    "rel_authors": [
-      {
-        "author_name": "Kristin Wickstrom",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "Valeria Vitelli",
-        "author_inst": "University of Oslo"
-      },
-      {
-        "author_name": "Ewan Carr",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Aleksander Rygh Holten",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "Rebecca Bendayan",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Andrew Henry Reiner",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "Daniel Bean",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Tom Searle",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Anthony Shek",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Zeljko Kraljevic",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "James T Teo",
-        "author_inst": "Kings College Hospital NHS Foundation Trust"
-      },
-      {
-        "author_name": "Richard Dobson",
-        "author_inst": "Kings College London"
-      },
-      {
-        "author_name": "Kristian Tonby",
-        "author_inst": "Oslo University Hospital"
-      },
-      {
-        "author_name": "Alvaro Kohn-Luque",
-        "author_inst": "University of Oslo"
-      },
-      {
-        "author_name": "Erik Koldberg Amundsen",
-        "author_inst": "Oslo University Hospital"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.03.26.21254391",
     "rel_title": "Vaccine effectiveness of the first dose of ChAdOx1 nCoV-19 and BNT162b2 against SARS-CoV-2 infection in residents of Long-Term Care Facilities (VIVALDI study)",
@@ -839760,6 +838260,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.03.24.21253923",
+    "rel_title": "Pattern of COVID-19 epidemics in Japan influenced by the control measures",
+    "rel_date": "2021-03-26",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.24.21253923",
+    "rel_abs": "BackgroundCOVID-19 has spread worldwide since its emergence in 2019. In contrast to many other countries with epidemics, Japan differed in that it avoided lockdowns and instead asked people for self-control. A travel campaign was conducted with a sizable budget, but the number of PCR tests was severely limited. These choices may have influenced the course of the epidemic.\n\nMethodsThe increase or decrease in the classes of SARS-CoV-2 variants was estimated by analyzing the published sequences with an objective multivariate analysis. This approach observes the samples in multiple directions, digesting complex differences into simpler forms. The results were compared over time with the number of confirmed cases, PCR tests, and overseas visitors. The kinetics of infection were analyzed using the logarithmic growth rate.\n\nResultsThe declared states of emergency failed to alter the movement of the growth rate. Three epidemic peaks were caused by domestically mutated variants. In other countries, there are few cases in which multiple variants have peaked. However, due to the relaxation of immigration restrictions, several infective variants have been imported from abroad and are currently competing for expansion, creating the fourth peak. By April 2021, these foreign variants exceeded 80%. The chaotic situation in Japan will continue for some time, in part because no effort has been made to identify asymptomatic carriers, and details of the vaccination program are undecided.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Tomokazu Konishi",
+        "author_inst": "Akita Prefectural University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.03.24.21253992",
     "rel_title": "Longitudinal immune profiling of a SARS-CoV-2 reinfection in a solid organ transplant recipient",
@@ -840933,125 +839452,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.03.25.21254320",
-    "rel_title": "Disparities in SARS-CoV-2 seroprevalence among individuals presenting for care in central North Carolina over a six-month period",
-    "rel_date": "2021-03-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.25.21254320",
-    "rel_abs": "BackgroundRobust community-level SARS-CoV-2 prevalence estimates have been difficult to obtain in the American South and outside of major metropolitan areas. Furthermore, though some previous studies have investigated the association of demographic factors such as race with SARS-CoV-2 exposure risk, fewer have correlated exposure risk to surrogates for socioeconomic status such as health insurance coverage.\n\nMethodsWe used a highly specific serological assay utilizing the receptor binding domain of the SARS-CoV-2 spike-protein to identify SARS-CoV-2 antibodies in remnant blood samples collected by the University of North Carolina Health system. We estimated the prevalence of SARS-CoV-2 in this cohort with Bayesian regression, as well as the association of critical demographic factors with higher prevalence odds.\n\nFindingsBetween April 21st and October 3rd of 2020, a total of 9,624 unique samples were collected from clinical sites in central NC and we observed a seroprevalence increase from 2{middle dot}9 (1{middle dot}7, 4{middle dot}3) to 9{middle dot}1 (7{middle dot}2, 11{middle dot}1) over the study period. Individuals who identified as Latinx were associated with the highest odds ratio of SARS-CoV-2 exposure at 7{middle dot}77 overall (5{middle dot}20, 12{middle dot}10). Increased odds were also observed among Black individuals and individuals without public or private health insurance.\n\nInterpretationOur data suggests that for this care-accessing cohort, SARS-CoV-2 seroprevalence was significantly higher than cumulative total cases reported for the study geographical area six months into the COVID-19 pandemic in North Carolina. The increased odds of seropositivity by ethnoracial grouping as well as health insurance highlights the urgent and ongoing need to address underlying health and social disparities in these populations.\n\nRESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed for studies published through March 21st, 2021. We used search terms that included \"COVID-19\", \"SARS-CoV-2\", \"prevalence\" and \"seroprevalence\". Our search resulted in 399 papers, from which we identified 58 relevant studies describing SARS-CoV-2 seroprevalence at sites around the United States from March 1 to December 9, 2020, 12 of which utilized remnant clinical samples and three of which overlapped with our study area. Most notably, one study of 4,422 asymptomatic inpatients and outpatients in central NC from April 28-June 19, 2020 found an estimated seroprevalence of 0{middle dot}7 -0{middle dot}8%, and another study of 177,919 inpatients and outpatients (3,817 from NC) from July 27-September 24, 2020 found an estimated seroprevalence of 2{middle dot}5 -6{middle dot}8%.\n\nAdded value of this studyThis is the largest SARS-CoV-2 seroprevalence cohort published to date in NC. Importantly, we used a Bayesian framework to account for uncertainty in antibody assay sensitivity and specificity and investigated seropositivity by important demographic variables that have not yet been studied in this context in NC. This study corroborates other reports that specific demographic factors including race, ethnicity and the lack of public or private insurance are associated with elevated risk of SARS-CoV-2 infection. Furthermore, in a subset of serum samples, we identify other SARS-CoV-2 antibodies elicited by these individuals, including functionally neutralizing antibodies.\n\nImplications of all the available evidenceIt is difficult to say the exact seroprevalence in the central North Carolina area, but a greater proportion of the population accessing healthcare has been infected by SARS-CoV-2 than is reflected by infection cases confirmed by molecular testing. Furthermore, local governments need to prioritize addressing the many forms of systemic racism and socioeconomic disadvantage that drive SARS-CoV-2 exposure risk, such as residential and occupational risk, and an urgent need to provide access to SARS-CoV-2 testing and vaccination to these groups.",
-    "rel_num_authors": 26,
-    "rel_authors": [
-      {
-        "author_name": "Cesar A. Lopez",
-        "author_inst": "Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA"
-      },
-      {
-        "author_name": "Clark H. Cunningham",
-        "author_inst": "Department of Genetics, University of North Carolina School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill NC 27599, USA"
-      },
-      {
-        "author_name": "Sierra Pugh",
-        "author_inst": "Department of Statistics, Colorado State University, Fort Collins, CO, 80523, USA"
-      },
-      {
-        "author_name": "Katerina Brandt",
-        "author_inst": "Department of Geography, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA; Carolina Population Center, Chapel Hill, NC 27516, USA"
-      },
-      {
-        "author_name": "Usaphea P. Vanna",
-        "author_inst": "Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA"
-      },
-      {
-        "author_name": "Matthew J. Delacruz",
-        "author_inst": "Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA"
-      },
-      {
-        "author_name": "Quique Guerra",
-        "author_inst": "Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA"
-      },
-      {
-        "author_name": "Samuel Jacob Goldstein",
-        "author_inst": "Department of Environmental Sciences and Engineering, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA"
-      },
-      {
-        "author_name": "Yixuan Jacob Hou",
-        "author_inst": "Department of Epidemiology, University of North Carolina at Chapel Hill School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27"
-      },
-      {
-        "author_name": "Margaret Gearhart",
-        "author_inst": "McLendon Clinical Laboratories, UNC Healthcare, Chapel Hill, NC 27599, USA"
-      },
-      {
-        "author_name": "Christine Wiethorn",
-        "author_inst": "Johnston Health Laboratories, Johnston Health, Smithfield, NC 27577"
-      },
-      {
-        "author_name": "Candace Pope",
-        "author_inst": "Johnston Health Laboratories, Johnston Health, Smithfield, NC 27577"
-      },
-      {
-        "author_name": "Carolyn Amditis",
-        "author_inst": "Rex Healthcare Laboratory, UNC Healthcare, Chapel Hill, NC 27607, USA"
-      },
-      {
-        "author_name": "Kathryn Pruitt",
-        "author_inst": "Chatham Clinical Laboratory, Chatham Hospital, Siler City, NC 27344, USA"
-      },
-      {
-        "author_name": "Cinthia Newberry-Dillon",
-        "author_inst": "Chatham Clinical Laboratory, Chatham Hospital, Siler City, NC 27344, USA"
-      },
-      {
-        "author_name": "John Schmitz",
-        "author_inst": "Department of Pathology & Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA"
-      },
-      {
-        "author_name": "Lakshmanane Premkumar",
-        "author_inst": "Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA"
-      },
-      {
-        "author_name": "Adaora A. Adimora",
-        "author_inst": "Department of Epidemiology, University of North Carolina at Chapel Hill School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27"
-      },
-      {
-        "author_name": "Michael Emch",
-        "author_inst": "Department of Geography, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA; Carolina Population Center, Chapel Hill, NC 27516, USA"
-      },
-      {
-        "author_name": "Ross Boyce",
-        "author_inst": "Department of Medicine, Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA"
-      },
-      {
-        "author_name": "Allison E. Aiello",
-        "author_inst": "Department of Epidemiology, University of North Carolina at Chapel Hill School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27"
-      },
-      {
-        "author_name": "Bailey K. Fosdick",
-        "author_inst": "Department of Statistics, Colorado State University, Fort Collins, CO, 80523, USA"
-      },
-      {
-        "author_name": "Daniel B Larremore",
-        "author_inst": "Department of Computer Science & BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80303, USA"
-      },
-      {
-        "author_name": "Aravinda M. de Silva",
-        "author_inst": "Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA"
-      },
-      {
-        "author_name": "Jonathan J. J. Juliano",
-        "author_inst": "Department of Epidemiology, University of North Carolina at Chapel Hill School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27"
-      },
-      {
-        "author_name": "Alena J. Markmann",
-        "author_inst": "Department of Medicine, Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill NC 27599, USA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.03.24.21253489",
     "rel_title": "Factors associated with COVID-19 vaccine receipt at two integrated healthcare systems in New York City: A Cross sectional study of healthcare workers",
@@ -841518,6 +839918,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.03.26.437014",
+    "rel_title": "Aberrant glycosylation of anti-SARS-CoV-2 IgG is a pro-thrombotic stimulus for platelets",
+    "rel_date": "2021-03-26",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.26.437014",
+    "rel_abs": "A subset of patients with COVID-19 become critically ill, suffering from severe respiratory problems and also increased rates of thrombosis. The causes of thrombosis in severely ill COVID-19 patients are still emerging, but the coincidence of critical illness with the timing of the onset of adaptive immunity could implicate an excessive immune response. We hypothesised that platelets might be susceptible to activation by anti-SARS-CoV-2 antibodies and contribute to thrombosis. We found that immune complexes containing recombinant SARS-CoV-2 spike protein and anti-spike IgG enhanced platelet-mediated thrombosis on von Willebrand Factor in vitro, but only when the glycosylation state of the Fc domain was modified to correspond with the aberrant glycosylation previously identified in patients with severe COVID-19. Furthermore, we found that activation was dependent on FcyRIIA and we provide in vitro evidence that this pathogenic platelet activation can be counteracted by therapeutic small molecules R406 (fostamatinib) and ibrutinib that inhibit tyrosine kinases syk and btk respectively or by the P2Y12 antagonist cangrelor.",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Alexander P Bye",
+        "author_inst": "University of Reading"
+      },
+      {
+        "author_name": "Willianne Hoepel",
+        "author_inst": "Amsterdam UMC"
+      },
+      {
+        "author_name": "Joanne L Mitchell",
+        "author_inst": "University of Birmingham"
+      },
+      {
+        "author_name": "Sophie Jegouic",
+        "author_inst": "University of Reading"
+      },
+      {
+        "author_name": "Silvia Loureiro",
+        "author_inst": "University of Reading"
+      },
+      {
+        "author_name": "Tanya Sage",
+        "author_inst": "University of Reading"
+      },
+      {
+        "author_name": "Steven de Taeye",
+        "author_inst": "Amsterdam UMC"
+      },
+      {
+        "author_name": "Marit van Gils",
+        "author_inst": "Amsterdam UMC"
+      },
+      {
+        "author_name": "Neline Kriek",
+        "author_inst": "University of Reading"
+      },
+      {
+        "author_name": "Nichola Cooper",
+        "author_inst": "Imperial College London"
+      },
+      {
+        "author_name": "Ian Jones",
+        "author_inst": "University of Reading"
+      },
+      {
+        "author_name": "Jeroen den Dunnen",
+        "author_inst": "Amsterdam UMC"
+      },
+      {
+        "author_name": "Jonathan M Gibbins",
+        "author_inst": "University of Reading"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2021.03.26.436314",
     "rel_title": "Immunoinformatic approach to design a vaccine against SARS-COV-2 membrane glycoprotein",
@@ -843074,33 +841541,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2021.03.25.437035",
-    "rel_title": "Computational assessment of the spike protein antigenicity reveals diversity in B cell epitopes but stability in T cell epitopes across SARS-CoV-2 variants",
-    "rel_date": "2021-03-25",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.25.437035",
-    "rel_abs": "Since its emergence into the human population at the end of 2019, SARS-CoV-2 has caused significant morbidity and mortality worldwide. Efforts to develop a protective vaccine against COVID-19 have yielded several vaccine platforms currently in distribution targeting the original SARS-CoV-2 spike protein sequence from the first cases of infection. In recent months, variants of SARS-CoV-2 have raised concerns that viral mutation may undermine vaccination efforts through viral escape of host immune memory acquired from infection or vaccination. We therefore used a computational approach to predict changes in spike protein antigenicity with respect to host B cell and CD8+ T cell immunity across six SARS-CoV-2 variants (D614G, B.1.1.7, B.1.351, P.1, B.1.429, and mink-related). Our epitope analysis using DiscoTope suggests possible changes in B cell epitopes in the S1 region of the spike protein across variants, in particular the B.1.1.7 and B.1.351 lineages, which may influence immunodominance. Additionally, we show that high-affinity MHC-I-binding peptides and glycosylation sites on the spike protein appear consistent between variants with the exception of an extra glycosylation site in the P.1 variant. Together, these analyses suggests T cell vaccine strategies have the most longevity before reformulation.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Anni Ge",
-        "author_inst": "Dalhousie University"
-      },
-      {
-        "author_name": "Melissa Rioux",
-        "author_inst": "Dalhousie University"
-      },
-      {
-        "author_name": "Alyson Ann Kelvin",
-        "author_inst": "VIDO (Vaccine and Infectious Disease Organization)"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2021.03.25.437083",
     "rel_title": "Target Capture Sequencing of SARS-CoV-2 Genomes Using the ONETest Coronaviruses Plus",
@@ -843515,6 +841955,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.03.15.21253567",
+    "rel_title": "Evaluation of pooling of samples for testing SARS-COV- 2 for mass screening of COVID-19",
+    "rel_date": "2021-03-24",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.15.21253567",
+    "rel_abs": "BackgroundThe current pandemic of SARS- COV- 2 virus, widely known as COVID-19 has affected millions of people around the world. The World Health Organization (WHO) has recommended vigorous testing to differentiate SARS-CoV-2 from other respiratory infections to aid in guiding appropriate care and management. Situations like this have demanded robust testing strategies and pooled testing of samples for SARS- COV- 2 virus has provided the solution to mass screening of people. The pooled testing strategy can be very effective in testing with limited resources, yet it comes with its own limitations. These limitations need critical consideration when it comes to testing of highly infectious disease like COVID -19.\n\nMethodsThe study evaluated the pooled testing of nasopharyngeal swabs for SARS- COV- 2 by comparing sensitivity of individual sample testing with 4 and 8 pool sample testing. Median cycle threshold (Ct) values were compared. The precision of pooled testing was assessed by doing an inter and intra assay of pooled samples. Coefficient of variance was calculated for inter and intra assay variability.\n\nResultsThe sensitivity becomes considerably low when the samples are pooled, there is a higher percentage of false negatives with higher pool size and when the patient viral load is low or weak positive samples. High variability was seen in the intra and inter assay, especially in weak positive samples and larger pool size.\n\nConclusionAs COVID - 19 numbers are still high and testing capacity needs to be high, we have to meticulously evaluate the testing strategy for each country depending on its testing capacity, infrastructure, economic strength, and need to make a serious call on cost effective strategy of resource saving and risk/ cost of missing positive patients.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Dr. Sally Mahmoud",
+        "author_inst": "Biogenix Lab G42, Abu Dhabi, UAE"
+      },
+      {
+        "author_name": "Ms.Esra Ibrahim",
+        "author_inst": "Biogenix Lab G42, Abu Dhabi, UAE"
+      },
+      {
+        "author_name": "Dr. Bhagyashree Thakre",
+        "author_inst": "Biogenix Lab G42, Abu Dhabi, UAE"
+      },
+      {
+        "author_name": "Dr.Juliet George Teddy",
+        "author_inst": "Biogenix Lab G42, Abu Dhabi, UAE"
+      },
+      {
+        "author_name": "Mrs.Preeti Raheja",
+        "author_inst": "Biogenix Lab G42, Abu Dhabi, UAE"
+      },
+      {
+        "author_name": "Dr. Subhashini Ganesan",
+        "author_inst": "G42 Healthcare, UAE"
+      },
+      {
+        "author_name": "Dr.Walid Zaher",
+        "author_inst": "G42 Healthcare, UAE"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.03.19.21253924",
     "rel_title": "VIRAL AND ANTIBODY TESTING FOR CORONAVIRUS DISEASE 2019 (COVID-19): FACTORS ASSOCIATED WITH POSITIVITY IN ELECTRONIC HEALTH RECORDS FROM THE UNITED STATES",
@@ -844696,105 +843179,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.03.23.436648",
-    "rel_title": "Phospholipidosis is a shared mechanism underlying the in vitro antiviral activity of many repurposed drugs against SARS-CoV-2",
-    "rel_date": "2021-03-24",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.23.436648",
-    "rel_abs": "Repurposing drugs as treatments for COVID-19 has drawn much attention. A common strategy has been to screen for established drugs, typically developed for other indications, that are antiviral in cells or organisms. Intriguingly, most of the drugs that have emerged from these campaigns, though diverse in structure, share a common physical property: cationic amphiphilicity. Provoked by the similarity of these repurposed drugs to those inducing phospholipidosis, a well-known drug side effect, we investigated phospholipidosis as a mechanism for antiviral activity. We tested 23 cationic amphiphilic drugs--including those from phenotypic screens and others that we ourselves had found--for induction of phospholipidosis in cell culture. We found that most of the repurposed drugs, which included hydroxychloroquine, azithromycin, amiodarone, and four others that have already progressed to clinical trials, induced phospholipidosis in the same concentration range as their antiviral activity; indeed, there was a strong monotonic correlation between antiviral efficacy and the magnitude of the phospholipidosis. Conversely, drugs active against the same targets that did not induce phospholipidosis were not antiviral. Phospholipidosis depends on the gross physical properties of drugs, and does not reflect specific target-based activities, rather it may be considered a confound in early drug discovery. Understanding its role in infection, and detecting its effects rapidly, will allow the community to better distinguish between drugs and lead compounds that more directly impact COVID-19 from the large proportion of molecules that manifest this confounding effect, saving much time, effort and cost.\n\nOne Sentence SummaryDrug-induced phospholipidosis is a single mechanism that may explain the in vitro efficacy of a wide-variety of therapeutics repurposed for COVID-19.",
-    "rel_num_authors": 21,
-    "rel_authors": [
-      {
-        "author_name": "Tia A Tummino",
-        "author_inst": "University of California, San Francisco"
-      },
-      {
-        "author_name": "Veronica V Rezelj",
-        "author_inst": "Institut Pasteur"
-      },
-      {
-        "author_name": "Benoit Fischer",
-        "author_inst": "Novartis Institutes for BioMedical Research"
-      },
-      {
-        "author_name": "Audrey Fischer",
-        "author_inst": "Novartis Institutes for BioMedical Research"
-      },
-      {
-        "author_name": "Blandine Monel",
-        "author_inst": "Institut Pasteur"
-      },
-      {
-        "author_name": "Thomas Vallet",
-        "author_inst": "Institut Pasteur"
-      },
-      {
-        "author_name": "Ziyang Zhang",
-        "author_inst": "University of California, San Francisco"
-      },
-      {
-        "author_name": "Assaf Alon",
-        "author_inst": "Harvard Medical School"
-      },
-      {
-        "author_name": "Jiankun Lyu",
-        "author_inst": "University of California, San Francisco"
-      },
-      {
-        "author_name": "Heiko Schadt",
-        "author_inst": "Novartis Institutes for BioMedical Research"
-      },
-      {
-        "author_name": "Kris M White",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Nevan J Krogan",
-        "author_inst": "University of California San Francisco"
-      },
-      {
-        "author_name": "Laszlo Urban",
-        "author_inst": "Novartis Institutes for BioMedical Research"
-      },
-      {
-        "author_name": "Kevan Shokat",
-        "author_inst": "University of California San Francisco"
-      },
-      {
-        "author_name": "Andrew Kruse",
-        "author_inst": "Harvard Medical School"
-      },
-      {
-        "author_name": "Adolfo Garc\u00eda-Sastre",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Olivier Schwartz",
-        "author_inst": "Institut Pasteur"
-      },
-      {
-        "author_name": "Francesca Moretti",
-        "author_inst": "Novartis Institutes for BioMedical Research"
-      },
-      {
-        "author_name": "Marco Vignuzzi",
-        "author_inst": "Institut Pasteur"
-      },
-      {
-        "author_name": "Francois Pognan",
-        "author_inst": "Novartis Institutes for BioMedical Research"
-      },
-      {
-        "author_name": "Brian K Shoichet",
-        "author_inst": "University of California, San Francisco"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "pharmacology and toxicology"
-  },
   {
     "rel_doi": "10.1101/2021.03.24.436620",
     "rel_title": "B.1.526 SARS-CoV-2 variants identified in New York City are neutralized by vaccine-elicited and therapeutic monoclonal antibodies",
@@ -845153,6 +843537,41 @@
     "type": "new results",
     "category": "bioinformatics"
   },
+  {
+    "rel_doi": "10.1101/2021.03.24.436822",
+    "rel_title": "Arginine Methylation Regulates SARS-CoV-2 Nucleocapsid Protein Function and Viral Replication",
+    "rel_date": "2021-03-24",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.24.436822",
+    "rel_abs": "Viral proteins are known to be methylated by host protein arginine methyltransferases (PRMTs) playing critical roles during viral infections. Herein, we show that PRMT1 methylates SARS-CoV-2 nucleocapsid (N) protein at residues R95 and R177 within RGG/RG sequences. Arginine methylation of N protein was confirmed by immunoblotting viral proteins extracted from SARS-CoV-2 virions isolated by cell culture. We demonstrate that arginine methylation of N protein is required for its RNA binding capacity, since treatment with a type I PRMT inhibitor (MS023) or substitution of R95K or R177K inhibited interaction with the 5-UTR of the SARS-CoV-2 genomic RNA. We defined the N interactome in HEK293 cells with or without MS023 treatment and identified PRMT1 and many of its RGG/RG substrates including the known interactor, G3BP1, and other components of stress granules (SG). Methylation of N protein at R95 regulates another function namely its property to suppress the formation of SGs. MS023 treatment or R95K substitution blocked N-mediated suppression of SGs. Also, the co-expression of methylarginine reader TDRD3 quenched N-mediated suppression of SGs in a dose-dependent manner. Finally, pre-treatment of VeroE6 cells with MS023 significantly reduced SARS-CoV-2 replication. With type I PRMT inhibitors being in clinical trials for cancer treatment, inhibiting arginine methylation to target the later stages of the viral life cycle such as viral genome packaging and assembly of virions may be an additional therapeutic application of these drugs.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Ting Cai",
+        "author_inst": "McGill University/Lady Davis Institute for Medical Research"
+      },
+      {
+        "author_name": "Zhenbao Yu",
+        "author_inst": "McGill University/Lady Davis Institute for Medical Research"
+      },
+      {
+        "author_name": "Zhen Wang",
+        "author_inst": "McGill University/Lady Davis Institute for Medical Research"
+      },
+      {
+        "author_name": "Chen Liang",
+        "author_inst": "McGill University/Lady Davis Institute for Medical Research"
+      },
+      {
+        "author_name": "Stephane Richard",
+        "author_inst": "McGill University/Lady Davis Institute for Medical Research"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "molecular biology"
+  },
   {
     "rel_doi": "10.1101/2021.03.16.21253753",
     "rel_title": "Rapid, widespread, and preferential increase of SARS-CoV-2 B.1.1.7 variant in Houston, TX, revealed by 8,857 genome sequences",
@@ -846340,45 +844759,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.03.16.21253632",
-    "rel_title": "Curtailing Covid-19 on a Dollar-a-Day in Malawi: Implications for the Ongoing Pandemic",
-    "rel_date": "2021-03-24",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.16.21253632",
-    "rel_abs": "Utilizing population-based data from the Covid-19 phone survey (N = 2, 262) of the Malawi Longitudinal Study of Families and Health (MLSFH) collected during June 2nd-August 17th, 2020, we investigate behavioral, economic and social responses to Covid-19 and focus on the crucial role that community leadership and trust in institutions play towards shaping these responses. We argue that the effective response of Malawi to limit the spread of the virus was facilitated by the engagement of local leaders to mobilize communities to adapt and adhere to Covid-19 prevention strategies. Village heads (VHs) played pivotal role in shaping individuals knowledge about the pandemic and the adaption of preventive health behaviors and were crucial for mitigating the negative economic and health consequences of the pandemic. We further show that trust in institutions is of particular importance in shaping individuals behavior during the pandemic, and these findings highlight the pivotal role of community leadership in fostering better compliance and adoption of public health measures essential to contain the virus. Overall, our findings point to distinctive patterns of pandemic response in a low-income sub-Saharan African rural population that emphasized local leadership as mediators of public health messages and policies. These lessons from the first pandemic wave remain relevant as in many low-income countries behavioral responses to Covid-19 will remain the primary prevention strategy for a foreseeable future.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Iliana V. Kohler",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Fabrice Kaempfen",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Alberto Ciancio",
-        "author_inst": "University of Lausanne"
-      },
-      {
-        "author_name": "James Mwera",
-        "author_inst": "Invest in Knowledge Initiative (IKI), Malawi"
-      },
-      {
-        "author_name": "Victor Mwapasa",
-        "author_inst": "College of Medicine, University of Malawi"
-      },
-      {
-        "author_name": "Hans-Peter Kohler",
-        "author_inst": "University of Pennsylvania"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.03.16.21252974",
     "rel_title": "Molecular Epidemiology of SARS-CoV-2 in Cyprus",
@@ -846729,6 +845109,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pediatrics"
   },
+  {
+    "rel_doi": "10.1101/2021.03.19.21253756",
+    "rel_title": "Characterizing Post-Acute Sequelae of SARS-CoV-2 Infection across Claims and Electronic Health Record Databases",
+    "rel_date": "2021-03-24",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253756",
+    "rel_abs": "Structured AbstractO_ST_ABSImportanceC_ST_ABSPost-acute sequelae of SARS-CoV-2 infection (PASC) is emerging as a major public health issue.\n\nObjectiveWe characterized the incidence of PASC, or related symptoms and diagnoses, for COVID-19 and influenza patients.\n\nDesignRetrospective cohort study.\n\nSettingOur data sources were the IBM MarketScan Commercial Claims and Encounters (CCAE), Optum Electronic Health Record (EHR) and Columbia University Irving Medical Center (CUIMC) databases that were transformed to the Observational Medical Outcome Partnership (OMOP) Common Data Model (CDM) and were part of the Observational Health Sciences and Informatics (OHDSI) network.\n\nParticipantsThe COVID-19 cohort consisted of patients with a diagnosis of COVID-19 or positive lab test of SARS-CoV-2 after January 1st 2020 with a follow up period of at least 30 days. The influenza cohort consisted of patients with a diagnosis of influenza between October 1, 2018 and May 1, 2019 with a follow up period of at least 30 days.\n\nInterventionInfection with COVID-19 or influenza.\n\nMain Outcomes and MeasuresPost-acute sequelae of SARS-CoV-2 infection (PASC), or related diagnoses, for COVID-19 and influenza patients.\n\nResultsIn aggregate, we characterized the post-acute experience for over 440,000 patients who were diagnosed with COVID-19 or tested positive for SARS-COV-2. The long term sequelae that had a higher incidence in the COVID-19 compared to Influenza cohorts were altered smell or taste, myocarditis, acute kidney injury, dyspnea and alopecia. Additionally, the long term incidences of respiratory illness, musculoskeletal disease, and psychiatric disorders for the COVID-19 population were higher than expected.\n\nConclusions and RelevanceThe long term sequelae of COVID-19 and influenza may be different. Further characterization of PASC on large scale observational healthcare databases is warranted.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Matthew E Spotnitz",
+        "author_inst": "Columbia University Irving Medical Center"
+      },
+      {
+        "author_name": "George Hripcsak",
+        "author_inst": "Columbia University Irving Medical Center"
+      },
+      {
+        "author_name": "Patrick B Ryan",
+        "author_inst": "Janssen Research and Development"
+      },
+      {
+        "author_name": "Karthik Natarajan",
+        "author_inst": "Columbia University Irving Medical Center"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.03.17.21253760",
     "rel_title": "Chronic diseases: Perceptions about Covid-19 risk and vaccination",
@@ -848306,37 +846717,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.03.21.21254064",
-    "rel_title": "In-person schooling and COVID-19 transmission in Canada's three largest cities",
-    "rel_date": "2021-03-23",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.21.21254064",
-    "rel_abs": "In North America and Europe, the Fall 2020 school term has coincided with the beginning of the second wave of the novel coronavirus (COVID-19) pandemic, sparking a heated debate about the role of in-person schooling for community transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This issue has immediate policy relevance for deciding how to operate schools safely as the pandemic unfolds, new variants of SARS-CoV-2 are circulating, and immunization coverage remains low. We contribute to this debate by presenting data on trends in COVID-19 weekly incidence among school-aged children 0-19 years old vis-a-vis other age groups during Fall 2020 in Canadas three largest cities: Montreal, Toronto and Calgary. We interpret these trends in light of the different back-to-school policies and other public health measures implemented in the three cities over the observation period.\n\nKEY POINTSO_LISchool closures are an effective measure to reduce the overall incidence of the novel coronavirus (COVID-19). Nonetheless, there is a general consensus that the decision to close schools to control the spread of COVID-19 should be used as last resort because of the negative impact on childrens development and mental health, and since they are less likely to have severe COVID-19 outcomes than adults.\nC_LIO_LIExisting evidence highlights the importance of adopting appropriate mitigation strategies for limiting COVID-19 community spread when returning to in-person schooling. To understand the association between in-person schooling and COVID-19 transmission given different mitigation strategies, especially universal masking and distance learning, we compare how the second wave of COVID-19 has affected school-aged children age 0-19 years old vis-a-vis other age groups in Montreal, Toronto and Calgary during Fall 2020.\nC_LIO_LIThe case of Montreal attests to the negative consequences of not implementing recommended migration strategies when reopening schools, even when public health measures such as gatherings restrictions are in place to maintain low levels of community transmission. On the contrary, school measures adopted in Toronto (optional distance learning and masking mandates), have limited the role of COVID-19 transmission among school-aged children for overall community transmission. In Calgary, this effect has been smaller, likely because public health measures to limit COVID-19 community spread were not introduced until early December 2020.\nC_LIO_LIOur findings have immediate policy relevance for deciding how to operate schools safely as the pandemic unfolds, new variants of SARS-CoV-2 are circulating, and immunization coverage remains low.\nC_LI",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Simona Bignami",
-        "author_inst": "Universite de Montreal"
-      },
-      {
-        "author_name": "Yacine Boujija",
-        "author_inst": "Universite de Montreal"
-      },
-      {
-        "author_name": "David Fisman",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "John Sandberg",
-        "author_inst": "George Washington University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.03.18.21253888",
     "rel_title": "Long Covid in adults discharged from UK hospitals after Covid-19: A prospective, multicentre cohort study using the ISARIC WHO Clinical Characterisation Protocol.",
@@ -848923,6 +847303,121 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.03.23.436564",
+    "rel_title": "Protein-primed RNA synthesis in SARS-CoVs and structural basis for inhibition by AT-527",
+    "rel_date": "2021-03-23",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.23.436564",
+    "rel_abs": "How viruses from the Coronaviridae family initiate viral RNA synthesis is unknown. Here we show that the SARS-CoV-1 and -2 Nidovirus RdRp-Associated Nucleotidyltransferase (NiRAN) domain on nsp12 uridylates the viral cofactor nsp8, forming a UMP-Nsp8 covalent intermediate that subsequently primes RNA synthesis from a poly(A) template; a protein-priming mechanism reminiscent of Picornaviridae enzymes. In parallel, the RdRp active site of nsp12 synthesizes a pppGpU primer, which primes (-)ssRNA synthesis at the precise genome-poly(A) junction. The guanosine analogue 5-triphosphate AT-9010 (prodrug: AT-527) tightly binds to the NiRAN and inhibits both nsp8-labeling and the initiation of RNA synthesis. A 2.98 [A] resolution Cryo-EM structure of the SARS-CoV-2 nsp12-nsp7-(nsp8)2 /RNA/NTP quaternary complex shows AT-9010 simultaneously binds to both NiRAN and RdRp active site of nsp12, blocking their respective activities. AT-527 is currently in phase II clinical trials, and is a potent inhibitor of SARS-CoV-1 and -2, representing a promising drug for COVID-19 treatment.",
+    "rel_num_authors": 25,
+    "rel_authors": [
+      {
+        "author_name": "Ashleigh Shannon",
+        "author_inst": "AFMB-CNRS-AMU"
+      },
+      {
+        "author_name": "Veronique Fattorini",
+        "author_inst": "AFMB-CNRS-AMU"
+      },
+      {
+        "author_name": "Bhawna Sama",
+        "author_inst": "AFMB-CNRS-AMU"
+      },
+      {
+        "author_name": "Barbara Selisko",
+        "author_inst": "AFMB-CNRS-AMU"
+      },
+      {
+        "author_name": "Mikael Feracci",
+        "author_inst": "AFMB-CNRS-AMU"
+      },
+      {
+        "author_name": "Camille Falcou",
+        "author_inst": "AFMB-CNRS-AMU"
+      },
+      {
+        "author_name": "Pierre Gauffre",
+        "author_inst": "AFMB-CNRS-AMU"
+      },
+      {
+        "author_name": "Priscila El Kazzi",
+        "author_inst": "AFMB-CNRS-AMU"
+      },
+      {
+        "author_name": "Etienne Decroly",
+        "author_inst": "AFMB-CNRS-AMU"
+      },
+      {
+        "author_name": "Nadia Rabah",
+        "author_inst": "AFMB-CNRS-AMU"
+      },
+      {
+        "author_name": "Karine Toulon",
+        "author_inst": "AFMB-CNRS-AMU"
+      },
+      {
+        "author_name": "Cecilia Eydoux",
+        "author_inst": "AFMB-CNRS-AMU"
+      },
+      {
+        "author_name": "Jean-Claude Guillemot",
+        "author_inst": "AFMB-CNRS-AMU"
+      },
+      {
+        "author_name": "Mathieu Noel",
+        "author_inst": "CNRS"
+      },
+      {
+        "author_name": "Francoise Debart",
+        "author_inst": "CNRS"
+      },
+      {
+        "author_name": "Jean-Jacques Vasseur",
+        "author_inst": "CNRS"
+      },
+      {
+        "author_name": "Adel Moussa",
+        "author_inst": "ATEA Pharmaceuticals"
+      },
+      {
+        "author_name": "Steven Good",
+        "author_inst": "ATEA Pharmaceuticals"
+      },
+      {
+        "author_name": "Kai Lin",
+        "author_inst": "ATEA Pharmaceuticals"
+      },
+      {
+        "author_name": "Jean-Pierre Sommadossi",
+        "author_inst": "ATEA Pharmaceuticals"
+      },
+      {
+        "author_name": "Yingxiao Zhu",
+        "author_inst": "WuxiBiortus"
+      },
+      {
+        "author_name": "Xiaodong Yan",
+        "author_inst": "WuxiBiortus"
+      },
+      {
+        "author_name": "Hui Shi",
+        "author_inst": "WuxiBiortus"
+      },
+      {
+        "author_name": "Francois Ferron",
+        "author_inst": "AFMB-CNRS-AMU"
+      },
+      {
+        "author_name": "Bruno Canard",
+        "author_inst": "AFMB-CNRS-AMU"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "biochemistry"
+  },
   {
     "rel_doi": "10.1101/2021.03.22.436476",
     "rel_title": "The Dual-Antigen Ad5 COVID-19 Vaccine Delivered as an Intranasal Plus Subcutaneous Prime Elicits Th1 Dominant T-Cell and Humoral Responses in CD-1 Mice",
@@ -850320,73 +848815,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.03.20.21254029",
-    "rel_title": "Psychosocial impact of the Covid-19 pandemic: Identification of most vulnerable populations.",
-    "rel_date": "2021-03-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.20.21254029",
-    "rel_abs": "With the aim of analyzing the psychosocial impact of Covid-19 pandemic on society in general and health care workers in particular, we developed a 74-question survey questionnaire which was shared through social media. After analyzing 56,656 responses obtained during the first pandemic peak, the results showed an early and important negative impact on family finances, fear of working with Covid-19 patients and ethical issues related to Covid-19 care among healthcare workers (HCW). We have identified 7 target groups at higher risk of impaired mental health and susceptible to benefiting from an intervention: women, under 42 years of age, people with care burden, socio-economically deprived groups, people with unskilled or unqualified jobs, Covid-19 patients, and HCW working with Covid-19 patients. These results should encourage the active implementation of specific strategies to increase resilience in these groups and to prepare an adequate organizational response.\n\nSummary boxO_ST_ABSWhat is already known?C_ST_ABSO_LIStudies in small cohorts have reported an important impact of the Covid-19 pandemic on the general population at several levels\nC_LIO_LIAccording to previous studies in small cohorts, approximately 20% of the population suffered from impaired mental health status due to the pandemic\nC_LI\n\nWhat are the new findings?O_LIWe have studied 56,656 survey questionnaires to assess the impact of the Covid-19 outbreak on health status, family finances, habits, general health and mental health status, and ethics, especially in health care workers\nC_LIO_LIWe have identified 7 target groups susceptible to benefitting from an intervention, and which should be taken into account when designing new contention measures against the pandemic\nC_LI\n\nWhat do the new findings imply?O_LIThe design and active implementation of interventions to build individual resilience, especially for the targeted populations described, and preparation of an appropriate organizational response are key\nC_LIO_LIThe results obtained in this project could help local and national Governments to design or adjust coping measures against future outbreaks\nC_LI",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Judith Farres",
-        "author_inst": "Anaxomics Biotech SL"
-      },
-      {
-        "author_name": "Jose Luis Ruiz",
-        "author_inst": "Anaxomics Biotech SL"
-      },
-      {
-        "author_name": "Jose Manuel Mas",
-        "author_inst": "Anaxomics Biotech SL"
-      },
-      {
-        "author_name": "Lilibeth Arias",
-        "author_inst": "Experimental Tuberculosis Unit (UTE). Fundacio Institut Germans Trias i Pujol (IGTP). CIBERES"
-      },
-      {
-        "author_name": "Maria-Rosa Sarrias",
-        "author_inst": "Innate Immunity Group. Fundacio Institut Germans Trias i Pujol (IGTP). CIBEREhD"
-      },
-      {
-        "author_name": "Carolina Armengol",
-        "author_inst": "Childhood Liver Oncology Group, Germans Trias I Pujol Research Institute (IGTP), CIBEREhD"
-      },
-      {
-        "author_name": "Pere-Joan Cardona",
-        "author_inst": "Experimental Tuberculosis Unit (UTE). Fundacio Institut Germans Trias i Pujol (IGTP). UAB. CIBERES"
-      },
-      {
-        "author_name": "Jose A Munoz-Moreno",
-        "author_inst": "Fundacio Lluita contra la SIDA (FLS) - Servei de Malalties Infeccioses, Hospital Germans Trias. UOC."
-      },
-      {
-        "author_name": "Miriam Vilaplana",
-        "author_inst": "Parc Sanitari Sant Joan de Du."
-      },
-      {
-        "author_name": "Belen Arranz",
-        "author_inst": "Parc Sanitari Sant Joan de Deu. Institut de Recerca Sant Joan de Deu. CIBERSAM"
-      },
-      {
-        "author_name": "Judith Usall",
-        "author_inst": "Parc Sanitari Sant Joan de Deu. Institut de Recerca Sant Joan de Deu"
-      },
-      {
-        "author_name": "Antoni Serrano-Blanco",
-        "author_inst": "Parc Sanitari Sant Joan de Deu. Institut de Recerca Sant Joan de Deu. CIBERESP"
-      },
-      {
-        "author_name": "Cristina Vilaplana",
-        "author_inst": "Experimental Tuberculosis Unit (UTE). Fundacio Institut Germans Trias i Pujol (IGTP). UAB. CIBERES"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.03.19.21253950",
     "rel_title": "Limit of detection in different matrices of nineteen commercially available rapid antigen tests for the detection of SARS-CoV-2",
@@ -850781,6 +849209,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.03.21.21253754",
+    "rel_title": "Role of Combining Anticoagulant and Antiplatelet Agents in COVID-19 Treatment: A Rapid Review",
+    "rel_date": "2021-03-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.21.21253754",
+    "rel_abs": "Although primarily affecting the respiratory system, COVID-19 causes multiple organ damage. One of its grave consequences is a prothrombotic state that manifests as thrombotic, microthrombotic, and thromboembolic events.Therefore, understanding the effect of antiplatelet and anticoagulation therapy in the context of COVID-19 treatment is important. The aim of this rapid review is to highlight the role of thrombosis in COVID-19 and provide new insights on the use of antithrombotic therapy in its management. A rapid systematic review was performed using preferred reporting items for systematic reviews. Papers published in English on antithrombotic agent use and COVID-19 complications were eligible. Results showed that the use of anticoagulants increased survival and reduced thromboembolic events in patients. However, despite the use of anticoagulants, patients still suffered thrombotic events likely due to heparin resistance. Data on antiplatelet use in combination with anticoagulants in the setting of COVID-19 is quite scarce. Current side effects of anticoagulation therapy emphasize the need to update treatment guidelines. In this rapid review, we address a possible modulatory role of antiplatelet and anticoagulant combination against COVID{square}19 pathogenesis. This combination may be an effective form of adjuvant therapy against COVID{square}19 infection. However, further studies are needed to elucidate potential risks and benefits associated with this combination.\n\nIt was not appropriate or possible to involve patients or the public in the design, or conduct, or reporting, or dissemination plans of our research",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Kamal Matli",
+        "author_inst": "LAUMCRH"
+      },
+      {
+        "author_name": "Raymond Farah",
+        "author_inst": "Lebanese University"
+      },
+      {
+        "author_name": "Mario Maalouf",
+        "author_inst": "LAU"
+      },
+      {
+        "author_name": "Christy Costanian",
+        "author_inst": "LAU"
+      },
+      {
+        "author_name": "Nibal Chamoun",
+        "author_inst": "LAU"
+      },
+      {
+        "author_name": "Georges Ghanem",
+        "author_inst": "LAUMCRH"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "cardiovascular medicine"
+  },
   {
     "rel_doi": "10.1101/2021.03.15.435423",
     "rel_title": "Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment",
@@ -852602,61 +851069,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.03.18.21253845",
-    "rel_title": "Heightened COVID-19 Vaccine Response following SARS-CoV-2 Infection",
-    "rel_date": "2021-03-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.18.21253845",
-    "rel_abs": "BackgroundCurrent recommendations in the United States are that subjects with a previous history of COVID-19 disease receive the full 2 dose mRNA vaccine regimen. We tested the hypothesis that humoral immune responses and reactogenicity to a SARS-CoV-2 mRNA vaccine (BNT-162b2) differ qualitatively and quantitatively in subjects with prior SARS-CoV-2 infection versus infection-naive subjects.\n\nMethodsHealth care workers (n=61) from a single academic institution with and without prior COVID-19 received two 30 {micro}g doses of BNT162b2 vaccine 3 weeks apart. The COVID group (n=30) received vaccine approximately 7 months post infection. IgG antibody against the Spike receptor-binding domain (RBD), serum neutralizing activity and vaccine adverse reactions were assessed every 2 weeks for 56 days after the 1st injection. A longitudinal design and long study duration allowed the onset, maximum response and initial decay rate of Spike IgG antibody to be assessed in each subject. In addition, Spike IgG antibody levels are expressed as {micro}g / mL to provide normal values for clinical decision making.\n\nFindingsSpike IgG responses were highly variable in both groups. However, the COVID group manifested rapid increases in Spike IgG antibody and serum neutralizing activity post 1st vaccine dose but little or no increase in Spike IgG or serum neutralizing activity after the 2nd dose. In fact, Spike IgG was maximum prior to the 2nd dose in 36% of the COVID group and 0% of controls. Peak IgG antibody was lower but appeared to fall more slowly in the COVID than in the control group. Finally, adverse systemic reactions e.g., fever, headache and malaise, after both the 1st and 2nd injection were more frequent and lasted longer in the COVID group than in the control group.\n\nConclusionsHealth care workers with prior COVID-19 demonstrate a robust, accelerated humoral immune response to the 1st dose of the COVID-19 mRNA vaccine but attenuated response to the 2nd dose. They also experience greater reactogenicity than controls. Accordingly, subjects with prior COVID-19 may require only a single dose of vaccine.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Steven G. Kelsen",
-        "author_inst": "Lewis Katz School of Medicine at Temple University, Philadelphia, PA  19140"
-      },
-      {
-        "author_name": "Alan Braverman",
-        "author_inst": "Lewis Katz School of Medicine at Temple University, Philadelphia, PA  19140"
-      },
-      {
-        "author_name": "Mark O. Aksoy",
-        "author_inst": "Lewis Katz School of Medicine at Temple University, Philadelphia, PA  19140"
-      },
-      {
-        "author_name": "Jacob Hayman",
-        "author_inst": "Lewis Katz School of Medicine at Temple University, Philadelphia, PA  19140"
-      },
-      {
-        "author_name": "Puja Patel",
-        "author_inst": "Lewis Katz School of Medicine at Temple University, Philadelphia, PA  19140"
-      },
-      {
-        "author_name": "Charu Rajput",
-        "author_inst": "Lewis Katz School of Medicine at Temple University, Philadelphia, PA  19140"
-      },
-      {
-        "author_name": "Huaqing Zhao",
-        "author_inst": "Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140"
-      },
-      {
-        "author_name": "Susan Fisher",
-        "author_inst": "Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140"
-      },
-      {
-        "author_name": "Michael Ruggieri",
-        "author_inst": "Lewis Katz School of Medicine at Temple University, Philadelphia, PA  19140"
-      },
-      {
-        "author_name": "Nina Gentile",
-        "author_inst": "Lewis Katz School of Medicine at Temple University, Philadelphia, PA  19140"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.03.18.21253903",
     "rel_title": "Development and validation of the long covid symptom and impact tools, a set of patient-reported instruments constructed from patients' lived experience",
@@ -852887,6 +851299,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.03.18.21253887",
+    "rel_title": "Effect of Increased Alcohol Consumption During COVID-19 Pandemic on Alcohol-related Liver Disease: A Modelling Study",
+    "rel_date": "2021-03-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.18.21253887",
+    "rel_abs": "ObjectivesThe burden of alcohol-related liver disease (ALD) is surging in the US. There is evidence that alcohol consumption increased during the early periods of the coronavirus disease-2019 (COVID-19) pandemic. We describe the impact of increased alcohol consumption on alcohol-related liver disease.\n\nDesignMicrosimulation model\n\nSettingModel parameters estimated from publicly available data sources, including national surveys on drug and alcohol use and published studies informing the impact of alcohol consumption on ALD severity.\n\nParticipantsUS residents\n\nMethodsWe extended a previously validated microsimulation model that estimated the short- and long-term effect of increased drinking during the COVID-19 pandemic in individuals in the US born between 1950-2012. We modelled short- and long-term outcomes of current drinking patterns during COVID-19 (status quo) using survey data of changes in alcohol consumption in a nationally representative sample between February and April 2020. We compared these outcomes with a counter-factual scenario wherein no COVID-19 occurs, and drinking patterns do not change. Reported outcomes are for individuals aged 18-65.\n\nMain outcome measuresALD-related deaths inclusive of HCC mortality, the prevalence and incidence of decompensated cirrhosis and hepatocellular carcinoma, and disability-adjusted life-years (DALYs)\n\nResultsIncreases in alcohol consumption during 2020 due to the COVID-19 pandemic are estimated to result in to 8,200 [95% UI 7,700 - 8,700] additional ALD-related deaths (1% increase compared with the counter-factual scenario), 17,100 [95% UI 16,100 - 18,200] cases of decompensated cirrhosis (2% increase) and 1,100 [95% UI 1,100 - 1,200] cases of HCC (1% increase) between 2020 and 2040. Between 2020 and 2023, alcohol consumption changes due to COVID-19 will lead to 100 [100-200] additional deaths and 2,200 [2,200-2,300] additional decompensations in patients suffering from alcohol-related liver disease.\n\nConclusionsA short-term increase in alcohol consumption during the COVID-19 pandemic can substantially increase long-term ALD-related morbidity and mortality. Our findings highlight the need for individuals and policymakers to make informed decisions to mitigate the impact of high-risk alcohol drinking in the US.\n\nSummary Box\"O_ST_ABSWhat is already known on this topicC_ST_ABSO_LIThe impact of an increase in alcohol consumption during coronavirus disease 2019 (COVID-19) on drinking trajectory changes and alcohol-related liver diseases is not known.\nC_LIO_LIStudies have reported increases in hospital admissions for alcohol-related liver disease or pancreatitis potentially related to COVID-19, increases in alcohol consumption, and exacerbation of pre-existing liver injury, though limited evidence exists for the long-term effect of increased drinking on alcohol-related liver cirrhosis and liver cancer in the USA.\nC_LI\n\nAdded value of this studyO_LIOur study provides new data on liver disease morbidity and mortality associated with increased consumption of alcohol during the COVID-19 pandemic.\nC_LIO_LIOur study suggests that drinking changes associated with the COVID-19 pandemic it is expected to lead to increases in both mortality and morbidity in the long term. to 8,200 additional ALD-related deaths, 17,100 cases of decompensated cirrhosis, and 1,100 cases of HCC between 2020 and 2040 2\nC_LI",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Jovan Julien",
+        "author_inst": "Georgia Institute of Technology, Massachusetts General Hospital"
+      },
+      {
+        "author_name": "Turgay Ayer",
+        "author_inst": "Department of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, GA"
+      },
+      {
+        "author_name": "Elliot Tapper",
+        "author_inst": "Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI"
+      },
+      {
+        "author_name": "Carolina Barbosa",
+        "author_inst": "RTI International, Research Triangle Park, NC"
+      },
+      {
+        "author_name": "William Dowd",
+        "author_inst": "RTI International, Research Triangle Park, NC"
+      },
+      {
+        "author_name": "Jagpreet Chhatwal",
+        "author_inst": "Harvard Medical School, Massachusetts General Hospital"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "gastroenterology"
+  },
   {
     "rel_doi": "10.1101/2021.03.18.21253902",
     "rel_title": "Smoking and Vaping Among a National Sample of U.S. Adults During the COVID-19 Pandemic",
@@ -854856,97 +853307,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.03.16.21253770",
-    "rel_title": "Accuracy of Computable Phenotyping Approaches for SARS-CoV-2 Infection and COVID-19 Hospitalizations from the Electronic Health Record",
-    "rel_date": "2021-03-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.16.21253770",
-    "rel_abs": "ObjectiveReal-world data have been critical for rapid-knowledge generation throughout the COVID-19 pandemic. To ensure high-quality results are delivered to guide clinical decision making and the public health response, as well as characterize the response to interventions, it is essential to establish the accuracy of COVID-19 case definitions derived from administrative data to identify infections and hospitalizations.\n\nMethodsElectronic Health Record (EHR) data were obtained from the clinical data warehouse of the Yale New Haven Health System (Yale, primary site) and 3 hospital systems of the Mayo Clinic (validation site). Detailed characteristics on demographics, diagnoses, and laboratory results were obtained for all patients with either a positive SARS-CoV-2 PCR or antigen test or ICD-10 diagnosis of COVID-19 (U07.1) between April 1, 2020 and March 1, 2021. Various computable phenotype definitions were evaluated for their accuracy to identify SARS-CoV-2 infection and COVID-19 hospitalizations.\n\nResultsOf the 69,423 individuals with either a diagnosis code or a laboratory diagnosis of a SARS-CoV-2 infection at Yale, 61,023 had a principal or a secondary diagnosis code for COVID-19 and 50,355 had a positive SARS-CoV-2 test. Among those with a positive laboratory test, 38,506 (76.5%) and 3449 (6.8%) had a principal and secondary diagnosis code of COVID-19, respectively, while 8400 (16.7%) had no COVID-19 diagnosis. Moreover, of the 61,023 patients with a COVID-19 diagnosis code, 19,068 (31.2%) did not have a positive laboratory test for SARS-CoV-2 in the EHR. Of the 20 cases randomly sampled from this latter group for manual review, all had a COVID-19 diagnosis code related to asymptomatic testing with negative subsequent test results. The positive predictive value (precision) and sensitivity (recall) of a COVID-19 diagnosis in the medical record for a documented positive SARS-CoV-2 test were 68.8% and 83.3%, respectively. Among 5,109 patients who were hospitalized with a principal diagnosis of COVID-19, 4843 (94.8%) had a positive SARS-CoV-2 test within the 2 weeks preceding hospital admission or during hospitalization. In addition, 789 hospitalizations had a secondary diagnosis of COVID-19, of which 446 (56.5%) had a principal diagnosis consistent with severe clinical manifestation of COVID-19 (e.g., sepsis or respiratory failure). Compared with the cohort that had a principal diagnosis of COVID-19, those with a secondary diagnosis had a more than 2-fold higher in-hospital mortality rate (13.2% vs 28.0%, P<0.001). In the validation sample at Mayo Clinic, diagnosis codes more consistently identified SARS-CoV-2 infection (precision of 95%) but had lower recall (63.5%) with substantial variation across the 3 Mayo Clinic sites. Similar to Yale, diagnosis codes consistently identified COVID-19 hospitalizations at Mayo, with hospitalizations defined by secondary diagnosis code with 2-fold higher in-hospital mortality compared to those with a primary diagnosis of COVID-19.\n\nConclusionsCOVID-19 diagnosis codes misclassified the SARS-CoV-2 infection status of many people, with implications for clinical research and epidemiological surveillance. Moreover, the codes had different performance across two academic health systems and identified groups with different risks of mortality. Real-world data from the EHR can be used to in conjunction with diagnosis codes to improve the identification of people infected with SARS-CoV-2.",
-    "rel_num_authors": 19,
-    "rel_authors": [
-      {
-        "author_name": "Rohan Khera",
-        "author_inst": "Yale School of Medicine"
-      },
-      {
-        "author_name": "Bobak Mortazavi",
-        "author_inst": "Texas A&M University"
-      },
-      {
-        "author_name": "Veer Sangha",
-        "author_inst": "Yale University"
-      },
-      {
-        "author_name": "Frederick Warner",
-        "author_inst": "Yale School of Medicine"
-      },
-      {
-        "author_name": "H Patrick Young",
-        "author_inst": "Yale School of Medicine"
-      },
-      {
-        "author_name": "Joseph S Ross",
-        "author_inst": "Yale School of Medicine"
-      },
-      {
-        "author_name": "Nilay D Shah",
-        "author_inst": "Mayo Clinic"
-      },
-      {
-        "author_name": "Elitza S Theel",
-        "author_inst": "Mayo Clinic"
-      },
-      {
-        "author_name": "William G Jenkinson",
-        "author_inst": "Mayo Clinic"
-      },
-      {
-        "author_name": "Camille A Knepper",
-        "author_inst": "Mayo Clinic"
-      },
-      {
-        "author_name": "Karen Wang",
-        "author_inst": "Yale School of Medicine"
-      },
-      {
-        "author_name": "David R Peaper",
-        "author_inst": "Yale School of Medicine"
-      },
-      {
-        "author_name": "Richard A Martinello",
-        "author_inst": "Yale School of Medicine"
-      },
-      {
-        "author_name": "Cynthia A Brandt",
-        "author_inst": "Yale School of Medicine"
-      },
-      {
-        "author_name": "Zhenqiu Lin",
-        "author_inst": "Yale School of Medicine"
-      },
-      {
-        "author_name": "Albert I Ko",
-        "author_inst": "Yale University School of Public Health"
-      },
-      {
-        "author_name": "Harlan M Krumholz",
-        "author_inst": "Yale School of Medicine"
-      },
-      {
-        "author_name": "Benjamin D Pollock",
-        "author_inst": "Mayo Clinic"
-      },
-      {
-        "author_name": "Wade L Schulz",
-        "author_inst": "Yale School of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health informatics"
-  },
   {
     "rel_doi": "10.1101/2021.03.17.21253739",
     "rel_title": "Adapting French COVID-19 vaccination campaign duration to variant dissemination",
@@ -855285,6 +853645,85 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.03.19.21253889",
+    "rel_title": "Risk of reinfection after seroconversion to SARS-CoV-2: A population-based propensity-score matched cohort study",
+    "rel_date": "2021-03-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253889",
+    "rel_abs": "ImportanceSerological assays detecting specific IgG antibodies generated against the Spike protein following Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection are being widely deployed in research studies and clinical practice. However, the duration and the effectiveness of the protection conferred by the immune response against future infection remains to be assessed in a large population.\n\nObjectiveTo estimate the incidence of newly acquired SARS-CoV-2 infections in seropositive individuals from a population-based sample as compared to seronegative controls.\n\nDesignRetrospective longitudinal propensity-score matched cohort study.\n\nSettingA seroprevalence survey including a population-based representative sample of the population from the canton of Geneva (Switzerland) was conducted between April and June 2020, immediately after the first pandemic wave. Each individual included in the seroprevalence survey was linked to a state centralized registry compiling virologically confirmed SARS-CoV-2 infections since the beginning of the pandemic.\n\nParticipantsParticipants aged twelve years old and over, who developed anti-spike IgG antibodies were matched one-to-two to seronegative controls, using a propensity-score including age, gender, immunodeficiency, body mass index, smoking status and education level.\n\nExposureSARS-CoV-2 seropositivity.\n\nMain outcomes and measuresOur primary outcome was virologically confirmed SARS-CoV-2 infections which occurred from serological status assessment in April-June 2020 to the end of the second pandemic wave (January 2021). Additionally, incidence of infections, rate of testing and proportion of positive tests were analysed.\n\nResultsAmong 8344 serosurvey participants, 498 seropositive individuals were selected and matched with 996 seronegative controls. After a mean follow-up of 35.6 (Standard Deviation, SD: 3.2) weeks, 7 out of 498 (1.4%) seropositive subjects had a positive SARS-CoV-2 test, of which 5 (1.0%) were considered as reinfections. By contrast, infection rate was significantly higher in seronegative individuals (15.5%, 154/996) during a similar mean follow-up of 34.7 (SD 3.2) weeks, corresponding to a 94% (95%CI 86% to 98%, P<0.001) reduction in the hazard of having a positive SARS-CoV-2 test for seropositive subjects.\n\nConclusions and relevanceSeroconversion after SARS-CoV-2 infection confers protection to successive viral contamination lasting at least 8 months. These findings could help global health authorities establishing priority for vaccine allocation.\n\nKey points\n\nQuestionDo SARS-CoV-2 antibodies confer protection against future infection?\n\nFindingsIn this retrospective matched cohort study nested in a representative sample of the general population of Geneva, Switzerland, we observed a 94% reduction in the hazard of being infected among participants with antibodies against SARS-CoV-2, when compared to seronegative controls, >8 months after initial serology assessment.\n\nMeaningSeroconversion to SARS-CoV-2 is associated with a large and sustained protection against reinfection.",
+    "rel_num_authors": 16,
+    "rel_authors": [
+      {
+        "author_name": "Antonio Leidi",
+        "author_inst": "Geneva University Hospitals"
+      },
+      {
+        "author_name": "Flora Koegler",
+        "author_inst": "Geneva University Hospitals"
+      },
+      {
+        "author_name": "Roxane Dumont",
+        "author_inst": "Geneva University Hospitals"
+      },
+      {
+        "author_name": "Richard Dubos",
+        "author_inst": "Geneva University Hospitals"
+      },
+      {
+        "author_name": "Maria-Eugenia Zaballa",
+        "author_inst": "Geneva University Hospitals"
+      },
+      {
+        "author_name": "Giovanni Piumatti",
+        "author_inst": "Geneva University Hospitals"
+      },
+      {
+        "author_name": "Matteo Coen",
+        "author_inst": "Geneva University Hospitals"
+      },
+      {
+        "author_name": "Amandine Berner",
+        "author_inst": "Geneva University Hospitals"
+      },
+      {
+        "author_name": "Pauline Darbellay Farhoumand",
+        "author_inst": "Geneva University Hospitals"
+      },
+      {
+        "author_name": "Pauline Vetter",
+        "author_inst": "Geneva University Hospitals"
+      },
+      {
+        "author_name": "Nicolas Vuilleumier",
+        "author_inst": "Geneva University Hospitals"
+      },
+      {
+        "author_name": "Laurent Kaiser",
+        "author_inst": "University of Geneva Hospitals"
+      },
+      {
+        "author_name": "Delphine Courvoisier",
+        "author_inst": "General Directorate of Health, Geneva, Switzerland"
+      },
+      {
+        "author_name": "Andrew Azman",
+        "author_inst": "Geneva University Hospitals"
+      },
+      {
+        "author_name": "Idris Guessous",
+        "author_inst": "Geneva University Hospitals"
+      },
+      {
+        "author_name": "Silvia Stringhini",
+        "author_inst": "Geneva University Hospitals"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.03.17.21253853",
     "rel_title": "Modelling the impact of rapid tests, tracing and distancing in lower-income countries suggest optimal policies varies with rural-urban settings",
@@ -856390,29 +854829,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.03.16.21253684",
-    "rel_title": "Long lockdowns and rainy days: Modeling the interactive roles of weather, behavior, and restrictions in COVID-19 transmission in the Netherlands",
-    "rel_date": "2021-03-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.16.21253684",
-    "rel_abs": "Extant research on the role of weather in COVID-19 has produced ambiguous results and much methodological debate. Following advice emerging from this methodological debate, we take a step further in modeling effects of weather on COVID-19 spread by including interactions between weather, behavior, baseline cases, and restrictions in our model. Our model was based on secondary infection, hospitalization, restriction, weather, and mobility data per day nested with safety region in the Netherlands. Our findings show significant but inconsistent interactions. The robust effects of weather on COVID-19 spread persisted over and above these interactions, highlighting the need to account for weather with nuance and caution in public policy, communication, and forecasting.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Ondrej Mitas",
-        "author_inst": "Breda University of Applied Sciences"
-      },
-      {
-        "author_name": "Alinda Kokkinou",
-        "author_inst": "Avans University of Applied Sciences"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.03.19.21253964",
     "rel_title": "Longitudinal assessment of diagnostic test performance over the course of acute SARS-CoV-2 infection",
@@ -856847,6 +855263,61 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2021.03.19.435740",
+    "rel_title": "The inhibitory effects of toothpaste and mouthwash ingredients on the interaction between the SARS-CoV-2 spike protein and ACE2, and the protease activity of TMPRSS2, in vitro",
+    "rel_date": "2021-03-19",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.19.435740",
+    "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters host cells when the viral spike protein is cleaved by transmembrane protease serine 2 (TMPRSS2) after binding to the host angiotensin-converting enzyme 2 (ACE2). Since ACE2 and TMPRSS2 are expressed in the mucosa of the tongue and gingiva, the oral cavity seems like it is an entry point for SARS-CoV-2. Daily oral care using mouthwash seems to play an important role in preventing SARS-CoV-2 infection. However, the relationship between daily oral care and the mechanisms of virus entry into host cells is unclear. In this study, we evaluated the inhibitory effects of ingredients that are generally contained in toothpaste and mouthwash on the interaction between the spike protein and ACE2 and on the serine protease activity of TMPRSS2 using an enzyme-linked immunosorbent assay and in vitro enzyme assay, respectively. Both assays detected inhibitory effects of sodium tetradecene sulfonate, sodium N-lauroyl-N-methyltaurate, sodium N-lauroylsarcosinate, sodium dodecyl sulfate, and copper gluconate. Molecular docking simulations suggested that these ingredients could bind to the inhibitor-binding site of ACE2. In addition, tranexamic acid and 6-aminohexanoic acid, which act as serine protease inhibitors, exerted inhibitory effects on TMPRSS2 protease activity. Further experimental and clinical studies are needed to further elucidate these mechanisms. Our findings support the possibility that toothpaste and mouthwash contain ingredients that inhibit SARS-CoV-2 infection.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Riho Tateyama-Makino",
+        "author_inst": "Research & Development Headquarters, Lion Corporation, Tokyo, Japan"
+      },
+      {
+        "author_name": "Mari Abe-Yutori",
+        "author_inst": "Research & Development Headquarters, Lion Corporation, Tokyo, Japan"
+      },
+      {
+        "author_name": "Taku Iwamoto",
+        "author_inst": "Research & Development Headquarters, Lion Corporation, Tokyo, Japan"
+      },
+      {
+        "author_name": "Kota Tsutsumi",
+        "author_inst": "Research & Development Headquarters, Lion Corporation, Tokyo, Japan"
+      },
+      {
+        "author_name": "Motonori Tsuji",
+        "author_inst": "Institute of Molecular Function, Saitama, Japan"
+      },
+      {
+        "author_name": "Satoru Morishita",
+        "author_inst": "Research & Development Headquarters, Lion Corporation, Tokyo, Japan"
+      },
+      {
+        "author_name": "Kei Kurita",
+        "author_inst": "Research & Development Headquarters, Lion Corporation, Tokyo, Japan"
+      },
+      {
+        "author_name": "Yukio Yamamoto",
+        "author_inst": "Research & Development Headquarters, Lion Corporation, Tokyo, Japan"
+      },
+      {
+        "author_name": "Eiji Nishinaga",
+        "author_inst": "Research & Development Headquarters, Lion Corporation, Tokyo, Japan"
+      },
+      {
+        "author_name": "Keiichi Tsukinoki",
+        "author_inst": "Division of Environmental Pathology, Department of Oral Science, Kanagawa Dental University, Kanagawa, Japan"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "molecular biology"
+  },
   {
     "rel_doi": "10.1101/2021.03.19.435959",
     "rel_title": "Common dandelion (Taraxacum officinale) efficiently blocks the interaction between ACE2 cell surface receptor and SARS-CoV-2 spike protein D614, mutants D614G, N501Y, K417N and E484K in vitro",
@@ -858372,25 +856843,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.03.15.21253667",
-    "rel_title": "Age specific COVID-19 undercount in Spain from the regional breakdown of 52-week accumulated mortality rates",
-    "rel_date": "2021-03-17",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.15.21253667",
-    "rel_abs": "Spanish NUTS3 region records of age specific weekly deaths since the year 2020, records of age specific COVID-19 deaths and age specific population since the year 2020 are used to estimate first age specific all-cause death rates and age specific COVID-19 undercount.\n\nResults shows a statistically significant impact of the pandemic in excess deaths for population aged 40 and elder. Statistically significant COVID-19 undercount is identified only for population aged 80 and elder. Very likely this is the result of the impact of the pandemic in institutionalized population at the early stages of the pandemic.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Jose Maria Martin-Olalla",
-        "author_inst": "Universidad de Sevilla"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.03.14.21253561",
     "rel_title": "Female gender and knowing a person positive for COVID-19 significantly increases fear levels in the Cuban population",
@@ -858653,6 +857105,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
+  {
+    "rel_doi": "10.1101/2021.03.15.21253581",
+    "rel_title": "Tocilizumab Effect in COVID-19 Hospitalized Patients: A Systematic Review and Meta-Analysis of Randomized Control Trials",
+    "rel_date": "2021-03-17",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.15.21253581",
+    "rel_abs": "Since the emergence of the first cases of COVID-19 viral pneumonia late 2019 several studies evaluated the benefits of different treatment modalities. Early in the pandemic, the interleukin 6 (IL-6) receptor antibody Tocilizumab was considered in view of the cytokine release syndrome associated with COVID-19 infection. Several early observational studies showed beneficial effect of treatment with Tocilizumab on mortality, however, results from well-designed randomized clinical trials (RCT) were contradicting.\n\nObjectivesTo perform a systematic literature review and meta-analysis of RCTs utilizing Tocilizumab in the treatment of COVID-19 pneumonia, with in-hospital mortality as a primary objective, while secondary objectives included composite outcome of mortality, intubation, or ICU admission, another secondary outcome was super added infection.\n\nMethodThis was a random effects model (DerSimonian and Laird) model of relative risk (RR), along with corresponding 95% confidence intervals, p values, and forest plots of both primary and secondary outcomes. A fixed effect sensitivity test was performed for the primary outcome, in addition to subgroup and meta-regression analyses with predefined criteria.\n\nResultsThe primary outcome of mortality showed statistically insignificant reduction of mortality with Tocilizumab (RR = 0.9, 95% CI: 0.8 - 1.01; p = 0.09) although with an unmistakable apparent clinical benefit. There was a significant reduction in the RR of the secondary composite outcome (RR = 0.83, 95% CI: 0.76 - 0.9; p < 0.001), and no difference between groups in super-added infection (RR = 0.77, 95% CI: 0.51 - 1.19; p = 0.24). Treatment protocol allowing a second dose was the only significant predictor of improved mortality in the meta-regression analysis. Certainty of evidence was reduced to moderate for the primary outcome and the secondary outcome of clinical deterioration, while it was reduced to low for the secondary outcome of super-added infection.\n\nConclusionModerate certainty of evidence suggest no statistically significant improvement of 28-30 day all-cause mortality of hospitalized COVID-19 patients treated with TCZ, although there may be clinically important value. Moderate certainty of evidence suggest lowered relative risk of a composite outcome of death or clinical deterioration, while, low grade evidence indicate no increase in the risk of super-added infection associated with TCZ treatment. A protocol allowing two doses of TCZ shows evidence of improved mortality as compared to a strictly single dose protocol.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Waleed Tharwat Aletreby",
+        "author_inst": "King Saud Medical City"
+      },
+      {
+        "author_name": "Basheer Abdulrahman",
+        "author_inst": "King Saud Medical City"
+      },
+      {
+        "author_name": "Ahmed Fouad Mady",
+        "author_inst": "King Saud Medical City. Faculty of Medicine Tanta University."
+      },
+      {
+        "author_name": "Alfateh Mohammed Noor",
+        "author_inst": "King Saud Medical City"
+      },
+      {
+        "author_name": "Mohammed H Lhmdi",
+        "author_inst": "King Saud Medical City"
+      },
+      {
+        "author_name": "Fahad Faqihi",
+        "author_inst": "King Saud Medical City"
+      },
+      {
+        "author_name": "Abdulrahman M Alharthy",
+        "author_inst": "King Saud Medical City"
+      },
+      {
+        "author_name": "Mohammed A Al-Odat",
+        "author_inst": "King Saud Medical City"
+      },
+      {
+        "author_name": "Dimitrios Karakitsos",
+        "author_inst": "King Saud Medical City, Critical Care Department, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA. \tDepartment of Medicine, Sou"
+      },
+      {
+        "author_name": "Ziad Memish",
+        "author_inst": "King saud Medical City,  \tHubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA. \tCollege of Medicine, Alfaisa"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.03.15.21253586",
     "rel_title": "Rapid base-specific calling of SARS-CoV-2 variants of concern using combined RT-PCR melting curve screening and SIRPH technology",
@@ -860042,121 +858549,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2021.03.17.435581",
-    "rel_title": "Longitudinal characterization of humoral and cellular immunity in hospitalized COVID-19 patients reveal immune persistence up to 9 months after infection",
-    "rel_date": "2021-03-17",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.17.435581",
-    "rel_abs": "BackgroundInsights into early, specific humoral and cellular responses to infection with SARS-CoV-2, as well as the persistence and magnitude of resulting immune memory is important amidst the ongoing pandemic. The combination of humoral and cellular immunity will most likely contribute to protection from reinfection or severe disease.\n\nMethodsHere, we conducted a longitudinal study on hospitalized moderate and severe COVID-19 patients from the acute phase of disease into convalescence at five- and nine-months post symptom onset. Utilizing flow cytometry, serological assays as well as B cell and T cell FluoroSpot assays, we assessed the magnitude and specificity of humoral and cellular immune memory during and after human SARS-CoV-2 infection.\n\nFindingsDuring acute COVID-19, we observed an increase in germinal center activity, a substantial expansion of antibodysecreting cells, and the generation of SARS-CoV-2-neutralizing antibodies. Despite gradually decreasing antibody levels, we show persistent, neutralizing antibody titers as well as robust specific memory B cell responses and polyfunctional T cell responses at five- and nine-months after symptom onset in both moderate and severe COVID-19 patients. Long-term SARS-CoV-2 specific responses were marked by preferential targeting of spike over nucleocapsid protein.\n\nConclusionsOur findings describe the initiation and, importantly, persistence of cellular and humoral SARS-CoV-2 specific immunological memory in hospitalized COVID-19 patients long after recovery, likely contributing towards protection against reinfection.",
-    "rel_num_authors": 25,
-    "rel_authors": [
-      {
-        "author_name": "John Tyler Sandberg",
-        "author_inst": "Center for Infectious Medicine, ANA Futura, Department of Medicine Huddinge, Karolinska Institutet, 171 77 Stockholm, Sweden."
-      },
-      {
-        "author_name": "Renata Varnait\u0117",
-        "author_inst": "Center for Infectious Medicine, ANA Futura, Department of Medicine Huddinge, Karolinska Institutet, 171 77 Stockholm, Sweden"
-      },
-      {
-        "author_name": "Wanda Christ",
-        "author_inst": "Center for Infectious Medicine, ANA Futura, Department of Medicine Huddinge, Karolinska Institutet, 171 77 Stockholm, Sweden"
-      },
-      {
-        "author_name": "Puran Chen",
-        "author_inst": "Center for Infectious Medicine, ANA Futura, Department of Medicine Huddinge, Karolinska Institutet, 171 77 Stockholm, Sweden"
-      },
-      {
-        "author_name": "Jagadeeswara Rao Muvva",
-        "author_inst": "Center for Infectious Medicine, ANA Futura, Department of Medicine Huddinge, Karolinska Institutet, 171 77 Stockholm, Sweden"
-      },
-      {
-        "author_name": "Kimia T Maleki",
-        "author_inst": "Center for Infectious Medicine, ANA Futura, Department of Medicine Huddinge, Karolinska Institutet, 171 77 Stockholm, Sweden"
-      },
-      {
-        "author_name": "Marina Garc\u00eda",
-        "author_inst": "Center for Infectious Medicine, ANA Futura, Department of Medicine Huddinge, Karolinska Institutet, 171 77 Stockholm, Sweden"
-      },
-      {
-        "author_name": "Majda Dzidic",
-        "author_inst": "Center for Infectious Medicine, ANA Futura, Department of Medicine Huddinge, Karolinska Institutet, 171 77 Stockholm, Sweden"
-      },
-      {
-        "author_name": "Elin Folkesson",
-        "author_inst": "Department of Infectious Diseases, Karolinska University Hospital, 171 76, Stockholm, Sweden;                                               Department of Medici"
-      },
-      {
-        "author_name": "Magdalena Skagerberg",
-        "author_inst": "Department of Infectious Diseases, Karolinska University Hospital, 171 76, Stockholm, Sweden; Department of Medicine Huddinge, Karolinska Institutet, 171 77, St"
-      },
-      {
-        "author_name": "Gustaf Ahl\u00e9n",
-        "author_inst": "Division of Clinical Microbiology, ANA Futura, Department of Laboratory Medicine, Karolinska Institutet, 171 77, Stockholm, Sweden"
-      },
-      {
-        "author_name": "Lars Frelin",
-        "author_inst": "Division of Clinical Microbiology, ANA Futura, Department of Laboratory Medicine, Karolinska Institutet, 171 77, Stockholm, Sweden"
-      },
-      {
-        "author_name": "Matti S\u00e4llberg",
-        "author_inst": "Division of Clinical Microbiology, ANA Futura, Department of Laboratory Medicine, Karolinska Institutet, 171 77, Stockholm, Sweden"
-      },
-      {
-        "author_name": "- The Karolinska COVID-19 Study Group",
-        "author_inst": "-"
-      },
-      {
-        "author_name": "Lars I Eriksson",
-        "author_inst": "Function Perioperative Medicine and Intensive Care, Karolinska University Hospital, 171 76, Stockholm, Sweden; Department of Physiology and Pharmacology, Karoli"
-      },
-      {
-        "author_name": "Olav Rooyackers",
-        "author_inst": "Function Perioperative Medicine and Intensive Care, Karolinska University Hospital, 171 76, Stockholm, Sweden; Department of Clinical Intervention and Technolog"
-      },
-      {
-        "author_name": "Anders S\u00f6nnerborg",
-        "author_inst": "Department of Infectious Diseases, Karolinska University Hospital, 171 76, Stockholm, Sweden; Department of Medicine Huddinge, Karolinska Institutet, 171 77, St"
-      },
-      {
-        "author_name": "Marcus Buggert",
-        "author_inst": "Center for Infectious Medicine, ANA Futura, Department of Medicine Huddinge, Karolinska Institutet, 171 77 Stockholm, Sweden"
-      },
-      {
-        "author_name": "Niklas K Bj\u00f6rkstr\u00f6m",
-        "author_inst": "Center for Infectious Medicine, ANA Futura, Department of Medicine Huddinge, Karolinska Institutet, 171 77 Stockholm, Sweden; Department of Clinical Microbiolog"
-      },
-      {
-        "author_name": "Soo Aleman",
-        "author_inst": "Department of Infectious Diseases, Karolinska University Hospital, 171 76, Stockholm, Sweden; Department of Medicine Huddinge, Karolinska Institutet, 171 77, St"
-      },
-      {
-        "author_name": "Kristoffer Str\u00e5lin",
-        "author_inst": "Department of Infectious Diseases, Karolinska University Hospital, 171 76, Stockholm, Sweden; Department of Medicine Huddinge, Karolinska Institutet, 171 77, St"
-      },
-      {
-        "author_name": "Jonas Klingstr\u00f6m",
-        "author_inst": "Center for Infectious Medicine, ANA Futura, Department of Medicine Huddinge, Karolinska Institutet, 171 77 Stockholm, Sweden"
-      },
-      {
-        "author_name": "Hans-Gustaf Ljunggren",
-        "author_inst": "Center for Infectious Medicine, ANA Futura, Department of Medicine Huddinge, Karolinska Institutet, 171 77 Stockholm, Sweden"
-      },
-      {
-        "author_name": "Kim Blom",
-        "author_inst": "Center for Infectious Medicine, ANA Futura, Department of Medicine Huddinge, Karolinska Institutet, 171 77 Stockholm, Sweden"
-      },
-      {
-        "author_name": "Sara Gredmark-Russ",
-        "author_inst": "Center for Infectious Medicine, ANA Futura, Department of Medicine Huddinge, Karolinska Institutet, 171 77 Stockholm, Sweden; Department of Infectious Diseases,"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2021.03.17.435637",
     "rel_title": "Epigallocatechin Gallate from Green Tea Effectively Blocks Infection of SARS-CoV-2 and New Variants by Inhibiting Spike Binding to ACE2 Receptor",
@@ -860675,6 +859067,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "oncology"
   },
+  {
+    "rel_doi": "10.1101/2021.03.15.21253598",
+    "rel_title": "U.S. adolescents' mental health and COVID-19-related changes in technology use, Fall 2020",
+    "rel_date": "2021-03-17",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.15.21253598",
+    "rel_abs": "Preliminary reports suggest that during COVID-19, adolescents mental health has worsened while technology and social media use has increased. Much data derives from early in the pandemic, when schools were uniformly remote and personal/family stressors related to the pandemic were limited. This cross-sectional study, conducted during Fall 2020, examines the correlation between mental wellbeing and COVID-19-related changes in technology use, along with influence of COVID-19-related stressors, school status (in-person versus remote), and social media use for coping purposes, among 978 U.S. adolescents. Results suggest self-reported daily social media and technology use increased significantly from prior to COVID-19 through Fall 2020. Increased social media use was significantly associated with higher levels of anxiety and depressive symptoms regardless of other theoretical moderators or confounders of mental health (e.g., demographics, school status, importance of technology, COVID-19-related stress). Despite literature suggesting that remote learning may result in adverse mental health outcomes, we did not find local school reopening to be associated with current depressive/anxiety symptoms, nor with COVID-19-related increases in technology use. Self-reported use of social media for coping purposes moderated the association between increased social media use and mental health symptoms; in other words, some social media use may have positive effects. Although much prior research has focused on social media use as a marker of stress, we also found that increased video gaming and TV/movie watching were also associated with internalizing symptoms, in accordance with others' work. Future research should explore in more granular detail what, if any, social media and technology use is protective during a pandemic, and for whom, to help tailor prevention efforts.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Taylor A Burke",
+        "author_inst": "Alpert Medical School of Brown University"
+      },
+      {
+        "author_name": "Emily R Kutok",
+        "author_inst": "Alpert Medical School of Brown University"
+      },
+      {
+        "author_name": "Shira Dunsiger",
+        "author_inst": "Brown University"
+      },
+      {
+        "author_name": "Nicole R Nugent",
+        "author_inst": "Brown University"
+      },
+      {
+        "author_name": "John V Patena",
+        "author_inst": "Alpert Medical School of Brown University"
+      },
+      {
+        "author_name": "Alison Riese",
+        "author_inst": "Alpert Medical School of Brown University"
+      },
+      {
+        "author_name": "Megan L Ranney",
+        "author_inst": "Alpert Medical School of Brown University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "psychiatry and clinical psychology"
+  },
   {
     "rel_doi": "10.1101/2021.03.15.21253574",
     "rel_title": "Understanding SARS-CoV-2 Infection and Dynamics with Long Term Wastewater based Epidemiological Surveillance",
@@ -862308,121 +860743,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "hiv aids"
   },
-  {
-    "rel_doi": "10.1101/2021.03.12.21252149",
-    "rel_title": "Durability of SARS-CoV-2-specific IgG responses in saliva for up to 8 months after infection",
-    "rel_date": "2021-03-15",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.12.21252149",
-    "rel_abs": "We evaluated the durability of IgG responses specific to SARS-CoV-2 nucleocapsid (N), receptor binding domain (RBD), and spike (S) antigens in saliva up to 8 months after RT-PCR-confirmed COVID-19 using a multiplex salivary assay. We estimated a half-life of 64 days (d) (95% CI: 49, 80 d) for N, 100 d for RBD (95% CI: 58, 141 d), and 148 d (95% CI: 62, 238 d) for S IgG responses in saliva, consistent with half-life estimates previously reported in blood. Saliva can serve as an alternative to blood to monitor humoral immune responses on a large scale following SARS-CoV-2 infection and vaccination for surveillance and assessment of population immunity.",
-    "rel_num_authors": 25,
-    "rel_authors": [
-      {
-        "author_name": "Pranay R. Randad",
-        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
-      },
-      {
-        "author_name": "Nora Pisanic",
-        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
-      },
-      {
-        "author_name": "Kate Kruczynski",
-        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
-      },
-      {
-        "author_name": "Tyrone Howard",
-        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
-      },
-      {
-        "author_name": "Magdielis Gregory Rivera",
-        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
-      },
-      {
-        "author_name": "Kristoffer Spicer",
-        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
-      },
-      {
-        "author_name": "Annukka A.R. Antar",
-        "author_inst": "Johns Hopkins University School of Medicine"
-      },
-      {
-        "author_name": "Tristan Penson",
-        "author_inst": "Johns Hopkins University School of Medicine"
-      },
-      {
-        "author_name": "David L. Thomas",
-        "author_inst": "Johns Hopkins University School of Medicine"
-      },
-      {
-        "author_name": "Andrew Pekosz",
-        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
-      },
-      {
-        "author_name": "Nelson Ndahiro",
-        "author_inst": "Johns Hopkins University Whiting School of Engineering"
-      },
-      {
-        "author_name": "Lateef Aliyu",
-        "author_inst": "Johns Hopkins University Whiting School of Engineering"
-      },
-      {
-        "author_name": "Michael J. Betenbaugh",
-        "author_inst": "Johns Hopkins University Whiting School of Engineering"
-      },
-      {
-        "author_name": "Hannah Manley",
-        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
-      },
-      {
-        "author_name": "Barbara Detrick",
-        "author_inst": "Johns Hopkins University School of Medicine"
-      },
-      {
-        "author_name": "Morgan Katz",
-        "author_inst": "Johns Hopkins University School of Medicine"
-      },
-      {
-        "author_name": "Sara Cosgrove",
-        "author_inst": "Johns Hopkins University School of Medicine"
-      },
-      {
-        "author_name": "Claire Rock",
-        "author_inst": "Johns Hopkins University School of Medicine"
-      },
-      {
-        "author_name": "Israel Zyskind",
-        "author_inst": "NYU Langone"
-      },
-      {
-        "author_name": "Jonathan I. Silverberg",
-        "author_inst": "George Washington University School of Medicine and Health Sciences"
-      },
-      {
-        "author_name": "Avi Z. Rosenberg",
-        "author_inst": "Johns Hopkins University School of Medicine"
-      },
-      {
-        "author_name": "Priya Duggal",
-        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
-      },
-      {
-        "author_name": "Yukari C. Manabe",
-        "author_inst": "Johns Hopkins University School of Medicine"
-      },
-      {
-        "author_name": "Matthew H. Collins",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Christopher D. Heaney",
-        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.03.12.435191",
     "rel_title": "A novel soluble ACE2 protein totally protects from lethal disease caused by SARS-CoV-2 infection",
@@ -862873,6 +861193,41 @@
     "type": "new results",
     "category": "biochemistry"
   },
+  {
+    "rel_doi": "10.1101/2021.03.14.435322",
+    "rel_title": "Effects of Mutations in the Receptor-Binding Domain of SARS-CoV-2 Spike on its Binding Affinity to ACE2 and Neutralizing Antibodies Revealed by Computational Analysis",
+    "rel_date": "2021-03-15",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.14.435322",
+    "rel_abs": "SARS-CoV-2 causing coronavirus disease 2019 (COVID-19) is responsible for one of the most deleterious pandemics of our time. The interaction between the ACE2 receptors at the surface of human cells and the viral Spike (S) protein triggers the infection making the receptor-binding domain (RBD) of the SARS-CoV-2 S-protein a focal target for the neutralizing antibodies (Abs). Despite the recent progress in the development and deployment of vaccines, the emergence of novel variants of SARS-CoV-2 insensitive to Abs produced in response to the vaccine administration and/or monoclonal ones represents upcoming jeopardy. Here, we assessed the possible effects of single and multiple mutations in the RBD of SARS-CoV-2 S-protein on its binding energy to various antibodies and the human ACE2 receptor. The performed computational analysis indicates that while single amino acid replacements in RBD may only cause partial impairment of the Abs binding, moreover, limited to specific epitopes, some variants of SARS-CoV-2 (with as few as 8 mutations), which are already present in the population, may potentially result in a much broader antigenic escape. We also identified a number of point mutations, which, in contrast to the majority of replacements, reduce RBD affinity to various antibodies without affecting its binding to ACE2. Overall, the results provide guidelines for further experimental studies aiming at the identification of the high-risk RBD mutations allowing for an antigenic escape.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Marine E Bozdaganyan",
+        "author_inst": "Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia; N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Scienc"
+      },
+      {
+        "author_name": "Olga S Sokolova",
+        "author_inst": "Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia; Biology Department, Shenzhen MSU-BIT University, Shenzhen, China"
+      },
+      {
+        "author_name": "Konstantin V Shaitan",
+        "author_inst": "Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia; N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Scienc"
+      },
+      {
+        "author_name": "Mikhail P Kirpichnikov",
+        "author_inst": "Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia"
+      },
+      {
+        "author_name": "Philipp S Orekhov",
+        "author_inst": "Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia;  Institute of Personalized Medicine, Sechenov University, Moscow, Russia"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "biophysics"
+  },
   {
     "rel_doi": "10.1101/2021.03.13.435222",
     "rel_title": "BNT162b2 mRNA COVID-19 vaccine induces antibodies of broader cross-reactivity than natural infection but recognition of mutant viruses is up to 10-fold reduced",
@@ -864802,77 +863157,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.03.13.21253510",
-    "rel_title": "Is there a serum proteome signature to predict mortality in severe COVID-19 patients?",
-    "rel_date": "2021-03-13",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.13.21253510",
-    "rel_abs": "Here we recorded serum proteome profiles of 33 COVID-19 patients admitted to respiratory and intensive care units because of respiratory failure. We received, for most patients, blood samples just after admission and at two more later timepoints. We focused on serum proteins different in abundance between the group of survivors and non-survivors and observed that a rather small panel of about a dozen proteins were significantly different in abundance between these two groups. The four structurally and functionally related type-3 cystatins AHSG, FETUB, HRG and KNG1 were all more abundant in the survivors. The family of inter--trypsin inhibitors, ITIH1, ITIH2, ITIH3 and ITIH4, were all found to be differentially abundant in between survivors and non-survivors, whereby ITIH1 and ITIH2 were more abundant in the survivor group and ITIH3 and ITIH4 more abundant in the non-survivors. ITIH1/ITIH2 and ITIH3/ITIH4 also did show opposite trends in protein abundance during disease progression. This panel of eight proteins, complemented with a few more, may represent a panel for mortality risk assessment and eventually even for treatment, by administration of exogenous proteins possibly aiding survival. Such administration is not unprecedented, as administration of exogenous inter--trypsin inhibitors is already used in the treatment of patients with severe sepsis and Kawasaki disease. The mortality risk panel defined here is in excellent agreement with findings in two recent COVID-19 serum proteomics studies on independent cohorts, supporting our findings. This panel may not be unique for COVID-19, as some of the proteins here annotated as mortality risk factors have previously been annotated as mortality markers in aging and in other diseases caused by different pathogens, including bacteria.",
-    "rel_num_authors": 14,
-    "rel_authors": [
-      {
-        "author_name": "Franziska Voellmy",
-        "author_inst": "Utrecht University"
-      },
-      {
-        "author_name": "Henk van den Toorn",
-        "author_inst": "Utrecht University"
-      },
-      {
-        "author_name": "Riccardo Zenezini Chiozzi",
-        "author_inst": "Utrecht University"
-      },
-      {
-        "author_name": "Ottavio Zucchetti",
-        "author_inst": "University of Ferrara"
-      },
-      {
-        "author_name": "Albetto Papi",
-        "author_inst": "University of Ferrara"
-      },
-      {
-        "author_name": "Carlo Alberto Volta",
-        "author_inst": "University of Ferrara"
-      },
-      {
-        "author_name": "Luisa Marracino",
-        "author_inst": "University of Ferrara"
-      },
-      {
-        "author_name": "Francesco Vieceli Dalla Sega",
-        "author_inst": "Maria Cecilia Hospital"
-      },
-      {
-        "author_name": "Francecsca Fortini",
-        "author_inst": "Maria Cecilia Hospital"
-      },
-      {
-        "author_name": "Gianluca Campo",
-        "author_inst": "University of Ferrara"
-      },
-      {
-        "author_name": "Marco Contoli",
-        "author_inst": "University of Ferrara"
-      },
-      {
-        "author_name": "Savino Spadaro",
-        "author_inst": "University of Ferrara"
-      },
-      {
-        "author_name": "Paola Rizzo",
-        "author_inst": "University of Ferrara"
-      },
-      {
-        "author_name": "Albert J.R. Heck",
-        "author_inst": "Utrecht University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.03.13.21253499",
     "rel_title": "Awake prone position in adult nonintubated patients with acute hypoxaemic respiratory failure secondary to COVID-19:A multi-centre feasibility randomized controlled trial",
@@ -865323,6 +863607,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
+  {
+    "rel_doi": "10.1101/2021.03.08.21252883",
+    "rel_title": "Outcome of Different Therapeutic Interventions in Mild COVID-19 Patients in a Single OPD Clinic of West Bengal: A Retrospective study",
+    "rel_date": "2021-03-12",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.08.21252883",
+    "rel_abs": "IntroductionWith over 87,273,380 cases being reported and 1,899,440 deaths worldwide as of 9th January 2021, Coronavirus disease 2019 (COVID-19) has become the worst-hit pandemic till date. Every day clinicians are bombarded with many new treatment options that claim to be better than the others.\n\nMaterials and methodsAfter screening the electronic database of COVID-19 patients retrospectively, 56 patients with mild COVID-19 infection matched the inclusion criteria and were divided into the four following groups - group having used Hydroxychloroquine (HCQ), group using doxycycline (DOX) + Ivermectin (IVR) combination, group receiving only azithromycin (AZ) and, group receiving only symptomatic treatment. The studys primary objective was to see Clinical response of well-being (CRWB) reporting time after initiating treatment onset between the four different treatment arms.\n\nResultsCRWB did not differ between the four groups receiving four different managements (p-value 0.846). There was significant correlation between blood levels of LDH (p-value 0.001), CRP (p-value 0.03) and D-dimer (p-value 0.04) with CRWB in IVR+DOX group and, between LDH (p-value 0.001), CRP (p-value 0.01) and age (p-value 0.035) with CRWB in the symptomatic management group.\n\nConclusionMild COVID-19 infection in patients having low-risk to progress can be managed symptomatically without any specific drug intervention.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Sayak Roy",
+        "author_inst": "Medica Superspeciality Hospital"
+      },
+      {
+        "author_name": "Shambo Samrat Samajdar",
+        "author_inst": "School of Tropical Medicine, Kolkata"
+      },
+      {
+        "author_name": "Santanu K Tripathi",
+        "author_inst": "School of Tropical Medicine, Kolkata; Dean (Academics) and Head, Dept of Pharmacology, Netaji Subhash Medical College & Hospital, Bihta, Patna"
+      },
+      {
+        "author_name": "Shatavisa Mukherjee",
+        "author_inst": "School of Tropical Medicine, Kolkata."
+      },
+      {
+        "author_name": "Kingshuk Bhattacharjee",
+        "author_inst": "Independent Biostatistician, Kolkata"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.03.08.21252784",
     "rel_title": "SARS-CoV-2 seroassay optimization and performance in a population with high background reactivity in Mali",
@@ -866712,57 +865031,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.03.09.21253204",
-    "rel_title": "Detection of SARS-CoV-2 lineage P.1 in patients from a region with exponentially increasing hospitalization rates in February 2021, Rio Grande do Sul, Southern Brazil",
-    "rel_date": "2021-03-12",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.09.21253204",
-    "rel_abs": "The emergence SARS-CoV-2 P.1 lineage has been coincidental with a rapid growth in hospitalization in the northern region of Brazil. An exponential growth of severe COVID-19 occurred in Rio Grande do Sul state, Southern Brazil in February-2021. Whole-genome sequencing revealed that the previously undetected P.1 lineage accounted for 88.9% of specimens collected from patients at a referral COVID-19 hospital. These findings raise concerns regarding a possible association between lineage P.1 and rapid growth in cases and hospitalizations.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Andreza Francisco Martins",
-        "author_inst": "Universidade Federal do Rio Grande do Sul"
-      },
-      {
-        "author_name": "Alexandre P. Zavascki",
-        "author_inst": "Universidade Federal do Rio Grande do Sul"
-      },
-      {
-        "author_name": "Priscila Lamb Wink",
-        "author_inst": "Hospital de Clinicas de Porto Alegre"
-      },
-      {
-        "author_name": "Fabiana Caroline Zempulski Volpato",
-        "author_inst": "Hospital de Clinicas de Porto Alegre"
-      },
-      {
-        "author_name": "Francielle Liz Monteiro",
-        "author_inst": "Hospital de Clinicas de Porto Alegre"
-      },
-      {
-        "author_name": "Clevia Rosset",
-        "author_inst": "Hospital de Clinicas de Porto Alegre"
-      },
-      {
-        "author_name": "Fernanda de-Paris",
-        "author_inst": "Hospital de Clinicas de Porto Alegre"
-      },
-      {
-        "author_name": "Alvaro Kruger Ramos",
-        "author_inst": "Universidade Federal do Rio Grande do Sul"
-      },
-      {
-        "author_name": "Afonso Luis Barth",
-        "author_inst": "Hospital de Clinicas de Porto Alegre"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.03.09.21253198",
     "rel_title": "Efficacy of SARS-CoV-2 Repeat Testing to Control Spread in Residential College Populations",
@@ -867197,6 +865465,169 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.03.09.21252822",
+    "rel_title": "Genomic epidemiology of SARS-CoV-2 in the United Arab Emirates reveals novel virus mutation, patterns of co-infection and tissue specific host responses",
+    "rel_date": "2021-03-12",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.09.21252822",
+    "rel_abs": "To unravel the source of SARS-CoV-2 introduction and the pattern of its spreading and evolution in the United Arab Emirates, we conducted meta-transcriptome sequencing of 1,067 nasopharyngeal swab samples collected between May 9th and Jun 29th, 2020 during the first peak of the local COVID-19 epidemic. We identified global clade distribution and eleven novel genetic variants that were almost absent in the rest of the world defined five subclades specific to the UAE viral population. Cross-settlement human-to-human transmission was related to the local business activity. Perhaps surprisingly, at least 5% of the population were co-infected by SARS-CoV-2 of multiple clades within the same host. We also discovered an enrichment of cytosine-to-uracil mutation among the viral population collected from the nasopharynx, that is different from the adenosine-to-inosine change previously reported in the bronchoalveolar lavage fluid samples and a previously unidentified upregulation of APOBEC4 expression in nasopharynx among infected patients, indicating the innate immune host response mediated by ADAR and APOBEC gene families could be tissue-specific. The genomic epidemiological and molecular biological knowledge reported here provides new insights for the SARS-CoV-2 evolution and transmission and points out future direction on host-pathogen interaction investigation.",
+    "rel_num_authors": 37,
+    "rel_authors": [
+      {
+        "author_name": "Rong Liu",
+        "author_inst": "BGI-Shenzhen, Shenzhen"
+      },
+      {
+        "author_name": "Pei Wu",
+        "author_inst": "BGI-Shenzhen, Shenzhen"
+      },
+      {
+        "author_name": "Pauline Ogrodzki",
+        "author_inst": "Group42 Healthcare, Abu Dhabi, United Arab Emirates"
+      },
+      {
+        "author_name": "Sally Mahmoud",
+        "author_inst": "Group42 Healthcare, Abu Dhabi, United Arab Emirates"
+      },
+      {
+        "author_name": "Ke Liang",
+        "author_inst": "MGI, BGI-Shenzhen, Shenzhen"
+      },
+      {
+        "author_name": "Pengjuan Liu",
+        "author_inst": "MGI, BGI-Shenzhen, Shenzhen"
+      },
+      {
+        "author_name": "Stephen S. Francis",
+        "author_inst": "Department of Neurological Surgery, University of California, San Francisco"
+      },
+      {
+        "author_name": "Hanif Khalak",
+        "author_inst": "Group42 Healthcare, Abu Dhabi, United Arab Emirates"
+      },
+      {
+        "author_name": "Denghui Liu",
+        "author_inst": "Laboratory of Health Intelligence, Huawei Technologies Co., Ltd"
+      },
+      {
+        "author_name": "Junhua Li",
+        "author_inst": "BGI-Shenzhen, Shenzhen"
+      },
+      {
+        "author_name": "Tao Ma",
+        "author_inst": "MGI, BGI-Shenzhen, Shenzhen"
+      },
+      {
+        "author_name": "Fang Chen",
+        "author_inst": "MGI, BGI-Shenzhen, Shenzhen"
+      },
+      {
+        "author_name": "Weibin Liu",
+        "author_inst": "BGI-Shenzhen, Shenzhen"
+      },
+      {
+        "author_name": "Xinyu Huang",
+        "author_inst": "MGI, BGI-Shenzhen, Shenzhen"
+      },
+      {
+        "author_name": "Wenjun He",
+        "author_inst": "Laboratory of Health Intelligence, Huawei Technologies Co., Ltd"
+      },
+      {
+        "author_name": "Zhaorong Yuan",
+        "author_inst": "Laboratory of Health Intelligence, Huawei Technologies Co., Ltd"
+      },
+      {
+        "author_name": "Nan Qiao",
+        "author_inst": "Laboratory of Health Intelligence, Huawei Technologies Co., Ltd"
+      },
+      {
+        "author_name": "Xin Meng",
+        "author_inst": "Laboratory of Health Intelligence, Huawei Technologies Co., Ltd"
+      },
+      {
+        "author_name": "Budoor Alqarni",
+        "author_inst": "Group42 Healthcare, Abu Dhabi, United Arab Emirates"
+      },
+      {
+        "author_name": "Javier Quilez",
+        "author_inst": "Group42 Healthcare, Abu Dhabi, United Arab Emirates"
+      },
+      {
+        "author_name": "Vinay Kusuma",
+        "author_inst": "Group42 Healthcare, Abu Dhabi, United Arab Emirates"
+      },
+      {
+        "author_name": "Long Lin",
+        "author_inst": "BGI-Shenzhen, Shenzhen"
+      },
+      {
+        "author_name": "Xin Jin",
+        "author_inst": "BGI-Shenzhen, Shenzhen"
+      },
+      {
+        "author_name": "Chongguang Yang",
+        "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven"
+      },
+      {
+        "author_name": "Xavier Anton",
+        "author_inst": "Group42 Healthcare, Abu Dhabi, United Arab Emirates"
+      },
+      {
+        "author_name": "Ashish Koshy",
+        "author_inst": "Group42 Healthcare, Abu Dhabi, United Arab Emirates"
+      },
+      {
+        "author_name": "Huanming Yang",
+        "author_inst": "BGI-Shenzhen, Shenzhen"
+      },
+      {
+        "author_name": "Xun Xu",
+        "author_inst": "BGI-Shenzhen, Shenzhen"
+      },
+      {
+        "author_name": "Jian Wang",
+        "author_inst": "BGI-Shenzhen, Shenzhen"
+      },
+      {
+        "author_name": "Peng Xiao",
+        "author_inst": "Group42 Healthcare, Abu Dhabi, United Arab Emirates"
+      },
+      {
+        "author_name": "Nawal Ahmed Mohamed Al Kaabi",
+        "author_inst": "SEHA, Abu Dhabi Health Services Co, Abu Dhabi, United Arab Emirates"
+      },
+      {
+        "author_name": "Mohammed Saifuddin Fasihuddin",
+        "author_inst": "SEHA, Abu Dhabi Health Services Co, Abu Dhabi, United Arab Emirates"
+      },
+      {
+        "author_name": "Francis Amirtharaj Selvaraj",
+        "author_inst": "SEHA, Abu Dhabi Health Services Co, Abu Dhabi, United Arab Emirates"
+      },
+      {
+        "author_name": "Stefan Weber",
+        "author_inst": "SEHA, Abu Dhabi Health Services Co, Abu Dhabi, United Arab Emirates"
+      },
+      {
+        "author_name": "Farida Ismail Al Hosani",
+        "author_inst": "Department of Health, Abu Dhabi, United Arab Emirates"
+      },
+      {
+        "author_name": "Siyang Liu",
+        "author_inst": "BGI-Shenzhen, Shenzhen"
+      },
+      {
+        "author_name": "Walid Abbas Zaher",
+        "author_inst": "Group42 Healthcare, Abu Dhabi, United Arab Emirates"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.03.09.21253216",
     "rel_title": "COVID-19: Optimal Allocation of Ventilator Supply under Uncertainty and Risk",
@@ -868346,77 +866777,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.03.10.21253321",
-    "rel_title": "Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State",
-    "rel_date": "2021-03-12",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.10.21253321",
-    "rel_abs": "Real-time epidemiological tracking of variants of interest can help limit the spread of more contagious forms of SARS-CoV-2, such as those containing the N501Y mutation. Typically, genetic sequencing is required to be able to track variants of interest in real-time. However, sequencing can take time and may not be accessible in all laboratories. Genotyping by RT-ddPCR offers an alternative to sequencing to rapidly detect variants of concern through discrimination of specific mutations such as N501Y that is associated with increased transmissibility. Here we describe the first cases of the B.1.1.7 lineage of SARS-CoV-2 detected in Washington State by using a combination of RT-PCR, RT-ddPCR, and next-generation sequencing. We screened 1,035 samples positive for SARS-CoV-2 by our CDC-based laboratory developed assay using ThermoFishers multiplex RT-PCR COVID-19 assay over four weeks from late December 2020 to early January 2021. S gene dropout candidates were subsequently assayed by RT-ddPCR to confirm four mutations within the S gene associated with the B.1.1.7 lineage: a deletion at amino acid (AA) 69-70 (ACATGT), deletion at AA 145, (TTA), N501Y mutation (TAT), and S982A mutation (GCA). All four targets were detected in two specimens, and follow-up sequencing revealed a total of 10 mutations in the S gene and phylogenetic clustering within the B.1.1.7 lineage. As variants of concern become increasingly prevalent, molecular diagnostic tools like RT-ddPCR can be utilized to quickly, accurately, and sensitively distinguish more contagious lineages of SARS-CoV-2.",
-    "rel_num_authors": 14,
-    "rel_authors": [
-      {
-        "author_name": "Garrett A. Perchetti",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Haiying Zhu",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Margaret G Mills",
-        "author_inst": "University of Washington Medical Center"
-      },
-      {
-        "author_name": "Lasata Shrestha",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Cassia Wagner",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Shah Mohamed Bakhash",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Michelle J Lin",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Hong Xie",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Meeili Huang",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Patrick C Mathias",
-        "author_inst": "University of Washington School of Medicine"
-      },
-      {
-        "author_name": "Trevor Bedford",
-        "author_inst": "Fred Hutchinson Cancer Research Center"
-      },
-      {
-        "author_name": "Keith Jerome",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Alexander L Greninger",
-        "author_inst": "University of Washington Medical Center"
-      },
-      {
-        "author_name": "Pavitra Roychoudhury",
-        "author_inst": "University of Washington"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.03.10.21253299",
     "rel_title": "SARS-CoV-2 Serology Status Detected by Commercialized Platforms Distinguishes Previous Infection and Vaccination Adaptive Immune Responses",
@@ -868707,6 +867067,101 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.03.11.21253226",
+    "rel_title": "Analysis of Accumulated SARS-CoV-2 Seroconversion in North Carolina: The COVID-19 Community Research Partnership",
+    "rel_date": "2021-03-12",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.11.21253226",
+    "rel_abs": "IntroductionThe COVID-19 Community Research Partnership is a population-based longitudinal syndromic and sero-surveillance study. The study includes over 17,000 participants from six healthcare systems in North Carolina who submitted over 49,000 serology results. The purpose of this study is to use these serology data to estimate the cumulative proportion of the North Carolina population that has either been infected with SARS-CoV-2 or developed a measurable humoral response to vaccination.\n\nMethodsAdult community residents were invited to participate in the study between April 2020 and February 2021. Demographic information was collected and daily symptom screen was completed using a secure, HIPPA-compliant, online portal. A portion of participants were mailed kits containing a lateral flow assay to be used in-home to test for presence of anti-SARS-CoV-2 IgM or IgG antibodies. The cumulative proportion of participants who tested positive at least once during the study was calculated. A standard Cox proportional hazards model was constructed to illustrate the probability of seroconversion over time up to December 20, 2020 (before vaccines available). A separate analysis was performed to describe the influence of vaccines during an extended period through February 15, 2021.\n\nResults17,688 participants contributed at least one serology result. Approximately two-thirds of the population were female and almost three-quarters were between 30 and 64 years of age. The average number of serology test results submitted per participant was 3.0 ({+/-}1.9). At December 20, 2020, the overall probability of seropositivity in the CCRP population was 32.6%. At February 15, 2021 the probability among healthcare workers and non-healthcare workers was 83% and 49%, respectively. An inflection upward in the probability of seropositivity was demonstrated around the end of December, suggesting an influence of vaccinations, especially for healthcare workers. Among healthcare workers, those in the oldest age category (60+ years) were 38% less likely to have seroconverted by February 15, 2021.\n\nConclusionsResults of this study suggest more North Carolina residents may have been infected with SARS-CoV-2 than the number of documented cases as determined by positive RNA or antigen tests. The influence of vaccinations on seropositivity among North Carolina residents is also demonstrated. Additional research is needed to fully characterize the impact of seropositivity on immunity and the ultimate course of the pandemic.",
+    "rel_num_authors": 20,
+    "rel_authors": [
+      {
+        "author_name": "John C Williamson",
+        "author_inst": "Wake Forest Baptist Health"
+      },
+      {
+        "author_name": "Thomas F Wierzba",
+        "author_inst": "Wake Forest Baptist Health"
+      },
+      {
+        "author_name": "Michele Santacatterina",
+        "author_inst": "George Washington Biostatistics Center"
+      },
+      {
+        "author_name": "Iqra Munawar",
+        "author_inst": "Wake Forest Baptist Health"
+      },
+      {
+        "author_name": "Austin L Seals",
+        "author_inst": "Wake Forest Baptist Health"
+      },
+      {
+        "author_name": "Christine Ann Pittman Ballard",
+        "author_inst": "Wake Forest Baptist Health"
+      },
+      {
+        "author_name": "Martha Alexander-Miller",
+        "author_inst": "Wake Forest Baptist Health"
+      },
+      {
+        "author_name": "Michael S Runyon",
+        "author_inst": "Atrium Health"
+      },
+      {
+        "author_name": "Lewis H McCurdy",
+        "author_inst": "Atrium Health"
+      },
+      {
+        "author_name": "Michael A Gibbs",
+        "author_inst": "Atrium Health"
+      },
+      {
+        "author_name": "Amina Ahmed",
+        "author_inst": "Atrium Health"
+      },
+      {
+        "author_name": "William H Lagarde",
+        "author_inst": "WakeMed Health and Hospitals"
+      },
+      {
+        "author_name": "Patrick D Maguire",
+        "author_inst": "New Hanover Regional Medical Center"
+      },
+      {
+        "author_name": "Robin King-Thiele",
+        "author_inst": "Campbell University"
+      },
+      {
+        "author_name": "Terri Hamrick",
+        "author_inst": "Campbell University"
+      },
+      {
+        "author_name": "Abdalla Ihmeidan",
+        "author_inst": "Campbell University"
+      },
+      {
+        "author_name": "Shakira Henderson",
+        "author_inst": "Vidant Health"
+      },
+      {
+        "author_name": "Diane Uschner",
+        "author_inst": "George Washington Biostatistics Center"
+      },
+      {
+        "author_name": "David M Herrington",
+        "author_inst": "Wake Forest Baptist Health"
+      },
+      {
+        "author_name": "John W Sanders",
+        "author_inst": "Wake Forest Baptist Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.03.11.21253356",
     "rel_title": "Optimal vaccination strategies for COVID-19 based on dynamical social networks with real-time updating",
@@ -870052,117 +868507,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.03.11.21253234",
-    "rel_title": "Comparison of SARS-CoV-2 detection in Saliva by real-time RT-PCR and RT-PCR/MALDI-TOF Methods",
-    "rel_date": "2021-03-12",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.11.21253234",
-    "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic has accelerated the need for rapid implementation of diagnostic assays for detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in respiratory specimens. While multiple molecular methods utilize nasopharyngeal specimens, supply chain constraints and need for easier and safer specimen collection warrant alternative specimen types, particularly saliva. Although saliva has been found to be a comparable clinical matrix for detection of SARS-CoV-2, evaluations of diagnostic and analytic performance across platforms for this specimen type are limited. Here, we compared two methods for SARS-CoV-2 detection in saliva: the Roche cobas(R) 6800/8800 SARS-CoV-2 real-time RT-PCR Test and the Agena Biosciences MassARRAY(R) SARS-CoV-2 Panel/MassARRAY(R) System. Overall, both systems had high agreement with one another, and both demonstrated high diagnostic sensitivity and specificity when compared to matched patient upper respiratory specimens. We also evaluated the analytical sensitivity of each platform and determined the limit of detection of the Roche assay was four times lower than that of Agena for saliva specimens (390.6 v. 1,562.5 copies/mL). Furthermore, across individual target components of each assay, T2 and N2 targets had the lowest limits of detection for each platform, respectively. Together, we demonstrate that saliva represents an appropriate specimen for SARS-CoV-2 detection in two technologies that have high agreement and differ in analytical sensitivities overall and across individual component targets. The addition of saliva as an acceptable specimen and understanding the sensitivity for testing on these platforms can further inform public health measures for screening and detection to combat the COVID-19 pandemic.",
-    "rel_num_authors": 24,
-    "rel_authors": [
-      {
-        "author_name": "Matthew M. Hernandez",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Radhika Banu",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Paras Shrestha",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Armi Patel",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Feng Chen",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Liyong Cao",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Shelcie Fabre",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Jessica Tan",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Heidi Lopez",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Numthip Chiu",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Biana Shifrin",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Inessa Zapolskaya",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Vanessa Flores",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Pui Yiu Lee",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Sergio Casta\u00f1eda",
-        "author_inst": "Universidad del Rosario"
-      },
-      {
-        "author_name": "Juan David Ram\u00edrez",
-        "author_inst": "Universidad del Rosario"
-      },
-      {
-        "author_name": "Jeffrey Jhang",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Giuliana Osorio",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Melissa R Gitman",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Michael D. Nowak",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "David L. Reich",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Carlos Cordon-Cardo",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Emilia M Sordillo",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Alberto E Paniz Mondolfi",
-        "author_inst": "Icahn School of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.03.09.21253220",
     "rel_title": "Leg-heel chest compression as an alternative for medical professionals in times of COVID-19",
@@ -870433,6 +868777,69 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.03.11.21253364",
+    "rel_title": "Analysis of severe outcomes associated with the SARS-CoV-2 Variant of Concern 202012/01 in England using ICNARC Case Mix Programme and QResearch databases.",
+    "rel_date": "2021-03-12",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.11.21253364",
+    "rel_abs": "BackgroundA new, more transmissible variant of SARS-CoV-2, variant of concern (VOC) 202012/01 or lineage B.1.1.7, has emerged in the UK. We estimate the risk of critical care admission, mortality in critical ill patients, and overall mortality associated with VOC B.1.1.7 compared with the original variant. We also compare clinical outcomes between these variants   groups.\n\nMethodsWe linked a large primary care (QResearch), the national critical care (ICNARC CMP) and the COVID-19 testing (PHE) database and extracted two cohorts. The first was used to explore the association between VOC B.1.1.7 and critical care admission and 28-day mortality. The second to determine the risk of mortality in critically ill patients with VOC B.1.1.7 compared to those without. We used Royston-Parmar models adjusted for age, sex, region, other socio-demographics and comorbidities (asthma, COPD, type I and II, hypertension). We reported information on types and duration of organ supports for the two variants   groups.\n\nFindingsThe first cohort included 198,420 patients. Of these, 80,494 had VOC B.1.1.7, 712 were critically ill and 630 died by 28 days. The second cohort included 3432 critically ill patients. Of these, 2019 had VOC B.1.1.7 and 822 died at the end of critical care. Using the first cohort, we estimated adjusted hazard ratios for critical care admission and mortality to be 1.99 (95% CI: 1.59, 2.49) and 1.59 (95% CI: 1.25-2.03) for VOC B.1.1.7 compared with the original variant group, respectively. The adjusted hazard ratio for mortality in critical care, estimated using the second cohort, was 0.93 (95% CI 0.76-1.15) for patients with VOC B.1.1.7, compared to those without.\n\nInterpretationVOC B.1.1.7 appears to be more severe. Patients with VOC B.1.1.7 are at increased risk of critical care admission and mortality compared with patients without. For patients receiving critical care, mortality appears independent of virus strain.\n\nRESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSA new variant of the SARS-CoV-2 virus, variant of concern (VOC) 202012/01, or lineage B.1.1.7, was detected in England in September 2020. The characteristics and outcomes of patients infected with VOC B.1.1.7 are not yet known. VOC B.1.1.7 has been associated with increased transmissibility. Early analyses have suggested infection with VOC B.1.1.7 may be associated with a higher risk of mortality compared with infection with other virus variants, but these analyses had either limited ability to adjust for key confounding variables or did not consider critical care admission. The effects of VOC B.1.1.7 on severe COVID-19 outcomes remain unclear.\n\nAdded value of this studyThis study found a 60% higher risk of 28-day mortality associated with infection with VOC B.1.1.7 in patients tested in the community in comparison with the original variant, when adjusted for key confounding variables. The risk of critical care admission for those with VOC B.1.1.7 is double the risk associated with the original variant. For patients receiving critical care, the infecting variant is not associated with the risk of mortality at the end of critical care.\n\nImplications of all the available evidenceThe higher mortality and rate of critical care admission associated with VOC B.1.1.7, combined with its known increased transmissibility, are likely to put health care systems under further stress. These effects may be mitigated by the ongoing vaccination programme.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Martina Patone",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Karen Thomas",
+        "author_inst": "Intensive Care National Audit & Research Centre"
+      },
+      {
+        "author_name": "Robert Hatch",
+        "author_inst": "Intensive Care National Audit & Research Centre"
+      },
+      {
+        "author_name": "Pui San Tan",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Weiqi Liao",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Carol Coupland",
+        "author_inst": "University of Nottingham"
+      },
+      {
+        "author_name": "Paul Mouncey",
+        "author_inst": "Intensive Care National Audit & Research Centre"
+      },
+      {
+        "author_name": "David Harrison",
+        "author_inst": "Intensive Care National Audit & Research Centre"
+      },
+      {
+        "author_name": "Kathryn Rowan",
+        "author_inst": "Intensive Care National Audit & Research Centre"
+      },
+      {
+        "author_name": "Peter Horby",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Peter Watkinson",
+        "author_inst": "Intensive Care National Audit & Research Centre"
+      },
+      {
+        "author_name": "Julia Hippisley-Cox",
+        "author_inst": "University of Oxford"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "primary care research"
+  },
   {
     "rel_doi": "10.1101/2021.03.11.21253348",
     "rel_title": "The role of connectivity on COVID-19 preventive approaches",
@@ -871561,53 +869968,6 @@
     "type": "new results",
     "category": "biophysics"
   },
-  {
-    "rel_doi": "10.1101/2021.03.08.21253143",
-    "rel_title": "Determining the risk of developing symptomatic covid-19 infection after attending hospital for radiological examinations: controlled cohort study",
-    "rel_date": "2021-03-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.08.21253143",
-    "rel_abs": "OBJECTIVETo determine whether brief attendance for outpatient radiological investigations is associated with increased risk of clinically significant coronavirus disease 2019 (covid-19) infection.\n\nDESIGNObservational cohort study with a historical control.\n\nSETTING2 large UK University Hospitals located in Nottingham and Cardiff.\n\nPARTICIPANTSAll 47,340 patients who attended an outpatient radiology appointment at Nottingham University Hospitals and University Hospital of Wales during the first wave of the pandemic in 2020, and 70,655 patients that comprised the control cohort who attended for outpatient radiology the same period in 2019.\n\nMAIN OUTCOME MEASURESThe risk of developing clinically significant covid-19 infection within 28-days of attending a radiological examination. Covid-19 infection rates for the 2020 cohort were compared against a control group who attended in 2019.\n\nRESULTS84 positive SARS-CoV-2 tests were temporally associated with 47,340 radiological examinations across two hospitals in 2020. This low infection rate was higher than the 2019 control cohort; OR 2.507 (1.766 - 3.559) and equates to an approximate 1 positive covid-19 infection per 1000 radiology investigations.\n\nCONCLUSIONSOur data suggests that attending hospitals for outpatient radiological investigations during the pandemic is associated with a very small absolute risk of acquiring clinically significant covid-19 infection. It is unlikely that this risk is directly attributable to radiology attendance, considering the reasons leading individuals to attend hospitals during the pandemic, the true attributable risk will likely be even lower.\n\nTRIAL REGISTRATIONClinicalTrials.gov NCT04544176",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Nikos Evangelou",
-        "author_inst": "University of Nottingham"
-      },
-      {
-        "author_name": "Sian Vaughan",
-        "author_inst": "Nottingham University Hospitals"
-      },
-      {
-        "author_name": "Aimee Hibbert",
-        "author_inst": "Nottingham University Hospitals"
-      },
-      {
-        "author_name": "Paul Morgan",
-        "author_inst": "University of Nottingham"
-      },
-      {
-        "author_name": "Matthijs Backx",
-        "author_inst": "Cardiff and Vale University Health Board"
-      },
-      {
-        "author_name": "Louise Berry",
-        "author_inst": "Nottingham University Hospitals"
-      },
-      {
-        "author_name": "Timothy Card",
-        "author_inst": "University of Nottingham"
-      },
-      {
-        "author_name": "Emma Tallantyre",
-        "author_inst": "Cardiff University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.03.08.21253144",
     "rel_title": "Factors influencing COVID rates at local authority level and contribution of variation in vaccine coverage",
@@ -871986,6 +870346,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.03.09.21253155",
+    "rel_title": "High-resolution epigenome analysis in nasal samples derived from children with respiratory viral infections reveals striking changes upon SARS-CoV-2 infection",
+    "rel_date": "2021-03-11",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.09.21253155",
+    "rel_abs": "BackgroundDNA methylation patterns of the human genome can be modified by environmental stimuli and provide dense information on gene regulatory circuitries. We studied genome-wide DNA methylation in nasal samples from infants (<6 months) applying whole-genome bisulfite sequencing (WGBS) to characterize epigenome response to 10 different respiratory viral infections including SARS-CoV-2.\n\nResultsWe identified virus-specific differentially methylated regions (vDMR) with human metapneumovirus (hMPV) and SARS-CoV-2 followed by Influenza B (Flu B) causing the weakest vs. strongest epigenome response with 496 vs. 78541 and 14361 vDMR, respectively. We found a strong replication rate of FluB (52%) and SARS-CoV-2 (42%) vDMR in independent samples indicating robust epigenome perturbation upon infection. Among the FluB and SARS-CoV-2 vDMRs, around 70% were hypomethylated and significantly enriched among epithelial cell-specific regulatory elements whereas the hypermethylated vDMRs for these viruses mapped more frequently to immune cell regulatory elements, especially those of the myeloid lineage. The hypermethylated vDMRs were also enriched among genes and genetic loci in monocyte activation pathways and monocyte count. Finally, we perform single-cell RNA-sequencing characterization of nasal mucosa in response to these two viruses to functionally analyze the epigenome perturbations. Which supports the trends we identified in methylation data and highlights and important role for monocytes.\n\nConclusionsAll together, we find evidence indicating genetic predisposition to innate immune response upon a respiratory viral infection. Our genome-wide monitoring of infant viral response provides first catalogue of associated host regulatory elements. Assessing epigenetic variation in individual patients may reveal evidence for viral triggers of childhood disease.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Konner Winkley",
+        "author_inst": "Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, Missouri, US"
+      },
+      {
+        "author_name": "Boryana Koseva",
+        "author_inst": "Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, Missouri, US"
+      },
+      {
+        "author_name": "Dithi Banerjee",
+        "author_inst": "Department of Pathology and Laboratory Medicine, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, Missouri, US"
+      },
+      {
+        "author_name": "Warren Cheung",
+        "author_inst": "Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, Missouri, US"
+      },
+      {
+        "author_name": "Rangaraj Selvarangan",
+        "author_inst": "Department of Pathology and Laboratory Medicine, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, Missouri, US"
+      },
+      {
+        "author_name": "Tomi Pastinen",
+        "author_inst": "Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, Missouri, US"
+      },
+      {
+        "author_name": "Elin Grundberg",
+        "author_inst": "Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, Missouri, US"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "genetic and genomic medicine"
+  },
   {
     "rel_doi": "10.1101/2021.03.08.21253135",
     "rel_title": "Predicting the Efficacy of COVID-19 Convalescent Plasma Donor Units with the Lumit Dx anti-Receptor Binding Domain Assay.",
@@ -873566,73 +871969,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.03.08.21253093",
-    "rel_title": "Anti-SARS-CoV-2 Serology persistence over time in COVID-19 Convalescent Plasma Donors.",
-    "rel_date": "2021-03-10",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.08.21253093",
-    "rel_abs": "BackgroundCharacterizing the kinetics of the antibody response to SARS{square}CoV{square}2 is of critical importance to developing strategies that may mitigate the public health burden of COVID-19. We sought to determine how circulating antibody levels change over time following natural infection.\n\nMethods/MaterialsWe conducted a prospective, longitudinal analysis of COVID-19 convalescent plasma (CCP) donors at multiple time points over a 9-month period. At each study visit, subjects either donated plasma or only had study samples drawn. In all cases, anti-SARS-CoV-2 donor testing was performed using semi-quantitative chemiluminescent immunoassays (ChLIA) targeting subunit 1 (S1) of the SARS-CoV-2 spike (S) protein, and an in-house fluorescence reduction neutralization assay (FRNA).\n\nResultsFrom April to November 2020 we enrolled 202 donors, mean age 47.3 {+/-}14.7 years, 55% female, 75% Caucasian. Most donors reported a mild clinical course (91%, n=171) without hospitalization. One hundred and five (105) (52%) donors presented for repeat visits with a median 42 (12-163) days between visits. The final visit occurred at a median 160 (53-273) days post-symptom resolution. Total anti-SARS-CoV-2 antibodies (Ab), SARS-CoV-2 specific IgG and neutralizing antibodies were detected in 97.5%, 91.1%, and 74% of donors respectively at initial presentation. Neutralizing Ab titers based on FRNA50 were positively associated with mean IgG levels (p = <0.0001). Mean IgG levels and neutralizing titers were positively associated with COVID-19 severity, increased donor age and BMI (p=0.0006 and p=0.0028, p=0.0083 and p=0.0363, (p=0.0008 and p=0.0018, respectively). Over the course of repeat visits, IgG decreased in 74.1% of donors; FRNA50 decreased in 44.4% and remained unchanged in 33.3% of repeat donors. A weak negative correlation was observed between total Ab levels and number of days post-symptom recovery (r = 0.09).\n\nConclusionAnti-SARS-CoV-2 antibodies were identified in 97% of convalescent donors at initial presentation. In a cohort that largely did not require hospitalization. IgG and neutralizing antibodies were positively correlated with age, BMI and clinical severity, and persisted for up to 9 months post-recovery from natural infection. On repeat presentation, IgG anti-SARS-CoV-2 levels decreased in 56% of repeat donors. Overall, these data suggest that CP donors possess a wide range of IgG and neutralizing antibody levels that are proportionally distributed across demographics, with the exception of age, BMI and clinical severity.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Valeria De Giorgi",
-        "author_inst": "National Institutes of Health (NIH), Clinical Center, Department of Transfusion Medicine, Bethesda, MD 20892"
-      },
-      {
-        "author_name": "Kamille A West",
-        "author_inst": "National Institutes of Health (NIH), Clinical Center, Department of Transfusion Medicine, Bethesda, MD 20892"
-      },
-      {
-        "author_name": "Amanda N Henning",
-        "author_inst": "National Institutes of Health (NIH), Clinical Center, Department of Transfusion Medicine, Bethesda, MD 20892"
-      },
-      {
-        "author_name": "Leonard Chen",
-        "author_inst": "National Institutes of Health (NIH), Clinical Center, Department of Transfusion Medicine, Bethesda, MD 20892"
-      },
-      {
-        "author_name": "Michael R Holbrook",
-        "author_inst": "National Institute of Allergy and Infectious Diseases (NIAID) Integrated Research Facility, National Institutes of Health (NIH), Frederick, MD 21702"
-      },
-      {
-        "author_name": "Robin Gross",
-        "author_inst": "National Institute of Allergy and Infectious Diseases (NIAID) Integrated Research Facility, National Institutes of Health (NIH), Frederick, MD 21702"
-      },
-      {
-        "author_name": "Janie Liang",
-        "author_inst": "National Institute of Allergy and Infectious Diseases (NIAID) Integrated Research Facility, National Institutes of Health (NIH), Frederick, MD 21702"
-      },
-      {
-        "author_name": "Elena Postnikova",
-        "author_inst": "National Institute of Allergy and Infectious Diseases (NIAID) Integrated Research Facility, National Institutes of Health (NIH), Frederick, MD 21702"
-      },
-      {
-        "author_name": "Joni Trenbeath",
-        "author_inst": "National Institutes of Health (NIH), Clinical Center, Department of Transfusion Medicine, Bethesda, MD 20892"
-      },
-      {
-        "author_name": "Sarah Pogue",
-        "author_inst": "National Institutes of Health (NIH), Clinical Center, Department of Transfusion Medicine, Bethesda, MD 20892"
-      },
-      {
-        "author_name": "Tania Scinto",
-        "author_inst": "National Institutes of Health (NIH), Clinical Center, Department of Transfusion Medicine, Bethesda, MD 20892"
-      },
-      {
-        "author_name": "Harvey J Alter",
-        "author_inst": "National Institutes of Health (NIH), Clinical Center, Department of Transfusion Medicine, Bethesda, MD 20892"
-      },
-      {
-        "author_name": "Cathy Conry Cantilena",
-        "author_inst": "National Institutes of Health (NIH), Clinical Center, Department of Transfusion Medicine, Bethesda, MD 20892"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.03.08.21253065",
     "rel_title": "Impact of previous COVID-19 on immune response after a single dose of BNT162b2 SARS-CoV-2 vaccine",
@@ -874135,6 +872471,85 @@
     "type": "new results",
     "category": "biophysics"
   },
+  {
+    "rel_doi": "10.1101/2021.03.09.434030",
+    "rel_title": "Development of Equine Immunoglobulin Fragment F(ab')2 with High Neutralizing Capability against SARS-CoV-2",
+    "rel_date": "2021-03-10",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.09.434030",
+    "rel_abs": "The ongoing pandemic, COVID-19, caused by SARS-CoV-2 has taken the world, and especially the scientific community by storm. While vaccines are being introduced into the market, there is also a pressing need to find potential drugs and therapeutic modules. Remdesivir is one of the antivirals currently being used with a limited window of action. As more drugs are being vetted, passive immunotherapy in the form of neutralizing antibodies can provide immediate action to combat the increasing numbers of COVID-positive cases. Herein, we demonstrate that equines hyper-immunized with chemically inactivated SARS-CoV-2 generate high titers of antibody with a strong virus neutralizing potential. ELISA performed with pooled antisera displayed highest immunoglobulin titer on 42 days post-immunization, at 1:51,200 dilutions. F(ab)2 immunoglobulin fragments generated from the pools also showed very high, antigen-specific affinity at 1:102,400 dilutions. Finally, in vitro virus neutralization assays confirmed that different pools of F(ab)2 fragments could successfully neutralize SARS-CoV-2 with titers well above 25,000, indicating the potential of this strategy in treating severe COVID-19 cases with high titers. The F(ab)2 was able to cross neutralize another SARS-CoV-2 strain, demonstrating its efficacy against the emerging viral variants and the importance of this approach in our efforts of eradication of COVID-19. In conclusion, this study demonstrates that virus-neutralizing antibodies raised in equines can potentially be used as a treatment regimen in the form of effective passive immunotherapy to combat COVID-19.",
+    "rel_num_authors": 16,
+    "rel_authors": [
+      {
+        "author_name": "Divya Gupta Ms",
+        "author_inst": "Centre for Cellular and Molecular Biology"
+      },
+      {
+        "author_name": "Farhan Ahmed Dr",
+        "author_inst": "University of Hyderabad"
+      },
+      {
+        "author_name": "Dixit Tandel Mr",
+        "author_inst": "Centre for Cellular and Molecular Biology, Academy of Scientific and Innovative Research"
+      },
+      {
+        "author_name": "Haripriya Parthasarathy Ms",
+        "author_inst": "Centre for Cellular and Molecular Biology"
+      },
+      {
+        "author_name": "Dhiviya Vedagiri Ms",
+        "author_inst": "Centre for Cellular and Molecular Biology, Academy of Scientific and Innovative Research"
+      },
+      {
+        "author_name": "Vishal Sah Mr",
+        "author_inst": "Centre for Cellular and Molecular Biology, Academy of Scientific and Innovative Research"
+      },
+      {
+        "author_name": "Krishna Mohan Bodduluru Dr",
+        "author_inst": "Vins Bioproducts Ltd"
+      },
+      {
+        "author_name": "Siddarth Shreedas Daga Mr",
+        "author_inst": "Vins Bioproducts Ltd"
+      },
+      {
+        "author_name": "Rafiq Ahmad Khan Mr",
+        "author_inst": "University of Hyderabad"
+      },
+      {
+        "author_name": "Chiranjeevi Kondiparthi Mr",
+        "author_inst": "Vins Bioproducts Ltd"
+      },
+      {
+        "author_name": "Prabhudas Savari Mr",
+        "author_inst": "Vins Bioproducts Ltd"
+      },
+      {
+        "author_name": "Sandesh Hajarilal Jain Dr",
+        "author_inst": "Vins Bioproducts Ltd"
+      },
+      {
+        "author_name": "Jaya Shreedas Daga Ms",
+        "author_inst": "Vins Bioproducts Ltd"
+      },
+      {
+        "author_name": "Shashikala Reddy Dr",
+        "author_inst": "Osmania Medical College"
+      },
+      {
+        "author_name": "Nooruddin Khan Dr",
+        "author_inst": "University of Hyderabad"
+      },
+      {
+        "author_name": "Krishnan Harinivas Harshan Dr",
+        "author_inst": "Centre for Cellular and Molecular Biology"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2021.03.09.434607",
     "rel_title": "The dual function monoclonal antibodies VIR-7831 and VIR-7832 demonstrate potent in vitro and in vivo activity against SARS-CoV-2",
@@ -875988,101 +874403,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.03.09.434497",
-    "rel_title": "Spike mutations in SARS-CoV-2 variants confer resistance to antibody neutralization",
-    "rel_date": "2021-03-09",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.09.434497",
-    "rel_abs": "New SARS-CoV-2 variants continue to emerge from the current global pandemic, some of which can replicate faster and with greater transmissibility and pathogenicity. In particular, UK501Y.V1 identified in UK, SA501Y.V2 in South Africa, and BR501Y.V3 in Brazil are raising serious concerns as they spread quickly and contain spike protein mutations that may facilitate escape from current antibody therapies and vaccine protection. Here, we constructed a panel of 28 SARS-CoV-2 pseudoviruses bearing single or combined mutations found in the spike protein of these three variants, as well as additional nine mutations that within or close by the major antigenic sites in the spike protein identified in the GISAID database. These pseudoviruses were tested against a panel of monoclonal antibodies (mAbs), including some approved for emergency use to treat SARS-CoV-2 infection, and convalescent patient plasma collected early in the pandemic. SA501Y.V2 pseudovirus was the most resistant, in magnitude and breadth, against mAbs and convalescent plasma, followed by BR501Y.V3, and then UK501Y.V1. This resistance hierarchy corresponds with Y144del and 242-244del mutations in the N-terminal domain as well as K417N/T, E484K and N501Y mutations in the receptor binding domain (RBD). Crystal structural analysis of RBD carrying triple K417N-E484K-N501Y mutations found in SA501Y.V2 bound with mAb P2C-1F11 revealed a molecular basis for antibody neutralization and escape. SA501Y.V2 and BR501Y.V3 also acquired substantial ability to use mouse and mink ACE2 for entry. Taken together, our results clearly demonstrate major antigenic shifts and potentially broadening the host range of SA501Y.V2 and BR501Y.V3, which pose serious challenges to our current antibody therapies and vaccine protection.",
-    "rel_num_authors": 20,
-    "rel_authors": [
-      {
-        "author_name": "Ruoke Wang",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Qi Zhang",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Jiwan Ge",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Wenlin Ren",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Riu Zhang",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Jun Lan",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Bin Ju",
-        "author_inst": "Shenzhen Third Peoples Hospital"
-      },
-      {
-        "author_name": "Bin Su",
-        "author_inst": "Beijing Youan Hospital"
-      },
-      {
-        "author_name": "Fengting Yu",
-        "author_inst": "Beijnig Ditan Hospital"
-      },
-      {
-        "author_name": "Peng Chen",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Huiyu Liao",
-        "author_inst": "Beijing Youan Hospital"
-      },
-      {
-        "author_name": "Yingmei Feng",
-        "author_inst": "Beijing Youan Hospital"
-      },
-      {
-        "author_name": "Xuemei Li",
-        "author_inst": "Beijing Youan Hospital"
-      },
-      {
-        "author_name": "Xuanling Shi",
-        "author_inst": "Tsinghua University School of Medicine"
-      },
-      {
-        "author_name": "Zheng Zhang",
-        "author_inst": "Shenzhen Third Peoples Hospital"
-      },
-      {
-        "author_name": "Fujie Zhang",
-        "author_inst": "Beijing Ditan Hospital"
-      },
-      {
-        "author_name": "Qiang Ding",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Tong Zhang",
-        "author_inst": "Beijing Youan Hospital"
-      },
-      {
-        "author_name": "Xinquan Wang",
-        "author_inst": "Tsinghua University"
-      },
-      {
-        "author_name": "Linqi Zhang",
-        "author_inst": "Tsinghua University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2021.03.08.434499",
     "rel_title": "The N501Y spike substitution enhances SARS-CoV-2 transmission",
@@ -876577,6 +874897,89 @@
     "type": "new results",
     "category": "bioinformatics"
   },
+  {
+    "rel_doi": "10.1101/2021.03.09.434219",
+    "rel_title": "The FDA-approved drug cobicistat synergizes with remdesivir to inhibit SARS-CoV-2 replication",
+    "rel_date": "2021-03-09",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.09.434219",
+    "rel_abs": "Combinations of direct-acting antivirals are needed to minimize drug-resistance mutations and stably suppress replication of RNA viruses. Currently, there are limited therapeutic options against the Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) and testing of a number of drug regimens has led to conflicting results. Here we show that cobicistat, which is an-FDA approved drug-booster that blocks the activity of the drug metabolizing proteins Cytochrome P450-3As (CYP3As) and P-glycoprotein (P-gp), inhibits SARS-CoV-2 replication. Cell-to-cell membrane fusion assays indicated that the antiviral effect of cobicistat is exerted through inhibition of spike protein-mediated membrane fusion. In line with this, incubation with low micromolar concentrations of cobicistat decreased viral replication in three different cell lines including cells of lung and gut origin. When cobicistat was used in combination with the putative CYP3A target and nucleoside analog remdesivir, a synergistic effect on the inhibition of viral replication was observed in cell lines and in a primary human colon organoid. The cobicistat/remdesivir combination was able to potently abate viral replication to levels comparable to mock-infected cells leading to an almost complete rescue of infected cell viability. These data highlight cobicistat as a therapeutic candidate for treating SARS-CoV-2 infection and as a potential building block of combination therapies for COVID-19.",
+    "rel_num_authors": 17,
+    "rel_authors": [
+      {
+        "author_name": "Iart Luca Shytaj",
+        "author_inst": "Department of Infectious Diseases, Federal University of Sao Paulo, Sao Paulo, Brazil."
+      },
+      {
+        "author_name": "Mohamed Fares",
+        "author_inst": "Department of Hydrobiology, Veterinary Research Division, National Research Centre, Cairo, Egypt."
+      },
+      {
+        "author_name": "Bojana Lucic",
+        "author_inst": "Department of Infectious Diseases, Integrative Virology, CIID, Heidelberg University, Heidelberg, Germany"
+      },
+      {
+        "author_name": "Lara Gallucci",
+        "author_inst": "Department of Infectious Diseases, Integrative Virology, CIID, Heidelberg University, Heidelberg, Germany."
+      },
+      {
+        "author_name": "Mahmoud M. Tolba",
+        "author_inst": "Pharmaceutical Division, Ministry of Health and Population, Faiyum, Egypt."
+      },
+      {
+        "author_name": "Liv Zimmermann",
+        "author_inst": "Department of Infectious Diseases, Virology, CIID, Heidelberg University Hospital, Heidelberg, Germany"
+      },
+      {
+        "author_name": "Ahmed  T. Ayoub",
+        "author_inst": "Department of Pharmaceutical Chemistry, Biomolecular Simulation Center, Heliopolis University, Cairo, Egypt."
+      },
+      {
+        "author_name": "Mirko Cortese",
+        "author_inst": "Department of Infectious Diseases, Molecular Virology, CIID, Heidelberg University, Heidelberg, Germany"
+      },
+      {
+        "author_name": "Christopher J. Neufeldt",
+        "author_inst": "Department of Infectious Diseases, Molecular Virology, CIID, Heidelberg University, Heidelberg, Germany"
+      },
+      {
+        "author_name": "Vibor Laketa",
+        "author_inst": "Department of Infectious Diseases, Virology, CIID, Heidelberg University Hospital, Heidelberg, Germany"
+      },
+      {
+        "author_name": "Petr Chlanda",
+        "author_inst": "Department of Infectious Diseases, Virology, CIID, Heidelberg University Hospital, Heidelberg, Germany"
+      },
+      {
+        "author_name": "Oliver T. Fackler",
+        "author_inst": "Department of Infectious Diseases, Integrative Virology, CIID, Heidelberg University, Heidelberg, Germany."
+      },
+      {
+        "author_name": "Steeve Boulant",
+        "author_inst": "Department of Infectious Diseases, Virology, CIID, Heidelberg University Hospital, Heidelberg, Germany"
+      },
+      {
+        "author_name": "Ralf Bartenschlager",
+        "author_inst": "Department of Infectious Diseases, Molecular Virology, CIID, Heidelberg University, Heidelberg, Germany"
+      },
+      {
+        "author_name": "Megan Stanifer",
+        "author_inst": "Department of Infectious Diseases, Molecular Virology, CIID, Heidelberg University, Heidelberg, Germany"
+      },
+      {
+        "author_name": "Andrea Savarino",
+        "author_inst": "Department of Infectious and Immune-Mediated Diseases, Italian Institute of Health, Rome, Italy."
+      },
+      {
+        "author_name": "Marina Lusic",
+        "author_inst": "Department of Infectious Diseases, Integrative Virology, CIID, Heidelberg University, Heidelberg, Germany."
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2021.03.08.433764",
     "rel_title": "Site-specific steric control of SARS-CoV-2 spike glycosylation",
@@ -878354,37 +876757,6 @@
     "type": "new results",
     "category": "genomics"
   },
-  {
-    "rel_doi": "10.1101/2021.03.07.434295",
-    "rel_title": "AI-driven prediction of SARS-CoV-2 variant binding trends from atomistic simulations",
-    "rel_date": "2021-03-08",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.07.434295",
-    "rel_abs": "We present a novel technique to predict binding affinity trends between two molecules from atomistic molecular dynamics simulations. The technique uses a neural network algorithm applied to a series of images encoding the distance between two molecules in time. We demonstrate that our algorithm is capable of separating with high accuracy non-hydrophobic mutations with low binding affinity from those with high binding affinity. Moreover, we show high accuracy in prediction using a small subset of the simulation, therefore requiring a much shorter simulation time. We apply our algorithm to the binding between several variants of the SARS-CoV-2 spike protein and the human receptor ACE2.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Sara Capponi",
-        "author_inst": "IBM Almaden Research Center"
-      },
-      {
-        "author_name": "Shangying Wang",
-        "author_inst": "IBM Almaden Research Center"
-      },
-      {
-        "author_name": "Eirk J Navarro",
-        "author_inst": "IBM Almaden Research Center"
-      },
-      {
-        "author_name": "Simone Bianco",
-        "author_inst": "IBM Almaden Research Center"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "new results",
-    "category": "biophysics"
-  },
   {
     "rel_doi": "10.1101/2021.03.04.21252889",
     "rel_title": "We also deserve help during the pandemic: The effect of the COVID-19 pandemic on foreign domestic workers in Hong Kong",
@@ -878667,6 +877039,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.03.04.21252880",
+    "rel_title": "Estimation and optimal control of the multi-scale dynamics of the Covid-19",
+    "rel_date": "2021-03-08",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.04.21252880",
+    "rel_abs": "This work aims at a better understanding and the optimal control of the spread of the new severe acute respiratory corona virus 2 (SARS-CoV-2). We first propose a multi-scale model giving insights on the virus population dynamics, the transmission process and the infection mechanism. We consider 10 compartments in the human population in order to take into accounts the effects of different specific mitigation policies: susceptible, infected, infectious, quarantined, hospitalized, treated, recovered, non-infectious dead, infectious dead, buried. The population of viruses is also partitioned into 10 compartments corresponding respectively to each of the first nine human population compartments and the free viruses available in the environment. Indeed, we have human to human virus transmission, human to environment virus transmission, environment to human virus transmission and self infection by susceptible individuals. We show the global stability of the disease free equilibrium if a given threshold[T] 0 is less or equal to 1 and we provide how to compute the basic reproduction number[R] 0. A convergence index[T] 1 is also defined in order to estimate the speed at which the disease extincts and an upper bound to the time of extinction is given. The existence of the endemic equilibrium is conditional and its description is provided. We evaluate the sensitivity of[R] 0,[T] 0 and[T] 1 to control parameters such as the maximal human density allowed per unit of surface, the rate of disinfection both for people and environment, the mobility probability, the wearing mask probability or efficiency, and the human to human contact rate which results from the previous one. Except the maximal human density allowed per unit of surface, all those parameters have significant effects on the qualitative dynamics of the disease. The most significant is the probability of wearing mask followed by the probability of mobility and the disinfection rate. According to a functional cost taking into consideration economic impacts of SARS-CoV-2, we determine and discuss optimal fighting strategies. The study is applied to real available data from Cameroon and an estimation of model parameters is done. After several simulations, social distancing and the disinfection frequency appear as the main elements of the optimal control strategy.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "David Jaures FOTSA MBOGNE",
+        "author_inst": "The University of Ngaoundere"
+      },
+      {
+        "author_name": "Stephane Yanick TCHOUMI",
+        "author_inst": "The University of Ngaoundere"
+      },
+      {
+        "author_name": "Yannick Kouakep Tchaptchie",
+        "author_inst": "EGCIM, University of Ngaoundere"
+      },
+      {
+        "author_name": "Vivient Corneille KAMLA",
+        "author_inst": "The University of Ngaoundere"
+      },
+      {
+        "author_name": "Jean Claude KAMGANG",
+        "author_inst": "The University of Ngaoundere"
+      },
+      {
+        "author_name": "Duplex Elvis HOUPA DANGA",
+        "author_inst": "The University of Ngaoundere"
+      },
+      {
+        "author_name": "Samuel BOWONG TSAKOU",
+        "author_inst": "The University of Douala"
+      },
+      {
+        "author_name": "David BEKOLLE",
+        "author_inst": "The University of Ngaoundere"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.03.03.21252855",
     "rel_title": "Bromhexine Hydrochloride Prophylaxis of COVID-19 for Medical Personnel: A Randomized Open-Label Study",
@@ -880104,69 +878523,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "allergy and immunology"
   },
-  {
-    "rel_doi": "10.1101/2021.03.05.21252835",
-    "rel_title": "High seroprevalence of anti-SARS-CoV-2 antibodies after the first wave of the COVID-19 pandemic in a vulnerable population in Perpignan, France",
-    "rel_date": "2021-03-08",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.05.21252835",
-    "rel_abs": "BackgroundIn March 2020, many cases of COVID-19 were reported in three socially deprived neighbourhoods of the city of Perpignan, in the south of France, where large sedentary gypsy communities live. A study to measure seroprevalence was conducted in July 2020 to assess the level of contamination in these neighbourhoods after the first wave of the pandemic, and to identify factors associated with seropositivity.\n\nMethodsSCoPe is a cross-sectional survey conducted in selected persons aged six years old and over living in three neighbourhoods in Perpignan. Households were selected by systematic sampling and participants by random sampling. Collected blood samples were tested for SARS-CoV-2 IgG and IgM antibodies using the EIecsys(R) immunoassay to target the coronaviruss spike protein. Antibody seroprevalence was estimated from weighted data and associated factors were investigated using multivariate logistic regression.\n\nResultsThe seroprevalence of anti-SARS-CoV-2 antibodies was 35.4% (95% CI: 30.2-41.0). Over a fifth of seropositive individuals (21.7% ([14.1-31.8]) did not report any COVID-19 symptom. People aged 15-64 years old were at greater risk of seropositivity than those aged 65 years or over. Obesity prevalence was 40.7% (35.8-45.8) and obese people were more likely to be seropositive (aOR=2.0 [1.1-3.8]). The risk of being seropositive was higher in households with clinical COVID-19 cases (One case: aOR=2.5 [1.3-5.0]). In the neighbourhood with the highest measured seroprevalence, people living in a dwelling with 1-2 rooms had a higher risk of being seropositive than those living in a 4-room house (aOR=2.8 [1.2-6.3]). Working during the lockdown was associated with a lower risk of seropositivity (aOR=0.2 [0.03-1.0]).\n\nConclusionTransmission prevalence of the SARS-COV-2 virus in this vulnerable population was very high during the COVID-19 pandemics first wave. Our results highlight the need to strengthen and adapt preventive measures by taking into account all social determinants of health, especially housing conditions.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Adeline Beaumont",
-        "author_inst": "Sant\u00e9 Publique France"
-      },
-      {
-        "author_name": "C\u00e9cile Durand",
-        "author_inst": "Sant\u00e9 Publique France"
-      },
-      {
-        "author_name": "Martine Ledrans",
-        "author_inst": "Sant\u00e9 Publique France"
-      },
-      {
-        "author_name": "Val\u00e9rie Schwoebel",
-        "author_inst": "Sant\u00e9 Publique France"
-      },
-      {
-        "author_name": "Harold Noel",
-        "author_inst": "Sant\u00e9 Publique France"
-      },
-      {
-        "author_name": "Yann Le Strat",
-        "author_inst": "Sant\u00e9 Publique France"
-      },
-      {
-        "author_name": "Donatien Diulius",
-        "author_inst": "Agence R\u00e9gionale de Sant\u00e9 Occitanie"
-      },
-      {
-        "author_name": "L\u00e9a Colombain",
-        "author_inst": "Centre Hospitalier de Perpignan"
-      },
-      {
-        "author_name": "Marie M\u00e9dus",
-        "author_inst": "Centre Hospitalier de Perpignan"
-      },
-      {
-        "author_name": "Philippe Gueudet",
-        "author_inst": "Centre Hospitalier de Perpignan"
-      },
-      {
-        "author_name": "Damien Mouly",
-        "author_inst": "Sant\u00e9 Publique France"
-      },
-      {
-        "author_name": "Hugues Auma\u00eetre",
-        "author_inst": "Centre Hospitalier de Perpignan"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.03.05.21249174",
     "rel_title": "Serological surveys to estimate cumulative incidence of SARS-CoV-2 infection in adults (Sero-MAss study), Massachusetts, July-August 2020",
@@ -880429,6 +878785,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "occupational and environmental health"
   },
+  {
+    "rel_doi": "10.1101/2021.03.06.21251482",
+    "rel_title": "A Rapid Method to Evaluate Pre-Travel Testing Programs for COVID-19: A Study in Hawaii",
+    "rel_date": "2021-03-08",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.06.21251482",
+    "rel_abs": "BackgroundPre-travel testing programs are being implemented around the world to curb COVID-19 and its variants from incoming travelers. A common approach is a single pre-travel test, 72 hours before departure, such as in Hawaii; however this raises concerns for those who are incubating or those infected after pre-travel testing or during transit. We need a rapid method to assess the effectiveness of pre-travel testing programs, and we use Hawaii as our case study.\n\nMethodsWe invited travelers departing from Kahului main airport at the end of their visit to Maui (major tourist destination among the Hawaiian islands) and performed COVID-19 PCR testing. Eligible participants needed a negative pre-travel test and a Hawaiian stay [&le;] 14 days. We designed for anonymous testing at the end of travel so that travel plans would be unaffected, and we aimed for [&ge;] 70% study participation.\n\nResultsAmong consecutive eligible travelers, 282 consented and 111 declined to participate, leading to a 72% (67-76%, 95% confidence interval) participation rate. Among 281 tested participants, two were positive with COVID-19, with an estimated positivity rate of 7 cases per 1,000 travelers. The top states of residence are California (58%) and Washington (21%). The mean length of stay was 7.7 {+/-} 0.2 days. Regarding pre-travel testing, 87% had non-nasopharyngeal tests and 66% had self-administered tests.\n\nConclusionsThis positivity rate leads to an estimated 17-30 infected travelers arriving daily to Maui in November-December 2020, and an estimated 52-70 infected travelers arriving daily to Hawaii during the same period. These counts surpass the Maui District Health Offices projected ability to accommodate 10 infected visitors daily in Maui; therefore, an additional mitigation layer for travelers is recommended. This rapid field study can be replicated widely in airports to assess effectiveness of pre-travel programs and can be expanded to evaluate COVID-19 importation and its variants.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Amy T. Hou",
+        "author_inst": "Medical Reserve Corps, Maui District Health Office, Hawaii Department of Health"
+      },
+      {
+        "author_name": "Genevieve C. Pang",
+        "author_inst": "Maui District Health Office, Hawaii Department of Health"
+      },
+      {
+        "author_name": "Kristin M. Mills",
+        "author_inst": "Maui District Health Office, Hawaii Department of Health"
+      },
+      {
+        "author_name": "Krizhna L. Bayudan",
+        "author_inst": "Medical Reserve Corps, Maui District Health Office, Hawaii Department of Health"
+      },
+      {
+        "author_name": "Dayna M. Moore",
+        "author_inst": "Medical Reserve Corps, Maui District Health Office, Hawaii Department of Health"
+      },
+      {
+        "author_name": "Luz P. Medina",
+        "author_inst": "Maui County Medical Society"
+      },
+      {
+        "author_name": "Lorrin W. Pang",
+        "author_inst": "Maui District Health Office, Hawaii Department of Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.03.06.21252994",
     "rel_title": "Meta-Analysis of the Dynamics of the Emergence of Mutations and Variants of SARS-CoV-2",
@@ -881834,45 +880233,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.03.03.21252867",
-    "rel_title": "Rapid increase of SARS-CoV-2 variant B.1.1.7 detected in sewage samples from England between October 2020 and January 2021",
-    "rel_date": "2021-03-07",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.03.21252867",
-    "rel_abs": "SARS-CoV-2 variants with multiple amino acid mutations in the spike protein are emerging in different parts of the world raising concerns on their possible impact on human immune response to the virus and vaccine efficacy against them. Recently, a variant named lineage B.1.1.7 was detected and shown to be rapidly spreading across the UK since November 2020. As surveillance for these SARS-CoV-2 variants of concern (VOCs) becomes critical, we have investigated the use of environmental surveillance (ES) for the rapid detection and quantification of B.1.1.7 viruses in sewage as a way of monitoring its expansion that is independent on the investigation of identified clinical cases. B.1.1.7 mutations in viral sequences from sewage were first identified in a sample collected in London on 10th November 2020 and shown to rapidly increase in frequency to >95% in January 2021, in agreement with clinical data over the same period. We show that ES can provide an early warning of VOCs becoming prevalent in the population and that, as well as B.1.1.7, our method can potentially detect VOCs B.1.351 and P.1, first identified in South Africa and Brazil, respectively, and other viruses also carrying critical spike mutation E484K, known to have an effect on virus antigenicity.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Thomas Wilton",
-        "author_inst": "National Institute for Biological Standards and Control"
-      },
-      {
-        "author_name": "Erika Bujaki",
-        "author_inst": "National Institute for Biological Standards and Control"
-      },
-      {
-        "author_name": "Dimitra Klapsa",
-        "author_inst": "National Institute for Biological Standards and Control"
-      },
-      {
-        "author_name": "Martin Fritzsche",
-        "author_inst": "National Institute for Biological Standards and Control"
-      },
-      {
-        "author_name": "Ryan Mate",
-        "author_inst": "National Institute for Biological Standards and Control"
-      },
-      {
-        "author_name": "Javier Martin",
-        "author_inst": "National Institute for Biological Standards and Control"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.03.04.21252885",
     "rel_title": "Prevalence of vitamin D is not associated with the COVID-19 epidemic in Europe. A judicial update of the existing evidence.",
@@ -882235,6 +880595,69 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2021.03.03.21252838",
+    "rel_title": "SARS-CoV-2 transmission in intercollegiate athletics not fully mitigated with daily antigen testing",
+    "rel_date": "2021-03-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.03.21252838",
+    "rel_abs": "BackgroundHigh frequency, rapid turnaround SARS-CoV-2 testing continues to be proposed as a way of efficiently identifying and mitigating transmission in congregate settings. However, two SARS-CoV-2 outbreaks occurred among intercollegiate university athletic programs during the fall 2020 semester despite mandatory directly observed daily antigen testing.\n\nMethodsDuring the fall 2020 semester, athletes and staff in both programs were tested daily using Quidels Sofia SARS Antigen Fluorescent Immunoassay (FIA), with positive antigen results requiring confirmatory testing with real-time reverse transcription polymerase chain reaction (RT-PCR). We used genomic sequencing to investigate transmission dynamics in these two outbreaks.\n\nResultsIn Outbreak 1, 32 confirmed cases occurred within a university athletics program after the index patient attended a meeting while infectious despite a negative antigen test on the day of the meeting. Among isolates sequenced from Outbreak 1, 24 (92%) of 26 were closely related, suggesting sustained transmission following an initial introduction event. In Outbreak 2, 12 confirmed cases occurred among athletes from two university programs that faced each other in an athletic competition despite receiving negative antigen test results on the day of the competition. Sequences from both teams were closely related and unique from strains circulating in the community, suggesting transmission during intercollegiate competition.\n\nConclusionsThese findings suggest that antigen testing alone, even when mandated and directly observed, may not be sufficient as an intervention to prevent SARS-CoV-2 outbreaks in congregate settings, and highlights the importance of supplementing serial antigen testing with appropriate mitigation strategies to prevent SARS-CoV-2 outbreak in congregate settings.\n\nSummaryHigh frequency, rapid turnaround SARS-CoV-2 testing continues to be proposed as a way of efficiently identifying and mitigating transmission in congregate settings. However, here we describe two SARS-CoV-2 outbreaks occurred among intercollegiate university athletic programs during the fall 2020 semester.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Gage Kahl Moreno",
+        "author_inst": "University of Wisconsin - Madison"
+      },
+      {
+        "author_name": "Katarina M Braun",
+        "author_inst": "University of Wisconsin-Madison"
+      },
+      {
+        "author_name": "Ian W Pray",
+        "author_inst": "Wisconsin Department of Health Services"
+      },
+      {
+        "author_name": "Hannah E Seagaloff",
+        "author_inst": "Wisconsin Department of Health Services"
+      },
+      {
+        "author_name": "Ailam Lim",
+        "author_inst": "University of Wisconsin - Madison"
+      },
+      {
+        "author_name": "Keith Poulsen",
+        "author_inst": "University of Wisconsin - Madison"
+      },
+      {
+        "author_name": "Jonathan Meiman",
+        "author_inst": "Wisconsin Department of Health Services"
+      },
+      {
+        "author_name": "James Borchers",
+        "author_inst": "Ohio State University"
+      },
+      {
+        "author_name": "Ryan P Westergaard",
+        "author_inst": "Wisconsin Department of Health Services"
+      },
+      {
+        "author_name": "Michael K Moll",
+        "author_inst": "University of Wisconsin - Madison"
+      },
+      {
+        "author_name": "Thomas Friedrich",
+        "author_inst": "University of Wisconsin Madison"
+      },
+      {
+        "author_name": "David H O'Connor",
+        "author_inst": "University of Wisconsin-Madison"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.03.03.21252861",
     "rel_title": "The COVID-19 health equity twindemic: Statewide epidemiologic trends of SARS-CoV-2 outcomes among racial minorities and in rural America",
@@ -883932,25 +882355,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.03.02.21252761",
-    "rel_title": "Comparing Vaccination Strategies in Canada Under Different Assumptions",
-    "rel_date": "2021-03-05",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.02.21252761",
-    "rel_abs": "This paper estimates the outcomes of two different COVID-19 vaccination strategies in Canada for the mRNA vaccines currently approved for Emergency Use Authorization (EUA), modelled on the vaccination and effectiveness of the Pfizer vaccine which is likely to be more widely administered in Canada. The first strategy is the manufacturer recommended standard of two doses (two-dose strategy) given within 21 days apart versus a strategy of giving a larger group a single dose of vaccine (first-dose-for-most strategy) by delaying the second injection.\n\nThree parameters are varied in the course of 36 estimation scenarios of the population-level effects of the two vaccination strategies. The first is the effectiveness of a single dose of vaccine at preventing disease, the second is the effectiveness of the vaccine at preventing transmission of the virus, and the third is the rate of transmission of the virus during the course of the simulations.\n\nOver the course of the different scenarios, the first-dose-for-most strategy was superior in reducing disease transmission in all scenarios where vaccination is assumed to have an effect on viral transmission. The results for fatalities was mixed, with the first-dose-for-most strategy being superior in cases where a higher first-dose effectiveness at preventing disease was assumed.\n\nFinally, in the best-guess scenarios where a 75% reduction in disease transmission and a 92.6% effectiveness at preventing disease from a single dose were used, the first-dose-for-most strategy was superior in a situation with reduced vaccine doses available, and switching to the first-dose-for-most strategy earlier helped to prevent a higher proportion of cases and deaths.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Timothy Ruse",
-        "author_inst": "Concordia University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.03.03.21252464",
     "rel_title": "Covid-19 impact on Parkinson's Disease patients treated by drugs or deep brain stimulation",
@@ -884281,6 +882685,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.03.02.21252746",
+    "rel_title": "Providing a safe, in-person, residential college experience during the COVID-19 pandemic",
+    "rel_date": "2021-03-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.02.21252746",
+    "rel_abs": "Due to the COVID-19 pandemic, higher education institutions were forced to make difficult decisions regarding the 2020-2021 academic year. Many institutions decided to have courses in an online remote format, others decided to attempt an in-person experience, while still others took a hybrid approach. Hope College (Holland, MI) decided that an in-person semester would be safer and more equitable for students. To achieve this at a residential college required broad collaboration across multiple stakeholders. Here, we share lessons learned and detail Hope Colleges model, including wastewater surveillance, comprehensive testing, contact tracing and isolation procedures, that allowed us to deliver on our commitment of an in-person, residential college experience.",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Scott A Travis",
+        "author_inst": "Hope College"
+      },
+      {
+        "author_name": "Aaron A Best",
+        "author_inst": "Hope College"
+      },
+      {
+        "author_name": "Kristyn S Bochniak",
+        "author_inst": "Hope College"
+      },
+      {
+        "author_name": "Nicole D Dunteman",
+        "author_inst": "Hope College"
+      },
+      {
+        "author_name": "Jennifer Fellinger",
+        "author_inst": "Hope College"
+      },
+      {
+        "author_name": "Peter D Folkert",
+        "author_inst": "Hope College"
+      },
+      {
+        "author_name": "Timothy Koberna",
+        "author_inst": "Hope College"
+      },
+      {
+        "author_name": "Benjamin G Kopek",
+        "author_inst": "Hope College"
+      },
+      {
+        "author_name": "Brent P Krueger",
+        "author_inst": "Hope College"
+      },
+      {
+        "author_name": "Jeff Pestun",
+        "author_inst": "Hope College"
+      },
+      {
+        "author_name": "Michael J Pikaart",
+        "author_inst": "Hope College"
+      },
+      {
+        "author_name": "Cindy Sabo",
+        "author_inst": "Hope College"
+      },
+      {
+        "author_name": "Alex J Schuitema",
+        "author_inst": "Hope College"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.03.02.21252290",
     "rel_title": "HiSpike: A high-throughput cost effective sequencing method for the SARS-CoV-2 spike gene",
@@ -885650,181 +884121,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2021.03.03.433558",
-    "rel_title": "Engineered SARS-CoV-2 receptor binding domain improves immunogenicity in mice and elicits protective immunity in hamsters",
-    "rel_date": "2021-03-04",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.03.433558",
-    "rel_abs": "Global containment of COVID-19 still requires accessible and affordable vaccines for low- and middle-income countries (LMICs).1 Recently approved vaccines provide needed interventions, albeit at prices that may limit their global access.2 Subunit vaccines based on recombinant proteins are suited for large-volume microbial manufacturing to yield billions of doses annually, minimizing their manufacturing costs.3 These types of vaccines are well-established, proven interventions with multiple safe and efficacious commercial examples.4-6 Many vaccine candidates of this type for SARS-CoV-2 rely on sequences containing the receptor-binding domain (RBD), which mediates viral entry to cells via ACE2.7,8 Here we report an engineered sequence variant of RBD that exhibits high-yield manufacturability, high-affinity binding to ACE2, and enhanced immunogenicity after a single dose in mice compared to the Wuhan-Hu-1 variant used in current vaccines. Antibodies raised against the engineered protein exhibited heterotypic binding to the RBD from two recently reported SARS-CoV-2 variants of concern (501Y.V1/V2). Presentation of the engineered RBD on a designed virus-like particle (VLP) also reduced weight loss in hamsters upon viral challenge.",
-    "rel_num_authors": 40,
-    "rel_authors": [
-      {
-        "author_name": "Neil C Dalvie",
-        "author_inst": "Massachusetts Institute of Technology"
-      },
-      {
-        "author_name": "Sergio A Rodriguez-Aponte",
-        "author_inst": "Massachusetts Institute of Technology"
-      },
-      {
-        "author_name": "Brittany L Hartwell",
-        "author_inst": "Massachusetts Institute of Technology"
-      },
-      {
-        "author_name": "Lisa H Tostanoski",
-        "author_inst": "Harvard Medical School"
-      },
-      {
-        "author_name": "Andrew M Biedermann",
-        "author_inst": "Massachusetts Institute of Technology"
-      },
-      {
-        "author_name": "Laura E Crowell",
-        "author_inst": "Massachusetts Institute of Technology"
-      },
-      {
-        "author_name": "Kawaljit Kaur",
-        "author_inst": "University of Kansas"
-      },
-      {
-        "author_name": "Ozan Kumru",
-        "author_inst": "University of Kansas"
-      },
-      {
-        "author_name": "Lauren Carter",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Jingyou Yu",
-        "author_inst": "Harvard Medical School"
-      },
-      {
-        "author_name": "Aiquan Chang",
-        "author_inst": "Harvard Medical School"
-      },
-      {
-        "author_name": "Katherine McMahan",
-        "author_inst": "Harvard Medical School"
-      },
-      {
-        "author_name": "Thomas Courant",
-        "author_inst": "Vaccine Formulation Institute"
-      },
-      {
-        "author_name": "Celia Lebas",
-        "author_inst": "Vaccine Formulation Institute"
-      },
-      {
-        "author_name": "Ashley A Lemnios",
-        "author_inst": "Massachusetts Institute of Technology"
-      },
-      {
-        "author_name": "Kristen A Rodrigues",
-        "author_inst": "Massachusetts Institute of Technology"
-      },
-      {
-        "author_name": "Murillo Silva",
-        "author_inst": "Massachusetts Institute of Technology"
-      },
-      {
-        "author_name": "Ryan S Johnston",
-        "author_inst": "Massachusetts Institute of Technology"
-      },
-      {
-        "author_name": "Christopher A Naranjo",
-        "author_inst": "Massachusetts Institute of Technology"
-      },
-      {
-        "author_name": "Mary Kate Tracey",
-        "author_inst": "Massachusetts Institute of Technology"
-      },
-      {
-        "author_name": "Joseph R Brady",
-        "author_inst": "Massachusetts Institute of Technology"
-      },
-      {
-        "author_name": "Charles A Whittaker",
-        "author_inst": "Massachusetts Institute of Technology"
-      },
-      {
-        "author_name": "Dongsoo Yun",
-        "author_inst": "Massachusetts Institute of Technology"
-      },
-      {
-        "author_name": "Swagata Kar",
-        "author_inst": "Bioqual"
-      },
-      {
-        "author_name": "Maciel Porto",
-        "author_inst": "Bioqual"
-      },
-      {
-        "author_name": "Megan Lok",
-        "author_inst": "Bioqual"
-      },
-      {
-        "author_name": "Hanne Andersen",
-        "author_inst": "Bioqual"
-      },
-      {
-        "author_name": "Mark G Lewis",
-        "author_inst": "Bioqual"
-      },
-      {
-        "author_name": "Kerry R Love",
-        "author_inst": "Massachusetts Institute of Technology"
-      },
-      {
-        "author_name": "Danielle L Camp",
-        "author_inst": "Massachusetts Institute of Technology"
-      },
-      {
-        "author_name": "Judith Maxwell Silverman",
-        "author_inst": "Gates Medical Research Institute"
-      },
-      {
-        "author_name": "Harry Kleanthous",
-        "author_inst": "Bill & Melinda Gates Foundation"
-      },
-      {
-        "author_name": "Sangeeta B Joshi",
-        "author_inst": "University of Kansas"
-      },
-      {
-        "author_name": "David B Volkin",
-        "author_inst": "University of Kansas"
-      },
-      {
-        "author_name": "Patrice M Dubois",
-        "author_inst": "Vaccine Formulation Institute"
-      },
-      {
-        "author_name": "Nicolas Collin",
-        "author_inst": "Vaccine Formulation Institute"
-      },
-      {
-        "author_name": "Neil P King",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Dan H Barouch",
-        "author_inst": "Harvard Medical School"
-      },
-      {
-        "author_name": "Darrell J Irvine",
-        "author_inst": "Massachusetts Institute of Technology"
-      },
-      {
-        "author_name": "J Christopher Love",
-        "author_inst": "Massachusetts Institute of Technology"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "molecular biology"
-  },
   {
     "rel_doi": "10.1101/2021.03.03.21252830",
     "rel_title": "Saliva testing is accurate for early-stage and presymptomatic COVID-19",
@@ -886139,6 +884435,45 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2021.03.04.433849",
+    "rel_title": "Efficient Inhibition of SARS-CoV-2 Using Chimeric Antisense Oligonucleotides through RNase L Activation",
+    "rel_date": "2021-03-04",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.04.433849",
+    "rel_abs": "There is an urgent need for effective antiviral drugs to alleviate the current COVID-19 pandemic. Here, we rationally designed and developed chimeric antisense oligonucleotides to degrade envelope and spike RNAs of SARS-CoV-2. Each oligonucleotide comprises a 3 antisense sequence for target recognition and a 5-phosphorylated 2-5 poly(A)4 for guided ribonuclease L (RNase L) activation. Since RNase L can potently cleave single strand RNA during innate antiviral response, the improved degradation efficiency of chimeric oligonucleotides was twice as much as classic antisense oligonucleotides in Vero cells, for both SARS-CoV-2 RNA targets. In pseudovirus infection models, one of chimeric oligonucleotides targeting spike RNA achieved potent and broad-spectrum inhibition of both SARS-CoV-2 and its recently reported N501Y and/or {Delta}H69/{Delta}V70 mutants. These results showed that the constructed chimeric oligonucleotides could efficiently degrade pathogenic RNA of SARS-CoV-2 facilitated by immune activation, showing promising potentials as antiviral nucleic acid drugs for COVID-19.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Xiaoxuan Su",
+        "author_inst": "State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University"
+      },
+      {
+        "author_name": "Wenxiao Ma",
+        "author_inst": "State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University"
+      },
+      {
+        "author_name": "Boyang Cheng",
+        "author_inst": "State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University"
+      },
+      {
+        "author_name": "Qian Wang",
+        "author_inst": "State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University"
+      },
+      {
+        "author_name": "Demin Zhou",
+        "author_inst": "State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University"
+      },
+      {
+        "author_name": "Xinjing Tang",
+        "author_inst": "State Key Laboratory of Natural and Biomimetic Drugs, the School of Pharmaceutical Sciences, Peking University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2021.03.04.433658",
     "rel_title": "Inhibiting SARS-CoV-2 infection in vitro by suppressing its receptor, angiotensin-converting enzyme 2, via aryl-hydrocarbon receptor signal",
@@ -887696,29 +886031,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.03.02.21252694",
-    "rel_title": "365 days with COVID-19 in Iran: data analysis and epidemic curves",
-    "rel_date": "2021-03-03",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.02.21252694",
-    "rel_abs": "BackgroundThe first confirmed cases of COVID-19 in Iran were reported on February 19, 2020. This study aimed to analyze the epidemic curves and to investigate the correlation between epidemic parameters and furthermore to analyze the impact of control measures on the spread of COVID-19 in Iran during 365 days of the epidemic.\n\nMethodsWe used data from February 20, 2020, to February 18, 2021, on the number of COVID-19 cases reported by Iranian governments. Pearson correlation coefficient was applied to investigate the correlation between different epidemic parameters. The number of daily deaths per daily new cases was averaged to calculate daily death rate and the same method was used to investigate the rate of daily positive tests. Furthermore, we employed two different methods to calculate the effective reproduction number using reported data.\n\nResultsThe results showed that there was a strong correlation between the number of daily deaths and the number of daily new cases (specially the admitted cases). The results also indicated that the mean of daily death rate of COVID-19 during 365 days was 4.9 percent, and averagely 13.9 percent of daily tests results were positive. Furthermore, epidemic curves showed that implementing strict social distancing measures effectively reduced the number of confirmed cases. The effective reproduction curve indicated that social distancing is still necessary to control the spread of COVID-19 in Iran.\n\nConclusionsAnalyzing the prevention and control measures indicated that the strict social distancing implemented by the government effectively reduces the number of new cases and deaths. The curve of reproduction number also showed that effective reproduction number is still above one; hence, it is necessary to continue strict social distancing and control travelling to prevent causing another wave of outbreak especially in Persian New Year.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Ebrahim Sahafizadeh",
-        "author_inst": "Persian Gulf University"
-      },
-      {
-        "author_name": "Saeed Talatian Azad",
-        "author_inst": "Persian Gulf University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.03.01.21252508",
     "rel_title": "Experiences of COVID-19 Recovered Patients - A Qualitative Case Study from a Hotspot in Saudi Arabia",
@@ -888197,6 +886509,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.03.02.21250607",
+    "rel_title": "Modeling University Reopening in Low Risk Countries During COVID-19",
+    "rel_date": "2021-03-03",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.02.21250607",
+    "rel_abs": "The safety of students worldwide remains a key issue during COVID-19. The reopening of universities in high risk countries during Fall 2020 resulted in numerous outbreaks. While regular screening and testing on campus can prevent the transmission of SARS-CoV-2, they are extremely challenging to implement due to various reasons such as cost and logistics. However, for low risk countries with minimal to no community spread, our study suggests that universities can fully reopen without testing, if students self-quarantine for 14 days on arrival and adopt proper nonpharmaceutical interventions (NPIs). This alternative strategy might save institutions millions of dollars. We adopt agent-based simulation to model virus transmission on campus and test the effectiveness of several NPIs when school reopens. Assuming one initially infected student, results indicate that transmission between roommates causes the most infections with visitors, ground floors, and elevators, being the next main contributors. Limiting density and/or population are not impactful at flattening the curve. However, adopting masks, minimizing movement, and increasing the frequency of cleaning can effectively minimize infection and prevent outbreak, allowing for classes and activities to resume as normal.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Jing Yang (Sunny) Xi",
+        "author_inst": "Tsinghua University"
+      },
+      {
+        "author_name": "Wai Kin (Victor) Chan",
+        "author_inst": "Tsinghua University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.03.03.21252286",
     "rel_title": "Impact of COVID-19 pandemic on Black, Asian and Minority Ethnic (BAME) communities: a qualitative study on the perspectives of BAME community leaders",
@@ -889982,137 +888317,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "intensive care and critical care medicine"
   },
-  {
-    "rel_doi": "10.1101/2021.02.26.21252256",
-    "rel_title": "Utility of a Clinical Scoring System for Point of Care Triaging in COVID-19 Pneumonia",
-    "rel_date": "2021-03-02",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.26.21252256",
-    "rel_abs": "BackgroundSurges in COVID-19 disease cases can rapidly overwhelm healthcare resources; triaging to appropriate levels of care can assist in resource planning. At the beginning of the pandemic, we developed a simple triage tool, the Temple COVID-19 Pneumonia Triage Tool (TemCOV) based on a combination of clinical and radiographic features that are readily available on presentation to categorize and predict illness severity.\n\nMethodsWe prospectively examined 579 sequential cases admitted to Temple University Hospital who were assigned severity categories on admission. Our primary outcome was to compare the performance of TemCOV in predicting patients who have the highest likely of admission to the ICU at 24 and at 72 hours to other standard triage tools: the National Early Warning System (NEWS), the Modified Early Warning System (MEWS) and the CURB65 score. Additional endpoints included need for invasive mechanical ventilation (IMV) within 72 hours, total hospital admission charges, and mortality.\n\nResults26% of patients fell within our highest risk Category 4 and were more likely to require ICU admission at 24 hours (OR 11.51) and 72 hours (OR 8.6). Additionally they had the highest likelihood of needing IMV (OR 29.47) and in-hospital mortality (OR 2.37)., TemCOV performed similar to MEWS in predicting ICU admission at 24 hours (receive operator characteristic (ROC) curve area under the curve (AUC) 0.77 vs. 0.74, p=0.21) but better than NEWS2 and CURB65 (ROC AUC 0.77 vs. 0.69 and 0.77 vs. 0.64, respectively, p<0.01). While all severity scores had a weak correlation to hospital charges, the TemCOV performed the best among all severity scores measured (r=0.18); median hospital charges for Category 4 patients was $170,468 ($96,972-$487,556).\n\nConclusionTemCOV is a simple triage score that can be used upon hospitalization in patients with COVID-19 that predicts the need for hospital resources such as ICU bed capacity, invasive mechanical ventilation and personnel staffing.",
-    "rel_num_authors": 29,
-    "rel_authors": [
-      {
-        "author_name": "Andrew J Gangemi",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Rohit Gupta",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Gustavo Fernandez-Romero",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Huaqing Zhao",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Maulin Patel",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Junad Chowdhury",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Massa Zantah",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Matthew Zheng",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Osheen Abramian",
-        "author_inst": "Cooper University Hospital"
-      },
-      {
-        "author_name": "Stephen Codella",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Linda Vien",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Eduardo Dominguez-Castillo",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Timothy Buckey",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Charles Earley",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Jourdan Frankovich",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Mali Jurkowski",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Zachary Jurkowski",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Nanzhou Guo",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Paige Stanley",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Brenton Halsey",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Jasleen Kahlon",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Navjot Kaur",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Roman Prosniak",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Maruti Kumaran",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Chandra Dass",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "David Fleece",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Michael R Jacobs",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "Gerard J Criner",
-        "author_inst": "Lewis Katz School of Medicine at Temple University"
-      },
-      {
-        "author_name": "- Temple University COVID-19 Research Group",
-        "author_inst": ""
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "intensive care and critical care medicine"
-  },
   {
     "rel_doi": "10.1101/2021.02.28.21252625",
     "rel_title": "Seasonal patterns COVID-19 and Flu Like Illnesses comparable",
@@ -890359,6 +888563,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.02.28.21252648",
+    "rel_title": "Shifting research priorities in maternal and child health in the COVID-19 pandemic era in India: a renewed focus on systems strengthening",
+    "rel_date": "2021-03-02",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.28.21252648",
+    "rel_abs": "BackgroundThe remarkable progress seen in maternal and child health (MCH) in India over the past two decades has been impacted by setbacks from the COVID-19 pandemic. We aimed to undertake a rapid assessment to identify key priorities for public health research in MCH in India within the context and aftermath of the COVID-19 pandemic.\n\nMethodsA web-based survey was developed to identify top research priorities in MCH. It consisted of 26 questions on six broad domains: vaccine preventable diseases, outbreak preparedness, primary healthcare integration, maternal health, neonatal health, and infectious diseases. Key stakeholders were invited to participate between September and November 2020. Participants assigned importance on a 5-point Likert scale, and assigned overall ranks to each sub-domain research priority. Descriptive statistics were used to examine Likert scale responses, and a ranking analysis was done to obtain an \"average ranking score\" and identify the top research priority under each domain.\n\nResultsAmongst the 84 respondents, 37% were public-health researchers, 25% healthcare providers, 20% academic faculty and 13% were policy makers. Across the six domains, most respondents considered conducting research on systems strengthening as extremely important. The highest ranked research priorities were strengthening the public sector workforce (vaccine preventable diseases), enhancing public-health surveillance networks (outbreak preparedness), nutrition support through community workers (primary care integration), encouraging at least 4-8 antenatal visits (maternal health), neonatal resuscitation to reduce birth asphyxia (neonatal health) and pediatric and maternal screening and treatment of tuberculosis (infectious diseases). Common themes identified through open-ended questions were also systems strengthening priorities across domains.\n\nConclusionsThe overall focus for research priorities in MCH in India during the COVID-19 pandemic is on strengthening existing services and service delivery, rather than novel research. Our results highlight pivotal steps within the roadmap for advancing and sustaining maternal and child health gains during the ongoing COVID-19 pandemic and beyond.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Kayur Mehta",
+        "author_inst": "Johns Hopkins University"
+      },
+      {
+        "author_name": "Sanjay Zodpey",
+        "author_inst": "Public Health Foundation of India"
+      },
+      {
+        "author_name": "Preetika Banerjee",
+        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
+      },
+      {
+        "author_name": "Stephanie L Pocius",
+        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
+      },
+      {
+        "author_name": "Baldeep Dhaliwal",
+        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
+      },
+      {
+        "author_name": "Andrea DeLuca",
+        "author_inst": "Amuptee Coalition"
+      },
+      {
+        "author_name": "Sangeeta Das Bhattacharya",
+        "author_inst": "Indian Institute of Technology Kharagpur"
+      },
+      {
+        "author_name": "Shailendra Hegde",
+        "author_inst": "Piramal Swasthya"
+      },
+      {
+        "author_name": "Paramita Sengupta",
+        "author_inst": "All India Institute of Medical Sciences Kalyani"
+      },
+      {
+        "author_name": "MADHU GUPTA",
+        "author_inst": "postgraduate institute of medical education and research"
+      },
+      {
+        "author_name": "Anita Shet",
+        "author_inst": "Johns Hopkins School of Public Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health policy"
+  },
   {
     "rel_doi": "10.1101/2021.03.01.21252652",
     "rel_title": "Early effectiveness of COVID-19 vaccination with BNT162b2 mRNA vaccine and ChAdOx1 adenovirus vector vaccine on symptomatic disease, hospitalisations and mortality in older adults in England",
@@ -891928,29 +890191,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.03.01.433503",
-    "rel_title": "Cytoplasmic domain and enzymatic activity of ACE2 is not required for PI4KB dependent endocytosis entry of SARS-CoV-2 into host cells",
-    "rel_date": "2021-03-02",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.01.433503",
-    "rel_abs": "The recent COVID-19 pandemic poses a global health emergency. Cellular entry of the causative agent SARS-CoV-2 is mediated by its spike protein interacting with cellular receptor- human angiotensin converting enzyme 2 (ACE2). Here, we used lentivirus based pseudotypes bearing spike protein to demonstrate that entry of SARS-CoV-2 into host cells is dependent on clathrin-mediated endocytosis, and phosphoinositides play essential role during this process. In addition, we showed that the intracellular domain and the catalytic activity of ACE2 is not required for efficient virus entry. These results provide new insights into SARS-CoV-2 cellular entry and present potential targets for drug development.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "LingJie Xu",
-        "author_inst": "Sichuan University"
-      },
-      {
-        "author_name": "Bing Liu",
-        "author_inst": "Imperial College London"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2021.03.02.21252203",
     "rel_title": "Performance evaluation of the Roche Elecsys Anti-SARS-CoV-2 S immunoassay",
@@ -892245,6 +890485,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.02.27.21252593",
+    "rel_title": "Surgical activity in England and Wales during the COVID-19 pandemic: a nationwide observational cohort study",
+    "rel_date": "2021-03-01",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.27.21252593",
+    "rel_abs": "ObjectivesTo report the volume of surgical activity and the number of cancelled surgical procedures during the COVID-19 pandemic.\n\nDesign and settingAnalysis of electronic health record data from the National Health Service (NHS) in England and Wales.\n\nMethodsWe used hospital episode statistics for all adult patients undergoing surgery between 1st January 2020 and 31st December 2020. We identified surgical procedures using a previously published list of procedure codes. Procedures were stratified by urgency of surgery as defined by NHS England. We calculated the deficit of surgical activity by comparing the expected number of procedures from the years 2016-2019 with the actual number of procedures in 2020. We estimated the cumulative number of cancelled procedures by 31st December 2021 according patterns of activity in 2020.\n\nResultsThe total number of surgical procedures carried out in England and Wales in 2020 was 3,102,674 compared to the predicted number of 4,671,338. This represents a 33.6% reduction in the national volume of surgical activity. There were 763,730 emergency surgical procedures (13.4% reduction), compared to 2,338,944 elective surgical procedures (38.6% reduction). The cumulative number of cancelled or postponed procedures was 1,568,664. We estimate that this will increase to 2,358,420 by 31st December 2021.\n\nConclusionsThe volume of surgical activity in England and Wales was reduced by 33.6% in 2020, resulting in over 1,568,664 cancelled operations. This deficit will continue to grow in 2021.\n\nSummary boxesO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIThe COVID-19 pandemic necessitated a rapid change in the provision of care, including the suspension of a large proportion of surgical activity\nC_LIO_LISurgical activity has yet to return to normal and has been further impacted by subsequent waves of the pandemic\nC_LIO_LIThis will lead to a large backlog of cases\nC_LI\n\nWhat this study addsO_LI3,102,674 surgical procedures were performed in England and Wales during 2020, a 33.6% reduction on the expected yearly surgical activity\nC_LIO_LIOver 1.5 million procedures were not performed, with this deficit likely to continue to grow to 2.3 million by the end of 2021\nC_LIO_LIThis deficit is the equivalent of more than 6 months of pre-pandemic surgical activity, requiring a monumental financial and logistic challenge to manage\nC_LI",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Thomas D Dobbs",
+        "author_inst": "Swansea University Medical School"
+      },
+      {
+        "author_name": "John A G Gibson",
+        "author_inst": "Swansea University Medical School"
+      },
+      {
+        "author_name": "Alexander J Fowler",
+        "author_inst": "Queen Mary, University of London"
+      },
+      {
+        "author_name": "Tom E Abbott",
+        "author_inst": "Queen Mary University of London"
+      },
+      {
+        "author_name": "Tasnin Shahid",
+        "author_inst": "Queen Mary University of London"
+      },
+      {
+        "author_name": "Fatemeh Torabi",
+        "author_inst": "Swansea University"
+      },
+      {
+        "author_name": "Rowena Griffiths",
+        "author_inst": "Swansea University"
+      },
+      {
+        "author_name": "Ronan A Lyons",
+        "author_inst": "Swansea University"
+      },
+      {
+        "author_name": "Rupert M Pearse",
+        "author_inst": "Queen Mary University of London"
+      },
+      {
+        "author_name": "Iain S Whitaker",
+        "author_inst": "Swansea University Medical School"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "surgery"
+  },
   {
     "rel_doi": "10.1101/2021.02.26.21252497",
     "rel_title": "Impact of the COVID-19 pandemic on cognitive function in Japanese community-dwelling older adults in a class for preventing cognitive decline",
@@ -893826,29 +892121,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2021.02.28.433287",
-    "rel_title": "The E3 Ubiquitin Ligase RNF5 Facilitates SARS-CoV-2 Membrane Protein-Mediated Virion Release",
-    "rel_date": "2021-03-01",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.28.433287",
-    "rel_abs": "As enveloped virus, SARS-CoV-2 membrane protein (M) mediates viral release from cellular membranes, but the molecular mechanisms of SARS-CoV-2 virions release remain poorly understood. Here, we performed RNAi screening and identified the E3 ligase RNF5 which mediates ubiquitination of SARS-CoV-2 M at residue K15 to enhance the interaction of viral envelope (E) with M. M-E complex ensures the uniform size of viral particles for viral maturation and mediates viral release. Moreover, overexpression of M induces complete autophagy which is dependent on RNF5-mediated ubiquitin modification. M inhibits the activity of lysosome protease, and uses autolysosomes for virion release. Consequently, all these results demonstrate that RNF5 mediates ubiquitin modification of SARS-CoV-2 M to stabilize the M-E complex and induce autophagy for virion release.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Zhen Yuan",
-        "author_inst": "Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030"
-      },
-      {
-        "author_name": "Binbin Ding",
-        "author_inst": "Huazhong University of Science and Technology"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2021.03.01.433428",
     "rel_title": "A Comparison of Performance for Different SARS-Cov-2 Sequencing Protocols",
@@ -894079,6 +892351,53 @@
     "type": "new results",
     "category": "scientific communication and education"
   },
+  {
+    "rel_doi": "10.1101/2021.02.27.21252577",
+    "rel_title": "Nationwide rollout reveals efficacy of epidemic control through digital contact tracing",
+    "rel_date": "2021-03-01",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.27.21252577",
+    "rel_abs": "Fueled by epidemiological studies of SARS-CoV-2, contact tracing by mobile phones has been put to use in many countries. A year into the pandemic, we lack conclusive evidence on its effectiveness. Here, we used a unique real world contact data set, collected during the rollout of the first Norwegian contact tracing app in the Spring of 2020, to address this gap. Our dataset involves millions of contacts between 12.5% of the adult population, and enabled us to measure the real-world app performance. The technological tracing efficacy was measured at 80%, and we estimated that at least 11.0% of the discovered close contacts could not be identified by manual contact tracing. The overall effectiveness of digital tracing depends strongly on app uptake, but significant impact can be achieved for moderate uptake numbers. Used as a supplement to manual tracing and other measures, digital tracing can be instrumental in controlling the pandemic. Our findings can thus help informing public health policies in the coming months.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Ahmed Elmokashfi",
+        "author_inst": "Simula Metropolitan CDE"
+      },
+      {
+        "author_name": "Joakim Sundnes",
+        "author_inst": "Simula Research Lab"
+      },
+      {
+        "author_name": "Amund Kvalbein",
+        "author_inst": "Simula Metropolitan CDE"
+      },
+      {
+        "author_name": "Valeriya Naumova",
+        "author_inst": "Simula Metropolitan CDE"
+      },
+      {
+        "author_name": "Sven-Arne Reinemo",
+        "author_inst": "Simula Metropolitan CDE"
+      },
+      {
+        "author_name": "Per Magne Florvaag",
+        "author_inst": "Simula Research Lab"
+      },
+      {
+        "author_name": "H\u00e5kon Kvale Stensland",
+        "author_inst": "Simula Research Lab, University of Oslo"
+      },
+      {
+        "author_name": "Olav Lysne",
+        "author_inst": "Simula Metropolitan CDE and Oslo Metropolitan University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.02.09.21249859",
     "rel_title": "A precise score for the regular monitoring of COVID-19 patients condition validated within the first two waves of the pandemic",
@@ -895256,73 +893575,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
-  {
-    "rel_doi": "10.1101/2021.02.27.21252571",
-    "rel_title": "Performance of RT-PCR on saliva specimens compared to nasopharyngeal swabs for the detection of SARS-CoV-2 in children: A prospective comparative clinical trial",
-    "rel_date": "2021-03-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.27.21252571",
-    "rel_abs": "BackgroundSaliva RT-PCR is an attractive alternative for the detection of SARS-CoV-2 in adults with much less known in children.\n\nMethodsChildren and adolescents with symptoms suggestive of COVID-19 were prospectively enrolled in a comparative clinical trial of saliva and nasopharyngeal (NP) RT-PCR between November and December 2020. Detection rates and sensitivities of saliva and NP RT-PCR were compared. Participants with discordant NP and saliva RT-PCR results including viral load (VL) were also analyzed.\n\nResultOut of 405 patients enrolled, 397 patients had two tests performed. Mean age was 12.7 years (range 1.2-17.9). Detection rates were 22.9% (95%CI 18.8-27.1%) by saliva RT-PCR, 25.4% (21.2-29.7%) by NP RT-PCR, and 26.7% (22.4-31.1%) by any test. The sensitivity of saliva was 85.2% (78.2-92.1%) when using NP as the gold standard; in contrast, when saliva was considered the gold standard, the sensitivity of NP was 94.5% (89.8-99.2%).For a NP RT-PCR VL threshold of [&ge;]103 and [&ge;]104 copies/ml, sensitivity of saliva increases to 88.7% and 95.2% respectively. Sensitivity of saliva and NP swabs was respectively 89.5% and 95.3% in patient with symptoms less than 4 days (p=0.249) and 70.0% and 95.0% in those with symptoms [&ge;] 4 to 7 days (p=0.096). The 15 patients who had an isolated positive NP RT-PCR were significantly younger (p=0.034), had a lower NP VL (median 5.6x103 vs 3.9x107, p<0.001), and were not able to drool saliva at the end of the sampling (p=0.002). VLs were significantly lower with saliva PCR than with NP RT-PCR (median 8.7 cp/ml x104; IQR 1.2x104-5.2x105; vs median 4.0x107cp/ml; IQR 8.6x105-1.x108; p<0.001).\n\nConclusionSaliva PCR shows diagnostic performances close to NP RT-PCR for SARS-CoV2 detection in most symptomatic outpatient children and adolescents.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Yves Fougere",
-        "author_inst": "Lausanne University Hospital"
-      },
-      {
-        "author_name": "Jean Marc Schwob",
-        "author_inst": "Tropical and Travel Medicine Unit, Center for Primary Care and Public Health (Unisante)"
-      },
-      {
-        "author_name": "Alix Miauton",
-        "author_inst": "Tropical and Travel Medicine Unit, Center for Primary Care and Public Health (Unisante)"
-      },
-      {
-        "author_name": "Francesca Hoegger",
-        "author_inst": "Service of Pediatrics, Department Women-Mother-Child, Lausanne University Hospital, Switzerland"
-      },
-      {
-        "author_name": "Onya Opota",
-        "author_inst": "Institute of Microbiology, University of Lausanne and Lausanne University Hospital"
-      },
-      {
-        "author_name": "Katia Jaton",
-        "author_inst": "Institute of Microbiology, Lausanne University Hospital, Switzerland"
-      },
-      {
-        "author_name": "Rene Brouillet",
-        "author_inst": "Institute of Microbiology, Lausanne University Hospital, Switzerland"
-      },
-      {
-        "author_name": "Gilbert Greub",
-        "author_inst": "University of Lausanne"
-      },
-      {
-        "author_name": "Blaise Genton",
-        "author_inst": "Tropical and Travel Medicine Unit, Center for Primary Care and Public Health (Unisante) and university of Lausanne"
-      },
-      {
-        "author_name": "Mario Gehri",
-        "author_inst": "Pediatric Infectious Diseases and Vaccinology Unit, Department Women-Mother-Child, Lausanne University Hospital, Switzerland"
-      },
-      {
-        "author_name": "Ilaria Taddeo",
-        "author_inst": "Pediatric Emergency Center, Vidy-Med, Lausanne, Switzerland"
-      },
-      {
-        "author_name": "Valerie D'Acremont",
-        "author_inst": "Centre for primary care and public health, University of Lausanne"
-      },
-      {
-        "author_name": "Sandra Andrea Asner",
-        "author_inst": "Pediatric Infectious Diseases and Vaccinology Unit, Department Women-Mother-Child, Lausanne University Hospital, Switzerland"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.02.25.21252493",
     "rel_title": "SARS-CoV-2 Total and Subgenomic RNA Viral Load in Hospitalized Patients",
@@ -895669,6 +893921,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "cardiovascular medicine"
   },
+  {
+    "rel_doi": "10.1101/2021.02.26.21252553",
+    "rel_title": "Vaccination and herd immunity thresholds in heterogeneous populations",
+    "rel_date": "2021-03-01",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.26.21252553",
+    "rel_abs": "It has been suggested, without rigorous mathematical analysis, that the classical vaccine-induced herd immunity threshold (HIT) assuming a homogeneous population can be substantially higher than the minimum HIT obtained when considering population heterogeneities. We investigated this claim by developing, and rigorously analyzing, a vaccination model that incorporates various forms of heterogeneity and compared it with a model of a homogeneous population. By employing a two-group vaccination model in heterogeneous populations, we theoretically established conditions under which heterogeneity leads to different HIT values, depending on the relative values of the contact rates for each group, the type of mixing between groups, relative vaccine efficacy, and the relative population size of each group. For example, under biased random mixing and when vaccinating a given group results in disproportionate prevention of higher transmission per capita, it is optimal to vaccinate that group before vaccinating other groups. We also found situations, under biased assortative mixing assumption, where it is optimal to vaccinate more than one group. We show that regardless of the form of mixing between groups, the HIT values assuming a heterogeneous population are always lower than the HIT values obtained from a corresponding model with a homogeneous population. Using realistic numerical examples and parametrization (e.g., assuming assortative mixing together with vaccine efficacy of 95% and basic reproduction number of 2.5), we demonstrate that the HIT value considering heterogeneity (e.g., biased assortative mixing) is significantly lower (40%) compared with a HIT value of (63%) assuming a homogeneous population.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Elamin H Elbasha",
+        "author_inst": "Merck Inc."
+      },
+      {
+        "author_name": "Abba B. Gumel",
+        "author_inst": "Arizona State University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.02.27.21252583",
     "rel_title": "Predicting the effects of COVID-19 related interventions in urban settings by combining activity-based modelling, agent-based simulation, and mobile phone data",
@@ -896942,137 +895217,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "intensive care and critical care medicine"
   },
-  {
-    "rel_doi": "10.1101/2021.02.24.21251664",
-    "rel_title": "Obesity may hamper SARS-CoV-2 vaccine immunogenicity",
-    "rel_date": "2021-02-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.24.21251664",
-    "rel_abs": "BackgroundThe first goal of the study was to analyse the antibody titre 7 days after the second dose of BNT162b2 vaccine in a group of 248 healthcare workers (HCW). The second goal was to analyse how the antibody titre changes in correlation with age, gender and BMI.\n\nMethodsParticipants were assigned to receive the priming dose at baseline and booster dose at day 21. Blood and nasopharyngeal swabs were collected at baseline and 7 days after second dose of vaccine.\n\nFindings248 HWCs were analysed, 158 women (63.7%) and 90 men (36.3%). After the second dose of BNT162b2 vaccine, 99.5% of participants developed a humoral immune response.\n\nThe geometric mean concentration of antibodies among the vaccinated subjects after booster dose (285.9 AU/mL 95% CI: 249.5-327.7); was higher than that of human convalescent sera (39.4 AU/mL, 95% CI: 33.1-46.9), with p<0.0001. The antibody titre was found to be higher in young and female participants. A strong correlation of BMI classes with antibody titres was noticed: humoral response was more efficient in the group with under- and normal-weight vs the group with pre- and obesity participants (p<0.0001 at T1).\n\nInterpretationThese findings imply that females, lean and young people have an increased capacity to mount humoral immune responses compared to males, overweight and the older population. Although further studies are needed, this data may have important implications for the development of vaccination strategies for COVID-19, particularly in obese people.\n\nFundingNone",
-    "rel_num_authors": 29,
-    "rel_authors": [
-      {
-        "author_name": "Raul Pellini",
-        "author_inst": "IRCCS Regina Elena National Cancer Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "Aldo Venuti",
-        "author_inst": "IRCCS Regina Elena National Cancer Institute"
-      },
-      {
-        "author_name": "Fulvia Pimpinelli",
-        "author_inst": "IRCCS San Gallicano Dermatological Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "Elva Abril",
-        "author_inst": "IRCCS San Gallicano Dermatological Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "GIovanni Blandino",
-        "author_inst": "IRCCS Regina Elena National Cancer Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "Flaminia Campo",
-        "author_inst": "IRCCS Regina Elena National Cancer Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "Laura Conti",
-        "author_inst": "IRCCS Regina Elena National Cancer Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "Armando De Virgilio",
-        "author_inst": "Humanitas University"
-      },
-      {
-        "author_name": "Federico De Marco",
-        "author_inst": "IRCCS Regina Elena National Cancer Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "Enea GIno Di Domenico",
-        "author_inst": "IRCCS San Gallicano Dermatological Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "Ornella Di Bella",
-        "author_inst": "Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "Simona Di Martino",
-        "author_inst": "IRCCS Regina Elena National Cancer Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "Fabrizio Ensoli",
-        "author_inst": "IRCCS San Gallicano Dermatological Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "Diana Giannarelli",
-        "author_inst": "IRCCS Regina Elena National Cancer Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "Chiara Mandoj",
-        "author_inst": "IRCCS Regina Elena National Cancer Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "Valentina Manciocco",
-        "author_inst": "IRCCS Regina Elena National Cancer Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "Paolo Marchesi",
-        "author_inst": "IRCCS Regina Elena National Cancer Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "Francesco Mazzola",
-        "author_inst": "IRCCS Regina Elena National Cancer Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "Silvia Moretto",
-        "author_inst": "IRCCS Regina Elena National Cancer Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "Gerardo Petruzzi",
-        "author_inst": "IRCCS Regina Elena National Cancer Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "Fabrizio Petrone",
-        "author_inst": "IRCCS Regina Elena National Cancer Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "Barbara Pichi",
-        "author_inst": "IRCCS Regina Elena National Cancer Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "Martina Pontone",
-        "author_inst": "IRCCS San Gallicano Dermatological Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "Jacopo Zocchi",
-        "author_inst": "IRCCS Regina Elena National Cancer Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "Antonello Vidiri",
-        "author_inst": "IRCCS Regina Elena National Cancer Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "Branka Vujovic",
-        "author_inst": "Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "GIulia Piaggio",
-        "author_inst": "IRCCS Regina Elena National Cancer Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "Aldo Morrone",
-        "author_inst": "IRCCS San Gallicano Dermatological Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      },
-      {
-        "author_name": "Gennaro Ciliberto",
-        "author_inst": "IRCCS Regina Elena National Cancer Institute, Istituti Fisioterapici Ospitalieri (IFO)"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "allergy and immunology"
-  },
   {
     "rel_doi": "10.1101/2021.02.24.21252368",
     "rel_title": "Longitudinal protection following natural SARS-CoV-2 infection and early vaccine responses: insights from a cohort of community based dental health care professionals",
@@ -897495,6 +895639,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
+  {
+    "rel_doi": "10.1101/2021.02.24.21252135",
+    "rel_title": "Risk factors for increased COVID-19 case-fatality in the United States: A county-level analysis during the first wave",
+    "rel_date": "2021-02-26",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.24.21252135",
+    "rel_abs": "The ongoing COVID-19 pandemic is causing significant morbidity and mortality across the US. In this ecological study, we identified county-level variables associated with the COVID-19 case-fatality rate (CFR) using publicly available datasets and a negative binomial generalized linear model. Variables associated with decreased CFR included a greater number of hospitals per 10,000 people, banning religious gatherings, a higher percentage of people living in mobile homes, and a higher percentage of uninsured people. Variables associated with increased CFR included a higher percentage of the population over age 65, a higher percentage of Black or African Americans, a higher asthma prevalence, and a greater number of hospitals in a county. By identifying factors that are associated with COVID-19 CFR in US counties, we hope to help officials target public health interventions and healthcare resources to locations that are at increased risk of COVID-19 fatalities.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Jess A. Millar",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Hanh Dung N. Dao",
+        "author_inst": "University of Oklahoma Health Sciences Center"
+      },
+      {
+        "author_name": "Marianne E. Stefopulos",
+        "author_inst": "Child Health Evaluative Sciences Program, SickKids Hospital"
+      },
+      {
+        "author_name": "Camila G. Estevam",
+        "author_inst": "State University of Campinas"
+      },
+      {
+        "author_name": "Katharine Fagan-Garcia",
+        "author_inst": "University of Alberta"
+      },
+      {
+        "author_name": "Diana H. Taft",
+        "author_inst": "University of California Davis"
+      },
+      {
+        "author_name": "Christopher Park",
+        "author_inst": "New York University"
+      },
+      {
+        "author_name": "Amaal Alruwaily",
+        "author_inst": "Independent Scholar"
+      },
+      {
+        "author_name": "Angel N. Desai",
+        "author_inst": "University of California Davis Medical Center"
+      },
+      {
+        "author_name": "Maimuna S. Majumder",
+        "author_inst": "Harvard Medical School and Boston Children's Hospital"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.02.24.21252316",
     "rel_title": "A national mixed-mode seroprevalence random population-based cohort on SARS-CoV-2 epidemic in France: the socio-epidemiological EpiCov study",
@@ -898972,33 +897171,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.02.25.432265",
-    "rel_title": "Visualization of SARS-CoV-2 Infection Scenes by 'Zero-Shot' Enhancements of Electron Microscopy Images",
-    "rel_date": "2021-02-25",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.25.432265",
-    "rel_abs": "Electron microscopy (EM) recordings of infected tissues serve to diagnose a disease, and they can contribute to our understanding of infection processes. Consequently, a large number of EM images of the interaction of SARS-CoV-2 viruses with cells have been made available by numerous labs. However, due to EM recording techniques at high resolution, images of infection scenes are very noisy and they appear two dimensional ( flat). Current research consequently aims (A) at methods that can remove noise, and (B) at techniques that allow for recovering a 3D impression of the virus or its parts. Here we discuss a novel method which can recover a spatial impression of a whole infection scene at high resolution. In contrast to previous approaches which aim at the reconstruction of single spike proteins or a single virus, the here used method can be applied to a single noisy EM image of an infection scene. As one example image, we show a high resolution image of SARS-CoV-2 viruses in Vero cell cultures (Fig. 1). The method we use is based on probabilistic machine learning algorithms which can operate in a  zero-shot setting, i.e., in a setting when just one noisy image (and no large and clean image corpus) is available. The probabilistic method we apply can estimate non-noisy images by inferring first order statistics (pixel means) across image patches using a previously learned probabilistic image representation. Estimating higher order statistics and appropriately chosen probabilistic models then allow for the generation of images that enhance details and give a spatial impression of a full nanoscopic scene.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Jakob Drefs",
-        "author_inst": "Machine Learning Lab, School of Medicine and Health Science, University Oldenburg, Germany."
-      },
-      {
-        "author_name": "Sebastian Salwig",
-        "author_inst": "Machine Learning Lab, School of Medicine and Health Science, University Oldenburg, Germany."
-      },
-      {
-        "author_name": "J\u00f6rg L\u00fccke",
-        "author_inst": "Machine Learning Lab, School of Medicine and Health Science, University Oldenburg, Germany."
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "bioinformatics"
-  },
   {
     "rel_doi": "10.1101/2021.02.24.432807",
     "rel_title": "Modeling SARS-CoV-2 nsp1-5'-UTR complex via the extended ensemble simulations",
@@ -899605,6 +897777,61 @@
     "type": "new results",
     "category": "cell biology"
   },
+  {
+    "rel_doi": "10.1101/2021.02.25.432762",
+    "rel_title": "The type 2 asthma mediator IL-13 inhibits SARS-CoV-2 infection of bronchial epithelium",
+    "rel_date": "2021-02-25",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.25.432762",
+    "rel_abs": "RationaleAsthma is associated with chronic changes in the airway epithelium, a key target of SARS-CoV-2. Many epithelial changes are driven by the type 2 cytokine IL-13, but the effects of IL-13 on SARS-CoV-2 infection are unknown.\n\nObjectivesWe sought to discover how IL-13 and other cytokines affect expression of genes encoding SARS-CoV-2-associated host proteins in human bronchial epithelial cells (HBECs) and determine whether IL-13 stimulation alters susceptibility to SARS-CoV-2 infection.\n\nMethodsWe used bulk and single cell RNA-seq to identify cytokine-induced changes in SARS-CoV-2-associated gene expression in HBECs. We related these to gene expression changes in airway epithelium from individuals with mild-moderate asthma and chronic obstructive pulmonary disease (COPD). We analyzed effects of IL-13 on SARS-CoV-2 infection of HBECs.\n\nMeasurements and Main ResultsTranscripts encoding 332 of 342 (97%) SARS-CoV-2-associated proteins were detected in HBECs ([&ge;]1 RPM in 50% samples). 41 (12%) of these mRNAs were regulated by IL-13 (>1.5-fold change, FDR < 0.05). Many IL-13-regulated SARS-CoV-2-associated genes were also altered in type 2 high asthma and COPD. IL-13 pretreatment reduced viral RNA recovered from SARS-CoV-2 infected cells and decreased dsRNA, a marker of viral replication, to below the limit of detection in our assay. Mucus also inhibited viral infection.\n\nConclusionsIL-13 markedly reduces susceptibility of HBECs to SARS-CoV-2 infection through mechanisms that likely differ from those activated by type I interferons. Our findings may help explain reports of relatively low prevalence of asthma in patients diagnosed with COVID-19 and could lead to new strategies for reducing SARS-CoV-2 infection.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Luke R Bonser",
+        "author_inst": "UCSF"
+      },
+      {
+        "author_name": "Walter L Eckalbar",
+        "author_inst": "UCSF"
+      },
+      {
+        "author_name": "Lauren Rodriguez",
+        "author_inst": "UCSF"
+      },
+      {
+        "author_name": "Jiangshan Shen",
+        "author_inst": "UCSF"
+      },
+      {
+        "author_name": "Kyung Duk Koh",
+        "author_inst": "UCSF"
+      },
+      {
+        "author_name": "Lorna T Zlock",
+        "author_inst": "UCSF"
+      },
+      {
+        "author_name": "Stephanie Christenson",
+        "author_inst": "UCSF"
+      },
+      {
+        "author_name": "Prescott G Woodruff",
+        "author_inst": "UCSF"
+      },
+      {
+        "author_name": "Walter E Finkbeiner",
+        "author_inst": "UCSF"
+      },
+      {
+        "author_name": "David J Erle",
+        "author_inst": "UCSF"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "cell biology"
+  },
   {
     "rel_doi": "10.1101/2021.02.22.21252240",
     "rel_title": "Non-pharmaceutical interventions and inoculation rate shape SARS-COV-2 vaccination campaign success",
@@ -900990,29 +899217,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.02.11.21251580",
-    "rel_title": "Mandatory public health measures for COVID-19 are associated with improved mortality, equity and economic outcomes",
-    "rel_date": "2021-02-24",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.11.21251580",
-    "rel_abs": "We review approaches to the COVID-19 pandemic in a systematic way by comparing countries/states representative of the mandatory vs. voluntary approach to non-pharmaceutical interventions in Europe and the US. We use a comparative tabular format to examine differences in mortality, economic impact and equity between regions with mandatory versus voluntary policies. Mandatory shelter-in-place policies were associated with 3 to 4 fold lower population adjusted mortality in the US model and 11 fold lower in the European one. We conclude that voluntary policies are less effective, based on historical precedent and the current analysis. Moreover, effects on health equity mirrored the increased mortality outcomes of voluntary policies and there was no apparent economic benefit associated with voluntary measures.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Brita Lundberg",
-        "author_inst": "Lundberg Health Advocates"
-      },
-      {
-        "author_name": "Kathryn McDonald",
-        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
-      }
-    ],
-    "version": "2",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.02.24.432734",
     "rel_title": "Targeting of the NLRP3 Inflammasome for early COVID-19",
@@ -901319,6 +899523,81 @@
     "type": "new results",
     "category": "bioinformatics"
   },
+  {
+    "rel_doi": "10.1101/2021.02.24.432656",
+    "rel_title": "SARS-CoV-2 ORF6 disturbs nucleocytoplasmic trafficking to advance the viral replication",
+    "rel_date": "2021-02-24",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.24.432656",
+    "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus responsible for the coronavirus disease 2019 pandemic. ORF6 is known to antagonize the interferon signaling by inhibiting the nuclear translocation of STAT1. Here we show that ORF6 acts as a virulence factor through two distinct strategies. First, ORF6 directly interacts with STAT1 in an IFN-independent manner to inhibit its nuclear translocation. Second, ORF6 directly binds to importin 1, which is a nuclear transport factor encoded by KPNA2, leading to a significant suppression of importin 1-mediated nuclear transport. Furthermore, we found that KPNA2 knockout enhances the viral replication, suggesting that importin 1 suppresses the viral propagation. Additionally, the analyses of gene expression data revealed that importin 1 levels decreased significantly in the lungs of older individuals. Taken together, SARS-CoV-2 ORF6 disrupts the nucleocytoplasmic trafficking to accelerate the viral replication, resulting in the disease progression, especially in older individuals.",
+    "rel_num_authors": 15,
+    "rel_authors": [
+      {
+        "author_name": "Yoichi Miyamoto",
+        "author_inst": "National Institutes of Biomedical Innovation, Health and Nutrition"
+      },
+      {
+        "author_name": "Yumi Itoh",
+        "author_inst": "Research Institute for Microbial Diseases, Osaka University"
+      },
+      {
+        "author_name": "Tatsuya Suzuki",
+        "author_inst": "Research Institute for Microbial Diseases, Osaka University"
+      },
+      {
+        "author_name": "Tomohisa Tanaka",
+        "author_inst": "Faculty of Medicine, University of Yamanashi"
+      },
+      {
+        "author_name": "Yusuke Sakai",
+        "author_inst": "Yamaguchi University"
+      },
+      {
+        "author_name": "Masaru Koido",
+        "author_inst": "The University of Tokyo"
+      },
+      {
+        "author_name": "Chiaki Hata",
+        "author_inst": "Cell Engineering Corporation"
+      },
+      {
+        "author_name": "Cai-Xia Wan",
+        "author_inst": "Cell Engineering Corporation"
+      },
+      {
+        "author_name": "Mayumi Otani",
+        "author_inst": "National Institutes of Biomedical Innovation, Health and Nutrition"
+      },
+      {
+        "author_name": "Kohji Moriishi",
+        "author_inst": "Faculty of Medicine, University of Yamanashi"
+      },
+      {
+        "author_name": "Taro Tachibana",
+        "author_inst": "Osaka City University"
+      },
+      {
+        "author_name": "Yoichiro Kamatani",
+        "author_inst": "The University of Tokyo"
+      },
+      {
+        "author_name": "Yoshihiro Yoneda",
+        "author_inst": "National Institutes of Biomedical Innovation, Health and Nutrition"
+      },
+      {
+        "author_name": "Toru Okamoto",
+        "author_inst": "Research Institute for Microbial Diseases, Osaka University"
+      },
+      {
+        "author_name": "Masahiro Oka",
+        "author_inst": "National Institutes of Biomedical Innovation, Health and Nutrition"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2021.02.24.432759",
     "rel_title": "Implications of central carbon metabolism in SARS-CoV-2 replication and disease severity",
@@ -902876,33 +901155,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "occupational and environmental health"
   },
-  {
-    "rel_doi": "10.1101/2021.02.20.21252131",
-    "rel_title": "The Association of Opening K-12 Schools and Colleges with the Spread of COVID-19 in the United States: County-Level Panel Data Analysis",
-    "rel_date": "2021-02-23",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.20.21252131",
-    "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThis paper empirically examines how the opening of K-12 schools and colleges is associated with the spread of COVID-19 using county-level panel data in the United States. Using data on foot traffic and K-12 school opening plans, we analyze how an increase in visits to schools and opening schools with different teaching methods (in-person, hybrid, and remote) is related to the 2-weeks forward growth rate of confirmed COVID-19 cases. Our debiased panel data regression analysis with a set of county dummies, interactions of state and week dummies, and other controls shows that an increase in visits to both K-12 schools and colleges is associated with a subsequent increase in case growth rates. The estimates indicate that fully opening K-12 schools with in-person learning is associated with a 5 (SE = 2) percentage points increase in the growth rate of cases. We also find that the positive association of K-12 school visits or in-person school openings with case growth is stronger for counties that do not require staff to wear masks at schools. These results have a causal interpretation in a structural model with unobserved county and time confounders. Sensitivity analysis shows that the baseline results are robust to timing assumptions and alternative specifications.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Victor Chernozhukov",
-        "author_inst": "MIT"
-      },
-      {
-        "author_name": "Hiroyuki Kasahara",
-        "author_inst": "University of British Columbia"
-      },
-      {
-        "author_name": "Paul Schrimpf",
-        "author_inst": "University of British Columbia"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health economics"
-  },
   {
     "rel_doi": "10.1101/2021.02.19.21252118",
     "rel_title": "Phased implementation of COVID-19 vaccination: rapid assessment of policy adoption, reach and effectiveness to protect the most vulnerable in the US",
@@ -903293,6 +901545,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.02.22.21251534",
+    "rel_title": "The spatio-temporal distribution of COVID-19 infection in England between January and June 2020.",
+    "rel_date": "2021-02-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.22.21251534",
+    "rel_abs": "The spatio-temporal dynamics of an outbreak provide important insights to help direct public health resources intended to control transmission. They also provide a focus for detailed epidemiological studies and allow the timing and impact of interventions to be assessed.\n\nA common approach is to aggregate case data to administrative regions. Whilst providing a good visual impression of change over space, this method masks spatial variation and assumes that disease risk is constant across space. Risk factors for COVID-19 (e.g. population density, deprivation and ethnicity) vary from place to place across England so it follows that risk will also vary spatially. Kernel density estimation compares the spatial distribution of cases relative to the underlying population, unfettered by arbitrary geographical boundaries, to produce a continuous estimate of spatially varying risk.\n\nUsing test results from healthcare settings in England (Pillar 1 of the UK Government testing strategy) and freely available methods and software, we estimated the spatial and spatio-temporal risk of COVID-19 infection across England for the first six months of 2020. Widespread transmission was underway when partial lockdown measures were introduced on the 23rd March 2020 and the greatest risk erred towards large urban areas. The rapid growth phase of the outbreak coincided with multiple introductions to England from the European mainland. The spatio-temporal risk was highly labile throughout.\n\nIn terms of controlling transmission, the most important practical application is the accurate identification of areas within regions that may require tailored intervention strategies. We recommend that this approach is absorbed into routine surveillance outputs in England. Further risk characterisation using widespread community testing (Pillar 2) data is needed as is the increased use of predictive spatial models at fine spatial scales.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Richard Elson",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Tilman M Davies",
+        "author_inst": "University of Otago"
+      },
+      {
+        "author_name": "Iain R Lake",
+        "author_inst": "University of East Anglia"
+      },
+      {
+        "author_name": "Roberto Vivancos",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Paula B Blomquist",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Andre Charlett",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Gavin Dabrera",
+        "author_inst": "Public Health England"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.02.20.20248421",
     "rel_title": "Nosocomial outbreak of SARS-CoV-2 in a 'non-COVID-19' hospital ward: virus genome sequencing as a key tool to understand cryptic transmission",
@@ -904770,53 +903065,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.02.22.21252235",
-    "rel_title": "Estimating the spreading and dominance of SARS-CoV-2 VOC 202012/01 (lineage B.1.1.7) across Europe",
-    "rel_date": "2021-02-23",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.22.21252235",
-    "rel_abs": "We develop a two strain, age-structured, compartmental model to assess the spreading potential of the B.1.1.7 variant across several European metropolitan areas and countries. The model accounts for B.1.1.7 introductions from the UK and different locations, as well as local mitigation policies in the time period 2020/09 - 2021/02. In the case of an increase of transmissibility of 50%, the B.1.1.7 variant has the potential to become dominant in all investigated areas by the end of March 2021.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Nicol\u00f2 Gozzi",
-        "author_inst": "University of Greenwich"
-      },
-      {
-        "author_name": "Matteo Chinazzi",
-        "author_inst": "Northeastern University"
-      },
-      {
-        "author_name": "Jessica T Davis",
-        "author_inst": "Northeastern University"
-      },
-      {
-        "author_name": "Kunpeng Mu",
-        "author_inst": "Northeastern University"
-      },
-      {
-        "author_name": "Ana Pastore y Piontti",
-        "author_inst": "Northeastern University"
-      },
-      {
-        "author_name": "Marco Ajelli",
-        "author_inst": "Indiana University"
-      },
-      {
-        "author_name": "Nicola Perra",
-        "author_inst": "University of Greenwich"
-      },
-      {
-        "author_name": "Alessandro Vespignani",
-        "author_inst": "Northeastern University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.02.22.21252205",
     "rel_title": "A rapid review of equity considerations in large-scale testing campaigns during infectious disease epidemics",
@@ -905379,6 +903627,89 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "occupational and environmental health"
   },
+  {
+    "rel_doi": "10.1101/2021.02.22.21252207",
+    "rel_title": "Critical COVID-19 represents an endothelial disease with high similarity to kidney disease on the molecular level",
+    "rel_date": "2021-02-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.22.21252207",
+    "rel_abs": "In patients with critical or mild COVID19 (WHO stages 6-8 [n=53] and stages 1-3 [n=66]), 593 urinary peptides significantly affected by disease severity were identified, reflecting the molecular pathophysiology associated with the course of the infection. The peptide profiles were similar compared with those observed in kidney disease, a prototype of target organ damage with major microvascular involvement, thereby confirming the observation that endothelial damage is a hallmark of COVID19. The clinical corollary is that COVID19 is an indication for anti-oxidative, anti-inflammatory and immunosuppressive treatment modalities protecting the endothelial lining.",
+    "rel_num_authors": 17,
+    "rel_authors": [
+      {
+        "author_name": "Justyna Siwy",
+        "author_inst": "Mosaiques-Diagnostics GmbH"
+      },
+      {
+        "author_name": "Ralph Wendt",
+        "author_inst": "Hospital St. Georg, Leipzig"
+      },
+      {
+        "author_name": "Amaya Albalat",
+        "author_inst": "University of Stirling, /UK"
+      },
+      {
+        "author_name": "Tianlin He",
+        "author_inst": "Mosaiques Diagnostics"
+      },
+      {
+        "author_name": "Harald Mischak",
+        "author_inst": "Mosaiques Diagnostics"
+      },
+      {
+        "author_name": "William Mullen",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Agnieszka Latosinska",
+        "author_inst": "Mosaiques Diagnostics"
+      },
+      {
+        "author_name": "Christoph Luebbert",
+        "author_inst": "University Leipzig"
+      },
+      {
+        "author_name": "Sven Kalbitz",
+        "author_inst": "Hospital St. Georg, Leipzig, Germany"
+      },
+      {
+        "author_name": "Alexandre Mebazaa",
+        "author_inst": "Universite de Paris, Paris, France."
+      },
+      {
+        "author_name": "Bjoern Peters",
+        "author_inst": "Department of Nephrology, Skaraborg Hospital, Skoevde, Sweden"
+      },
+      {
+        "author_name": "Bernd Stegmayr",
+        "author_inst": "Department of Public Health and Clinical Medicine, Umea University, Umea, Sweden"
+      },
+      {
+        "author_name": "Goce Spasovski",
+        "author_inst": "Department of Nephrology, Medical Faculty, University St.Cyril and Methodius, Skopje, Republic of N. Macedonia"
+      },
+      {
+        "author_name": "Thorsten Wiech",
+        "author_inst": "Nephropathology Section, Institute for Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany"
+      },
+      {
+        "author_name": "Jan Staessen",
+        "author_inst": "Alliance for the Promotion of Preventive Medicine (APPREMED), Mechelen, Belgium."
+      },
+      {
+        "author_name": "Johannes Wolf",
+        "author_inst": "Department of Laboratory Medicine, Hospital St. Georg, Leipzig, Germany"
+      },
+      {
+        "author_name": "Joachim Beige",
+        "author_inst": "Department of Infectious Diseases/Tropical Medicine, Nephrology and Rheumatology, Hospital St. Georg, Leipzig, Germany"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.02.22.21252236",
     "rel_title": "High-resolution longitudinal serum proteome trajectories in COVID-19 reveal patients-specific seroconversion",
@@ -906688,37 +905019,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2021.02.21.432165",
-    "rel_title": "Comparative Perturbation-Based Modeling of the SARS-CoV-2 Spike Protein Binding with Host Receptor and Neutralizing Antibodies : Structurally Adaptable Allosteric Communication Hotspots Define Spike Sites Targeted by Global Circulating Mutations",
-    "rel_date": "2021-02-22",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.21.432165",
-    "rel_abs": "In this study, we used an integrative computational approach focused on comparative perturbation-based modeling to examine molecular mechanisms and determine functional signatures underlying role of functional residues in the SARS-CoV-2 spike protein that are targeted by novel mutational variants and antibody-escaping mutations. Atomistic simulations and functional dynamics analysis are combined with alanine scanning and mutational sensitivity profiling for the SARS-CoV-2 spike protein complexes with the ACE2 host receptor are REGN-COV2 antibody cocktail (REG10987+REG10933). Using alanine scanning and mutational sensitivity analysis, we have shown that K417, E484 and N501 residues correspond to key interacting centers with a significant degree of structural and energetic plasticity that allow mutants in these positions to afford the improved binding affinity with ACE2. Through perturbation-based network modeling and community analysis of the SARS-CoV-2 spike protein complexes with ACE2 we demonstrate that E406, N439, K417 and N501 residues serve as effector centers of allosteric interactions and anchor major inter-molecular communities that mediate long-range communication in the complexes. The results provide support to a model according to which mutational variants and antibody-escaping mutations constrained by the requirements for host receptor binding and preservation of stability may preferentially select structurally plastic and energetically adaptable allosteric centers to differentially modulate collective motions and allosteric interactions in the complexes with the ACE2 enzyme and REGN-COV2 antibody combination. This study suggests that SARS-CoV-2 spike protein may function as a versatile and functionally adaptable allosteric machine that exploits plasticity of allosteric regulatory centers to fine-tune response to antibody binding without compromising activity of the spike protein.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Gennady Verkhivker",
-        "author_inst": "Chapman University School of Pharmacy"
-      },
-      {
-        "author_name": "Steve Agajanian",
-        "author_inst": "Chapman University"
-      },
-      {
-        "author_name": "Deniz Yazar Oztas",
-        "author_inst": "Chapman University"
-      },
-      {
-        "author_name": "Grace Gupta",
-        "author_inst": "Chapman University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "biophysics"
-  },
   {
     "rel_doi": "10.1101/2021.02.18.21251992",
     "rel_title": "Demographic benchmarks for equitable coverage of the COVID-19 vaccination program among priority populations",
@@ -907025,6 +905325,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.02.20.432081",
+    "rel_title": "Nanoceutical Fabric Prevents COVID-19 Spread through Expelled Respiratory Droplets: A Combined Computational, Spectroscopic and Anti-microbial Study",
+    "rel_date": "2021-02-22",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.20.432081",
+    "rel_abs": "Centers for Disease Control and Prevention (CDC) warns the use of one-way valves or vents in free masks for potential threat of spreading COVID-19 through expelled respiratory droplets. Here, we have developed a nanoceutical cotton fabric duly sensitized with non-toxic zinc oxide nanomaterial for potential use as membrane filter in the one way valve for the ease of breathing without the threat of COVID-19 spreading. A detailed computational study revealed that zinc oxide nanoflowers (ZnO NF) with almost two-dimensional petals trap SARS-CoV-2 spike proteins, responsible to attach to ACE-2 receptors in human lung epithelial cells. The study also confirm significant denaturation of the spike proteins on the ZnO surface, revealing removal of virus upon efficient trapping. Following the computational study, we have synthesized ZnO NF on cotton matrix using hydrothermal assisted strategy. Electron microscopic, steady-state and picosecond resolved spectroscopic studies confirm attachment of ZnO NF to the cotton (i.e., cellulose) matrix at atomic level to develop the nanoceutical fabric. A detailed antimicrobial assay using Pseudomonas aeruginosa bacteria (model SARS-CoV-2 mimic) reveals excellent anti-microbial efficiency of the developed nanoceutical fabric. To our understanding the novel nanoceutical fabric used in one-way valve of a face mask would be the choice to assure breathing comfort along with source control of COVID-19 infection. The developed nanosensitized cloth can also be used as antibacterial/anti CoV-2 washable dress material in general.\n\nGRAPHICAL ABSTRACT O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY\n\nA novel nanoceutical cotton fabric duly sensitized with non-toxic zinc oxide nanoflower can potentially be used as membrane filter in the one way valve of face mask to assure breathing comfort along with source control of COVID-19 infection. The nanoceutical fabric denatures the SARS-CoV-2 spike protein and makes the microorganism ineffective.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Aniruddha Adhikari",
+        "author_inst": "S N Bose National Centre for Basic Sciences"
+      },
+      {
+        "author_name": "Uttam Pal",
+        "author_inst": "SN Bose National Centre for Basic Sciences"
+      },
+      {
+        "author_name": "Sayan Bayan",
+        "author_inst": "SN Bose National Centre for Basic Sciences"
+      },
+      {
+        "author_name": "Susmita Mondal",
+        "author_inst": "SN Bose National Centre for Basic Sciences"
+      },
+      {
+        "author_name": "Ria Ghosh",
+        "author_inst": "SN Bose National Centre for Basic Sciences"
+      },
+      {
+        "author_name": "Soumendra Darbar",
+        "author_inst": "Deys Medical Stores (Mfg.) Ltd"
+      },
+      {
+        "author_name": "Tanusri Saha-Dasgupta",
+        "author_inst": "SN Bose National Centre for Basic Sciences"
+      },
+      {
+        "author_name": "Samit Kumar Ray",
+        "author_inst": "SN Bose National Centre for Basic Sciences"
+      },
+      {
+        "author_name": "Samir Kumar Pal",
+        "author_inst": "SN Bose National Centre for Basic Sciences"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2021.02.22.432359",
     "rel_title": "SARS-CoV-2 B.1.1.7 and B.1.351 Spike variants bind human ACE2 with increased affinity",
@@ -908298,57 +906649,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.02.18.21251442",
-    "rel_title": "Visuospatial processing impairment following mild COVID-19",
-    "rel_date": "2021-02-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.18.21251442",
-    "rel_abs": "Severe Acute Respiratory Syndrome Coronavirus 2 infection causes coronavirus disease 2019. COVID-19 was an unknown infection that reached pandemic proportions in 2020 and has shown to bring long-term negative consequences. Here, we used a case-control design to investigate the performance of relatively young people recovered from COVID 19 in objective neuropsychological tests. We found significant differences between groups for all measures of the ROCFT with a large difference in the copy, a moderate difference in immediate recall, and a large difference in delayed recall. No significant differences were found for the measures from all the other five neuropsychological tests used.About one quarter of COVID 19 patients were below the 10th percentile according to normative data.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "JONAS JARDIM DE PAULA",
-        "author_inst": "UFMG"
-      },
-      {
-        "author_name": "Rachel Elisa R.P. Paiva",
-        "author_inst": "UFMG"
-      },
-      {
-        "author_name": "Danielle de Souza Costa",
-        "author_inst": "UFMG"
-      },
-      {
-        "author_name": "Nathalia Gualberto Souza e Silva",
-        "author_inst": "UFMG"
-      },
-      {
-        "author_name": "Daniela Valadao Rosa",
-        "author_inst": "UFMG"
-      },
-      {
-        "author_name": "Jose Nelio Januario",
-        "author_inst": "UFMG"
-      },
-      {
-        "author_name": "Luciana Costa Silva",
-        "author_inst": "Laboratorio Hermes Pardini"
-      },
-      {
-        "author_name": "Debora Marques Miranda",
-        "author_inst": "UFMG"
-      },
-      {
-        "author_name": "Marco Aurelio Romano-Silva",
-        "author_inst": "UFMG"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "psychiatry and clinical psychology"
-  },
   {
     "rel_doi": "10.1101/2021.02.18.21251368",
     "rel_title": "Early Identification of SARS-CoV-2 Emergence in the DoD via Retrospective Analysis of 2019-2020 Upper Respiratory Illness Samples",
@@ -908603,6 +906903,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.02.18.21251793",
+    "rel_title": "Accessible LAMP-Enabled Rapid Test (ALERT) for detecting SARS-CoV-2",
+    "rel_date": "2021-02-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.18.21251793",
+    "rel_abs": "The COVID-19 pandemic has highlighted bottlenecks in large-scale, frequent testing of populations for infections. PCR-based diagnostic tests are expensive, reliant on expensive centralized labs, can take days to deliver results, and are prone to backlogs and supply shortages. Antigen tests, that bind and detect the surface proteins of a virus, are rapid and inexpensive but suffer from high false negative rates. To address this problem, we have created an inexpensive, simple, and robust 60-minute Do-It-Yourself (DIY) workflow to detect viral RNA from nasal swabs or saliva with high sensitivity (0.1 to 2 viral particles/{micro}l) and specificity (>97% True Negative Rate) utilizing reverse transcription loop-mediated isothermal amplification (RT-LAMP).\n\nOur workflow, ALERT (Accessible LAMP-Enabled Rapid Test), incorporates the following features: 1) Increased shelf-life and ambient temperature storage by using wax layers to isolate enzymes from reaction, 2) Improved specificity by using sequence-specific QUASR reporters, 3) Increased sensitivity through use of a magnetic wand to enable pipette-free concentration of sample RNA and cell debris removal, 4) Quality control with a nasopharyngeal-specific mRNA target, and 5) Co-detection of other respiratory viruses, such as Influenza B, by duplexing QUASR-modified RT-LAMP primer sets.\n\nThe flexible nature of the ALERT workflow allows easy, at-home and point-of-care testing for individuals and higher-throughput processing for centralized labs and hospitals. With minimal effort, SARS-CoV-2-specific primer sets can be swapped out for other targets to repurpose ALERT to detect other viruses, microorganisms or nucleic acid-based markers.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Ali Bekta\u015f",
+        "author_inst": "Oakland Genomics Center"
+      },
+      {
+        "author_name": "Mike F. Covington",
+        "author_inst": "Oakland Genomics Center, 355 30th St. Oakland, CA, 94609, USA, and Amaryllis Nucleics, 355 30th St, Oakland, CA, 94609, USA"
+      },
+      {
+        "author_name": "Guy Aidelberg",
+        "author_inst": "Universit\u00e9 de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), F-75006 Paris, France"
+      },
+      {
+        "author_name": "Anibal Arce",
+        "author_inst": "Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Cat\u00f3lica de Chile, Santiago 7820244, Chil"
+      },
+      {
+        "author_name": "Tamara Matute",
+        "author_inst": "Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Cat\u00f3lica de Chile, Santiago 7820244, Chil"
+      },
+      {
+        "author_name": "Isaac N\u00fa\u00f1ez",
+        "author_inst": "Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Cat\u00f3lica de Chile, Santiago 7820244, Chil"
+      },
+      {
+        "author_name": "Julia Walsh",
+        "author_inst": "School of Public Health, University of California Berkeley, Berkeley, CA, 94720, USA"
+      },
+      {
+        "author_name": "David Boutboul",
+        "author_inst": "Clinical Immunology Department, U976 HIPI, H\u00f4pital Saint Louis, Universit\u00e9 de Paris, Paris, France"
+      },
+      {
+        "author_name": "Ariel B. Lindner",
+        "author_inst": "Universit\u00e9 de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), F-75006 Paris, France"
+      },
+      {
+        "author_name": "Fern\u00e1n Federici",
+        "author_inst": "Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Cat\u00f3lica de Chile, Santiago 7820244, Chil"
+      },
+      {
+        "author_name": "Anitha Jayaprakash",
+        "author_inst": "Oakland Genomics Center, 355 30th St. Oakland, CA, 94609, USA and Girihlet Inc, 355 30th St, Oakland, CA, 94609, USA"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.02.18.21251243",
     "rel_title": "A Multivariate Forecasting Model for the COVID-19 Hospital Census Based on Local Infection Incidence",
@@ -909820,41 +908179,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.02.16.21251819",
-    "rel_title": "The rise of SARS-CoV-2 variant B.1.1.7 in Israel intensifies the role of surveillance and vaccination in elderly",
-    "rel_date": "2021-02-19",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.16.21251819",
-    "rel_abs": "Since the emergence of the SARS-CoV-2 pandemic various generic variants have been described. Of specific interest is a new variant, which was observed in England during December 2020 and is now termed B.1.1.7. This variant is now associated with increased infectivity and therefore its spread within the community is of great importance. The Israeli government established three noteworthy programs namely, mass PCR testing, focused protection of the elderly and more recently an unparalleled prioritized vaccination program. In this study we analyzed primary data of >300,000 RT-PCR samples collected throughout December 6th 2020 until February 10th 2021 in the general community and nursing homes. We identified that within a period of six weeks, the B.1.1.7 variant was capable of out competing the wildtype SARS-CoV-2 strain to become the main strain. Furthermore, we show that the transmission of B.1.1.7 in the 60+ population reached a near complete halt, due to an ongoing surveillance testing program in nursing homes and the vaccination program of Israel. Thus, proactive protection programs such as routine surveillance and monitoring of populations at risk combined with prioritized vaccination, is achievable and will result in a reduction of severe illness and subsequent death.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Ariel Munitz",
-        "author_inst": "1Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801 Israel"
-      },
-      {
-        "author_name": "Matan Yechezkel",
-        "author_inst": "Laboratory for Epidemic Modeling and Analysis, Department of Industrial Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv, 6997801 Israel"
-      },
-      {
-        "author_name": "Yoav Dickstein",
-        "author_inst": "Electra-TAU laboratory, Omer, Israel"
-      },
-      {
-        "author_name": "Dan Yamin",
-        "author_inst": "Laboratory for Epidemic Modeling and Analysis, Department of Industrial Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv, 6997801 Israel"
-      },
-      {
-        "author_name": "Motti Gerlic",
-        "author_inst": "Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801 Israel"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.02.16.21251641",
     "rel_title": "Size and duration of COVID-19 clusters go along with a high SARS-CoV-2 viral load : a spatio-temporal investigation in Vaud state, Switzerland",
@@ -910137,6 +908461,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.02.16.21251676",
+    "rel_title": "Incidence and Outcomes of Pulmonary embolism among hospitalized COVID-19 patients",
+    "rel_date": "2021-02-19",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.16.21251676",
+    "rel_abs": "BackgroundPatients with COVID-19 may be at high risk for thrombotic complications due to excess inflammatory response and stasis of blood flow. This study aims to assess the incidence of pulmonary embolism among hospitalized patients with COVID-19, risk factors and the impact on survival.\n\nMethodA retrospective case-control study was conducted at Al-Noor Specialist Hospital in, Saudi Arabia between March 15, 2020, and June 15, 2020. Patients with confirmed COVID-19 diagnosis by a real-time polymerase chain reaction (PCR) and confirmed diagnosis of pulmonary embolism by Computed Tomography pulmonary angiogram (CTPA) formed the case group. Patients with confirmed COVID-19 diagnosis by a real-time polymerase chain reaction (PCR) and without confirmed diagnose of pulmonary embolism formed the control group. Logistic regression analysis was used to identify predictors of pulmonary embolism and its survival.\n\nResultsA total of 159 patients participated were included in the study, of which 51 were the cases (patients with pulmonary embolism) and 108 patients formed the control group (patients without pulmonary embolism). The incidence of PE among hospitalized was around 32%. Smoking history, low level of oxygen saturation and higher D-dimer values were important risk factors that were associated with a higher risk of developing PE (p< 0.05). Higher respiratory rate was associated with higher odds of death, and decrease the possibility of survival among hospitalised patients with PE.\n\nConclusionPulmonary embolism is common among hospitalized patients with COVID-19. Preventive measures should be considered for hospitalized patients with smoking history, low level of oxygen saturation, high D-dimer values, and high respiratory rate.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Omaima Badr",
+        "author_inst": "Al Noor Specialist Hospital, Mecca"
+      },
+      {
+        "author_name": "Hassan Alwafi",
+        "author_inst": "Umm Al qura university"
+      },
+      {
+        "author_name": "Wael Elrefaey",
+        "author_inst": "Al Noor Specialist Hospital, Mecca"
+      },
+      {
+        "author_name": "Abdallah Y Naser",
+        "author_inst": "Isra University"
+      },
+      {
+        "author_name": "Mohammed Shabrawishi",
+        "author_inst": "Al Noor Specialist Hospital, Mecca"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "respiratory medicine"
+  },
   {
     "rel_doi": "10.1101/2021.02.16.21250657",
     "rel_title": "Worries about COVID-19 infection and psychological distress at work and while commuting",
@@ -911458,53 +909817,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.02.17.21251953",
-    "rel_title": "COVID-19 associated autoimmunity is a feature of severe respiratory disease - a Bayesian analysis.",
-    "rel_date": "2021-02-19",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.17.21251953",
-    "rel_abs": "BackgroundSerological and clinical features with similarities to systemic autoimmunity have been reported in severe COVID-19, but there is a lack of studies that include contemporaneous controls who do not have COVID-19.\n\nMethodsObservational cohort study of adult patients admitted to an intensive care unit with acute respiratory failure. Patients were divided into COVID+ and COVID- based on SARS-CoV-2 PCR from nasopharyngeal swabs and/or endotracheal aspirates. No COVID-19 specific interventions were given. The primary clinical outcome was death in the ICU within 3 months; secondary outcomes included in-hospital death and disease severity measures. Measurements including autoantibodies, were done longitudinally. ANOVA and Fishers exact test were used with =0.05, with a false discovery rate of q=0.05. Bayesian analysis was performed to provide credible estimates of the possible states of nature compatible with our results.\n\nResults22 COVID+ and 20 COVID- patients were recruited, 69% males, median age 60.5 years. Overall, 64% had anti-nuclear antibodies, 38% had antigen-specific autoantibodies, 31% had myositis related autoantibodies, and 38% had high levels of anti-cytokine autoantibodies. There were no statistically significant differences between COVID+ and COVID- for any of the clinical or autoantibody parameters. A specific pattern of anti-nuclear antibodies was associated with worse clinical severity for both cohorts.\n\nConclusionsSevere COVID+ patients have similar humoral autoimmune features as comparably ill COVID- patients, suggesting that autoantibodies are a feature of critical illness regardless of COVID-19 status. The clinical significance of autoimmune serology and the correlation with severity in critical illness remains to be elucidated.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Uriel Trahtemberg",
-        "author_inst": "St. Michael's Hospital"
-      },
-      {
-        "author_name": "Robert Rottapel",
-        "author_inst": "St Michael's Hospital"
-      },
-      {
-        "author_name": "Claudia C Dos Santos",
-        "author_inst": "St Michael's Hospital"
-      },
-      {
-        "author_name": "Alex P Di Battista",
-        "author_inst": "St Michael's Hospital"
-      },
-      {
-        "author_name": "Arthur S Slutsky",
-        "author_inst": "St Michael's Hospital"
-      },
-      {
-        "author_name": "Andrew J Baker",
-        "author_inst": "St Michael's Hospital"
-      },
-      {
-        "author_name": "Marvin J Fritzler",
-        "author_inst": "Cumming School of Medicine, University of Calgary"
-      },
-      {
-        "author_name": "- COLOBILI - COVID19 Longitudinal Biomarkers of Lung Injury Study Group",
-        "author_inst": ""
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "intensive care and critical care medicine"
-  },
   {
     "rel_doi": "10.1101/2021.02.18.21251809",
     "rel_title": "The unexpected dynamics of COVID-19 in Manaus, Brazil: Herd immunity versus interventions",
@@ -911907,6 +910219,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.02.17.21251725",
+    "rel_title": "Assessment of knowledge, attitude and practices among Accredited Social Health Activists (ASHAs) towards COVID-19: a descriptive cross-sectional study in Tripura, India",
+    "rel_date": "2021-02-19",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.17.21251725",
+    "rel_abs": "With the surge in COVID-19 cases, community healthcare workers (CHW) remain pivotal for proper dissemination of awareness of disease transmission and infection control measures among the communities in low- and middle-income countries. In this context, lack of adequate knowledge and appropriate attitude among the CHW can directly influence the COVID-19 management programme. Therefore, the present study was designed to assess the knowledge, attitude and practices towards COVID-19 among the CHW of India known as Accredited Social Health Activists (ASHAs). A descriptive cross-sectional was conducted in the state of Tripura, Northeast India, among ASHAs with 14-, 4- and 3-item self-administered questionnaire for knowledge, attitude and practice. Around 61.2% of participants had the mean correct answer rate and the mean score of knowledge was 8.57{+/-} 2.25 ({+/-}SD). As per Blooms cut-off, it was observed that only 10% of the ASHAs had adequate knowledge, 30.9% showed positive attitude and 88% adhered to the good practices. It was observed that the indigenous ASHAs were 1.79 times more likely to adhere to the good practice of wearing masks during filed visits in the community (OR: 1.791, 95% CI: 1.059-3.028, p=0.030). Multinomial regression analysis showed that practice was significantly associated with fear of getting infected during service and the communitys fearfulness of ASHAs spreading the disease. Urgent addressing of the provisions of support, guidance and training of grassroot level healthcare workers in rural tough terrains can ensure robust output from the existing community healthcare workers in future pandemic-like emergencies.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "PURVITA CHOWDHURY",
+        "author_inst": "Model Rural Health Research Unit (MRHRU), Tripura"
+      },
+      {
+        "author_name": "Subrata Baidya",
+        "author_inst": "Agartala Government Medical College, Tripura & Model Rural Health Research Unit (MRHRU), Tripura"
+      },
+      {
+        "author_name": "Debosmita Paul",
+        "author_inst": "Model Rural Health Research Unit (MRHRU), Tripura"
+      },
+      {
+        "author_name": "Pinki Debbarma",
+        "author_inst": "Kherengbar Hospital, Khumulwng, Tripura"
+      },
+      {
+        "author_name": "Biraj Kalita",
+        "author_inst": "Model Rural Health Research Unit (MRHRU), Tripura"
+      },
+      {
+        "author_name": "Sanjoy Karmakar",
+        "author_inst": "Model Rural Health Research Unit (MRHRU), Tripura"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.02.17.21251957",
     "rel_title": "Change in vaccine willingness in Australia: August 2020 to January 2021",
@@ -913172,101 +911523,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
-  {
-    "rel_doi": "10.1101/2021.02.15.21251764",
-    "rel_title": "SARS-CoV-2 Seroprevalence Survey Among District Residents Presenting for Serologic Testing at Three Community Based Test Sites in Washington, DC, July to August, 2020",
-    "rel_date": "2021-02-18",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.15.21251764",
-    "rel_abs": "BackgroundThe District of Columbia (DC), a major metropolitan area, continues to see community transmission of SARS-CoV-2. While serologic testing does not indicate current SARS-CoV-2 infection, it can indicate prior infection and help inform local policy and health guidance. The DC Department of Health (DC Health) conducted a community-based survey to estimate DCs SARS-CoV-2 seroprevalence and identify seropositivity-associated factors.\n\nMethodsA mixed-methods cross-sectional serology survey was conducted among a convenience sample of DC residents during July 27-August 21, 2020. Free serology testing was offered at three public test sites. Participants completed an electronic questionnaire on household and demographic characteristics, COVID-like illness (CLI) since January 1, 2020, comorbidities, and SARS-CoV-2 exposures. Univariate and bivariate analyses were conducted to describe the sample population and assess factors associated with seropositivity.\n\nResultsAmong a sample of 671 participants, 51 individuals were seropositive, yielding an estimated seroprevalence of 7.6%. More than half (56.9%) of the seropositive participants reported no prior CLI; nearly half (47.1%) had no prior SARS-CoV-2 testing. Race/ethnicity, prior SARS-CoV-2 testing, prior CLI, employment status, and contact with confirmed COVID-19 cases were associated with seropositivity (P<0.05). Among those reporting prior CLI, loss of taste or smell, duration of CLI, fewer days between CLI and serology test, or prior viral test were associated with seropositivity (P[&le;]0.006).\n\nConclusionsThese findings indicate many seropositive individuals reported no symptoms consistent with CLI since January or any prior SARS-CoV-2 testing. This underscores the potential for cases to go undetected in the community and suggests wider-spread transmission than previously reported in DC.\n\nWhat is already known on this subject?Traditional case-based detection and syndromic surveillance efforts might not identify mildly symptomatic or asymptomatic SARS-CoV-2 infections. This is particularly true among people in the general population who do not have increased risk of severe illness or might not be tested otherwise. Consequently, the true population prevalence of prior SARS-CoV-2 infections might not be known.\n\nWhat this study adds?A community-based seroprevalence survey conducted in Washington, DC, during July 27-August 21, 2020 estimated that 7.6% of the convenience sample had antibodies to SARS-CoV-2, indicating prior infection. At the time of this survey, most of the participants reported that they had not been previously infected with or tested for SARS-CoV-2. These findings highlight both the value of serologic surveillance in complementing other surveillance methods, and the importance of continued prevention and mitigation measures, such as maintaining physical distances of at least 6 feet, avoiding crowds and poorly ventilated spaces, practicing frequent hand hygiene, and wearing face masks properly and consistently around people who do not live with you.",
-    "rel_num_authors": 20,
-    "rel_authors": [
-      {
-        "author_name": "Adrienne Sherman",
-        "author_inst": "Department of Health, Government of the District of Columbia; Council of State and Territorial Epidemiologists Applied Epidemiology Fellowship Program"
-      },
-      {
-        "author_name": "Jacqueline Reuben",
-        "author_inst": "Department of Health, Government of the District of Columbia"
-      },
-      {
-        "author_name": "Naomi S David",
-        "author_inst": "Centers for Disease Control and Prevention, COVID-19 Response Team"
-      },
-      {
-        "author_name": "Delores P Quasie-Woods",
-        "author_inst": "Department of Health, Government of the District of Columbia; Centers for Disease Control and Prevention Foundation"
-      },
-      {
-        "author_name": "Jayleen K. L. Gunn",
-        "author_inst": "Centers for Disease Control and Prevention COVID-19 Response Team; Commissioned Corps Activity, United States Public Health Service"
-      },
-      {
-        "author_name": "Carrie F Nielson",
-        "author_inst": "Centers for Disease Control and Prevention COVID-19 Response Team; Commissioned Corps Activity, United States Public Health Service"
-      },
-      {
-        "author_name": "Patricia Lloyd",
-        "author_inst": "1 Department of Health, Government of the District of Columbia"
-      },
-      {
-        "author_name": "Abraham Yohannes",
-        "author_inst": "Department of Health, Government of the District of Columbia"
-      },
-      {
-        "author_name": "Mary Puckett",
-        "author_inst": "Centers for Disease Control and Prevention, COVID-19 Response Team"
-      },
-      {
-        "author_name": "Jo Anna Powell",
-        "author_inst": "Centers for Disease Control and Prevention, COVID-19 Response Team"
-      },
-      {
-        "author_name": "Sarah Leonard",
-        "author_inst": "Centers for Disease Control and Prevention, COVID-19 Response Team"
-      },
-      {
-        "author_name": "Preetha Iyengar",
-        "author_inst": "Department of Health, Government of the District of Columbia"
-      },
-      {
-        "author_name": "Fern Johnson-Clarke",
-        "author_inst": "Department of Health, Government of the District of Columbia"
-      },
-      {
-        "author_name": "Anthony Tran",
-        "author_inst": "Department of Forensic Sciences, Public Health Laboratory, Government of the District of Columbia"
-      },
-      {
-        "author_name": "Matthew McCarroll",
-        "author_inst": "Department of Forensic Sciences, Public Health Laboratory, Government of the District of Columbia"
-      },
-      {
-        "author_name": "Pushker Raj",
-        "author_inst": "Department of Forensic Sciences, Public Health Laboratory, Government of the District of Columbia"
-      },
-      {
-        "author_name": "John Davies-Cole",
-        "author_inst": "Department of Health, Government of the District of Columbia"
-      },
-      {
-        "author_name": "Jenifer Smith",
-        "author_inst": "Department of Forensic Sciences, Public Health Laboratory, Government of the District of Columbia"
-      },
-      {
-        "author_name": "James A Ellison",
-        "author_inst": "Centers for Disease Control and Prevention, COVID-19 Response Team"
-      },
-      {
-        "author_name": "LaQuandra Nesbitt",
-        "author_inst": "Department of Health, Government of the District of Columbia"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.02.15.21251511",
     "rel_title": "Mapping of SARS-CoV-2 Brain Invasion and Histopathology in COVID-19 Disease",
@@ -913741,6 +911997,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "respiratory medicine"
   },
+  {
+    "rel_doi": "10.1101/2021.02.15.21251586",
+    "rel_title": "Epidemiology of COVID-19 infection amongst workers in Primary Healthcare in Qatar",
+    "rel_date": "2021-02-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.15.21251586",
+    "rel_abs": "BackgroundCOVID-19 transmission was significant amongst Healthcare workers worldwide.\n\nAimThis study aims to estimate the risk of exposure for COVID-19 across Primary Healthcare workers in the State of Qatar. Methods: A cross-sectional descriptive study was conducted to study the burden of COVID-19 among staff working at PHCC during the COVID-19 pandemic from March 1 to October 31, 2020.\n\nResults1,048 (87.4%)of the infected HCWs belonged to the age group below 45 years, and 488 (40.7%) HCWs were females. 450 (37.5%) were HCWs clinical staff working in one of the 27 PHCC HCs; Despite the increased patient footfall and risk environment, the COVID HCs had an attack rate of 10.1%, which is not significantly different from the average attack rate of 8.9% among staff located in other HCs (p-value =0.26). Storekeepers, engineering & maintenance staff, housekeeping staff, support staff, and security staff (outsourced positions) had the highest positivity rates, 100%, 67.2%, 47.1%, 32.4%, and 29.5% respective positivity rates.\n\nConclusionsThe elevated risk of infection amongst outsourced healthcare workers can be explained by environmental factors such as living conditions. On the other hand, better containment within clinical healthcare workers can be attributed to strict safety training and compliance with preventative measures which is recommended to be implemented across all settings.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Mohamed Al Kuwari",
+        "author_inst": "Primary Healthcare Corporation"
+      },
+      {
+        "author_name": "Mariam AbdelMalik",
+        "author_inst": "Primary HealthCare Corporation"
+      },
+      {
+        "author_name": "Asma Al Nuaimi",
+        "author_inst": "PrimaryHealthCare Corporation"
+      },
+      {
+        "author_name": "Jazeel AbdelMajeed",
+        "author_inst": "PrimaryHealthCare Corporation"
+      },
+      {
+        "author_name": "Hamad Romaihi",
+        "author_inst": "Primary Healtcare Corporation"
+      },
+      {
+        "author_name": "sandy semaan",
+        "author_inst": "Primary Healthcare Corporation"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.02.17.431721",
     "rel_title": "Immune characterization and profiles of SARS-CoV-2 infected patients",
@@ -914986,61 +913281,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.02.11.21251129",
-    "rel_title": "Are there significant correlations between climate factors and the spread of COVID-19 for less densely populated and less polluted regions?",
-    "rel_date": "2021-02-17",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.11.21251129",
-    "rel_abs": "This study analyzes the correlation between the spread of COVID-19 and meteorological variables (air temperature, relative humidity, wind speed, and precipitation) in urban-rural cities located in southeastern Brazil. Spearmans correlation coefficients were used for the statistical analysis. Results show that air temperature and wind speed were positively correlated with COVID-19 cases, while air relative humidity showed negative correlation. As seen in several recent studies, climate factors and the spread of COVID-19 seem to be related. Our study corroborates this hypothesis for less densely populated and less polluted regions. We hope that our findings help worldwide scientific efforts towards understanding this disease and how it spreads in different regions.\n\nHighlightsO_LIClimate and COVID-19s spread were also correlated in less-densely populated regions.\nC_LIO_LIBoth maximum and minimum temperatures are strongly correlated with cases of covid-19.\nC_LIO_LIOne hypothesis for the strong association could be the high minimum temperatures in the subtropical region.\nC_LIO_LIWind speed is also positively correlated with COVID-19, while air humidity is negatively related.\nC_LIO_LIMitigation policies against the spread of COVID-19 should be based on local climate profiles.\nC_LI",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Marcelo de Paula Correa",
-        "author_inst": "Universidade Federal de Itajuba"
-      },
-      {
-        "author_name": "Ana Leticia Campos Yamamoto",
-        "author_inst": "Universidade Federal de Itajuba"
-      },
-      {
-        "author_name": "Luiz Felipe Silva",
-        "author_inst": "Universidade Federal de Itajuba"
-      },
-      {
-        "author_name": "Ivana Bastos",
-        "author_inst": "Universidade Federal de Itajuba"
-      },
-      {
-        "author_name": "Talis Matias",
-        "author_inst": "Universidade Federal de Alfenas"
-      },
-      {
-        "author_name": "Raquel Pereira",
-        "author_inst": "Universidade Federal de Itajuba"
-      },
-      {
-        "author_name": "Flavia Fagundes",
-        "author_inst": "Universidade Federal de Itajuba"
-      },
-      {
-        "author_name": "Alysson Ribeiro",
-        "author_inst": "Universidade Federal de Itajuba"
-      },
-      {
-        "author_name": "Joaquim Moraes",
-        "author_inst": "Universidade Federal de Itajuba"
-      },
-      {
-        "author_name": "Filipe Silva",
-        "author_inst": "Universidade Federal de Itajuba"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.02.17.431566",
     "rel_title": "E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies",
@@ -915555,6 +913795,89 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2021.02.16.430500",
+    "rel_title": "Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants",
+    "rel_date": "2021-02-17",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.16.430500",
+    "rel_abs": "The protective efficacy of neutralizing antibodies (nAbs) elicited during natural infection with SARS-CoV-2 and by vaccination based on its spike protein has been compromised with emergence of the recent SARS-CoV-2 variants. Residues E484 and K417 in the receptor-binding site (RBS) are both mutated in lineages first described in South Africa (B.1.351) and Brazil (B.1.1.28.1). The nAbs isolated from SARS-CoV-2 patients are preferentially encoded by certain heavy-chain germline genes and the two most frequently elicited antibody families (IGHV3-53/3-66 and IGHV1-2) can each bind the RBS in two different binding modes. However, their binding and neutralization are abrogated by either the E484K or K417N mutation, whereas nAbs to the cross-reactive CR3022 and S309 sites are largely unaffected. This structural and functional analysis illustrates why mutations at E484 and K417 adversely affect major classes of nAbs to SARS-CoV-2 with consequences for next-generation COVID-19 vaccines.",
+    "rel_num_authors": 17,
+    "rel_authors": [
+      {
+        "author_name": "Meng Yuan",
+        "author_inst": "The Scripps Research Institute"
+      },
+      {
+        "author_name": "Deli Huang",
+        "author_inst": "The Scripps Research Institute"
+      },
+      {
+        "author_name": "Chang-Chun D. Lee",
+        "author_inst": "The Scripps Research Institute"
+      },
+      {
+        "author_name": "Nicholas C. Wu",
+        "author_inst": "University of Illinois at Urbana-Champaign"
+      },
+      {
+        "author_name": "Abigail M. Jackson",
+        "author_inst": "The Scripps Research Institute"
+      },
+      {
+        "author_name": "Xueyong Zhu",
+        "author_inst": "The Scripps Research Institute"
+      },
+      {
+        "author_name": "Hejun Liu",
+        "author_inst": "The Scripps Research Institute"
+      },
+      {
+        "author_name": "Linghang Peng",
+        "author_inst": "The Scripps Research Institute"
+      },
+      {
+        "author_name": "Marit J. van Gils",
+        "author_inst": "Amsterdam UMC"
+      },
+      {
+        "author_name": "Rogier W. Sanders",
+        "author_inst": "Amsterdam UMC"
+      },
+      {
+        "author_name": "Dennis R. Burton",
+        "author_inst": "The Scripps Research Institute"
+      },
+      {
+        "author_name": "S Momsen Reincke",
+        "author_inst": "Deutsches Zentrum f\u00fcr Neurodegenerative Erkrankungen"
+      },
+      {
+        "author_name": "Harald Pr\u00fcss",
+        "author_inst": "Deutsches Zentrum f\u00fcr Neurodegenerative Erkrankungen"
+      },
+      {
+        "author_name": "Jakob Kreye",
+        "author_inst": "Deutsches Zentrum f\u00fcr Neurodegenerative Erkrankungen"
+      },
+      {
+        "author_name": "David Nemazee",
+        "author_inst": "The Scripps Research Institute"
+      },
+      {
+        "author_name": "Andrew B. Ward",
+        "author_inst": "The Scripps Research Institute"
+      },
+      {
+        "author_name": "Ian A. Wilson",
+        "author_inst": "The Scripps Research Institute"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2021.02.17.431625",
     "rel_title": "A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features",
@@ -916919,33 +915242,6 @@
     "type": "new results",
     "category": "biochemistry"
   },
-  {
-    "rel_doi": "10.1101/2021.02.16.431364",
-    "rel_title": "Identification of common key genes and pathways between Covid-19 and lung cancer by using protein-protein interaction network analysis",
-    "rel_date": "2021-02-16",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.16.431364",
-    "rel_abs": "COVID-19 is indeed an infection that is caused by a recently found coronavirus group, a type of virus proven to cause human respiratory diseases. The high mortality rate was observed in patients who had pre-existing health conditions like cancer. However, the molecular mechanism of SARS-CoV-2 infection in lung cancer patients was not discovered yet at the pathway level. This study was about determining the common key genes of COVID-19 and lung cancer through network analysis. The hub genes associated with COVID-19 and lung cancer were identified through Protein-Protein interaction analysis. The hub genes are ALB, CXCL8, FGF2, IL6, INS, MMP2, MMP9, PTGS2, STAT3 and VEGFA. Through gene enrichment, it is identified both COVID-19 and lung cancer have a common pathway in EGFR tyrosine kinase inhibitor resistance, IL-17 signalling pathway, AGE-RAGE signalling pathway in diabetic complications, HIF-1 signalling pathway and pathways in cancer.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Kang Soon Nana",
-        "author_inst": "Management and Science University, Malaysia"
-      },
-      {
-        "author_name": "Kalimuthu Karuppanan",
-        "author_inst": "University of Oxford, Oxford, UK"
-      },
-      {
-        "author_name": "Suresh Kumar",
-        "author_inst": "Management and Science University, Malaysia"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "bioinformatics"
-  },
   {
     "rel_doi": "10.1101/2021.02.15.431198",
     "rel_title": "Single-Domain SARS-CoV-2 S1 and RBD Antibodies Isolated from Immunized Llama Effectively Bind Targets of the Wuhan, UK, and South African Strains in vitro",
@@ -917179,6 +915475,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.02.12.21251479",
+    "rel_title": "Severe COVID-19 pneumonia and barotrauma: From the frying pan into the fire.",
+    "rel_date": "2021-02-16",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.12.21251479",
+    "rel_abs": "AimCOVID-19 pneumonia with ARDS (C-ARDS) has a high mortality. Preliminary reports indicate a higher incidence of barotrauma in patients with C-ARDS[1] both on invasive mechanical ventilation (iMV) and non-invasive ventilation (NIV) This study examines the incidence and risk factors for barotrauma and change in outcomes after barotrauma in patients with severe C-ARDS on positive pressure respiratory support (PPRS).\n\nMethods and materialsThis is a retrospective study of C-ARDS associated barotrauma over 5 months in patients on PPRS in a tertiary COVID care center. The type of barotrauma, intervention, related factors, such as type of respiratory support (iMV vs NIV), airway pressure prior to the occurrence of barotrauma, and post-barotrauma outcomes were analyzed.\n\nResultsA total of 38/410 (9.3%) C-ARDS patients on PPRS [mean age 57.82 {+/-} 13.3 years, 32 males (84.2%)] developed barotrauma. Of these, 20 patients (52.6%) were on NIV and 18 (47.4%) patients were iMV on standard recommended settings. The median P/F ratio of patients on MV at the time of barotrauma was 116.4 (IQR 72.4, 193.25). The details of barotrauma were as follows: 24 patients had pneumothorax (PTX), 2 had pneumo-mediastinum and 12 had subcutaneous emphysema. Overall, 24/38 (63.2%) patients, including 15/18 (83.3%) on MV succumbed to their illness. The barotrauma happened a median of 6.5 days (IQR 4.75,13) after admission and 15 days (IQR 10.25,18.0) from symptom onset. The median duration from barotrauma to death was 7 days (IQR 2.25, 8.0) and barotrauma to discharge (for survivors) was 12.5 days (IQR 8.0, 21.25). All patients received steroids and 11/38 (28.9%) received additional immunosuppression with tocilizumab.\n\nConclusionA high incidence of barotrauma was seen in this large series of severe C-ARDS patients on PPRS. Barotrauma led to further deterioration in the clinical status leading to a fatal outcome in the majority of the MV patients, despite prompt treatment.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Hariprasad Kalpakam",
+        "author_inst": "Apollo Hospitals Bangalore"
+      },
+      {
+        "author_name": "Sameer Bansal",
+        "author_inst": "Apollo Specialty Hospital, Bangalore"
+      },
+      {
+        "author_name": "Nithya . Suresh",
+        "author_inst": "Apollo hospitals"
+      },
+      {
+        "author_name": "Samson Kade",
+        "author_inst": "Apollo Specialty Hospitals, Bangalore, India"
+      },
+      {
+        "author_name": "Anmol Thorbole",
+        "author_inst": "Apollo Hospitals, Bangalore, India"
+      },
+      {
+        "author_name": "Ravindra M Mehta",
+        "author_inst": "Apollo Super Specialty Hospital"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "intensive care and critical care medicine"
+  },
   {
     "rel_doi": "10.1101/2021.02.10.21251484",
     "rel_title": "An analysis of school absences in England during the Covid-19 pandemic",
@@ -918488,57 +916823,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2021.02.15.431237",
-    "rel_title": "SARS-CoV2 envelop proteins reshape the serological responses of COVID-19 patients",
-    "rel_date": "2021-02-15",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.15.431237",
-    "rel_abs": "The SARS-CoV-2 pandemic has elicited a unique international mobilization of the scientific community to better understand this coronavirus and its associated disease and to develop efficient tools to combat infection. Similar to other coronavirae, SARS-CoV-2 hijacks the host cell complex secretory machinery to produce properly folded viral proteins that will compose the nascent virions; including Spike, Envelope and Membrane proteins, the most exposed membrane viral proteins to the host immune system. Antibody response is part of the anti-viral immune arsenal that infected patients develop to fight viral particles in the body. Herein, we investigate the immunogenic potential of Spike (S), Envelope (E) and Membrane (M) proteins using a human cell-based system to mimic membrane insertion and N-glycosylation. We show that both S and M proteins elicit the production of specific IgG, IgM and IgA in SARS-CoV-2 infected patients. Elevated Ig responses were observed in COVID+ patients with moderate and severe forms of the disease. Finally, when SARS-CoV-2 Spike D614 and G614 variants were compared, reduced Ig binding was observed with the Spike G614 variant. Altogether, this study underlines the needs for including topological features in envelop proteins to better characterize the serological status of COVID+ patients, points towards an unexpected immune response against the M protein and shows that our assay could represent a powerful tool to test humoral responses against actively evolving SARS-CoV-2 variants and vaccine effectiveness.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Sophie Martin",
-        "author_inst": "Inserm U1242 Oncogenesis Stress Signaling, Centre Eugene Marquis, Rennes, France"
-      },
-      {
-        "author_name": "Christopher Heslan",
-        "author_inst": "Department of Virology, CHU Pontchaillou, Rennes, France"
-      },
-      {
-        "author_name": "Gwenaele Jegou",
-        "author_inst": "Inserm U1242 Oncogenesis Stress Signaling, Centre Eugene Marquis, Rennes, France"
-      },
-      {
-        "author_name": "Leif A. Eriksson",
-        "author_inst": "Department of Chemistry & Molecular Biology, University of Gothenburg, Goteborg, Sweden"
-      },
-      {
-        "author_name": "Matthieu Le Gallo",
-        "author_inst": "Inserm U1242 Oncogenesis Stress Signaling, Centre Eugene Marquis, Rennes, France"
-      },
-      {
-        "author_name": "Vincent Thibault",
-        "author_inst": "Department of Virology, CHU Pontchaillou, Rennes, France"
-      },
-      {
-        "author_name": "Eric Chevet",
-        "author_inst": "Inserm U1242 Oncogenesis Stress Signaling, Centre Eugene Marquis, Rennes, France"
-      },
-      {
-        "author_name": "Florence Godey",
-        "author_inst": "Inserm U1242 Oncogenesis Stress Signaling, Centre Eugene Marquis, Rennes, France"
-      },
-      {
-        "author_name": "Tony Avril",
-        "author_inst": "Inserm U1242 Oncogenesis Stress Signaling, Centre Eugene Marquis, Rennes, France"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "cell biology"
-  },
   {
     "rel_doi": "10.1101/2021.02.11.21251584",
     "rel_title": "Recent and forecast post-COVID trends in hospital activity in England amongst 0 to 24 year olds: analyses using routine hospital administrative data",
@@ -919013,6 +917297,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.02.11.21251562",
+    "rel_title": "Population Age-Ineligible for COVID-19 Vaccine in the United States: Implications for State, County, and Race/Ethnicity Vaccination Targets",
+    "rel_date": "2021-02-15",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.11.21251562",
+    "rel_abs": "BackgroundWe examined the geographic and racial/ethnic distribution of the SARS-CoV-2 vaccine age-ineligible population (0-15 years old) in the U.S., and calculated the proportion of the age-eligible population that will need to be vaccinated in a given geo-demographic group in order to achieve either 60% or 75% vaccine coverage for that population as a whole.\n\nMethodsUS Census Bureau population estimates for 2019 were used to calculate the percent vaccine ineligible and related measures for counties, states, and the nation as a whole. Vaccination targets for the 30 largest counties by population were calculated. Study measures were calculated for racial/ethnic populations at the national (n=7) and state (n=6) levels.\n\nResultsPercent of population ineligible for vaccine varied widely both geographically and by race/ethnicity. State values ranged from 15.8% in Vermont to 25.7% in Utah, while percent ineligible of the major racial/ethnic groups was 16.4% of non-Hispanic whites, 21.6% of non-Hispanic Blacks, and 27.5% of Hispanics. Achievement of total population vaccine coverage of at least 75% will require vaccinating more than 90% of the population aged 16 years and older in 29 out of 30 of the largest counties in the U.S.\n\nConclusionsThe vaccine-ineligibility of most children for the next 1-2 years, coupled with reported pervasive vaccine hesitancy among adults, especially women and most minorities, means that achievement of adequate levels of vaccine coverage will be very difficult for many vulnerable geographic areas and for several racial/ethnic minority groups, particularly Hispanics, Blacks, and American Indians.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Elizabeth B Pathak",
+        "author_inst": "Women's Institute for Independent Social Enquiry"
+      },
+      {
+        "author_name": "Janelle Menard",
+        "author_inst": "Women's Institute for Independent Social Enquiry (www.wiise-usa.org)"
+      },
+      {
+        "author_name": "Rebecca B Garcia",
+        "author_inst": "Premise Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.02.10.21251526",
     "rel_title": "Impacts of school closures on physical and mental health of children and young people: a systematic review",
@@ -920102,53 +918413,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "allergy and immunology"
   },
-  {
-    "rel_doi": "10.1101/2021.02.10.21251458",
-    "rel_title": "Human liver organoid derived intra-hepatic bile duct cells support SARS-CoV-2 infection and replication and its comparison with SARS-CoV",
-    "rel_date": "2021-02-15",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.10.21251458",
-    "rel_abs": "BackgroundAlthough the main route of infection for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the respiratory tract, liver injury is also commonly seen in many patients, as evidenced by deranged parenchymal liver enzymes. Furthermore, patients with severe liver disease have been shown to have higher mortality. Overall, the mechanism behind the liver injury remains unclear.\n\nApproach and resultsWe showed that intra-hepatic bile duct cells could be grown using a human liver organoid platform. The cholangiocytes were not only susceptible to SARS-CoV-2 infection, they also supported efficient viral replication. We also showed that SARS-CoV-2 replication was much higher than SARS-CoV.\n\nConclusionOur findings suggested direct cytopathic viral damage being a mechanism for SARS-CoV-2 liver injury.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Vincent Chi-Hang Lui",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Kenrie Pui-Yan Hui",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Rosanna Ottakandathil Babu",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Haibing Yue",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Patrick Ho-Yu Chung",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Paul KH Tam",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Michael Chi-Wai Chan",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Kenenth Kak-Yuen Wong",
-        "author_inst": "The University of Hong Kong"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "gastroenterology"
-  },
   {
     "rel_doi": "10.1101/2021.02.11.21251553",
     "rel_title": "Performance characteristics of five antigen-detecting rapid diagnostic test (Ag-RDT) for SARS-CoV-2 asymptomatic infection: a head-to-head benchmark comparison",
@@ -920631,6 +918895,41 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2021.02.12.430933",
+    "rel_title": "Rapidly Increasing SARS-CoV-2 Neutralization by Intravenous Immunoglobulins Produced from Plasma Collected During the 2020 Pandemic",
+    "rel_date": "2021-02-12",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.12.430933",
+    "rel_abs": "Immunoglobulin (IG) lots (N=176) released since March 2020 were tested for SARS-CoV-2 neutralizing antibodies, with first positive results for September 2020 lots, mean = 1.8 IU/ml, 46% of lots positive. From there, values steadily increased, in correlation with the cumulative COVID-19 incidence, to reach a mean of 36.7 IU/ml and 93% of lots positive by January 2021. Extrapolating the correlation, IGs could reach an anti-SARS-CoV-2 potency of ~400 IU/ml by July 2021. At that stage, prophylactic IG treatment for primary/secondary immunodeficiency could contain similar doses of anti-SARS-CoV-2 as convalescent plasma which is used for treatment of COVID-19.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Maria R. Farcet",
+        "author_inst": "Baxter AG, part of Takeda"
+      },
+      {
+        "author_name": "Michael Karbiener",
+        "author_inst": "Baxter AG, part of Takeda"
+      },
+      {
+        "author_name": "Julia Schwaiger",
+        "author_inst": "Baxter AG, part of Takeda"
+      },
+      {
+        "author_name": "Reinhard Ilk",
+        "author_inst": "Baxter AG, part of Takeda"
+      },
+      {
+        "author_name": "Thomas R. Kreil",
+        "author_inst": "Baxter AG, part of Takeda"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2021.02.11.430866",
     "rel_title": "A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection",
@@ -922009,64 +920308,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.02.10.21251474",
-    "rel_title": "A participatory modelling approach for investigating the spread of COVID-19 in countries of the Eastern Mediterranean Region to support public health decision-making",
-    "rel_date": "2021-02-12",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.10.21251474",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Keyrellous Adib",
-        "author_inst": "World Health Organization Eastern Mediterranean Regional Office"
-      },
-      {
-        "author_name": "Penelope A Hancock",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Aysel Rahimli",
-        "author_inst": "World Health Organisation Regional Office for the Eastern Mediterranean"
-      },
-      {
-        "author_name": "Bridget Mugisa",
-        "author_inst": "World Health Organization Eastern Mediterranean Regional Office"
-      },
-      {
-        "author_name": "Fayez Abdulrazeq",
-        "author_inst": "World Health Organization Eastern Mediterranean Regional Office"
-      },
-      {
-        "author_name": "Noha Farag",
-        "author_inst": "Centers for Disease Control and Prevention Center for Global Health"
-      },
-      {
-        "author_name": "Ricardo Aguas",
-        "author_inst": "University of Oxford Centre for Tropical Medicine and Global Health"
-      },
-      {
-        "author_name": "Lisa J White",
-        "author_inst": "University of Oxford, Nuffield Department of Medicine"
-      },
-      {
-        "author_name": "Rana Hajjeh",
-        "author_inst": "World Health Organisation Regional Office for the Eastern Mediterranean"
-      },
-      {
-        "author_name": "Lubna Al Ariqi",
-        "author_inst": "World Health Organisation Regional Office for the Eastern Mediterranean"
-      },
-      {
-        "author_name": "Pierre Nabeth",
-        "author_inst": "World Health Organisation Regional Office for the Eastern Mediterranean"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.02.10.21251480",
     "rel_title": "Symptom reporting in over 1 million people: community detection of COVID-19",
@@ -922351,6 +920592,28 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.02.10.21251533",
+    "rel_title": "County-Specific, Real-Time Projection of the Effect of Business Closures on the COVID-19 Pandemic",
+    "rel_date": "2021-02-12",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.10.21251533",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Dominic Yurk",
+        "author_inst": "California Institute of Technology"
+      },
+      {
+        "author_name": "Yaser Abu-Mostafa",
+        "author_inst": "California Institute of Technology"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.02.10.21251543",
     "rel_title": "Is Covid-19 seroprevalence different in health care workers as per their risk of exposure? A study from a tertiary care hospital in National Capital Region of India",
@@ -924022,153 +922285,6 @@
     "type": "new results",
     "category": "molecular biology"
   },
-  {
-    "rel_doi": "10.1101/2021.02.11.21249258",
-    "rel_title": "Tocilizumab in patients admitted to hospital with COVID-19 (RECOVERY): preliminary results of a randomised, controlled, open-label, platform trial",
-    "rel_date": "2021-02-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.11.21249258",
-    "rel_abs": "Findings: Between 23 April 2020 and 25 January 2021, 4116 adults were included in the assessment of tocilizumab, including 562 (14%) patients receiving invasive mechanical ventilation, 1686 (41%) receiving non-invasive respiratory support, and. 1868 (45%) receiving no respiratory support other than oxygen. Median CRP was 143 [IQR 107-205] mg/L and 3385 (82%) patients were receiving systemic corticosteroids at randomisation. Overall, 596 (29%) of the 2022 patients allocated tocilizumab and 694 (33%) of the 2094 patients allocated to usual care died within 28 days (rate ratio 0.86; 95% confidence interval [CI] 0.77-0.96; p=0.007). Consistent results were seen in all pre-specified subgroups of patients, including those receiving systemic corticosteroids. Patients allocated to tocilizumab were more likely to be discharged from hospital alive within 28 days (54% vs. 47%; rate ratio 1.23; 95% CI 1.12-1.34; p<0.0001). Among those not receiving invasive mechanical ventilation at baseline, patients allocated tocilizumab were less likely to reach the composite endpoint of invasive mechanical ventilation or death (33% vs. 38%; risk ratio 0.85; 95% CI 0.78-0.93; p=0.0005). Interpretation: In hospitalised COVID-19 patients with hypoxia and systemic inflammation, tocilizumab improved survival and other clinical outcomes regardless of the level of respiratory support received and in addition to the use of systemic corticosteroids.",
-    "rel_num_authors": 33,
-    "rel_authors": [
-      {
-        "author_name": "Peter W Horby",
-        "author_inst": "Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom"
-      },
-      {
-        "author_name": "Mark Campbell",
-        "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom"
-      },
-      {
-        "author_name": "Natalie Staplin",
-        "author_inst": "MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom"
-      },
-      {
-        "author_name": "Enti Spata",
-        "author_inst": "MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom"
-      },
-      {
-        "author_name": "Jonathan R Emberson",
-        "author_inst": "MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom"
-      },
-      {
-        "author_name": "Guilherme Pessoa-Amorim",
-        "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom"
-      },
-      {
-        "author_name": "Leon Peto",
-        "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom"
-      },
-      {
-        "author_name": "Christopher E Brightling",
-        "author_inst": "Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, United Kingdom"
-      },
-      {
-        "author_name": "Rahuldeb Sarkar",
-        "author_inst": "Medway Foundation NHS Trust, Gillingham, United Kingdom; King?s College London, London, United Kingdom"
-      },
-      {
-        "author_name": "Koshy Thomas",
-        "author_inst": "Basildon and Thurrock Hospitals NHS Foundation Trust, Basildon, United Kingdom"
-      },
-      {
-        "author_name": "Vandana Jeebun",
-        "author_inst": "Department of Respiratory Medicine, North Tees & Hartlepool NHS Foundation Trust, Stockton-on-Tees, United Kingdom"
-      },
-      {
-        "author_name": "Abdul Ashish",
-        "author_inst": "Wrightington Wigan and Leigh NHS Foundation Trust, Wigan, United Kingdom"
-      },
-      {
-        "author_name": "Redmond Tully",
-        "author_inst": "Royal Oldham Hospital, Northern Care Alliance, Oldham, United Kingdom"
-      },
-      {
-        "author_name": "David Chadwick",
-        "author_inst": "Centre for Clinical Infection, James Cook University Hospital, Middlesbrough, United Kingdom"
-      },
-      {
-        "author_name": "Muhammad Sharafat",
-        "author_inst": "North West Anglia NHS Foundation Trust, Peterborough, United Kingdom"
-      },
-      {
-        "author_name": "Richard Stewart",
-        "author_inst": "Milton Keynes University Hospital, Milton Keynes, United Kingdom"
-      },
-      {
-        "author_name": "Banu Rudran",
-        "author_inst": "Luton & Dunstable University Hospital, Luton, United Kingdom"
-      },
-      {
-        "author_name": "J Kenneth Baillie",
-        "author_inst": "Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom"
-      },
-      {
-        "author_name": "Maya H Buch",
-        "author_inst": "Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom"
-      },
-      {
-        "author_name": "Lucy C Chappell",
-        "author_inst": "School of Life Sciences, Kings College London, London, United Kingdom"
-      },
-      {
-        "author_name": "Jeremy N Day",
-        "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom"
-      },
-      {
-        "author_name": "Saul N Furst",
-        "author_inst": "NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, "
-      },
-      {
-        "author_name": "Thomas Jaki",
-        "author_inst": "Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom"
-      },
-      {
-        "author_name": "Katie Jeffery",
-        "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom"
-      },
-      {
-        "author_name": "Edmund Juszczak",
-        "author_inst": "School of Medicine, University of Nottingham, Nottingham, United Kingdom"
-      },
-      {
-        "author_name": "Wei Shen Lim",
-        "author_inst": "Respiratory Medicine Department, Nottingham University Hospitals NHS Foundation Trust, Nottingham, United Kingdom"
-      },
-      {
-        "author_name": "Alan Montgomery",
-        "author_inst": "School of Medicine, University of Nottingham, Nottingham, United Kingdom"
-      },
-      {
-        "author_name": "Andrew Mumford",
-        "author_inst": "School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom"
-      },
-      {
-        "author_name": "Kathryn Rowan",
-        "author_inst": "Intensive Care National Audit and Research Centre, London, United Kingdom"
-      },
-      {
-        "author_name": "Guy Thwaites",
-        "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom"
-      },
-      {
-        "author_name": "Marion Mafham",
-        "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom"
-      },
-      {
-        "author_name": "Richard Haynes",
-        "author_inst": "MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom"
-      },
-      {
-        "author_name": "Martin J Landray",
-        "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.02.08.21251344",
     "rel_title": "Novel SARS-CoV-2 spike variant identified through viral genome sequencing of the pediatric Washington D.C. COVID-19 outbreak",
@@ -924667,6 +922783,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.02.08.21251352",
+    "rel_title": "Assessment of Post SARS CoV 2 Fatigue among Physicians Working in COVID Designated Hospitals in Dhaka, Bangladesh",
+    "rel_date": "2021-02-10",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.08.21251352",
+    "rel_abs": "BackgroundFatigue has been observed after a number of infectious disease outbreaks around the world. After the outbreak of SARS CoV-2 in Wuhan, China in 2019, the disease turned into a pandemic very rapidly. Mental health is a key issue associated with such outbreaks. To explore the fatigue level among physicians working in designated public and private hospitals in Bangladesh, we conducted a matched case-control study of post-SARS-CoV-2 fatigue.\n\nMethodIn this study 105 physicians who were diagnosed as COVID-19 infected, got treatment, and declared cured at least 6 weeks before the interview date, were recruited as cases and the same number of age and designation matched healthy physicians as control who are working in the same hospital. Case and control were selected in 1:1 ratio from each of the hospitals. The study population was selected by inclusion and exclusion criteria after taking informed written consent. Data collection was done by a semi-structured questionnaire. Diagnosis of COVID--19 infection was done by detection of SARS CoV-2 antigen by RT-PCR from reference laboratories in Bangladesh or by HRCT Chest.\n\nResultAround two-thirds of the physicians were male (67.6% versus 32.4%). Most of them aged less than forty years (80.5%). The cases had a greater number of comorbid conditions than those who were negative. The FSS score (mean) was much higher for cases (36.7 {+/-} 5.3 versus 19.3 {+/-} 3.8) than the control group with a statistically significant difference with no significant gender differentiation. Similarly, around 67.7% of the previously COVID positive physicians represented in the highest FSS score tertile compared to the respondents in the control group had a mean score of less than 3. The difference was also highly significant.\n\nConclusionPhysicians, who had a previous history of COVID-19 infection had a higher total and mean FSS score, signifying a more severe level of fatigue than the physicians who had never been COVID-19 positive while working in the same hospital irrespective of their age and sex.",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "A T M Hasibul Hasan",
+        "author_inst": "National Institute of Neurosciences and Hospital"
+      },
+      {
+        "author_name": "Muhammad Sougatul Islam",
+        "author_inst": "BioTED"
+      },
+      {
+        "author_name": "Nushrat Khan",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Nazmul Hoque Munna",
+        "author_inst": "Mugda Medical College Hospital"
+      },
+      {
+        "author_name": "Wahidur Rahman Choton",
+        "author_inst": "Mymensingh Medical College and Hospital"
+      },
+      {
+        "author_name": "Mostofa Kamal Arefin",
+        "author_inst": "Dhaka Medical College Hospital"
+      },
+      {
+        "author_name": "Mohammad Abdullah Az Zubayer Khan",
+        "author_inst": "National Institute of Laboratory Medicine and Referral Centre"
+      },
+      {
+        "author_name": "Mohaimen Mansur",
+        "author_inst": "Institute of Statistical Research and Training, Dhaka University"
+      },
+      {
+        "author_name": "Rashedul Hassan",
+        "author_inst": "Green Life Medical College & Hospital"
+      },
+      {
+        "author_name": "Numera Siddiqui",
+        "author_inst": "Dhaka Medical College & Hospital"
+      },
+      {
+        "author_name": "Muhammad Shamsul Arefin",
+        "author_inst": "National Institute of Neurosciences & Hospital"
+      },
+      {
+        "author_name": "Nayema Afroje",
+        "author_inst": "50 Bed District Hospital, Kishoreganj"
+      },
+      {
+        "author_name": "Md. Salequl Islam",
+        "author_inst": "Jahangirnagar University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "psychiatry and clinical psychology"
+  },
   {
     "rel_doi": "10.1101/2021.02.08.21250113",
     "rel_title": "Association between COVID-19, mobility and environment in Sao Paulo, Brazil",
@@ -926184,29 +924367,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "cardiovascular medicine"
   },
-  {
-    "rel_doi": "10.1101/2021.02.08.21251339",
-    "rel_title": "Multivariate spatio-temporal analysis of the global COVID-19 pandemic",
-    "rel_date": "2021-02-09",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.08.21251339",
-    "rel_abs": "The Covid-19 pandemic has caused significant mortality and disruption on a global scale not seen in living memory. Understanding the spatial and temporal vectors of transmission as well as similarities in the trajectories of recorded cases and deaths across countries can aid in understanding the benefit or otherwise of varying interventions and control strategies on virus transmission. It can also highlight emerging globa trends as they occur. Data on number of cases and deaths across the globe have been made available through a variety of databases and provide a wide range of opportunities for the application of multivariate statistical methods to extract information on similarity or difference from them. Here we conduct spatial and temporal multivariate statistical analyses of global Covid-19 cases and deaths for the period spanning January to August 2020, using a variety of distance based multivariate methods to cluster countries according to similar temporal trends in cases and deaths resulting from COVID-19. We also use novel air passenger data as a proxy for movement between countries. The air passenger movement can act as an important vector of transmission and thus scaling covariance matrices before conducting dimension reduction techniques can account for known structures in the data and help highlight important residual spatial and/or temporal trends that may then be attributable to the success of interventions or other cultural differences. Global temporal structure is found to be of significantly more importance than local spatial structure in terms of global dynamics. Our results highlight a significant global change in case and mortality daynamics from early-August, consistent in timing with the emergence of new strains with highger levels of transmission. We propose the methodology offers great potential in real-time analysis of complex, noisy spatio-temporal data and the extraction of emerging changes in pandemic dynamics that can support policy and decision makers.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Wen Xiang",
-        "author_inst": "University of Glasgow"
-      },
-      {
-        "author_name": "Ben Swallow",
-        "author_inst": "University of Glasgow"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.02.07.21251291",
     "rel_title": "Rapid Impact Analysis of B 1.1.7 Variant on the Spread of SARS-CoV-2 in North Carolina",
@@ -926493,6 +924653,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.02.08.21251070",
+    "rel_title": "The protective association between statins use and adverse outcomes among COVID-19 patients: a systematic review and meta-analysis",
+    "rel_date": "2021-02-09",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.08.21251070",
+    "rel_abs": "IntroductionStatins may reduce a cytokine storm, which has been hypothesized as a possible mechanism of severe COVID-19 pneumonia. The aim of this study was to conduct a systematic review and meta-analysis to report on adverse outcomes among COVID-19 patients by statin usage.\n\nMethodsLiteratures were searched from January 2019 to December 2020 to identify studies that reported the association between statin usage and adverse outcomes, including mortality, ICU admissions, and mechanical ventilation. Studies were meta-analyzed for mortality by the subgroups of ICU status and statin usage before and after COVID-19 hospitalization. Studies reporting an odds ratio (OR) and hazard ratio (HR) were analyzed separately.\n\nResultsThirteen cohorts, reporting on 110,078 patients, were included in this meta-analysis. Individuals who used statins before their COVID-19 hospitalization showed a similar risk of mortality, compared to those who did not use statins (HR 0.80, 95% CI: 0.50, 1.28; OR 0.62, 95% CI: 0.38, 1.03). Patients who were administered statins after their COVID-19 diagnosis were at a lower risk of mortality (HR 0.53, 95% CI: 0.46, 0.61; OR 0.57, 95% CI: 0.43, 0.75). The use of statins did not reduce the mortality of COVID-19 patients admitted to the ICU (OR 0.65; 95% CI: 0.26, 1.64). Among non-ICU patients, statin users were at a lower risk of mortality relative to non-statin users (HR 0.53, 95% CI: 0.46, 0.62; OR 0.64, 95% CI: 0.46, 0.88).\n\nConclusionPatients administered statins after COVID-19 diagnosis or non-ICU admitted patients were at lower risk of mortality relative to non-statin users.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Ronald Chow",
+        "author_inst": "Yale School of Public Health, Yale University, New Haven, CT, United States of America; Yale New Haven Health, Yale School of Medicine, Yale University, New Hav"
+      },
+      {
+        "author_name": "James Im",
+        "author_inst": "Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada"
+      },
+      {
+        "author_name": "Nicholas Chiu",
+        "author_inst": "Beth Israel Deaconess Medical Center, Harvard Medical School, Harvard University, Boston, MA, United States of America"
+      },
+      {
+        "author_name": "Leonard Chiu",
+        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, United States of America"
+      },
+      {
+        "author_name": "Rahul Aggarwal",
+        "author_inst": "Beth Israel Deaconess Medical Center, Harvard Medical School, Harvard University, Boston, MA, United States of America"
+      },
+      {
+        "author_name": "Jihui Lee",
+        "author_inst": "Weill Cornell Medicine, New York, NY, United States of America"
+      },
+      {
+        "author_name": "Young-Geun Choi",
+        "author_inst": "Sookmyung Womens Hospital, Seoul, Korea"
+      },
+      {
+        "author_name": "Elizabeth Horn Prsic",
+        "author_inst": "Yale New Haven Health, Yale School of Medicine, Yale University, New Haven, CT, United States of America"
+      },
+      {
+        "author_name": "Hyun Joon Shin",
+        "author_inst": "Lemuel Shattuck Hospital, Massachusetts Department of Public Health, Jamaica Plain, MA, United States of America; Brigham and Women's Hospital, Boston, MA, Unit"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.02.08.21251332",
     "rel_title": "Current quantitative polymerase chain reaction to detect severe acute respiratory syndrome coronavirus 2 may give positive results for other described coronavirus",
@@ -927898,29 +926109,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.02.04.21250767",
-    "rel_title": "Introduction of a hand dermatitis clinic to reduce occupational dermatoses during the covid-19 pandemic.",
-    "rel_date": "2021-02-08",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.04.21250767",
-    "rel_abs": "BackgroundThe SARS-Co-V pandemic has necessitated strict hand hygiene practices in healthcare settings. An increased incidence of staff presentations of occupational dermatitis in our institutions prompted the establishment of a drop-in access daily hand dermatitis clinic.\n\nObjectiveto document the incidence and severity of cases of occupational dermatitis arising in healthcare workers during the first wave of the pandemic, and to reduce the impact of this with early assessment and treatment.\n\nMethodsan open-access daily staff clinic run by dermatologists was established, and demographic and clinical data collected from each clinical encounter.\n\nResults532 staff attended the clinic over a 6 week period. This compared to 7 staff presenting to occupational health over the same period in 2019. The majority were females 81%,and ward based 51%. ITU and A&E staff represented 15%. The prevalence of occupational hand dermatitis was 88%. 52% were classed as mild, 26% as moderate 26% and 9% severe/very severe.\n\nConclusionsthe pandemic and associated hand hygiene practices have led to a substantial increase in presentations of occupational hand dermatitis. A drop-in clinic proved an effective way of allowing staff to access treatment in a timely fashion.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Sarah Walsh",
-        "author_inst": "King's College Hospital NHS Foundation Trust"
-      },
-      {
-        "author_name": "Siobhan Carey",
-        "author_inst": "King's College Hospital NHS Foundation Trust"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "dermatology"
-  },
   {
     "rel_doi": "10.1101/2021.02.04.21251176",
     "rel_title": "Assessment of Vaccination and Underreporting on COVID-19 Infections in Turkey Based On Effective Reproduction Number",
@@ -928195,6 +926383,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.02.04.21251171",
+    "rel_title": "Mapping internet activity in Australian cities during COVID-19 lockdown: how occupational factors drive inequality",
+    "rel_date": "2021-02-08",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.04.21251171",
+    "rel_abs": "During the COVID-19 pandemic, evidence has accumulated that movement restrictions enacted to combat virus spread produce disparate consequences along socioeconomic lines. We investigate the hypothesis that people engaged in financially secure employment are better able to adhere to mobility restrictions, due to occupational factors that link the capacity for flexible work arrangements to income security. We use high-resolution spatial data on household internet traffic as a surrogate for adaptation to home-based work, together with the geographical clustering of occupation types, to investigate the relationship between occupational factors and increased internet traffic during work hours under lockdown in two Australian cities. By testing our hypothesis based on the observed trends, and exploring demographic factors associated with divergences from our hypothesis, we are left with a picture of unequal impact dominated by two major influences: the types of occupations in which people are engaged, and the composition of households and families. During lockdown, increased internet traffic was correlated with income security and, when school activity was conducted remotely, to the proportion of families with children. Our findings suggest that response planning and provision of social and economic support for residents within lockdown areas should explicitly account for income security and household structure. Overall, the results we present contribute to the emerging picture of the impacts of COVID-19 on human behaviour, and will help policy makers to understand the balance between public health and social impact in making decisions about mitigation policies.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Cameron Zachreson",
+        "author_inst": "The University of Melbourne"
+      },
+      {
+        "author_name": "Erika Martino",
+        "author_inst": "The University of Melbourne"
+      },
+      {
+        "author_name": "Martin Tomko",
+        "author_inst": "The University of Melbourne"
+      },
+      {
+        "author_name": "Freya M Shearer",
+        "author_inst": "The University of Melbourne"
+      },
+      {
+        "author_name": "Rebecca Bentley",
+        "author_inst": "The University of Melbourne"
+      },
+      {
+        "author_name": "Nicholas Geard",
+        "author_inst": "The University of Melbourne"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.02.05.21251197",
     "rel_title": "Development and validation of an algorithm to estimate the risk of severe complications of COVID-19 to prioritise vaccination",
@@ -929764,33 +927991,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
-  {
-    "rel_doi": "10.1101/2021.02.06.21251270",
-    "rel_title": "Clinical and Economic Impact of Widespread Rapid Testing to Decrease SARS-CoV-2 Transmission",
-    "rel_date": "2021-02-08",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.06.21251270",
-    "rel_abs": "BackgroundThe value of frequent, rapid testing to reduce community transmission of SARS-CoV-2 is poorly understood.\n\nObjectiveTo define performance standards and predict the clinical, epidemiological, and economic outcomes of nationwide, home-based, antigen testing.\n\nDesignA simple compartmental epidemic model estimated viral transmission, clinical history, and resource use, with and without testing.\n\nData SourcesParameter values and ranges informed by Centers for Disease Control guidance and published literature.\n\nTarget PopulationUnited States population.\n\nTime Horizon60 days.\n\nPerspectiveSocietal.Costs include: testing, inpatient care, and lost workdays.\n\nInterventionHome-based SARS-CoV-2 antigen testing.\n\nOutcome MeasuresCumulative infections and deaths, numbers isolated and/or hospitalized, and total costs.\n\nResults of Base-Case AnalysisWithout a testing intervention, the model anticipates 15 million infections, 125,000 deaths, and $10.4 billion in costs ($6.5 billion inpatient; $3.9 billion lost productivity) over a 60-day horizon. Weekly availability of testing may avert 4 million infections and 19,000 deaths, raising costs by $21.5 billion. Lower inpatient outlays ($5.9 billion) would partially offset additional testing expenditures ($12.0 billion) and workdays lost ($13.9 billion), yielding incremental costs per infection (death) averted of $5,400 ($1,100,000).\n\nResults of Sensitivity AnalysisOutcome estimates vary widely under different behavioral assumptions and testing frequencies. However, key findings persist across all scenarios: large reductions in infections, mortality, and hospitalizations; and costs per death averted roughly an order of magnitude lower than commonly accepted willingness-to-pay values per statistical life saved ($5-17 million).\n\nLimitationsAnalysis restricted to at-home testing and limited by uncertainties about test performance.\n\nConclusionHigh-frequency home testing for SARS-CoV-2 using an inexpensive, imperfect test could contribute to pandemic control at justifiable cost and warrants consideration as part of a national containment strategy.\n\nPrimary Funding SourcesDr. Paltiel was supported by grant R37DA015612 from the National Institute on Drug Abuse of the National Institutes of Health.\n\nDr. Sax was supported by grant R01AI042006 from the National Institute of Allergy and Infectious Diseases of the National Institutes of Health.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "A David Paltiel",
-        "author_inst": "Yale School of Public Health"
-      },
-      {
-        "author_name": "Amy Zheng",
-        "author_inst": "Harvard Medical School"
-      },
-      {
-        "author_name": "Paul E. Sax",
-        "author_inst": "Brigham and Womens Hospital and Harvard Medical School"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.02.07.21251062",
     "rel_title": "Performance of three SARS-CoV-2 immunoassays, three rapid lateral flow tests and a novel bead-based affinity surrogate test for the detection of SARS-CoV-2 antibodies in human serum",
@@ -930193,6 +928393,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.02.07.21250586",
+    "rel_title": "The impact of mobility network properties on predicted epidemic dynamics in Dhaka and Bangkok",
+    "rel_date": "2021-02-08",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.07.21250586",
+    "rel_abs": "1Properties of city-level commuting networks are expected to influence epidemic potential of cities and modify the speed and spatial trajectory of epidemics when they occur. In this study, we use aggregated mobile phone user data to reconstruct commuter mobility networks for Bangkok (Thailand) and Dhaka (Bangladesh), two megacities in Asia with populations of 16 and 21 million people, respectively. We model the dynamics of directly-transmitted infections (such as SARS-CoV2) propagating on these commuting networks, and find that differences in network structure between the two cities drive divergent predicted epidemic trajectories: the commuting network in Bangkok is composed of geographically-contiguous modular communities and epidemic dispersal is correlated with geographic distance between locations, whereas the network in Dhaka has less distinct geographic structure and epidemic dispersal is less constrained by geographic distance. We also find that the predicted dynamics of epidemics vary depending on the local topology of the network around the origin of the outbreak. Measuring commuter mobility, and understanding how commuting networks shape epidemic dynamics at the city level, can support surveillance and preparedness efforts in large cities at risk for emerging or imported epidemics.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Tyler S Brown",
+        "author_inst": "Massachusetts General Hospital"
+      },
+      {
+        "author_name": "Kenth Eng\u00f8-Monsen",
+        "author_inst": "Telenor Group"
+      },
+      {
+        "author_name": "Mathew V Kiang",
+        "author_inst": "Stanford University School of Medicine, Department of Epidemiology and Population Health"
+      },
+      {
+        "author_name": "Ayesha S Mahmud",
+        "author_inst": "University of California, Berkeley, Demography Department"
+      },
+      {
+        "author_name": "Richard J Maude",
+        "author_inst": "Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University"
+      },
+      {
+        "author_name": "Caroline O Buckee",
+        "author_inst": "Harvard T.H. Chan School of Public Health, Center for Communicable Disease Dynamics"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.02.06.21251265",
     "rel_title": "COVIDHunter: An Accurate, Flexible, and Environment-Aware Open-Source COVID-19 Outbreak Simulation Model",
@@ -931626,145 +929865,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.02.04.21249959",
-    "rel_title": "Combination therapy of Tocilizumab and steroid for management of COVID-19 associated cytokine release syndrome: A single center experience from Pune, Western India",
-    "rel_date": "2021-02-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.04.21249959",
-    "rel_abs": "BackgroundCytokine release syndrome (CRS) or cytokine storm is thought to be the cause of inflammatory lung damage, worsening pneumonia and death in patients with COVID-19. Steroids (Methylprednisolone or Dexamethasone) and Tocilizumab (TCZ), an interleukin-6 receptor antagonist, are approved for the treatment of CRS in India. The aim of this study was to evaluate the efficacy and safety of combination therapy of TCZ and steroids in COVID-19 associated CRS.\n\nMethodsThis retrospective cohort study was conducted at a tertiary level private hospital in Pune, India between 2nd April and 2nd November 2020. All patients administered TCZ and steroids for treatment of CRS were included. The primary endpoint was incidence of all-cause mortality. Secondary outcomes studied were need for mechanical ventilation and incidence of infectious complications. Baseline and time-dependent risk factors significantly associated with death were identified by Relative risk estimation.\n\nResultsOut of 2831 admitted patients, 515 (24.3% females) were administered TCZ and steroids. Median age of the cohort was 57 (IQR: 46.5, 66) years. Almost 72 % patients had preexisting co-morbidities. Median time to TCZ administration since onset of symptoms was 9 days (IQR: 7, 11). 63% patients needed intensive care unit (ICU) admission. Mechanical ventilation was required in 242 (47%) patients. Of these, 44.2% (107/242) recovered and were weaned off the ventilator. There were 135 deaths (26.2%), while 380 patients (73.8%) had clinical improvement. Infectious complications like hospital acquired pneumonia, bloodstream bacterial and fungal infections were observed in 2.13 %, 2.13 % and 0.06 % patients respectively. Age [&ge;] 60 years (p=0.014), presence of co-morbidities like hypertension (p = 0.011), IL-6 [&ge;] 100 pg/ml (p = 0.002), D-dimer [&ge;] 1000 ng/ml (p < 0.0001), CT severity index [&ge;] 18 (p < 0.0001) and systemic complications like lung fibrosis (p = 0.019), cardiac arrhythmia (p < 0.0001), hypotension (p < 0.0001) and encephalopathy (p < 0.0001) were associated with increased risk of death.\n\nConclusionsCombination therapy of TCZ and Steroids is likely to be safe and effective in the management of COVID-19 associated cytokine release syndrome. Efficacy of this anti-inflammatory combination therapy needs to be validated in randomized controlled clinical trials.",
-    "rel_num_authors": 31,
-    "rel_authors": [
-      {
-        "author_name": "Ameet Dravid",
-        "author_inst": "Noble Hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Reema Kashiva",
-        "author_inst": "Noble Hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Zafer Khan",
-        "author_inst": "Noble Hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Danish Memon",
-        "author_inst": "Noble Hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Aparna Kodre",
-        "author_inst": "Noble Hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Prashant Potdar",
-        "author_inst": "Noble Hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Milind Mane",
-        "author_inst": "Noble hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Rakesh Borse",
-        "author_inst": "Noble hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Vishal Pawar",
-        "author_inst": "Noble hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Dattatraya Patil",
-        "author_inst": "Noble hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Debashis Banerjee",
-        "author_inst": "Noble hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Kailas Bhoite",
-        "author_inst": "Noble hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Reshma Pharande",
-        "author_inst": "Noble Hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Suraj Kalyani",
-        "author_inst": "Noble Hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Prathamesh Raut",
-        "author_inst": "Noble Hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Madhura Bapte",
-        "author_inst": "Noble Hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Anshul Mehta",
-        "author_inst": "Noble Hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "M Sateesh Reddy",
-        "author_inst": "Noble Hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Krushnadas Bhayani",
-        "author_inst": "Noble Hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "S S Laxmi",
-        "author_inst": "Noble Hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "P D Vishnu",
-        "author_inst": "Noble Hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Shipra Srivastava",
-        "author_inst": "Noble Hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Shubham Khandelwal",
-        "author_inst": "Noble Hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Sailee More",
-        "author_inst": "Noble Hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Rohit Shinde",
-        "author_inst": "Noble Hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Mohit Pawar",
-        "author_inst": "Noble Hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Amol Harshe",
-        "author_inst": "Noble Hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Sagar Kadam",
-        "author_inst": "Noble Hospital and Research Center, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Uma Mahajan",
-        "author_inst": "VMK Diagnostics private limited, Pune, State - Maharashtra, India"
-      },
-      {
-        "author_name": "Gaurav Joshi",
-        "author_inst": "Independent Statistical Consultant, Chicago, USA"
-      },
-      {
-        "author_name": "Dilip Mane",
-        "author_inst": "Noble Hospital and Research Center, Pune, State - Maharashtra, India."
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.02.06.430041",
     "rel_title": "Subgenomic RNAs as molecular indicators of asymptomatic SARS-CoV-2 infection",
@@ -932151,6 +930251,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.02.02.21251042",
+    "rel_title": "Mental Health, Substance Use, and Suicidal Ideation Among Unpaid Caregivers in the United States During the COVID-19 Pandemic: Relationships to Age, Race/Ethnicity, Employment, and Caregiver Intensity",
+    "rel_date": "2021-02-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.02.21251042",
+    "rel_abs": "ObjectivesTo estimate the prevalence of unpaid caregiving during the coronavirus disease 2019 (COVID-19) pandemic, and to identify factors associated with adverse mental health symptoms, substance use, and suicidal ideation in this population, which provides critical support in health care systems by providing care to older adults and those with chronic conditions.\n\nMethodsIn June 2020, Internet-based surveys with questions about demographics, caregiving responsibilities, and mental health were administered to US adults aged [&ge;]18 years. Demographic quota sampling and survey weighting to improve cross-sectional sample representativeness of age, gender, and race/ethnicity. Prevalence ratios for adverse mental health symptoms were estimated using multivariable Poisson regressions.\n\nResultsOf 9,896 eligible invited adults, 5,412 (54.7%) completed surveys; 5,011 (92.6%) respondents met screening criteria and were analysed, including 1,362 (27.2%) caregivers. Caregivers had higher prevalences of adverse mental health symptoms than non-caregivers, including anxiety or depressive disorder symptoms (57.6% vs 21.5%, respectively, p<0.0001) having recently seriously considered suicide (33.4% vs 3.7%, p<0.0001). Symptoms were more common among caregivers who were young vs older adults (e.g., aged 18-24 vs [&ge;]65 years, aPR 2.75, 95% CI 1.95-3.88, p<0.0001), Hispanic or Latino vs non-Hispanic White (1.14, 1.04-1.25, p=0.0044), living with vs without disabilities (1.18, 1.10-1.26, p<0.0001), and with moderate and high vs low Caregiver Intensity Index scores (2.31, 1.65-3.23; 2.81, 2.00-3.94; both p<0.0001). Suicidal ideation was more prevalent among non-Hispanic Black vs non-Hispanic White caregivers (1.48, 1.15-1.90, p=0.0022).\n\nConclusionsCaregivers, who accounted for one in four US adult respondents in this nationally representative sample, more commonly reported adverse mental health symptoms than non-caregivers. Increased visibility of and access to mental health care resources are urgently needed to address mental health challenges of caregiving.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Mark \u00c9 Czeisler",
+        "author_inst": "Monash University"
+      },
+      {
+        "author_name": "Alexandra Drane",
+        "author_inst": "ARCHANGELS"
+      },
+      {
+        "author_name": "Sarah S. Winnay",
+        "author_inst": "ARCHANGELS"
+      },
+      {
+        "author_name": "Emily R. Capodilupo",
+        "author_inst": "WHOOP, Inc."
+      },
+      {
+        "author_name": "Charles A. Czeisler",
+        "author_inst": "Brigham & Women's Hospital"
+      },
+      {
+        "author_name": "Shantha M.W. Rajaratnam",
+        "author_inst": "Monash University"
+      },
+      {
+        "author_name": "Mark E. Howard",
+        "author_inst": "Austin Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "psychiatry and clinical psychology"
+  },
   {
     "rel_doi": "10.1101/2021.02.03.21251068",
     "rel_title": "Estimating vaccine confidence levels among future healthcare workers and their trainers: A quantitative study protocol",
@@ -933484,69 +931627,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.02.03.21251095",
-    "rel_title": "How did COVID-19 measures impact sexual behaviour and access to STI&HIV services in Panama? Results from a national cross-sectional online survey",
-    "rel_date": "2021-02-05",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.03.21251095",
-    "rel_abs": "ObjectivesTo describe perceived changes in sexual behaviours, including virtual sex (sexting and cybersex), and access to HIV/STI testing and care during COVID-19 measures in Panama. Methods We conducted an online cross-sectional survey from August 8 to September 12, 2020, among adults ([&ge;]18 years) residing in Panama. Participants were recruited through social media. Questions included demographics, access to HIV/STI testing and HIV care and sexual behaviours three months before COVID-19 social distancing measures and during social distancing measures (COVID-19 measures). Logistic regression was used to identify associations between variables and behavioural changes.\n\nResultsWe recruited 960 participants; 526 (54.8%) identified as cis-women, 366 (38.1%) cis-men, and 68 (7.1%) non-binary or another gender; median age was 28y (IQR:23-37y), 531/957 (55.5%) were of mixed-ethnicity (mixed-Indigenous/European/Afro-descendant ancestry). Before COVID-19 measures, virtual sex was reported by 38.5% (181/470) cis-women, 58.4% (184/315) cis-men and 45.0% (27/60) non-binary participants; during COVID-19 measures, virtual sex increased among 17.2% cis-women, 24.7% cis-men and 8.9% non-binary participants. During COVID-19 measures, 230/800 [28.8%] of participants reported decreased casual sex compared to pre-COVID-19 measures. Compared to pre-COVID-19 measures, decreased casual sex were reported more frequently during COVID-19 measures by cis-men compared to cis-women (39.2% versus 22.9%, urban/rural adjusted odds ratio [AOR]=2.17, 95% confidence interval [CI]:1.57-3.01); and by Afro-descendant compared to mixed-ethnicity participants (40.0% versus 29.8%, AOR=1.78, 95%CI:1.07-2.94). Compared to no change in virtual sex (16.8%), increase in virtual sex (38.5%, AOR=1.78, 95%CI:1.10-2.88); and decreased virtual sex (86.7%, AOR=16.53, 95%CI:7.74-35.27) were associated with decreased casual sex encounters. During COVID-19 measures, HIV/STI testing could not be obtained by 58.0%(58/100) participants who needed a test, and interrupted HIV care was reported by 53.3% (8/15) HIV-positive participants.\n\nConclusionsCOVID-19 measures in Panama were associated with a decrease in casual sex among cis-men and Afro-descendant peoples, whilst access to HIV/STI testing and care was seriously disrupted.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Amanda Gabster",
-        "author_inst": "London School of Hygiene and Tropical Medicine, Instituto Conmemorativo Gorgas de Estudios de la Salud"
-      },
-      {
-        "author_name": "Jennifer Toller Erausquin",
-        "author_inst": "University of North Carolina Greensboro, School of Health and Human Sciences"
-      },
-      {
-        "author_name": "Kristien Michielsen",
-        "author_inst": "Universiteit Gent, Faculty of Medicine and Health Sciences"
-      },
-      {
-        "author_name": "Philippe Mayaud",
-        "author_inst": "London School of Hygiene and Tropical Medicine,  Faculty of Infectious and Tropical Diseases"
-      },
-      {
-        "author_name": "Juan Miguel Pascale",
-        "author_inst": "Instituto Conmemorativo Gorgas de Estudios de la Salud; Universidad de Panama, Facultad de Medicina"
-      },
-      {
-        "author_name": "Carles Pericas Escale",
-        "author_inst": "Universiteit Gent, Faculty of Medicine and Health Sciences"
-      },
-      {
-        "author_name": "Michael Marks",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Jennifer Katz",
-        "author_inst": "Instituto Conmemorativo Gorgas de Estudios de la Salud"
-      },
-      {
-        "author_name": "Gonzalo Cabezas Talavero",
-        "author_inst": "Instituto Conmemorativo Gorgas de Estudios de la Salud"
-      },
-      {
-        "author_name": "Marilu de Argote",
-        "author_inst": "Instituto Conmemorativo Gorgas de Estudios de la Salud"
-      },
-      {
-        "author_name": "Anet Murillo Estrada",
-        "author_inst": "Instituto Conmemorativo Gorgas de Estudios de la Salud"
-      },
-      {
-        "author_name": "Joseph D Tucker",
-        "author_inst": "University of North Carolina at Chapel Hill, London School of Hygiene and Tropical Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.02.03.21251004",
     "rel_title": "Ethnic differences in COVID-19 mortality during the first two waves of the Coronavirus Pandemic: a nationwide cohort study of 29 million adults in England",
@@ -933825,6 +931905,1201 @@
     "type": "new results",
     "category": "pharmacology and toxicology"
   },
+  {
+    "rel_doi": "10.1101/2021.02.03.21250974",
+    "rel_title": "Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the US",
+    "rel_date": "2021-02-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.03.21250974",
+    "rel_abs": "Short-term probabilistic forecasts of the trajectory of the COVID-19 pandemic in the United States have served as a visible and important communication channel between the scientific modeling community and both the general public and decision-makers. Forecasting models provide specific, quantitative, and evaluable predictions that inform short-term decisions such as healthcare staffing needs, school closures, and allocation of medical supplies. Starting in April 2020, the US COVID-19 Forecast Hub (https://covid19forecasthub.org/) collected, disseminated, and synthesized tens of millions of specific predictions from more than 90 different academic, industry, and independent research groups. A multi-model ensemble forecast that combined predictions from dozens of different research groups every week provided the most consistently accurate probabilistic forecasts of incident deaths due to COVID-19 at the state and national level from April 2020 through October 2021. The performance of 27 individual models that submitted complete forecasts of COVID-19 deaths consistently throughout this year showed high variability in forecast skill across time, geospatial units, and forecast horizons. Two-thirds of the models evaluated showed better accuracy than a naive baseline model. Forecast accuracy degraded as models made predictions further into the future, with probabilistic error at a 20-week horizon 3-5 times larger than when predicting at a 1-week horizon. This project underscores the role that collaboration and active coordination between governmental public health agencies, academic modeling teams, and industry partners can play in developing modern modeling capabilities to support local, state, and federal response to outbreaks.\n\nSignificance StatementThis paper compares the probabilistic accuracy of short-term forecasts of reported deaths due to COVID-19 during the first year and a half of the pandemic in the US. Results show high variation in accuracy between and within stand-alone models, and more consistent accuracy from an ensemble model that combined forecasts from all eligible models. This demonstrates that an ensemble model provided a reliable and comparatively accurate means of forecasting deaths during the COVID-19 pandemic that exceeded the performance of all of the models that contributed to it. This work strengthens the evidence base for synthesizing multiple models to support public health action.",
+    "rel_num_authors": 295,
+    "rel_authors": [
+      {
+        "author_name": "Estee Y Cramer",
+        "author_inst": "University of Massachusetts, Amherst"
+      },
+      {
+        "author_name": "Evan L Ray",
+        "author_inst": "University of Massachusetts, Amherst"
+      },
+      {
+        "author_name": "Velma K Lopez",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Johannes Bracher",
+        "author_inst": "Chair of Econometrics and Statistics, Karlsruhe Institute of Technology; Computational Statistics Group, Heidelberg Institute for Theoretical Studies"
+      },
+      {
+        "author_name": "Andrea Brennen",
+        "author_inst": "IQT"
+      },
+      {
+        "author_name": "Alvaro J Castro Rivadeneira",
+        "author_inst": "University of Massachusetts, Amherst"
+      },
+      {
+        "author_name": "Aaron Gerding",
+        "author_inst": "University of Massachusetts, Amherst"
+      },
+      {
+        "author_name": "Tilmann Gneiting",
+        "author_inst": "Institute of Stochastics, Karlsruhe Institute of Technology"
+      },
+      {
+        "author_name": "Katie H House",
+        "author_inst": "University of Massachusetts, Amherst"
+      },
+      {
+        "author_name": "Yuxin Huang",
+        "author_inst": "University of Massachusetts, Amherst"
+      },
+      {
+        "author_name": "Dasuni Jayawardena",
+        "author_inst": "University of Massachusetts, Amherst"
+      },
+      {
+        "author_name": "Abdul H Kanji",
+        "author_inst": "University of Massachusetts, Amherst"
+      },
+      {
+        "author_name": "Ayush Khandelwal",
+        "author_inst": "University of Massachusetts, Amherst"
+      },
+      {
+        "author_name": "Khoa Le",
+        "author_inst": "University of Massachusetts, Amherst"
+      },
+      {
+        "author_name": "Anja Muehlemann",
+        "author_inst": "Institute of Mathematical Statistics and Actuarial Science, University of Bern"
+      },
+      {
+        "author_name": "Jarad Niemi",
+        "author_inst": "Iowa State University"
+      },
+      {
+        "author_name": "Apurv Shah",
+        "author_inst": "University of Massachusetts, Amherst"
+      },
+      {
+        "author_name": "Ariane Stark",
+        "author_inst": "University of Massachusetts, Amherst"
+      },
+      {
+        "author_name": "Yijin Wang",
+        "author_inst": "University of Massachusetts, Amherst"
+      },
+      {
+        "author_name": "Nutcha Wattanachit",
+        "author_inst": "University of Massachusetts, Amherst"
+      },
+      {
+        "author_name": "Martha W Zorn",
+        "author_inst": "University of Massachusetts, Amherst"
+      },
+      {
+        "author_name": "Youyang Gu",
+        "author_inst": "Unaffiliated"
+      },
+      {
+        "author_name": "Sansiddh Jain",
+        "author_inst": "Wadhwani Institute of Artificial Intelligence"
+      },
+      {
+        "author_name": "Nayana Bannur",
+        "author_inst": "Wadhwani Institute of Artificial Intelligence"
+      },
+      {
+        "author_name": "Ayush Deva",
+        "author_inst": "Wadhwani Institute of Artificial Intelligence"
+      },
+      {
+        "author_name": "Mihir Kulkarni",
+        "author_inst": "Wadhwani Institute of Artificial Intelligence"
+      },
+      {
+        "author_name": "Srujana Merugu",
+        "author_inst": "Wadhwani Institute of Artificial Intelligence"
+      },
+      {
+        "author_name": "Alpan Raval",
+        "author_inst": "Wadhwani Institute of Artificial Intelligence"
+      },
+      {
+        "author_name": "Siddhant Shingi",
+        "author_inst": "Wadhwani Institute of Artificial Intelligence"
+      },
+      {
+        "author_name": "Avtansh Tiwari",
+        "author_inst": "Wadhwani Institute of Artificial Intelligence"
+      },
+      {
+        "author_name": "Jerome White",
+        "author_inst": "Wadhwani Institute of Artificial Intelligence"
+      },
+      {
+        "author_name": "Neil F Abernethy",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Spencer Woody",
+        "author_inst": "University of Texas at Austin"
+      },
+      {
+        "author_name": "Maytal Dahan",
+        "author_inst": "Texas Advanced Computing Center"
+      },
+      {
+        "author_name": "Spencer Fox",
+        "author_inst": "University of Texas at Austin"
+      },
+      {
+        "author_name": "Kelly Gaither",
+        "author_inst": "Texas Advanced Computing Center"
+      },
+      {
+        "author_name": "Michael Lachmann",
+        "author_inst": "Santa Fe Institute"
+      },
+      {
+        "author_name": "Lauren Ancel Meyers",
+        "author_inst": "University of Texas at Austin"
+      },
+      {
+        "author_name": "James G Scott",
+        "author_inst": "University of Texas at Austin"
+      },
+      {
+        "author_name": "Mauricio Tec",
+        "author_inst": "University of Texas at Austin"
+      },
+      {
+        "author_name": "Ajitesh Srivastava",
+        "author_inst": "University of Southern California"
+      },
+      {
+        "author_name": "Glover E George",
+        "author_inst": "US Army Engineer Research and Development Center"
+      },
+      {
+        "author_name": "Jeffrey C Cegan",
+        "author_inst": "US Army Engineer Research and Development Center"
+      },
+      {
+        "author_name": "Ian D Dettwiller",
+        "author_inst": "US Army Engineer Research and Development Center"
+      },
+      {
+        "author_name": "William P England",
+        "author_inst": "US Army Engineer Research and Development Center"
+      },
+      {
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+        "author_inst": "Google Cloud"
+      },
+      {
+        "author_name": "Jinsung Yoon",
+        "author_inst": "Google Cloud"
+      },
+      {
+        "author_name": "Leyou Zhang",
+        "author_inst": "Google Cloud"
+      },
+      {
+        "author_name": "Sam Abbott",
+        "author_inst": "London School of Hygiene & Tropical Medicine"
+      },
+      {
+        "author_name": "Nikos I Bosse",
+        "author_inst": "London School of Hygiene & Tropical Medicine"
+      },
+      {
+        "author_name": "Sebastian Funk",
+        "author_inst": "London School of Hygiene & Tropical Medicine"
+      },
+      {
+        "author_name": "Joel Hellewell",
+        "author_inst": "London School of Hygiene & Tropical Medicine"
+      },
+      {
+        "author_name": "Sophie R Meakin",
+        "author_inst": "London School of Hygiene & Tropical Medicine"
+      },
+      {
+        "author_name": "Katharine Sherratt",
+        "author_inst": "London School of Hygiene & Tropical Medicine"
+      },
+      {
+        "author_name": "Mingyuan Zhou",
+        "author_inst": "The University of Texas at Austin"
+      },
+      {
+        "author_name": "Rahi Kalantari",
+        "author_inst": "The University of Texas at Austin"
+      },
+      {
+        "author_name": "Teresa K Yamana",
+        "author_inst": "Columbia University"
+      },
+      {
+        "author_name": "Sen Pei",
+        "author_inst": "Columbia University"
+      },
+      {
+        "author_name": "Jeffrey Shaman",
+        "author_inst": "Columbia University"
+      },
+      {
+        "author_name": "Michael L Li",
+        "author_inst": "Operations Research Center, Massachusetts Institute of Technology"
+      },
+      {
+        "author_name": "Dimitris Bertsimas",
+        "author_inst": "Sloan School of Management, Massachusetts Institute of Technology"
+      },
+      {
+        "author_name": "Omar Skali Lami",
+        "author_inst": "Operations Research Center, Massachusetts Institute of Technology"
+      },
+      {
+        "author_name": "Saksham Soni",
+        "author_inst": "Operations Research Center, Massachusetts Institute of Technology"
+      },
+      {
+        "author_name": "Hamza Tazi Bouardi",
+        "author_inst": "Operations Research Center, Massachusetts Institute of Technology"
+      },
+      {
+        "author_name": "Turgay Ayer",
+        "author_inst": "Emory University Medical School; Georgia Insitute of Technology"
+      },
+      {
+        "author_name": "Madeline Adee",
+        "author_inst": "MGH"
+      },
+      {
+        "author_name": "Jagpreet Chhatwal",
+        "author_inst": "MGH"
+      },
+      {
+        "author_name": "Ozden O Dalgic",
+        "author_inst": "Value Analytics Labs"
+      },
+      {
+        "author_name": "Mary A Ladd",
+        "author_inst": "MGH"
+      },
+      {
+        "author_name": "Benjamin P Linas",
+        "author_inst": "Boston University School of Medicine"
+      },
+      {
+        "author_name": "Peter Mueller",
+        "author_inst": "MGH"
+      },
+      {
+        "author_name": "Jade Xiao",
+        "author_inst": "Georgia Insitute of Technology"
+      },
+      {
+        "author_name": "Yuanjia Wang",
+        "author_inst": "Columbia University"
+      },
+      {
+        "author_name": "Qinxia Wang",
+        "author_inst": "Columbia University"
+      },
+      {
+        "author_name": "Shanghong Xie",
+        "author_inst": "Columbia University"
+      },
+      {
+        "author_name": "Donglin Zeng",
+        "author_inst": "UNC Chapel Hill"
+      },
+      {
+        "author_name": "Alden Green",
+        "author_inst": "Carnegie Mellon University"
+      },
+      {
+        "author_name": "Jacob Bien",
+        "author_inst": "University of Southern California"
+      },
+      {
+        "author_name": "Logan Brooks",
+        "author_inst": "Carnegie Mellon University"
+      },
+      {
+        "author_name": "Addison J Hu",
+        "author_inst": "Carnegie Mellon University"
+      },
+      {
+        "author_name": "Maria Jahja",
+        "author_inst": "Carnegie Mellon University"
+      },
+      {
+        "author_name": "Daniel McDonald",
+        "author_inst": "University of British Columbia"
+      },
+      {
+        "author_name": "Balasubramanian Narasimhan",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Collin Politsch",
+        "author_inst": "Carnegie Mellon University"
+      },
+      {
+        "author_name": "Samyak Rajanala",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Aaron Rumack",
+        "author_inst": "Carnegie Mellon University"
+      },
+      {
+        "author_name": "Noah Simon",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Ryan J Tibshirani",
+        "author_inst": "Carnegie Mellon University"
+      },
+      {
+        "author_name": "Rob Tibshirani",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Valerie Ventura",
+        "author_inst": "Carnegie Mellon University"
+      },
+      {
+        "author_name": "Larry Wasserman",
+        "author_inst": "Carnegie Mellon University"
+      },
+      {
+        "author_name": "Eamon B O'Dea",
+        "author_inst": "University of Georgia"
+      },
+      {
+        "author_name": "John M Drake",
+        "author_inst": "University of Georgia"
+      },
+      {
+        "author_name": "Robert Pagano",
+        "author_inst": "Unaffiliated"
+      },
+      {
+        "author_name": "Quoc T Tran",
+        "author_inst": "Walmart Inc."
+      },
+      {
+        "author_name": "Lam Si Tung Ho",
+        "author_inst": "Dalhousie University"
+      },
+      {
+        "author_name": "Huong Huynh",
+        "author_inst": "Virtual Power System Inc."
+      },
+      {
+        "author_name": "Jo W Walker",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Rachel B Slayton",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Michael A Johansson",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Matthew Biggerstaff",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Nicholas G Reich",
+        "author_inst": "University of Massachusetts, Amherst"
+      }
+    ],
+    "version": "1",
+    "license": "cc0",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.02.05.429917",
     "rel_title": "Catching SARS-CoV-2 by sequence hybridization: a comparative analysis",
@@ -935158,29 +934433,6 @@
     "type": "new results",
     "category": "molecular biology"
   },
-  {
-    "rel_doi": "10.1101/2021.02.04.429769",
-    "rel_title": "Modulation of SARS-CoV-2 Spike-induced Unfolded Protein Response (UPR) in HEK293T cells by selected small chemical molecules",
-    "rel_date": "2021-02-04",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.04.429769",
-    "rel_abs": "Coronaviruses (CoV) exploits the endoplasmic reticulum (ER) of the host cells for replication and in doing so, increases ER stress. evokes Unfolded Protein Response (UPR) and possibly autophagy, which could all attribute to the pathophysiology of the viral infections. To date, little is known about the roles of ER stress, UPR, and autophagy in SARS-CoV-2 infection. Here we over-expressed the viral Spike (S) protein in cultured HEK293T cells, as it has been shown that such protein is largely responsible for UPR activation in other CoV-infected cells. We noticed, in the transfected cells, heightened ER stress, activation of the PERK-eIF2 arm of the UPR, induction of autophagy and cell death. When we treated the transfected cells with Tauroursodeoxycholic acid (TUDCA), 4-phenyl butyric acid (PBA), Salubrinal, Trazadone hydrochloride, and Dibenzoylmethane (DBM), we saw reduced the BiP/GRP78 levels, but only PBA and TUDCA could significantly diminish the levels of peIF2 and autophagy expression.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Bijina Balakrishnan",
-        "author_inst": "University of Utah"
-      },
-      {
-        "author_name": "Kent Lai",
-        "author_inst": "University of Utah"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "biochemistry"
-  },
   {
     "rel_doi": "10.1101/2021.02.01.21250853",
     "rel_title": "IN-HOSPITAL CONTINUATION WITH ANGIOTENSIN RECEPTOR BLOCKERS IS ASSOCIATED WITH A LOWER MORTALITY RATE THAN CONTINUATION WITH ANGIOTENSIN CONVERTING ENZYME INHIBITORS IN COVID-19 PATIENTS A RETROSPECTIVE COHORT STUDY",
@@ -935395,6 +934647,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.02.01.21250877",
+    "rel_title": "Optimal time to return to normality: parallel use of COVID-19 vaccines and circuit breakers",
+    "rel_date": "2021-02-03",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.01.21250877",
+    "rel_abs": "By January 2020, the COVID-19 illness has caused over two million deaths. Countries have restricted disease spread through non-pharmaceutical interventions (e.g., social distancing). More severe \"lockdowns\" have also been required. Although lockdowns keep people safer from the virus, they substantially disrupt economies and individual well-being. Fortunately, vaccines are becoming available. Yet, vaccination programs may take several months to implement, requiring further time for individuals to develop immunity following inoculation. To prevent health services being overwhelmed it may be necessary to implement further lockdowns in conjunction with vaccination. Here, we investigate optimal approaches for vaccination under varying lockdown lengths and/or severities to prevent COVID-19-related deaths exceeding critical thresholds. We find increases in vaccination rate cause a disproportionately larger decrease in lockdowns: with vaccination, severe lockdowns can reduce infections by up to 89%. Notably, we include demographics, modelling three groups: vulnerable, front-line workers, and non-vulnerable. We investigate the sequence of vaccination. One counter-intuitive finding is that even though the vulnerable group is high risk, demographically, this is a small group (per person, vaccination occurs more slowly) so vaccinating this group first achieves limited gains in overall disease control. Better disease control occurs by vaccinating the non-vulnerable group with longer and/or more severe lockdowns.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Michael Bonsall",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Chris Huntingford",
+        "author_inst": "UK Centre for Ecology and Hydrology, Wallingford"
+      },
+      {
+        "author_name": "Thomas Rawson",
+        "author_inst": "Dept of Zoology, University of Oxford"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.02.01.21250900",
     "rel_title": "RAY: CRISPR diagnostic for rapid and accurate detection of SARS-CoV2 variants on a paper strip",
@@ -937208,77 +936487,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "occupational and environmental health"
   },
-  {
-    "rel_doi": "10.1101/2021.02.01.21250963",
-    "rel_title": "Risk factors for SARS-CoV-2 infection among farmworkers in Monterey County, California",
-    "rel_date": "2021-02-03",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.01.21250963",
-    "rel_abs": "ImportanceEssential workers in agriculture and food production have been severely affected by the ongoing COVID-19 pandemic.\n\nObjectiveTo identify risk factors associated with SARS-CoV-2 shedding and antibody response in farmworkers in California.\n\nDesignThis cross-sectional study collected survey data and determined current SARS-CoV-2 shedding and seropositivity among 1,107 farmworkers in Californias Salinas Valley from 16 July to 30 November 2020.\n\nSettingFarmworkers receiving transcription-mediated amplification (TMA) tests for SARS-CoV-2 infection at federally qualified community clinics and community sites were invited to participate in our study.\n\nParticipantsIndividuals were eligible if they were not pregnant, [&ge;]18 years old, had conducted farm work since the pandemic started, and were proficient in English or Spanish.\n\nExposuresSociodemographic, household, community, and workplace characteristics.\n\nMain Outcome(s) and Measure(s)Current (as indicated by TMA positivity) and historical (as indicated by IgG seropositivity) SARS-CoV-2 infection.\n\nResultsMost farmworkers enrolled in the study were born in Mexico, had primary school or lower levels of educational attainment, and were overweight or obese. Current SARS-CoV-2 shedding was associated in multivariable analyses with attained only primary or lower educational levels (RR=1.32; 95% CI: 0.99-1.76), speaking an indigenous language at home (RR=1.30; 0.97-1.73), working in the fields (RR=1.60; 1.03-2.50), and exposure to known or suspected COVID-19 case at home (RR=2.98; 2.06-4.32) or in the workplace (RR=1.59; 1.18-2.14). Antibody detection was associated with residential exposures including living in crowded housing (RR=1.23; 0.98-1.53), with children (RR=1.40; 1.1-1.76) or unrelated roommates (RR=1.40; 1.19-1.64), and with a known or suspected COVID-19 case (RR=1.59; 1.13-2.24). Those who were obese (RR=1.65; 1.01-2.70) or diabetic (RR=1.31; 0.98-1.75) were also more likely to be seropositive. Farmworkers who lived in rural areas other than Greenfield (RR=0.58; 0.47-0.71), worked indoors (RR=0.68; 0.61-0.77), or whose employer provided them with information on how to protect themselves at work (RR=0.59; 0.40-0.86) had lower risk of prior infection.\n\nConclusions and RelevanceOur findings suggest both residential and workplace exposures are contributing to SARS-CoV-2 infection among farmworkers in California. Urgent distribution of COVID-19 vaccines is warranted given this populations increased risk of infection and the essential nature of their work.",
-    "rel_num_authors": 14,
-    "rel_authors": [
-      {
-        "author_name": "Ana M Mora",
-        "author_inst": "Center for Environmental Research and Children's Health, School of Public Health, University of California, Berkeley"
-      },
-      {
-        "author_name": "Joseph A Lewnard",
-        "author_inst": "Division of Epidemiology, School of Public Health, University of California, Berkeley"
-      },
-      {
-        "author_name": "Katherine Kogut",
-        "author_inst": "Center for Environmental Research and Children's Health, School of Public Health, University of California, Berkeley, Berkeley, California"
-      },
-      {
-        "author_name": "Stephen Rauch",
-        "author_inst": "Center for Environmental Research and Children's Health, School of Public Health, University of California, Berkeley, Berkeley, California"
-      },
-      {
-        "author_name": "Norma Morga",
-        "author_inst": "Clinica de Salud del Valle de Salinas"
-      },
-      {
-        "author_name": "Samantha Hernandez",
-        "author_inst": "Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley"
-      },
-      {
-        "author_name": "Marcus P Yong",
-        "author_inst": "Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley"
-      },
-      {
-        "author_name": "Karen Huen",
-        "author_inst": "Center for Environmental Research and Children's Health, School of Public Health, University of California, Berkeley, Berkeley, California"
-      },
-      {
-        "author_name": "Cynthia Chang",
-        "author_inst": "Center for Environmental Research and Children's Health, School of Public Health, University of California, Berkeley"
-      },
-      {
-        "author_name": "Nicholas P Jewell",
-        "author_inst": "Department of Medical Statistics, London School of Hygiene and Tropical Medicine, London, United Kingdom"
-      },
-      {
-        "author_name": "Nina Holland",
-        "author_inst": "Center for Environmental Research and Children's Health, School of Public Health, University of California, Berkeley"
-      },
-      {
-        "author_name": "Eva Harris",
-        "author_inst": "Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley"
-      },
-      {
-        "author_name": "Maximiliano Cuevas",
-        "author_inst": "Clinica de Salud del Valle de Salinas"
-      },
-      {
-        "author_name": "Brenda Eskenazi",
-        "author_inst": "Center for Environmental Research and Children's Health, School of Public Health, University of California, Berkeley"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "occupational and environmental health"
-  },
   {
     "rel_doi": "10.1101/2021.02.02.21250796",
     "rel_title": "Scientists' opinion, attitudes, and consensus towards immunity passports",
@@ -937649,6 +936857,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.02.02.21250985",
+    "rel_title": "Rapid vaccination and early reactive partial lockdown will minimize deaths from emerging highly contagious SARS-CoV-2 variants",
+    "rel_date": "2021-02-03",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.02.21250985",
+    "rel_abs": "The goals of SARS-CoV-2 vaccination programs are to maximally reduce cases and deaths, and to limit the amount of time required under lockdown. Using a mathematical model calibrated to data from King County Washington but generalizable across states, we simulated multiple scenarios with different vaccine efficacy profiles, vaccination rates, and case thresholds for triggering and relaxing partial lockdowns. We assumed that a contagious variant is currently present at low levels. In all scenarios, it rapidly becomes dominant by early summer. Low case thresholds for triggering partial lockdowns during current and future waves of infection strongly predict lower total numbers of COVID-19 infections, hospitalizations and deaths in 2021. However, in regions with relatively higher current seroprevalence, there is a predicted delay in onset of a subsequent surge in new variant infections. For all vaccine efficacy profiles, increasing vaccination rate lowers the total number of infections and deaths, as well as the total number of days under partial lockdown. Due to variable current estimates of emerging variant infectiousness, vaccine efficacy against these variants, vaccine refusal, and future adherence to masking and physical distancing, we project considerable uncertainty regarding the timing and intensity of subsequent waves of infection. Nevertheless, under all plausible scenarios, rapid vaccination and early implementation of partial lockdown are the two most critical variables to save the greatest number of lives.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Daniel B Reeves",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      },
+      {
+        "author_name": "Chloe Bracis",
+        "author_inst": "Universite Grenoble Alpes"
+      },
+      {
+        "author_name": "David A Swan",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      },
+      {
+        "author_name": "Mia Moore",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      },
+      {
+        "author_name": "Dobromir Dimitrov",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      },
+      {
+        "author_name": "Joshua T Schiffer",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.02.01.21250839",
     "rel_title": "Extremely high SARS-CoV-2 seroprevalence in a strictly-Orthodox Jewish community in the UK",
@@ -939210,53 +938457,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2021.02.03.429625",
-    "rel_title": "A high-throughput radioactivity-based assay for screening SARS-CoV-2 nsp10-nsp16 complex",
-    "rel_date": "2021-02-03",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.03.429625",
-    "rel_abs": "Frequent outbreaks of novel coronaviruses (CoVs), highlighted by the current SARS-CoV-2 pandemic, necessitate the development of therapeutics that could be easily and effectively administered world-wide. The conserved mRNA-capping process enables CoVs to evade their host immune system and is a target for antiviral development. Nonstructural protein (nsp) 16 in complex with nsp10 catalyzes the final step of coronaviral mRNA-capping through its 2-O-methylation activity. Like other methyltransferases, SARS-CoV-2 nsp10-nsp16 complex is druggable. However, the availability of an optimized assay for high-throughput screening (HTS) is an unmet need. Here, we report the development of a radioactivity-based assay for methyltransferase activity of nsp10-nsp16 complex in a 384-well format, and kinetic characterization, and optimization of the assay for HTS (Z'-factor: 0.83). Considering the high conservation of nsp16 across known CoV species, the potential inhibitors targeting SARS-CoV-2 nsp10-nsp16 complex may also be effective against other emerging pathogenic CoVs.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Aliakbar Khalili Yazdi",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Fengling Li",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Kanchan Devkota",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Sumera Perveen",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Pegah Ghiabi",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Taraneh Hajian",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Albina Bolotokova",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Masoud Vedadi",
-        "author_inst": "University of Toronto"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "biochemistry"
-  },
   {
     "rel_doi": "10.1101/2021.02.03.429510",
     "rel_title": "Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2",
@@ -939727,6 +938927,29 @@
     "type": "new results",
     "category": "scientific communication and education"
   },
+  {
+    "rel_doi": "10.1101/2021.02.03.429201",
+    "rel_title": "'Phytopathological strolls' in the dual context of COVID-19 lockdown and IYPH2020: transforming constraints into an opportunity for public education about plant pathogens",
+    "rel_date": "2021-02-03",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.03.429201",
+    "rel_abs": "The experience presented here relates to 2020, a particularly timely year for plant disease-related communication ( International Year of Plant Health IYPH2020), but also a unique year because of the COVID-19 pandemic. Our goal was to illustrate the diversity and beauty of fungal plant pathogens through a naturalist approach that could be followed by any amateur. We achieved this end through  phytopathological strolls, in which we observed and determined the origin of symptoms on diseased plants found in our garden, in the local streets, in nearby open spaces, and sharing this matter with a broad public. The lockdown imposed in France created an additional motivation to take up the challenge, and to involve our children, even under strong constraints, such as movement restrictions. We observed and described fungal pathogens through hundreds of photographs, shared our findings with a large audience on Twitter, and received feedback. The material used was deliberately simple and transportable: a digital reflex camera, an old microscope, a mobile phone, some books and an Internet connexion. Between March 17, 2020 and June 20, 2021 we found 196 plant pathogens, including 97 rusts, 27 powdery mildews and 28 septoria-like diseases. We discuss here the importance of promoting searches for plant pathogens, their description and conservation, through a combination of classical approaches and digital tools in tune with the times, such as Twitter, by treating pathogen identification like a detective game and, more surprisingly, by making use of the addictive nature of collection approaches, drawing a parallel with Pokemon Go.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Fr\u00e9d\u00e9ric Suffert",
+        "author_inst": "INRAE"
+      },
+      {
+        "author_name": "Muriel Suffert",
+        "author_inst": "EPPO"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2021.02.02.429476",
     "rel_title": "LIFE AND WORK OF RESEARCHERS TRAPPED IN THE COVID-19PANDEMIC VICIOUS CYCLE",
@@ -940972,105 +940195,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2021.02.01.429108",
-    "rel_title": "Nelfinavir markedly improves lung pathology in SARS-CoV-2-infected Syrian hamsters despite a lack of an antiviral effect",
-    "rel_date": "2021-02-01",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.01.429108",
-    "rel_abs": "In response to the ongoing COVID-19 pandemic, repurposing of drugs for the treatment of SARS-CoV-2 infections is being explored. The HIV protease inhibitor Nelfinavir, widely prescribed in combination with other HIV inhibitors, has been shown to inhibit in vitro SARS-CoV-2 replication. We here report on the effect of Nelfinavir in the Syrian hamster SARS-CoV-2 infection model. Although treatment of infected hamsters with either 15 or 50 mg/kg BID Nelfinavir [for four consecutive days, initiated on the day of infection] does not reduce viral RNA loads nor infectious virus titres in the lungs compared to the vehicle control, the drug reduced virus-induced lung pathology to nearly the baseline scores of healthy animals. A substantial interstitial infiltration of neutrophils is observed in the lungs of treated (both infected and uninfected) animals. The protective effect of Nelfinavir on SARS-CoV-2-induced lung pathology (at doses that are well tolerated and that result in exposures nearing those observed in HIV-infected patients) may lay the foundation for clinical studies with this widely used drug.",
-    "rel_num_authors": 21,
-    "rel_authors": [
-      {
-        "author_name": "Caroline S. Foo",
-        "author_inst": "KU Leuven"
-      },
-      {
-        "author_name": "Rana Abdelnabi",
-        "author_inst": "KU Leuven"
-      },
-      {
-        "author_name": "Suzanne J.F. Kaptein",
-        "author_inst": "KU Leuven"
-      },
-      {
-        "author_name": "Xin Zhang",
-        "author_inst": "KU Leuven"
-      },
-      {
-        "author_name": "Sebastiaan ter Horst",
-        "author_inst": "KU Leuven"
-      },
-      {
-        "author_name": "Raf Mols",
-        "author_inst": "KU Leuven"
-      },
-      {
-        "author_name": "Leen Delang",
-        "author_inst": "KU Leuven"
-      },
-      {
-        "author_name": "Joana Rocha-Pereira",
-        "author_inst": "KU Leuven"
-      },
-      {
-        "author_name": "Lotte Coelmont",
-        "author_inst": "KU Leuven"
-      },
-      {
-        "author_name": "Pieter Leyssen",
-        "author_inst": "KU Leuven"
-      },
-      {
-        "author_name": "Kai Dallmeier",
-        "author_inst": "KU Leuven"
-      },
-      {
-        "author_name": "Valentijn Vergote",
-        "author_inst": "KU Leuven"
-      },
-      {
-        "author_name": "Elisabeth Heylen",
-        "author_inst": "KU Leuven"
-      },
-      {
-        "author_name": "Laura Vangeel",
-        "author_inst": "KU Leuven"
-      },
-      {
-        "author_name": "Arnab K. Chatterjee",
-        "author_inst": "Calibr, Scripps Research"
-      },
-      {
-        "author_name": "Pieter Annaert",
-        "author_inst": "KU Leuven"
-      },
-      {
-        "author_name": "Patrick Augustijns",
-        "author_inst": "KU Leuven"
-      },
-      {
-        "author_name": "Steven De Jonghe",
-        "author_inst": "KU Leuven"
-      },
-      {
-        "author_name": "Dirk Jochmans",
-        "author_inst": "KU Leuven"
-      },
-      {
-        "author_name": "Birgit Weynand",
-        "author_inst": "UZ Leuven"
-      },
-      {
-        "author_name": "Johan Neyts",
-        "author_inst": "KU Leuven"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2021.01.31.429010",
     "rel_title": "Environmentally-induced mdig is a major contributor to the severity of COVID-19 through fostering expression of SARS-CoV-2 receptor NRPs and glycan metabolism",
@@ -941425,6 +940549,65 @@
     "type": "new results",
     "category": "biochemistry"
   },
+  {
+    "rel_doi": "10.1101/2021.01.30.428979",
+    "rel_title": "Production of SARS-CoV-2 virus-like particles in insect cells",
+    "rel_date": "2021-02-01",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.30.428979",
+    "rel_abs": "Coronavirus disease (COVID-19) causes a serious threat to human health. To production of SARS-COV-2 virus-like particles (VLPs) in insect cells for vaccine development and scientific research. The E, M and S genes were cloned into multiple cloning sites of the new triple expression plasmid with one p10 promoter, two pPH promoters and three multiple cloning sites. The plasmid was transformed into DH10 BacTM Escherichia coli competent cells to obtain recombinant bacmid. Then the recombinant bacmid was transfected in ExpiSf9 insect cells to generate recombinant baculovirus. After ExpiSf9 infected with the recombinant baculovirus, the E, M, and S protein co-expressed in insect cells. Finally, SARS-CoV-2 VLPs were self-assembled in insect cells after infection. The morphology and the size of SARS-CoV-2 VLPs are similar to the native virions.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Youjun mi",
+        "author_inst": "lanzhou university"
+      },
+      {
+        "author_name": "Tao Xie",
+        "author_inst": "lanzhou university"
+      },
+      {
+        "author_name": "BingDong Zhu",
+        "author_inst": "Lanzhou university"
+      },
+      {
+        "author_name": "JiYing tan",
+        "author_inst": "LanZhou University"
+      },
+      {
+        "author_name": "XueFeng Li",
+        "author_inst": "LanZhou University"
+      },
+      {
+        "author_name": "YanPing Luo",
+        "author_inst": "LanZhou University"
+      },
+      {
+        "author_name": "Fei Li",
+        "author_inst": "LanZhou University"
+      },
+      {
+        "author_name": "HongXia Niu",
+        "author_inst": "LanZhou Uiversity"
+      },
+      {
+        "author_name": "JiangYuan Han",
+        "author_inst": "LanZhou University"
+      },
+      {
+        "author_name": "Wei Lv",
+        "author_inst": "LanZhou University"
+      },
+      {
+        "author_name": "Juan Wang",
+        "author_inst": "LanZhou University"
+      }
+    ],
+    "version": "1",
+    "license": "",
+    "type": "new results",
+    "category": "bioengineering"
+  },
   {
     "rel_doi": "10.1101/2021.01.28.21250718",
     "rel_title": "Prediction Models for Severe Manifestations and Mortality due to COVID-19: A Rapid Systematic Review",
@@ -942710,69 +941893,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.01.29.21250660",
-    "rel_title": "Correlation of SARS-CoV-2 serology and clinical phenotype amongst hospitalised children in a tertiary children's hospital in India",
-    "rel_date": "2021-02-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.29.21250660",
-    "rel_abs": "IntroductionChildren usually present with minimal or no symptoms of SARS-CoV-2 infection. Antibody responses to SARS-CoV-2 in children from low- and middle-income countries (LMIC) have not been well described. We describe the prevalence of anti-SARS-CoV-2 antibodies and clinical phenotype of seropositive children admitted to a tertiary childrens hospital in South India.\n\nMethodsTo determine the seropositivity and describe the clinical characteristics of SARS-CoV-2 infection amongst hospitalised children, we performed a prospective clinical data collection and blood sampling of children admitted to Kanchi Kamakoti CHILDS Trust Hospital, Chennai, India over 4 months of the COVID-19 pandemic. In seropositive children, we compared antibody titres between children with and without PIMS-TS.\n\nResultsOf 463 children, 91 (19.6%) were seropositive. The median (range) age of seropositive children was 5 years (1 month - 17 years). Clinical presentation was consistent with Paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 infection (PIMS-TS) in 48% (44/91) of seropositive children. The median (range) antibody titre was 54.8 (11.1-170.9) AU/ml among all seropositive children. The median antibody titre among the children with PIMS-TS (60.3 AU/mL) was significantly (p=0.01) higher when compared to the children without PIM-TS (54.8 AU/mL).\n\nConclusionWe describe the antibody responses to SARS-CoV-2 amongst hospitalised children in a LMIC tertiary childrens hospital. Almost half of the seropositive children had PIMS-TS. Antibody levels may be helpful in the diagnosis and disease stratification of PIMS-TS.\n\nLay summaryChildren usually present with minimal or no symptoms of SARS-CoV-2 infection. However, Paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 infection (PIMS-TS) has emerged as a distinctive paediatric illness related to SARS-CoV-2. Recently, antibody testing for SARS-CoV-2 is being used increasingly as a diagnostic test for PIMS-TS. However, data on the antibody responses to SARS-CoV-2 in children is sparse. We therefore, attempted to identify the seropositivity and describe the clinical spectrum of SARS-CoV-2 infection amongst infants and children getting hospitalised in a childrens hospital in south India. Nearly one-fifth of the hospitalised children tested serology positive over 4 months. Antibody levels in children with PIMS-TS were significantly higher in comparison to the other two groups (acute SARS-CoV-2 infection and children without PIMS-TS). Results from our study suggest that all children are at risk of SARS-CoV-2 infection though they may present with mild illness or no symptoms. We also observed that antibody testing may have a possible role in diagnosis of PIMS-TS.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Aishwarya Venkataraman",
-        "author_inst": "Kanchi Kamakoti CHILDS Trust Hospital, Chennai, India"
-      },
-      {
-        "author_name": "Balasubramanian S",
-        "author_inst": "Kanchi Kamakoti CHILDS Trust Hospital, Chennai, India"
-      },
-      {
-        "author_name": "Sulochana Putilibai",
-        "author_inst": "Kanchi Kamakoti CHILDS Trust Hospital, Chennai, India"
-      },
-      {
-        "author_name": "Lakshan Raj S",
-        "author_inst": "Kanchi Kamakoti CHILDS Trust Hospital"
-      },
-      {
-        "author_name": "Sumanth Amperayani",
-        "author_inst": "Kanchi Kamakoti CHILDS Trust Hospital, Chennai, India"
-      },
-      {
-        "author_name": "Senthilnathan S",
-        "author_inst": "Kanchi Kamakoti CHILDS Trust Hospital, Chennai, India"
-      },
-      {
-        "author_name": "Anand Manoharan",
-        "author_inst": "The CHILDS Trust Medical Research Foundation (CTMRF)"
-      },
-      {
-        "author_name": "Arokia Sophi",
-        "author_inst": "Kanchi Kamakoti CHILDS Trust Hospital, Chennai, India"
-      },
-      {
-        "author_name": "Amutha R",
-        "author_inst": "Kanchi Kamakoti CHILDS Trust Hospital, Chennai, India"
-      },
-      {
-        "author_name": "Kalaimaran Sadasivam",
-        "author_inst": "Kanchi Kamakoti CHILDS Trust Hospital"
-      },
-      {
-        "author_name": "Anu Goenka",
-        "author_inst": "Bristol Royal Hospital for Children, UK."
-      },
-      {
-        "author_name": "Ramanan A V",
-        "author_inst": "Bristol Royal Hospital for Children, UK."
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "pediatrics"
-  },
   {
     "rel_doi": "10.1101/2021.01.30.21250083",
     "rel_title": "Increasing but inadequate intention to receive Covid-19 vaccination over the first 50 days of impact of the more infectious variant and roll-out of vaccination in UK: indicators for public health messaging",
@@ -943115,6 +942235,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "rehabilitation medicine and physical therapy"
   },
+  {
+    "rel_doi": "10.1101/2021.01.29.21250757",
+    "rel_title": "Updated SARS-CoV-2 Single Nucleotide Variants and Mortality Association",
+    "rel_date": "2021-02-01",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.29.21250757",
+    "rel_abs": "Since its outbreak in December 2019, COVID-19 has caused 100,5844,555 cases and 2,167,313 deaths as of Jan 27, 2021. Comparing our previous study of SARS-CoV-2 single nucleotide variants (SNVs) before June 2020, we found out that the SNV clustering had changed considerably since June 2020. Apart from that the group SNVs represented by two non-synonymous mutations A23403G (S: D614G) and C14408T (ORF1ab: P4715L) became dominant and carried by over 95% genomes, a few emerging groups of SNVs were recognized with sharply increased monthly occurrence ratios up to 70% in November 2020. Further investigation revealed that several SNVs were strongly associated with the mortality, but they presented distinct distribution in specific countries, e.g., Brazil, USA, Saudi Arabia, India, and Italy. SNVs including G25088T, T25A, G29861T and G29864A were adopted in a regularized logistic regression model to predict the mortality status in Brazil with the AUC of 0.84. Protein structure analysis showed that the emerging subgroups of non-synonymous SNVs and those mortality-related ones in Brazil were located on protein surface area. The clashes in protein structure introduced by these mutations might in turn affect virus pathogenesis through conformation changes, leading to the difference in transmission and virulence. Particularly, we found that SNVs tended to occur in intrinsic disordered regions (IDRs) of Spike (S) and ORF1ab, suggesting a critical role of SNVs in protein IDRs to determine protein folding and immune evasion.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Shuyi Fang",
+        "author_inst": "Indiana University"
+      },
+      {
+        "author_name": "Sheng Liu",
+        "author_inst": "Indiana University School of Medicine"
+      },
+      {
+        "author_name": "Jikui Shen",
+        "author_inst": "Johns Hopkins University"
+      },
+      {
+        "author_name": "Alex Z Lu",
+        "author_inst": "Park Tudor School, Indianapolis, Indiana USA"
+      },
+      {
+        "author_name": "Yucheng Zhang",
+        "author_inst": "Indiana University School of Medicine"
+      },
+      {
+        "author_name": "Kailing Li",
+        "author_inst": "Indiana University"
+      },
+      {
+        "author_name": "Juli Liu",
+        "author_inst": "Indiana University School of Medicine"
+      },
+      {
+        "author_name": "Lei Yang",
+        "author_inst": "Indiana University School of Medicine"
+      },
+      {
+        "author_name": "Chang-Deng Hu",
+        "author_inst": "Purdue University"
+      },
+      {
+        "author_name": "Jun Wan",
+        "author_inst": "Indiana University School of Medicine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health informatics"
+  },
   {
     "rel_doi": "10.1101/2021.01.29.20248125",
     "rel_title": "Estimating the COVID-19 Prevalence in Spain with Indirect Reporting via Open Surveys",
@@ -944288,45 +943463,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.01.30.21250555",
-    "rel_title": "Impact of COVID-19 restrictions on the postpartum experience of women living in Eastern Canada: A mixed method cohort study",
-    "rel_date": "2021-02-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.30.21250555",
-    "rel_abs": "ObjectivesTo (1) compare changes in self-efficacy, social support, postpartum anxiety and postpartum depression in Canadian women collected before (Cohort 1) and during the COVID-19 pandemic (Cohort 2); (2) explore the women felt related to having a newborn during the pandemic; and (3) explore ways that women coped.\n\nMethodsPrior to the pandemic (October 1, 2019-January 1, 2020), an online survey was conducted with women had given birth within the past six months in one of the three Eastern Canadian Maritime provinces (Cohort 1). A second, similar survey was conducted between August 1, 2020 and October 31, 2020 (Cohort 2) during a period of provincial pandemic response to COVID-19.\n\nResultsFor Cohort 1, 561 women completed the survey and 331 women in Cohort 2. Cohorts were similar in terms of age of women, parity, and age of newborn. There were no significant differences for self-efficacy, social support, postpartum anxiety, and depression between the cohorts. Difficulties that women reported as a result of COVID-19 restrictions included lack of support from family and friends, fear of COVID-19 exposure, feeling isolated and uncertain, negative impact on perinatal care experience, and hospital restrictions. Having support from partners and families, in-person/virtual support, as well as self-care and the low prevalence of COVID-19 during the summer of 2020 helped women cope.\n\nConclusionWhile there was no significant difference in pre-pandemic and during pandemic psychosocial outcomes, there were still challenges and negative impacts that women identified. Consideration of vulnerable populations is important when making public health recommendations.\n\nWhat is already known on this subject?Previous work has shown the importance of social support in the postpartum transition in developing parenting self-efficacy and decreasing postpartum anxiety and depression. However, during the COVID-19 pandemic, womens mental health, particularly during the perinatal period, has seen an increases in rates of postpartum anxiety and depression.\n\nWhat this study adds?This study is able to compare self-efficacy, social support, postpartum anxiety and depression between two cohorts of postpartum women living in Eastern Canada - pre-COVID-19 pandemic and during. While there was no significant difference in pre-pandemic and during pandemic psychosocial outcomes, there were still challenges and negative impacts that women identified.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Justine Dol",
-        "author_inst": "Dalhousie University"
-      },
-      {
-        "author_name": "Brianna Richardson",
-        "author_inst": "Dalhousie University"
-      },
-      {
-        "author_name": "Megan Aston",
-        "author_inst": "Dalhousie University"
-      },
-      {
-        "author_name": "Douglas McMillan",
-        "author_inst": "IWK Health Centre"
-      },
-      {
-        "author_name": "Gail Tomblin Murphy",
-        "author_inst": "Nova Scotia Health Authority"
-      },
-      {
-        "author_name": "Marsha Campbell-Yeo",
-        "author_inst": "Dalhousie University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.01.31.21250859",
     "rel_title": "Prognosis and hematological findings in patients with COVID-19 in an Amazonian population of Peru",
@@ -944593,6 +943729,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.01.29.21250653",
+    "rel_title": "Robust spike antibody responses and increased reactogenicity in seropositive individuals after a single dose of SARS-CoV-2 mRNA vaccine",
+    "rel_date": "2021-02-01",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.29.21250653",
+    "rel_abs": "An important question is arising as COVID-19 vaccines are getting rolled out: Should individuals who already had a SARS-CoV-2 infection receive one or two shots of the currently authorized mRNA vaccines. In this short report, we show that the antibody response to the first vaccine dose in individuals with pre-existing immunity is equal to or even exceeds the titers found in naive individuals after the second dose. We also show that the reactogenicity is significantly higher in individuals who have been infected with SARS-CoV-2 in the past. Changing the policy to give these individuals only one dose of vaccine would not negatively impact on their antibody titers, spare them from unnecessary pain and free up many urgently needed vaccine doses.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Florian Krammer",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Komal Srivastava",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "- PARIS team",
+        "author_inst": ""
+      },
+      {
+        "author_name": "Viviana Simon",
+        "author_inst": "Icahn School of Medicine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "allergy and immunology"
+  },
   {
     "rel_doi": "10.1101/2021.01.28.21250666",
     "rel_title": "Structural basis of fitness of emerging SARS-COV-2 variants and considerations for screening, testing and surveillance strategy to contain their threat.",
@@ -946214,73 +945381,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2021.01.29.428442",
-    "rel_title": "A single dose of replication-competent VSV-vectored vaccine expressing SARS-CoV-2 S1 protects against virus replication in a hamster model of severe COVID-19",
-    "rel_date": "2021-01-30",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.29.428442",
-    "rel_abs": "The development of effective countermeasures against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the agent responsible for the COVID-19 pandemic, is a priority. We designed and produced ConVac, a replication-competent vesicular stomatitis virus (VSV) vaccine vector that expresses the S1 subunit of SARS-CoV-2 spike protein. We used golden Syrian hamsters as animal model of severe COVID-19 to test the efficacy of the ConVac vaccine. A single vaccine dose elicited high levels of SARS-CoV-2 specific binding and neutralizing antibodies; following intranasal challenge with SARS-CoV-2, animals were protected from weight loss and viral replication in the lungs. No enhanced pathology was observed in vaccinated animals upon challenge, but some inflammation was still detected. The data indicate rapid control of SARS-CoV-2 replication by the S1-based VSV-vectored SARS-CoV-2 ConVac vaccine.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Delphine C. Malherbe",
-        "author_inst": "University of Texas Medical Branch"
-      },
-      {
-        "author_name": "Drishya Kurup",
-        "author_inst": "Thomas Jefferson University"
-      },
-      {
-        "author_name": "Christoph Wirblich",
-        "author_inst": "Thomas Jefferson University"
-      },
-      {
-        "author_name": "Adam J. Ronk",
-        "author_inst": "University of Texas Medical Branch"
-      },
-      {
-        "author_name": "Chad Mire",
-        "author_inst": "University of Texas Medical Branch"
-      },
-      {
-        "author_name": "Natalia Kuzmina",
-        "author_inst": "University of Texas Medical Branch"
-      },
-      {
-        "author_name": "Noor Shaik",
-        "author_inst": "Thomas Jefferson University"
-      },
-      {
-        "author_name": "Sivakumar Periasamy",
-        "author_inst": "University of Texas Medical Branch"
-      },
-      {
-        "author_name": "Matthew A. Hyde",
-        "author_inst": "Galveston National Laboratory"
-      },
-      {
-        "author_name": "Julie M. Williams",
-        "author_inst": "Galveston National Laboratory"
-      },
-      {
-        "author_name": "Pei-Yong Shi",
-        "author_inst": "University of TexasMedical Branch"
-      },
-      {
-        "author_name": "Matthias J Schnell",
-        "author_inst": "Thomas Jefferson University"
-      },
-      {
-        "author_name": "Alexander Bukreyev",
-        "author_inst": "University of Texas Medical Branch at Galveston"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2021.01.25.21249942",
     "rel_title": "Development and external validation of prognostic models for COVID-19 to support risk stratification in secondary care",
@@ -946787,6 +945887,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.01.26.21250533",
+    "rel_title": "Lumipulse G SARS-CoV-2 Ag Assay Evaluation for SARS-CoV-2 Antigen Detection Using 594 Nasopharyngeal Swab Samples from Different Testing Groups",
+    "rel_date": "2021-01-29",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.26.21250533",
+    "rel_abs": "Compared to RT-PCR, lower performance of antigen detection assays, including the Lumipulse G SARS-CoV-2 Ag assay, may depend on specific testing scenarios. We tested 594 nasopharyngeal swab samples from individuals with COVID-19 (RT-PCR cycle threshold [Ct] values [&le;]40) or non-COVID-19 (Ct values [&le;]40) diagnoses. RT-PCR positive samples were assigned to diagnostic, screening, or monitoring groups of testing. With a limit of detection of 1.2 x 104 SARS-CoV-2 RNA copies/ml, Lumipulse showed positive percent agreement (PPA) of 79.9% (155/194) and negative percent agreement of 99.3% (397/400), whereas PPAs were 100% for samples with Ct values of <18 or 18-<25 and 92.5% for samples with Ct values of 25-<30. By three groups, Lumipulse showed PPA of 87.0% (60/69), 81.1% (43/53), or 72.2% (52/72), respectively, whereas PPA was 100% for samples with Ct values of <18 or 18-<25, and was 94.4%, 80.0%, or 100% for samples with Ct values of 25-<30, respectively. RT-PCR positive samples were also tested for SARS-CoV-2 subgenomic RNA and, by three groups, testing showed that PPA was 63.8% (44/69), 62.3% (33/53), or 33.3% (24/72), respectively. PPAs dropped to 55.6%, 20.0%, or 41.7% for samples with Ct values of 25-<30, respectively. All 101 samples with a subgenomic RNA positive result had a Lumipulse assays antigen positive result, whereas only 54 (58.1%) of remaining 93 samples had a Lumipulse assays antigen positive result. In conclusion, Lumipulse assay was highly sensitive in samples with low RT-PCR Ct values, implying repeated testing to reduce consequences of false-negative results.",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Giulia Menchinelli",
+        "author_inst": "Universit\u00e0 Cattolica del S. Cuore"
+      },
+      {
+        "author_name": "Licia Bordi",
+        "author_inst": "National Institute for Infectious Diseases"
+      },
+      {
+        "author_name": "Flora Marzialiotti",
+        "author_inst": "Fondazione Policlinico Universitario A. Gemelli, IRCCS"
+      },
+      {
+        "author_name": "Ivana Palucci",
+        "author_inst": "Catholic University of the Sacred Hearth"
+      },
+      {
+        "author_name": "Maria R. Capobianchi",
+        "author_inst": "National Institute for Infectious Diseases"
+      },
+      {
+        "author_name": "Giuseppe Sberna",
+        "author_inst": "National Institute for Infectious Diseases L. Spallanzani-IRCCS"
+      },
+      {
+        "author_name": "Eleonora Lalle",
+        "author_inst": "National Institute for Infectious Diseases"
+      },
+      {
+        "author_name": "Lucio Romano",
+        "author_inst": "Fondazione Policlinico Universitario A. Gemelli, IRCCS"
+      },
+      {
+        "author_name": "Giulia De Angelis",
+        "author_inst": "Catholic University"
+      },
+      {
+        "author_name": "Simona Marchetti",
+        "author_inst": "Fondazione Policlinico Universitario A. Gemelli, IRCCS"
+      },
+      {
+        "author_name": "Maurizio Sanguinetti",
+        "author_inst": "Fondazione Policlinico Universitario"
+      },
+      {
+        "author_name": "Paola Cattani",
+        "author_inst": "Fondazione Policlinico Universitario A. Gemelli, IRCCS"
+      },
+      {
+        "author_name": "Brunella Posteraro",
+        "author_inst": "Universit\u00e0 Cattolica del S. Cuore"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.01.26.21250580",
     "rel_title": "THE AIRBORNE CONTAGIOUSNESS OF RESPIRATORY VIRUSES: A COMPARATIVE ANALYSIS AND IMPLICATIONS FOR MITIGATION",
@@ -947940,29 +947107,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.01.27.21250604",
-    "rel_title": "The World Mortality Dataset: Tracking excess mortality across countries during the COVID-19 pandemic",
-    "rel_date": "2021-01-29",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.27.21250604",
-    "rel_abs": "Comparing the impact of the COVID-19 pandemic between countries or across time is difficult because the reported numbers of cases and deaths can be strongly affected by testing capacity and reporting policy. Excess mortality, defined as the increase in all-cause mortality relative to the expected mortality, is widely considered as a more objective indicator of the COVID-19 death toll. However, there has been no global, frequently-updated repository of the all-cause mortality data across countries. To fill this gap, we have collected weekly, monthly, or quarterly all-cause mortality data from 94 countries and territories, openly available as the regularly-updated World Mortality Dataset. We used this dataset to compute the excess mortality in each country during the COVID-19 pandemic. We found that in several worst-affected countries (Peru, Ecuador, Bolivia, Mexico) the excess mortality was above 50% of the expected annual mortality. At the same time, in several other countries (Australia, New Zealand) mortality during the pandemic was below the usual level, presumably due to social distancing measures decreasing the non-COVID infectious mortality. Furthermore, we found that while many countries have been reporting the COVID-19 deaths very accurately, some countries have been substantially underreporting their COVID-19 deaths (e.g. Nicaragua, Russia, Uzbekistan), sometimes by two orders of magnitude (Tajikistan). Our results highlight the importance of open and rapid all-cause mortality reporting for pandemic monitoring.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Ariel Karlinsky",
-        "author_inst": "Hebrew University Jerusalem Israel; Kohelet Economic Forum Jerusalem Israel; Midaat Israel"
-      },
-      {
-        "author_name": "Dmitry Kobak",
-        "author_inst": "Institute for Ophthalmic Research, University of Tubingen, Germany"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.01.27.20240309",
     "rel_title": "Beyond the new normal: assessing the feasibility of vaccine-based elimination of SARS-CoV-2",
@@ -948253,6 +947397,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "obstetrics and gynecology"
   },
+  {
+    "rel_doi": "10.1101/2021.01.27.21250153",
+    "rel_title": "The prevalence of olfactory dysfunction and its associated factors in patients with COVID-19 infection",
+    "rel_date": "2021-01-29",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.27.21250153",
+    "rel_abs": "ObjectiveTo determine the prevalence of olfactory dysfunctions, mainly, anosmia and to identify its associated factors in patients with COVID-19 infection.\n\nStudy designA hospital-based prospective observational cohort study\n\nSettingA COVID dedicated hospital, Square Hospitals Ltd., Dhaka, Bangladesh.\n\nMethodsWe collected patients information including laboratory-confirmed COVID-19 test results. We used Pearson Chi-square test and logistic regression model to assess the associations between demographic and clinical characteristics and olfactory outcomes.\n\nResultsOut of 600 COVID-19 positive patients, 38.7% were diagnosed with olfactory dysfunction. Our analyses showed that patients age, smoking status, cough, dyspnea, sore throat, asthenia, and nausea or vomiting were significantly associated with the anosmia. We observed the risk of developing anosmia was greater in younger patients than in older patients, and this risk decreased as age increased [odds ratio (OR) range for different age groups: 1.26 to 1.08]. Smoking patients were 1.73 times more likely to experience anosmia than non-smoking patients [OR=1.73, 95% confidence interval (CI) = 1.01-2.98]. In addition, patients complained asthenia had a significantly double risk of developing the anosmia [OR = 1.96, CI = 1.23-3.06].\n\nConclusionsOur study shows that about 39% of patients diagnosed with olfactory dysfunction. Patients age, smoking status, and asthenia are significantly positively associated with the anosmia. Since anosmia can be a significant marker for the diagnosis of COVID-19, we suggest regular screening of olfactory dysfunction in patients with early symptoms of COVID-19, particularly younger patients, smoker, and complained asthenia.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Md. Mehedi Hasan",
+        "author_inst": "Square Hospitals Ltd."
+      },
+      {
+        "author_name": "Naima Ahmed Tamanna",
+        "author_inst": "Jagannath University"
+      },
+      {
+        "author_name": "Mohammad Nasimul Jamal",
+        "author_inst": "Square Hospitals Ltd."
+      },
+      {
+        "author_name": "Md. Jamal Uddin",
+        "author_inst": "Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "otolaryngology"
+  },
   {
     "rel_doi": "10.1101/2021.01.27.21250487",
     "rel_title": "Self-Reported Mask Wearing Greatly Exceeds Directly Observed Use: Urgent Need for Policy Intervention in Kenya",
@@ -949750,77 +948925,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2021.01.27.428478",
-    "rel_title": "Early therapy with remdesivir and antibody combinations improves COVID-19 disease in mice",
-    "rel_date": "2021-01-28",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.27.428478",
-    "rel_abs": "Improving the standard of clinical care for individuals infected with SARS-CoV-2 variants is a global health priority. Small molecule antivirals like remdesivir (RDV) and biologics such as human monoclonal antibodies (mAb) have demonstrated therapeutic efficacy against SARS-CoV-2, the causative agent of COVID-19. However, it is not known if combination RDV/mAb will improve outcomes over single agent therapies or whether antibody therapies will remain efficacious against variants. In kinetic studies in a mouse-adapted model of ancestral SARS-CoV-2 pathogenesis, we show that a combination of two mAbs in clinical trials, C144 and C135, have potent antiviral effects against even when initiated 48 hours after infection. The same antibody combination was also effective in prevention and therapy against the B.1.351 variant of concern (VOC). Combining RDV and antibodies provided a modest improvement in outcomes compared to single agents. These data support the continued use of RDV to treat SARS-CoV-2 infections and support the continued clinical development of the C144 and C135 antibody combination to treat patients infected with SARS-CoV-2 variants.",
-    "rel_num_authors": 14,
-    "rel_authors": [
-      {
-        "author_name": "David Martinez",
-        "author_inst": "The University of North Carolina at Chapel Hill"
-      },
-      {
-        "author_name": "Alexandra Schaefer",
-        "author_inst": "University of North Carolina at Chapel Hill"
-      },
-      {
-        "author_name": "Sarah R. Leist",
-        "author_inst": "University of North Carolina at Chapel Hill"
-      },
-      {
-        "author_name": "Dapeng Li",
-        "author_inst": "Duke University"
-      },
-      {
-        "author_name": "Kendra Gully",
-        "author_inst": "University of North Carolina at Chapel Hill"
-      },
-      {
-        "author_name": "Joy Feng",
-        "author_inst": "Gilead Sciences Inc"
-      },
-      {
-        "author_name": "Elaine Bunyan",
-        "author_inst": "Gilead Sciences Inc"
-      },
-      {
-        "author_name": "Danielle Porter",
-        "author_inst": "Gilead Sciences Inc"
-      },
-      {
-        "author_name": "Tomas Cihlar",
-        "author_inst": "Gilead Sciences Inc"
-      },
-      {
-        "author_name": "Stephanie Montgomery",
-        "author_inst": "University of North Carolina at Chapel Hill"
-      },
-      {
-        "author_name": "Barton Haynes",
-        "author_inst": "Duke University"
-      },
-      {
-        "author_name": "Ralph S. Baric",
-        "author_inst": "University of North Carolina at Chapel Hill"
-      },
-      {
-        "author_name": "Michel C. Nussenzweig",
-        "author_inst": "The Rockefeller University"
-      },
-      {
-        "author_name": "Timothy P. Sheahan",
-        "author_inst": "University of North Carolina at Chapel Hill"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2021.01.28.428521",
     "rel_title": "Modeling mutational effects on biochemical phenotypes using convolutional neural networks: application to SARS-CoV-2",
@@ -950211,6 +949315,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "endocrinology"
   },
+  {
+    "rel_doi": "10.1101/2021.01.25.21250040",
+    "rel_title": "COVID-19-related disruptions to routine vaccination services in India: perspectives from pediatricians",
+    "rel_date": "2021-01-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.25.21250040",
+    "rel_abs": "Background and ObjectiveThe COVID-19 pandemic has led to disruptions to routine immunization programs in India and around the world, setting the stage for potentially serious outbreaks of vaccine-preventable diseases.\n\nMethodsWe surveyed pediatric healthcare providers in India in 2 rounds in April-June and September 2020 to understand how COVID-19 control measures may have impacted routine vaccination.\n\nResultsRespondents were predominantly pediatricians working in primary, secondary or tertiary healthcare centers, across 21 Indian states and two union territories. Among the 424 (survey 1) and 141 (survey 2) respondents, 33.4% and 7.8%, respectively, reported near complete suspension of vaccination services due to COVID-19. A 50% or greater drop in vaccination services was reported by 83.1% of respondents in June, followed by 32.6% four months later, indicating slow recovery of services. By September 2020, 83.6% were aware of updated guidelines on safe provision of immunization services, although awareness of specific catch-up vaccination plans was low, and 76.6% expressed concern about a vaccine coverage gap that could potentially lead to increased non-COVID-19 illnesses and deaths.\n\nConclusionsPandemic-related disruptions to vaccination services were reported by pediatricians across India. Concerted efforts are needed from governing and academic groups to ensure that routine immunization and catch-up programs are implemented during this pandemic, which can sustain gains in vaccination coverage and provide a robust blueprint for the national roll-out of the COVID-19 vaccine.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Anita Shet",
+        "author_inst": "Johns Hopkins School of Public Health"
+      },
+      {
+        "author_name": "Baldeep Dhaliwal",
+        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
+      },
+      {
+        "author_name": "Preetika Banerjee",
+        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
+      },
+      {
+        "author_name": "Kelly Carr",
+        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
+      },
+      {
+        "author_name": "Andrea DeLuca",
+        "author_inst": "Amputee Coalition, Washington DC, USA"
+      },
+      {
+        "author_name": "Carl Britto",
+        "author_inst": "St Johns Research Institute, Bangalore, India"
+      },
+      {
+        "author_name": "Rajeev Seth",
+        "author_inst": "Bal Umang Drishya Sanstha, New Delhi, India"
+      },
+      {
+        "author_name": "Bakul Parekh",
+        "author_inst": "Indian Academy of Pediatrics"
+      },
+      {
+        "author_name": "GV Basavaraj",
+        "author_inst": "Indian Academy of Pediatrics"
+      },
+      {
+        "author_name": "Digant Shastri",
+        "author_inst": "Indian Academy of Pediatrics"
+      },
+      {
+        "author_name": "Piyush Gupta",
+        "author_inst": "Indian Academy of Pediatrics"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "pediatrics"
+  },
   {
     "rel_doi": "10.1101/2021.01.26.21250518",
     "rel_title": "Impact of COVID-19 on education, health and lifestyle behaviour of Brazilian urology residents",
@@ -951608,57 +950771,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.01.21.21249623",
-    "rel_title": "Genomic insights into early SARS-CoV-2 strains isolated in Reunion Island",
-    "rel_date": "2021-01-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.21.21249623",
-    "rel_abs": "The relative isolation of many island communities provides some protection from the COVID-19 pandemic, as imported cases can be limited and traced effectively. Until recently, this was true for the population of the French overseas department, Reunion Island, where only limited numbers of autochthonous cases were observed prior to August 2020. Since the report of the first case of COVID-19, contact tracing has been carried out for each new case identified in Reunion Island to identify transmission and clusters. To contribute to the public health response and understand the diffusion of SARS-Cov-2 strains in Reunion Island, we established in-house genome sequencing capability in Reunion using Oxford nanopore technology (MinION) as an inexpensive option for genomic typing of SARS-CoV-2 lineages on the island, and cross-validated typing results between viral isolation methods and different sequencing technologies. The results of our work during the early phase of the epidemics are presented herein.\n\nArticle Summary LineThe COVID-19 pandemic has had an unprecedented impact on the global community. Here we provide epidemiological and genomic details of the early stages of the pandemic on Reunion Island.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "David A Wilkinson",
-        "author_inst": "Universite de La Reunion, CNRS, IRD, INSERM"
-      },
-      {
-        "author_name": "Camille Lebarbenchon",
-        "author_inst": "UMR Processus Infectieux en Milieu Insulaire Tropical"
-      },
-      {
-        "author_name": "Celestine Atyame",
-        "author_inst": "UMR Processus Infectieux en Milieu Insulaire Tropical"
-      },
-      {
-        "author_name": "Sarah Hafsia",
-        "author_inst": "UMR Processus Infectieux en Milieu Insulaire Tropical"
-      },
-      {
-        "author_name": "Marie-Christine Jaffar-Bandjee",
-        "author_inst": "Centre Hospitalier Universitaire de la Reunion, Saint-Denis, France"
-      },
-      {
-        "author_name": "Luce Menudier",
-        "author_inst": "Sante Publique France, Saint Denis, France"
-      },
-      {
-        "author_name": "Sebastien Tanaka",
-        "author_inst": "Assistance Publique-Hopitaux de Paris (AP-HP), Department of Anesthesiology and Critical Care Medicine, Bichat-Claude Bernard Hospital, Paris, France"
-      },
-      {
-        "author_name": "Olivier Meilhac",
-        "author_inst": "Reunion Island University, French Institute of Health and Medical Research (INSERM), U1188 Diabetes atherothrombosis Reunion Indian Ocean (DeTROI), CYROI Platef"
-      },
-      {
-        "author_name": "Patrick Mavingui",
-        "author_inst": "Universite de La Reunion. Unite Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical (UMR PIMIT)"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.01.20.21250173",
     "rel_title": "The usefulness of a quantitative olfactory test for the detection of COVID-19.",
@@ -951881,6 +950993,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pediatrics"
   },
+  {
+    "rel_doi": "10.1101/2021.01.20.21250204",
+    "rel_title": "Rule of thumb in human intelligence for assessing the COVID-19 outbreak in Japan",
+    "rel_date": "2021-01-26",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.20.21250204",
+    "rel_abs": "BackgroundThe COVID-19 outbreak in Japan exhibited its third peak at the end of 2020. Mathematical modelling and developed AI cannot explain several peaks in a single year.\n\nObjectThis study was conducted to evaluate a rule of thumb for prediction from past wave experiences.\n\nMethodWe rescaled the number of newly infected patients as 100% at the peak and checked similarities among waves. Then we extrapolated the courses of the third and later waves.\n\nResultsResults show some similarity around the second and the third waves. Based on this similarity, we expected the bottom of the third wave will show 2131 newly positive patients including asymptomatic patients at around the end of February, 2021.\n\nDiscussion and ConclusionWe can infer the course of the third wave from similarity with the second wave. Mathematical modelling has been unable to do it, even when AI was used for prediction. Performance of the rule of thumb used with human intelligence might be superior to that of AI under these circumstances.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Junko Kurita",
+        "author_inst": "Tokiwa University, Ibaraki, Japan"
+      },
+      {
+        "author_name": "Tamie Sugawara",
+        "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan"
+      },
+      {
+        "author_name": "Yasushi Ohkusa",
+        "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.01.22.21250302",
     "rel_title": "Willingness to volunteer of medical students during the COVID-19 pandemic: Assessment at a tertiary care hospital in India",
@@ -953286,69 +952425,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.01.24.20248381",
-    "rel_title": "Dynamic change and clinical relevance of post-infectious SARS-CoV-2 antibody responses.",
-    "rel_date": "2021-01-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.24.20248381",
-    "rel_abs": "BackgroundAlthough reports suggest that most individuals with COVID-19 develop detectable antibodies post infection, the kinetics, durability, and relative differences between IgM and IgG responses beyond the first few weeks after symptom onset remain poorly understood.\n\nMethodsWithin a large, well-phenotyped, diverse, prospective cohort of subjects with and without SARS-CoV-2 PCR-confirmed infection and historical controls derived from cohorts with high prevalence of viral coinfections and samples taken during prior flu seasons, we measured SARS-CoV-2 serological responses (both IgG and IgM) using commercially available assays. We calculated sensitivity and specificity, relationship with disease severity and mapped the kinetics of antibody responses over time using generalised additive models.\n\nResultsWe analysed 1,001 samples from 752 subjects, 327 with confirmed SARS-CoV-2 (29.7% with severe disease) spanning a period of 90 days from symptom onset. Sensitivity was lower (44.1-47.1%) early (<10 days) after symptom onset but increased to >80% after 10 days. IgM positivity increased earlier than IgG-targeted assays but positivity peaked between day 32 and 38 post onset of symptoms and declined thereafter, a dynamic that was confirmed when antibody levels were analysed, with more rapid decline observed with IgM. Early (<10 days) IgM but not IgG levels were significantly higher in those who subsequently developed severe disease (signal / cut-off 4.20 (0.75-17.93) versus 1.07 (0.21-5.46), P=0.048).\n\nConclusionsThis study suggests that post-infectious antibody responses in those with confirmed COVID-19 begin to decline relatively early post infection and suggests a potential role for higher IgM levels early in infection predicting subsequent disease severity.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Patrick WG Mallon",
-        "author_inst": "University College Dublin"
-      },
-      {
-        "author_name": "Willard Tinago",
-        "author_inst": "University College Dublin"
-      },
-      {
-        "author_name": "Alejandro Garcia Leon",
-        "author_inst": "University College Dublin"
-      },
-      {
-        "author_name": "Kathleen McCann",
-        "author_inst": "University College Dublin"
-      },
-      {
-        "author_name": "Grace Kenny",
-        "author_inst": "University College Dublin"
-      },
-      {
-        "author_name": "Padraig McGettrick",
-        "author_inst": "University College Dublin"
-      },
-      {
-        "author_name": "Sandra Green",
-        "author_inst": "University College Dublin"
-      },
-      {
-        "author_name": "Rosanna Inzitiari",
-        "author_inst": "University College Dublin"
-      },
-      {
-        "author_name": "Aoife Cotter",
-        "author_inst": "University College Dublin"
-      },
-      {
-        "author_name": "Stefano Savinelli",
-        "author_inst": "University College Dublin"
-      },
-      {
-        "author_name": "Eoin R Feeney",
-        "author_inst": "University College Dublin"
-      },
-      {
-        "author_name": "Peter Doran",
-        "author_inst": "University College Dublin"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.01.22.20249050",
     "rel_title": "A High-throughput Microsphere-based Immunoassay of Anti-SARS-CoV-2 IgM Testing for COVID-19 Diagnostics",
@@ -953803,6 +952879,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "respiratory medicine"
   },
+  {
+    "rel_doi": "10.1101/2021.01.25.21250233",
+    "rel_title": "Contamination of air and surfaces in workplaces with SARS-CoV-2 virus: a systematic review",
+    "rel_date": "2021-01-26",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.25.21250233",
+    "rel_abs": "ObjectivesThis systematic review aimed to evaluate the evidence for air and surface contamination of workplace environments with SARS-CoV-2 RNA and the quality of the methods used to identify actions necessary to improve the quality of the data.\n\nMethodsWe searched Web of Science and Google Scholar until 24th December 2020 for relevant articles and extracted data on methodology and results.\n\nResultsThe vast majority of data come from healthcare settings, with typically around 6 % of samples having detectable concentrations of SARS-CoV-2 RNA and almost none of the samples collected had viable virus. There were a wide variety of methods used to measure airborne virus, although surface sampling was generally undertaken using nylon flocked swabs. Overall, the quality of the measurements was poor. Only a small number of studies reported the airborne concentration of SARS-CoV-2 virus RNA, mostly just reporting the detectable concentration values without reference to the detection limit. Imputing the geometric mean air concentration assuming the limit of detection was the lowest reported value, suggests typical concentrations in health care settings may be around 0.01 SARS-CoV-2 virus RNA copies/m3. Data on surface virus loading per unit area were mostly unavailable.\n\nConclusionThe reliability of the reported data is uncertain. The methods used for measuring SARS-CoV-2 and other respiratory viruses in work environments should be standardised to facilitate more consistent interpretation of contamination and to help reliably estimate worker exposure.\n\nKey messagesO_LIWhat is already known about this subject?\nO_LILow level contamination of air and surfaces in hospitals with SARS-CoV-2 RNA have been reported during the Covid-19 pandemic.\nC_LIO_LILimited data have published from non-healthcare settings.\nC_LI\nC_LIO_LIWhat are the new findings?\nO_LITypically, around 6% of air and surface samples in hospitals were positive for SARS-COV-2 RNA, although there is very limited data for non-healthcare settings.\nC_LIO_LIThe quality of the available measurement studies is generally poor, with little consistency in the sampling and analytical methods used.\nC_LIO_LIFew studies report the concentration of SARS-CoV-2 in air or as surface loading of virus RNA, and very few studies have reported culture of the virus.\nC_LIO_LIThe best estimate of typical air concentrations in health care settings is around 0.01 SARS-CoV-2 virus RNA copies/m3\nC_LI\nC_LIO_LIHow might this impact on policy or clinical practice in the foreseeable future?\nO_LIThere should be concerted efforts to standardise the methods used for measuring SARS-CoV-2 and other respiratory viruses in work environments.\nC_LI\nC_LI",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "John Cherrie",
+        "author_inst": "Institute of Occupational Medicine"
+      },
+      {
+        "author_name": "Mark Cherrie",
+        "author_inst": "Institute of Occupational Medicine"
+      },
+      {
+        "author_name": "Alice Davis",
+        "author_inst": "Institute of Occupational Medicine"
+      },
+      {
+        "author_name": "David Holmes",
+        "author_inst": "Institute of Occupational Medicine"
+      },
+      {
+        "author_name": "Sean Semple",
+        "author_inst": "University of Stirling"
+      },
+      {
+        "author_name": "Susanne Steinle",
+        "author_inst": "Institute of Occupational Medicine"
+      },
+      {
+        "author_name": "Ewan MacDonald",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Ginny Moore",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Miranda Loh",
+        "author_inst": "Institute of Occupational Medicine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "occupational and environmental health"
+  },
   {
     "rel_doi": "10.1101/2021.01.25.20248984",
     "rel_title": "Impulse dispersion of aerosols during playing wind instruments",
@@ -955192,61 +954319,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.01.26.21250520",
-    "rel_title": "Impact of social restrictions during the COVID-19 pandemic on the physical activity levels of older adults: an analysis of the CHARIOT COVID-19 Rapid Response Study",
-    "rel_date": "2021-01-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.26.21250520",
-    "rel_abs": "ObjectivesPhysical inactivity is more common in older adults, is associated with social isolation and loneliness, and contributes to increased morbidity and mortality. We examined the effect of social restrictions, implemented to reduce transmission of COVID-19 in the UK (lockdown), on physical activity (PA) levels of older adults, and the demographic, lifestyle and social predictors of this change.\n\nDesignBaseline analysis of a survey-based prospective cohort study\n\nSettingAdults enrolled in the Cognitive Health in Ageing Register for Investigational and Observational Trials (CHARIOT) cohort from GP practices in North West London were invited to participate from April to July 2020.\n\nParticipants6,219 cognitively healthy adults aged 50 to 92 years completed the survey.\n\nMain outcome measuresSelf-reported PA before and after lockdown, as measured by Metabolic Equivalent of Task (MET) minutes. Associations of PA with demographic, lifestyle and social factors, mood and frailty.\n\nResultsMean PA was significantly lower following lockdown, from 3,519 MET minutes/week to 3,185 MET minutes/week (p<0.001). After adjustment for confounders and pre-lockdown PA, lower levels of PA after lockdown were found in those who were over 85 years old (640 [95% CI: 246 to 1034] MET minutes/week less); were divorced or single (240 [95% CI: 120 to 360] MET minutes/week less); living alone (277 [95% CI: 152 to 402] MET minutes/week less); reported feeling lonely often (306 [95% CI: 60 to 552] MET minutes/week less); and showed symptoms of depression (1007 [95% CI: 1401 to 612] MET minutes/week less) compared to those aged 50-64 years, married, co-habiting, and not reporting loneliness or depression, respectively.\n\nConclusions and ImplicationsMarkers of social isolation, loneliness and depression were associated with lower PA following lockdown in the UK. Interventions to improve PA in older adults should take account of social and community factors, and targeted strategies to increase physical activity in socially isolated, lonely and depressed older adults should be considered.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "David Salman",
-        "author_inst": "MSk lab and Department of Primary Care and Public Health, Imperial College London"
-      },
-      {
-        "author_name": "Thomas Beaney",
-        "author_inst": "Department of Primary Care and Public Health, Imperial College London"
-      },
-      {
-        "author_name": "Catherine Robb",
-        "author_inst": "Ageing Epidemiology Research Unit (AGE), School of Public Health, Imperial College London"
-      },
-      {
-        "author_name": "Celeste A. de Jager Loots",
-        "author_inst": "Ageing Epidemiology Research Unit (AGE), School of Public Health, Imperial College London"
-      },
-      {
-        "author_name": "Parthenia Giannakopoulou",
-        "author_inst": "Ageing Epidemiology Research Unit (AGE), School of Public Health, Imperial College London"
-      },
-      {
-        "author_name": "Chi Udeh-Momoh",
-        "author_inst": "Ageing Epidemiology Research Unit (AGE), School of Public Health, Imperial College London"
-      },
-      {
-        "author_name": "Sara Ahmadi-Abhari",
-        "author_inst": "Ageing Epidemiology Research Unit (AGE), School of Public Health, Imperial College London"
-      },
-      {
-        "author_name": "Azeem Majeed",
-        "author_inst": "Department of Primary Care and Public Health London, Imperial College London and Public Health Directorate, Imperial College Healthcare NHS Trust, London, UK"
-      },
-      {
-        "author_name": "Lefkos T Middleton",
-        "author_inst": "Ageing Epidemiology Research Unit (AGE), School of Public Health, Imperial College London and Public Health Directorate, Imperial College Healthcare NHS Trust, "
-      },
-      {
-        "author_name": "Alison H McGregor",
-        "author_inst": "MSk lab, Imperial College London"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.01.26.21249335",
     "rel_title": "Elevated HScore is Associated with Poor Clinical Outcomes in COVID-19, Even in the Absence of Secondary Hemophagocytic Lymphohistiocytosis.",
@@ -955589,6 +954661,101 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2021.01.25.428137",
+    "rel_title": "Increased Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7 to Antibody Neutralization",
+    "rel_date": "2021-01-26",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.25.428137",
+    "rel_abs": "The COVID-19 pandemic has ravaged the globe, and its causative agent, SARS-CoV-2, continues to rage. Prospects of ending this pandemic rest on the development of effective interventions. Single and combination monoclonal antibody (mAb) therapeutics have received emergency use authorization1-3, with more in the pipeline4-7. Furthermore, multiple vaccine constructs have shown promise8, including two with ~95% protective efficacy against COVID-199,10. However, these interventions were directed toward the initial SARS-CoV-2 that emerged in 2019. The recent emergence of new SARS-CoV-2 variants B.1.1.7 in the UK11 and B.1.351 in South Africa12 is of concern because of their purported ease of transmission and extensive mutations in the spike protein. We now report that B.1.1.7 is refractory to neutralization by most mAbs to the N-terminal domain (NTD) of spike and relatively resistant to a few mAbs to the receptor-binding domain (RBD). It is not more resistant to convalescent plasma or vaccinee sera. Findings on B.1.351 are more worrisome in that this variant is not only refractory to neutralization by most NTD mAbs but also by multiple individual mAbs to the receptor-binding motif on RBD, largely due to an E484K mutation. Moreover, B.1.351 is markedly more resistant to neutralization by convalescent plasma (9.4 fold) and vaccinee sera (10.3-12.4 fold). B.1.351 and emergent variants13,14 with similar spike mutations present new challenges for mAb therapy and threaten the protective efficacy of current vaccines.",
+    "rel_num_authors": 20,
+    "rel_authors": [
+      {
+        "author_name": "Pengfei Wang",
+        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
+      },
+      {
+        "author_name": "Manoj S Nair",
+        "author_inst": "Columbia University"
+      },
+      {
+        "author_name": "Lihong Liu",
+        "author_inst": "Columbia University Irving Medical Center"
+      },
+      {
+        "author_name": "Sho Iketani",
+        "author_inst": "Columbia University Irving Medical Center"
+      },
+      {
+        "author_name": "Yang Luo",
+        "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA"
+      },
+      {
+        "author_name": "Yicheng Guo",
+        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
+      },
+      {
+        "author_name": "Maple Wang",
+        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
+      },
+      {
+        "author_name": "Jian Yu",
+        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
+      },
+      {
+        "author_name": "Baoshan Zhang",
+        "author_inst": "Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA."
+      },
+      {
+        "author_name": "Peter D Kwong",
+        "author_inst": "Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA; Department of Biochemistry, Columbia University, New York, NY, USA."
+      },
+      {
+        "author_name": "Barney S Graham",
+        "author_inst": "Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA"
+      },
+      {
+        "author_name": "John R Mascola",
+        "author_inst": "Vaccine Research Center, NIAID, NIH"
+      },
+      {
+        "author_name": "Jennifer Y Chang",
+        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
+      },
+      {
+        "author_name": "Michael T Yin",
+        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
+      },
+      {
+        "author_name": "Magdalena E Sobieszczyk",
+        "author_inst": "Columbia University Medical Center"
+      },
+      {
+        "author_name": "Christos A Kyratsous",
+        "author_inst": "Regeneron Pharmaceuticals, Inc."
+      },
+      {
+        "author_name": "Lawrence Shapiro",
+        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
+      },
+      {
+        "author_name": "Zizhang Sheng",
+        "author_inst": "Columbia University"
+      },
+      {
+        "author_name": "Yaoxing Huang",
+        "author_inst": "Columbia University"
+      },
+      {
+        "author_name": "David D Ho",
+        "author_inst": "Columbia University Irving Medical Center"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2021.01.26.428251",
     "rel_title": "A single intranasal dose of chimpanzee adenovirus-vectored vaccine protects against SARS-CoV-2 infection in rhesus macaques",
@@ -956878,165 +956045,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.01.21.21249825",
-    "rel_title": "SARS-CoV-2 Control on a Large Urban College Campus Without Mass Testing",
-    "rel_date": "2021-01-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.21.21249825",
-    "rel_abs": "ObjectiveA small percentage of universities and colleges conduct mass SARS-CoV-2 testing. However, universal testing is resource-intensive, strains national testing capacity, and false negative tests can encourage unsafe behaviors.\n\nParticipantsA large urban university campus.\n\nMethodsVirus control centered on three pillars: mitigation, containment, and communication, with testing of symptomatic and a random subset of asymptomatic students.\n\nResultsRandom surveillance testing demonstrated a prevalence among asymptomatic students of 0.4% throughout the term. There were two surges in cases that were contained by enhanced mitigation and communication combined with targeted testing. Cumulative cases totaled 445 for the term, most resulting from unsafe undergraduate student behavior and among students living off-campus. A case rate of 232/10,000 undergraduates equaled or surpassed several peer institutions that conducted mass testing.\n\nConclusionsAn emphasis on behavioral mitigation and communication can control virus transmission on a large urban campus combined with a limited and targeted testing strategy.",
-    "rel_num_authors": 36,
-    "rel_authors": [
-      {
-        "author_name": "Christopher P O'Donnell",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Katherine Brownlee",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Elise Martin",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Joe Suyama",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Steven Middle Name(s)/Initial(s) Albert",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Steven Anderson",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Sai H Bhatte",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Kenyon Bonner",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Chad Burton",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Micaela F Corn",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Heather Eng",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Bethany J Flage",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Jay Frerotte",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Goundappa K Balasubramani",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Catherine L Haggerty",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Joel Haight",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Lee H Harrison",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Amy Hartman",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Thomas Hitter",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Wendy C King",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Kate Ledger",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Jane W Marsh",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Margaret C McDonald",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Bethany R Miga",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Kimberly D Moses",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Anne W Newman",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Meg Ringler",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Mark S Roberts",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Terrie Sax",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Anantha Shekhar",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Matthew Sterne",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Tyler J Tenney",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Marian Vanek",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Alan Wells",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "Sally Wenzel",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "John V Williams",
-        "author_inst": "University of Pittsburgh"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.01.20.20243782",
     "rel_title": "COVID-19 Diagnostic Testing For All - Using Non-Dilutive Saliva Sample Collection, Stabilization and Ambient Transport Devices",
@@ -957359,6 +956367,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.01.24.21250416",
+    "rel_title": "Social, economic, and environmental factors influencing the basic reproduction number of COVID-19 across countries",
+    "rel_date": "2021-01-25",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.24.21250416",
+    "rel_abs": "ObjectiveTo assess whether the basic reproduction number (R0) of COVID-19 is different across countries and what national-level demographic, social, and environmental factors characterize initial vulnerability to the virus.\n\nMethodsWe fit logistic growth curves to reported daily case numbers, up to the first epidemic peak. This fitting estimates R0. We then use a generalized additive model to discern the effects, and include 5 random effect covariates to account for potential differences in testing and reporting that can bias the estimated R0.\n\nFindingsWe found that the mean R0 is 1.70 (S.D. 0.57), with a range between 1.10 (Ghana) and 3.52 (South Korea). We identified four factors-population between 20-34 years old (youth), population residing in urban agglomerates over 1 million (city), social media use to organize offline action (social media), and GINI income inequality-as having strong relationships with R0. An intermediate level of youth and GINI inequality are associated with high R0, while high city population and high social media use are associated with high R0. Environmental and climate factors were not found to have strong relationships with R0.\n\nConclusionStudies that aim to measure the effectiveness of interventions should account for the intrinsic differences between populations.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Jude Dzevela Kong",
+        "author_inst": "York University"
+      },
+      {
+        "author_name": "Edward Tekwa",
+        "author_inst": "Rutgers University"
+      },
+      {
+        "author_name": "Sarah Gignoux-Wolfsohn",
+        "author_inst": "6Smithsonian Environmental Research Center, Edgewater"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.01.22.21250304",
     "rel_title": "Rates of serious clinical outcomes in survivors of hospitalisation with COVID-19: a descriptive cohort study within the OpenSAFELY platform",
@@ -958952,37 +957987,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2021.01.25.427846",
-    "rel_title": "SARS-CoV-2 receptor binding mutations and antibody mediated immunity.",
-    "rel_date": "2021-01-25",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.25.427846",
-    "rel_abs": "SARS-CoV-2 mutations can impact infectivity, viral load, and overall morbidity/mortality during infection. In this analysis, we look at the mutational landscape of the SARS-CoV-2 receptor binding domain, a structure that is antigenic and allows for viral binding to the host. We analyze 104193 GISAID sequences acquired on October 15th, 2020 with a majority of sequences (96%) containing point mutations. We report high frequency mutations with improved binding affinity to ACE2 including S477N, N439K, V367F, and N501Y and address the potential impact of RBD mutations on antibody binding. The high frequency S477N mutation is present in 6.7% of all SARS-CoV-2 sequences, co-occurs with D614G, and is currently present in 14 countries. To address RBD-antibody interactions we take a subset of human derived antibodies and define their interacting residues using PDBsum. Our analysis shows that adaptive immunity against SARS-CoV-2 enlists broad coverage of the RBD suggesting that antibody mediated immunity should be sufficient to resolve infection in the presence of RBD point mutations that conserve structure.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Marios Mejdani",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Kiandokht Haddadi",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Chester Pham",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Radhakrishnan Mahadevan",
-        "author_inst": "University of Toronto"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "bioinformatics"
-  },
   {
     "rel_doi": "10.1101/2021.01.25.428125",
     "rel_title": "The CXCR6/CXCL16 axis links inflamm-aging to disease severity in COVID-19 patients",
@@ -959257,6 +958261,49 @@
     "type": "new results",
     "category": "genomics"
   },
+  {
+    "rel_doi": "10.1101/2021.01.24.427089",
+    "rel_title": "Meta-analysis reveals consistent immune response patterns in COVID-19 infected patients at single-cell resolution",
+    "rel_date": "2021-01-24",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.24.427089",
+    "rel_abs": "A number of single-cell RNA studies looking at the human immune response to the coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been recently published. However, the number of samples used in each individual study typically is small, moreover the technologies and protocols used in different studies vary, thus somewhat restricting the range of conclusions that can be made with high confidence. To better capture the cellular gene expression changes upon SARS-CoV-2 infection at different levels and stages of disease severity and to minimise the effect of technical artefacts, we performed meta-analysis of data from 9 previously published studies, together comprising 143 human samples, and a set of 16 healthy control samples (10X). In particular, we used generally accepted immune cell markers to discern specific cell subtypes and to look at the changes of the cell proportion over different disease stages and their consistency across the studies. While half of the observations reported in the individual studies can be confirmed across multiple studies, half of the results seem to be less conclusive. In particular, we show that the differentially expressed genes consistently point to upregulation of type I Interferon signal pathway and downregulation of the mitochondrial genes, alongside several other reproducibly consistent changes. We also confirm the presence of expanded B-cell clones in COVID-19 patients, however, no consistent trend in T-cell clonal expansion was observed.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Manik Garg",
+        "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)"
+      },
+      {
+        "author_name": "Xu Li",
+        "author_inst": "School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, P.R. China"
+      },
+      {
+        "author_name": "Pablo Andres Moreno Cortez",
+        "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)"
+      },
+      {
+        "author_name": "Irene Papatheodorou",
+        "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)"
+      },
+      {
+        "author_name": "Yuelong Shu",
+        "author_inst": "School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, P.R. China"
+      },
+      {
+        "author_name": "Alvis Brazma",
+        "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)"
+      },
+      {
+        "author_name": "Zhichao Miao",
+        "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI)"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "confirmatory results",
+    "category": "bioinformatics"
+  },
   {
     "rel_doi": "10.1101/2021.01.24.427965",
     "rel_title": "An Autoantigen Atlas from Human Lung HFL1 Cells Offers Clues to Neurological and Diverse Autoimmune Manifestations of COVID-19",
@@ -960382,57 +959429,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.01.21.21250258",
-    "rel_title": "Theoretical framework for retrospective studies of the effectiveness of SARS-CoV-2 vaccines",
-    "rel_date": "2021-01-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.21.21250258",
-    "rel_abs": "Observational studies of the effectiveness of vaccines to prevent COVID-19 are needed to inform real-world use. These are now in planning amid the ongoing rollout of SARS-CoV-2 vaccines globally. While traditional case-control (TCC) and test-negative design (TND) studies feature prominently among strategies used to assess vaccine effectiveness, such studies may encounter important threats to validity. Here we review the theoretical basis for estimation of vaccine direct effects under TCC and TND frameworks, addressing specific natural history parameters of SARS-CoV-2 infection and COVID-19 relevant to these designs. Bias may be introduced by misclassification of cases and controls, particularly when clinical case criteria include common, non-specific indicators of COVID-19. When using diagnostic assays with high analytical sensitivity for SARS-CoV-2 detection, individuals testing positive may be counted as cases even if their symptoms are due to other causes. The TCC may be particularly prone to confounding due to associations of vaccination with healthcare-seeking behavior or risk of infection. The TND reduces but may not eliminate this confounding, for instance if individuals who receive vaccination seek care or testing for less-severe infection. These circumstances indicate the two study designs cannot be applied naively to datasets gathered through public health surveillance or administrative sources. We suggest practical strategies to reduce bias in vaccine effectiveness estimates at the study design and analysis stages.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Joseph A Lewnard",
-        "author_inst": "University of California Berkeley"
-      },
-      {
-        "author_name": "Manish M Patel",
-        "author_inst": "CDC"
-      },
-      {
-        "author_name": "Nicholas P Jewell",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Jennifer R Verani",
-        "author_inst": "CDC"
-      },
-      {
-        "author_name": "Miwako Kobayashi",
-        "author_inst": "CDC"
-      },
-      {
-        "author_name": "Mark Tenforde",
-        "author_inst": "CDC"
-      },
-      {
-        "author_name": "Natalie E Dean",
-        "author_inst": "University of Florida"
-      },
-      {
-        "author_name": "Benjamin J Cowling",
-        "author_inst": "University of Hong Kong"
-      },
-      {
-        "author_name": "Benjamin A Lopman",
-        "author_inst": "Emory University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.01.21.21250237",
     "rel_title": "Agent-Based Simulation of Covid-19 Vaccination Policies in CovidSIMVL",
@@ -960739,6 +959735,77 @@
     "type": "new results",
     "category": "bioinformatics"
   },
+  {
+    "rel_doi": "10.1101/2021.01.22.427737",
+    "rel_title": "Human embryonic stem cell-derived cardiomyocytes express SARS-CoV-2 host entry proteins: screen to identify inhibitors of infection",
+    "rel_date": "2021-01-22",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.22.427737",
+    "rel_abs": "Patients with cardiovascular comorbidities are more susceptible to severe infection with SARS-CoV-2, known to directly cause pathological damage to cardiovascular tissue. We outline a screening platform using human embryonic stem cell-derived cardiomyocytes, confirmed to express the protein machinery critical for SARS-CoV-2 infection, and a pseudotyped virus system. The method has allowed us to identify benztropine and DX600 as novel inhibitors of SARS-CoV-2 infection.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Thomas L Williams",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Maria T Colzani",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Robyn GC Macrae",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Emma L Robinson",
+        "author_inst": "University of Colorado Denver"
+      },
+      {
+        "author_name": "Stuart Bloor",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Edward JD Greenwood",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Jun Ru Zhan",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Gregory Strachan",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Rhoda E Kuc",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Duuamene Nyimanu",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Janet J Maguire",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Paul J Lehner",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Sanjay Sinha",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Anthony P Davenport",
+        "author_inst": "University of Cambridge"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "pharmacology and toxicology"
+  },
   {
     "rel_doi": "10.1101/2021.01.22.427567",
     "rel_title": "Bispecific antibody prevents SARS-CoV-2 escape and protects mice from disease",
@@ -962008,57 +961075,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "anesthesia"
   },
-  {
-    "rel_doi": "10.1101/2021.01.17.21249993",
-    "rel_title": "Modelling the Long-Term Effects of Covid-19 Cancer Services Disruption on Patient Outcome in Scotland",
-    "rel_date": "2021-01-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.17.21249993",
-    "rel_abs": "BackgroundModelling the long-term effects of disruption of cancer services and minimising any excess cancer mortality due to the Covid-19 pandemic is of great importance. Here we adapted a stage-shift model to inform service planning decisions within NHS Scotland for the   Detect Cancer Early tumours, breast, colorectal and lung cancer which represent 46% of all cancers diagnosed in Scotland.\n\nMethods & DataLung, colorectal and breast cancer incidence data for years 2017-18 were obtained from Public Health Scotland Cancer Quality Performance Indicators (QPI), to define a baseline scenario. The most current stage-specific 5-year survival data came from 2009-2014 national cancer registry and South East Scotland Cancer Network (SCAN) QPI audit datasets. The Degeling et al., inverse stage-shift model was adapted to estimate changes in stage at diagnosis, excess mortality and life-years lost from delays to diagnosis and treatment due to Covid-19-related health services disruption. Three and 6-month periods of disruption were simulated to demonstrate the model predictions.\n\nResultsApproximately, 1-9% reductions in stage I/II presentations leading up to 2-10% increases in stage III/IV presentations are estimated across the three cancer types. A 6-month period of service disruption is predicted to lead to excess deaths at 5 years of 32.5 (31.1, 33.9) per 1000 cases for lung cancer, 16.5 (7.9, 24.3) for colorectal cancer and 31.6 (28.5, 34.4) for breast cancer.\n\nConclusionsDisruption of cancer diagnostic services can lead to significant excess deaths in following years. Increasing diagnostic and capacity for cancer services to deal with the backlog of care are needed. Real time monitoring of incidence and referral patterns over the disruption and post-disruption period to reduce excess deaths including more rapid incidence data by stage and other key tumour/clinical characteristics at presentation for key cancer cases (on a quarterly basis). Real time monitoring in cancer care and referral patterns should help inform what type of interventions are needed to reduce excess mortality and whether different population subgroups require public health messaging campaigns. Specific mitigation measures can be the subject of additional modelling analysis to assess the benefits and inform service planning decision making.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Jonine Figueroa",
-        "author_inst": "University of Edinburgh"
-      },
-      {
-        "author_name": "Ewan Gray",
-        "author_inst": "University of Edinburgh"
-      },
-      {
-        "author_name": "Yasuko Maeda",
-        "author_inst": "University of Edinburgh"
-      },
-      {
-        "author_name": "Peter S Hall",
-        "author_inst": "University of Edinburgh"
-      },
-      {
-        "author_name": "Melanie Mackean",
-        "author_inst": "Edinburgh Cancer Centre, Western General Hospital"
-      },
-      {
-        "author_name": "Kenneth Elder",
-        "author_inst": "Edinburgh Cancer Center, Western General Hospital"
-      },
-      {
-        "author_name": "Farhat Din",
-        "author_inst": "University of Edinburgh"
-      },
-      {
-        "author_name": "Malcolm G Dunlop",
-        "author_inst": "Institute of Genetics and Molecular Medicine"
-      },
-      {
-        "author_name": "David Weller",
-        "author_inst": "University of Edinburgh"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.01.17.21249990",
     "rel_title": "Population-based seroprevalence of SARS-CoV-2 antibodies in a high-altitude setting in Peru",
@@ -962269,6 +961285,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.01.18.21250025",
+    "rel_title": "COVID-19 in 823 Transplant patients: A Systematic Scoping Review",
+    "rel_date": "2021-01-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.18.21250025",
+    "rel_abs": "BackgroundManagement of COVID-19 in transplant patients is a big challenge. Data on immunosuppression management, clinical picture, and outcomes are lacking.\n\nObjectivesTo summarize the current literature on COVID-19 in transplant patients especially the data regarding the immunosuppression protocols, clinical presentation, and outcomes.\n\nSearch strategyA systematic search of MEDLINE, EBSCO, CENTRAL, CINAHL, LitCovid, Web of Science, and Scopus electronic databases. The references of the relevant studies were also searched. The search was last updated on June 3, 2020.\n\nSelection CriteriaPrimary reports of solid organ transplant patients who developed COVID-19. An overlap of cases in different reports was checked.\n\nData collection and analysisA descriptive summary of immunosuppression therapy (before and after COVID-19), clinical presentation (symptoms, imaging, laboratory, and disease severity), management (oxygen therapy, antiviral, and antibacterial), major outcomes (Intensive care admission, invasive mechanical ventilation, acute kidney injury), and mortality.\n\nMain resultsWe identified 74 studies reporting 823 cases of solid organ transplantation with COVID-19. Among 372 patients, 114 (30.6%) were mild COVID-19, 101 (27.2%) moderate, and 157 (42.2%) severe or critical.\n\nMajor outcomes included intensive care unit admission, invasive ventilation, and acute kidney injury, which occurred in 121 (14.7%), 97 (11.8%), and 63 (7.7%) of patients, respectively. Mortality was reported in 160 (19.4%) patients. Missing individual data hindered making clinical correlations.\n\nConclusionCOVID-19 in solid organ transplant patients probably has a more disease severity, worse major outcomes (Intensive care admission, invasive ventilation, acute kidney injury), and higher mortality than in non-transplant patients.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Moataz Maher Emara",
+        "author_inst": "Department of Anesthesiology and Intensive Care and Pain medicine, Mansoura University, Egypt"
+      },
+      {
+        "author_name": "Mahmoud Elsedeiq",
+        "author_inst": "Department of Anesthesiology and Intensive Care and Pain Medicine, Mansoura University, Egypt"
+      },
+      {
+        "author_name": "Mohamed Elmorshedi",
+        "author_inst": "Department of Anesthesiology and Intensive Care and Pain Medicine, Mansoura University, Egypt"
+      },
+      {
+        "author_name": "Hamed Neamatallah",
+        "author_inst": "Department of Anesthesiology and Intensive Care and Pain Medicine, Mansoura University, Egypt"
+      },
+      {
+        "author_name": "Mostafa Abdelkhalek",
+        "author_inst": "Department of Anesthesiology and Intensive Care and Pain Medicine, Mansoura University, Egypt"
+      },
+      {
+        "author_name": "Amr Yassen",
+        "author_inst": "Department of Anesthesiology and Intensive Care and Pain Medicine, Mansoura University, Egypt"
+      },
+      {
+        "author_name": "Ashraf Nabhan",
+        "author_inst": "Department of Obstetrics and Gynecology, Faculty of Medicine, Ain Shams University, Cairo, Egypt"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "transplantation"
+  },
   {
     "rel_doi": "10.1101/2021.01.18.21250050",
     "rel_title": "Analysis of communities of countries with similar dynamics of the COVID-19 pandemic evolution",
@@ -963386,53 +962445,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.01.18.21250071",
-    "rel_title": "The impacts of COVID-19 vaccine timing, number of doses, and risk prioritization on mortality in the US",
-    "rel_date": "2021-01-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.18.21250071",
-    "rel_abs": "As COVID-19 vaccination begins worldwide, policymakers face critical trade-offs. Using a mathematical model of COVID-19 transmission, we find that timing of the rollout is expected to have a substantially greater impact on mortality than risk-based prioritization and uptake and that prioritizing first doses over second doses may be life saving.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Xutong Wang",
-        "author_inst": "University of Texas at Austin"
-      },
-      {
-        "author_name": "Zhanwei Du",
-        "author_inst": "University of Texas at Austin"
-      },
-      {
-        "author_name": "Kaitlyn Johnson",
-        "author_inst": "University of Texas at Austin"
-      },
-      {
-        "author_name": "Remy Pasco",
-        "author_inst": "University of Texas at Austin"
-      },
-      {
-        "author_name": "Spencer Fox",
-        "author_inst": "University of Texas at Austin"
-      },
-      {
-        "author_name": "Michael Lachmann",
-        "author_inst": "Santa Fe Institute"
-      },
-      {
-        "author_name": "Jason S McLellan",
-        "author_inst": "University of Texas at Austin"
-      },
-      {
-        "author_name": "Lauren Ancel Meyers",
-        "author_inst": "The University of Texas at Austin"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.01.18.21250032",
     "rel_title": "Remote care for mental health: qualitative study with service users, carers and staff during the COVID-19 pandemic",
@@ -963727,6 +962739,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "nephrology"
   },
+  {
+    "rel_doi": "10.1101/2021.01.18.21249976",
+    "rel_title": "Covid-19 respiratory protection: the filtration efficiency assessment of decontaminated FFP2 masks responding to associated shortages",
+    "rel_date": "2021-01-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.18.21249976",
+    "rel_abs": "During the Covid-19 pandemic, healthcare workers were extremely vulnerable to infection with the virus and needed continuous protection. One of the most effective and widely used means of protection was the FFP2 respirator. Unfortunately, this crisis created a shortage of these masks, prompting hospitals to explore opportunities to reuse them after decontamination.\n\nAn approach for assessing the filtration efficiency of decontaminated FFP2 masks has been proposed and applied to evaluate the possibilities of their safe reuse. The decontamination processes adopted are those based on moist heat or hydrogen peroxide. The approach introduces efficiency measures that define the filtration and protection capacity of the masks, which characterize both chemical and structural changes, and encompasses many techniques including scanning electron microscopy (SEM), Fourier transforms infrared spectroscopy (FTIR), and thermogravimetric analysis (TGA). The test protocol was applied to mask samples that had endured different decontamination cycles and the results of their efficiency measures were compared to brand-new masks performances.\n\nThe main result was that chemical and structural characterization of the decontaminated masks have shown no substantial change or deformation of their filter media structures. Indeed, the respiratory resistance test has shown that the results of both the FFP2 masks that have undergone a hydrogen peroxide disinfection cycle or a steam autoclave cycle remained constant with a small variation of 10 Pa from the EN149 standard. The chemical characterization, on the other hand, has shown that the filter media of the decontaminated masks remains unchanged, with no detectable chemical derivatives in its constituents.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "benboubker moussa",
+        "author_inst": "USMBA,Fez,Morocco"
+      },
+      {
+        "author_name": "Bouchra Omokhtar",
+        "author_inst": "USMBA,Fez,Morocco"
+      },
+      {
+        "author_name": "Fouzia hmami",
+        "author_inst": "USMBA,Fez,Morocco"
+      },
+      {
+        "author_name": "Khalil El mabrouk",
+        "author_inst": "UEMF,Fez,Morocco"
+      },
+      {
+        "author_name": "Leena El alami",
+        "author_inst": "USMBA,Fez,Morocco"
+      },
+      {
+        "author_name": "Btissam Arhoune",
+        "author_inst": "USMBA,Fez,Morocco"
+      },
+      {
+        "author_name": "Mohammed Faouzi Belahcen",
+        "author_inst": "USMBA,Fez,Morocco"
+      },
+      {
+        "author_name": "Ahmed Aboutajeddine",
+        "author_inst": "USMBA,Fez,Morocco"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "occupational and environmental health"
+  },
   {
     "rel_doi": "10.1101/2021.01.18.21249433",
     "rel_title": "The burden of nosocomial covid-19: results from the Wales multi-centre retrospective observational study of 2518 hospitalised adults.",
@@ -965356,45 +964415,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2021.01.20.21250150",
-    "rel_title": "Exploring overcrowding trends in an inner city emergence department in the UK before and during COVID-19 epidemic",
-    "rel_date": "2021-01-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.20.21250150",
-    "rel_abs": "BackgroundWe compared impact of three pre-COVID-19 interventions and of the COVID-19 UK-epidemic and the first UK national lockdown on overcrowding within University College London Hospital Emergency Department (UCLH ED). The three interventions: target the influx of patients at ED (A), reduce the pressure on in-patients beds (B) and improve ED processes to improve the flow of patents out from ED (C).\n\nMethodsWe analysed the change in overcrowding metrics (daily attendances, the proportion of people leaving within four hours of arrival (four-hours target) and the reduction in overall waiting time) across three analysis. The first analysis used data 01/04/2017-31/12-2019 to calculate changes over a period of six months before and after the start of interventions A-C. The second and third analyses focused on evaluating the impact of the COVID-19 epidemic, comparing the first 10 months in 2020 and 2019, and of the first national lockdown (23/03/2020-31/05/2020).\n\nResultsPre-COVID-19 all interventions led to small reductions in waiting time (17%, p<0.001 for A and C;9%, p=0.322 for B) but also to a small decrease in the number of patients leaving within four hours of arrival (6.6%,7.4%,6.2% respectively A-C,p<0.001).\n\nIn presence of the COVID-19 pandemic, attendance and waiting time were reduced (40% and 8%;p<0.001), and the number of people leaving within four hours of arrival was increased (6%,p<0.001). During the first lockdown, there was 65% reduction in attendance, 22% reduction in waiting time and 8% increase in number of people leaving within 4 hours of arrival (p<0.001). Crucially, when the lockdown was lifted, there was an increase (6.5%,p<0.001) in the percentage of people leaving within four hours, together with a larger (12.5%,p<0.001) decrease in waiting time. This occurred despite the increase of 49.6%(p<0.001) in attendance after lockdown ended.\n\nConclusionsThe mixed results pre-COVID-19 (significant improvements in waiting time with some interventions but not improvement in the four-hours target), may be due to a  spill-over effect where clogging up one part of the ED system affects other parts. Hence multifaceted interventions and a system-wide approach to improve the pathway of flow through the ED system is necessary.\n\nDuring 2020 and in presence of the COVID-19 epidemic, a shift in public behaviour with anxiety over attending hospitals and higher use of virtual consultations, led to notable drop in UCLH ED attendance and consequential curbing of overcrowding.\n\nImportantly, once the lockdown was lifted, although there was an increase in arrivals at UCLH ED, overcrowding metrics were reduced. Thus, the combination of shifted public behaviour and the restructuring changes during COVID-19 epidemic, maybe be able to curb future ED overcrowding, but longer timeframe analysis is required to confirm this.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Jasmina Panovska-Griffiths",
-        "author_inst": "UCL"
-      },
-      {
-        "author_name": "Jack Ross",
-        "author_inst": "University College London NHS Foundation Trust"
-      },
-      {
-        "author_name": "Samer Elkhodair",
-        "author_inst": "University College London NHS Foundation Trust"
-      },
-      {
-        "author_name": "Christopher Baxter-Derrington",
-        "author_inst": "University College London NHS Foundation Trust"
-      },
-      {
-        "author_name": "Chris Laing",
-        "author_inst": "University College London NHS Foundation Trust"
-      },
-      {
-        "author_name": "Rosalind Raine",
-        "author_inst": "University College London NHS Foundation Trust"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "emergency medicine"
-  },
   {
     "rel_doi": "10.1101/2021.01.19.21250128",
     "rel_title": "Sleep in Frontline Healthcare Workers on Social Media During the COVID-19 Pandemic",
@@ -965717,6 +964737,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.01.19.21250137",
+    "rel_title": "A Label-Free SARS-CoV-2 Surrogate Virus Neutralization Test and a Longitudinal Study of Antibody Characteristics in COVID-19 Patients",
+    "rel_date": "2021-01-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.19.21250137",
+    "rel_abs": "Background. The laboratory-based methods to measure the SARS-CoV-2 humoral response include virus neutralization tests (VNTs) to determine antibody neutralization potency. For ease of use and universal applicability, surrogate virus neutralization tests (sVNTs) based on antibody-mediated blockage of molecular interactions have been proposed. Methods. A surrogate virus neutralization test established on a label-free immunoassay platform (LF-sVNT). The LF-sVNT analyzes the binding ability of RBD to ACE2 after neutralizing RBD with antibodies in serum. Results. The LF-sVNT neutralizing antibody titers (IC50) were determined from serum samples (n=246) from COVID-19 patients (n=113), as well as the IgG concentrations and the IgG avidity indices. Although there is variability in the kinetics of the IgG concentrations and neutralizing antibody titers between individuals, there is an initial rise, plateau and then in some cases a gradual decline at later timepoints after 40 days post-symptom onset. The IgG avidity indices, in the same cases, plateau after the initial rise and did not show a decline. Conclusions. The LF-sVNT can be a valuable tool in clinical laboratories for the assessment of the presence of neutralizing antibodies to COVID-19. This study is the first to provide longitudinal neutralizing antibody titers beyond 200 days post-symptom onset. Despite the decline of IgG concentration and neutralizing antibody titer, IgG avidity index increases, reaches a plateau and then remains constant up to 8 months post-infection. The decline of antibody neutralization potency can be attributed to the reduction in antibody quantity rather than the deterioration of antibody avidity, a measure of antibody quality.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Yiqi Ruben Luo",
+        "author_inst": "University of California San Francisco"
+      },
+      {
+        "author_name": "Cassandra Yun",
+        "author_inst": "University of California San Francisco"
+      },
+      {
+        "author_name": "Indrani Chakraborty",
+        "author_inst": "Gator Bio"
+      },
+      {
+        "author_name": "Alan H.B. Wu",
+        "author_inst": "University of California San Francisco"
+      },
+      {
+        "author_name": "Kara Lake Lynch",
+        "author_inst": "University of California San Francisco"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.01.19.21250114",
     "rel_title": "Modeling the population effects of epitope specific escape mutations in SARS-CoV-2 to guide vaccination strategies",
@@ -967182,45 +966237,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pathology"
   },
-  {
-    "rel_doi": "10.1101/2021.01.16.21249925",
-    "rel_title": "Correlates of and changes in aerobic physical activity and strength training before and after the onset of COVID-19 pandemic in the UK. Findings from the HEBECO study.",
-    "rel_date": "2021-01-18",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.16.21249925",
-    "rel_abs": "ObjectivesUnderstanding changes in moderate to vigorous aerobic physical activity (MVPA) and strength training (MSA) from before to after (pre-/post-) the onset of the Covid-19 pandemic in the UK (first lockdown) and their correlates can inform interventions.\n\nMethodsCross-sectional analysis of retrospective and concurrent data on MVPA/MSA pre- and post-Covid-19 (until 14th June 2020) among 2,657 UK adults. The associations between socio-demographic and health characteristics, MVPA/MSA pre-Covid-19, living and exercise conditions and meeting WHO recommended levels for MVPA/MSA/both (vs meeting neither), and changes in MVPA/MSA from pre-to post-Covid-19 following stratification for pre-Covid-19 MVPA/MSA levels were evaluated.\n\nResultsA third of adults maintained (30.4%), decreased (36.2%) or increased (33.4%) their MVPA levels post-Covid-19. For MSA, the percentages were 61.6%, 18.2%, and 20.2%, respectively. MVPA increased or decreased by an average of 150min/week, and MSA by 2 days/week. Meeting both MSA+MVPA recommendations during lockdown (vs. meeting neither) was positively associated with meeting MVPA+MSA pre-lockdown (aOR=16.11,95%CI=11.24-23.07), and post-16-years of age education (aOR=1.57,1.14-2.17), and negatively associated with being obese (aOR=0.49,0.33-0.73), older age (65+ vs [&le;]34; aOR=.53.32-.87), and annual household income <50.000GBP (vs [&ge;]50.000GBP; aOR=0.65,0.46-0.91). The odds for decreasing MVPA were significantly lower for white ethnicity, post-16-years of age education, access to garden/balcony, and higher for those who were in total isolation. The odds for decreasing MSA were significantly higher for those who were overweight or obese.\n\nConclusionAerobic and strength training were differently impacted during the first UK lockdown, with poorer outcomes associated with older age, lower education, and higher body mass index.\n\nO_TEXTBOXWhat are the new findingsO_LIAt the start of the Covid-19 pandemic, a third of UK adults decreased and a third increased moderate-to-vigorous physical activity; the corresponding proportions for muscle strength training were 18% and 20%.\nC_LIO_LIOlder adults were more likely to maintain inactivity from before to start of the pandemic.\nC_LIO_LIAdults with higher body mass index were at risk of not meeting WHO recommendations for weekly levels of strength and aerobic training, and at decreasing muscle strength training in this period.\nC_LIO_LIThose with lower incomes, no post-16-years of age education, ethnic minority background and living in total isolation had poorer physical activity outcomes.\nC_LI\n\nC_TEXTBOX",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Aleksandra Herbec",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Verena Schneider",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Abi Fisher",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Dimitra Kale",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Lion Shahab",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Phillippa Lally",
-        "author_inst": "University College London"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.01.16.426965",
     "rel_title": "Fluorescent Glycan Fingerprinting of SARS2 Spike Proteins",
@@ -967743,6 +966759,45 @@
     "type": "new results",
     "category": "genetics"
   },
+  {
+    "rel_doi": "10.1101/2021.01.18.427092",
+    "rel_title": "A national analysis of trends in COVID-19 infection and clinical management in Veterans Health Administration medical facilities",
+    "rel_date": "2021-01-18",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.18.427092",
+    "rel_abs": "OBJECTIVEWe explored longitudinal trends in sociodemographic characteristics, reported symptoms, laboratory findings, pharmacological and non-pharmacological treatment, comorbidities, and 30-day in-hospital mortality among hospitalized patients with coronavirus disease 2019 (COVID-19).\n\nMETHODSThis retrospective cohort study included 43,267 patients diagnosed with COVID-19 in the Veterans Health Administration between 03/01/20 and 08/31/20 and followed until 09/30/20. We focused our analysis on patients that were subsequently hospitalized, and categorized them into groups based on the month of hospitalization. We summarized our findings through descriptive statistics. We used a nonparametric rank-sum test for trend to examine any differences in the distribution of our study variables across the six months.\n\nRESULTSDuring our study period, 8,240 patients were hospitalized, and 1,081 (13.1%) died within 30 days of admission. Hospitalizations increased over time, but the proportion of patients that died consistently declined from March (N=221/890, 24.8%) to August (N=111/1,396, 8.0%). Patients hospitalized in March compared to August were younger on average, mostly black, and symptomatic. They also had a higher frequency of baseline comorbidities, including hypertension and diabetes, and were more likely to present with abnormal laboratory findings including low lymphocyte counts and elevated creatinine. Lastly, receipt of mechanical ventilation and Hydroxychloroquine declined from March to August, while treatment with Dexamethasone and Remdesivir increased.\n\nCONCLUSIONWe found evidence of declining COVID-19 severity and fatality over time within a national health care system.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Maya Aboumrad",
+        "author_inst": "White River Junction VA Medical Center"
+      },
+      {
+        "author_name": "Brian Shiner",
+        "author_inst": "White River Junction VA Medical Center"
+      },
+      {
+        "author_name": "Natalie Riblet",
+        "author_inst": "White River Junction VA Medical Center"
+      },
+      {
+        "author_name": "Hugh Huizenga",
+        "author_inst": "White River Junction VA Medical Center"
+      },
+      {
+        "author_name": "Nabin Neupane",
+        "author_inst": "White River Junction VA Medical Center"
+      },
+      {
+        "author_name": "Yinong Young-Xu",
+        "author_inst": "White River Junction VA Medical Center"
+      }
+    ],
+    "version": "1",
+    "license": "cc0",
+    "type": "new results",
+    "category": "scientific communication and education"
+  },
   {
     "rel_doi": "10.1101/2021.01.15.21249691",
     "rel_title": "SARS-CoV-2 viral load distribution in different patient populations and age groups reveals that viral loads increase with age.",
@@ -969707,145 +968762,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.01.14.21249801",
-    "rel_title": "Factor V is an immune inhibitor that is expressed at increased levels in leukocytes of patients with severe Covid-19",
-    "rel_date": "2021-01-15",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.14.21249801",
-    "rel_abs": "Severe Covid-19 is associated with elevated plasma Factor V (FV) and increased risk of thromboembolism. We report that neutrophils, T regulatory cells (Tregs), and monocytes from patients with severe Covid-19 express FV, and expression correlates with T cell lymphopenia. In vitro full length FV, but not FV activated by thrombin cleavage, suppresses T cell proliferation. Increased and prolonged FV expression by cells of the innate and adaptive immune systems may contribute to lymphopenia in severe Covid-19. Activation by thrombin destroys the immunosuppressive properties of FV. Anticoagulation in Covid-19 patients may have the unintended consequence of suppressing the adaptive immune system.",
-    "rel_num_authors": 31,
-    "rel_authors": [
-      {
-        "author_name": "Jun Wang",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Prasanti Kotagiri",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Paul Lyons",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Federica Mescia",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Laura Bergamaschi",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Lorinda Turner",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Rafia Al-Lamki",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Michael D Morgan",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Fernando J Calero-Nieto",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Karsten Bach",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Nicole Mende",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Nicola K Wilson",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Emily R Watts",
-        "author_inst": "University of Edinburgh"
-      },
-      {
-        "author_name": "- Cambridge Institute of Therapeutic Immunology and Infectious Disease - NIHR Covid BioResource",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Patrick Chinnery",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Nathalie Kingston",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Sofia Papadia",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Kathleen Stirrups",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Neil Walker",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Ravindra K Gupta",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Mark Toshner",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Michael Weekes",
-        "author_inst": "Cambridge University"
-      },
-      {
-        "author_name": "James A Nathan",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Sarah Walmsley",
-        "author_inst": "University of Edinburgh"
-      },
-      {
-        "author_name": "Willem Hendrik Ouwehand",
-        "author_inst": "Prof"
-      },
-      {
-        "author_name": "Mary Kasanicki",
-        "author_inst": "Cambridge University Hospitals"
-      },
-      {
-        "author_name": "Berthold Gottgens",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "John C Marioni",
-        "author_inst": "EMBL-EBI"
-      },
-      {
-        "author_name": "Smith GC Smith",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Jordan S Pober",
-        "author_inst": "Yale University"
-      },
-      {
-        "author_name": "John R Bradley",
-        "author_inst": "University of Cambridge"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.01.15.21249879",
     "rel_title": "Anticipating the curve: can online symptom-based data reflect COVID-19 case activity in Ontario, Canada?",
@@ -970244,6 +969160,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.01.14.21249853",
+    "rel_title": "The Use of Procalcitonin as an Antimicrobial Stewardship Tool and a Predictor of Disease Severity in COVID-19",
+    "rel_date": "2021-01-15",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.14.21249853",
+    "rel_abs": "In our study, procalcitonin was associated with both antibiotic use and duration in patients with COVID-19, as well as established biochemical markers of COVID-19 disease severity and oxygen requirement, suggesting a potential role for procalcitonin in COVID-19 antimicrobial stewardship.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "George Peter Drewett",
+        "author_inst": "Austin Health"
+      },
+      {
+        "author_name": "Olivia C Smibert",
+        "author_inst": "Austin Health"
+      },
+      {
+        "author_name": "Natasha E Holmes",
+        "author_inst": "Austin Health"
+      },
+      {
+        "author_name": "Jason A Trubiano",
+        "author_inst": "Austin Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.01.14.21249836",
     "rel_title": "Persistently increased systemic ACE2 activity and Furin levels are associated with increased inflammatory response in smokers with SARS-CoV-2 COVID-19",
@@ -971661,173 +970608,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.01.11.20248765",
-    "rel_title": "Early immune pathology and persistent dysregulation characterise severe COVID-19",
-    "rel_date": "2021-01-15",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.11.20248765",
-    "rel_abs": "In a study of 207 SARS-CoV2-infected individuals with a range of severities followed over 12 weeks from symptom onset, we demonstrate that an early robust bystander CD8 T cell immune response, without systemic inflammation, is characteristic of asymptomatic or mild disease. Those presenting to hospital had delayed bystander responses and systemic inflammation already evident at around symptom onset. Such early evidence of inflammation suggests immunopathology may be inevitable in some individuals, or that preventative intervention might be needed before symptom onset. Viral load does not correlate with the development of this pathological response, but does with its subsequent severity. Immune recovery is complex, with profound persistent cellular abnormalities correlating with a change in the nature of the inflammatory response, where signatures characteristic of increased oxidative phosphorylation and reactive-oxygen species-associated inflammation replace those driven by TNF and IL-6. These late immunometabolic inflammatory changes and unresolved immune defects may have clinical implications.",
-    "rel_num_authors": 38,
-    "rel_authors": [
-      {
-        "author_name": "Laura Bergamaschi",
-        "author_inst": "Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK"
-      },
-      {
-        "author_name": "Federica Mescia",
-        "author_inst": "Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK"
-      },
-      {
-        "author_name": "Lorinda Turner",
-        "author_inst": "Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK"
-      },
-      {
-        "author_name": "Aimee Hanson",
-        "author_inst": "Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK"
-      },
-      {
-        "author_name": "Prasanti Kotagiri",
-        "author_inst": "Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK"
-      },
-      {
-        "author_name": "Benjamin J. Dunmore",
-        "author_inst": "Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK"
-      },
-      {
-        "author_name": "Helene Ruffieux",
-        "author_inst": "MRC Biostatistics Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK"
-      },
-      {
-        "author_name": "Aloka DeSa",
-        "author_inst": "Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK"
-      },
-      {
-        "author_name": "Oisin Huhn",
-        "author_inst": "Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK"
-      },
-      {
-        "author_name": "Michael D Morgan",
-        "author_inst": "Cancer Research UK, Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK"
-      },
-      {
-        "author_name": "Pehuen Pereyra Gerber",
-        "author_inst": "Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK"
-      },
-      {
-        "author_name": "Mark R. Wills",
-        "author_inst": "Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK"
-      },
-      {
-        "author_name": "Stephen Baker",
-        "author_inst": "Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK"
-      },
-      {
-        "author_name": "Fernando J Calero Nieto",
-        "author_inst": "Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK"
-      },
-      {
-        "author_name": "Rainer Doffinger",
-        "author_inst": "Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK"
-      },
-      {
-        "author_name": "Gordon Dougan",
-        "author_inst": "Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK"
-      },
-      {
-        "author_name": "Anne Elmer",
-        "author_inst": "Cambridge Clinical Research Centre, NIHR Clinical Research Facility, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge CB2 "
-      },
-      {
-        "author_name": "Ian G Goodfellow",
-        "author_inst": "Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK"
-      },
-      {
-        "author_name": "Ravindra K. Gupta",
-        "author_inst": "Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK"
-      },
-      {
-        "author_name": "Myra Hosmillo",
-        "author_inst": "Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK"
-      },
-      {
-        "author_name": "Kelvin Hunter",
-        "author_inst": "Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK"
-      },
-      {
-        "author_name": "Nathalie Kingston",
-        "author_inst": "Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK"
-      },
-      {
-        "author_name": "Paul J. Lehner",
-        "author_inst": "Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK"
-      },
-      {
-        "author_name": "Nicholas J. Matheson",
-        "author_inst": "Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK"
-      },
-      {
-        "author_name": "Jeremy K. Nicholson",
-        "author_inst": "The Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Murdoch, Western Australia WA 6150, Australia"
-      },
-      {
-        "author_name": "Anna M. Petrunkina",
-        "author_inst": "Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK"
-      },
-      {
-        "author_name": "Sylvia Richardson",
-        "author_inst": "MRC Biostatistics Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK"
-      },
-      {
-        "author_name": "Caroline Saunders",
-        "author_inst": "Cambridge Clinical Research Centre, NIHR Clinical Research Facility, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge CB2 "
-      },
-      {
-        "author_name": "James E.D. Thaventhiran",
-        "author_inst": "Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK"
-      },
-      {
-        "author_name": "Erik J.M. Toonen",
-        "author_inst": "R&D Department, Hycult Biotech, 5405 PD Uden, The Netherlands"
-      },
-      {
-        "author_name": "Michael P. Weekes",
-        "author_inst": "Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK"
-      },
-      {
-        "author_name": "- CambridgeInstituteofTherapeuticImmunologyandInfectiousDisease-NationalInstituteofHealthResearch(CITI",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Berthold Gottgens",
-        "author_inst": "Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK"
-      },
-      {
-        "author_name": "Mark Toshner",
-        "author_inst": "Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK"
-      },
-      {
-        "author_name": "Christoph Hess",
-        "author_inst": "Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK"
-      },
-      {
-        "author_name": "John R. Bradley",
-        "author_inst": "Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK"
-      },
-      {
-        "author_name": "Paul A. Lyons",
-        "author_inst": "Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK"
-      },
-      {
-        "author_name": "Kenneth G.C. Smith",
-        "author_inst": "Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.01.11.20248882",
     "rel_title": "Modelling the effect of lockdown",
@@ -972250,6 +971030,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
+  {
+    "rel_doi": "10.1101/2021.01.11.21249324",
+    "rel_title": "A national survey of potential acceptance of COVID-19 vaccines in healthcare workers in Egypt",
+    "rel_date": "2021-01-15",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.11.21249324",
+    "rel_abs": "BackgroundSince the start of COVID-19 outbreak investigators are competing to develop and exam vaccines against COVID-19. It would be valuable to protect the population especially health care employees from COVID-19 infection. The success of COVID-19 vaccination programs will rely heavily on public willingness to accept the vaccine.\n\nAimsThis study aimed to describe the existing COVID-19 vaccine approval landscape among the health care providers and to identify the most probable cause of agreement or disagreement of COVID-19 vaccine.\n\nMethodsA cross-sectional online survey was done.\n\nResultsThe present study included 496 health care employees, 55% were at age group from 18-45 years old. History of chronic diseases was recorded in 40.4%, and definite history of drug/food allergy in 10.1%. Only 13.5% totally agree to receive the vaccine, 32.4% somewhat agree and 40.9% disagreed to take the vaccine. Causes of disagreement were none safety, fear of genetic mutation and recent techniques and believe that the vaccine is not effective (57%, 20.2%, 17.7% and 16.6% respectively). The most trusted vaccine was the mRNA based vaccine. The age of health care employees and the presence of comorbidities or chronic diseases were the main factors related to COVID-19 acceptance (P<0.001 and 0.02 respectively).\n\nConclusionVaccine hesitancy is not uncommon in healthcare employees in Egypt and this may be an alarming barrier of vaccine acceptance in the rest of population. There is an urgent need to start campaigns to increase the awareness of the vaccine importance.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Aliae AR Mohamed-Hussein",
+        "author_inst": "Faculty of medicine, Assiut University"
+      },
+      {
+        "author_name": "islam g sayed",
+        "author_inst": "Aswan University"
+      },
+      {
+        "author_name": "nahed Makhlouf",
+        "author_inst": "Faculty of medicine, Assiut University"
+      },
+      {
+        "author_name": "Hoda Makhlouf",
+        "author_inst": "Assiut Faculty of Medicine"
+      },
+      {
+        "author_name": "Howaida Abd El Aal",
+        "author_inst": "Assiut Faculty of Nursing"
+      },
+      {
+        "author_name": "Karima Kholief",
+        "author_inst": "Assiut Faculty of Medicine"
+      },
+      {
+        "author_name": "Mahmoud M Saad",
+        "author_inst": "Assiut Faculty of Medicine"
+      },
+      {
+        "author_name": "Doaa Abdeltawab Abdellal",
+        "author_inst": "Assiut Faculty of Medicine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.01.12.20248726",
     "rel_title": "Changes in the Health of Adolescent Athletes: A Comparison of Health Measures Collected Before and During the CoVID-19 Pandemic",
@@ -973731,41 +972558,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "cardiovascular medicine"
   },
-  {
-    "rel_doi": "10.1101/2021.01.13.21249447",
-    "rel_title": "The impact of the first wave of COVID-19 on those with lifelong conditions: a case study of congenital heart disease",
-    "rel_date": "2021-01-15",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.13.21249447",
-    "rel_abs": "ObjectivesGlobally, health care systems have been stretched to the limit by the COVID-19 pandemic. Significant changes have had to be made to the way in which non-COVID-19 related care has been delivered. Our objective was to understand, from the perspective of patients with a chronic, life-long condition (congenital heart disease, CHD) and their parents/carers, the impact of COVID-19 on the delivery of care, how changes were communicated and whether health care providers should do anything differently in a subsequent wave of COVID-19 infections.\n\nDesign and settingA series of asynchronous discussion forums set up and moderated by three patient charities via their Facebook pages.\n\nParticipantsPatients with CHD and parents/carers of patients with CHD.\n\nMain outcome measuresQualitative responses to questions posted on the discussion forums.\n\nResultsThe forums ran over a 6-week period and involved 111 participants. Following thematic analysis of the transcripts, we identified three themes and ten subthemes related to individual condition-related factors, patient-related factors and health professional/centre factors that may have influenced how patients and parents/carers experienced changes to service delivery as a result of COVID-19.\n\nConclusionsOur findings, whilst collected in relation to patients with CHD, are not necessarily specific to this population and we believe reflect the experiences of many thousands of people with life-long conditions in the UK. Drawing on what participants told us in the discussion forums, we have developed recommendations related to communication, service delivery and support during the pandemic that would, we think, improve patients experience of care and, potentially, their outcomes. Although the data were collected specifically in relation to COVID-19, a number of these recommendations are relevant to the wider delivery of care to patients with chronic underlying health conditions and reflect principles of good communication and service delivery.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Jo Wray",
-        "author_inst": "Great Ormond Street Hospital for Children NHS Foundation Trust"
-      },
-      {
-        "author_name": "Christina Pagel",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Adrian H Chester",
-        "author_inst": "The Magdi Yacoub Institute"
-      },
-      {
-        "author_name": "Fiona Kennedy",
-        "author_inst": "Barts Health NHS Trust"
-      },
-      {
-        "author_name": "Sonya Crowe",
-        "author_inst": "University College London"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "cardiovascular medicine"
-  },
   {
     "rel_doi": "10.1101/2021.01.12.21249697",
     "rel_title": "Mortality of Diabetes-related Acute Metabolic Emergencies in COVID-19 patients: a systematic review and meta-analysis",
@@ -974020,6 +972812,25 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2021.01.08.21249273",
+    "rel_title": "Modeling the COVID-19 transmission in Italy: The roles of asymptomatic cases, social distancing, and lockdowns",
+    "rel_date": "2021-01-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.08.21249273",
+    "rel_abs": "The SEIR model of COVID-19 is developed to investigate the roles of physical distancing, lockdowns and asymptomatic cases in Italy. In doing so, two types of policies including behavioral measures and lockdown measures are embedded in the model. Compared with existing models, the model successfully reproduces similar multiple observed outputs such as infected and recovered patients in Italy by July 2020. This study concludes that the first policy is important once the number of infected cases is relatively low. However, once the number of infected cases is very high so the society cannot identify infected and disinfected people, the second policy must be applied soon. It is thus this study suggests that relaxed lockdowns lead to the second wave of the COVID-19 around the world. It is hoped that the model can enhance our understanding on the roles of behavioral measures, lockdowns, and undocumented cases, so-called asymptomatic cases, on the COVID-19 flow.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Muhamad Khairulbahri",
+        "author_inst": "Bandung Institute of Technology"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.01.09.20248472",
     "rel_title": "Magnitude, change over time, demographic characteristics and geographic distribution of excess deaths among nursing home residents during the first wave of COVID-19 in France: a nationwide cohort study",
@@ -975713,69 +974524,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.01.11.21249435",
-    "rel_title": "Monitoring the proportion infected by SARS-CoV-2 from age-stratified hospitalisation and serological data",
-    "rel_date": "2021-01-13",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.11.21249435",
-    "rel_abs": "BackgroundRegional monitoring of the proportion infected by SARS-CoV-2 is important to guide local management of the epidemic, but is difficult in the absence of regular nationwide serosurveys.\n\nMethodsWe developed a method to reconstruct in real-time the proportion infected by SARS-CoV-2 and the proportion of infections being detected from the joint analysis of age-stratified seroprevalence, hospitalisation and case data. We applied our approach to the 13 French metropolitan regions.\n\nFindingsWe estimate that 5.7% [5.1%-6.4%] of adults in metropolitan France had been infected by SARS-CoV-2 by May 2020. This proportion remained stable until August and increased to 12.6% [11.2%-14.3%] by the end of November. With 23.8% [21.2%-26.8%] infected in the Paris region compared to 4.0% [3.5% - 4.6%] in Brittany, regional variations remained large (Coefficient of Variation CV: 0.53) although less so than in May (CV: 0.74). The proportion infected was twice higher (17.6% [13.4%-22.7%]) in 20-49 y.o. than in 50+ y.o (8.0% [5.7% - 11.5%]). Forty percent [33.7% - 45.4%] of infections in adults were detected in June-August compared to 55.7% [48.7% - 63.1%] in September-November. Our method correctly predicted seroprevalence in 11 regions in which only hospitalisation data were used.\n\nInterpretationIn the absence of contemporary serosurvey, our real-time monitoring indicates that the proportion infected by SARS-CoV-2 may be above 20% in some French regions.\n\nFundingEU RECOVER, ANR, Fondation pour la Recherche Medicale, Inserm.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Nathanael Hoze",
-        "author_inst": "Institut Pasteur"
-      },
-      {
-        "author_name": "Juliette Paireau",
-        "author_inst": "Institut Pasteur"
-      },
-      {
-        "author_name": "Nathanael Lapidus",
-        "author_inst": "Sorbonne Universite"
-      },
-      {
-        "author_name": "Cecile Tran Kiem",
-        "author_inst": "Institut Pasteur"
-      },
-      {
-        "author_name": "Henrik Salje",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Gianluca Severi",
-        "author_inst": "INSERM"
-      },
-      {
-        "author_name": "Mathilde Touvier",
-        "author_inst": "INSERM"
-      },
-      {
-        "author_name": "Marie Zins",
-        "author_inst": "INSERM"
-      },
-      {
-        "author_name": "Xavier de Lamballerie",
-        "author_inst": "Ai-Marseille univ -Inserm - IRD"
-      },
-      {
-        "author_name": "Daniel Levy-Bruhl",
-        "author_inst": "Sante publique France"
-      },
-      {
-        "author_name": "Fabrice Carrat",
-        "author_inst": "INSERM"
-      },
-      {
-        "author_name": "Simon Cauchemez",
-        "author_inst": "Institut Pasteur"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.01.10.21249557",
     "rel_title": "Vaccination in a two-group epidemic model",
@@ -976078,6 +974826,69 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.01.11.21249626",
+    "rel_title": "Aerosol tracer testing in the cabin of wide-bodied Boeing 767 and 777 aircraft to simulate exposure potential of infectious particulate such as SARS-CoV-2",
+    "rel_date": "2021-01-13",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.11.21249626",
+    "rel_abs": "The COVID-19 pandemic has reintroduced questions regarding the potential risk of SARS-CoV-2 exposure amongst passengers on an aircraft. Quantifying risk with computational fluid dynamics models or contact tracing methods alone is challenging, as experimental results for inflight biological aerosols is lacking. Using fluorescent aerosol tracers and real time optical sensors, coupled with DNA-tagged tracers for aerosol deposition, we executed ground and inflight testing on Boeing 767 and 777 airframes.\n\nAnalysis here represents tracer particles released from a simulated infected passenger, in multiple rows and seats, to determine the exposure risk via penetration into breathing zones in that row and numerous rows ahead and behind the index case. We completed over 65 releases of 180,000,000 fluorescent particles from the source, with 40+ Instantaneous Biological Analyzer and Collector sensors placed in passenger breathing zones for real-time measurement of simulated virus particle penetration.\n\nResults from both airframes showed a minimum reduction of 99.54% of 1 {micro}m aerosols from the index source to the breathing zone of a typical passenger seated directly next to the source. An average 99.97 to 99.98% reduction was measured for the breathing zones tested in the 767 and 777, respectively. Contamination of surfaces from aerosol sources was minimal, and DNA-tagged 3 {micro}m tracer aerosol collection techniques agreed with fluorescent methodologies.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Sean M Kinahan",
+        "author_inst": "University of Nebraska Medical Center"
+      },
+      {
+        "author_name": "David B Silcott",
+        "author_inst": "S3I LLC"
+      },
+      {
+        "author_name": "Blake E Silcott",
+        "author_inst": "S3I LLC."
+      },
+      {
+        "author_name": "Ryan M Silcott",
+        "author_inst": "S3I LLC"
+      },
+      {
+        "author_name": "Peter J Silcott",
+        "author_inst": "S3I LLC"
+      },
+      {
+        "author_name": "Braden J Silcott",
+        "author_inst": "S3I LLC"
+      },
+      {
+        "author_name": "Steven L Distelhorst",
+        "author_inst": "National Strategic Research Institute"
+      },
+      {
+        "author_name": "Vicki L Herrera",
+        "author_inst": "University of Nebraska Medical Center"
+      },
+      {
+        "author_name": "Danielle N Rivera",
+        "author_inst": "National Strategic Research Institute"
+      },
+      {
+        "author_name": "Kevin K Crown",
+        "author_inst": "National Strategic Research Institute"
+      },
+      {
+        "author_name": "Gabriel A Lucero",
+        "author_inst": "National Strategic Research Institute"
+      },
+      {
+        "author_name": "Joshua Santarpia",
+        "author_inst": "University of Nebraska Medical Center"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.01.05.21249196",
     "rel_title": "Genomic and mobility data reveal mass population movement as a driver of SARS-CoV-2 dissemination and diversity in Bangladesh",
@@ -977247,101 +976058,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2021.01.09.21249263",
-    "rel_title": "Pragmatic, open-label, single-center, randomized, phase II clinical trial to evaluate the efficacy and safety of methylprednisolone pulses and tacrolimus in patients with severe pneumonia secondary to COVID-19: the TACROVID trial protocol",
-    "rel_date": "2021-01-12",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.09.21249263",
-    "rel_abs": "IntroductionSome COVID-19 patients evolve to severe lung injury and systemic hyperinflammatory syndrome triggered by both the coronavirus infection and the subsequent host-immune response. Accordingly, the use of immunomodulatory agents has been suggested but still remains controversial. Our working hypothesis is that methylprednisolone pulses and tacrolimus may be an effective and safety drug combination for treating severe COVID-19 patients.\n\nMethods and analysisTACROVID is a randomized, open-label, single-center, phase II trial to evaluate the efficacy and safety of methylprednisolone pulses and tacrolimus plus standard of care (SoC) versus SoC alone, in patients at advanced stage of COVID-19 disease with lung injury and systemic hyperinflammatory response. Patients are randomly assigned (1:1) to one of two arms (42 patients in each group). The primary aim is to assess the time to clinical stability after initiating randomization. Clinical stability is defined as body temperature [&le;] 37.5{degrees}C, and PaO2/FiO2 > 400 and/or SatO2/FiO2 > 300, and respiratory rate [&le;]24 rpm; for 48 consecutive hours.\n\nDiscussionMethylprednisolone and tacrolimus might be beneficial to treat those COVID-19 patients progressing into severe pulmonary failure and systemic hyperinflammatory syndrome. The rationale for its use is the fast effect of methylprednisolone pulses and the ability of tacrolimus to inhibit both the CoV-2 replication and the secondary cytokine storm. Interestingly, both drugs are low-cost and can be manufactured on a large scale; thus, if effective and safe, a large number of patients could be treated in developed and developing countries.\n\nTrial registration numberNCT04341038 / EudraCT: 2020-001445-39",
-    "rel_num_authors": 20,
-    "rel_authors": [
-      {
-        "author_name": "Xavier Solanich",
-        "author_inst": "Bellvitge University Hospital"
-      },
-      {
-        "author_name": "Arnau Antoli",
-        "author_inst": "Bellvitge University Hospital"
-      },
-      {
-        "author_name": "Nuria Padulles",
-        "author_inst": "Bellvitge University Hospital"
-      },
-      {
-        "author_name": "Marta Fanlo",
-        "author_inst": "Bellvitge University Hospital"
-      },
-      {
-        "author_name": "Adriana Iriarte",
-        "author_inst": "Bellvitge University Hospital"
-      },
-      {
-        "author_name": "Francesca Mitjavila",
-        "author_inst": "Bellvitge University Hospital"
-      },
-      {
-        "author_name": "Olga Capdevila",
-        "author_inst": "Bellvitge university Hospital"
-      },
-      {
-        "author_name": "Maria Molina",
-        "author_inst": "Bellvitge University Hospital"
-      },
-      {
-        "author_name": "Joan Sabater",
-        "author_inst": "Bellvitge University Hospital"
-      },
-      {
-        "author_name": "Jordi Bas",
-        "author_inst": "Bellvitge University Hospital"
-      },
-      {
-        "author_name": "Anna Mensa-Vilaro",
-        "author_inst": "Clinic Hospital"
-      },
-      {
-        "author_name": "Jordi Niubo",
-        "author_inst": "Bellvitge University Hospital"
-      },
-      {
-        "author_name": "Nahum Calvo",
-        "author_inst": "Bellvitge University Hospital"
-      },
-      {
-        "author_name": "Santiago Bolivar",
-        "author_inst": "Bellvitge University Hospital"
-      },
-      {
-        "author_name": "Raul Rigo-Bonnin",
-        "author_inst": "Bellvitge University Hospital"
-      },
-      {
-        "author_name": "Laura Arregui",
-        "author_inst": "Bellvitge University Hospital"
-      },
-      {
-        "author_name": "Cristian Tebe",
-        "author_inst": "Bellvitge Biomedical Research Institute"
-      },
-      {
-        "author_name": "Pilar Hereu",
-        "author_inst": "Bellvitge University Hospital"
-      },
-      {
-        "author_name": "Sebastian Videla",
-        "author_inst": "Bellvitge University Hospital"
-      },
-      {
-        "author_name": "Xavier Corbella",
-        "author_inst": "Hospital Universitari de Bellvitge"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.01.09.21249494",
     "rel_title": "Assessments of heavy lift UAV quadcopter drone to support COVID 19 vaccine cold chain delivery for indigenous people in remote areasin South East Asia",
@@ -977616,6 +976332,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.01.09.21249505",
+    "rel_title": "Wastewater Virus Detection Complements Clinical COVID-19 Testing to Limit Spread of Infection at Kenyon College",
+    "rel_date": "2021-01-12",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.09.21249505",
+    "rel_abs": "In-person college instruction during the 2020 pandemic required effective and economical monitoring of COVID-19 prevalence. Kenyon College and the Village of Gambier conducted measurement of SARS-CoV-2 RNA from the village wastewater plant and from an on-campus sewer line. Wastewater RNA detection revealed virus prevalence leading to individual testing and case identification. Wastewater surveillance also showed when case rates had subsided, thus limiting the need for individual clinical testing. Overall, wastewater virus surveillance allows more targeted use of individual testing and increases community confidence in student population management.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Daniel Barich",
+        "author_inst": "Kenyon College"
+      },
+      {
+        "author_name": "Joan L Slonczewski",
+        "author_inst": "Kenyon College"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2021.01.09.21249508",
     "rel_title": "Exploration of interethnic variation in the ibuprofen metabolizing enzyme CYP2C9: a cautionary guide for treatment of COVID-19 symptoms",
@@ -978997,93 +977736,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "intensive care and critical care medicine"
   },
-  {
-    "rel_doi": "10.1101/2021.01.08.425999",
-    "rel_title": "The landscape of human brain immune response in patients with severe COVID-19",
-    "rel_date": "2021-01-11",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.08.425999",
-    "rel_abs": "In coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the relationship between brain tropism, neuroinflammation and host immune response has not been well characterized. We analyzed 68,557 single-nucleus transcriptomes from three brain regions (dorsolateral prefrontal cortex, medulla oblongata and choroid plexus) and identified an increased proportion of stromal cells and monocytes in the choroid plexus of COVID-19 patients. Differential gene expression, pseudo-temporal trajectory and gene regulatory network analyses revealed microglial transcriptome perturbations, mediating a range of biological processes, including cellular activation, mobility and phagocytosis. Quantification of viral spike S1 protein and SARS-CoV-2 transcripts did not support the notion of brain tropism. Overall, our findings suggest extensive neuroinflammation in patients with acute COVID-19.\n\nOne Sentence SummarySingle-nucleus transcriptome analysis suggests extensive neuroinflammation in human brain tissue of patients with acute coronavirus disease 2019.",
-    "rel_num_authors": 18,
-    "rel_authors": [
-      {
-        "author_name": "John F Fullard",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Hao-chih Lee",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Georgios Voloudakis",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Shengbao Suo",
-        "author_inst": "Harvard Medical School"
-      },
-      {
-        "author_name": "Zhiping Shao",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Cyril Peter",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Behnam Javidfar",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Wen Zhang",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Shan Jiang",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Andre Corvelo",
-        "author_inst": "New York Genome Center"
-      },
-      {
-        "author_name": "Emma Woodoff-Leith",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Dushyant P Purohit",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Gabriel E Hoffman",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Schahram Akbarian",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Mary Fowkes",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "John Crary",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Guo-Cheng Yuan",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Panos Roussos",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "new results",
-    "category": "neuroscience"
-  },
   {
     "rel_doi": "10.1101/2021.01.11.426080",
     "rel_title": "Immunological and cardio-vascular pathologies associated with SARS-CoV-2 infection in golden syrian hamster",
@@ -979526,6 +978178,133 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2021.01.09.426032",
+    "rel_title": "Immunogenicity and efficacy of the COVID-19 candidate vector vaccine MVA SARS 2 S in preclinical vaccination",
+    "rel_date": "2021-01-11",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.09.426032",
+    "rel_abs": "The severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) has emerged as the infectious agent causing the pandemic coronavirus disease 2019 (COVID-19) with dramatic consequences for global human health and economics. Previously, we reached clinical evaluation with our vector vaccine based on vaccinia virus MVA against the Middle East respiratory syndrome coronavirus (MERS-CoV), which causes an infection in humans similar to SARS and COVID-19. Here, we describe the construction and preclinical characterization of a recombinant MVA expressing full-length SARS-CoV-2 spike (S) protein (MVA-SARS-2-S). Genetic stability and growth characteristics of MVA-SARS-2-S, plus its robust synthesis of S antigen, make it a suitable candidate vaccine for industrial scale production. Vaccinated mice produced S antigen-specific CD8+ T cells and serum antibodies binding to S glycoprotein that neutralized SARS-CoV-2. Prime-boost vaccination with MVA-SARS-2-S protected mice sensitized with a human ACE2-expressing adenovirus from SARS-CoV-2 infection. MVA-SARS-2-S is currently being investigated in a phase I clinical trial as aspirant for developing a safe and efficacious vaccine against COVID-19.\n\nSignificance StatementThe highly attenuated vaccinia virus MVA is licensed as smallpox vaccine, and as vector it is a component of the approved Adenovirus-MVA-based prime-boost vaccine against Ebola virus disease. Here we provide results from testing the COVID-19 candidate vaccine MVA-SARS-2-S, a poxvirus-based vector vaccine that proceeded to clinical evaluation. When administered by intramuscular inoculation, MVA-SARS-2-S expresses and safely delivers the full-length SARS-CoV-2 spike (S) protein, inducing balanced SARS-CoV-2-specific cellular and humoral immunity, and protective efficacy in vaccinated mice. Substantial clinical experience has already been gained with MVA vectors using homologous and heterologous prime-boost applications, including the immunization of children and immunocompromised individuals. Thus, MVA-SARS-2-S represents an important resource for developing further optimized COVID-19 vaccines.",
+    "rel_num_authors": 28,
+    "rel_authors": [
+      {
+        "author_name": "Alina Tscherne",
+        "author_inst": "Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany"
+      },
+      {
+        "author_name": "Jan Hendrik Schwarz",
+        "author_inst": "Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany"
+      },
+      {
+        "author_name": "Cornelius Rohde",
+        "author_inst": "Institute of Virology, Philipps University Marburg, Marburg, Germany"
+      },
+      {
+        "author_name": "Alexandra Kupke",
+        "author_inst": "Institute of Virology, Philipps University Marburg, Marburg, Germany"
+      },
+      {
+        "author_name": "Georgia Kalodimou",
+        "author_inst": "Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany"
+      },
+      {
+        "author_name": "Leonard Limpinsel",
+        "author_inst": "Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany"
+      },
+      {
+        "author_name": "Nisreen M.A. Okba",
+        "author_inst": "Erasmus MC"
+      },
+      {
+        "author_name": "Berislav Bosnjak",
+        "author_inst": "Institute of Immunology, Hannover Medical School, Hannover, Germany"
+      },
+      {
+        "author_name": "Inga Sandrock",
+        "author_inst": "Institute of Immunology, Hannover Medical School, Hannover, Germany"
+      },
+      {
+        "author_name": "Sandro Halwe",
+        "author_inst": "Institute of Virology, Philipps University Marburg, Marburg, Germany"
+      },
+      {
+        "author_name": "Lucie Sauerhering",
+        "author_inst": "Institute of Virology, Philipps University Marburg, Marburg, Germany"
+      },
+      {
+        "author_name": "Katrin Printz",
+        "author_inst": "Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany"
+      },
+      {
+        "author_name": "Liangliang Nan",
+        "author_inst": "Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany"
+      },
+      {
+        "author_name": "Elke Duell",
+        "author_inst": "Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany"
+      },
+      {
+        "author_name": "Sylvia Jany",
+        "author_inst": "Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany"
+      },
+      {
+        "author_name": "Astrid Freudenstein",
+        "author_inst": "Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany"
+      },
+      {
+        "author_name": "Joerg Schmidt",
+        "author_inst": "Institute of Virology, Philipps University Marburg, Marburg, Germany"
+      },
+      {
+        "author_name": "Anke Werner",
+        "author_inst": "Institute of Virology, Philipps University Marburg, Marburg, Germany"
+      },
+      {
+        "author_name": "Michelle Gellhorn",
+        "author_inst": "Institute of Virology, Philipps University Marburg, Marburg, Germany"
+      },
+      {
+        "author_name": "Michael Kluever",
+        "author_inst": "Institute of Virology, Philipps University Marburg, Marburg, Germany"
+      },
+      {
+        "author_name": "Wolfgang Guggemos",
+        "author_inst": "Munich Clinic Schwabing, Academic Teaching Hospital, LMU Munich, Munich, Germany"
+      },
+      {
+        "author_name": "Michael Seilmaier",
+        "author_inst": "Munich Clinic Schwabing, Academic Teaching Hospital, LMU Munich, Munich, Germany"
+      },
+      {
+        "author_name": "Clemens Wendtner",
+        "author_inst": "Munich Clinic Schwabing, Academic Teaching Hospital, LMU Munich, Munich, Germany"
+      },
+      {
+        "author_name": "Reinhold Foerster",
+        "author_inst": "Institute of Immunology, Hannover Medical School, Hannover, Germany"
+      },
+      {
+        "author_name": "Bart Haagmans",
+        "author_inst": "Erasmus Medical Center"
+      },
+      {
+        "author_name": "Stephan Becker",
+        "author_inst": "Institute of Virology, Philipps University Marburg, Marburg, Germany"
+      },
+      {
+        "author_name": "Gerd Sutter",
+        "author_inst": "Division of Virology, Department of Veterinary Sciences, LMU Munich, Munich, Germany"
+      },
+      {
+        "author_name": "Asisa Volz",
+        "author_inst": "University of Veterinary Medicine Hannover"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2021.01.11.426209",
     "rel_title": "COVID-19 Severity Is Associated with Differential Antibody Fc-mediated Innate Immune Functions",
@@ -981207,109 +979986,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
-  {
-    "rel_doi": "10.1101/2021.01.06.21249282",
-    "rel_title": "COVID-19 Rapid Antigen Test at hospital admission associated to the knowledge of individual risk factors allow overcoming the difficulty of managing suspected patients in hospitals",
-    "rel_date": "2021-01-08",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.06.21249282",
-    "rel_abs": "Early diagnosis of SARS-CoV-2 is essential to limiting the spread of the virus and managing infected patients during hospitalization. The sensitivity of RT-qPCR is contested by the fact that it is time-consuming, executed by trained technicians in proper environment for material extraction. Here, we evaluated the first SARS-CoV-2 antigen test recommended by the World Health Organization at September, 2020 as an alternative for immediate diagnosis of symptomatic and suspected patients at a hospital in Brazil during the epidemic peak. All patients were submitted to RT-qPCR and rapid antigen test using nasopharyngeal swabs rigorously collected at the same time. Demographics, baseline comorbidities, symptoms and outcomes were considered. Prediction analysis revealed that previous stroke, chronic obstructive pulmonary disease, desaturation and tachypnea were the most relevant determinants of the death of COVID-19 patients. Comparison between the rapid antigen test and RT-qPCR revealed an overall PPV of 97%, extended to 100% when performed between 4 and 15 days of symptoms, with an accuracy of 90-91% from days 1 to 7 and a  Substantial agreement. The rapid antigen test presented no inconclusive result. Among the discordant results and RT-qPCR inconclusives, 72% presented bilateral multifocal ground-glass opacities on imaging and other exams alterations. The median time to obtain RT-qPCR results was 83.6 hours, against 15 minutes for the rapid test, precious time for deciding on patient isolation and management. Knowledge of the risk factors and a rapid diagnosis upon patient admission is critical to reduce mortality of COVID-19 patients, hospital internal costs and in-hospital transmission.",
-    "rel_num_authors": 22,
-    "rel_authors": [
-      {
-        "author_name": "Priscilla S Filgueiras",
-        "author_inst": "Universidade Federal de Minas Gerais"
-      },
-      {
-        "author_name": "Camila A Corsini",
-        "author_inst": "Oswaldo Cruz Foundation"
-      },
-      {
-        "author_name": "Nathalie  Bonatti Franco Almeida",
-        "author_inst": "Centro de Pesquisas Rene Rachou"
-      },
-      {
-        "author_name": "Jessica V Assis",
-        "author_inst": "Oswaldo Cruz Foundation"
-      },
-      {
-        "author_name": "Maria Luysa C Pedrosa",
-        "author_inst": "Oswaldo Cruz Foundation"
-      },
-      {
-        "author_name": "Alana K de Oliveira",
-        "author_inst": "Oswaldo Cruz Foundation"
-      },
-      {
-        "author_name": "Raquel NH Amorim",
-        "author_inst": "Oswaldo Cruz Foundation"
-      },
-      {
-        "author_name": "Daniel AP de Miranda",
-        "author_inst": "Oswaldo Cruz Foundation"
-      },
-      {
-        "author_name": "Lucelia A Coutinho",
-        "author_inst": "Oswaldo Cruz Foundation"
-      },
-      {
-        "author_name": "Sarah VC Gomes",
-        "author_inst": "Oswaldo Cruz Foundation"
-      },
-      {
-        "author_name": "Natalia G Custodio",
-        "author_inst": "Oswaldo Cruz Foundation"
-      },
-      {
-        "author_name": "Douglas H da Silva",
-        "author_inst": "Hospital da Baleia"
-      },
-      {
-        "author_name": "Gabriela PV Santos",
-        "author_inst": "Hospital da Baleia"
-      },
-      {
-        "author_name": "Raphael A Silva",
-        "author_inst": "Hospital da Baleia"
-      },
-      {
-        "author_name": "Maria Izabella VARC Medeiros",
-        "author_inst": "Hospital da Baleia"
-      },
-      {
-        "author_name": "Priscila VCC Reis",
-        "author_inst": "Hospital da Baleia"
-      },
-      {
-        "author_name": "Adelina J Lourenco",
-        "author_inst": "Hospital da Baleia"
-      },
-      {
-        "author_name": "Cecilia MF Bicalho",
-        "author_inst": "Hospital da Baleia"
-      },
-      {
-        "author_name": "Raquel Vilela",
-        "author_inst": "Faculdade de Farmacia, Av. Pres. Antonio Carlos, 6627, Pampulha"
-      },
-      {
-        "author_name": "Hercules P Neves",
-        "author_inst": "Oswaldo Cruz Foundation"
-      },
-      {
-        "author_name": "Gabriel R Fernandes",
-        "author_inst": "Oswaldo Cruz Foundation"
-      },
-      {
-        "author_name": "Rafaella Fortini Queiroz Grenfell",
-        "author_inst": "Oswaldo Cruz Foundation"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2021.01.06.21249280",
     "rel_title": "Mobilefuge: A low-cost, portable, open source, 3D-printed centrifuge that can be used for purification of saliva samples for SARS-CoV2 detection",
@@ -981692,6 +980368,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2021.01.06.21249349",
+    "rel_title": "Identifying silent COVID-19 infections among children is critical for controlling the pandemic",
+    "rel_date": "2021-01-08",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.06.21249349",
+    "rel_abs": "ImportanceA significant proportion of COVID-19 transmission occurs silently during the pre-symptomatic and asymptomatic stages of infection. Children, while being important drivers of silent transmission, are not included in the current COVID-19 vaccination campaigns.\n\nObjectiveTo investigate the benefits of identifying silent infections among children as a proxy for their vaccination.\n\nDesignThis study used an age-structured disease transmission model, parameterized with census data and estimates from published literature, to simulate the synergistic effect of interventions in reducing attack rates over the course of one year.\n\nSettingA synthetic population representative of the United States (US) demographics.\n\nParticipantsSix age groups of 0-4, 5-10, 11-18, 19-49, 50-64, 65+ years based on US census data.\n\nInterventionsIn addition to the isolation of symptomatic cases within 24 hours of symptom onset, vaccination of adults was implemented to reach a 40%-60% coverage over the course of one year with an efficacy of 95% against symptomatic and severe COVID-19.\n\nMain Outcomes and MeasuresThe combinations of proportion and speed for detecting silent infections among children which would suppress future attack rates below 5%.\n\nResultsIn the base-case scenarios with an effective reproduction number Re = 1.2, a targeted approach that identifies 11% and 14% of silent infections among children within 2 or 3 days post-infection, respectively, would bring attack rates under 5% with 40% vaccination coverage of adults. If silent infections among children remained undetected, achieving the same attack rates would require an unrealistically high vaccination coverage (at least 81%) of this age group, in addition to 40% vaccination coverage of adults. The effect of identifying silent infections was robust in sensitivity analyses with respect to vaccine efficacy against infection and reduced susceptibility of children to infection.\n\nConclusions and RelevanceIn this simulation modeling study of a synthetic US population, in the absence of vaccine availability for children, a targeted approach to rapidly identify silent COVID-19 infections in this age group was estimated to significantly mitigate disease burden. Without measures to interrupt transmission chains from silent infections, vaccination of adults is unlikely to contain the outbreaks in the near term.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhat is the effect of a targeted strategy for identification of silent COVID-19 infections among children in the absence of their vaccination?\n\nFindingsIn this simulation modeling study, it was found that identifying 10-20% of silent infections among children within three days post-infection would bring attack rates below 5% if only adults were vaccinated. If silent infections among children remained undetected, achieving the same attack rate would require an unrealistically high vaccination coverage (over 80%) of this age group, in addition to vaccination of adults.\n\nMeaningRapid identification of silent infections among children can achieve comparable effects as would their vaccination.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Seyed M. Moghadas",
+        "author_inst": "York University"
+      },
+      {
+        "author_name": "Meagan C. Fitzpatrick",
+        "author_inst": "University of Maryland"
+      },
+      {
+        "author_name": "Affan Shoukat",
+        "author_inst": "Yale University"
+      },
+      {
+        "author_name": "Kevin Zhang",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Alison P. Galvani",
+        "author_inst": "Yale University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2021.01.06.21249352",
     "rel_title": "OpenSAFELY NHS Service Restoration Observatory 1: describing trends and variation in primary care clinical activity for 23.3 million patients in England during the first wave of COVID-19",
@@ -983077,41 +981788,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.01.07.21249380",
-    "rel_title": "Epidemiological differences in the impact of COVID-19 vaccination in the United States and China",
-    "rel_date": "2021-01-08",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.07.21249380",
-    "rel_abs": "BackgroundThe objective of this study was to forecast the impact of COVID-19 vaccination in the United States (US) and China, two countries at different epidemic phases.\n\nMethodsA mathematical model describing SARS-CoV-2 transmission and disease progression was used to investigate vaccine impact. Impact was assessed both for a vaccine that prevents infection (VES = 95%) and a vaccine that prevents only disease (VEP = 95%).\n\nResultsFor VES = 95% and gradual easing of restrictions, vaccination in the US reduced the peak incidence of infection, disease, and death by >55% and cumulative incidence by >32%, and in China by >77% and >65%, respectively. Nearly three vaccinations were needed to avert one infection in the US, but only one was needed in China. For VEP = 95%, benefits of vaccination were half those for VES = 95%. In both countries, the impact of vaccination was substantially enhanced with rapid scale-up, vaccine coverage >50%, and slower or no easing of restrictions, particularly in the US.\n\nConclusionsCOVID-19 vaccination can flatten, delay, and/or prevent future epidemic waves. However, vaccine impact is destined to be heterogeneous across countries because of an underlying \"epidemiologic inequity\" that reduces benefits for countries already at high incidence, such as the US. Despite 95% efficacy, actual vaccine impact could be meager in such countries, if vaccine scale-up is slow, acceptance of the vaccine is poor, or restrictions are eased prematurely.\n\nOne Sentence SummaryVaccine impact will be heterogeneous across countries disadvantaging countries at high incidence. This heterogeneity can be alleviated with rapid vaccination scale-up and limited easing of restrictions.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Monia Makhoul",
-        "author_inst": "Weill Cornell Medicine-Qatar, Doha, Qatar"
-      },
-      {
-        "author_name": "Hiam Chemaitelly",
-        "author_inst": "Weill Cornell Medicine-Qatar, Doha, Qatar"
-      },
-      {
-        "author_name": "Houssein H. Ayoub",
-        "author_inst": "Qatar University, Doha, Qatar"
-      },
-      {
-        "author_name": "Shaheen Seedat",
-        "author_inst": "Weill Cornell Medicine-Qatar, Doha, Qatar"
-      },
-      {
-        "author_name": "Laith J Abu-Raddad",
-        "author_inst": "Weill Cornell Medicine-Qatar, Doha, Qatar"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2021.01.07.21249401",
     "rel_title": "Timeliness of U.S. mortality data releases during the COVID-19 pandemic: delays are associated with electronic death registration system and elevated weekly mortality",
@@ -983361,6 +982037,129 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2021.01.08.425915",
+    "rel_title": "Ad26.COV2.S-elicited immunity protects against G614 spike variant SARS-CoV-2 infection in Syrian hamsters and does not enhance respiratory disease in challenged animals with breakthrough infection after sub-optimal vaccine dosing",
+    "rel_date": "2021-01-08",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.08.425915",
+    "rel_abs": "Previously we have shown that a single dose of recombinant adenovirus serotype 26 (Ad26) vaccine expressing a prefusion stabilized SARS-CoV-2 spike antigen (Ad26.COV2.S) is immunogenic and provides protection in Syrian hamster and non-human primate SARS-CoV-2 infection models. Here, we investigated the immunogenicity, protective efficacy and potential for vaccine-associated enhanced respiratory disease (VAERD) mediated by Ad26.COV2.S in a moderate disease Syrian hamster challenge model, using the currently most prevalent G614 spike SARS-CoV-2 variant. Vaccine doses of 1x109 vp and 1x1010 vp elicited substantial neutralizing antibodies titers and completely protected over 80% of SARS-CoV-2 inoculated Syrian hamsters from lung infection and pneumonia but not upper respiratory tract infection. A second vaccine dose further increased neutralizing antibody titers which was associated with decreased infectious viral load in the upper respiratory tract after SARS-CoV-2 challenge. Suboptimal non-protective immune responses elicited by low-dose A26.COV2.S vaccination did not exacerbate respiratory disease in SARS-CoV-2-inoculated Syrian hamsters with breakthrough infection. In addition, dosing down the vaccine allowed to establish that binding and neutralizing antibody titers correlate with lower respiratory tract protection probability. Overall, these pre-clinical data confirm efficacy of a 1-dose vaccine regimen with Ad26.COV2.S in this G614 spike SARS-CoV-2 virus variant Syrian hamster model, show the added benefit of a second vaccine dose, and demonstrate that there are no signs of VAERD under conditions of suboptimal immunity.",
+    "rel_num_authors": 27,
+    "rel_authors": [
+      {
+        "author_name": "Joan E.M. van der Lubbe",
+        "author_inst": "Janssen Vaccines & Prevention"
+      },
+      {
+        "author_name": "Sietske K. Rosendahl Huber",
+        "author_inst": "Janssen Vaccines & Prevention B.V., Leiden, The Netherlands"
+      },
+      {
+        "author_name": "Aneesh Vijayan",
+        "author_inst": "Janssen Vaccines & Prevention B.V., Leiden, The Netherlands"
+      },
+      {
+        "author_name": "Liesbeth Dekking",
+        "author_inst": "Janssen Vaccines & Prevention B.V., Leiden, The Netherlands"
+      },
+      {
+        "author_name": "Ella van Huizen",
+        "author_inst": "Janssen Vaccines & Prevention B.V., Leiden, The Netherlands"
+      },
+      {
+        "author_name": "Jessica Vreugdenhil",
+        "author_inst": "Janssen Vaccines & Prevention B.V., Leiden, The Netherlands"
+      },
+      {
+        "author_name": "Ying Choi",
+        "author_inst": "Janssen Vaccines & Prevention B.V., Leiden, The Netherlands"
+      },
+      {
+        "author_name": "Miranda R.M. Baert",
+        "author_inst": "Janssen Vaccines & Prevention B.V., Leiden, The Netherlands"
+      },
+      {
+        "author_name": "Karin Feddes-de Boer",
+        "author_inst": "Janssen Vaccines & Prevention B.V., Leiden, The Netherlands"
+      },
+      {
+        "author_name": "Ana Izquierdo Gil",
+        "author_inst": "Janssen Vaccines & Prevention B.V., Leiden, The Netherlands"
+      },
+      {
+        "author_name": "Marjolein van Heerden",
+        "author_inst": "Janssen Non-Clinical Safety B.V., Beerse, Belgium"
+      },
+      {
+        "author_name": "Tim J. Dalebout",
+        "author_inst": "Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands"
+      },
+      {
+        "author_name": "Sebenzile K. Myeni",
+        "author_inst": "Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands"
+      },
+      {
+        "author_name": "Marjolein Kikkert",
+        "author_inst": "Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands"
+      },
+      {
+        "author_name": "Eric J. Snijder",
+        "author_inst": "Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands"
+      },
+      {
+        "author_name": "Leon de Waal",
+        "author_inst": "Viroclinics Biosciences B.V., Viroclinics Xplore, Schaijk, The Netherlands"
+      },
+      {
+        "author_name": "Koert J. Stittelaar",
+        "author_inst": "Wageningen Bioveterinary Research, Lelystad, The Netherlands"
+      },
+      {
+        "author_name": "Jeroen T.B.M. Tolboom",
+        "author_inst": "Janssen Vaccines & Prevention B.V., Leiden, The Netherlands"
+      },
+      {
+        "author_name": "Jan Serroyen",
+        "author_inst": "Janssen Vaccines & Prevention B.V., Leiden, The Netherlands"
+      },
+      {
+        "author_name": "Leacky Muchene",
+        "author_inst": "Janssen Vaccines & Prevention B.V., Leiden, The Netherlands"
+      },
+      {
+        "author_name": "Leslie van der Fits",
+        "author_inst": "Janssen Vaccines & Prevention B.V., Leiden, The Netherlands"
+      },
+      {
+        "author_name": "Lucy Rutten",
+        "author_inst": "Janssen Vaccines & Prevention B.V., Leiden, The Netherlands"
+      },
+      {
+        "author_name": "Johannes P.M. Langedijk",
+        "author_inst": "Janssen Vaccines & Prevention B.V., Leiden, The Netherlands"
+      },
+      {
+        "author_name": "Dan H. Barouch",
+        "author_inst": "Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA"
+      },
+      {
+        "author_name": "Hanneke Schuitemaker",
+        "author_inst": "Janssen Vaccines & Prevention B.V., Leiden, The Netherlands"
+      },
+      {
+        "author_name": "Roland C. Zahn",
+        "author_inst": "Janssen Vaccines & Prevention B.V., Leiden, The Netherlands"
+      },
+      {
+        "author_name": "Frank Wegmann",
+        "author_inst": "Janssen Vaccines & Prevention B.V., Leiden, The Netherlands"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2021.01.08.21249439",
     "rel_title": "Inflight Transmission of COVID-19 Based on Aerosol Dispersion Data",
@@ -984542,33 +983341,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2021.01.05.21249284",
-    "rel_title": "Twitter Discourse on Nicotine as Potential Prophylactic or Therapeutic for COVID-19",
-    "rel_date": "2021-01-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.05.21249284",
-    "rel_abs": "BackgroundAn unproven \"nicotine hypothesis\" that indicates nicotines therapeutic potential for COVID-19 has been proposed in recent literature. This study is about Twitter posts that misinterpret this hypothesis to make baseless claims about benefits of smoking and vaping in the context of COVID-19. We quantify the presence of such misinformation and characterize the tweeters who post such messages.\n\nMethodsTwitter premium API was used to download tweets (n = 17,533) that match terms indicating (a) nicotine or vaping themes, (b) a prophylactic or therapeutic effect, and (c) COVID-19 (January-July 2020) as a conjunctive query. A constraint on the length of the span of text containing the terms in the tweets allowed us to focus on those that convey the therapeutic intent. We hand-annotated these filtered tweets and built a classifier that identifies tweets that extrapolate the nicotine hypothesis to smoking/vaping with a positive predictive value of 85%. We analyzed the frequently used terms in author bios, top Web links, and hashtags of such tweets.\n\nResults21% of our filtered COVID-19 tweets indicate a vaping or smoking-based prevention/treatment narrative. Qualitative analyses show a variety of ways therapeutic claims are being made and tweeter bios reveal pre-existing notions of positive stances toward vaping.\n\nConclusionThe social media landscape is a double-edged sword in tobacco communication. Although it increases information reach, consumers can also be subject to confirmation bias when exposed to inadvertent or deliberate framing of scientific discourse that may border on misinformation. This calls for circumspection and additional planning in countering such narratives as the COVID-19 pandemic continues to ravage our world. Our results also serve as a cautionary tale in how social media can be leveraged to spread misleading information about tobacco products in the wake of pandemics.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Ramakanth Kavuluru",
-        "author_inst": "University of Kentucky"
-      },
-      {
-        "author_name": "Jiho Noh",
-        "author_inst": "University of Kentucky"
-      },
-      {
-        "author_name": "Shyanika W Rose",
-        "author_inst": "University of Kentucky"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health informatics"
-  },
   {
     "rel_doi": "10.1101/2021.01.05.21249216",
     "rel_title": "Prevalence and Factors associated with Mental health impact of COVID-19 Pandemic in Bangladesh: A survey-based cross-sectional study",
@@ -985063,6 +983835,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.01.05.21249131",
+    "rel_title": "Ivermectin shows clinical benefits in mild to moderate Covid19 disease: A randomised controlled double blind dose response study in Lagos.",
+    "rel_date": "2021-01-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.05.21249131",
+    "rel_abs": "IntroductionIn vitro studies have shown the efficacy of Ivermectin (IV) to inhibit the SARS - CoV-2 viral replication, but questions remained as to In-vivo applications. We set out to explore the efficacy and safety of Ivermectin in persons infected with COVID19.\n\nMethodsWe conducted a translational proof of concept (PoC) randomized, double blind placebo controlled, dose response, parallel group study of IV efficacy in RT - PCR proven COVID 19 positive patients. 62 patients were randomized to 3 treatment groups. (A) IV 6mg regime, (B)IV 12 mg regime (given Q84hrs for 2weeks) (C, control) Lopinavir/Ritonavir. All groups plus standard of Care.\n\nResultsThe Days to COVID negativity [DTN] was significantly and dose dependently reduced by IV (p = 0.0066). The DTN for Control were, = 9.1+/-5.2, for A 6.0 +/- 2.9, and for B 4.6 +/-3.2. 2 Way repeated measures ANOVA of ranked COVID 19 + / - scores at 0, 84, 168, 232 hours showed a significant IV treatment effect (p=0.035) and time effect (p <0.0001). IV also tended to increase SPO2 % compared to controls, p = 0.073, 95% CI - 0.39 to 2.59 and increased platelet count compared to C (p = 0.037) 95%CI 5.55 - 162.55 x 103/ml. The platelet count increase was inversely correlated to DTN (r = -0.52, p = 0.005). No SAE was reported.\n\nConclusions12 mg IV regime may have superior efficacy. IV should be considered for use in clinical management of SARS-Cov-2, and may find applications in community prophylaxis in high-risk areas.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Olufemi Emmanuel Babalola",
+        "author_inst": "Department of Ophthalmology, Bingham University, Karu-Jos, Nigeria"
+      },
+      {
+        "author_name": "Christopher Olusanjo Bode",
+        "author_inst": "Department of Surgery,Faculty of Clinical Sciences, College of Medicine & Lagos University Teaching Hospital, Lagos, Nigeria"
+      },
+      {
+        "author_name": "Adesuyi Adeyinka Ajayi",
+        "author_inst": "Division of Hypertension and Clinical pharmacology, Keck Department of Medicine, Baylor College of Medicine Texas, USA"
+      },
+      {
+        "author_name": "Felix M Alakaloko",
+        "author_inst": "Department of Surgery, Lagos University Teaching Hospital, Lagos, Nigeria"
+      },
+      {
+        "author_name": "Iorhen Ephraim Akase",
+        "author_inst": "Department of Medicine, Lagos University Teaching Hospital"
+      },
+      {
+        "author_name": "Erere Otrofanowei",
+        "author_inst": "Department of Medicine, Faculty of Clinical Sciences, College of Medicine/ Lagos University Teaching Hospital"
+      },
+      {
+        "author_name": "Olumuyiwa Babalola Salu",
+        "author_inst": "Centre for Human and Zoonotic Virology, Central Research Laboratory/Department of Medical Microbiology and Parasitology, College of Medicine, University of Lago"
+      },
+      {
+        "author_name": "Wasiu Lanre Adeyemo",
+        "author_inst": "Department of Oral and Maxillofacial Surgery, College of Medicine, University of Lagos"
+      },
+      {
+        "author_name": "Adesoji O Ademuyiwa",
+        "author_inst": "Department of Surgery, Faculty of Clinical Sciences, College of Medicine & Lagos University Teaching Hospital, Lagos, Nigeria"
+      },
+      {
+        "author_name": "Sunday A Omilabu",
+        "author_inst": "Centre for Human and Zoonotic Virology, Central Research Laboratory/Department of Medical Microbiology and Parasitology, College of Medicine, University of Lago"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.01.05.21249293",
     "rel_title": "Modelling Decay of Population Immunity With Proposed Second Dose Deferral Strategy",
@@ -986200,33 +985027,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2021.01.04.21249241",
-    "rel_title": "The Effect of Frames on COVID-19 Vaccine Hesitancy",
-    "rel_date": "2021-01-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.04.21249241",
-    "rel_abs": "In order to control the spread of infectious diseases such as COVID-19, it will be important to develop a communication strategy to counteract \"vaccine hesitancy\". This paper reports the results of a survey experiment testing the impacts of several types of message content: the safety and efficacy of the vaccine itself, the likelihood that others will take the vaccine, and the possible role of politics in promoting the vaccine. In an original survey of 1123 American M-Turk respondents, we provided six different information conditions suggesting the safety and efficacy of the vaccine, the lack of safety/efficacy of the vaccine, the suggestion that most others would take the vaccine, the suggestion that most others would not take the vaccine, the suggestion that the vaccine is being promoted to gain greater control over individual freedom, and the suggestion that it is being rushed for political motivations. We compared the responses for those in the treatment groups with a control group who received no additional information. In comparison to the control group, those who received information about the safety/efficacy of the vaccine were more likely to report that they would take the vaccine, those who received information that others were reluctant to take the vaccine were more likely to report that they themselves would not take it, that other Americans would not take it, and that it was not important to get the vaccine, and those who received information about political influences on vaccine development expressed hesitancy to take it. Communication of effective messages about the vaccine will be essential for public health agencies that seek to promote vaccine take-up.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Risa Palm",
-        "author_inst": "Georgia State University"
-      },
-      {
-        "author_name": "Toby Bolsen",
-        "author_inst": "Georgia State University"
-      },
-      {
-        "author_name": "Justin Kingsland",
-        "author_inst": "Georgia State University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health policy"
-  },
   {
     "rel_doi": "10.1101/2021.01.05.20248202",
     "rel_title": "Coronavirus-19 and coagulopathy: A Systematic Review",
@@ -986497,6 +985297,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2021.01.03.21249175",
+    "rel_title": "Modelling COVID -19 Transmission in a Hemodialysis Centre Using Simulation Generated Contacts Matrices",
+    "rel_date": "2021-01-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.03.21249175",
+    "rel_abs": "The COVID-19 pandemic has been particularly threatening to the patients with end-stage kidney disease (ESKD) on intermittent hemodialysis and their care providers. Hemodialysis patients who receive life-sustaining medical therapy in healthcare settings, face unique challenges as they need to be at a dialysis unit three or more times a week, where they are confined to specific settings and tended to by dialysis nurses and staff with physical interaction and in close proximity. Despite the importance and critical situation of the dialysis units, modelling studies of the SARS-CoV-2 spread in these settings are very limited. In this paper, we have used a combination of discrete event and agent-based simulation models, to study the operations of a typical large dialysis unit and generate contact matrices to examine outbreak scenarios. We present the details of the contact matrix generation process and demonstrate how the simulation calculates a micro-scale contact matrix comprising the number and duration of contacts at a micro-scale time step. We have used the contacts matrix in an agent-based model to predict disease transmission under different scenarios. The results show that micro-simulation can be used to estimate contact matrices, which can be used effectively for disease modelling in dialysis and similar settings.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Mohammadali Tofighi",
+        "author_inst": "York University (ADERSIM) and Ale-Taha Institute of Higher Education"
+      },
+      {
+        "author_name": "Ali Asgary",
+        "author_inst": "York University (ADERSIM)"
+      },
+      {
+        "author_name": "Asad A. Merchant",
+        "author_inst": "University Health Network (UHN)"
+      },
+      {
+        "author_name": "Mohammad Ali Shafiee",
+        "author_inst": "University Health Network (UHN)"
+      },
+      {
+        "author_name": "Mahdi M. Najafabadi",
+        "author_inst": "York University (ADERSIM)"
+      },
+      {
+        "author_name": "Nazanin Nadri",
+        "author_inst": "York University (ADERSIM)"
+      },
+      {
+        "author_name": "Mehdi Aarabi",
+        "author_inst": "University Health Network (UHN)"
+      },
+      {
+        "author_name": "Jane Heffernan",
+        "author_inst": "York University"
+      },
+      {
+        "author_name": "Jianhong Wu",
+        "author_inst": "York University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2021.01.04.21249227",
     "rel_title": "Antithrombotic Therapy in COVID-19: Systematic Summary of Ongoing or Completed Randomized Trials",
@@ -987562,29 +986413,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2021.01.05.425441",
-    "rel_title": "Crystallographic molecular replacement using an in silico-generated search model of SARS-CoV-2 ORF8",
-    "rel_date": "2021-01-05",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.05.425441",
-    "rel_abs": "The majority of crystal structures are determined by the method of molecular replacement (MR). The range of application of MR is limited mainly by the need for an accurate search model. In most cases, pre-existing experimentally determined structures are used as search models. In favorable cases, ab initio predicted structures have yielded search models adequate for molecular replacement. The ORF8 protein of SARS-CoV-2 represents a challenging case for MR using an ab initio prediction because ORF8 has an all {beta}-sheet fold and few orthologs. We previously determined experimentally the structure of ORF8 using the single anomalous dispersion (SAD) phasing method, having been unable to find an MR solution to the crystallographic phase problem. Following a report of an accurate prediction of the ORF8 structure, we assessed whether the predicted model would have succeeded as an MR search model. A phase problem solution was found, and the resulting structure was refined, yielding structural parameters equivalent to the original experimental solution.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Thomas G Flower",
-        "author_inst": "UC Berkeley"
-      },
-      {
-        "author_name": "James H Hurley",
-        "author_inst": "UC Berkeley"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "biophysics"
-  },
   {
     "rel_doi": "10.1101/2021.01.03.424883",
     "rel_title": "Rejuveinix Mitigates Sepsis-Associated Oxidative Stress in the Brain of Mice: Clinical Impact Potential in COVID-19 and Nervous System Disorders",
@@ -987915,6 +986743,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "hematology"
   },
+  {
+    "rel_doi": "10.1101/2020.12.29.20248975",
+    "rel_title": "COVID-19: Can early home treatment with Azithromycin alone or with Zinc help prevent hospitalisation, death, and long-COVID-19? A review",
+    "rel_date": "2021-01-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.29.20248975",
+    "rel_abs": "IntroductionThe effects of the SARS-CoV-2 pandemic continues to disrupt health systems worldwide, leading to population lockdowns in many countries. Preventing hospitalisation, death and long-COVID-19 with repurposed drugs remains a priority. Hydroxychloroquine (HCQ) and azithromycin (AZM) are the most commonly used in ambulatory care, with divergent results. With the aim of decentralizing early treatment to family practitioners, we addressed the question: Can early home treatment with AZM alone or with zinc help prevent hospitalisation, death, and long-COVID-19?\n\nMethodologyWe conducted a scoping review of articles published from 31st December 2019 to 5th November 2020 in Pubmed, Google Scholar, MedRxiv, and BioRxiv databases, and a review of undergoing clinical trials published in the Clinicaltrial.gov database.\n\nResultsMany studies report on outpatient treatment with a combination of AZM + HCQ versus AZM alone, and few studies propose the addition of Zinc (Zn) to AZM. In addition, we identified 5 clinical trials currently recruiting individuals for early outpatient treatment with AZM. However, we failed in identifying any study or clinical trial conducted with family practitioners responding to our question.\n\nDiscussionThe antiviral, anti-inflammatory, immunomodulatory benefits of AZM + Zn make this drugs combination a good candidate therapy to treat flu-like-COVID-19 and atypical pneumoniae. The antibacterial action of AZM can also help disrupting the bacteria/virus cooperation that is poorly documented. Considering pros and cons of macrolide use (including antimicrobial resistance), we call for early use of this therapy by family practitioners for home treatment of individuals presenting mild or moderate symptoms under rigorous scientific guidance to prevent hospitalisation, death and long-COVID.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Philippe LEPERE",
+        "author_inst": "University of Geneva"
+      },
+      {
+        "author_name": "Bruno Escarguel",
+        "author_inst": "Saint Joseph Hospital, Marseille, France"
+      },
+      {
+        "author_name": "Selda Yolartiran",
+        "author_inst": "Saint Joseph Hospital, Marseille, France"
+      },
+      {
+        "author_name": "Claude Escarguel",
+        "author_inst": "Association Biologie et Cooperation, France"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.12.28.20248967",
     "rel_title": "Postlockdown Dynamics of COVID-19 in New York, Florida, Arizona, and Wisconsin",
@@ -989160,29 +988019,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.12.29.20248986",
-    "rel_title": "Insights into the molecular mechanism of anticancer drug ruxolitinib repurposable in COVID-19 therapy",
-    "rel_date": "2021-01-04",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.29.20248986",
-    "rel_abs": "Due to non-availability of specific therapeutics against COVID-19, repurposing of approved drugs is a reasonable option. Cytokines imbalance in COVID-19 resembles cancer; exploration of anti-inflammatory agents, might reduce COVID-19 mortality. The current study investigates the effect of ruxolitinib treatment in SARS-CoV-2 infected alveolar cells compared to the uninfected one from the GSE5147507 dataset. The protein-protein interaction network, biological process and functional enrichment of differentially expressed genes were studied using STRING App of the Cytoscape software and R programming tools. The present study indicated that ruxolitinib treatment elicited similar response equivalent to that of SARS-CoV-2 uninfected situation by inducing defense response in host against virus infection by RLR and NOD like receptor pathways. Further, the effect of ruxolitinib in SARS-CoV-2 infection was mainly caused by significant suppression of IFIH1, IRF7 and MX1 genes as well as inhibition of DDX58/IFIH1-mediated induction of interferon-I and -II signalling.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Manisha Mandal",
-        "author_inst": "MGM Medical College, India"
-      },
-      {
-        "author_name": "Shyamapada Mandal",
-        "author_inst": "University of Gour Banga, India"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.12.30.20249033",
     "rel_title": "Imprecise assessment of mask use may obscure associations with SARS-CoV-2 positivity",
@@ -989425,6 +988261,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.12.30.20248908",
+    "rel_title": "Unsupervised Discovery of Risk Profiles on Negative and Positive COVID-19 Hospitalized Patients",
+    "rel_date": "2021-01-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.30.20248908",
+    "rel_abs": "COVID-19 is a viral disease that affects people in different ways: Most people will develop mild symptoms; others will require hospitalization, and a few others will die. Hence identifying risk factors is vital to assist physicians in the treatment decision. The objective of this paper is to determine whether unsupervised analysis of risk factors of positive and negative COVID-19 subjects may be useful for the discovery of a small set of reliable and clinically relevant risk-profiles. We selected 13367 positive and 19958 negative hospitalized patients from the Mexican Open Registry. Registry patients were described by 13 risk factors, three different outcomes, and COVID-19 test results. Hence, the dataset could be described by 6144 different risk-profiles per age group. To discover the most common risk-profiles, we propose the use of unsupervised learning. The data was split into discovery (70%) and validation (30%) sets. The discovery set was analyzed using the partition around medoids (PAM) method and robust consensus clustering was used to estimate the stable set of risk-profiles. We validated the reliability of the PAM models by predicting the risk-profile of the validation set subjects. The clinical relevance of the risk-profiles was evaluated on the validation set by characterizing the prevalence of the three patient outcomes: pneumonia diagnosis, ICU, or death. The analysis discovered six positives and five negative COVID-19 risk-profiles with strong statistical differences among them. Henceforth PAM clustering with consensus mapping is a viable method for unsupervised risk-profile discovery among subjects with critical respiratory health issues.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Fahimeh Nezhadmoghadam",
+        "author_inst": "Tec de Monterrey"
+      },
+      {
+        "author_name": "Jose Tamez-Pena",
+        "author_inst": "Tec de Monterrey"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.12.29.20248990",
     "rel_title": "Identical trends of SARS-Cov-2 transmission and retail and transit mobility during non-lockdown periods",
@@ -990478,49 +989337,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2021.01.02.20248576",
-    "rel_title": "Covid-19 Pandemic and Behavioural Response To Self-Medication Practice In Western Uganda",
-    "rel_date": "2021-01-04",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.02.20248576",
-    "rel_abs": "BackgroundSelf-medication has become is a serious public health problem globally posing great risks, especially with the increasing number of cases of COVID-19 disease in Uganda. This is may be partly because of the absence of a recognized treatment for the disease, however, the prevalence and nature differ from country to country which may influence human behavioural responses.\n\nAimThis study aimed to investigated the beharioural response of the community towards self- medication practices during this COVID-19 pandemic and lockdown.\n\nMethodsA cross sectional household and online survey was conducted during the months of June-to- August. The study was conducted among adult between age 18 above in communities of western Uganda who consented to participate in the study. Study participants were selected using a convenience sampling technique and sampling was done by sending a structured online questionnaire via Google forms and a printed copies questionnaire made available to other participants that did not use the online questionnaire\n\nResultsThe percentage of respondents that know about self-medication is (97%) and those that practice self-medication are approximately (88%). 97% of respondents have heard about self-medication either through health workers, media, family members, friends and/or school while 3% said they have not heard about self-medication. The percentage of respondents who practiced self- medication during COVID-19 pandemic is 57% while those that did not is 43%. There is statistically difference in the number of those that practice self-medication and those that do not p < 0.005 at 95% confidence interval. Also there was a statistically significant decrease in the number of respondents that practice self-medication during COVID-19 pandemic lockdown compare to the practice before the pandemic lockdown p < 0.05 at 95% confidence interval.\n\nConclusionOur investigation showed adequate knowledge of self-medication and high level of self- medication practice with a decrease in self-medication practices during the COVID-19 pandemic lockdown compared to the practice before the lockdown.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Samuel Sunday Dare",
-        "author_inst": "Kabale University"
-      },
-      {
-        "author_name": "Ejike Daniel Eze",
-        "author_inst": "Kabale University"
-      },
-      {
-        "author_name": "Isaac Echoru",
-        "author_inst": "Kabale University"
-      },
-      {
-        "author_name": "Ibe Michael Usman",
-        "author_inst": "Kampala International University Western Campus"
-      },
-      {
-        "author_name": "Fred Ssempijja",
-        "author_inst": "Kampala International University Western Campus"
-      },
-      {
-        "author_name": "Edmund Eriya Bukenya",
-        "author_inst": "Kabale University"
-      },
-      {
-        "author_name": "Robinson Ssebuufu",
-        "author_inst": "Kampala International University Western Campus"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2021.01.02.21249137",
     "rel_title": "Knowledge, attitude and practice toward COVID-19 among healthcare workers in public health facilities, Eastern Ethiopia",
@@ -990771,6 +989587,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2021.01.03.20248715",
+    "rel_title": "Humoral and cell-mediated response in colostrum after exposure to severe acute respiratory syndrome coronavirus 2",
+    "rel_date": "2021-01-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.03.20248715",
+    "rel_abs": "BackgroundColostrum provides an immune sharing between a mother and her infant. The transfer in colostrum of antibodies against SARS-CoV-2 and the elicited cytokines may provide crucial protection to the infant. There is limited literature on the immune response to SARS-CoV-2 present in colostrum.\n\nObjectiveTo evaluate the presence of antibodies specific to SARS-CoV-2 and the associated cytokines in colostrum from women who tested positive for the virus.\n\nStudy DesignBetween March and September 2020 we obtained bilateral colostrum samples collected on spot cards within 48 hours of delivery from 15 new mothers who had previously tested positive for SARS-CoV-2. Five of these 15 COVID-19 positive women also provided bilateral liquid colostrum within 1-2 days of providing the spot card samples. Archived bilateral colostrum samples collected from 8 women during 2011-2013 were used as pre-COVID-19 controls. All samples were tested for reactivity to the Receptor Binding Domain (RBD) of the SARS-CoV-2 spike protein using an ELISA that measures SARS-CoV-2 RBD-specific IgA, IgG, and IgM, and for concentrations of 10 inflammatory cytokines (IFN{gamma}, TNF, IL-1{beta}, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-13) using a multiplex electrochemiluminescent sandwich assay.\n\nResultsBilateral colostrum samples from 73%, 73% and 33% of the 15 COVID-19 mothers exhibited IgA, IgG, and IgM reactivity to RBD respectively. Colostrum samples from two of the 8 pre-pandemic controls showed IgA and IgG reactivity to RBD. Additionally, COVID-19 mothers had significantly higher levels of 9 of the 10 inflammatory markers (all except IFN{gamma}) as compared to the pre-COVID-19 controls. Comparable results were obtained with both the spot card-eluates and liquid samples.\n\nConclusionsA strong humoral immune response is present in the colostrum of women who were infected with SARS-CoV-2 before delivering. High levels of 9 inflammatory markers were also present in the colostrum. The evolution and duration of the antibody response, as well as dynamics of the cytokine response, remain to be determined. Our results also indicate that future large-scale studies can be conducted with milk easily collected on paper spot cards.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Vignesh Narayanaswamy",
+        "author_inst": "University of Massachusetts Amherst"
+      },
+      {
+        "author_name": "Brian Pentecost",
+        "author_inst": "University of Massachusetts Amherst"
+      },
+      {
+        "author_name": "Dominique Alfandari",
+        "author_inst": "University of Massachusetts Amherst"
+      },
+      {
+        "author_name": "Emily Chin",
+        "author_inst": "University of Massachusetts Medical School Worcester"
+      },
+      {
+        "author_name": "Kathleen Minor",
+        "author_inst": "University of Massachusetts Medical School Worcester"
+      },
+      {
+        "author_name": "Alyssa Kastrinakis",
+        "author_inst": "University of Massachusetts Medical School Worcester"
+      },
+      {
+        "author_name": "Tanya Lieberman",
+        "author_inst": "University of Massachusetts Amherst"
+      },
+      {
+        "author_name": "Kathleen F Arcaro",
+        "author_inst": "University of Massachusetts Amherst"
+      },
+      {
+        "author_name": "Heidi Leftwich",
+        "author_inst": "University of Massachusetts Medical School Worcester"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "obstetrics and gynecology"
+  },
   {
     "rel_doi": "10.1101/2021.01.03.21249170",
     "rel_title": "Nested pool testing strategy for the reliable identification of individuals infected with SARS-CoV-2",
@@ -992364,49 +991231,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2021.01.02.425072",
-    "rel_title": "Sequencing of Sars-CoV-2 genome using different Nanopore chemistries",
-    "rel_date": "2021-01-02",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.02.425072",
-    "rel_abs": "Nanopore sequencing has emerged as a rapid and cost-efficient tool for diagnostic and epidemiological surveillance of SARS-CoV-2 during the COVID-19 pandemic. This study compared results from sequencing the SARS-CoV-2 genome using R9 vs R10 flow cells and Rapid Barcoding Kit (RBK) vs Ligation Sequencing Kit (LSK). The R9 chemistry provided a lower error rate (3.5%) than R10 chemistry (7%). The SARS-CoV-2 genome includes few homopolymeric regions. Longest homopolymers were composed of 7 (TTTTTTT) and 6 (AAAAAA) nucleotides. The R10 chemistry resulted in a lower rate of deletions in timine and adenine homopolymeric regions than R9, at expenses of a larger rate (~10%) of mismatches in these regions.\n\nThe LSK had a larger yield than RBK, and provided longer reads than RBK. It also resulted in a larger percentage of aligned reads (99% vs 93%) and also in a complete consensus genome.\n\nThe results from this study suggest that the LSK used on a R9 flow cell could maximize the yield and accuracy of the consensus sequence when used in epidemiological surveillance of SARS-CoV-2.\n\nKeypointsO_LISequencing SARS-CoV-2 genome is of great importance for the pandemic surveillance\nC_LIO_LINanopore offers a low cost and accurate method to sequence SARS-CoV-2 genome\nC_LIO_LILigation sequencing is preferred rather than the rapid kit using transposases\nC_LI",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Oscar Gonzalez-Recio",
-        "author_inst": "Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria, O.A., M.P. INIA"
-      },
-      {
-        "author_name": "Monica Gutierrez-Rivas",
-        "author_inst": "Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria, O.A., M.P. INIA"
-      },
-      {
-        "author_name": "Ramon Peiro-Pastor",
-        "author_inst": "Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria, O.A., M.P. - INIA."
-      },
-      {
-        "author_name": "Pilar Aguilera-Sepulveda",
-        "author_inst": "Centro de Investigacion en Sanidad Animal (INIA-CISA)"
-      },
-      {
-        "author_name": "Cristina Cano-Gomez",
-        "author_inst": "Centro de Investigacion en Sanidad Animal (INIA-CISA)"
-      },
-      {
-        "author_name": "Miguel Angel Jimenez-Clavero",
-        "author_inst": "Centro de Investigacion en Sanidad Animal (INIA-CISA)"
-      },
-      {
-        "author_name": "Jovita Fernandez-Pinero",
-        "author_inst": "Centro de Investigacion en Sanidad Animal (INIA-CISA),"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.12.31.424961",
     "rel_title": "Comprehensive analysis of the host-virus interactome of SARS-CoV-2",
@@ -992685,6 +991509,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.12.27.20248896",
+    "rel_title": "Vaccination and Non-Pharmaceutical Interventions: when can the UK relax about COVID-19?",
+    "rel_date": "2021-01-02",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.27.20248896",
+    "rel_abs": "BackgroundThe announcement of efficacious vaccine candidates against SARS-CoV-2 has been met with worldwide acclaim and relief. Many countries already have detailed plans for vaccine targeting based on minimising severe illness, death and healthcare burdens. Normally, relatively simple relationships between epidemiological parameters, vaccine efficacy and vaccine uptake predict the success of any immunisation programme. However, the dynamics of vaccination against SARS-CoV-2 is made more complex by age-dependent factors, changing levels of infection and the potential relaxation of non-pharmaceutical interventions (NPIs) as the perceived risk declines.\n\nMethodsIn this study we use an age-structured mathematical model, matched to a range of epidemiological data in the UK, that also captures the roll-out of a two-dose vaccination programme targeted at specific age groups.\n\nFindingsWe consider the interaction between the UK vaccination programme and future relaxation (or removal) of NPIs. Our predictions highlight the population-level risks of early relaxation leading to a pronounced wave of infection, hospital admissions and deaths. Only vaccines that offer high infection-blocking efficacy with high uptake in the general population allow relaxation of NPIs without a huge surge in deaths.\n\nInterpretationWhile the novel vaccines against SARS-CoV-2 offer a potential exit strategy for this outbreak, this is highly contingent on the infection-blocking (or transmission-blocking) action of the vaccine and the population uptake, both of which need to be carefully monitored as vaccine programmes are rolled out in the UK and other countries.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSVaccination has been seen as a key tool in the fight against SARS-CoV-2. The vaccines already developed represent a major technological achievement and have been shown to generate significant immune responses, as well as offering considerable protection against disease. However, to date there is limited information on the degree of infection-blocking these vaccines are likely to induce. Mathematical models have already successfully been used to consider age- and risk-structured targeting of vaccination, highlighting the importance of prioritising older and high-risk individuals.\n\nAdded value of this studyTranslating current knowledge and uncertainty of vaccine behaviour into meaningful public health messages requires models that fully capture the within-country epidemiology as well as the complex roll-out of a two-dose vaccination programme. We show that under reasonable assumptions for vaccine efficacy and uptake the UK is unlikely to reach herd immunity, which means that non-pharmaceutical interventions cannot be released without generating substantial waves of infection.\n\nImplications of all the available evidenceVaccination is likely to provide substantial individual protection to those receiving two doses, but the degree of protection to the wider population is still uncertain. While substantial immunisation of the most vulnerable groups will allow for some relaxation of controls, this must be done gradually to prevent large scale public health consequences.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Sam Moore",
+        "author_inst": "University of Warwick"
+      },
+      {
+        "author_name": "Edward M Hill",
+        "author_inst": "University of Warwick"
+      },
+      {
+        "author_name": "Michael Tildesley",
+        "author_inst": "University of Warwick"
+      },
+      {
+        "author_name": "Louise M Dyson",
+        "author_inst": "University of Warwick"
+      },
+      {
+        "author_name": "Matt J Keeling",
+        "author_inst": "University of Warwick"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.12.26.20248855",
     "rel_title": "Quantitative plasma proteomics of survivor and non-survivor COVID-19 patients admitted to hospital unravels potential prognostic biomarkers and therapeutic targets",
@@ -993698,41 +992557,6 @@
     "type": "new results",
     "category": "bioengineering"
   },
-  {
-    "rel_doi": "10.1101/2020.12.29.424534",
-    "rel_title": "A novel fermented Yi traditional medicine efficiently suppresses the replication of SARS-CoV-2 in vitro",
-    "rel_date": "2020-12-30",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.29.424534",
-    "rel_abs": "Currently, the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a worldwide epidemic, causing more than 80 million infections and more than 1.7 million deaths. The pandemic has led to the closure of enterprises and schools in many countries, resulting in serious disruption of the global economy and social activities. Remdesivir is currently approved by the FDA for the treatment of COVID-19, but the WHO declared that Remdesivir is almost ineffective against COVID-19. The research and development of vaccines has made great progress, but it will take at least several months for safe and effective vaccines to be widely used clinically. Clinical studies revealed that some Traditional Chinese Medicines, such as Lianhua Qingwen Capsule and Huoxiang Zhengqi Water, exhibited excellent therapeutic effect on COVID-19. However, until now, there is still no cure for COVID-19. Therefore, there is an urgent need to find medicines that can effectively fight against the SARS-CoV-2. In this study, JIE BEN No. 10 (JB10), a fermentation broth produced by Yi traditional medicine fermentation technology, was explored for its anti-coronavirus activity. The in vitro data showed that JB10 could significantly suppresses the replication of the SARS-CoV-2 with an EC50 of 769.1 times dilution and a selection index of 42.68. Further studies indicated that JB10 had significant anti-inflammatory and antioxidant activities. The analysis of active components suggested that JB10 contained a large amount of superoxide dismutase (SOD), flavones, polyphenols, crude polysaccharide, etc. which may explain the anti-coronavirus activity, anti-inflammatory and antioxidant effects. Our study provides a new potentially therapeutic strategy for COVID-19.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Shisong Fang",
-        "author_inst": "Shenzhen Center for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Benhong Xu",
-        "author_inst": "Shenzhen Center for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Xiangrong Song",
-        "author_inst": "Sichuan University"
-      },
-      {
-        "author_name": "Yongmei Xie",
-        "author_inst": "Sichuan University"
-      },
-      {
-        "author_name": "Xifei Yang",
-        "author_inst": "Shenzhen Center for Disease Control and Prevention"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.12.30.424862",
     "rel_title": "Screening a library of FDA-approved and bioactive compounds for antiviral activity against SARS-CoV-2",
@@ -994059,6 +992883,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.12.24.20248814",
+    "rel_title": "S gene dropout patterns in SARS-CoV-2 tests suggest spread of the H69del/V70del mutation in the US.",
+    "rel_date": "2020-12-30",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.24.20248814",
+    "rel_abs": "Recently, multiple novel strains of SARS-CoV-2 have been found to share the same deletion of amino acids H69 and V70 in the virus S gene. This includes strain B.1.1.7 / SARS-CoV-2 VUI 202012/01, which has been found to be more infectious than other strains of SARS-CoV-2, and its increasing presence has resulted in new lockdowns in and travel restrictions leaving the UK. Here, we analyze 2 million RT-PCR SARS-CoV-2 tests performed at Helix to identify the rate of S gene dropout, which has been recently shown to occur in tests from individuals infected with strains of SARS-CoV-2 that carry the H69del/V70del mutation. We observe a rise in S gene dropout in the US starting in early October, with 0.25% of our daily SARS-CoV-2-positive tests exhibiting this pattern during the first week. The rate of positive samples with S gene dropout has grown slowly over time, with last week exhibiting the highest level yet, at 0.5%. Focusing on the 14 states for which we have sufficient sample size to assess the frequency of this rare event (n>1000 SARS-CoV-2-positive samples), we see a recent expansion in the Eastern part of the US, concentrated in MA, OH, and FL. However, we cannot say from these data whether the S gene dropout samples we observe here represent the B.1.1.7. strain. Only with an expansion of genomic surveillance sequencing in the US will we know for certain the prevalence of the B.1.1.7 strain in the US.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Nicole L Washington",
+        "author_inst": "Helix"
+      },
+      {
+        "author_name": "Simon White",
+        "author_inst": "Helix"
+      },
+      {
+        "author_name": "Kelly m Schiabor Barrett",
+        "author_inst": "Helix"
+      },
+      {
+        "author_name": "Elizabeth T Cirulli",
+        "author_inst": "Helix"
+      },
+      {
+        "author_name": "Alexandre Bolze",
+        "author_inst": "Helix"
+      },
+      {
+        "author_name": "James T Lu",
+        "author_inst": "Helix"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.12.23.20245316",
     "rel_title": "Smoking and SARS-CoV-2 Impair Dendritic Cells and Regulate DC-SIGN Expression in Tissues",
@@ -995515,89 +994378,6 @@
     "type": "new results",
     "category": "biophysics"
   },
-  {
-    "rel_doi": "10.1101/2020.12.28.424590",
-    "rel_title": "Lentiviral vector-based SARS-CoV-2 pseudovirus enables analysis of neutralizing activity in COVID-19 convalescent plasma",
-    "rel_date": "2020-12-29",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.28.424590",
-    "rel_abs": "As the COVID-19 pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to spread around the globe, effective vaccination protocols are under deployment. Alternatively, the use of convalescent plasma (CP) therapy relies on the transfer of the immunoglobulin repertoire of a donor that has recovered from the disease as a means of passive vaccination. While the lack of an effective antiviral treatment inadvertently increases the interest in CP products, initial clinical evaluation on COVID-19 patients revealed that critical factors determining the outcome of CP therapy need to be defined clearly if clinical efficacy is to be expected. Measurement of neutralizing activity against SARS-CoV-2 using wildtype virus presents a reliable functional assay but the availability of suitable BSL3 facilities for virus culture restricts its applicability. Instead, the use of pseudovirus particles containing elements from the SARS-CoV-2 virus is widely applied to determine the activity of CP or other neutralizing agents such as monoclonal antibodies.\n\nIn this study, we present our approach to optimize GFP-encoding lentiviral particles pseudotyped with the SARS-CoV-2 Spike and Membrane proteins for use in neutralization assays. Our results show the feasibility of pseudovirus production using a C-terminal truncated Spike protein which is greatly enhanced by the incorporation of the D614G mutation. Moreover, we report that the use of Sodium Butyrate during lentiviral vector production dramatically increases pseudovirus titers. Analysis of CP neutralizing activity against particles pseudotyped with wildtype or D614G mutant Spike protein in the presence or absence the M protein revealed differential activity in CP samples that did not necessarily correlate with the amount of anti-SARS-CoV-2 antibodies.\n\nOur results indicate that the extent of neutralizing activity in CP samples depends on the quality rather than the quantity of the humoral immune responses and varies greatly between donors. Functional screening of neutralizing activity using pseudovirus-based neutralization assays must be accepted as a critical tool for choosing CP donors if clinical efficacy is to be maximized.",
-    "rel_num_authors": 17,
-    "rel_authors": [
-      {
-        "author_name": "Cevriye Pamukcu",
-        "author_inst": "Bogazici University"
-      },
-      {
-        "author_name": "Elif Celik",
-        "author_inst": "Bogazici University"
-      },
-      {
-        "author_name": "Ebru Zeynep Ergun",
-        "author_inst": "Bogazici University"
-      },
-      {
-        "author_name": "Zeynep Sena Karahan",
-        "author_inst": "Bogazici University"
-      },
-      {
-        "author_name": "Gozde Turkoz",
-        "author_inst": "Bogazici University"
-      },
-      {
-        "author_name": "Merkaya Aras",
-        "author_inst": "Bogazici University"
-      },
-      {
-        "author_name": "Canan Eren",
-        "author_inst": "Marmara University"
-      },
-      {
-        "author_name": "Uluhan Sili",
-        "author_inst": "Marmara University"
-      },
-      {
-        "author_name": "Huseyin Bilginer",
-        "author_inst": "Marmara University"
-      },
-      {
-        "author_name": "Ilke Suder",
-        "author_inst": "Bogazici University"
-      },
-      {
-        "author_name": "Baris Can Mandaci",
-        "author_inst": "Bogazici University"
-      },
-      {
-        "author_name": "Baran Dingiloglu",
-        "author_inst": "Istanbul Technical University"
-      },
-      {
-        "author_name": "Ozge Tatli",
-        "author_inst": "Istanbul Technical University"
-      },
-      {
-        "author_name": "Gizem Dinler Doganay",
-        "author_inst": "Istanbul Technical University"
-      },
-      {
-        "author_name": "Safa Baris",
-        "author_inst": "Marmara University"
-      },
-      {
-        "author_name": "Nesrin Ozoren",
-        "author_inst": "Bogazici University"
-      },
-      {
-        "author_name": "Tolga Sutlu",
-        "author_inst": "Bogazici University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2020.12.29.424698",
     "rel_title": "An Ultrasensitive Biosensor for Quantifying the Interaction of SARS-CoV-2 and Its Receptor ACE2 in Cells and in vitro",
@@ -995791,6 +994571,97 @@
     "type": "new results",
     "category": "pharmacology and toxicology"
   },
+  {
+    "rel_doi": "10.1101/2020.12.28.424554",
+    "rel_title": "Human neutralizing antibodies against SARS-CoV-2 require intact Fc effector functions and monocytes for optimal therapeutic protection",
+    "rel_date": "2020-12-28",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.28.424554",
+    "rel_abs": "SARS-CoV-2 has caused the global COVID-19 pandemic. Although passively delivered neutralizing antibodies against SARS-CoV-2 show promise in clinical trials, their mechanism of action in vivo is incompletely understood. Here, we define correlates of protection of neutralizing human monoclonal antibodies (mAbs) in SARS-CoV-2-infected animals. Whereas Fc effector functions are dispensable when representative neutralizing mAbs are administered as prophylaxis, they are required for optimal protection as therapy. When given after infection, intact mAbs reduce SARS-CoV-2 burden and lung disease in mice and hamsters better than loss-of-function Fc variant mAbs. Fc engagement of neutralizing antibodies mitigates inflammation and improves respiratory mechanics, and transcriptional profiling suggests these phenotypes are associated with diminished innate immune signaling and preserved tissue repair. Immune cell depletions establish that neutralizing mAbs require monocytes for therapeutic efficacy. Thus, potently neutralizing mAbs require Fc effector functions for maximal therapeutic benefit during therapy to modulate protective immune responses and mitigate lung disease.",
+    "rel_num_authors": 19,
+    "rel_authors": [
+      {
+        "author_name": "Emma S. Winkler",
+        "author_inst": "Washington University"
+      },
+      {
+        "author_name": "Pavlo Gilchuk",
+        "author_inst": "Vanderbilt University"
+      },
+      {
+        "author_name": "Jinsheng Yu",
+        "author_inst": "Washington University"
+      },
+      {
+        "author_name": "Adam L. Bailey",
+        "author_inst": "Washington University"
+      },
+      {
+        "author_name": "Rita E. Chen",
+        "author_inst": "Washington University"
+      },
+      {
+        "author_name": "Seth J. Zost",
+        "author_inst": "Vanderbilt University"
+      },
+      {
+        "author_name": "Hyesun Jang",
+        "author_inst": "University of Georgia"
+      },
+      {
+        "author_name": "Ying Huang",
+        "author_inst": "University of Georgia"
+      },
+      {
+        "author_name": "James D. Allen",
+        "author_inst": "University of Georgia"
+      },
+      {
+        "author_name": "James Brett Case",
+        "author_inst": "Washington University"
+      },
+      {
+        "author_name": "Rachel E. Sutton",
+        "author_inst": "Vanderbilt University"
+      },
+      {
+        "author_name": "Robert H. Carnahan",
+        "author_inst": "Vanderbilt University"
+      },
+      {
+        "author_name": "Tamarand L. Darling",
+        "author_inst": "Washington University"
+      },
+      {
+        "author_name": "Adrianus C. M. Boon",
+        "author_inst": "Washington University"
+      },
+      {
+        "author_name": "Matthias Mack",
+        "author_inst": "University Hospital Regensburg"
+      },
+      {
+        "author_name": "Richard D. Head",
+        "author_inst": "Washington University"
+      },
+      {
+        "author_name": "Ted M. Ross",
+        "author_inst": "University of Georgia"
+      },
+      {
+        "author_name": "James E. Crowe Jr.",
+        "author_inst": "Vanderbilt University"
+      },
+      {
+        "author_name": "Michael Diamond",
+        "author_inst": "Washington University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2020.12.28.424451",
     "rel_title": "SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma",
@@ -997296,29 +996167,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.12.23.20248808",
-    "rel_title": "Characteristic spatial scales of SARS-CoV-2 pandemics: lessons from mass rapid antigen testing in Slovakia",
-    "rel_date": "2020-12-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.23.20248808",
-    "rel_abs": "Mass antigen testing in Slovakia conducted in October and November 2020 is a source of important data. We perform its statistical analysis and study epidemic geographical patterns. We observe exponentially distributed test positivity and exponential trends in its geographical distribution, and its approximately 10 km spatial characteristic correlation length. A small correlation between positivity in two consecutive testing rounds appeared on the municipalities level but it significantly increased on the counties level. Recent 7-day PCR tests incidence per capita served as a good proxy for antigen test positivity. Positivity of non-residents was higher than of residents when mass testing was offered only in municipalities with the highest positivity in previous rounds. Reduction in positivity in repeated testing increased with the positivity in the earlier round. Our results contribute to better understanding of pandemic data, and aid an assessment of mass testing efficiency, and planning of mitigation measures.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Katarina Bodova",
-        "author_inst": "Comenius University"
-      },
-      {
-        "author_name": "Richard Kollar",
-        "author_inst": "Comenius University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.12.23.20248798",
     "rel_title": "Support and follow-up needs of patients discharged from Intensive Care after severe COVID-19: a mixed-methods study of the views of UK general practitioners and intensive care staff during the pandemic's first wave",
@@ -997569,6 +996417,25 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2020.12.23.424283",
+    "rel_title": "The SARS-CoV-2 S1 spike protein mutation N501Y alters the protein interactions with both hACE2 and human derived antibody: A Free energy of perturbation study",
+    "rel_date": "2020-12-26",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.23.424283",
+    "rel_abs": "The N501Y and K417N mutations in spike protein of SARS-CoV-2 and their combination arise questions but the data about their mechanism of action at molecular level is limited. Here, we present Free energy perturbation (FEP) calculations for the interactions of the spike S1 receptor binding domain (RBD) with both the ACE2 receptor and an antibody derived from COVID-19 patients. Our results shown that the S1 RBD-ACE2 interactions were significantly increased whereas those with the STE90-C11 antibody dramatically decreased; about over 100 times. The K417N mutation had much more pronounced effect and in a combination with N501Y fully abolished the antibody effect. This may explain the observed in UK and South Africa more spread of the virus but also raise an important question about the possible human immune response and the success of already available vaccines.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Filip Fratev",
+        "author_inst": "Micar Innovation (Micar21)"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "molecular biology"
+  },
   {
     "rel_doi": "10.1101/2020.12.23.424172",
     "rel_title": "Pulmonary stromal expansion and intra-alveolar coagulation are primary causes of Covid-19 death",
@@ -999002,125 +997869,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2020.12.22.20248691",
-    "rel_title": "Automated processing of thermal imaging to detect COVID-19",
-    "rel_date": "2020-12-24",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.22.20248691",
-    "rel_abs": "Rapid and sensitive screening tools for SARS-CoV-2 infection are essential to limit the spread of COVID-19 and to properly allocate national resources. Here, we developed a new point-of-care, non-contact thermal imaging tool to detect COVID-19, based on image-processing algorithms and machine learning analysis. We captured thermal images of the back of individuals with and without COVID-19 using a portable thermal camera that connects directly to smartphones. Our novel image processing algorithms automatically extracted multiple texture and shape features of the thermal images and achieved an area under the curve (AUC) of 0.85 in detecting COVID-19 with up to 92% sensitivity. Thermal imaging scores were inversely correlated with clinical variables associated with COVID-19 disease progression. We show, for the first time, that a hand-held thermal imaging device can be used to detect COVID-19. Non-invasive thermal imaging could be used to screen for COVID-19 in out-of-hospital settings, especially in low-income regions with limited imaging resources.\n\nHIGHLIGHTSO_LIAutomated processing of thermal images of the back can be used to detect COVID-19 with up to 92% sensitivity.\nC_LIO_LIThe extracted texture features of the thermal image are associated with COVID-19 disease progression and lung injury.\nC_LIO_LIA portable thermal camera that connects directly to smartphones can be used to detect COVID-19.\nC_LIO_LINon-invasive thermal imaging could be used to screen for COVID-19 in out-of-hospital settings and regions with limited imaging resources.\nC_LI\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=68 SRC=\"FIGDIR/small/20248691v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (15K):\norg.highwire.dtl.DTLVardef@1afd708org.highwire.dtl.DTLVardef@14e5a5eorg.highwire.dtl.DTLVardef@10ede4corg.highwire.dtl.DTLVardef@1248470_HPS_FORMAT_FIGEXP  M_FIG C_FIG",
-    "rel_num_authors": 26,
-    "rel_authors": [
-      {
-        "author_name": "Rafael Y. Brzezinski",
-        "author_inst": "Sheba Medical Center and Tel Aviv University"
-      },
-      {
-        "author_name": "Neta Rabin",
-        "author_inst": "Tel Aviv University"
-      },
-      {
-        "author_name": "Nir Lewis",
-        "author_inst": "Sheba Medical Center and Tel Aviv University"
-      },
-      {
-        "author_name": "Racheli Peled",
-        "author_inst": "Sheba Medical Center and Tel Aviv University"
-      },
-      {
-        "author_name": "Ariel Kerpel",
-        "author_inst": "Sheba Medical Center and Tel Aviv University"
-      },
-      {
-        "author_name": "Avishai M. Tsur",
-        "author_inst": "Sheba Medical Center and Tel Aviv University"
-      },
-      {
-        "author_name": "Omer Gendelman",
-        "author_inst": "Sheba Medical Center and Tel Aviv University"
-      },
-      {
-        "author_name": "Nili Naftali-Shani",
-        "author_inst": "Sheba Medical Center and Tel Aviv University"
-      },
-      {
-        "author_name": "Irina Gringauz",
-        "author_inst": "Sheba Medical Center and Tel Aviv University"
-      },
-      {
-        "author_name": "Howard Amital",
-        "author_inst": "Sheba Medical Center and Tel Aviv University"
-      },
-      {
-        "author_name": "Avshalom Leibowitz",
-        "author_inst": "Sheba Medical Center and Tel Aviv University"
-      },
-      {
-        "author_name": "Haim Mayan",
-        "author_inst": "Sheba Medical Center and Tel Aviv University"
-      },
-      {
-        "author_name": "Ilan Ben-Zvi",
-        "author_inst": "Sheba Medical Center and Tel Aviv University"
-      },
-      {
-        "author_name": "Eyal Heler",
-        "author_inst": "Sheba Medical Center and Tel Aviv University"
-      },
-      {
-        "author_name": "Liran Shechtman",
-        "author_inst": "Sheba Medical Center and Tel Aviv University"
-      },
-      {
-        "author_name": "Ori Rogovski",
-        "author_inst": "Tel Aviv Sourasky Medical Center and Tel Aviv University"
-      },
-      {
-        "author_name": "Shani Shenhar-Tsarfaty",
-        "author_inst": "Tel Aviv Sourasky Medical Center and Tel Aviv University"
-      },
-      {
-        "author_name": "Eli Konen",
-        "author_inst": "Sheba Medical Center and Tel Aviv University"
-      },
-      {
-        "author_name": "Edith M. Marom",
-        "author_inst": "Sheba Medical Center and Tel Aviv University"
-      },
-      {
-        "author_name": "Avinoah Ironi",
-        "author_inst": "Sheba Medical Center and Tel Aviv University"
-      },
-      {
-        "author_name": "Galia Rahav",
-        "author_inst": "Sheba Medical Center and Tel Aviv University"
-      },
-      {
-        "author_name": "Yair Zimmer",
-        "author_inst": "Afeka Tel Aviv Academic College of Engineering"
-      },
-      {
-        "author_name": "Ehud Grossman",
-        "author_inst": "Sheba Medical Center and Tel Aviv University"
-      },
-      {
-        "author_name": "Zehava Ovadia-Blechman",
-        "author_inst": "Afeka Tel Aviv Academic College of Engineering"
-      },
-      {
-        "author_name": "Jonathan Leor",
-        "author_inst": "Sheba Medical Center and Tel Aviv University"
-      },
-      {
-        "author_name": "Oshrit Hoffer",
-        "author_inst": "Afeka Tel Aviv Academic College of Engineering"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "radiology and imaging"
-  },
   {
     "rel_doi": "10.1101/2020.12.22.20248501",
     "rel_title": "Prevalence of bacterial pathogens and potential role in COVID-19 severity in patients admitted to intensive care units in Brazil",
@@ -999467,6 +998215,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "genetic and genomic medicine"
   },
+  {
+    "rel_doi": "10.1101/2020.12.17.20248360",
+    "rel_title": "Identifying communities at risk for COVID-19-related burden across 500 U.S. Cities and within New York City",
+    "rel_date": "2020-12-24",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.17.20248360",
+    "rel_abs": "BackgroundWhile it is well-known that older individuals with certain comorbidities are at highest risk for complications related to COVID-19 including hospitalization and death, we lack tools to identify communities at highest risk with fine-grained spatial and temporal resolution. Information collected at a county level obscures local risk and complex interactions between clinical comorbidities, the built environment, population factors, and other social determinants of health.\n\nMethodsWe develop a robust COVID-19 Community Risk Score (C-19 Risk Score) that summarizes the complex disease co-occurrences for individual census tracts with unsupervised learning, selected on their basis for association with risk for COVID complications, such as death. We mapped the C-19 Risk Score onto neighborhoods in New York City and associated the score with C-19 related death. We further predict the C-19 Risk Score using satellite imagery data to map the built environment in C-19 Risk.\n\nResultsThe C-19 Risk Score describes 85% of variation in co-occurrence of 15 diseases that are risk factors for COVID complications among 26K census tract neighborhoods (median population size of tracts: 4,091). The C-19 Risk Score is associated with a 40% greater risk for COVID-19 related death across NYC (April and September 2020) for a 1SD change in the score (Risk Ratio for 1SD change in C19 Risk Score: 1.4, p < .001). Satellite imagery coupled with social determinants of health explain nearly 90% of the variance in the C-19 Risk Score in the United States in held-out census tracts (R2 of 0.87).\n\nConclusionsThe C-19 Risk Score localizes COVID-19 risk at the census tract level and predicts COVID-19 related morbidity and mortality.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Chirag J Patel",
+        "author_inst": "XY Health, Inc"
+      },
+      {
+        "author_name": "Andrew Deonarine",
+        "author_inst": "XY.Health, Inc"
+      },
+      {
+        "author_name": "Genevieve Lyons",
+        "author_inst": "XY.Health, Inc"
+      },
+      {
+        "author_name": "Chirag Lakhani",
+        "author_inst": "XY.Health, Inc."
+      },
+      {
+        "author_name": "Arjun K Manrai",
+        "author_inst": "XY.Health, Inc."
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health informatics"
+  },
   {
     "rel_doi": "10.1101/2020.12.23.20248514",
     "rel_title": "Risk factors for community transmission of SARS-CoV-2. A cross-sectional study in 116,678 people.",
@@ -1000672,61 +999455,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.12.23.20248789",
-    "rel_title": "SARS-CoV-2 Testing in Florida, Illinois, and Maryland: Access and Barriers",
-    "rel_date": "2020-12-24",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.23.20248789",
-    "rel_abs": "ObjectiveTo characterize the SARS-CoV-2 testing cascade and associated barriers in three US states.\n\nMethodsWe recruited participants from Florida, Illinois, and Maryland ([~]1000/state) for an online survey September 16 - October 15, 2020. The survey covered demographics, COVID-19 symptoms, and experiences around SARS-CoV-2 PCR testing in the prior 2 weeks. Logistic regression was used to analyze associations with outcomes of interest.\n\nResultsOverall, 316 (10%) of 3,058 respondents wanted/needed a test in the two weeks prior to the survey. Of these, 166 (53%) were able to get tested and 156 (94%) received results; 53% waited [&ge;] 8 days to get results from when they wanted/needed a test. There were no significant differences by state. Among those wanting/needing a test, getting tested was significantly less common among men (aOR: 0.46) and those reporting black race (aOR: 0.53) and more common in those reporting recent travel (aOR: 3.35).\n\nConclusionsThere is an urgent need for a national communication strategy on who should get tested and where one can get tested. Additionally, measures need to be taken to improve access and reduce turn-around-time.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Steven J. Clipman",
-        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
-      },
-      {
-        "author_name": "Amy Wesolowski",
-        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
-      },
-      {
-        "author_name": "Shruti H. Mehta",
-        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
-      },
-      {
-        "author_name": "Smisha Agarwal",
-        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
-      },
-      {
-        "author_name": "Sarah E. Cobey",
-        "author_inst": "University of Chicago"
-      },
-      {
-        "author_name": "Derek A.T. Cummings",
-        "author_inst": "University of Florida"
-      },
-      {
-        "author_name": "Dustin G. Gibson",
-        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
-      },
-      {
-        "author_name": "Alain B. Labrique",
-        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
-      },
-      {
-        "author_name": "Gregory D. Kirk",
-        "author_inst": "Johns Hopkins University School of Medicine"
-      },
-      {
-        "author_name": "Sunil S. Solomon",
-        "author_inst": "Johns Hopkins University School of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.12.23.20248761",
     "rel_title": "Forecasting intensive care unit demand during the COVID-19 pandemic: A spatial age-structured microsimulation model",
@@ -1001128,6 +999856,85 @@
     "type": "new results",
     "category": "bioinformatics"
   },
+  {
+    "rel_doi": "10.1101/2020.12.23.424232",
+    "rel_title": "Remdesivir-Ivermectin combination displays synergistic interaction with improved in vitro antiviral activity against SARS-CoV-2",
+    "rel_date": "2020-12-24",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.23.424232",
+    "rel_abs": "A key element for the prevention and management of COVID-19 is the development of effective therapeutics. Drug combination strategies of repurposed drugs offer several advantages over monotherapies, including the potential to achieve greater efficacy, the potential to increase the therapeutic index of drugs and the potential to reduce the emergence of drug resistance. Here, we report on the in vitro synergistic interaction between two FDA approved drugs, remdesivir and ivermectin resulting in enhanced antiviral activity against SARS-CoV-2. These findings warrant further investigations into the clinical potential of this combination, together with studies to define the underlying mechanism.",
+    "rel_num_authors": 16,
+    "rel_authors": [
+      {
+        "author_name": "Laura Jeffreys",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Shaun H Pennington",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Jack Duggan",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Claire H Caygill",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Rose C Lopeman",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Alastair Breen",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Jessica Jinks",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Alison Ardrey",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Samantha Donnellan",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Edward I Patterson",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Grant I Hughes",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "W. David Hong",
+        "author_inst": "University of Liverpool"
+      },
+      {
+        "author_name": "Ghaith Aljayyoussi",
+        "author_inst": "Liverpool School of tropical Medicine"
+      },
+      {
+        "author_name": "Andrew Owen",
+        "author_inst": "University of Liverpool"
+      },
+      {
+        "author_name": "Steve A Ward",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Giancarlo A Biagini",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2020.12.23.424169",
     "rel_title": "SARS-CoV-2 sensing by RIG-I and MDA5 links epithelial infection to macrophage inflammation",
@@ -1002605,89 +1001412,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.12.21.20191346",
-    "rel_title": "Direct RNA nanopore sequencing of SARS-CoV-2 extracted from critical material from swabs",
-    "rel_date": "2020-12-23",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20191346",
-    "rel_abs": "BackgroundIn consideration of the increasing prevalence of COVID-19 cases in several countries and the resulting demand for unbiased sequencing approaches, we performed a direct RNA sequencing experiment using critical oropharyngeal swab samples collected from Italian patients infected with SARS-CoV-2 from the Palermo region in Sicily.\n\nMethodsHere, we identified the sequences SARS-CoV-2 directly in RNA extracted from critical samples using the Oxford Nanopore MinION technology without prior cDNA retro-transcription.\n\nResultsUsing an appropriate bioinformatics pipeline, we could identify mutations in the nucleocapisid (N) gene, which have been reported previously in studies conducted in other countries.\n\nConclusionTo the best of our knowledge, the technique used in this study has not been used for SARS-CoV-2 detection previously owing to the difficulties in the extraction of RNA of sufficient quantity and quality from routine oropharyngeal swabs.\n\nDespite these limitations, this approach provides the advantages of true native RNA sequencing, and does not include amplification steps that could introduce systematic errors.\n\nThis study can provide novel information relevant to the current strategies adopted in SARS-CoV-2 next-generation sequencing.\n\nWe deposited the gene sequence in the NCBI database under the following URL:https://www.ncbi.nlm.nih.gov/nuccore/MT457389",
-    "rel_num_authors": 17,
-    "rel_authors": [
-      {
-        "author_name": "Davide Vacca",
-        "author_inst": "University of Palermo"
-      },
-      {
-        "author_name": "Antonino Fiannaca",
-        "author_inst": "National Research Council of Italy"
-      },
-      {
-        "author_name": "Fabio Tramuto",
-        "author_inst": "University of Palermo"
-      },
-      {
-        "author_name": "Valeria Cancila",
-        "author_inst": "University of Palermo"
-      },
-      {
-        "author_name": "Laura La Paglia",
-        "author_inst": "National Research Council of Italy"
-      },
-      {
-        "author_name": "Walter Mazzucco",
-        "author_inst": "University of Palermo"
-      },
-      {
-        "author_name": "Alessandro Gulino",
-        "author_inst": "University of Palermo"
-      },
-      {
-        "author_name": "Massimo La Rosa",
-        "author_inst": "National Research Council of Italy"
-      },
-      {
-        "author_name": "Carmelo Massimo Maida",
-        "author_inst": "University of Palermo"
-      },
-      {
-        "author_name": "Gaia Morello",
-        "author_inst": "University of Palermo"
-      },
-      {
-        "author_name": "Beatrice Belmonte",
-        "author_inst": "University of Palermo"
-      },
-      {
-        "author_name": "Alessandra Casuccio",
-        "author_inst": "University of Palermo"
-      },
-      {
-        "author_name": "Rosario Maugeri",
-        "author_inst": "University of Palermo"
-      },
-      {
-        "author_name": "Gerardo Iacopino",
-        "author_inst": "University of Palermo"
-      },
-      {
-        "author_name": "Francesco Vitale",
-        "author_inst": "University of Palermo"
-      },
-      {
-        "author_name": "Claudio Tripodo",
-        "author_inst": "University of Palermo"
-      },
-      {
-        "author_name": "Alfonso Urso",
-        "author_inst": "National Research Council of Italy"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.12.21.20248645",
     "rel_title": "Renin-angiotensin system blockers and mortality in COVID-19: a territory-wide study from Hong Kong",
@@ -1002958,6 +1001682,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
+  {
+    "rel_doi": "10.1101/2020.12.16.423122",
+    "rel_title": "Immune-Based Prediction of COVID-19 Severity and Chronicity Decoded Using Machine Learning",
+    "rel_date": "2020-12-22",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.16.423122",
+    "rel_abs": "Individuals with systemic symptoms long after COVID-19 has cleared represent approximately ~10% of all COVID-19 infected individuals. Here we present a bioinformatics approach to predict and model the phases of COVID so that effective treatment strategies can be devised and monitored. We investigated 144 individuals including normal individuals and patients spanning the COVID-19 disease continuum. We collected plasma and isolated PBMCs from 29 normal individuals, 26 individuals with mild-moderate COVID-19, 25 individuals with severe COVID-19, and 64 individuals with Chronic COVID-19 symptoms. Immune subset profiling and a 14-plex cytokine panel were run on all patients. Data was analyzed using machine learning methods to predict and distinguish the groups from each other.Using a multi-class deep neural network classifier to better fit our prediction model, we recapitulated a 100% precision, 100% recall and F1 score of 1 on the test set. Moreover, a first score specific for the chronic COVID-19 patients was defined as S1 = (IFN-{gamma} + IL-2)/ CCL4-MIP-1{beta}. Second, a score specific for the severe COVID-19 patients was defined as S2 = (10*IL-10 + IL-6) - (IL-2 + IL-8). Severe cases are characterized by excessive inflammation and dysregulated T cell activation, recruitment, and counteracting activities. While chronic patients are characterized by a profile able to induce the activation of effector T cells with pro-inflammatory properties and the capacity of generating an effective immune response to eliminate the virus but without the proper recruitment signals to attract activated T cells.\n\nSummaryImmunologic Modeling of Severity and Chronicity of COVID-19",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Bruce Patterson",
+        "author_inst": "IncellDx"
+      },
+      {
+        "author_name": "Jose Guevara-Coto",
+        "author_inst": "Universidad de Costa Rica"
+      },
+      {
+        "author_name": "Ram Yogendra",
+        "author_inst": "ECA Wellness"
+      },
+      {
+        "author_name": "Edgar B. Francisco",
+        "author_inst": "IncellDx, Inc"
+      },
+      {
+        "author_name": "emily long",
+        "author_inst": "incelldx, Inc"
+      },
+      {
+        "author_name": "Amruta Pise",
+        "author_inst": "IncellDx, Inc"
+      },
+      {
+        "author_name": "Hallison Rodrigues",
+        "author_inst": "IncellDx, Inc"
+      },
+      {
+        "author_name": "Purvi Parikh",
+        "author_inst": "NYU"
+      },
+      {
+        "author_name": "Javier Mora",
+        "author_inst": "Universidad de Costa Rica"
+      },
+      {
+        "author_name": "Rodrigo A. Mora-Rodriguez",
+        "author_inst": "Universidad de Costa Rica"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2020.12.22.20248696",
     "rel_title": "A comparative analysis of COVID-19 mortality rate across the globe: An extensive analysis of the associated factors",
@@ -1004247,29 +1003026,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.12.21.20248431",
-    "rel_title": "How optimal allocation of limited testing capacity changes epidemic dynamics",
-    "rel_date": "2020-12-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248431",
-    "rel_abs": "Insufficient testing capacity continues to be a critical bottleneck in the worldwide fight against COVID-19. Optimizing the deployment of limited testing resources has therefore emerged as a keystone problem in pandemic response planning. Here, we use a modified SEIR model to optimize testing strategies under a constraint of limited testing capacity. We define pre-symptomatic, asymptomatic, and symptomatic infected classes, and assume that positively tested individuals are immediately moved into quarantine. We further define two types of testing. Clinical testing focuses only on the symptomatic class. Non-clinical testing detects pre- and asymptomatic individuals from the general population, and an \"information\" parameter governs the degree to which such testing can be focused on high infection risk individuals. We then solve for the optimal mix of clinical and non-clinical testing as a function of both testing capacity and the information parameter. We find that purely clinical testing is optimal at very low testing capacities, supporting early guidance to ration tests for the sickest patients. Additionally, we find that a mix of clinical and non-clinical testing becomes optimal as testing capacity increases. At high but empirically observed testing capacities, a mix of clinical testing and unfocused (information=0) non-clinical testing becomes optimal. We further highlight the advantages of early implementation of testing programs, and of combining optimized testing with contact reduction interventions such as lockdowns, social distancing, and masking.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Justin M Calabrese",
-        "author_inst": "Center for Advanced Systems Understanding (CASUS)"
-      },
-      {
-        "author_name": "Jeffery Demers",
-        "author_inst": "Department of Biology, University of Maryland"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.12.21.20248241",
     "rel_title": "Mathematical Models for Assessing Vaccination Scenarios in Several Provinces in Indonesia",
@@ -1004480,6 +1003236,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.12.20.20248581",
+    "rel_title": "Early empirical assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020",
+    "rel_date": "2020-12-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.20.20248581",
+    "rel_abs": "Two new SARS-CoV-2 lineages with the N501Y mutation in the receptor binding domain of the spike protein have rapidly become prevalent in the UK. We estimated that the earlier 501Y lineage without amino acid deletion {Delta}69/{Delta}70 circulating mainly between early September to mid-November was 10% (6-13%) more transmissible than the 501N lineage, and the currently dominant 501Y lineage with amino acid deletion {Delta}69/{Delta}70 circulating since late September was 75% (70-80%) more transmissible than the 501N lineage.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Kathy Leung",
+        "author_inst": "The University of Hong Kong"
+      },
+      {
+        "author_name": "Marcus HH Shum",
+        "author_inst": "The University of Hong Kong"
+      },
+      {
+        "author_name": "Gabriel M Leung",
+        "author_inst": "The University of Hong Kong"
+      },
+      {
+        "author_name": "Tommy TY Lam",
+        "author_inst": "The University of Hong Kong"
+      },
+      {
+        "author_name": "Joseph T Wu",
+        "author_inst": "The University of Hong Kong"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.12.21.20248153",
     "rel_title": "Changes in hospital prescribing activity at a specialist children's hospital during the COVID-19 pandemic - an observational study",
@@ -1005753,149 +1004544,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.12.21.20248409",
-    "rel_title": "COVID-19 in-hospital mortality in South Africa: the intersection of communicable and non-communicable chronic diseases in a high HIV prevalence setting",
-    "rel_date": "2020-12-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248409",
-    "rel_abs": "BackgroundThe interaction between COVID-19, non-communicable diseases, and chronic infectious diseases such as HIV and tuberculosis (TB) are unclear, particularly in low- and middle-income countries in Africa. South Africa has a national adult HIV prevalence of 19% and TB prevalence of 0.7%. Using a nationally representative hospital surveillance system in South Africa, we investigated the factors associated with in-hospital mortality among individuals with COVID-19.\n\nMethodsUsing data from national active hospital surveillance, we describe the demographic characteristics, clinical features, and in-hospital mortality among hospitalised individuals testing positive for SARS-CoV-2, during 5 March 2020 to 27 March 2021. Chained equation multiple imputation was used to account for missing data and random effect multivariable logistic regression models were used to assess the role of HIV-status and underlying comorbidities on in-hospital COVID-19 mortality.\n\nFindingsAmong the 219,265 individuals admitted with laboratory confirmed SARS-Cov-2, 51,037 (23.3%) died. Most commonly observed comorbidities among individuals with available data were hypertension (61,098/163,350; 37.4%), diabetes (43,885/159,932; 27.4%), and HIV (13,793/151,779; %), while TB was reported in 3.6% (5,282/146,381) of individuals. While age was the most important predictor, other factors associated with in-hospital COVID-19 mortality were HIV infection [aOR 1.34, 95% CI: 1.27-1.43), past TB [aOR 1.26, 95% CI: 1.15-1.38), current TB [aOR 1.42, 95% CI: 1.22-1.64) and both past and current TB [aOR 1.48, 95% CI: 1.32-1.67) compared to never TB, as well as other described risk factors for COVID-19, such as male sex, non-white race, and chronic underlying hypertension, diabetes, chronic cardiac disease, chronic renal disease, and malignancy. After adjusting for other factors, PLWH not on ART [aOR 1.45, 95% CI: 1.22-1.72] were more likely to die in-hospital compared to PLWH on ART. Among PLWH, the prevalence of other comorbidities was 29.2% compared to 30.8% among HIV-uninfected individuals. Increasing number of comorbidities was associated with increased mortality risk in both PLWH and HIV-uninfected individuals.\n\nInterpretationIdentified high risk individuals (older individuals and those with chronic comorbidities and PLWH, particularly those not on ART) would benefit from COVID-19 prevention programmes such as vaccine prioritisation, as well as early referral and treatment.\n\nFundingSouth African National Government\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSSince the emergence of the COVID-19 pandemic, studies have identified older age, male sex and presence of underlying comorbidities including heart disease and diabetes as risk factors for severe disease and death. There are very few studies, however, carried out in low- and middle-income countries (LMIC) in Africa, many of whom have high poverty rates, limited access to healthcare, and high prevalence of chronic communicable diseases, such as HIV and tuberculosis (TB). Data are also limited from settings with limited access to HIV treatment programmes. Early small cohort studies mainly from high income countries were not conclusive on whether HIV or TB are risk factors for disease severity and death in COVID-19 patients. Large population cohort studies from South Africas Western Cape province and the United Kingdom (UK) have found people living with HIV (PLWH) to have a moderately increased risk of COVID-19 associated mortality. Of these, only the Western Cape study presented data on mortality risk associated with presence of high viral load or immunosuppression, and found similar levels of severity irrespective of these factors. Recent meta-analyses have confirmed the association of HIV with COVID-19 mortality. No studies reported on the interaction between HIV-infection and other non-communicable comorbidities on COVID-19 associated mortality.\n\nWe performed separate literature searches on PubMed using the following terms: \"COVID-19\" \"risk factors\" and \"mortality\"; \"HIV\" \"COVID-19\" and \"mortality\"; \"TB\" \"COVID-19\" and \"mortality\". All searches included publications from December 1, 2019 until May 5, 2021, without language restrictions. Pooled together, we identified 2,786 published papers. Additionally, we performed two literature searches on MedRxiv using the terms \"HIV\" \"COVID-19\" and \"mortality\", and \"TB\" \"COVID-19\" and \"mortality\" from April 25, 2020 until May 5, 2021, without language restrictions. Pooled together, we identified 7,744 pre-prints.\n\nAdded value of this studyAmong a large national cohort of almost 220,000 individuals hospitalised with COVID-19 in a setting with 19% adult HIV prevalence and 0.7%TB prevalence, we found that along with age, sex and other comorbidities, HIV and TB were associated with a moderately increased risk of in-hospital mortality. We found increasing risk of in-hospital mortality among PLWH not on ART compared to those on ART. Among PLWH, the prevalence of other comorbidities was high (29%) and the effect of increasing numbers of comorbidities on mortality was similar in PLWH and HIV-uninfected individuals. Our study included 13,793 PLWH from all provinces in the country with varying levels of access to HIV treatment programmes.\n\nImplications of all the available evidenceThe evidence suggests that PLWH and TB-infected individuals should be prioritised for COVID-19 prevention and treatment programmes, particularly those with additional comorbidities. Increasing age and presence of chronic underlying illness are important additional factors associated with COVID-19 mortality in a middle-income African setting. The completeness of data is a limitation of this national surveillance system, and additional data are needed to confirm these findings.",
-    "rel_num_authors": 32,
-    "rel_authors": [
-      {
-        "author_name": "WAASILA JASSAT",
-        "author_inst": "National Institute for Communicable Diseases"
-      },
-      {
-        "author_name": "Cheryl Cohen",
-        "author_inst": "National Institute for Communicable Diseases"
-      },
-      {
-        "author_name": "Stefano Tempia",
-        "author_inst": "NICD"
-      },
-      {
-        "author_name": "Maureen Masha",
-        "author_inst": "Right to Care"
-      },
-      {
-        "author_name": "Susan Goldstein",
-        "author_inst": "South Africa Medical Research Council (SAMRC) Centre for Health Economics and Decision Science-PRICELESS SA, School of Public Health, University of the Witwater"
-      },
-      {
-        "author_name": "Tendesayi Kufa-Chakezha",
-        "author_inst": "National Institute for Communicable Diseases"
-      },
-      {
-        "author_name": "Pelagia Murangandi",
-        "author_inst": "United Centers for Disease Prevention and Control"
-      },
-      {
-        "author_name": "Dana Savulescu",
-        "author_inst": "National Institute for Communicable Diseases"
-      },
-      {
-        "author_name": "Sibongile Walaza",
-        "author_inst": "National Institute for Communicable Diseases"
-      },
-      {
-        "author_name": "Jamy-Lee Bam",
-        "author_inst": "Western Cape Government: Health, Health Impact Assessment Directorate"
-      },
-      {
-        "author_name": "Mary-Ann Davies",
-        "author_inst": "Western Cape Government: Health, Health Impact Assessment Directorate"
-      },
-      {
-        "author_name": "Hans W Prozesky",
-        "author_inst": "Tygerberg Hospital and Division of Infectious Disease, University of Stellenbosch"
-      },
-      {
-        "author_name": "Jonathan Naude",
-        "author_inst": "Mitchells Plain District Hospital"
-      },
-      {
-        "author_name": "Trevor Mnguni",
-        "author_inst": "Khayelitsha District Hospital"
-      },
-      {
-        "author_name": "Charlene A Lawrence",
-        "author_inst": "Western Cape Department of Health"
-      },
-      {
-        "author_name": "Hlengani Mathema",
-        "author_inst": "National Institute for Communicable Diseases"
-      },
-      {
-        "author_name": "Jarrod Zamparini",
-        "author_inst": "University of Witwatersrand"
-      },
-      {
-        "author_name": "John Black",
-        "author_inst": "Walter Sisulu University"
-      },
-      {
-        "author_name": "Ruchika Mehta",
-        "author_inst": "Klerksdorp Tshepong Hospital"
-      },
-      {
-        "author_name": "Arifa Parker",
-        "author_inst": "Tygerberg Hospital"
-      },
-      {
-        "author_name": "Perpetual Chikobvu",
-        "author_inst": "Free State Department of Health"
-      },
-      {
-        "author_name": "Halima Dawood",
-        "author_inst": "Grey's Hospital"
-      },
-      {
-        "author_name": "Ntshengedzeni Muvhango",
-        "author_inst": "Limpopo Department of Health"
-      },
-      {
-        "author_name": "Riaan Strydom",
-        "author_inst": "Northern Cape Department of Health"
-      },
-      {
-        "author_name": "Tsholofelo Adelekan",
-        "author_inst": "Gauteng Department of Health"
-      },
-      {
-        "author_name": "Bhekizizwe Mdlovu",
-        "author_inst": "Mpumalanga Department of Health"
-      },
-      {
-        "author_name": "Nirvasha Moodley",
-        "author_inst": "KwaZulu Natal Department of Health"
-      },
-      {
-        "author_name": "Eunice L Nemavhandu",
-        "author_inst": "Eastern Cape Department of Health"
-      },
-      {
-        "author_name": "Paul Rheeder",
-        "author_inst": "University of Pretoria"
-      },
-      {
-        "author_name": "Jacqueline Venturas",
-        "author_inst": "University of Witwatersrand"
-      },
-      {
-        "author_name": "Nombulelo Magula",
-        "author_inst": "University of KwaZulu-Natal"
-      },
-      {
-        "author_name": "Lucille Blumberg",
-        "author_inst": "National Institute for Communicable Diseases"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.12.21.20248642",
     "rel_title": "Identification of SARS-CoV-2-specific immune alterations in acutely ill patients",
@@ -1006602,6 +1005250,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.12.21.20248288",
+    "rel_title": "Comparative analysis of loop-mediated isothermal amplification (LAMP)-based assays for rapid detection of SARS-CoV-2 genes",
+    "rel_date": "2020-12-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248288",
+    "rel_abs": "The COVID-19 pandemic caused by SARS-CoV-2 has infected millions worldwide and there is an urgent need to increase our diagnostic capacity to identify infected cases. Although RT-qPCR remains the gold standard for SARS-CoV-2 detection, this method requires specialised equipment in a diagnostic laboratory and has a long turn-around time to process the samples. To address this, several groups have recently reported development of loop-mediated isothermal amplification (LAMP) as a simple, low cost and rapid method for SARS-CoV-2 detection. Herein we present a comparative analysis of three LAMP-based assays that target different regions of the SARS-CoV-2: ORF1ab RdRP, ORF1ab nsp3 and Gene N. We perform a detailed assessment of their sensitivity, kinetics and false positive rates for SARS-CoV-2 diagnostics in LAMP or RT-LAMP reactions, using colorimetric or fluorescent detection. Our results independently validate that all three assays can detect SARS-CoV-2 in 30 minutes, with robust accuracy at detecting as little as 1000 RNA copies and the results can be visualised simply by color changes. We also note the shortcomings of these LAMP-based assays, including variable results with shorter reaction time or lower load of SARS-CoV-2, and false positive results in some experimental conditions. Overall for RT-LAMP detection, the ORF1ab RdRP and ORF1ab nsp3 assays have higher sensitivity and faster kinetics for detection, whereas the Gene N assay exhibits no false positives in 30 minutes reaction time. This study provides validation of the performance of LAMP-based assays for SARS-CoV-2 detection, which have important implications in development of point-of-care diagnostic for SARS-CoV-2.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Daniel Urrutia-Cabrera",
+        "author_inst": "Centre for Eye Research Australia, University of Melbourne"
+      },
+      {
+        "author_name": "Roxanne Hsiang-Chi Liou",
+        "author_inst": "Centre for Eye Research Australia, University of Melbourne"
+      },
+      {
+        "author_name": "Jianxiong Chan",
+        "author_inst": "Monash University"
+      },
+      {
+        "author_name": "Sandy Shen-Chi Hung",
+        "author_inst": "Centre for Eye Research Australia, University of Melbourne"
+      },
+      {
+        "author_name": "Alex W Hewitt",
+        "author_inst": "Centre for Eye Research Australia, University of Melbourne"
+      },
+      {
+        "author_name": "Keith Martin",
+        "author_inst": "Centre for Eye Research Australia, University of Melbourne"
+      },
+      {
+        "author_name": "Patrick Kwan",
+        "author_inst": "Monash University"
+      },
+      {
+        "author_name": "Raymond Ching-Bong Wong",
+        "author_inst": "Centre for Eye Research Australia Ltd/ University of Melbourne"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.12.21.20248140",
     "rel_title": "Rapid Detection of SARS-CoV-2 Antigen from Serum in a Hospitalized Population",
@@ -1007995,117 +1006690,6 @@
     "type": "new results",
     "category": "genomics"
   },
-  {
-    "rel_doi": "10.1101/2020.12.22.20242362",
-    "rel_title": "SARS-CoV-2 testing of 11,884 healthcare workers at an acute NHS hospital trust in England: a retrospective analysis",
-    "rel_date": "2020-12-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.22.20242362",
-    "rel_abs": "Healthcare workers (HCWs) are known to be at increased risk of infection with SARS-CoV-2, although whether these risks are equal across all roles is uncertain. Here we report a retrospective analysis of a large real-world dataset obtained from 10 March to 6 July 2020 in an NHS Foundation Trust in England with 17,126 employees. 3,338 HCWs underwent symptomatic PCR testing (14.4% positive, 2.8% of all staff) and 11,103 HCWs underwent serological testing for SARS-CoV-2 IgG (8.4% positive, 5.5% of all staff). Seropositivity was lower than other hospital settings in England but higher than community estimates. Increased test positivity rates were observed in HCWs from BAME backgrounds and residents in areas of higher social deprivation. A logistic regression model adjusting for these factors showed significant increases in the odds of testing positive in certain occupational groups, most notably domestic services staff, nurses and health-care assistants. PCR testing of symptomatic HCWs appeared to underestimate overall infection levels, probably due to asymptomatic seroconversion. Clinical outcomes were reassuring, with only a small minority of HCWs with COVID-19 requiring hospitalisation (2.3%) or ICU management (0.7%) and with no deaths. Despite a relatively low level of HCW infection compared to other UK cohorts, there were nevertheless important differences in test positivity rates between occupational groups, robust to adjustment for demographic factors such as ethnic background and social deprivation. Quantitative and qualitative studies are needed to better understand the factors contributing to this risk. Robust informatics solutions for HCW exposure data are essential to inform occupational monitoring.",
-    "rel_num_authors": 24,
-    "rel_authors": [
-      {
-        "author_name": "Aidan T. Hanrath",
-        "author_inst": "Newcastle University"
-      },
-      {
-        "author_name": "Ina Schim van der Loef",
-        "author_inst": "Newcastle University"
-      },
-      {
-        "author_name": "Dennis W. Lendrem",
-        "author_inst": "Newcastle University"
-      },
-      {
-        "author_name": "Kenneth F. Baker",
-        "author_inst": "Newcastle University"
-      },
-      {
-        "author_name": "David A. Price",
-        "author_inst": "The Newcastle upon Tyne Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Peter McDowall",
-        "author_inst": "The Newcastle upon Tyne Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Kiera McDowall",
-        "author_inst": "The Newcastle upon Tyne Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Susan Cook",
-        "author_inst": "The Newcastle upon Tyne Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Peter Towns",
-        "author_inst": "The Newcastle upon Tyne Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Ulrich Schwab",
-        "author_inst": "The Newcastle upon Tyne Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Adam Evans",
-        "author_inst": "The Newcastle upon Tyne Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Jill Dixon",
-        "author_inst": "The Newcastle upon Tyne Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Jennifer Collins",
-        "author_inst": "The Newcastle upon Tyne NHS Foundation Trust"
-      },
-      {
-        "author_name": "Shirelle Burton-Fanning",
-        "author_inst": "The Newcastle upon Tyne Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "David Saunders",
-        "author_inst": "The Newcastle upon Tyne Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Jayne Harwood",
-        "author_inst": "The Newcastle upon Tyne Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Julie Samuel",
-        "author_inst": "The Newcastle upon Tyne Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Matthias L. Schmid",
-        "author_inst": "The Newcastle upon Tyne Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Lucia Pareja-Cebrian",
-        "author_inst": "The Newcastle upon Tyne Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Ewan Hunter",
-        "author_inst": "The Newcastle upon Tyne Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Elizabeth Murphy",
-        "author_inst": "The Newcastle upon Tyne Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Yusri Taha",
-        "author_inst": "The Newcastle upon Tyne Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Brendan A. I. Payne",
-        "author_inst": "Newcastle University"
-      },
-      {
-        "author_name": "Christopher J A Duncan",
-        "author_inst": "Newcastle University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.12.22.423917",
     "rel_title": "T cell activation, highly armed cytotoxic cells and a sharp shift in monocytes CD300 receptors expression is characteristic of patients with severe COVID-19",
@@ -1008572,6 +1007156,57 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2020.12.20.423603",
+    "rel_title": "Fatty Acid Synthase inhibition prevents palmitoylation of SARS-CoV2 SpikeProtein and improves survival of mice infected with murine hepatitis virus.",
+    "rel_date": "2020-12-21",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.20.423603",
+    "rel_abs": "The Spike protein of SARS-CoV2 and other coronaviruses mediate host cell entry and are S-acylated on multiple phylogenetically conserved cysteine residues. Multiple protein acyltransferase enzymes of the ZDHHC family have been reported to modify Spike proteins post-translationally. Using resin-assisted capture mass spectrometry, we demonstrate that the Spike protein is S-acylated in SARS-CoV2 infected human and monkey cells. We further show that increased abundance of the human acyltransferase ZDHHC5 results in increased S-acylation of the SARS-CoV2 Spike protein, whereas ZDHHC5 knockout cells had a 40% reduction in the incorporation of an alkynyl-palmitate using click chemistry detection. We also find that the S-acylation of the Spike protein is not limited to palmitate, as clickable versions of myristate and stearate were also found on the immunocaptured protein. Yet, ZDHHC5 was highly selective for palmitate, suggesting that other ZDHHC enzymes mediated the incorporation of other fatty acyl chains. Thus, since multiple ZDHHC isoforms may modify the Spike protein, we examined the ability of the fatty acid synthase inhibitor TVB-3166 to prevent the S-acylation of the Spike proteins of SARS-CoV-2 and human CoV-229E. Treating cells with TVB-3166 inhibited S-acylation of ectopically expressed SARS-CoV2 Spike and attenuated the ability of SARS-CoV2 and human CoV-229E to spread in vitro. Additionally, treatment of mice with a comparatively low dose of TVB-3166 promoted survival from an otherwise fatal murine coronavirus infection. Our findings further substantiate the necessity of CoV Spike protein S-acylation and the potential use of fatty acid synthase inhibitors.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Katrina Mekhail",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Minhyoung Lee",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Michael Sugiyama",
+        "author_inst": "Ryerson University"
+      },
+      {
+        "author_name": "Audrey Astori",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Jonathan St-Germain",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Elyse Latreille",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Costin N Antonescu",
+        "author_inst": "Ryerson University"
+      },
+      {
+        "author_name": "Brian Raught",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Greg D Fairn",
+        "author_inst": "University of Toronto"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "cell biology"
+  },
   {
     "rel_doi": "10.1101/2020.12.20.422820",
     "rel_title": "In vitro measurements of protein-protein interactions show that antibody affinity governs the inhibition of SARS-CoV-2 spike/ACE2 binding in convalescent serum",
@@ -1009840,217 +1008475,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "genetic and genomic medicine"
   },
-  {
-    "rel_doi": "10.1101/2020.12.18.20248226",
-    "rel_title": "Failure to replicate the association of rare loss-of-function variants in type I IFN immunity genes with severe COVID-19",
-    "rel_date": "2020-12-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.18.20248226",
-    "rel_abs": "A recent report found that rare predicted loss-of-function (pLOF) variants across 13 candidate genes in TLR3- and IRF7-dependent type I IFN pathways explain up to 3.5% of severe COVID-19 cases. We performed whole-exome or whole-genome sequencing of 1,934 COVID-19 cases (713 with severe and 1,221 with mild disease) and 15,251 ancestry-matched population controls across four independent COVID-19 biobanks. We then tested if rare pLOF variants in these 13 genes were associated with severe COVID-19. We identified only one rare pLOF mutation across these genes amongst 713 cases with severe COVID-19 and observed no enrichment of pLOFs in severe cases compared to population controls or mild COVID-19 cases. We find no evidence of association of rare loss-of-function variants in the proposed 13 candidate genes with severe COVID-19 outcomes.",
-    "rel_num_authors": 49,
-    "rel_authors": [
-      {
-        "author_name": "Gundula Povysil",
-        "author_inst": "Columbia University"
-      },
-      {
-        "author_name": "Guillaume Butler-Laporte",
-        "author_inst": "McGill University"
-      },
-      {
-        "author_name": "Ning Shang",
-        "author_inst": "Columbia University"
-      },
-      {
-        "author_name": "Chen Weng",
-        "author_inst": "Columbia University"
-      },
-      {
-        "author_name": "Atlas Khan",
-        "author_inst": "Columbia University"
-      },
-      {
-        "author_name": "Manal Alaamery",
-        "author_inst": "King Abdulaziz City for Science and Technology"
-      },
-      {
-        "author_name": "Tomoko Nakanishi",
-        "author_inst": "McGill University"
-      },
-      {
-        "author_name": "Sirui Zhou",
-        "author_inst": "Lady Davis Institute for Medical Research"
-      },
-      {
-        "author_name": "Vincenzo Forgetta",
-        "author_inst": "Lady Davis Institute for Medical Research"
-      },
-      {
-        "author_name": "Robert Eveleigh",
-        "author_inst": "Lady Davis Institute for Medical Research"
-      },
-      {
-        "author_name": "Mathieu Bourgey",
-        "author_inst": "McGill University"
-      },
-      {
-        "author_name": "Naveed Aziz",
-        "author_inst": "Canadian COVID Genomics Network"
-      },
-      {
-        "author_name": "Steven Jones",
-        "author_inst": "Canadian COVID Genomics Network"
-      },
-      {
-        "author_name": "Bartha Knoppers",
-        "author_inst": "Canadian COVID Genomics Network"
-      },
-      {
-        "author_name": "Stephen Scherer",
-        "author_inst": "Canadian COVID Genomics Network"
-      },
-      {
-        "author_name": "Lisa Strug",
-        "author_inst": "Canadian COVID Genomics Network"
-      },
-      {
-        "author_name": "Pierre Lepage",
-        "author_inst": "McGill University"
-      },
-      {
-        "author_name": "Jiannis Ragoussis",
-        "author_inst": "McGill University"
-      },
-      {
-        "author_name": "Guillaume Bourque",
-        "author_inst": "McGill University"
-      },
-      {
-        "author_name": "Jahad Alghamdi",
-        "author_inst": "King Saud bin Abdulaziz University for Health Sciences"
-      },
-      {
-        "author_name": "Nora Aljawini",
-        "author_inst": "King Saud bin Abdulaziz University for Health Sciences"
-      },
-      {
-        "author_name": "Nour Albes",
-        "author_inst": "King Saud bin Abdulaziz University for Health Sciences"
-      },
-      {
-        "author_name": "Hani M. Al-Afghani",
-        "author_inst": "Taibah University"
-      },
-      {
-        "author_name": "Bader Alghamdi",
-        "author_inst": "King Saud bin Abdulaziz University for Health Sciences"
-      },
-      {
-        "author_name": "Mansour Almutair",
-        "author_inst": "King Saud bin Abdulaziz University for Health Sciences"
-      },
-      {
-        "author_name": "Ebrahim Sabri Mahmoud",
-        "author_inst": "King Abdulaziz City for Science and Technology"
-      },
-      {
-        "author_name": "Leen Abu Safie",
-        "author_inst": "King Abdulaziz City for Science and Technology"
-      },
-      {
-        "author_name": "Hadeel El Bardisy",
-        "author_inst": "King Abdulaziz City for Science and Technology"
-      },
-      {
-        "author_name": "Fawz S. Al Harthi",
-        "author_inst": "King Abdulaziz City for Science and Technology"
-      },
-      {
-        "author_name": "Abdulraheem Alshareef",
-        "author_inst": "Taibah University"
-      },
-      {
-        "author_name": "Bandar Ali Suliman",
-        "author_inst": "King Faisal Specialist Hospital and Research Centre"
-      },
-      {
-        "author_name": "Saleh Alqahtani",
-        "author_inst": "King Faisal Specialist Hospital and Research Centre"
-      },
-      {
-        "author_name": "Abdulaziz AlMalik",
-        "author_inst": "King Abdulaziz City for Science and Technology"
-      },
-      {
-        "author_name": "May M. Alrashed",
-        "author_inst": "King Saud University"
-      },
-      {
-        "author_name": "Salam Massadeh",
-        "author_inst": "King Abdulaziz City for Science and Technology"
-      },
-      {
-        "author_name": "Vincent Mooser",
-        "author_inst": "McGill University"
-      },
-      {
-        "author_name": "Mark Lathrop",
-        "author_inst": "McGill University"
-      },
-      {
-        "author_name": "Yaseen Arabi",
-        "author_inst": "King Abdulaziz City for Science and Technology"
-      },
-      {
-        "author_name": "Hamdi Mbarek",
-        "author_inst": "Qatar Foundation"
-      },
-      {
-        "author_name": "Chadi Saad",
-        "author_inst": "Qatar Foundation"
-      },
-      {
-        "author_name": "Wadha Al-Muftah",
-        "author_inst": "Qatar Foundation"
-      },
-      {
-        "author_name": "Radja Badji",
-        "author_inst": "Qatar Foundation"
-      },
-      {
-        "author_name": "Asma Al Thani",
-        "author_inst": "Qatar Foundation"
-      },
-      {
-        "author_name": "Said I. Ismail",
-        "author_inst": "Qatar Foundation"
-      },
-      {
-        "author_name": "Ali G. Gharavi",
-        "author_inst": "Columbia University"
-      },
-      {
-        "author_name": "Malak S. Abedalthagafi",
-        "author_inst": "King Abdulaziz City for Science and Technology"
-      },
-      {
-        "author_name": "J Brent Richards",
-        "author_inst": "McGill University"
-      },
-      {
-        "author_name": "David B. Goldstein",
-        "author_inst": "Columbia University"
-      },
-      {
-        "author_name": "Krzysztof Kiryluk",
-        "author_inst": "Columbia University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "genetic and genomic medicine"
-  },
   {
     "rel_doi": "10.1101/2020.12.18.20248461",
     "rel_title": "SARS-CoV-2-Specific Antibody Profiles Distinguish Patients with Moderate from Severe COVID-19",
@@ -1010425,6 +1008849,93 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.12.18.423106",
+    "rel_title": "Furin cleaves SARS-CoV-2 spike-glycoprotein at S1/S2 and S2'for viral fusion/entry: indirect role for TMPRSS2",
+    "rel_date": "2020-12-20",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.18.423106",
+    "rel_abs": "The spike (S)-protein of SARS-CoV-2 binds ACE2 and requires proteolytic \"priming\" at PRRAR685{downarrow} into S1 and S2 (cleavage at S1/S2), and \"fusion-activation\" at a S2 site for viral entry. In vitro, Furin cleaved peptides mimicking the S1/S2 cleavage site more efficiently than at the putative S2, whereas TMPRSS2 inefficiently cleaved both sites. In HeLa cells Furin-like enzymes mainly cleaved at S1/S2 during intracellular protein trafficking, and S2 processing by Furin at KPSKR815{downarrow} was strongly enhanced by ACE2, but not for the optimized S2 KRRKR815{downarrow} mutant (S2), whereas individual/double KR815AA mutants were retained in the endoplasmic reticulum. Pharmacological Furin-inhibitors (Boston Pharmaceuticals, BOS-inhibitors) effectively blocked endogenous S-protein processing in HeLa cells. Furthermore, we show using pseudotyped viruses that while entry by a \"pH-dependent\" endocytosis pathway in HEK293 cells did not require Furin processing at S1/S2, a \"pH-independent\" viral entry in lung-derived Calu-3 cells was sensitive to inhibitors of Furin (BOS) and TMPRSS2 (Camostat). Consistently, these inhibitors potently reduce infectious viral titer and cytopathic effects, an outcome enhanced when both compounds were combined. Quantitative analyses of cell-to-cell fusion and spike processing revealed the key importance of the Furin sites for syncytia formation. Our assays showed that TMPRSS2 enhances fusion and proteolysis at S2 in the absence of cleavage at S1/S2, an effect that is linked to ACE2 shedding by TMPRSS2. Overall, our results indicate that Furin and TMPRSS2 play synergistic roles in generating fusion-competent S-protein, and in promoting viral entry, supporting the combination of Furin and TMPRSS2 inhibitors as potent antivirals against SARS-CoV-2.\n\nIMPORTANCESARS-CoV-2 is the etiological agent of COVID-19 that resulted in >5 million deaths. The spike protein (S) of the virus directs infection of the lungs and other tissues by binding the angiotensin-converting enzyme 2 (ACE2) receptor. For effective infection, the S-protein is cleaved at two sites: S1/S2 and S2. Cleavage at S1/S2, induces a conformational change favoring the recognition of ACE2. The S2 cleavage is critical for cell-to-cell fusion and virus entry into host cells. Our study contributes to a better understanding of the dynamics of interaction between Furin and TMPRSS2 during SARS-CoV-2 entry and suggests that the combination of a non-toxic Furin inhibitor with a TMPRSS2 inhibitor could significantly reduce viral entry in lung cells, as evidenced by an average synergistic [~]95% reduction of viral infection. This represents a powerful novel antiviral approach to reduce viral spread in individuals infected by SARS-CoV-2 or future related coronaviruses.",
+    "rel_num_authors": 18,
+    "rel_authors": [
+      {
+        "author_name": "Rachid Essalmani",
+        "author_inst": "IRCM"
+      },
+      {
+        "author_name": "Jaspreet Jain",
+        "author_inst": "IRCM"
+      },
+      {
+        "author_name": "Delia Susan-Resiga",
+        "author_inst": "IRCM"
+      },
+      {
+        "author_name": "Ursula Andreo",
+        "author_inst": "IRCM"
+      },
+      {
+        "author_name": "Alexandra Evagelidis",
+        "author_inst": "IRCM"
+      },
+      {
+        "author_name": "Rabeb Mouna Derbali",
+        "author_inst": "IRCM"
+      },
+      {
+        "author_name": "David Huynh",
+        "author_inst": "IRCM"
+      },
+      {
+        "author_name": "Frederic Dallaire",
+        "author_inst": "IRCM"
+      },
+      {
+        "author_name": "Melanie Laporte",
+        "author_inst": "IRCM"
+      },
+      {
+        "author_name": "Adrien Delpal",
+        "author_inst": "AFMB Polytech"
+      },
+      {
+        "author_name": "Priscila Sutto-Ortiz",
+        "author_inst": "AFMB Polytech"
+      },
+      {
+        "author_name": "Bruno Coutard",
+        "author_inst": "UVE: Aix-Marseille"
+      },
+      {
+        "author_name": "Claudine Mapa",
+        "author_inst": "Boston Pharmaceuticals"
+      },
+      {
+        "author_name": "Keith Wilcoxen",
+        "author_inst": "Boston Pharmaceuticals"
+      },
+      {
+        "author_name": "Etienne Decroly",
+        "author_inst": "UVE: Aix-Marseille"
+      },
+      {
+        "author_name": "Tram Pham",
+        "author_inst": "IRCM"
+      },
+      {
+        "author_name": "Eric A. Cohen",
+        "author_inst": "IRCM"
+      },
+      {
+        "author_name": "Nabil G. Seidah",
+        "author_inst": "IRCM"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "biochemistry"
+  },
   {
     "rel_doi": "10.1101/2020.12.19.423584",
     "rel_title": "Identification of NPC1 as a novel SARS-CoV-2 intracellular target",
@@ -1011774,89 +1010285,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.12.18.20248265",
-    "rel_title": "Risk of thrombotic complications in influenza versus COVID-19 hospitalized patients",
-    "rel_date": "2020-12-19",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.18.20248265",
-    "rel_abs": "BackgroundWhereas accumulating studies on COVID-19 patients report high incidences of thrombotic complications, large studies on clinically relevant thrombosis in patients with other respiratory tract infections are lacking. How this high risk in COVID-19 patients compares to those observed in hospitalized patients with other viral pneumonias such as influenza is unknown.\n\nObjectivesTo assess the incidence of venous and arterial thrombotic complications in hospitalized influenza patients as opposed to that observed in hospitalized COVID-19 patients.\n\nMethodsRetrospective cohort study; we used data from Statistics Netherlands (study period: 2018) on thrombotic complications in hospitalized influenza patients. In parallel, we assessed the cumulative incidence of thrombotic complications - adjusted for competing risk of death - in patients with COVID-19 in three Dutch hospitals (February 24th - April 26th 2020).\n\nResultsOf the 13.217 hospitalized influenza patients, 437 (3.3%) were diagnosed with thrombotic complications, versus 66 (11%) of the 579 hospitalized COVID-19 patients. The 30-day cumulative incidence of any thrombotic complication in influenza was 11% (95%CI 9.4-12) versus 25% (95%CI 18-32) in COVID-19. For venous thrombotic complications (VTE) and arterial thrombotic complications alone, these numbers were respectively 3.6% (95%CI 2.7-4.6) and 7.5% (95%CI 6.3-8.8) in influenza versus 23% (95%CI 16-29) and 4.4% (95%CI 1.9-8.8) in COVID-19.\n\nConclusionsThe incidence of thrombotic complications in hospitalized influenza patients was lower than in hospitalized COVID-19 patients. This difference was mainly driven by a high risk of VTE complications in the COVID-19 patients admitted to ICU. Remarkably, influenza patients were more often diagnosed with arterial thrombotic complications.\n\nEssentialsO_LIIt is unknown how COVID-19 compares to patients with other virus infections regarding thrombosis.\nC_LIO_LIHospitalized patients with influenza and COVID-19 were evaluated and compared to each other.\nC_LIO_LI30-day cumulative incidence of thrombosis was lower in influenza (11%) than in COVID-19 (25%).\nC_LIO_LIDifference was mainly driven by a high risk of VTE in COVID-19 patients admitted to the ICU.\nC_LI",
-    "rel_num_authors": 17,
-    "rel_authors": [
-      {
-        "author_name": "Milou AM Stals",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Marco JJH Grootenboers",
-        "author_inst": "Amphia Hospital Breda"
-      },
-      {
-        "author_name": "Coen van Guldener",
-        "author_inst": "Amphia Hospital Breda"
-      },
-      {
-        "author_name": "Fleur HJ Kaptein",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Sander JE Braken",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Qingui Chen",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Gordon Chu",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Erik M van Driel",
-        "author_inst": "Alrijne Hospital Leiderdorp"
-      },
-      {
-        "author_name": "Antonio Iglesias del Sol",
-        "author_inst": "Alrijne Hospital Leiderdorp"
-      },
-      {
-        "author_name": "Evert de Jonge",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "K Merijn Kant",
-        "author_inst": "Amphia Hospital Breda"
-      },
-      {
-        "author_name": "Fleur Pals",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Myrthe MA Toorop",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Suzanne C Cannegieter",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Frederikus A Klok",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Menno V Huisman",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "- Dutch COVID and Thrombosis Coalition (DCTC)",
-        "author_inst": ""
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.12.18.20248317",
     "rel_title": "The COSEVAST Study: Unravelling the role of Arterial Stiffness in COVID-19 Disease severity.",
@@ -1012067,6 +1010495,105 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.12.16.20248180",
+    "rel_title": "Seroprevalence of anti-SARS-CoV-2 IgG antibodies, risk factors for infection and associated symptoms in Geneva, Switzerland: a population-based study",
+    "rel_date": "2020-12-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.16.20248180",
+    "rel_abs": "BackgroundPopulation-based serological surveys provide a means for assessing the immunologic landscape of a community, without the biases related to health-seeking behaviors and testing practices typically associated with rt-PCR testing. This study assesses SARS-CoV-2 seroprevalence over the first epidemic wave in Canton Geneva, Switzerland, as well as biological and socio-economic risk factors for infection and symptoms associated with IgG seropositivity.\n\nMethods and findingsBetween April 6 and June 30, 2020, former participants of a yearly representative cross-sectional survey of the 20-75-year-old population of the canton of Geneva were invited to participate in a seroprevalence study, along with household members five years and older. We collected blood and tested it for anti-SARS-CoV-2 immunoglobulins G (IgG). Questionnaires were self-administered. We estimated seroprevalence with a Bayesian model accounting for test performance and sampling design. We included 8344 participants (53.5% women, mean age 46.9 years). The population-level seroprevalence over the 12-week study period was 7.8 % (95% Credible Interval (CrI) 6.8-8.9), accounting for sex, age and household random effects. Seroprevalence was highest among 18-49 year olds (9.5%, 95%CrI 8.1-10.9), with young children (5-9 years) and those >65 years having significantly lower seroprevalence (4.3% and 4.7-5.4% respectively). Men were more likely to be seropositive than women (relative risk 1.2, 95%CrI 1.1-1.4). Odds of seropositivity were reduced for female retirees (0.46, 95%CI 0.23-0.93) and unemployed men (0.35, 95%CI 0.13-1.0) compared to employed individuals, and for current smokers (0.36, 95%CI 0.23-0.55) compared to never-smokers. We found no significant association between occupation, level of education, neighborhood income and the risk of being seropositive. Symptoms most strongly associated with seropositivity were anosmia/dysgeusia, loss of appetite, fever, fatigue and myalgia and/or arthralgia. Thirteen percent of seropositive participants reported no symptoms.\n\nConclusionsOur results confirm a low population seroprevalence of anti-SARS-CoV-2 antibodies after the first wave in Geneva, a region hard hit by the COVID-19 pandemic. Socioeconomic factors were not associated with seropositivity in this sample. The elderly and young children were less frequently seropositive, though it is not clear how biology and behaviors shape these differences. These specificities should be considered when assessing the need for targeted public health measures.",
+    "rel_num_authors": 21,
+    "rel_authors": [
+      {
+        "author_name": "Aude Richard",
+        "author_inst": "Division of Primary Care, Geneva University Hospitals, Geneva, Switzerland"
+      },
+      {
+        "author_name": "Ania Wisniak",
+        "author_inst": "Division of Primary Care, Geneva University Hospitals, Geneva, Switzerland"
+      },
+      {
+        "author_name": "Javier Perez-Saez",
+        "author_inst": "Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland"
+      },
+      {
+        "author_name": "Henri Garrison-Desany",
+        "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA"
+      },
+      {
+        "author_name": "Dusan Petrovic",
+        "author_inst": "Division of Primary Care, Geneva University Hospitals, Geneva, Switzerland"
+      },
+      {
+        "author_name": "Giovanni Piumatti",
+        "author_inst": "Division of Primary Care, Geneva University Hospitals, Geneva, Switzerland"
+      },
+      {
+        "author_name": "Helene Baysson",
+        "author_inst": "Division of Primary Care, Geneva University Hospitals, Geneva, Switzerland"
+      },
+      {
+        "author_name": "Attilio Picazio",
+        "author_inst": "Division of Primary Care, Geneva University Hospitals, Geneva, Switzerland"
+      },
+      {
+        "author_name": "Francesco Pennacchio",
+        "author_inst": "Division of Primary Care, Geneva University Hospitals, Geneva, Switzerland"
+      },
+      {
+        "author_name": "David De Ridder",
+        "author_inst": "Division of Primary Care, Geneva University Hospitals, Geneva, Switzerland"
+      },
+      {
+        "author_name": "Francois Chappuis",
+        "author_inst": "Division of Tropical and Humanitarian Medicine, Geneva University Hospitals, Geneva, Switzerland"
+      },
+      {
+        "author_name": "Nicolas Vuilleumier",
+        "author_inst": "Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland"
+      },
+      {
+        "author_name": "Nicola Low",
+        "author_inst": "University of BernInstitute of Social and Preventive Medicine, Faculty of Medicine, University of Bern, Bern, Switzerland"
+      },
+      {
+        "author_name": "Samia Hurst",
+        "author_inst": "Institute for Ethics, History, and the Humanities, Faculty of Medicine, University of Geneva, Geneva, Switzerland"
+      },
+      {
+        "author_name": "Isabella Eckerle",
+        "author_inst": "Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland"
+      },
+      {
+        "author_name": "Antoine Flahault",
+        "author_inst": "Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland"
+      },
+      {
+        "author_name": "Laurent Kaiser",
+        "author_inst": "Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland"
+      },
+      {
+        "author_name": "Anderw S Azman",
+        "author_inst": "Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland"
+      },
+      {
+        "author_name": "Idris Guessous",
+        "author_inst": "Division of Primary Care, Geneva University Hospitals, Geneva, Switzerland"
+      },
+      {
+        "author_name": "Silvia Stringhini",
+        "author_inst": "Division of Primary Care, Geneva University Hospitals, Geneva, Switzerland"
+      },
+      {
+        "author_name": "- SEROCOV-POP study group",
+        "author_inst": ""
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.12.16.20248134",
     "rel_title": "No evidence of association between schools and SARS-CoV-2 second wave in Italy.",
@@ -1013660,33 +1012187,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.12.16.20248359",
-    "rel_title": "Covid-19 Vaccine Efficacy: Accuracy, Uncertainty and Projection of Cases",
-    "rel_date": "2020-12-18",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.16.20248359",
-    "rel_abs": "BackgroundTwo vaccine candidates for coronavirus disease 2019 (Covid-19) have been announced by Pfizer-BioNTech and Moderna with above 90% efficacy. The efficacy of each vaccine changes between reports with no accuracy assessment.\n\nMethodsWe examined data in both vaccine trials, provided 95% confidence intervals, and projected the cases that would be prevented in communities of multi-million population.\n\nResultsThe 95% confidence intervals reveal that the true vaccine efficacy could be as low as 86% for stated efficacy of 94.4% in an interim report, indicating the inaccuracy and uncertainty of efficacy point estimate. Both vaccines achieve an efficacy above 89% by the 95% confidence interval in updated reports. The Moderna vaccine would prevent more than 50,260 cases in communities of 1 million people with 1 year exposure.\n\nConclusionsPoint estimates of vaccine efficacy transmit limited information. Corresponding statements of uncertainty, such as confidence intervals, should be provided and included in discussions of societal impact. The Covid-19 vaccines announced to date would prevent a substantial number of cases even at lower ends of the intervals.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Wenjiang Fu",
-        "author_inst": "University of Houston"
-      },
-      {
-        "author_name": "Jieni Li",
-        "author_inst": "University of Houston"
-      },
-      {
-        "author_name": "Paul Scheet",
-        "author_inst": "MD Anderson Cancer Center"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.12.17.20248377",
     "rel_title": "Voxel-level forecast system for lesion development in patients with COVID-19",
@@ -1013993,6 +1012493,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.12.16.20248357",
+    "rel_title": "Understanding the net benefit of antigen-based rapid diagnostic tests for COVID-19: An enhanced decision-curve analysis",
+    "rel_date": "2020-12-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.16.20248357",
+    "rel_abs": "BackgroundSARS-CoV-2 antigen-detection rapid diagnostic tests (Ag-RDTs) can diagnose COVID-19 rapidly and at low cost, but their lower sensitivity than nucleic acid amplification testing (NAAT) has limited clinical adoption.\n\nMethodsWe compared Ag-RDT, NAAT, and clinical judgment alone for diagnosing symptomatic COVID-19. We considered an outpatient setting (10% COVID-19 prevalence among the patients tested, 3-day NAAT turnaround) and a hospital setting (40% prevalence, 24-hour NAAT turnaround). We simulated transmission from cases and contacts and relationships between time, viral burden, transmission, and case detection. We compared diagnostic approaches using a measure of net benefit that incorporated both clinical and public health benefits and harms of intervention.\n\nResultsIn the outpatient setting, we estimated that using Ag-RDT instead of NAAT to test 200 individuals could have a net benefit equivalent to preventing all symptomatic transmission from one person with COVID-19 (one \"transmission-equivalent\"). In the hospital setting, net benefit analysis favored NAAT, and testing 25 patients with NAAT instead of Ag-RDT achieved one \"transmission-equivalent\" of incremental benefit. In both settings, Ag-RDT was preferred to NAAT if NAAT turnaround time exceeded two days. Both Ag-RDT and NAAT provided greater net benefit than management based on clinical judgment alone, unless intervention carried minimal harm and was provided equally regardless of diagnostic approach.\n\nConclusionsFor diagnosis of symptomatic COVID-19, the speed of diagnosis with Ag-RDT is likely to outweigh its lower accuracy compared to NAAT wherever NAAT turnaround times are two days or longer. This advantage may be even greater if Ag-RDTs are also less expensive.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Emily A Kendall",
+        "author_inst": "Johns Hopkins University School of Medicine"
+      },
+      {
+        "author_name": "Nimalan Arinaminpathy",
+        "author_inst": "Imperial College London"
+      },
+      {
+        "author_name": "Jilian A Sacks",
+        "author_inst": "FIND"
+      },
+      {
+        "author_name": "Yukari C Manabe",
+        "author_inst": "Johns Hopkins University School of Medicine"
+      },
+      {
+        "author_name": "Sabine Dittrich",
+        "author_inst": "FIND"
+      },
+      {
+        "author_name": "Samuel G Schumacher",
+        "author_inst": "FIND"
+      },
+      {
+        "author_name": "David W Dowdy",
+        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.12.16.20248343",
     "rel_title": "Impaired ICOS signaling between Tfh and B cells distinguishes hospitalized from ambulatory CoViD-19 patients",
@@ -1015218,29 +1013761,6 @@
     "type": "new results",
     "category": "scientific communication and education"
   },
-  {
-    "rel_doi": "10.1101/2020.12.15.422890",
-    "rel_title": "Ruling the Roost: Avian Species Reclaim Urban Habitat During India's COVID Lockdown",
-    "rel_date": "2020-12-16",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.15.422890",
-    "rel_abs": "As we retreated to our dwellings in the \"anthropause\" of spring 2020, did other species return to our urban centres? We leverage an increase in balcony birdwatching, a million eBird entries, and difference-in-difference techniques to test if avian species richness rose during Indias COVID lockdown. We find that birdwatchers in Indias 20 most populous cities observed 8-17% more species during the lockdown. Most additional observations occurred after a two-week lag, signaling greater abundance instead of improved detection. More frequent appearances of at-risk, rare, and common species were recorded, implying that making our cities more wildlife friendly can protect threatened species in addition to urban specialists. Our contributions are: 1) to isolate and estimate a causal impact of reducing human activity on avian diversity, 2) to improve the external validity of this literature in rapidly urbanizing bio-diverse developing countries, and, 3) to illustrate a method separating abundance from detection in observational avian surveys.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Raahil Madhok",
-        "author_inst": "University of British Columbia"
-      },
-      {
-        "author_name": "Sumeet Gulati",
-        "author_inst": "University of British Columbia"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "ecology"
-  },
   {
     "rel_doi": "10.1101/2020.12.14.20248201",
     "rel_title": "Comparison of Healthcare costs and benefits of the UK's Covid-19 response with four European countries: Decision Modelling Study",
@@ -1015615,6 +1014135,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.12.14.20248209",
+    "rel_title": "The Presence of Ambulatory Hypoxia as an Early Predictor of Moderate to Severe COVID-19 Disease",
+    "rel_date": "2020-12-16",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.14.20248209",
+    "rel_abs": "BackgroundThe importance of ambulatory hypoxia without resting hypoxia in COVID-19 is unknown. Ambulatory hypoxia without resting hypoxia may help objectively identify high-risk patients hospitalized with COVID-19. Interventions may be initiated earlier with sufficient lead-time between development of ambulatory hypoxia and other outcome measures.\n\nMethodsWe performed a retrospective study of adult patients hospitalized with COVID-19 from March 1, 2020 to October 30, 2020 in ten hospitals in an integrated academic medical system in the Chicagoland area. We analyzed patients who had daily ambulatory oximetry measurements, excluding patients who had first ambulatory oximetry measurements after the use of oxygen therapies (nasal cannula or advanced oxygen therapies). We determined the association of ambulatory hypoxia without resting hypoxia with the eventual need for nasal cannula or advanced oxygen therapies (defined as high flow nasal cannula, Bi-PAP, ventilator, or extracorporeal membrane oxygenation). We also calculated the time between development of ambulatory hypoxia and the need for oxygen therapies.\n\nResultsOf 531 patients included in the study, 132 (24.9%) had ambulatory hypoxia. Presence of ambulatory hypoxia was strongly associated with subsequent use of nasal cannula (OR 4.8, 95% CI 2.8 - 8.4) and advanced oxygen therapy (IRR 7.7, 95% CI 3.4 - 17.5). Ambulatory hypoxia preceded nasal cannula use by a median 12.5 hours [IQR 3.25, 29.25] and advanced oxygenation therapies by 54 hours [IQR 25, 82].\n\nConclusionAmbulatory hypoxia without resting hypoxia may serve as an early, non-invasive physiologic marker for the likelihood of developing moderate to severe COVID-19 and help clinicians triage patients and initiate earlier interventions.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Ajay Bhasin",
+        "author_inst": "Northwestern Univeristy"
+      },
+      {
+        "author_name": "Melissa Bregger",
+        "author_inst": "Northwestern University"
+      },
+      {
+        "author_name": "Mark Kluk",
+        "author_inst": "Northwestern University"
+      },
+      {
+        "author_name": "Peter Park",
+        "author_inst": "Northwestern University"
+      },
+      {
+        "author_name": "Joseph Feinglass",
+        "author_inst": "Northwestern University"
+      },
+      {
+        "author_name": "Jeffrey Barsuk",
+        "author_inst": "Northwestern University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.12.14.20248192",
     "rel_title": "A Comprehensive Clinical Description of Pediatric SARS-CoV-2 Infection in Western Pennsylvania",
@@ -1017016,37 +1015575,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.12.14.422718",
-    "rel_title": "Remdesivir is a delayed translocation inhibitor of SARS CoV-2 replication in vitro",
-    "rel_date": "2020-12-16",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.14.422718",
-    "rel_abs": "Remdesivir is a nucleoside analog approved by the FDA for treatment of COVID-19. Here, we present a 3.9-[A]-resolution cryoEM reconstruction of a remdesivir-stalled RNA-dependent RNA polymerase complex, revealing full incorporation of three copies of remdesivir monophosphate (RMP) and a partially incorporated fourth RMP in the active site. The structure reveals that RMP blocks RNA translocation after incorporation of three bases following RMP, resulting in delayed chain termination, which can guide the rational design of improved antiviral drugs.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Jack PK Bravo",
-        "author_inst": "University of Texas at Austin"
-      },
-      {
-        "author_name": "Tyler L Dangerfield",
-        "author_inst": "University of Texas at Austin"
-      },
-      {
-        "author_name": "David W Taylor",
-        "author_inst": "University of Texas at Austin"
-      },
-      {
-        "author_name": "Kenneth A Johnson",
-        "author_inst": "University of Texas at Austin"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "biochemistry"
-  },
   {
     "rel_doi": "10.1101/2020.12.15.412809",
     "rel_title": "Cyclic gallium-68 labeled peptides for specific detection of human angiotensin-converting enzyme 2",
@@ -1017465,6 +1015993,29 @@
     "type": "new results",
     "category": "bioengineering"
   },
+  {
+    "rel_doi": "10.1101/2020.12.16.423071",
+    "rel_title": "One Year of SARS-CoV-2: How Much Has the Virus Changed?",
+    "rel_date": "2020-12-16",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.16.423071",
+    "rel_abs": "SARS-CoV-2 coronavirus has caused a world-wide crisis with profound effects on both healthcare and the economy. In order to combat the COVID-19 pandemic, research groups have shared viral genome sequence data through the GISAID initiative. We collected and computationally profiled [~]223,000 full SARS-CoV-2 proteome sequences from GISAID over one year for emergent nonsynonymous mutations. Our analysis shows that SARS-CoV-2 proteins are mutating at substantially different rates, with most viral proteins exhibiting little mutational variability. As anticipated, our calculations capture previously reported mutations occurred in the first period of the pandemic, such as D614G (Spike), P323L (NSP12), and R203K/G204R (Nucleocapsid), but also identify recent mutations like A222V and L18F (Spike) and A220V (Nucleocapsid). Our comprehensive temporal and geographical analyses show two periods with different mutations in the SARS-CoV-2 proteome: December 2019 to June 2020 and July to November 2020. Some mutation rates differ also by geography; the main mutations in the second period occurred in Europe. Furthermore, our structure-based molecular analysis provides an exhaustive assessment of mutations in the context of 3D protein structure. Emerging sequence-to-structure data is beginning to reveal the site-specific mutational tolerance of SARS-CoV2 proteins as the virus continues to spread around the globe.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Santiago Vilar",
+        "author_inst": "Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine"
+      },
+      {
+        "author_name": "Daniel G. Isom",
+        "author_inst": "University of Miami, Miller School of Medicine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "bioinformatics"
+  },
   {
     "rel_doi": "10.1101/2020.12.16.20248308",
     "rel_title": "The effectiveness of Non Pharmaceutical Interventions in reducing the outcomes of the COVID-19 epidemic in the UK, an observational and modelling study.",
@@ -1018766,25 +1017317,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.12.11.20231829",
-    "rel_title": "Current forecast of COVID-19: a Bayesian and Machine Learning approaches",
-    "rel_date": "2020-12-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.11.20231829",
-    "rel_abs": "We address the estimation of the effective reproductive number Rt based on serological data using Bayesian inference. We also explore the Bayesian learning paradigm to estimate Rt. We calculate Rt for the top five most affected principal regions of Mexico. We present a forecast of the spread of coronavirus in Mexico based on a contact tracing model using Bayesian inference inspired in a data-driven approach. We investigate the health profile of individuals diagnosed with coronavirus in order to predict their type of patient care (inpatient or outpatient) and survival. Specifically, we analyze the comorbidity associated with coronavirus using Machine Learning. We implemented two classifiers, the first one, to predict the type of care procedure a diagnosed person with coronavirus presenting chronic diseases will obtain: outpatient or hospitalized. Second one, a classifier for the survival of the patient: survived or deceased. We present two techniques to deal with these kinds of unbalanced dataset related with outpatient/hospitalized and survived/deceased cases, occurring in general for these type coronavirus datasets in the world, in order obtain to a better performance for the classification.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Kernel Prieto",
-        "author_inst": "Instituto de Matematicas, Universidad Nacional Autonoma de Mexico"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.12.11.20247742",
     "rel_title": "Changes in cardiovascular disease monitoring in English primary care during the COVID-19 pandemic: an observational cohort study",
@@ -1019083,6 +1017615,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.12.13.20248142",
+    "rel_title": "COVID-19 vaccines that reduce symptoms but do not block infection need higher coverage and faster rollout to achieve population impact",
+    "rel_date": "2020-12-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.13.20248142",
+    "rel_abs": "BackgroundSeveral COVID-19 vaccine candidates are in the final stage of testing. Interim trial results for two vaccines suggest at least 90% efficacy against symptomatic disease (VEDIS). It remains unknown whether this efficacy is mediated predominately by lowering SARS-CoV-2 infection susceptibility (VESUSC) or development of symptoms after infection (VESYMP). A vaccine with high VESYMP but low VESUSC has uncertain population impact.\n\nMethodsWe developed a mathematical model of SARS-CoV-2 transmission, calibrated to demographic, physical distancing and epidemic data from King County, Washington. Different rollout scenarios starting December 2020 were simulated assuming different combinations of VESUSC and VESYMP resulting in up to 100% VEDIS with constant vaccine effects over 1 year. We assumed no further increase in physical distancing despite expanding case numbers and no reduction of infectivity upon infection conditional on presence of symptoms. Proportions of cumulative infections, hospitalizations and deaths prevented over 1 year from vaccination start are reported.\n\nResultsRollouts of 1M vaccinations (5,000 daily) using vaccines with 50% VEDIS are projected to prevent 30%-58% of infections and 38%-58% of deaths over one year. In comparison, vaccines with 90% VEDIS are projected to prevent 47%-78% of the infections and 58%-77% of deaths over one year. In both cases, there is a greater reduction if VEDIS is mediated mostly by VESUSC. The use of a \"symptom reducing\" vaccine will require twice as many people vaccinated than a \"susceptibility reducing\" vaccine with the same 90% VEDIS to prevent 50% of the infections and death over one year. Delaying the start of the vaccination by 3 months decreases the expected population impact by approximately 40%.\n\nConclusionsVaccines which prevent COVID-19 disease but not SARS-CoV-2 infection, and thereby shift symptomatic infections to asymptomatic infections, will prevent fewer infections and require larger and faster vaccination rollouts to have population impact, compared to vaccines that reduce susceptibility to infection. If uncontrolled transmission across the U.S. continues, then expected vaccination in Spring 2021 will provide only limited benefit.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "David A Swan",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      },
+      {
+        "author_name": "Chloe Bracis",
+        "author_inst": "Universit\u00e9 Grenoble Alpes"
+      },
+      {
+        "author_name": "Holly Janes",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      },
+      {
+        "author_name": "Mia Moore",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      },
+      {
+        "author_name": "Laura Matrajt",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      },
+      {
+        "author_name": "Daniel B Reeves",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      },
+      {
+        "author_name": "Eileen Burns",
+        "author_inst": "Independent Researcher"
+      },
+      {
+        "author_name": "Deborah Donnell",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      },
+      {
+        "author_name": "Myron S Cohen",
+        "author_inst": "University of North Carolina at Chapel Hill"
+      },
+      {
+        "author_name": "Joshua Schiffer",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      },
+      {
+        "author_name": "Dobromir T Dimitrov",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.12.13.20248147",
     "rel_title": "Association of Mortality and Aspirin Prescription for COVID-19 Patients at the Veterans Health Administration",
@@ -1020412,37 +1019003,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.12.11.20245357",
-    "rel_title": "Prevalence of Occupation Associated with Increased Mobility During COVID-19 Pandemic",
-    "rel_date": "2020-12-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.11.20245357",
-    "rel_abs": "ObjectiveIdentifying geographic-level prevalence of occupations associated with mobility during local stay-at-home pandemic mandate.\n\nMethodsA spatio-temporal ecological framework was applied to determine census-tracts that had significantly higher rates of occupations likely to be deemed essential: food-service, business and finance, healthcare support, and maintenance. Real-time mobility data was used to determine the average daily percent of residents not leaving their place of residence. Spatial regression models were constructed for each occupation proportion among census-tracts within a large urban area.\n\nResultsAfter adjusting for demographics, results indicate census-tracts with higher proportion of food-service workers, healthcare support employees, and office administration staff are likely to have increased mobility.\n\nConclusionsIncreased mobility among communities is likely to exacerbate COVID-19 mitigation efforts. This increase in mobility was also found associated with specific demographics suggesting it may be occurring among underserved and vulnerable populations. We find that prevalence of essential employment presents itself as a candidate for driving inequity in morbidity and mortality of COVID-19.\n\nThree-question SummaryO_LIEmployees and workers deemed essential during the COVID-19 pandemic are likely to endure additional risk of infection due to community exposure. While preliminary reports are still quantifying this risk, we set out to examine if prevalence of specific occupations could be used to evaluate overall community-level risk based on stay-at-home mandate adherence.\nC_LIO_LIStudy results suggest that that not only are certain occupation geo-spatially associated with movement outside the home but are also associated with demographic characteristics likely to contribute to inequity of COVID-19 morbidity.\nC_LIO_LIOften, nuanced inequities are lost in the larger data samples, being able to identify possible inequities from other sources such as prevalence of occupation among communities, remains an important and applicable alternative.\nC_LI",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Enbal Shacham",
-        "author_inst": "Saint Louis University, College for Public Health and Social Justice"
-      },
-      {
-        "author_name": "Stephen Scroggins",
-        "author_inst": "Saint Louis University"
-      },
-      {
-        "author_name": "Matthew Ellis",
-        "author_inst": "Saint Louis University, College for Public Health and Social Justice"
-      },
-      {
-        "author_name": "Alexander Garza",
-        "author_inst": "SSM Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.12.13.20248122",
     "rel_title": "Screening for high amounts of SARS-CoV-2 identifies pre-symptomatic subjects among healthy healthcare workers",
@@ -1020917,6 +1019477,61 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2020.12.13.420406",
+    "rel_title": "Identification of bis-benzylisoquinoline alkaloids as SARS-CoV-2 entry inhibitors from a library of natural products in vitro",
+    "rel_date": "2020-12-14",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.13.420406",
+    "rel_abs": "Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major public health issue. To screen for antiviral drugs for COVID-19 treatment, we constructed a SARS-CoV-2 spike (S) pseudovirus system using an HIV-1-based lentiviral vector with a luciferase reporter gene to screen 188 small potential antiviral compounds. Using this system, we identified nine compounds, specifically, bis-benzylisoquinoline alkaloids, that potently inhibited SARS-CoV-2 pseudovirus entry, with EC50 values of 0.1-10 M. Mechanistic studies showed that these compounds, reported as calcium channel blockers (CCBs), inhibited Ca2+-mediated membrane fusion and consequently suppressed coronavirus entry. These candidate drugs showed broad-spectrum efficacy against the entry of several coronavirus pseudotypes (SARS-CoV, MERS-CoV, SARS-CoV-2 [S-D614, S-G614, N501Y.V1 and N501Y.V2]) in different cell lines (293T, Calu-3, and A549). Antiviral tests using native SARS-CoV-2 in Vero E6 cells confirmed that four of the drugs (SC9/cepharanthine, SC161/hernandezine, SC171, and SC185/neferine) reduced cytopathic effect and supernatant viral RNA load. Among them, cepharanthine showed the strongest anti-SARS-CoV-2 activity. Collectively, this study offers new lead compounds for coronavirus antiviral drug discovery.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Chang-Long He",
+        "author_inst": "Chongqing Medical University"
+      },
+      {
+        "author_name": "Lu-Yi Huang",
+        "author_inst": "Chongqing Medical University"
+      },
+      {
+        "author_name": "Kai Wang",
+        "author_inst": "Chongqing Medical University"
+      },
+      {
+        "author_name": "Chen-Jian Gu",
+        "author_inst": "Fudan University"
+      },
+      {
+        "author_name": "Jie Hu",
+        "author_inst": "Chongqing Medical University"
+      },
+      {
+        "author_name": "Gui-Ji Zhang",
+        "author_inst": "Chongqing Medical University"
+      },
+      {
+        "author_name": "Wei Xu",
+        "author_inst": "Fudan University"
+      },
+      {
+        "author_name": "You-Hua Xie",
+        "author_inst": "Fudan University"
+      },
+      {
+        "author_name": "Ni Tang",
+        "author_inst": "Chongqing Medical University"
+      },
+      {
+        "author_name": "Ai-Long Huang",
+        "author_inst": "Chongqing Medical University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2020.12.13.422511",
     "rel_title": "Hepatitis C Virus Drugs Simeprevir and Grazoprevir Synergize with Remdesivir to Suppress SARS-CoV-2 Replication in Cell Culture",
@@ -1022133,73 +1020748,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.12.08.20246017",
-    "rel_title": "Factors associated with clinical severity in Emergency Department patients presenting with symptomatic SARS-CoV-2 infection.",
-    "rel_date": "2020-12-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.08.20246017",
-    "rel_abs": "ObjectiveTo measure the association of race, ethnicity, comorbidities, and insurance status with need for hospitalization of symptomatic Emergency Department (ED) patients with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection.\n\nMethodsThis study is a retrospective case-series of symptomatic patients presenting to a single ED with laboratory-confirmed SARS-CoV-2 infection from March 12-August 9, 2020. We collected patient-level information regarding demographics, public insurance status (Medicare or Medicaid), comorbidities, level of care, and mortality using a structured chart review. We compared demographics and comorbidities of patients who were (1) able to convalesce at home, (2) required admission to general medical service, (3) required admission to intensive care unit (ICU), or (4) died within 30 days of the index visit. Multivariable logistic regression analyses were performed to report adjusted odds ratios (aOR) and the associated 95% confidence intervals (95% CI) with hospital admission versus ED discharge home.\n\nResultsIn total, 993 patients who presented to the ED with symptoms were included in the analysis with 370 (37.3%) patients requiring hospital admission and 70 (7.1%) patients requiring ICU care. Patients requiring admission were more likely to be Black or African American, to be Hispanic or Latino, or to have public insurance (either Medicaid or Medicare.) On multivariable logistic regression analysis comparing which patients required hospital admission, African-American race (aOR 1.4, 95% CI 0.7-2.8) and Hispanic ethnicity (aOR 1.1, 95% CI 0.5-2.0) were not associated with need for admission but, public insurance (Medicaid: aOR 3.4, 95% CI 2.2-5.4; Medicare: aOR 2.6, 95% CI 1.2-5.3; Medicaid and Medicare: aOR 3.6 95% CI 2.1-6.2) and the presence of hypertension (aOR 1.8, 95% CI 1.2-2.7), diabetes (aOR 1.6, 95% CI 1.1-2.5), obesity (aOR 1.7, 95% CI 1.1-2.5), heart failure (aOR 3.9, 95% CI 1.4-11.2), and hyperlipidemia (aOR 1.8, 95% CI 1.2-2.9) were identified as independent predictors of hospital admission.\n\nConclusionComorbidities and public insurance are predictors of more severe illness for patients with SARS-CoV-2. This study suggests that the disparities in severity seen in COVID-19 among African Americans and Hispanics are likely to be closely related to low socioeconomic status and chronic health conditions and do not reflect an independent predisposition to disease severity.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Sophia Newton",
-        "author_inst": "George Washington University School of Medicine & Health Sciences"
-      },
-      {
-        "author_name": "Benjamin Zollinger",
-        "author_inst": "George Washington University School of Medicine & Health Sciences"
-      },
-      {
-        "author_name": "Jincong Freeman",
-        "author_inst": "George Washington University Milken Institute School of Public Health"
-      },
-      {
-        "author_name": "Seamus Moran",
-        "author_inst": "George Washington University School of Medicine & Health Sciences"
-      },
-      {
-        "author_name": "Alexandra Helfand",
-        "author_inst": "George Washington University School of Medicine & Health Sciences"
-      },
-      {
-        "author_name": "Kayla Authelet",
-        "author_inst": "George Washington University School of Medicine & Health Sciences"
-      },
-      {
-        "author_name": "Matthew McHarg",
-        "author_inst": "George Washington University School of Medicine & Health Sciences"
-      },
-      {
-        "author_name": "Nataly Montano Vargas",
-        "author_inst": "George Washington University School of Medicine & Health Sciences"
-      },
-      {
-        "author_name": "Robert Shesser",
-        "author_inst": "George Washington University School of Medicine & Health Sciences"
-      },
-      {
-        "author_name": "Joanna Cohen",
-        "author_inst": "Children's National Medical Center"
-      },
-      {
-        "author_name": "Derek A.T. Cummings",
-        "author_inst": "University of Florida"
-      },
-      {
-        "author_name": "Yan Ma",
-        "author_inst": "George Washington University Milken Institute School of Public Health,"
-      },
-      {
-        "author_name": "Andrew C Meltzer",
-        "author_inst": "George Washington University School of Medicine & Health Sciences"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.12.08.20245894",
     "rel_title": "Why the SARS-CoV-2 antibody test results may be misleading: insights from a longitudinal analysis of COVID-19",
@@ -1022642,6 +1021190,121 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.12.08.20246314",
+    "rel_title": "Antibody landscape against SARS-CoV-2 proteome revealed significant differences between non-structural/ accessory proteins and structural proteins",
+    "rel_date": "2020-12-11",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.08.20246314",
+    "rel_abs": "The immunogenicity of SARS-CoV-2 proteome is largely unknown, especially for non-structural proteins and accessory proteins. Here we collected 2,360 COVID-19 sera and 601 control sera. We analyzed these sera on a protein microarray with 20 proteins of SARS-CoV-2, built an antibody response landscape for IgG and IgM. We found that non-structural proteins and accessory proteins NSP1, NSP7, NSP8, RdRp, ORF3b and ORF9b elicit prevalent IgG responses. The IgG patterns and dynamic of non-structural/ accessory proteins are different from that of S and N protein. The IgG responses against these 6 proteins are associated with disease severity and clinical outcome and declined sharply about 20 days after symptom onset. In non-survivors, sharp decrease of IgG antibodies against S1 and N protein before death was observed. The global antibody responses to non-structural/ accessory proteins revealed here may facilitate deeper understanding of SARS-CoV-2 immunology.\n\nHighlightsO_LIAn antibody response landscape against SARS-CoV-2 proteome was constructed\nC_LIO_LINon-structural/accessory proteins elicit prevalent antibody responses but likely through a different mechanism to that of structural proteins\nC_LIO_LIIgG antibodies against non-structural/accessory proteins are more associated with disease severity and clinical outcome\nC_LIO_LIFor non-survivors, the levels of IgG antibodies against S1 and N decline significantly before death\nC_LI",
+    "rel_num_authors": 25,
+    "rel_authors": [
+      {
+        "author_name": "Yang Li",
+        "author_inst": "Shanghai Jiao Tong University"
+      },
+      {
+        "author_name": "Zhaowei Xu",
+        "author_inst": "Shanghai Jiao Tong University"
+      },
+      {
+        "author_name": "Qing Lei",
+        "author_inst": "Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Danyun Lai",
+        "author_inst": "Shanghai Jiao Tong University"
+      },
+      {
+        "author_name": "Hongyan Hou",
+        "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Hewei Jiang",
+        "author_inst": "Shanghai Jiao Tong University"
+      },
+      {
+        "author_name": "yunxiao Zheng",
+        "author_inst": "Shanghai Jiao Tong University"
+      },
+      {
+        "author_name": "Xuening Wang",
+        "author_inst": "Shanghai Jiao Tong University"
+      },
+      {
+        "author_name": "Jiaoxiang Wu",
+        "author_inst": "Tongren Hospital, Shanghai Jiao Tong University School of Medicine"
+      },
+      {
+        "author_name": "Mingliang Ma",
+        "author_inst": "Shanghai Jiao Tong University"
+      },
+      {
+        "author_name": "Bo Zhang",
+        "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Hong Chen",
+        "author_inst": "Shanghai Jiao Tong University"
+      },
+      {
+        "author_name": "Caizheng Yu",
+        "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Junbiao Xue",
+        "author_inst": "Shanghai Jiao Tong University"
+      },
+      {
+        "author_name": "Nainang Zhang",
+        "author_inst": "Shanghai Jiao Tong University"
+      },
+      {
+        "author_name": "Huan Qi",
+        "author_inst": "Shanghai Jiao Tong University"
+      },
+      {
+        "author_name": "Shujuan Guo",
+        "author_inst": "Shanghai Jiao Tong University"
+      },
+      {
+        "author_name": "Yandi Zhang",
+        "author_inst": "Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Xiaosong Lin",
+        "author_inst": "Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Zongjie Yao",
+        "author_inst": "Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Huiming Sheng",
+        "author_inst": "Tongren Hospital, Shanghai Jiao Tong University School of Medicine"
+      },
+      {
+        "author_name": "Ziyong Sun",
+        "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Feng Wang",
+        "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Xionglin Fan",
+        "author_inst": "Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Sheng-ce Tao",
+        "author_inst": "Shanghai Jiao Tong University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "allergy and immunology"
+  },
   {
     "rel_doi": "10.1101/2020.12.08.20238154",
     "rel_title": "Bayesian back-calculation and nowcasting for line list data during the COVID-19 pandemic",
@@ -1023987,37 +1022650,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pathology"
   },
-  {
-    "rel_doi": "10.1101/2020.12.09.20246371",
-    "rel_title": "Research on Recognition Method of COVID-19 Images Based on Deep Learning",
-    "rel_date": "2020-12-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.09.20246371",
-    "rel_abs": "In view of the large demand for new coronary pneumonia covid19 image recognition samples,the recognition accuracy is not ideal.In this paper,a new coronary pneumonia positive image recognition method proposed based on small sample recognition. First, the CT image pictures are preprocessed, and the pictures are converted into the picture formats which are required for transfer learning. Secondly, perform small-sample image enhancement and expansion on the converted picture, such as miscut transformation, random rotation and translation, etc.. Then, multiple migration models are used to extract features and then perform feature fusion. Finally,the model is adjusted by fine-tuning.Then train the model to obtain experimental results. The experimental results show that our method has excellent recognition performance in the recognition of new coronary pneumonia images,even with only a small number of CT image samples.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "dongshen ji",
-        "author_inst": "Lanzhou University of Technology"
-      },
-      {
-        "author_name": "yanzhong zhao",
-        "author_inst": "Lanzhou University Of Technology"
-      },
-      {
-        "author_name": "zhujun zhang",
-        "author_inst": "Lanzhou University of Technology"
-      },
-      {
-        "author_name": "qianchuan zhao",
-        "author_inst": "Lanzhou University of Technology,Tsinghua University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.12.09.20246520",
     "rel_title": "Impact of Nasopharyngeal Specimen Quality on SARS-CoV-2 Test Performance",
@@ -1024400,6 +1023032,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.12.09.20246538",
+    "rel_title": "The trade-off between mobility and vaccination for COVID-19 control: a metapopulation modeling approach",
+    "rel_date": "2020-12-11",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.09.20246538",
+    "rel_abs": "November 2020 received a string of encouraging results from leading vaccine developers raising hopes for the imminent availability of an effective and safe vaccine against the SARS-CoV-2. In the present work, we discuss the theoretical impact of introducing a vaccine across a range of scenarios. In particular, we investigate how vaccination coverage, efficacy, and delivery time affect the control of the transmission dynamics in comparison to mobility restrictions. The analysis is based on a metapopulation epidemic model structured by risk. We perform a global sensitivity analysis using the Sobol method. Our analysis suggest that the reduction of mobility among patches play a significant role in the mitigation of the disease close to the effect of immunization coverage of 30% achieved in 4 months. Moreover, for an immunization coverage between 20%-50% achieved in the first half of 2021 with a vaccine efficacy between 70%-95%, the percentage reduction in the total number of SARS-CoV-2 infections is between 30%-50% by the end of 2021 in comparison with the no vaccination scenario.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Fernando Saldana",
+        "author_inst": "Universidad Nacional Autonoma de Mexico"
+      },
+      {
+        "author_name": "Jorge X. Velasco-Hernandez",
+        "author_inst": "Universidad Nacional Autonoma de Mexico"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.12.10.20244699",
     "rel_title": "Will the COVID-19 pandemic lead to a tsunami of suicides? A Swedish nationwide analysis of historical and 2020 data",
@@ -1025697,73 +1024352,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.12.11.20247528",
-    "rel_title": "Understanding patterns of adherence to COVID-19 mitigation measures: A qualitative interview study.",
-    "rel_date": "2020-12-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.11.20247528",
-    "rel_abs": "In an effort to reduce the spread of COVID-19, the UK government has introduced a series of mitigation measures. The success of these measures in preventing transmission is dependent on adherence, which is currently considered to be low. Evidence highlights the disproportionate impact of mitigation measures on individuals from Black, Asian and minority ethnic (BAME) communities, as well as among those on a low income, and an understanding of barriers to adherence in these populations is needed. In this qualitative study we examined patterns of adherence to mitigation measures and reasons underpinning these behaviors among people on low income and those from BAME communities.\n\nSemi-structured interviews were conducted with 20 participants from BAME and low-income White backgrounds. The topic guide was designed to explore how individuals are adhering to social distancing and self-isolation measures during the COVID-19 pandemic, and to explore in detail the reasons underpinning this behavior. Data were analyzed using  thematic analysis following which charts were used to help compare concepts within and between participants and develop an understanding of patterns of adherence.\n\nParticipants were confused by the constantly changing and seemingly contradictory rules and guidance. As a result, decisions were made about how best to protect themselves and their household from COVID-19, and from the detrimental impact of lockdown restrictions. This was not always in line with government advice. We identified three categories of adherence to lockdown measures 1) caution motivated super-adherence 2) risk-adapted partial-adherence and 3) necessity-driven partial-adherence. Decisions about adherence considered potential for exposure to the virus, ability to reduce risk through use of protective measures, and perceived importance of/need for the behavior.\n\nThis research highlights a need for a more nuanced understanding of adherence to lockdown measures. Provision of practical and financial support could reduce the number of people who have to engage in necessity-driven partial-adherence. Information about viral transmission could help people assess the risk associated with partial-adherence more accurately. More evidence is required on population level risks of people adopting risk-adapted partial-adherence.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Sarah Denford",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Kate S Morton",
-        "author_inst": "University of Southampton"
-      },
-      {
-        "author_name": "Helen Lambert",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Juan Zhang",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Louise E. Smith",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "James G Rubin",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Shenghan Cai",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Tingting Zhang",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Charlotte Robin",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Gemma Lasseter",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Matthew Hickman",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Isabel Oliver",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Lucy Yardley",
-        "author_inst": "University of Bristol"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.12.11.20236919",
     "rel_title": "Addressing Personal Protective Equipment (PPE) Decontamination: Methylene Blue and Light Inactivates SARS-CoV-2 on N95 Respirators and Masks with Maintenance of Integrity and Fit",
@@ -1026306,6 +1024894,49 @@
     "type": "new results",
     "category": "biochemistry"
   },
+  {
+    "rel_doi": "10.1101/2020.12.11.416818",
+    "rel_title": "Duplex formation between the template and the nascent strand in the transcription-regulating sequences determines the site of template switching in SARS - CoV-2",
+    "rel_date": "2020-12-11",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.11.416818",
+    "rel_abs": "Recently published transcriptomic data of the SARS-CoV-2 coronavirus show that there is a large variation in the frequency and steady state levels of subgenomic mRNA sequences. This variation is derived from discontinuous subgenomic RNA synthesis where the polymerase switches template from a 3 proximal genome body sequence to a 5 untranslated leader sequence. This leads to a fusion between the common 5 leader sequence and a 3 proximal body sequence in the RNA product. This process revolves around a common core sequence (CS) that is present at both the template sites that make up the fusion junction. Base-pairing between the leader CS and the nascent complementary minus strand body CS, and flanking regions (together called the transcription regulating sequence, TRS) is vital for this template switching event. However, various factors can influence the site of template switching within the same TRS duplex. Here, we model the duplexes formed between the leader and complementary body TRS regions, hypothesising the role of the stability of the TRS duplex in determining the major sites of template switching for the most abundant mRNAs. We indicate that the stability of secondary structures and the speed of transcription play key roles in determining the probability of template switching in the production of subgenomic RNAs.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Amanda B Buckingham",
+        "author_inst": "University of Cambridge, Department of Medicine, Level 5 Addenbrookes Hospital, Hills Rd, Cambridge, CB2 0QQ"
+      },
+      {
+        "author_name": "Fanny Salasc",
+        "author_inst": "University of Cambridge Department of Medicine, Level 5 Addenbrookes Hospital, Hills Rd, Cambridge, CB2 0QQ"
+      },
+      {
+        "author_name": "Gennaro Iaconis",
+        "author_inst": "University of Cambridge Department of Medicine, Level 5 Addenbrookes Hospital, Hills Rd, Cambridge, CB2 0QQ"
+      },
+      {
+        "author_name": "Isobel Jarvis",
+        "author_inst": "University of Cambridge Department of Medicine, Level 5 Addenbrookes Hospital, Hills Rd, Cambridge, CB2 0QQ"
+      },
+      {
+        "author_name": "Harriet C T Groom",
+        "author_inst": "University of Cambridge Department of Medicine, Level 5 Addenbrookes Hospital, Hills Rd, Cambridge, CB2 0QQ"
+      },
+      {
+        "author_name": "Julia Kenyon",
+        "author_inst": "University of Cambridge Department of Medicine, Level 5 Addenbrookes Hospital, Hills Rd, Cambridge, CB2 0QQ"
+      },
+      {
+        "author_name": "Andrew M L Lever",
+        "author_inst": "University of Cambridge Department of Medicine, Level 5 Addenbrookes Hospital, Hills Rd, Cambridge, CB2 0QQ"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "bioinformatics"
+  },
   {
     "rel_doi": "10.1101/2020.12.11.421784",
     "rel_title": "Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations",
@@ -1027863,25 +1026494,6 @@
     "type": "new results",
     "category": "cell biology"
   },
-  {
-    "rel_doi": "10.1101/2020.12.07.20238253",
-    "rel_title": "Theoretical Epidemic Laws Based on Data of COVID-19 Pandemic",
-    "rel_date": "2020-12-09",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.07.20238253",
-    "rel_abs": "The standard growth model of epidemic evolution such as the Richards generalized logistic function is remarkably successful because it agrees with almost all previous epidemic data. Yet, it fails to explain intervention measures for mitigations of the ongoing coronavirus 2019 disease (COVID-19) pandemic. It also fails to replicate an endemic phase that occurs in many countries epidemic curves (time series data of daily new cases). These discrepancies demonstrate that new epidemic laws are required to understand, predict and mitigate the COVID-19 pandemic. Here we show that almost all COVID-19 evolution can be modeled by three innovative epidemic laws. Specifically, based on the world COVID-19 data, we first divide an epidemic curve into three phases: an exponential growth phase, an exponential decay phase, and a constant endemic phase. We next integrate the growth and the decay phases into the first epidemic law with interventions as a model parameter. This law is completely opposite to the Richards generalized logistic function in terms of intervention measures. We then combine the first epidemic law with the endemic phase to form the second epidemic law, which makes the curve of cumulative cases increase linearly as time tends to infinity. The third epidemic law states if an epidemic is composed of multiple epidemic waves, the superposition principle applies. These laws were confirmed by the COVID-19 data from 18 countries including undeveloped, developing and developed countries. Finally, we pave the way for future research to incorporate the proposed theory into the classic SIR model. We anticipate that the results from this research can provide a scientific base for governments to mitigate the COVID-19 and other epidemic disasters.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Junke Guo",
-        "author_inst": "University of Nebraska-Lincoln"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.12.07.20245514",
     "rel_title": "Smoking, distress and COVID-19 in England: cross-sectional population surveys from 2016 to 2020",
@@ -1028280,6 +1026892,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.12.08.20245910",
+    "rel_title": "SARS-CoV-2 infections in kindergartens and associated households at the start of the second wave in Berlin, Germany - a cross sectional study",
+    "rel_date": "2020-12-09",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.08.20245910",
+    "rel_abs": "ObjectivesThe comparatively large proportion of asymptomatic SARS-CoV-2 infections in the youngest children opens up the possibility that kindergartens represent reservoirs of infection. However, actual surveys in kindergartens beyond individual outbreaks are rare. At the beginning of the second pandemic wave in Berlin, Germany, i.e., end of September 2020, we screened SARS-CoV-2 infections among kindergarten children, staff and connected household members.\n\nMethodsTwelve kindergartens were randomly selected in the Berlin metropolitan area, and a total of 720 participants were recruited (155 pre-school children, 78 staff, 487 household members). Participants were briefly examined and interviewed, and SARS-CoV-2 infections and anti-SARS-Cov-2 IgG antibodies were assessed.\n\nResultsSigns and symptoms, largely resembling common cold, were present in 24.2% of children and 28.9% of staff. However, no SARS-CoV-2 infection was detected among 701 PCR-tested individuals, and only one childcare worker showed IgG seroreactivity (0.15%; 1/672).\n\nConclusionsAgainst a backdrop of increased pandemic activity in the community, this cross-sectional study does not suggest that kindergartens are silent transmission reservoirs. Nevertheless, at increasing pandemic activity, reinforced precautionary measures and repeated routine testing appears advisable.",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Marlene Thielecke",
+        "author_inst": "Charite Universitaetsmedizin Berlin, Institute of Tropical Medicine and International Health"
+      },
+      {
+        "author_name": "Stefanie Theuring",
+        "author_inst": "Charite Universitaetsmedizin Berlin, Institute of Tropical Medicine and International Health"
+      },
+      {
+        "author_name": "Welmoed van Loon",
+        "author_inst": "Charite Universitaetsmedizin Berlin, Institute of Tropical Medicine and International Health"
+      },
+      {
+        "author_name": "Franziska Hommes",
+        "author_inst": "Charite Universitaetsmedizin Berlin, Institute of Tropical Medicine and International Health"
+      },
+      {
+        "author_name": "Marcus A. Mall",
+        "author_inst": "Charite Universitaetsmedizin Berlin, Department of Pediatric Pulmonology, Immunology and Critical Care Medicine"
+      },
+      {
+        "author_name": "Alexander Rosen",
+        "author_inst": "Charite Universitaetsmedizin Berlin, Department of Pediatric Pulmonology, Immunology and Critical Care Medicine"
+      },
+      {
+        "author_name": "Falko Boehringer",
+        "author_inst": "Labor Berlin  Charite Vivantes Services GmbH"
+      },
+      {
+        "author_name": "Christof von Kalle",
+        "author_inst": "Charite Universitaetsmedizin Berlin, Clinical Study Center"
+      },
+      {
+        "author_name": "Valerie Kirchberger",
+        "author_inst": "Charite Universitaetsmedizin Berlin, Medical Directorate"
+      },
+      {
+        "author_name": "Tobias Kurth",
+        "author_inst": "Charite Universitaetsmedizin Berlin, Institute of Public Health"
+      },
+      {
+        "author_name": "Joachim Seybold",
+        "author_inst": "Charite Universitaetsmedizin Berlin, Medical Directorate"
+      },
+      {
+        "author_name": "Frank P. Mockenhaupt",
+        "author_inst": "Charite Universitaetsmedizin Berlin, Institute of Tropical Medicine and International Health"
+      },
+      {
+        "author_name": "- BECOSS Study Group",
+        "author_inst": ""
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.12.08.20245753",
     "rel_title": "A novel multi-omics-based identification of symptoms, comorbid conditions, and possible long-term complications in COVID-19",
@@ -1029544,41 +1028223,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.12.07.20243881",
-    "rel_title": "Inadequate intention to receive Covid-19 vaccination: indicators for public health messaging needed to improve uptake in UK",
-    "rel_date": "2020-12-08",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.07.20243881",
-    "rel_abs": "Data promising effective Covid-19 vaccines have accelerated the UKs mass vaccination programme. The UK publics attitudes to the governments prioritisation list are unknown, and achieving critical population immunity will require the remaining majority to accept both vaccination and the delay in access of up to a year or more. This cross-sectional observational study sent an online questionnaire to registrants of the UK National Health Services largest personal health record. Question items covered willingness for Covid-19 vaccine uptake and attitudes to prioritisation. Among 9,122 responses, 71.5% indicated wanting a vaccine, below what previous modelling indicated as critical levels for progressing towards herd immunity. 22.7% disagreed with the prioritisation list, though 70.3% were against being able to expedite vaccination through payment. Age and female gender were, respectively, strongly positively and negatively associated with wanting a vaccine. Teachers and Black, Asian and Minority Ethnic (BAME) groups were most cited by respondents for prioritisation. This study identifies factors to inform the public health messaging critical to improving uptake.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Patrik Bachtiger",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Alexander Adamson",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "William A Maclean",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Jennifer K Quint",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Nicholas S Peters",
-        "author_inst": "Imperial College London"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.12.07.20245308",
     "rel_title": "Integrative analyses identify susceptibility genes underlying COVID-19 hospitalization",
@@ -1030013,6 +1028657,77 @@
     "type": "new results",
     "category": "zoology"
   },
+  {
+    "rel_doi": "10.1101/2020.12.08.415836",
+    "rel_title": "Anti-SARS-CoV-2 activity of Andrographis paniculata extract and its major component Andrographolide in human lung epithelial cells and cytotoxicity evaluation in major organ cell representatives",
+    "rel_date": "2020-12-08",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.08.415836",
+    "rel_abs": "The coronavirus disease 2019 (COVID-19) caused by a novel coronavirus (SARS-CoV-2) has become a major health problem affecting more than fifty million cases with over one million deaths globally. The effective antivirals are still lacking. Here, we optimized a high-content imaging platform and the plaque assay for viral output study using the legitimate model of human lung epithelial cells, Calu-3, to determine anti-SARS-CoV-2 activity of Andrographis paniculata extract and its major component andrographolide. SARS-CoV-2 at 25TCID50 was able to reach the maximal infectivity of 95% in Calu-3 cells. Post-infection treatment of A. paniculata and andrographolide in SARS-CoV-2 infected Calu-3 cells significantly inhibited the production of infectious virions with the IC50 of 0.036 g/mL and 0.034 M, respectively, as determined by plaque assay. The cytotoxicity profile developed over the cell line representatives of major organs, including liver (HepG2 and imHC), kidney (HK-2), intestine (Caco-2), lung (Calu-3) and brain (SH-SY5Y), showed the CC50 of >100 g/mL for A. paniculata extract and 13.2-81.5 M for andrographolide, respectively, corresponding to the selectivity index over 380. In conclusion, this study provided experimental evidence in favor of A. paniculata and andrographolide for further development as a monotherapy or in combination with other effective drugs against SARS-CoV-2 infection.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Khanit Sa-ngiamsuntorn",
+        "author_inst": "Department of Biochemistry, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand."
+      },
+      {
+        "author_name": "Ampa Suksatu",
+        "author_inst": "Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400 Thailand"
+      },
+      {
+        "author_name": "Yongyut Pewkliang",
+        "author_inst": "Section for Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand"
+      },
+      {
+        "author_name": "Piyanoot Thongsri",
+        "author_inst": "Section for Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand"
+      },
+      {
+        "author_name": "Phongthon Kanjanasirirat",
+        "author_inst": "Excellent Center for Drug Discovery (ECDD), Faculty of Science, Mahidol University, Bangkok, 10400, Thailand"
+      },
+      {
+        "author_name": "Suwimon Manopwisedjaroen",
+        "author_inst": "Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400 Thailand"
+      },
+      {
+        "author_name": "Sitthivut Charoensutthivarakul",
+        "author_inst": "School of Bioinnovation and Bio Based Product Intelligence, Faculty of Science, Mahidol University, Bangkok 10400, Thailand"
+      },
+      {
+        "author_name": "Patompon Wongtrakoongate",
+        "author_inst": "Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand"
+      },
+      {
+        "author_name": "Supaporn Pitiporn",
+        "author_inst": "ChaoPhya Abhaibhubejhr Hospital, Prachin Buri 25000, Thailand"
+      },
+      {
+        "author_name": "Phisit Khemawoot",
+        "author_inst": "Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Samutprakarn 10540 Thailand"
+      },
+      {
+        "author_name": "Somchai Chutipongtanate",
+        "author_inst": "Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University"
+      },
+      {
+        "author_name": "Suparerk Borwornpinyo",
+        "author_inst": "Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand"
+      },
+      {
+        "author_name": "Arunee Thitithanyanont",
+        "author_inst": "Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400 Thailand"
+      },
+      {
+        "author_name": "Suradej Hongeng",
+        "author_inst": "Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2020.12.08.415018",
     "rel_title": "Extended in vitro inactivation of SARS-CoV-2 by titanium dioxide surface coating",
@@ -1031029,45 +1029744,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.12.04.20244020",
-    "rel_title": "Shift work is associated with positive COVID-19 status in hospitalised patients",
-    "rel_date": "2020-12-07",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.04.20244020",
-    "rel_abs": "IntroductionShift work is associated with both mental, and physical ill health, including lung disease and infections. However, the impact of shift work on significant COVID-19 illness has not be assessed. We therefore investigated whether shift work is associated with COVID-19.\n\nMethods501,000 UK biobank participants were linked to secondary care SARS-CoV-2 PCR results from public health England. Healthcare workers and those without an occupational history were excluded from analysis.\n\nResultsMultivariate logistic regression taking into account age, sex, ethnicity and deprivation index revealed that irregular shift work (OR 2.42 95%CI 1.92-3.05), permanent shift work (OR 2.5, 95%CI 1.95-3.19), day shift work (OR 2.01, 95%CI 1.55-2.6), irregular night shift work (OR 3.04, 95%CI 2.37-3.9) and permanent night shift work (OR 2.49, 95%CI 1.67-3.7) were all associated with positive COVID-19 tests compared to participants that did not perform shift work. This relationship persisted after adding sleep duration, chronotype, pre-morbid disease, BMI, alcohol and smoking. Work factors (proximity to a colleague combined with estimated disease exposure) were positively correlated with COVID-19 incidence (r2=0.248, p=0.02). If this was added to the model shift work frequency remained significantly associated with COVID-19. To control for non-measured occupational factors the incidence of COVID-19 in shift workers was compared to colleagues in the same job who did not do shift work. Shift workers had a higher incidence of COVID-19 (p<0.01).\n\nConclusionsShift work is associated with a higher likelihood of in-hospital COVID-19 positivity. This risk could potentially be mitigated via additional workplace precautions or vaccination.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Robert Maidstone",
-        "author_inst": "The university of Oxford"
-      },
-      {
-        "author_name": "Simon G Anderson",
-        "author_inst": "University of West Indies"
-      },
-      {
-        "author_name": "David W Ray",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Martin K Rutter",
-        "author_inst": "The University of Manchester"
-      },
-      {
-        "author_name": "Hannah J Durrington",
-        "author_inst": "University of Manchester"
-      },
-      {
-        "author_name": "John F Blaikley",
-        "author_inst": "The University of Manchester"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "respiratory medicine"
-  },
   {
     "rel_doi": "10.1101/2020.12.04.20242073",
     "rel_title": "Sulodexide in the treatment of patients with early stages of COVID-19: a randomised controlled trial",
@@ -1031330,6 +1030006,77 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.12.05.20244673",
+    "rel_title": "Handling and accuracy of four rapid antigen tests for the diagnosis of SARS-CoV-2 compared to RT-qPCR.",
+    "rel_date": "2020-12-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.05.20244673",
+    "rel_abs": "BackgroundSARS-CoV-2 molecular diagnostics is facing material shortages and long turnaround times due to exponential increase of testing demand.\n\nObjectiveWe evaluated the analytic performance and handling of four rapid Antigen Point of Care Tests (AgPOCTs) I-IV (Distributors: (I) Roche, (II) Abbott, (III) MEDsan and (IV) Siemens).\n\nMethods100 RT-PCR negative and 84 RT-PCR positive oropharyngeal swabs were prospectively collected and used to determine performance and accuracy of these AgPOCTs. Handling was evaluated by 10 healthcare workers/users through a questionnaire.\n\nResultsThe median duration from symptom onset to sampling was 6 days (IQR 2-12 days). The overall relative sensitivity was 49.4%, 44.6%, 45.8% and 54.9 % for tests I, II, III and IV, respectively. In the high viral load subgroup (containing >106 copies of SARS-CoV-2 /swab, n=26), AgPOCTs reached sensitivities of 92.3% or more (range 92.3%-100%). Specificity was 100% for tests I, II and IV and 97% for test III. Regarding handling, test I obtained the overall highest scores, while test II was considered to have the most convenient components. Of note, users considered all assays, with the exception of test I, to pose a significant risk for contamination by drips or spills.\n\nDiscussionBesides some differences in sensitivity and handling, all four AgPOCTs showed acceptable performance in high viral load samples. However, due to the significantly lower sensitivity compared to RT-qPCR, a careful consideration of pro and cons of AgPOCT has to be taken into account before clinical implementation.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Flaminia Olearo",
+        "author_inst": "University Medical Center Hamburg-Eppendorf, Hamburg, Germany"
+      },
+      {
+        "author_name": "Dominik Noerz",
+        "author_inst": "University Medical Center Hamburg-Eppendorf"
+      },
+      {
+        "author_name": "Fabian Heinrich",
+        "author_inst": "University Medical Center Hamburg-Eppendorf, Hamburg, Germany"
+      },
+      {
+        "author_name": "Jan Peter Sutter",
+        "author_inst": "University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany"
+      },
+      {
+        "author_name": "Kevin Roedel",
+        "author_inst": "University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany"
+      },
+      {
+        "author_name": "Alexander Schultze",
+        "author_inst": "University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany"
+      },
+      {
+        "author_name": "Julian Schulze Zur Wiesch",
+        "author_inst": "University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany"
+      },
+      {
+        "author_name": "Platon Braun",
+        "author_inst": "University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany"
+      },
+      {
+        "author_name": "Lisa Oesterreich",
+        "author_inst": "Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany"
+      },
+      {
+        "author_name": "Benno Kreuels",
+        "author_inst": "University Medical Center Hamburg-Eppendorf, Hamburg, Germany"
+      },
+      {
+        "author_name": "Dominic Wichmann",
+        "author_inst": "University Medical Center Hamburg-Eppendorf, Hamburg, Germany"
+      },
+      {
+        "author_name": "Martin Aepfelbacher",
+        "author_inst": "University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany"
+      },
+      {
+        "author_name": "Susanne Pfefferle",
+        "author_inst": "University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany"
+      },
+      {
+        "author_name": "Marc Luetgehetmann",
+        "author_inst": "University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.12.07.20245241",
     "rel_title": "Lack of antibodies against seasonal coronavirus OC43 nucleocapsid protein identifies patients at risk of critical COVID-19",
@@ -1032527,53 +1031274,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.12.04.412098",
-    "rel_title": "Significant inactivation of SARS-CoV-2 by a green tea catechin, a catechin-derivative and galloylated theaflavins in vitro",
-    "rel_date": "2020-12-06",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.04.412098",
-    "rel_abs": "Potential effects of teas and their constituents on SARS-CoV-2 infection were studied in vitro. Infectivity of SARS-CoV-2 was significantly reduced by a treatment with green tea, roasted green tea or oolong tea. Most remarkably, exposure to black tea for 1 min decreased virus titer to an undetectable level (less than 1/1,000 of untreated control). An addition of (-) epigallocatechin gallate (EGCG) significantly inactivated SARS-CoV-2, while theasinensin A (TSA) and galloylated theaflavins including theaflavin 3, 3-di-gallate (TFDG) had more remarkable anti-viral activities. Virus treated with TSA at 500 M or TFDG at 100 M showed less than 1/10,000 infectivity compared with untreated virus. TSA and TFDG significantly inhibited interaction between recombinant ACE2 and RGD of S protein. These results strongly suggest that EGCG, and more remarkably TSA and galloylated theaflavins, inactivate the novel coronavirus.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Eriko Ohgitani",
-        "author_inst": "Department of Immunology, Kyoto Prefectural University of Medicine"
-      },
-      {
-        "author_name": "Masaharu Shin-Ya",
-        "author_inst": "Department of Immunology, Kyoto Prefectural University of Medicine"
-      },
-      {
-        "author_name": "Masaki Ichitani",
-        "author_inst": "Central Research Institute, ITO EN, Ltd."
-      },
-      {
-        "author_name": "Makoto Kobayashi",
-        "author_inst": "Central Research Institute, ITO EN, Ltd."
-      },
-      {
-        "author_name": "Takanobu Takihara",
-        "author_inst": "Central Research Institute, ITO EN, Ltd."
-      },
-      {
-        "author_name": "Masaya Kawamoto",
-        "author_inst": "Department of Immunology, Kyoto Prefectural University of Medicine"
-      },
-      {
-        "author_name": "Hitoshi Kinugasa",
-        "author_inst": "Central Research Institute, ITO EN, Ltd."
-      },
-      {
-        "author_name": "Osam Mazda",
-        "author_inst": "Department of Immunology, Kyoto Prefectural University of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.12.04.410589",
     "rel_title": "Elevated SARS-CoV-2 Antibodies Distinguish Severe Disease in Early COVID-19 Infection",
@@ -1033000,6 +1031700,105 @@
     "type": "new results",
     "category": "genetics"
   },
+  {
+    "rel_doi": "10.1101/2020.12.04.410092",
+    "rel_title": "Ribavirin shows antiviral activity against SARS-CoV-2 and downregulates the activity of TMPRSS2 and the expression of ACE2 in vitro",
+    "rel_date": "2020-12-05",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.04.410092",
+    "rel_abs": "Ribavirin is a guanosine analog and has a broad-spectrum antiviral activity against RNA viruses. Based on this, we aimed to show the anti-SARS-CoV-2 activity of this drug molecule via in vitro, in silico and molecular techniques. Ribavirin showed antiviral activity in Vero E6 cells following SARS-CoV-2 infection. In silico analysis suggested that Ribarivin has a broad-spectrum impact on Vero E6 cells. According to the detailed molecular techniques, Ribavirin was shown to decrease TMPRSS2 expression both at mRNA and protein level 48 hours after treatment. The suppressive effect of Ribavirin in ACE2 protein expression was shown to be dependent on cell types. Finally, proteolytic activity assays showed that Ribavirin also showed an inhibitory effect on TMPRSS2 enzyme. As a conclusion, Ribavirin is a potential antiviral drug for the treatment against SARS-CoV-2, and it interferes with the effect of TMPRSS2 and ACE2 expression.",
+    "rel_num_authors": 21,
+    "rel_authors": [
+      {
+        "author_name": "Mehmet Altay Unal",
+        "author_inst": "Ankara University Stem Cell Institute"
+      },
+      {
+        "author_name": "Ceylan Verda Bitirim",
+        "author_inst": "Ankara University Stem Cell Institute"
+      },
+      {
+        "author_name": "Gokce Yagmur Summak",
+        "author_inst": "Ankara University Stem Cell Institute"
+      },
+      {
+        "author_name": "Sidar Bereketoglu",
+        "author_inst": "Ankara University, Faculty of Science, Department of Biology"
+      },
+      {
+        "author_name": "Inci Cevher Zeytin",
+        "author_inst": "Ankara University Stem Cell Institute"
+      },
+      {
+        "author_name": "Omur Besbinar",
+        "author_inst": "Ankara University Stem Cell Institute"
+      },
+      {
+        "author_name": "Cansu Gurcan",
+        "author_inst": "Ankara University Stem Cell Institute"
+      },
+      {
+        "author_name": "Dunya Aydos",
+        "author_inst": "Ankara University Stem Cell Institute"
+      },
+      {
+        "author_name": "Ezgi Goksoy",
+        "author_inst": "Ankara University Stem Cell Institute"
+      },
+      {
+        "author_name": "Ebru Kocakaya",
+        "author_inst": "Ankara University Stem Cell Institute"
+      },
+      {
+        "author_name": "Zeynep Eran",
+        "author_inst": "Ankara University Stem Cell Institute"
+      },
+      {
+        "author_name": "Merve Murat",
+        "author_inst": "Ankara University Stem Cell Institute"
+      },
+      {
+        "author_name": "Nil Demir",
+        "author_inst": "Ankara University Stem Cell Institute"
+      },
+      {
+        "author_name": "Julia Somers",
+        "author_inst": "Oregon Health & Sciences Univerity Department of Molecular and Medical Genetics"
+      },
+      {
+        "author_name": "Emek Demir",
+        "author_inst": "Oregon Health & Sciences Univerity Department of Molecular and Medical Genetics"
+      },
+      {
+        "author_name": "Hasan Nazir",
+        "author_inst": "Ankara University, Faculty of Science, Department of Chemistry"
+      },
+      {
+        "author_name": "Sibel Aysil Ozkan",
+        "author_inst": "Ankara University, Faculty of Pharmacy, Department of Analytical Chemistry"
+      },
+      {
+        "author_name": "Aykut Ozkul",
+        "author_inst": "Ankara University, Faculty of Veterinary, Department of Virology"
+      },
+      {
+        "author_name": "Alpay Azap",
+        "author_inst": "Ankara University, School of Medicine, Department of Infectious Diseases and Clinical Microbiology"
+      },
+      {
+        "author_name": "Acelya Yilmazer",
+        "author_inst": "Ankara University Stem Cell Institute; Ankara University, Faculty of Engineering, Department of Biomedical Engineering"
+      },
+      {
+        "author_name": "Kamil Can Akcali",
+        "author_inst": "Ankara University Stem Cell Institute; Ankara University, School of Medicine, Department of Biophysics"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "pharmacology and toxicology"
+  },
   {
     "rel_doi": "10.1101/2020.12.04.412155",
     "rel_title": "Chromatin remodeling in peripheral blood cells reflects COVID-19 symptom severity",
@@ -1034541,121 +1033340,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.12.03.407031",
-    "rel_title": "Circulating ACE2-expressing Exosomes Block SARS-CoV-2 Virus Infection as an Innate Antiviral Mechanism",
-    "rel_date": "2020-12-04",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.03.407031",
-    "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus disease 2019 (COVID-19) with innate and adaptive immune response triggered in such patients by viral antigens. Both convalescent plasma and engineered high affinity human monoclonal antibodies have shown therapeutic potential to treat COVID-19. Whether additional antiviral soluble factors exist in peripheral blood remain understudied. Herein, we detected circulating exosomes that express the SARS-CoV-2 viral entry receptor angiotensin-converting enzyme 2 (ACE2) in plasma of both healthy donors and convalescent COVID-19 patients. We demonstrated that exosomal ACE2 competes with cellular ACE2 for neutralization of SARS-CoV-2 infection. ACE2-expressing (ACE2+) exosomes blocked the binding of the viral spike (S) protein RBD to ACE2+ cells in a dose dependent manner, which was 400- to 700-fold more potent than that of vesicle-free recombinant human ACE2 extracellular domain protein (rhACE2). As a consequence, exosomal ACE2 prevented SARS-CoV-2 pseudotype virus tethering and infection of human host cells at a 50-150 fold higher efficacy than rhACE2. A similar antiviral activity of exosomal ACE2 was further demonstrated to block wild-type live SARS-CoV-2 infection. Of note, depletion of ACE2+ exosomes from COVID-19 patient plasma impaired the ability to block SARS-CoV-2 RBD binding to host cells. Our data demonstrate that ACE2+ exosomes can serve as a decoy therapeutic and a possible innate antiviral mechanism to block SARS-CoV-2 infection.",
-    "rel_num_authors": 25,
-    "rel_authors": [
-      {
-        "author_name": "Lamiaa El-Shennawy",
-        "author_inst": "Northwestern University"
-      },
-      {
-        "author_name": "Andrew D. Hoffmann",
-        "author_inst": "Northwestern University"
-      },
-      {
-        "author_name": "Nurmaa K. Dashzeveg",
-        "author_inst": "Northwestern University"
-      },
-      {
-        "author_name": "Paul J. Mehl",
-        "author_inst": "Northwestern University"
-      },
-      {
-        "author_name": "Zihao Yu",
-        "author_inst": "Northwestern University"
-      },
-      {
-        "author_name": "Valerie L. Tokars",
-        "author_inst": "Northwestern University"
-      },
-      {
-        "author_name": "Vlad Nicolaescu",
-        "author_inst": "The University of Chicago"
-      },
-      {
-        "author_name": "Carolina Ostiguin",
-        "author_inst": "Northwestern University"
-      },
-      {
-        "author_name": "Yuzhi Jia",
-        "author_inst": "Northwestern University"
-      },
-      {
-        "author_name": "Lin Li",
-        "author_inst": "Northwestern University"
-      },
-      {
-        "author_name": "Kevin Furlong",
-        "author_inst": "The University of Chicago"
-      },
-      {
-        "author_name": "Chengsheng Mao",
-        "author_inst": "Northwestern University"
-      },
-      {
-        "author_name": "Jan Wysocki",
-        "author_inst": "Northwestern University"
-      },
-      {
-        "author_name": "Daniel Batlle",
-        "author_inst": "Northwestern University"
-      },
-      {
-        "author_name": "Thomas J Hope",
-        "author_inst": "Northwestern University"
-      },
-      {
-        "author_name": "Yang Shen",
-        "author_inst": "Texas A&M University"
-      },
-      {
-        "author_name": "Yuan Luo",
-        "author_inst": "Northwestern University"
-      },
-      {
-        "author_name": "Young Chae",
-        "author_inst": "Northwestern University"
-      },
-      {
-        "author_name": "Hui Zhang",
-        "author_inst": "Northwestern University"
-      },
-      {
-        "author_name": "Suchitra Swaminathan",
-        "author_inst": "Northwestern University"
-      },
-      {
-        "author_name": "Glenn C. Randall",
-        "author_inst": "The University of Chicago"
-      },
-      {
-        "author_name": "Alexis R Demonbreun",
-        "author_inst": "Northwestern University"
-      },
-      {
-        "author_name": "Michael G Ison",
-        "author_inst": "Northwestern University"
-      },
-      {
-        "author_name": "Deyu Fang",
-        "author_inst": "Northwestern University"
-      },
-      {
-        "author_name": "Huiping Liu",
-        "author_inst": "Northwestern University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2020.12.04.407510",
     "rel_title": "Comparative analysis of antigen-specific anti-SARS-CoV-2 antibody isotypes in COVID-19 patients",
@@ -1034934,6 +1033618,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.12.03.20243345",
+    "rel_title": "Long Covid and the role of physical activity: a qualitative study",
+    "rel_date": "2020-12-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.03.20243345",
+    "rel_abs": "ObjectivesTo explore the lived experience of Long Covid with particular focus on the role of physical activity\n\nDesignQualitative study using semi-structured interviews\n\nParticipants18 people living with Long Covid (9 male, 9 female; aged between 18-74; 10 White British, 3 White Other, 3 Asian, 1 Black, 1 mixed ethnicity) recruited via a UK-based research interest database for people with Long Covid\n\nSettingTelephone interviews with 17 participants living in the UK and 1 participant living in the US\n\nResultsFour themes were generated. Theme one highlights the physical and social isolation experienced by people with Long Covid, compounded by a lack of support and advice from medical professionals. Theme two describes how participants sought information and validation through online sources and communities. Theme three captures the challenges associated with managing physical and cognitive effects of Long Covid including fatigue and  brain fog whilst trying to resume and maintain activities of daily living and other forms of exercise. Theme four illustrates the battle with self-concept to accept reduced function (even temporarily) and the fear of permanent reduction in physical and cognitive ability.\n\nConclusionsThis study provides insight into the challenges of managing physical activity alongside the extended symptoms associated with Long Covid. Findings highlight the need for greater consensus around physical activity-related advice for people with Long Covid and improved support to resume activities considered important for wellbeing.\n\nArticle Summary\n\nStrengths and limitations of this studyO_LITo our knowledge, this paper is the first to explore the role of physical activity in the lived experience of Long Covid using a qualitative approach\nC_LIO_LIThe study design enabled in-depth inquiry of lived experiences in a diverse sample\nC_LIO_LIInductive thematic analysis ensured descriptions and interpretations of the lived experience were tested and found to be grounded in the data\nC_LIO_LIParticipants were recruited from members of a Long Covid research interest database who registered via an on-line form, meaning study findings might not capture the views of digitally excluded populations\nC_LI\n\nFunding statementThis work was supported by Sheffield Hallam University.\n\nCompeting interestsAll authors have completed the ICMJE uniform disclosure form at www.icmje.org/coi_disclosure.pdf and declare: no support from any organization for the submitted work; no financial relationships with any organizations that might have an interest in the submitted work in the previous three years; no other relationships or activities that could appear to have influenced the submitted work.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Helen Humphreys",
+        "author_inst": "Sheffield Hallam University"
+      },
+      {
+        "author_name": "Laura Kilby",
+        "author_inst": "Sheffield Hallam University"
+      },
+      {
+        "author_name": "Nik Kudiersky",
+        "author_inst": "Sheffield Hallam University"
+      },
+      {
+        "author_name": "Robert Copeland",
+        "author_inst": "Sheffield Hallam University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.12.03.20243550",
     "rel_title": "The application of Hybrid deep learning Approach to evaluate chest ray images for the diagnosis of pneumonia in children",
@@ -1036103,33 +1034818,6 @@
     "type": "new results",
     "category": "pharmacology and toxicology"
   },
-  {
-    "rel_doi": "10.1101/2020.12.03.20243196",
-    "rel_title": "Mental health problems in the general population during and after the first lockdown phase due to the SARS-Cov-2 pandemic: Rapid review of multi-wave studies",
-    "rel_date": "2020-12-04",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.03.20243196",
-    "rel_abs": "AimsThe SARS-Cov-2 pandemic and the lockdown response are assumed to have increased mental health problems in general populations compared to pre-pandemic times. The aim of this paper is to review studies on the course of mental health problems during and after the first lockdown phase.\n\nMethodsWe conducted a rapid review of multi-wave studies in general populations with time points during and after the first lockdown phase. Repeated cross-sectional and longitudinal studies that utilized validated instruments were included. The main outcome was whether indicators of mental health problems have changed during and after the first lockdown phase. The study was registered with PROSPERO No. CRD42020218640.\n\nResults23 studies with 56 indicators were included in the qualitative review. Studies that reported data from pre-pandemic assessments through lockdown indicated an increase in mental health problems. During lockdown no uniform trend could be identified. After lockdown mental health problems decreased slightly.\n\nConclusionsAs mental health care utilization indicators and data on suicides do not suggest an increase in demand during the first lockdown phase, we regard the increase in mental health problems as general distress that is to be expected during a global health crisis. Several methodological, pandemic-related, response-related and health policy-related factors need to be considered when trying to gain a broader perspective on the impact of the first wave of the pandemic and the first phase of lockdown on general populations mental health.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Dirk Richter",
-        "author_inst": "Bern University Hospital for Mental Health"
-      },
-      {
-        "author_name": "Steffi Riedel-Heller",
-        "author_inst": "University of Leipzig, Institute of Social Medicine, Occupational Health and Public Health (ISAP), Leipzig, Germany"
-      },
-      {
-        "author_name": "Simeon Zuercher",
-        "author_inst": "Bern University Hospital for Mental Health, Bern, Switzerland"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "psychiatry and clinical psychology"
-  },
   {
     "rel_doi": "10.1101/2020.12.04.411389",
     "rel_title": "Elevated temperature inhibits SARS-CoV-2 replication in respiratory epithelium independently of the induction of IFN-mediated innate immune defences",
@@ -1036500,6 +1035188,205 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.11.30.20239095",
+    "rel_title": "Establishment of CORONET; COVID-19 Risk in Oncology Evaluation Tool to identify cancer patients at low versus high risk of severe complications of COVID-19 infection upon presentation to hospital",
+    "rel_date": "2020-12-03",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.30.20239095",
+    "rel_abs": "BackgroundCancer patients are at increased risk of severe COVID-19. As COVID-19 presentation and outcomes are heterogeneous in cancer patients, decision-making tools for hospital admission, severity prediction and increased monitoring for early intervention are critical.\n\nObjectiveTo identify features of COVID-19 in cancer patients predicting severe disease and build a decision-support online tool; COVID-19 Risk in Oncology Evaluation Tool (CORONET)\n\nMethodData was obtained for consecutive patients with active cancer with laboratory confirmed COVID-19 presenting in 12 hospitals throughout the United Kingdom (UK). Univariable logistic regression was performed on pre-specified features to assess their association with admission ([&ge;]24 hours inpatient), oxygen requirement and death. Multivariable logistic regression and random forest models (RFM) were compared with patients randomly split into training and validation sets. Cost function determined cut-offs were defined for admission/death using RFM. Performance was assessed by sensitivity, specificity and Brier scores (BS). The CORONET model was then assessed in the entire cohort to build the online CORONET tool.\n\nResultsTraining and validation sets comprised 234 and 66 patients respectively with median age 69 (range 19-93), 54% males, 46% females, 71% vs 29% had solid and haematological cancers. The RFM, selected for further development, demonstrated superior performance over logistic regression with AUROC predicting admission (0.85 vs. 0.78) and death (0.76 vs. 0.72). C-reactive protein was the most important feature predicting COVID-19 severity. CORONET cut-offs for admission and mortality of 1.05 and 1.8 were established. In the training set, admission prediction sensitivity and specificity were 94.5% and 44.3% with BS 0.118; mortality sensitivity and specificity were 78.5% and 57.2% with BS 0.364. In the validation set, admission sensitivity and specificity were 90.7% and 42.9% with BS 0.148; mortality sensitivity and specificity were 92.3% and 45.8% with BS 0.442. In the entire cohort, the CORONET decision support tool recommended admission of 99% of patients requiring oxygen and of 99% of patients who died.\n\nConclusions and RelevanceCORONET, a decision support tool validated in hospitals throughout the UK showed promise in aiding decisions regarding admission and predicting COVID-19 severity in patients with cancer presenting to hospital. Future work will validate and refine the tool in further datasets.",
+    "rel_num_authors": 46,
+    "rel_authors": [
+      {
+        "author_name": "Rebecca J Lee Dr",
+        "author_inst": "The Christie NHS Foundation Trust, Wilmslow road, M20 4BX; The University of Manchester, Oxford road, M13 9PL"
+      },
+      {
+        "author_name": "Cong Zhou Dr",
+        "author_inst": ". Digital experimental cancer medicine and Bioinformatics and Biostatistics teams, Cancer Research UK Manchester Institute Cancer Biomarker Centre, The Universi"
+      },
+      {
+        "author_name": "Oskar Wysocki Dr",
+        "author_inst": "The University of Manchester, Oxford road, M13 9PL; Digital experimental cancer medicine team, Manchester Centre for Cancer Biomarker Sciences, Alderley Park, S"
+      },
+      {
+        "author_name": "Rohan Shotton Dr",
+        "author_inst": "The Christie NHS Foundation Trust, Wilmslow road, M20 4BX"
+      },
+      {
+        "author_name": "Ann Tivey Dr",
+        "author_inst": "The Christie NHS Foundation Trust, Wilmslow road, M20 4BX"
+      },
+      {
+        "author_name": "Louise Lever Dr",
+        "author_inst": "The University of Manchester, Oxford road, M13 9PL"
+      },
+      {
+        "author_name": "Joshua Woodcock Dr",
+        "author_inst": "The University of Manchester, Oxford road, M13 9PL"
+      },
+      {
+        "author_name": "Angelos Angelakas Dr",
+        "author_inst": "University Hospitals of Morecambe Bay, Kendal LA9 7RG"
+      },
+      {
+        "author_name": "Theingi Aung Dr",
+        "author_inst": "Weston Park Cancer Centre, Sheffield Teaching Hospitals NHS foundation Trust, Sheffield S10 2JF"
+      },
+      {
+        "author_name": "Kathryn Banfill Dr",
+        "author_inst": "The Christie NHS Foundation Trust, Wilmslow road, M20 4BX; The University of Manchester, Oxford road, M13 9PL"
+      },
+      {
+        "author_name": "Mark Baxter Dr",
+        "author_inst": "University of Dundee, Dundee DD1 4HN"
+      },
+      {
+        "author_name": "Talvinder Bhogal Dr",
+        "author_inst": "The Clatterbridge Cancer Centre NHS Foundation Trust, Liverpool, UK"
+      },
+      {
+        "author_name": "Hayley Boyce Dr",
+        "author_inst": "Weston Park Cancer Centre, Sheffield Teaching Hospitals NHS foundation Trust, Sheffield S10 2JF"
+      },
+      {
+        "author_name": "Ellen Copson Dr",
+        "author_inst": "Cancer Sciences Academic Unit, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD"
+      },
+      {
+        "author_name": "Elena Dickens Dr",
+        "author_inst": "Oncology Department, University Hospitals of Leicester NHS Trust, Leicester, LE1 5WW"
+      },
+      {
+        "author_name": "Leonie Eastlake Dr",
+        "author_inst": "University Hospitals Plymouth NHS Trust, Plymouth, PL6 8DH"
+      },
+      {
+        "author_name": "Hannah Frost Ms",
+        "author_inst": ". Digital experimental cancer medicine and Bioinformatics and Biostatistics teams, Cancer Research UK Manchester Institute Cancer Biomarker Centre, The Universi"
+      },
+      {
+        "author_name": "Fabio Gomes Dr",
+        "author_inst": "The Christie NHS Foundation Trust, Wilmslow road, M20 4BX"
+      },
+      {
+        "author_name": "Donna Graham Dr",
+        "author_inst": "The Christie NHS Foundation Trust, Wilmslow road, M20 4BX"
+      },
+      {
+        "author_name": "Christina Hague Dr",
+        "author_inst": "The Christie NHS Foundation Trust, Wilmslow road, M20 4BX"
+      },
+      {
+        "author_name": "Michelle Harrison Dr",
+        "author_inst": "Ninewells Hospital, Dundee DD2 1SG"
+      },
+      {
+        "author_name": "Laura Horsley Dr",
+        "author_inst": "The Christie NHS Foundation Trust, Wilmslow road, M20 4BX"
+      },
+      {
+        "author_name": "Prerana Huddar Dr",
+        "author_inst": "Lancashire Teaching Hospitals NHS Trust, Preston PR2 9HT"
+      },
+      {
+        "author_name": "Zoe Hudson Dr",
+        "author_inst": "Bristol Haematology and Oncology Centre, Bristol BS2 8ED"
+      },
+      {
+        "author_name": "Sam Khan Dr",
+        "author_inst": "Oncology Department, University Hospitals of Leicester NHS Trust, Leicester, LE1 5WW; Leicester Cancer Research Centre, University of Leicester, Leicester, LE2 "
+      },
+      {
+        "author_name": "Umair T Khan Dr",
+        "author_inst": "Clatterbridge Cancer Centre, 65 Pembroke Place, Liverpool, L7 8YA; The University of Liverpool, Liverpool, L69 3BX"
+      },
+      {
+        "author_name": "Alec Maynard Dr",
+        "author_inst": "Sheffield Teaching Hospitals NHS foundation Trust, Sheffield S10 2JF"
+      },
+      {
+        "author_name": "Hayley McKenzie Dr",
+        "author_inst": "Cancer Sciences Academic Unit, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD"
+      },
+      {
+        "author_name": "Tim Robinson Dr",
+        "author_inst": "Bristol Haematology and Oncology Centre, Bristol BS2 8ED"
+      },
+      {
+        "author_name": "Michael Rowe Dr",
+        "author_inst": "Sunrise Centre, Royal Cornwall Hospital, Truro, Cornwall, TR1 3LJ"
+      },
+      {
+        "author_name": "Anne Thomas Prof",
+        "author_inst": "Oncology Department, University Hospitals of Leicester NHS Trust, Leicester, LE1 5WW; Leicester Cancer Research Centre, University of Leicester, Leicester, LE2 "
+      },
+      {
+        "author_name": "Lance Turtle",
+        "author_inst": "Institute of Infection, Ecological and Veterinary Sciences, University of Liverpool and Tropical and Infectious Diseases Unit, Liverpool University Hospitals"
+      },
+      {
+        "author_name": "Roseleen Sheehan Dr",
+        "author_inst": "Sheffield Teaching Hospitals NHS foundation Trust, Sheffield S10 2JF"
+      },
+      {
+        "author_name": "Alexander Stockdale",
+        "author_inst": "Institute of Infection, Ecological and Veterinary Sciences, University of Liverpool and Tropical and Infectious Diseases Unit, Liverpool University Hospitals"
+      },
+      {
+        "author_name": "Jamie Weaver Dr",
+        "author_inst": "The Christie NHS Foundation Trust, Wilmslow road, M20 4BX"
+      },
+      {
+        "author_name": "Sophie Williams Dr",
+        "author_inst": "Sheffield Teaching Hospitals NHS foundation Trust, Sheffield S10 2JF"
+      },
+      {
+        "author_name": "Caroline Wilson Dr",
+        "author_inst": "Sheffield Teaching Hospitals NHS foundation Trust, Sheffield S10 2JF"
+      },
+      {
+        "author_name": "Richard Hoskins Dr",
+        "author_inst": "The University of Manchester, Oxford road, M13 9PL"
+      },
+      {
+        "author_name": "Julie Stevenson Dr",
+        "author_inst": ". Digital experimental cancer medicine and Bioinformatics and Biostatistics teams, Cancer Research UK Manchester Institute Cancer Biomarker Centre, The Universi"
+      },
+      {
+        "author_name": "Paul Fitzpartick Dr",
+        "author_inst": ". Digital experimental cancer medicine and Bioinformatics and Biostatistics teams, Cancer Research UK Manchester Institute Cancer Biomarker Centre, The Universi"
+      },
+      {
+        "author_name": "Carlo Palmieri Prof",
+        "author_inst": "Clatterbridge Cancer Centre, 65 Pembroke Place, Liverpool, L7 8YA"
+      },
+      {
+        "author_name": "Donal Landers Dr",
+        "author_inst": ". Digital experimental cancer medicine and Bioinformatics and Biostatistics teams, Cancer Research UK Manchester Institute Cancer Biomarker Centre, The Universi"
+      },
+      {
+        "author_name": "Tim Cooksley Dr",
+        "author_inst": "The Christie NHS Foundation Trust, Wilmslow road, M20 4BX"
+      },
+      {
+        "author_name": "Caroline Dive Prof",
+        "author_inst": "Cancer Research UK Manchester Institute Cancer Biomarker Centre, Alderley Park, SK10 4TG"
+      },
+      {
+        "author_name": "Andre Freitas Dr",
+        "author_inst": "The University of Manchester, Oxford road, M13 9PL; Digital experimental cancer medicine team, Manchester Centre for Cancer Biomarker Sciences, Alderley Park, S"
+      },
+      {
+        "author_name": "Anne C Armstrong Dr",
+        "author_inst": "The Christie NHS Foundation Trust, Wilmslow road, M20 4BX; The University of Manchester, Oxford road, M13 9PL"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "oncology"
+  },
   {
     "rel_doi": "10.1101/2020.12.01.20241828",
     "rel_title": "Accuracy of automated computer aided-risk scoring systems to estimate the risk of COVID-19 and in-hospital mortality: a retrospective cohort study",
@@ -1037369,45 +1036256,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.12.01.20241760",
-    "rel_title": "Associations between vaping and Covid-19: cross-sectional findings from the HEBECO study",
-    "rel_date": "2020-12-03",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.01.20241760",
-    "rel_abs": "AimsTo explore i) associations between vaping and self-reported diagnosed/suspected Covid-19; ii) changes in vaping since Covid-19 and factors associated with these changes; iii) whether Covid-19 motivated current or recent ex-vapers to quit.\n\nMethodsCross-sectional online survey of 2791 UK adults recruited 30/04/2020-14/06/2020. Participants self-reported data on sociodemographic characteristics, diagnosed/suspected Covid-19, vaping status, changes in vaping and motivation to quit vaping since Covid-19.\n\nResultsThere were no differences in diagnosed/suspected Covid-19 between never, current and ex-vapers. Bayes factors indicated there was sufficient evidence to rule out small negative (protective) associations between vaping status and diagnosed/suspected Covid-19. Among current vapers (n=397), 9.7% (95% CI 6.8-12.6%) reported vaping less than usual since Covid-19, 42.0% (37.2-46.9%) reported vaping more, and 48.3% (43.4-53.2%) reported no change. In adjusted analyses, vaping less was associated with being female (aOR=3.40, 95% CI 1.73-6.71), not living with children (aOR=4.93, 1.15-21.08) and concurrent smoking (aOR=8.77, 3.04-25.64), while vaping more was associated with being younger (aOR=5.26, 1.37-20.0), living alone (aOR=2.08, 1.14-3.85), and diagnosed/suspected Covid-19 (aOR=4.72, 2.60-8.62). Of current vapers, 32.2% (95% CI 27.5-36.8%) were motivated to quit vaping since Covid-19, partly motivated by Covid-19, and 17.4%, (9.7-26.3%) of recent ex-vapers quit vaping due to Covid-19.\n\nConclusionsAmong UK adults, self-reported diagnosed/suspected Covid-19 was not associated with vaping status. Half of current vapers changed their vaping consumption since Covid-19, with the majority reporting an increase, and a minority was motivated to quit due to Covid-19.\n\nRegistrationThe analysis plan was pre-registered, and it is available at https://osf.io/6j8z3/\n\nHighlightsO_LINo difference found in diagnosed/suspected Covid-19 between never, current and ex-vapers\nC_LIO_LIHalf of current vapers changed their vaping consumption since Covid-19\nC_LIO_LIMotivation to quit vaping was partly related to Covid-19\nC_LI",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Dimitra Kale",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Aleksandra Herbec",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Olga Perski",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Sarah E Jackson",
-        "author_inst": "UCL"
-      },
-      {
-        "author_name": "Jamie Brown",
-        "author_inst": "UCL"
-      },
-      {
-        "author_name": "Lion Shahab",
-        "author_inst": "UCL"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.12.01.20241877",
     "rel_title": "Impact of social distancing regulations and epidemic risk perception on social contact and SARS-CoV-2 transmission potential in rural South Africa: analysis of repeated cross-sectional surveys",
@@ -1037742,6 +1036590,41 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2020.12.02.408575",
+    "rel_title": "In Vitro Analysis of the Anti-viral Potential of nasal spray constituents against SARS-CoV-2",
+    "rel_date": "2020-12-03",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.02.408575",
+    "rel_abs": "Viral pandemics have taken a significant toll on humanity and the world now is contending with the SARS-CoV-2 epidemic. Readily available economical preventive measures should be immediately explored. Xylitol has been reported to reduce the severity of viral infections as well as the severity of pneumonia, and increase the survivability of animal subjects. Since pneumonia and acute respiratory distress syndrome are potentially fatal complications of COVID-19, the present study tested the in vitro effectiveness of xylitol against SARS-CoV-2. Virus titers and LRV of SARS-CoV-2, were incubated with a single concentration of nasal spray. Toxicity was observed in the top dilution (1/10). Virus was seen below that dilution so it did not affect calculations of virus titer or LRV. After a 25-minute contact time, the nasal spray (11% Pure Xylitol, 0.85%NaCL (Saline), and 0.20% grapefruit seed extract) reduced virus from 4.2 to 1.7 log10 CCID50 per 0.1 mL, a statistically significant reduction (P<0.001) of 2.5 log10 CCID50. STEM Images obtained at the BIoCryo Laboratory revealed virus contained on the cell wall but none intra-cellular, possibly due to D-xylose (xylitol) production of glycoaminoglycans decoy targets. Xylitol and grapefruit seed extract are not exotic nor expensive rare high technology answers to viral epidemics. The potential in saving lives and the economies of the world by using X-GSE combination therapy should inspire large clinical trials, especially in those nations whereas the healthcare system would be dangerously compromised by the adoption of less effective and significantly more financially demanding therapies. Because there are no risk factors in using the X/GSE combination therapy, and the nasal spray is over the counter available without a prescription, and the spray allows for comfortable long term mask-wearing, adoption of this preventive anti-viral therapy should be encouraged.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Mark L Cannon",
+        "author_inst": "Northwestern University"
+      },
+      {
+        "author_name": "Jonna B Westover",
+        "author_inst": "Utah State University"
+      },
+      {
+        "author_name": "Reiner Bleher",
+        "author_inst": "Northwestern University"
+      },
+      {
+        "author_name": "Marcos A Sanchez-Gonzalez",
+        "author_inst": "Lake Erie College of Osteopathic Medicine"
+      },
+      {
+        "author_name": "Gustavo Ferrer",
+        "author_inst": "Nova Southeastern University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "confirmatory results",
+    "category": "molecular biology"
+  },
   {
     "rel_doi": "10.1101/2020.12.03.410233",
     "rel_title": "Horizontal gene transfer and recombination analysis of SARS-CoV-2 genes helps discover its close relatives and shed light on its origin",
@@ -1038863,33 +1037746,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
-  {
-    "rel_doi": "10.1101/2020.11.30.20241174",
-    "rel_title": "Modeling the effectiveness of olfactory testing to limit SARS-2-CoV transmission",
-    "rel_date": "2020-12-02",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.30.20241174",
-    "rel_abs": "A central problem in the COVID-19 pandemic is that there is not enough testing to prevent infectious spread of SARS-CoV-2, causing surges and lockdowns with human and economic toll. Molecular tests that detect viral RNAs or antigens will be unable to rise to this challenge unless testing capacity increases by at least an order of magnitude while decreasing turnaround times. Here, we evaluate an alternative strategy based on the monitoring of olfactory dysfunction, a symptom identified in 76-83% of SARS-CoV-2 infections--including those with no other symptoms--when a standardized olfaction test is used. We model how screening for olfactory dysfunction, with reflexive molecular tests, could be beneficial in reducing community spread of SARS-CoV-2 by varying testing frequency and the prevalence, duration, and onset time of olfactory dysfunction. We find that monitoring olfactory dysfunction could reduce spread via regular screening, and could reduce risk when used at point-of-entry for single-day events. In light of these estimated impacts, and because olfactory tests can be mass produced at low cost and self-administered, we suggest that screening for olfactory dysfunction could be a high impact and cost-effective method for broad COVID-19 screening and surveillance.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Daniel B Larremore",
-        "author_inst": "University of Colorado Boulder"
-      },
-      {
-        "author_name": "Derek Toomre",
-        "author_inst": "Yale University School of Medicine"
-      },
-      {
-        "author_name": "Roy Parker",
-        "author_inst": "University of Colorado Boulder"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.12.01.20241349",
     "rel_title": "Performance of saliva specimens for the molecular detection of SARS-CoV-2 in the community setting: does sample collection method matter?",
@@ -1039184,6 +1038040,89 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.11.30.20241208",
+    "rel_title": "Rapid and accurate point-of-care testing for SARS-CoV2 antibodies",
+    "rel_date": "2020-12-02",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.30.20241208",
+    "rel_abs": "The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has grown into worst public health crisis since the 1918 influenza pandemic. As COVID-19 continues to spread around the world, there is urgent need for a rapid, yet accurate antibody test to identify infected individuals in populations to inform health decisions. We have developed a rapid, accurate and cost-effective serologic test based on antibody-dependent agglutination of antigen-coated latex particles, which uses [~]5 {micro}l plasma and takes <5 min to complete with no instrument required. The simplicity of this test makes it ideal for point-of-care (POC) use at the community level. When validated using plasma samples that are positive or negative for SARS-CoV-2, the agglutination assay detected antibodies against the receptor-binding domain of the spike (S-RBD) or the nucleocapsid (N) protein of SARS-CoV-2 with 100% specificity and [~]98% sensitivity. Furthermore, we found that the strength of the S-RBD antibody response measured by the agglutination assay correlated with the efficiency of the plasma in blocking RBD binding to the angiotensin converting enzyme 2 (ACE2) in a surrogate neutralization assay, suggesting that the agglutination assay may be used to identify individuals with virus-neutralizing antibodies. Intriguingly, we found that >92% of patients had detectable antibodies on the day of positive viral RNA test, suggesting that seroconversion may occur earlier than previously thought and that the agglutination antibody test may complement RNA testing for POC diagnosis of SARS-CoV-2 infection.",
+    "rel_num_authors": 17,
+    "rel_authors": [
+      {
+        "author_name": "Shawn SC Li",
+        "author_inst": "Western University"
+      },
+      {
+        "author_name": "Sally Esmail",
+        "author_inst": "Western University"
+      },
+      {
+        "author_name": "Michael Knauer",
+        "author_inst": "Western University"
+      },
+      {
+        "author_name": "Husam Abdoh",
+        "author_inst": "Western University"
+      },
+      {
+        "author_name": "Benjamin Chin-Yee",
+        "author_inst": "Western University"
+      },
+      {
+        "author_name": "Lori Lowes",
+        "author_inst": "Western University"
+      },
+      {
+        "author_name": "Courtney Voss",
+        "author_inst": "Western University"
+      },
+      {
+        "author_name": "Benjamin Hedley",
+        "author_inst": "Western University"
+      },
+      {
+        "author_name": "Vipin Bhayana",
+        "author_inst": "Western University"
+      },
+      {
+        "author_name": "Ian Chin-Yee",
+        "author_inst": "Western University"
+      },
+      {
+        "author_name": "Alma Seitova",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Ashley Hutchinson",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Farhad Yusifov",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Tatiana Skarina",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Elena Evdokimova",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Suzanne Ackloo",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Peter Stogios",
+        "author_inst": "University of Toronto"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.11.30.20218560",
     "rel_title": "Convalescent Plasma in COVID-19. Mortality-Safety First Results of the Prospective Multicenter FALP 001-2020 Trial",
@@ -1040525,85 +1039464,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.12.01.406306",
-    "rel_title": "Neutrophil and monocyte dysfunctional effector response towards bacterial challenge in critically-ill COVID-19 patients",
-    "rel_date": "2020-12-01",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.01.406306",
-    "rel_abs": "COVID-19 displays diverse disease severities and symptoms. Elevated inflammation mediated by hypercytokinemia induces a detrimental dysregulation of immune cells. However, there is limited understanding of how SARS-CoV-2 pathogenesis impedes innate immune signaling and function against secondary bacterial infections. We assessed the influence of COVID-19 hypercytokinemia on the functional responses of neutrophils and monocytes upon bacterial challenges from acute and corresponding recovery COVID-19 ICU patients. We show that severe hypercytokinemia in COVID-19 patients correlated with bacterial superinfections. Neutrophils and monocytes from acute COVID-19 patients showed severely impaired microbicidal capacity, reflected by abrogated ROS and MPO production as well as reduced NETs upon bacterial challenges. We observed a distinct pattern of cell surface receptor expression on both neutrophils and monocytes leading to a suppressive autocrine and paracrine signaling during bacterial challenges. Our data provide insights into the innate immune status of COVID-19 patients mediated by their hypercytokinemia and its transient effect on immune dysregulation upon subsequent bacterial infections",
-    "rel_num_authors": 16,
-    "rel_authors": [
-      {
-        "author_name": "Srikanth Mairpady Shambat",
-        "author_inst": "University Hospital Zurich, Switzerland"
-      },
-      {
-        "author_name": "Alejandro Gomez-Mejia",
-        "author_inst": "University Hospital Zurich, University of Zurich, Switzerland"
-      },
-      {
-        "author_name": "Tiziano A. Schweizer",
-        "author_inst": "University Hospital Zurich, University of Zurich, Switzerland"
-      },
-      {
-        "author_name": "Markus Huemer",
-        "author_inst": "University Hospital Zurich, University of Zurich, Switzerland"
-      },
-      {
-        "author_name": "Chun-Chi Chang",
-        "author_inst": "University Hospital Zurich, University of Zurich, Switzerland"
-      },
-      {
-        "author_name": "Claudio Acevedo",
-        "author_inst": "University Hospital Zurich, Switzerland"
-      },
-      {
-        "author_name": "Judith Bergada Pijuan",
-        "author_inst": "University Hospital Zurich, Switzerland"
-      },
-      {
-        "author_name": "Clement Vulin",
-        "author_inst": "University Hospital of Zurich, University of Zurich, Switzerland"
-      },
-      {
-        "author_name": "Nataliya Miroshnikova",
-        "author_inst": "University Hospital Zurich, Switzerland"
-      },
-      {
-        "author_name": "Daniel A. Hofmanner",
-        "author_inst": "University Hospital Zurich, Switzerland"
-      },
-      {
-        "author_name": "Pedro D. Wendel Garcia",
-        "author_inst": "University Hospital Zurich"
-      },
-      {
-        "author_name": "Matthias P. Hilty",
-        "author_inst": "University of Zurich, Switzerland"
-      },
-      {
-        "author_name": "Philipp Karl Buehler",
-        "author_inst": "University Hospital Zurich, University of Zurich"
-      },
-      {
-        "author_name": "Reto A. Schuepbach",
-        "author_inst": "University Hospital of Zurich, University of Zurich, Switzerland"
-      },
-      {
-        "author_name": "Silvio  D Brugger",
-        "author_inst": "University Hospital Zurich, University of Zurich"
-      },
-      {
-        "author_name": "Annelies S. Zinkernagel",
-        "author_inst": "University Hospital of Zurich, University of Zurich, Switzerland"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2020.12.01.405662",
     "rel_title": "Differential effects of antiseptic mouth rinses on SARS-CoV-2 infectivity in vitro",
@@ -1041402,6 +1040262,65 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2020.12.01.407007",
+    "rel_title": "Multimodal Single-Cell Omics Analysis of COVID-19 Sex Differences in Human Immune Systems",
+    "rel_date": "2020-12-01",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.01.407007",
+    "rel_abs": "Sex differences in the risk of SARS-CoV-2 infection have been controversial and the underlying mechanisms of COVID-19 sexual dimorphism remain understudied. Here we inspected sex differences in SARS-CoV-2 positivity, hospitalization, admission to the intensive care unit (ICU), sera immune profiling, and two single-cell RNA-sequencing (snRNA-seq) profiles from nasal tissues and peripheral blood mononuclear cells (PBMCs) of COVID-19 patients with varying degrees of disease severity. Our propensity score-matching observations revealed that male individuals have a 29% increased likelihood of SARS-CoV-2 positivity, with a hazard ration (HR) 1.32 (95% confidence interval [CI] 1.18-1.48) for hospitalization and HR 1.51 (95% CI 1.24-1.84) for admission to ICU. Sera from male patients at hospital admission had decreased lymphocyte count and elevated inflammatory markers (C-reactive protein, procalcitonin, and neutrophils). We found that SARS-CoV-2 entry factors, including ACE2, TMPRSS2, FURIN and NRP1, have elevated expression in nasal squamous cells from males with moderate and severe COVID-19. Cell-cell network proximity analysis suggests possible epithelium-immune cell interactions and immune vulnerability underlying a higher mortality in males with COVID-19. Monocyte-elevated expression of Toll like receptor 7 (TLR7) and Bruton tyrosine kinase (BTK) is associated with severe outcomes in males with COVID-19. These findings provide basis for understanding immune responses underlying sex differences, and designing sex-specific targeted treatments and patient care for COVID-19.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Yuan Hou",
+        "author_inst": "Cleveland Clinic"
+      },
+      {
+        "author_name": "Yadi Zhou",
+        "author_inst": "Cleveland Clinic"
+      },
+      {
+        "author_name": "Michaela Gack",
+        "author_inst": "Cleveland Clinic Florida"
+      },
+      {
+        "author_name": "Justin Lathia",
+        "author_inst": "Cleveland Clinic"
+      },
+      {
+        "author_name": "Asha Kallianpur",
+        "author_inst": "Cleveland Clinic"
+      },
+      {
+        "author_name": "Reena Mehra",
+        "author_inst": "Cleveland Clinic"
+      },
+      {
+        "author_name": "Timothy Chan",
+        "author_inst": "Cleveland Clinic"
+      },
+      {
+        "author_name": "Jae U. Jung",
+        "author_inst": "Cleveland Clinic"
+      },
+      {
+        "author_name": "Lara Jehi",
+        "author_inst": "Cleveland Clinic"
+      },
+      {
+        "author_name": "Charis Eng",
+        "author_inst": "Cleveland Clinic Genomic Medicine Institute"
+      },
+      {
+        "author_name": "Feixiong Cheng",
+        "author_inst": "Cleveland Clinic"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "systems biology"
+  },
   {
     "rel_doi": "10.1101/2020.11.26.20232728",
     "rel_title": "COVID-19 Antigen Rapid Test as Screening Strategy at the Points-of-Entry: Experience in Lazio Region, Central Italy, August-October 2020.",
@@ -1042607,37 +1041526,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "otolaryngology"
   },
-  {
-    "rel_doi": "10.1101/2020.11.26.20239327",
-    "rel_title": "Changing case fatality risk for COVID-19 over time in selected European countries",
-    "rel_date": "2020-11-30",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.26.20239327",
-    "rel_abs": "ObjectivesTo illustrate the development of the case fatality risk (CFR) for COVID-19 over time using different assumptions for calculating the CFR.\n\nDesignObservational study.\n\nSetting\n\nSelected European countries, 28 January to October 29 2020.\n\nParticipantsLaboratory-confirmed COVID-19 cases and deaths due to COVID-19\n\nMain outcome measurecase fatality risk (CFR)\n\nResultsWe show that the CFR has considerably decreased over time. This seems to be driven not only by increased testing but also by a reduced CFR among cases older than 60 years. Our data also confirm a significantly higher fatality risk for men than for women. The decline in the CFR is even more pronounced when only cases and deaths occurring in a specified time window are considered. This alternative estimation method has the advantage that early data where the bias due to the incomplete ascertainment of cases was arguably largest do not affect CFR estimates later on. We find similar results for other European countries.\n\nConclusionCFR estimates vary considerably depending on the underlying assumptions concerning their calculation. Reliable CFR estimates should not be based on cumulative numbers from the beginning of the pandemic but rather be based on more recent data only.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Heiko Becher",
-        "author_inst": "University Medical Center Hamburg-Eppendorf"
-      },
-      {
-        "author_name": "Katharina Olszewski",
-        "author_inst": "University Medical Center Hamburg-Eppendorf"
-      },
-      {
-        "author_name": "Sarah Wiegel",
-        "author_inst": "University Medical Center Hamburg-Eppendorf"
-      },
-      {
-        "author_name": "Olaf Mueller",
-        "author_inst": "Institute of Global Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.11.26.20152520",
     "rel_title": "Design of COVID-19 Staged Alert Systems to Ensure Healthcare Capacity with Minimal Closures",
@@ -1042900,6 +1041788,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.11.26.20239418",
+    "rel_title": "Predictors of QT Interval Prolongation in Critically-ill Patients with SARS-CoV-2 Infection Treated with Hydroxychloroquine",
+    "rel_date": "2020-11-30",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.26.20239418",
+    "rel_abs": "BackgroundHydroxychloroquine (HCQ) has been described as a potential treatment for SARS-CoV-2 infection. However, there are safety concerns regarding its QT interval and pro-arrhythmic effects.\n\nObjectiveThis trial aimed to determine the predictors of QT interval prolongation and pro-arrhythmic effects in patients hospitalized for SARS-CoV-2 infection and receiving HCQ.\n\nMethodsWe performed a retrospective observational study of 45 critically-ill patients hospitalized because of SARS-CoV-2 infection and treated with 800 mg of HCQ at day 1 and 400 mg on days 2-5. Clinical aspects and outcomes, basal and final corrected QT (QTc) interval, and the incidence of arrhythmias and arrhythmogenic death were observed. Independent predictors of QTc prolongation were identified using multivariable logistic regression analysis. QT interval prolongation was considered substantial at final QTc [&ge;] 480 ms.\n\nResultsThe mean age was 60.9 {+/-} 16.67 years and 28 (62.2%) patients were men. Basal QTc was 442 {+/-} 28 ms, and the final QTc interval was 458 {+/-} 34 ms, for a mean QTc interval variation of 15 {+/-} 11 ms. There was no arrhythmogenic death. The need for hemodialysis remained a statistically significant predictor of QT interval enlargement (odds ratio, 10.34; 95% confidence interval, 1.04 - 102.18; p = 0.045).\n\nConclusionsHCQ promotes mild to moderate QT interval prolongation. The risk of QT interval prolongation is higher among patients with acute renal failure requiring hemodialysis.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Frederico Scuotto",
+        "author_inst": "Hospital Samaritano Higien\u00f3polis, United Health Group - S\u00e3o Paulo, SP, Brazil"
+      },
+      {
+        "author_name": "Rog\u00e9rio Marra",
+        "author_inst": "Hospital Samaritano Higien\u00f3polis, United Health Group - S\u00e3o Paulo, SP, Brazil"
+      },
+      {
+        "author_name": "Lilian Leite de Almeida",
+        "author_inst": "Hospital Samaritano Higien\u00f3polis, United Health Group - S\u00e3o Paulo, SP, Brazil"
+      },
+      {
+        "author_name": "Mariana Santa Rita Soares",
+        "author_inst": "Hospital Samaritano Higien\u00f3polis, United Health Group - S\u00e3o Paulo, SP, Brazil"
+      },
+      {
+        "author_name": "Gabriela Kurita Silva",
+        "author_inst": "Hospital Samaritano Higien\u00f3polis, United Health Group - S\u00e3o Paulo, SP, Brazil"
+      },
+      {
+        "author_name": "Luiz Carlos Paul",
+        "author_inst": "Hospital Samaritano Higien\u00f3polis, United Health Group - S\u00e3o Paulo, SP, Brazil"
+      },
+      {
+        "author_name": "Guilherme Drummond Fenelon Costa",
+        "author_inst": "Hospital Samaritano Higien\u00f3polis, United Health Group - S\u00e3o Paulo, SP, Brazil"
+      },
+      {
+        "author_name": "Cl\u00e1udio Cirenza",
+        "author_inst": "Hospital Samaritano Higien\u00f3polis, United Health Group - S\u00e3o Paulo, SP, Brazil"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "intensive care and critical care medicine"
+  },
   {
     "rel_doi": "10.1101/2020.11.27.20239657",
     "rel_title": "Quantifying superspreading for COVID-19 using Poisson mixture distributions",
@@ -1044193,25 +1043128,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.11.27.20239772",
-    "rel_title": "CoVid-19: The Second Wave is not due to Cooling-down in Autumn",
-    "rel_date": "2020-11-30",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.27.20239772",
-    "rel_abs": "In analogy to influenza the second wave of the CoVid-19 disease is generally considered as being triggered by cooling-down in autumn and enhanced aerosol distribution. Here, the time histories of the total case numbers in three European states are quantitatively compared with those of Argentina by a generally applicable fit procedure. It turns out that Argentina on the southern hemisphere sees the second wave simultaneously with similar parameters as Europe. This discards the assumption of the influence of atmospheric cooling in winter and puts into question present models of SARS-CoV-2 spreading.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Walter Langel",
-        "author_inst": "Universitaet Greifswald"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.11.27.20239244",
     "rel_title": "Prevalence of SARS-CoV-2 in household members and other close contacts of COVID-19 cases: a serologic study in canton of Vaud, Switzerland",
@@ -1044426,6 +1043342,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.11.29.20240614",
+    "rel_title": "AI4CoV: Matching COVID-19 Patients to Treatment Options Using Artificial Intelligence",
+    "rel_date": "2020-11-30",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.29.20240614",
+    "rel_abs": "We developed AI4CoV, a novel AI system to match thousands of COVID-19 clinical trials to patients based on each patients eligibility to clinical trials in order to help physicians select treatment options for patients. AI4CoV leveraged Natural Language Processing (NLP) and Machine Learning to parse through eligibility criteria of trials and patients clinical manifestations in their clinical notes, both presented in English text, to accomplish 92.76% AUROC on a cross-validation test with 3,156 patient-trial pairs labeled with ground truth of suitability. Our retrospective multiple-site review shows that according to AI4CoV, severe patients of COVID-19 generally have less treatment options suitable for them than mild and moderate patients and that suitable and unsuitable treatment options are different for each patient. Our results show that the general approach of AI4CoV is useful during the early stage of a pandemic when the best treatments are still unknown.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Andrew I Hsu",
+        "author_inst": "AI4WARD Inc."
+      },
+      {
+        "author_name": "Amber Yeh",
+        "author_inst": "AI4WARD Inc."
+      },
+      {
+        "author_name": "Shao-Lang Chen",
+        "author_inst": "AI4WARD Inc."
+      },
+      {
+        "author_name": "Jerry J Yeh",
+        "author_inst": "AI4WARD Inc."
+      },
+      {
+        "author_name": "DongQing Lv",
+        "author_inst": "2.\tDepartment of Respiratory Medicine, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Taizhou, China"
+      },
+      {
+        "author_name": "Jane Yung-jen Hsu",
+        "author_inst": "Department of Computer Science & Information Engineering, National Taiwan University, Taiwan"
+      },
+      {
+        "author_name": "Pai Jung Huang",
+        "author_inst": "Institute of Medical Science and Technology, Taipei Medical University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health informatics"
+  },
   {
     "rel_doi": "10.1101/2020.11.29.20240606",
     "rel_title": "A Retrospective Longitudinal Study of COVID-19 as Seen by a Large Urban Hospital in Chicago",
@@ -1045691,57 +1044650,6 @@
     "type": "new results",
     "category": "systems biology"
   },
-  {
-    "rel_doi": "10.1101/2020.11.25.20238535",
-    "rel_title": "A double-edged sword - Telemedicine for maternal care during COVID-19: Findings from a global mixed methods study of healthcare providers",
-    "rel_date": "2020-11-29",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.25.20238535",
-    "rel_abs": "IntroductionThe COVID-19 pandemic has led to a rapid and wide implementation of telemedicine for provision of maternal and newborn health care worldwide. Studies conducted before the pandemic, mainly deriving from high-income countries, showed telemedicine was a safe and cost-effective tool for delivering healthcare under certain conditions. The objective of this study was to document the experiences of healthcare professionals globally with the provision of telemedicine for maternal and newborn healthcare during the COVID-19 pandemic.\n\nMethodsWe analysed responses received to the second round of a global, online survey of maternal and newborn health professionals, disseminated through professional networks and social media in 11 languages. Data were collected between July 5, 2020 and September 10, 2020. The questionnaire included questions regarding background, preparedness for and response to COVID-19 and experiences with providing telemedicine during the pandemic. Descriptive statistics and qualitative thematic analysis were used concurrently to analyse responses, disaggregated by country income level.\n\nResultsResponses from 1,060 maternal and newborn health professional were analysed. Among the sample, 58% reported using telemedicine, with the lowest proportion reported by professionals working in low-income countries (24%). Two fifths of telemedicine users reported not receiving guidelines on the provision of care through technology. Key practices along the continuum of maternal and newborn healthcare provided through telemedicine included online group birth preparedness classes, antenatal and postnatal care by video/phone, setting up a COVID-19 helpline at maternity wards, and online psychosocial counselling. Challenges reported technological barriers, lack of technological literacy, financial and language barriers, lack of nonverbal feedback, and distrust from patients. Maternal and newborn health providers considered telemedicine to be an important alternative to in-person consultations to maintain care provision during the COVID-19 pandemic. However, they also emphasized the lower quality of care and risk of increasing the already existing inequalities in access to healthcare.\n\nConclusionsTelemedicine has been applied globally to address the disruptions of care provision during the COVID-19 pandemic. However, some crucial aspects of maternal and newborn healthcare seem difficult to deliver by telemedicine. Pitfalls of health care provision by telemedicine include exacerbated inequalities in access to care, patient-provider communication problems, and a financial burden for certain healthcare workers and women. More research regarding the effectiveness, efficacy, and quality of telemedicine for maternal health care in different contexts is highly needed before considering long-term adaptations in provision of care away from face to face interactions. Clear guidelines for care provision and approaches to minimising socio-economic and technological inequalities in access to care are urgently needed.\n\nSummary boxO_ST_ABSWhat is already known?C_ST_ABSO_LITelemedicine is the delivery of healthcare services by healthcare professionals from distance through using information and communication technologies for the exchange of valid and correct information.\nC_LIO_LITelemedicine for maternal and newborn health can safely be used to deliver certain components of care in highly controlled settings where the technology is available and accessible to patients\nC_LIO_LITelemedicine has been applied rapidly and on a wide scale during the COVID-19 pandemic to replace face to face visits along the continuum of maternal and newborn health care.\nC_LI\n\nWhat are the new findings?O_LIMaternal and newborn healthcare providers globally considered telemedicine of benefit during the pandemic and applied it on a wide scale for different aspects of maternal and newborn healthcare.\nC_LIO_LIThe rapid adaptation to provision of care via telemedicine was not optimally supported by guidelines, training for health providers, adequate equipment, reimbursement for cost of connectivity and insurance payments for care provided remotely.\nC_LIO_LIHealthcare providers reported not being able to reach a substantial group of families by telemedicine and encountered different barriers in providing high quality maternity care by telemedicine due to challenges present worldwide, but more prominent in low- and middle-income countries.\nC_LI\n\nWhat do the new findings imply?O_LIPre-existing inequalities in terms of access to high quality care might have increased by the large scale and rapid implementation of telemedicine during the COVID-19 pandemic in different settings.\nC_LIO_LIAccess to telemedicine for women was hampered by various factors such as internet connection problems, lack of the necessary equipment, digital illiteracy and distrust.\nC_LIO_LIIn-depth research is needed to formalise evidence-based guidelines for the implementation of telemedicine along the continuum of maternal and newborn care as lessons learned for building back beyond the COVID-19 pandemic and also for future emergency preparedness.\nC_LI",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Anna Galle",
-        "author_inst": "International Centre for Reproductive Health, Department of Public Health and Primary Care, Ghent University"
-      },
-      {
-        "author_name": "Aline Semaan",
-        "author_inst": "Institute of Tropical Medicine, Antwerp Belgium"
-      },
-      {
-        "author_name": "Elise Huysmans",
-        "author_inst": "Institute of Tropical Medicine, Antwerp Belgium"
-      },
-      {
-        "author_name": "Constance Audet",
-        "author_inst": "Institute of Tropical Medicine, Antwerp Belgium"
-      },
-      {
-        "author_name": "Anteneh Asefa",
-        "author_inst": "Institute of Tropical Medicine, Antwerp Belgium"
-      },
-      {
-        "author_name": "Therese Delvaux",
-        "author_inst": "Institute of Tropical Medicine, Antwerp Belgium"
-      },
-      {
-        "author_name": "Bosede B Afolabi",
-        "author_inst": "College of Medicine, University of Lagos, Nigeria"
-      },
-      {
-        "author_name": "Alison El Ayadi",
-        "author_inst": "University of California, San Francisco; San Francisco, USA"
-      },
-      {
-        "author_name": "Lenka Benova",
-        "author_inst": "Institute of Tropical Medicine, Antwerp Belgium"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "sexual and reproductive health"
-  },
   {
     "rel_doi": "10.1101/2020.11.25.20237883",
     "rel_title": "Clinical and immunological benefits of convalescent plasma therapy in severe COVID-19: insights from a single center open label randomised control trial",
@@ -1046076,6 +1044984,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.11.25.20238675",
+    "rel_title": "Autosomal Dominant Polycystic Kidney Disease does not significantly alter major COVID-19 outcomes among veterans",
+    "rel_date": "2020-11-29",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.25.20238675",
+    "rel_abs": "Chronic kidney disease (CKD), as well as its common causes (e.g., diabetes and obesity), are recognized risk factors for severe COVID-19 illness. To explore whether the most common inherited cause of CKD, autosomal dominant polycystic kidney disease (ADPKD), is also an independent risk factor, we studied data from the VA health system and the VA COVID-19-shared resources (e.g., ICD codes, demographics, pre-existing conditions, pre-testing symptoms, and post-testing outcomes). Among 61 COVID-19-positive ADPKD patients, 21 (34.4%) were hospitalized, 10 (16.4%) were admitted to ICU, 4 (6.6%) required ventilator, and 4 (6.6%) died by August 18, 2020. These rates were comparable to patients with other cystic kidney diseases and cystic liver-only diseases. ADPKD was not a significant risk factor for any of the four outcomes in multivariable logistic regression analyses when compared with other cystic kidney diseases and cystic liver-only diseases. In contrast, diabetes was a significant risk factor for hospitalization [OR 2.30 (1.61, 3.30), p<0.001], ICU admission [OR 2.23 (1.47, 3.42), p<0.001], and ventilator requirement [OR 2.20 (1.27, 3.88), p=0.005]. Black race significantly increased the risk for ventilator requirement [OR 2.00 (1.18, 3.44), p=0.011] and mortality [OR 1.60 (1.02, 2.51), p=0.040]. We also examined the outcome of starting dialysis after COVID-19 confirmation. The main risk factor for starting dialysis was CKD [OR 6.37 (2.43, 16.7)] and Black race [OR 3.47 (1.48, 8.1)]. After controlling for CKD, ADPKD did not significantly increase the risk for newly starting dialysis comparing with other cystic kidney diseases and cystic liver-only diseases. In summary, ADPKD did not significantly alter major COVID-19 outcomes among veterans when compared to other cystic kidney and liver patients.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Xiangqin Cui",
+        "author_inst": "Emory University and Atlanta VA Medical Center"
+      },
+      {
+        "author_name": "Julia W. Gallini",
+        "author_inst": "Foundation for Atlanta Veterans Education and Research"
+      },
+      {
+        "author_name": "Christine L. Jasien",
+        "author_inst": "Atlanta VA Mecial Center"
+      },
+      {
+        "author_name": "Michal Mrug",
+        "author_inst": "University of Alabama at Birmingham and Birmingham VA Medical Center"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "neurology"
+  },
   {
     "rel_doi": "10.1101/2020.11.25.20236752",
     "rel_title": "Symptom-based prediction model of SARS-1 CoV-2 infection developed from self-reported symptoms of SARS-CoV-2-infected individuals in an online survey",
@@ -1046973,37 +1045912,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.11.24.20237305",
-    "rel_title": "Which policies most effectively reduce SARS-CoV-2 transmission in schools?",
-    "rel_date": "2020-11-27",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.24.20237305",
-    "rel_abs": "IntroductionNew York City (NYC) has the largest public school system in the United States (US). During the SARS-CoV-2 pandemic, NYC was the first major US city to open schools for in-person learning in the 2020-2021 academic year. Several policies were implemented to reduce the risk of in-school transmission, including infection control measures (facemasks, physical distancing, enhanced indoor ventilation, cohorting of small groups, and hand hygiene), option of all-remote instruction, alternative options for how class schedules would rotate in-person and remote instruction, daily symptom screening, and testing 10-20% of students and staff weekly or monthly depending on local case rates. We sought to determine which of these policies had the greatest impact on reducing the risk of in-school transmission.\n\nMethodsWe evaluated the impact of each policy by referring to global benchmarks for the secondary attack rate (SAR) of SARS-CoV-2 in school settings and by simulating the potential for transmission in NYCs rotating cohort schedules, in which teachers could act as \"bridges\" across rotating cohorts. We estimated the impact of (1) infection control measures, (2) providing an option of all-remote instruction, (3) choice of class scheduling for in-person learners, (4) daily symptom screening, (5) testing to curtail transmission, and (6) testing to identify school outbreaks. Each policy was assessed independently of other policies, with the exception of symptom screening and random testing, which were assessed both independently and jointly.\n\nResultsAmong the policies analyzed, the greatest transmission reduction was associated with the infection control measures, followed by small class cohorts with an option for all-remote instruction, symptom screening, and finally randomly testing 10-20% of school attendees. Assuming adult staff are the primary source of within-school SARS-CoV-2 transmission, weekly testing of staff could be at least as effective as symptom screening, and potentially more so if testing days occur in the beginning of the workweek with results available by the following day. A combination of daily symptom screening and testing on the first workday of each week could reduce transmission by 70%.\n\nConclusionsAdherence to infection control is the highest priority for safe school re-opening. Further transmission reduction can be achieved through small rotating class cohorts with an option for remote learning, widespread testing at the beginning of the work week, and daily symptom screening and self-isolation. Randomly testing 10-20% of attendees weekly or monthly does not meaningfully curtail transmission and may not detect outbreaks before they have spread beyond a handful of individuals. School systems considering re-opening during the SARS-CoV-2 pandemic or similarly virulent respiratory disease outbreaks should consider these relative impacts when setting policy priorities.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Anna Bershteyn",
-        "author_inst": "New York University Grossman School of Medicine"
-      },
-      {
-        "author_name": "Hae-Young Kim",
-        "author_inst": "New York University Grossman School of Medicine"
-      },
-      {
-        "author_name": "Jessica B. McGillen",
-        "author_inst": "New York University Grossman School of Medicine"
-      },
-      {
-        "author_name": "R. Scott Braithwaite",
-        "author_inst": "New York University Grossman School of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health policy"
-  },
   {
     "rel_doi": "10.1101/2020.11.24.20235721",
     "rel_title": "Cytokine ranking via mutual information algorithm correlates cytokine profiles with disease severity in patients with COVID-19",
@@ -1047234,6 +1046142,117 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "occupational and environmental health"
   },
+  {
+    "rel_doi": "10.1101/2020.11.19.20234237",
+    "rel_title": "Association of Toll-like receptor 7 variants with life-threatening COVID-19 disease in males",
+    "rel_date": "2020-11-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.19.20234237",
+    "rel_abs": "BackgroundCOVID-19 clinical presentation ranges from asymptomatic to fatal outcome. This variability is due in part to host genome specific mutations. Recently, two families in which COVID-19 segregates like an X-linked recessive monogenic disorder environmentally conditioned by SARS-CoV-2 have been reported leading to identification of loss-of-function variants in TLR7.\n\nObjectiveWe sought to determine whether the two families represent the tip of the iceberg of a subset of COVID-19 male patients.\n\nMethodsWe compared male subjects with extreme phenotype selected from the Italian GEN-COVID cohort of 1178 SARS-CoV-2-infected subjects (<60y, 79 severe cases versus 77 control cases). We applied the LASSO Logistic Regression analysis, considering only rare variants on the young male subset, picking up TLR7 as the most important susceptibility gene.\n\nResultsRare TLR7 missense variants were predicted to impact on protein function in severely affected males and in none of the asymptomatic subjects. We then investigated a similar white European cohort in Spain, confirming the impact of TRL7 variants. A gene expression profile analysis in peripheral blood mononuclear cells after stimulation with TLR7 agonist demonstrated a reduction of mRNA level of TLR7, IRF7, ISG15, IFN-{square} and IFN-{gamma} in COVID-19 patients compared with unaffected controls demonstrating an impairment in type I and II INF responses.\n\nConclusionYoung males with TLR7 loss-of-function mutations and severe COVID-19 in the two reported families represent only a fraction of a broader and complex host genome situation. Specifically, missense mutations in the X-linked recessive TLR7 disorder may significantly contribute to disease susceptibility in up to 4% of severe COVID-19.\n\nClinical ImplicationIn this new yet complex scenario, our observations provide the basis for a personalized interferon-based therapy in patients with rare TLR7 variants.\n\nCAPSULE SUMMARYOur results in large cohorts from Italy and Spain showed that X-linked recessive TLR7 disorder may represent the cause of disease susceptibility to COVID-19 in up to 4% of severely affected young male cases.",
+    "rel_num_authors": 24,
+    "rel_authors": [
+      {
+        "author_name": "Chiara Fallerini",
+        "author_inst": "Medical Genetics, University of Siena; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy"
+      },
+      {
+        "author_name": "Sergio Daga",
+        "author_inst": "Medical Genetics, University of Siena; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy"
+      },
+      {
+        "author_name": "Stefania Mantovani",
+        "author_inst": "Division of Infectious Diseases and Immunology, Department of Medical Sciences and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy"
+      },
+      {
+        "author_name": "Elisa Benetti",
+        "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy"
+      },
+      {
+        "author_name": "Aurora Pujol",
+        "author_inst": "Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain; CIBERER, Centro de Investigacion Biomedica en Red de En"
+      },
+      {
+        "author_name": "Nicola Picchiotti",
+        "author_inst": "Department of Mathematics, University of Pavia, Pavia, Italy; University of Siena, DIISM-SAILAB, Siena, Italy"
+      },
+      {
+        "author_name": "Agatha Schluter",
+        "author_inst": "Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain; CIBERER, Centro de Investigacion Biomedica en Red de En"
+      },
+      {
+        "author_name": "Laura Planas-Serra",
+        "author_inst": "Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain; CIBERER, Centro de Investigacion Biomedica en Red de En"
+      },
+      {
+        "author_name": "Jesus Troya",
+        "author_inst": "Infanta Leonor University Hospital, Madrid, Spain"
+      },
+      {
+        "author_name": "Margherita Baldassarri",
+        "author_inst": "Medical Genetics, University of Siena; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy"
+      },
+      {
+        "author_name": "Francesca Fava",
+        "author_inst": "Medical Genetics, University of Siena; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Genetica Medica"
+      },
+      {
+        "author_name": "Serena Ludovisi",
+        "author_inst": "Division of Infectious Diseases and Immunology, Department of Medical Sciences and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; D"
+      },
+      {
+        "author_name": "Francesco Castelli",
+        "author_inst": "Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili Hospital, Brescia, Italy"
+      },
+      {
+        "author_name": "Maria Eugenia Quiros-Roldan",
+        "author_inst": "Department of Infectious and Tropical Diseases, University of Brescia and ASST Spedali Civili Hospital, Brescia, Italy"
+      },
+      {
+        "author_name": "Massimo Vaghi",
+        "author_inst": "Chirurgia Vascolare, Ospedale Maggiore di Crema, Italy"
+      },
+      {
+        "author_name": "Stefano Rusconi",
+        "author_inst": "III Infectious Diseases Unit, ASST-FBF-Sacco, Milan, Italy; Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy"
+      },
+      {
+        "author_name": "Matteo Siano",
+        "author_inst": "Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy"
+      },
+      {
+        "author_name": "Maria Bandini",
+        "author_inst": "Department of Preventive Medicine, Azienda USL Toscana Sud Est, Italy"
+      },
+      {
+        "author_name": "Simone Furini",
+        "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy"
+      },
+      {
+        "author_name": "Francesca Mari",
+        "author_inst": "Medical Genetics, University of Siena; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Genetica Medica"
+      },
+      {
+        "author_name": "- GEN-COVID Multicenter Study",
+        "author_inst": ""
+      },
+      {
+        "author_name": "Alessandra Renieri",
+        "author_inst": "Medical Genetics, University of Siena; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Genetica Medica"
+      },
+      {
+        "author_name": "Mario U Mondelli",
+        "author_inst": "Division of Infectious Diseases and Immunology, Department of Medical Sciences and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; D"
+      },
+      {
+        "author_name": "Elisa Frullanti",
+        "author_inst": "Medical Genetics, University of Siena; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "genetic and genomic medicine"
+  },
   {
     "rel_doi": "10.1101/2020.11.25.20144139",
     "rel_title": "Disentangling the roles of human mobility and deprivation on the transmission dynamics of COVID-19 using a spatially explicit simulation model.",
@@ -1048903,41 +1047922,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.11.24.20237750",
-    "rel_title": "Nurses' burnout and associated risk factors during the COVID-19 pandemic: a systematic review and meta-analysis",
-    "rel_date": "2020-11-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.24.20237750",
-    "rel_abs": "BackgroundDuring the COVID-19 pandemic, physical and mental health of the nurses is greatly challenged since they work under unprecedented pressure and they are more vulnerable to the harmful effects of the disease.\n\nAimTo examine the impact of the COVID-19 pandemic on nurses burnout and to identify associated risk factors.\n\nMethodsWe followed the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines for this systematic review and meta-analysis. PubMed, Scopus, ProQuest and pre-print services (medR{chi}iv and PsyArXiv) were searched from January 1, 2020 to November 15, 2020 and we removed duplicates. We applied a random effect model to estimate pooled effects since the heterogeneity between results was very high.\n\nFindingsFourteen studies, including 17,390 nurses met the inclusion criteria. Five standardized and valid questionnaires were used to measure burnout among nurses; Maslach Burnout Inventory, Copenhagen Burnout Inventory, Professional Quality of Life Scale version 5, Mini-Z, and Spanish Burnout Inventory. The overall prevalence of emotional exhaustion was 34.1% (95% confidence interval [CI]: 22.5-46.6%), of depersonalization was 12.6% (95% CI: 6.9-19.7%), and of lack of personal accomplishment was 15.2% (95% CI: 1.4-39.8%). The following factors were associated with increased nurses burnout: younger age, higher educational level, higher degree, decreased social support, having a relative/friend diagnosed with COVID-19, low family and colleagues readiness to cope with COVID-19 outbreak, increased perceived threat of Covid-19, longer working time in quarantine areas, working in a high-risk environment (a COVID-19 designated hospital, a COVID-19 unit, etc.), working in hospitals with inadequate and insufficient material and human resources, decreased working safety while caring for COVID-19 patients, increased workload, decreased self-confidence in self-protection, and lower levels of specialized training regarding COVID-19, job experience, and self-confidence in caring for COVID-19.\n\nConclusionNurses experience high levels of burnout during the COVID-19 pandemic, while several sociodemographic, social and occupational factors affect this burnout. Several interventions need to be implemented to mitigate mental health impact of the COVID-19 pandemic on nurses, e.g. screening for mental health illness and early supportive interventions for high-risk nurses, immediate access to mental health care services, social support to reduce feelings of isolation, sufficient personal protective equipment for all nurses to provide security etc. Governments, health care organizations and policy makers should act in this direction to prepare health care systems, individuals and nurses for a better response against the COVID-19 pandemic.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Petros A Galanis",
-        "author_inst": "National and Kapodistrian University of Athens"
-      },
-      {
-        "author_name": "Irene Vraka",
-        "author_inst": "P & A Kyriakou Children's Hospital"
-      },
-      {
-        "author_name": "Despoina Fragkou",
-        "author_inst": "National and Kapodistrian University of Athens"
-      },
-      {
-        "author_name": "Angeliki Bilali",
-        "author_inst": "P & A Kyriakou Children's Hospital"
-      },
-      {
-        "author_name": "Daphne Kaitelidou",
-        "author_inst": "National and Kapodistrian University of Athens"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "nursing"
-  },
   {
     "rel_doi": "10.1101/2020.11.23.394114",
     "rel_title": "A Nasal Spray Solution of Grapefruit Seed Extract plus Xylitol Displays Virucidal Activity Against SARS-Cov-2 In Vitro",
@@ -1049416,6 +1048400,37 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2020.11.21.20236216",
+    "rel_title": "Use of alternative RNA storage and extraction reagents and development of a hybrid PCR-based method for SARS-CoV-2 detection",
+    "rel_date": "2020-11-24",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.21.20236216",
+    "rel_abs": "The COVID-19 pandemic has presented multiple healthcare challenges, one of which is adequately meeting the need for large-scale diagnostic testing. The most commonly used assays for detection of SARS-CoV-2, including those recommended by the Center for Disease Control and Prevention (CDC), rely on a consistent set of core reagents. This has put a serious strain on the reagent supply chain, resulting in insufficient testing. It has also led to restricted animal testing, even though there are now multiple reports of animals, particularly cats, ferrets and minks, contracting the disease. We aimed to address the diagnostic bottleneck by developing a PCR-based SARS-CoV-2 detection assay for cats (and, potentially, other animals) which avoids the use of most common reagents, such as collection kits optimized for RNA stabilization, RNA isolation kits and TaqMan-based RT-PCR reagents. We demonstrated that an inexpensive solid-phase reversible immobilization (SPRI) method can be used for RNA extraction from feline samples collected with DNAGenoteks ORAcollect RNA OR-100 and PERFORMAgene DNA PG-100 sample collection kits, optimized for RNA or DNA stabilization, respectively. We developed a dual method SARS-CoV-2 detection assay relying on SYBR RT-PCR and Sanger sequencing, using the same set of custom synthesized oligo primers. We validated our tests specificity with a commercially available SARS-CoV-2 plasmid positive control, as well as two in-house positive control RNA samples. Our assays sensitivity was determined to be 10 viral copies per reaction. Our results suggest that a simple SPRI-dependent RNA extraction protocol and certain sample collection kits not specifically optimized for RNA stabilization could potentially be used in cases where reagent shortages are hindering adequate COVID-19 testing. These  alternative reagents could be used in combination with our COVID-19 testing method, which relies on inexpensive and readily available SYBR RT-PCR and non-fluorescent PCR reagents. Depending on the detection goals and the laboratory setup available, the SYBR RT-PCR method and the Sanger sequencing based method can be used alone or in conjunction, for improved accuracy. Although the test is intended for animal use, it is, in theory, possible to use it with human samples, especially those with higher viral loads.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Julie Yang",
+        "author_inst": "Basepaws"
+      },
+      {
+        "author_name": "Elias Salfati",
+        "author_inst": "Basepaws"
+      },
+      {
+        "author_name": "Damian Kao",
+        "author_inst": "Basepaws"
+      },
+      {
+        "author_name": "Yuliana Mihaylova",
+        "author_inst": "Basepaws"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.11.22.20236414",
     "rel_title": "The variation of genome sites associated with severe COVID-19 across populations: the worldwide and national pattern",
@@ -1050673,73 +1049688,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.11.23.20237057",
-    "rel_title": "Antigen rapid tests, nasopharyngeal PCR and saliva PCR to detect SARS-CoV-2: a prospective comparative clinical trial",
-    "rel_date": "2020-11-24",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.23.20237057",
-    "rel_abs": "BackgroundNasopharyngeal antigen Rapid Diagnostic Tests (RDTs) and saliva RT-PCR have shown variable performance to detect SARS-CoV-2.\n\nMethodsIn October 2020, we conducted a prospective trial involving patients presenting at testing centers with symptoms of COVID-19. We compared detection rates and performance of RDT, saliva PCR and nasopharyngeal (NP) PCR.\n\nResultsOut of 949 patients enrolled, 928 patients had all three tests. Detection rates were 35.2% (95%CI 32.2-38.4%) by RDT, 39.8% (36.6-43.0%) by saliva PCR, 40.1% (36.9-43.3%) by NP PCR, and 41.5% (38.3-44.7%) by any test. For those with viral loads (VL) [&ge;]106 copies/ml, detection rates were 30.3% (27.3-33.3), 31.4% (28.4-34.5), 31.5% (28.5-34.6), and 31.6% (28.6-34.7%) respectively.\n\nSensitivity of RDT compared to NP PCR was 87.4% (83.6-90.6%) for all positive patients and 96.5% (93.6-98.3%) for those with VL[&ge;]106. Sensitivity of STANDARD-Q(R), Panbio and COVID-VIRO(R) Ag tests were 92.9% (86.4-96.9%), 86.1% (78.6-91.7%) and 84.1% (76.9-89.7%), respectively. For those with VL[&ge;]106, sensitivities were 96.6% (90.5-99.3%), 97.8% (92.1-99.7%) and 95.3% (89.4-98.5%) respectively. Specificity of RDT was 100% (99.3-100%) compared to any PCR. RDT sensitivity was similar <4 days (87.8%) and [&ge;]4 days (85.7%) after symptoms onset (p=0.6). Sensitivities of saliva and NP PCR were 95.7% (93.1-97.5%) and 96.5% (94.1-98.1%), respectively, compared to the other PCR.\n\nConclusionsThe high performance of RDTs allows rapid identification of COVID cases with immediate isolation of the vast majority of contagious individuals. RDT could be a game changer in primary care practices, and even more so in resource-constrained settings. PCR on saliva can replace NP PCR.\n\nClinicalTrial.gov Identifier: NCT04613310",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Jean-Marc Schwob",
-        "author_inst": "Center for primary care and public health, University of Lausanne (Unisante)"
-      },
-      {
-        "author_name": "Alix Miauton",
-        "author_inst": "Center for primary care and public health, University of Lausanne (Unisante)"
-      },
-      {
-        "author_name": "Dusan Petrovic",
-        "author_inst": "Center for primary care and public health, University of Lausanne (Unisante)"
-      },
-      {
-        "author_name": "Jean Perdrix",
-        "author_inst": "Center for primary care and public health, University of Lausanne (Unisante)"
-      },
-      {
-        "author_name": "Nicolas Senn",
-        "author_inst": "Center for primary care and public health, University of Lausanne (Unisante)"
-      },
-      {
-        "author_name": "Katia Jaton",
-        "author_inst": "Institute of microbiology, University hospital of Lausanne"
-      },
-      {
-        "author_name": "Onya Opota",
-        "author_inst": "Institute of microbiology, University hospital of Lausanne"
-      },
-      {
-        "author_name": "Alain Maillard",
-        "author_inst": "Vidy-Med"
-      },
-      {
-        "author_name": "Gianni Minghelli",
-        "author_inst": "Vidy-Med"
-      },
-      {
-        "author_name": "Jacques Cornuz",
-        "author_inst": "Centre for primary care and public health, University of Lausanne (Unisante)"
-      },
-      {
-        "author_name": "Gilbert Greub",
-        "author_inst": "Institute of microbiology, University hospital of Lausanne"
-      },
-      {
-        "author_name": "Blaise Genton",
-        "author_inst": "Centre for primary care and public health, University of Lausanne (Unisante)"
-      },
-      {
-        "author_name": "Valerie D'Acremont",
-        "author_inst": "Centre for primary care and public health, University of Lausanne (Unisante)"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.11.23.20236901",
     "rel_title": "SalivaSTAT: Direct-PCR and pooling of saliva samples collected in healthcare and community setting for SARS-CoV-2 mass surveillance.",
@@ -1051006,6 +1049954,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.11.23.20237487",
+    "rel_title": "How closely is COVID-19 related to HCoV, SARS, and MERS? : Clinical comparison of coronavirus infections and identification of risk factors influencing the COVID-19 severity using common data model (CDM)",
+    "rel_date": "2020-11-24",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.23.20237487",
+    "rel_abs": "BackgroundSouth Korea was one of the epicenters for both the 2015 Middle East Respiratory Syndrome and 2019 COVID-19 outbreaks. However, there has been a lack of published literature, especially using the Electronic Medical Records (EMR), that provides a comparative summary of the prognostic factors present in the coronavirus-derived diseases. Therefore, in this study, we aimed to evaluate the distinct clinical traits between the infected patients of different coronaviruses to observe the extent of resemblance within the clinical features and to identify unique factors by disease severity that may influence the prognosis of COVID-19 patients.\n\nMethodsWe utilized the common data model (CDM), which is the database that houses the standardized EMR. We set COVID-19 as a reference group in comparative analyses. For statistical methods, we used Levenes test, one-way Anova test, Scheffe post-hoc test, Games-howell post-hoc test, and Students t-test for continuous variables, and chi-squared test and Fishers exact test for categorical variables. With the variables that reflected similarity in more than two comparisons between the disease groups yet significantly different between the COVID-19 severity groups, we performed univariate logistic regression to identify which common manifestations in coronaviruses are risk factors for severe COVID-19 outcomes.\n\nFindingsWe collected the records of 2840 COVID-19 patients, 67 MERS patients (several suspected cases included), 43 SARS suspected patients, and 87 HCoV patients. We found that a significantly higher number of COVID-19 patients had been diagnosed with comorbidities compared to the MERS and HCoV groups (48.5% vs. 10.4 %, p < 0.001 and 48.5% vs. 35.6%, p < 0.05) and also that the non-mild COVID-19 patients reported more comorbidities than the mild group (55.7% vs. 47.8%, p < 0.05). There were overall increases in the levels of fibrinogen in both sets of disease and severity groups. The univariate logistic regression showed that the male sex (OR: 1.66; CI: 1.29-2.13, p < 0.001), blood type A (OR: 1.80; CI: 1.40-2.31, p < 0.001), renal disease (OR: 3.27; CI: 2.34-4.55, p < 0.001), decreased creatinine level (OR: 2.05; CI: 1.45-2.88, p < 0.001), and elevated fibrinogen level (OR: 1.59, CI: 1.21-2.09, p < 0.001) are associated with the severe COVID-19 prognosis, whereas the patients reporting gastrointestinal symptoms (OR: 0.42; CI: 0.23-0.72, p < 0.01) and increased alkaline phosphatase (OR: 0.73; CI: 0.56-0.94, p < 0.05) are more less likely to experience complications and other severe outcomes from the SARS-CoV-2 infection.\n\nInterpretationThe present study observed the highest resemblance between the COVID-19 and SARS groups as clinical manifestations that were present in SARS group were linked to the severity of COVID-19. In particular, male individuals with blood type A and previous diagnosis of kidney failure were shown to be more susceptible to developing the poorer outcomes during COVID-19 infection, with a presentation of elevated level of fibrinogen.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Yeon Hee Kim",
+        "author_inst": "Biomedical Research Institute, Seoul National University Hospital"
+      },
+      {
+        "author_name": "Ye-Hee Ko",
+        "author_inst": "Biomedical Research Institute, Seoul National University Hospital"
+      },
+      {
+        "author_name": "Sooyoung Kim",
+        "author_inst": "Biomedical Research Institute, Seoul National University Hospital"
+      },
+      {
+        "author_name": "Kwangsoo Kim",
+        "author_inst": "Transdisciplinary Department of Medicine & Advanced Technology, Seoul National University Hospital"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.11.24.20237719",
     "rel_title": "Seroprevalence of SARS-CoV-2 infection in the craft and manual worker population of Qatar",
@@ -1052351,61 +1051330,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "medical education"
   },
-  {
-    "rel_doi": "10.1101/2020.11.20.20235598",
-    "rel_title": "Comparing Machine Learning Algorithms for Predicting ICU Admission and Mortality in COVID-19",
-    "rel_date": "2020-11-23",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.20.20235598",
-    "rel_abs": "As predicting the trajectory of COVID-19 disease is challenging, machine learning models could assist physicians determine high-risk individuals. This study compares the performance of 18 machine learning algorithms for predicting ICU admission and mortality among COVID-19 patients. Using COVID-19 patient data from the Mass General Brigham (MGB) healthcare database, we developed and internally validated models using patients presenting to Emergency Department (ED) between March-April 2020 (n = 1144) and externally validated them using those individuals who encountered ED between May-August 2020 (n = 334). We show that ensemble-based models perform better than other model types at predicting both 5-day ICU admission and 28-day mortality from COVID-19. CRP, LDH, and procalcitonin levels were important for ICU admission models whereas eGFR <60 ml/min/1.73m2, ventilator use, and potassium levels were the most important variables for predicting mortality. Implementing such models would help in clinical decision-making for future COVID-19 and other infectious disease outbreaks.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Sonu Subudhi",
-        "author_inst": "Department of Medicine/Gastroenterology Division, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts"
-      },
-      {
-        "author_name": "Ashish Verma",
-        "author_inst": "Department of Medicine/Renal Division, Brigham and Women Hospital and Harvard Medical School, Boston, Massachusetts"
-      },
-      {
-        "author_name": "Ankit B. Patel",
-        "author_inst": "Department of Medicine/Renal Division, Brigham and Women Hospital and Harvard Medical School, Boston, Massachusetts"
-      },
-      {
-        "author_name": "Charles C. Hardin",
-        "author_inst": "Department of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts"
-      },
-      {
-        "author_name": "Melin J. Khandekar",
-        "author_inst": "Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts"
-      },
-      {
-        "author_name": "Hang Lee",
-        "author_inst": "Biostatistics Center, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts"
-      },
-      {
-        "author_name": "Triantafyllos Stylianopoulos",
-        "author_inst": "Cancer Biophysics Laboratory, Department of Mechanical and Manufacturing Engineering, University of Cyprus, Nicosia, Cyprus"
-      },
-      {
-        "author_name": "Lance L. Munn",
-        "author_inst": "Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts"
-      },
-      {
-        "author_name": "Sayon Dutta",
-        "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts"
-      },
-      {
-        "author_name": "Rakesh K. Jain",
-        "author_inst": "Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health informatics"
-  },
   {
     "rel_doi": "10.1101/2020.11.20.20235697",
     "rel_title": "Long-Term Persistence of Spike Antibody and Predictive Modeling of Antibody Dynamics Following Infection with SARS-CoV-2",
@@ -1052668,6 +1051592,81 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.11.20.20231696",
+    "rel_title": "Antibody response patterns in COVID-19 patients with different levels of disease severity-Japan",
+    "rel_date": "2020-11-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.20.20231696",
+    "rel_abs": "BackgroundWe analyzed antibody response patterns according to level of disease severity in patients with novel coronavirus disease 2019 (COVID-19) in Japan.\n\nMethodsWe analyzed 611 serum specimens from 231 patients with COVID-19 (mild, 170; severe, 31; critical, 30). IgM and IgG antibodies against nucleocapsid protein (N) and spike 1 protein (S1) were detected by enzyme-linked immunosorbent assays.\n\nFindingsThe peaks of fitting curves for the OD values of IgM and IgG antibodies against N appeared simultaneously, while those against S1 were delayed compared with N. The OD values of IgM against N and IgG against both N and S1 were significantly higher in the severe and critical cases than in the mild cases at 11 days after symptom onset. The seroconversion rates of IgG were higher than those of IgM against both N and S1 during the clinical course based on the optimal cut-off values defined in this study. The seroconversion rates of IgG and IgM against N and S1 were higher in the severe and critical cases than in the mild cases.\n\nConclusionOur findings show that a stronger antibody response occurred in COVID-19 patients with greater disease severity and there were low seroconversion rates of antibodies against N and S1 in the mild cases. The antibody response patterns in our population suggest a second infection pattern, leading us to hypothesize that cross-reactivity occurs between SARS-CoV-2 and past infection with other human coronaviruses.",
+    "rel_num_authors": 15,
+    "rel_authors": [
+      {
+        "author_name": "Kazuo Imai",
+        "author_inst": "Saitama Medical University"
+      },
+      {
+        "author_name": "Yutaro Kitagawa",
+        "author_inst": "Saitama Medical University Hospital"
+      },
+      {
+        "author_name": "Sakiko Tabata",
+        "author_inst": "Self-Defense Forces Central Hospital"
+      },
+      {
+        "author_name": "Katsumi Kubota",
+        "author_inst": "Saitama Medical University Hospital"
+      },
+      {
+        "author_name": "Mayu Ikeda",
+        "author_inst": "Self-Defense Forces Central Hospital"
+      },
+      {
+        "author_name": "Masaru Matuoka",
+        "author_inst": "Saitama Medical University Hospital"
+      },
+      {
+        "author_name": "Kazuyasu Miyoshi",
+        "author_inst": "Self-Defense Forces Central Hospital"
+      },
+      {
+        "author_name": "Jun Sakai",
+        "author_inst": "Saitama Medical University"
+      },
+      {
+        "author_name": "Noriomi Ishibashi",
+        "author_inst": "Saitama Medical University"
+      },
+      {
+        "author_name": "Norihito Tarumoto",
+        "author_inst": "Saitama Medical University"
+      },
+      {
+        "author_name": "Shinichi Takeuchi",
+        "author_inst": "Saitama Medical University Hospital"
+      },
+      {
+        "author_name": "Toshimitsu Ito",
+        "author_inst": "Self-Defense Forces Central Hospital"
+      },
+      {
+        "author_name": "Shigefumi Maesaki",
+        "author_inst": "Saitama Medical University"
+      },
+      {
+        "author_name": "Kaku Tamura",
+        "author_inst": "Self-Defense Forces Central Hospital"
+      },
+      {
+        "author_name": "Takuya Maeda",
+        "author_inst": "Saitama Medical University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.11.20.20235390",
     "rel_title": "Improved RT-PCR SARS-Cov2 results interpretation by indirect determination of cut-off cycle threshold value.",
@@ -1053769,37 +1052768,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2020.11.23.394312",
-    "rel_title": "The multidisciplinary nature of COVID-19 research",
-    "rel_date": "2020-11-23",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.23.394312",
-    "rel_abs": "ObjectiveWe analyzed the scientific output after COVID-19 and contrasted it with studies published in the aftermath of seven epidemics/pandemics: Severe Acute Respiratory Syndrome (SARS), Influenza A virus H5N1 and Influenza A virus H1N1 human infections, Middle East Respiratory Syndrome (MERS), Ebola virus disease, Zika virus disease, and Dengue.\n\nDesign/Methodology/ApproachWe examined bibliometric measures for COVID-19 and the rest of studied epidemics/pandemics. Data were extracted from Web of Science, using its journal classification scheme as a proxy to quantify the multidisciplinary coverage of scientific output. We proposed a novel Thematic Dispersion Index (TDI) for the analysis of pandemic early stages.\n\nResults/DiscussionThe literature on the seven epidemics/pandemics before COVID-19 has shown explosive growth of the scientific production and continuous impact during the first three years following each emergence or re-emergence of the specific infectious disease. A subsequent decline was observed with the progressive control of each health emergency. We observed an unprecedented growth in COVID-19 scientific production. TDI measured for COVID-19 (29,4) in just six months, was higher than TDI of the rest (7,5 to 21) during the first three years after epidemic initiation.\n\nConclusionsCOVID-19 literature showed the broadest subject coverage, which is clearly a consecuence of its social, economic, and political impact. The proposed indicator (TDI), allowed the study of multidisciplinarity, differentiating the thematic complexity of COVID-19 from the previous seven epidemics/pandemics.\n\nOriginality/ValueThe multidisciplinary nature and thematic complexity of COVID-19 research were successfully analyzed through a scientometric perspective.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Ricardo Arencibia-Jorge",
-        "author_inst": "UNAM, Mexico."
-      },
-      {
-        "author_name": "Lourdes Garcia-Garcia",
-        "author_inst": "INSP, Mexico."
-      },
-      {
-        "author_name": "Ernesto Galban-Rodriguez",
-        "author_inst": "CIGB, Cuba."
-      },
-      {
-        "author_name": "Humberto Carrillo-Calvet",
-        "author_inst": "UNAM, Mexico."
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "scientific communication and education"
-  },
   {
     "rel_doi": "10.1101/2020.11.22.393587",
     "rel_title": "A Synthetic Defective Interfering SARS-CoV-2",
@@ -1054178,6 +1053146,61 @@
     "type": "new results",
     "category": "scientific communication and education"
   },
+  {
+    "rel_doi": "10.1101/2020.11.20.20235440",
+    "rel_title": "Coagulation factors and COVID-19 severity: Mendelian randomization analyses and supporting evidence",
+    "rel_date": "2020-11-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.20.20235440",
+    "rel_abs": "BackgroundThe evolving pandemic of COVID-19 is arousing alarm to public health. According to epidemiological and observational studies, coagulopathy was frequently seen in severe COVID-19 patients, yet the causality from specific coagulation factors to COVID-19 severity and the underlying mechanism remain elusive.\n\nMethodsFirst, we leveraged Mendelian randomization (MR) analyses to assess causal relationship between 12 coagulation factors and severe COVID-19 illness based on two genome-wide association study (GWAS) results of COVID-19 severity. Second, we curated clinical evidence supporting causal associations between COVID-19 severity and particular coagulation factors which showed significant results in MR analyses. Third, we validated our results in an independent cohort from UK Biobank (UKBB) using polygenic risk score (PRS) analysis and logistic regression model. For all MR analyses, GWAS summary-level data were used to ascertain genetic effects on exposures against disease risk.\n\nResultsWe revealed that genetic predisposition to the antigen levels of von Willebrand factor (VWF) and the activity levels of its cleaving protease ADAMTS13 were causally associated with COVID-19 severity, wherein elevated VWF antigen level (P = 0.005, odds ratio (OR) = 1.35, 95% confidence interval (CI): 1.09-1.68 in the Severe COVID-19 GWAS Group cohort; P = 0.039, OR = 1.21, 95% CI: 1.01-1.46 in the COVID-19 Host Genetics Initiative cohort) and lowered ADAMTS13 activity (P = 0.025, OR = 0.69, 95% CI: 0.50-0.96 in the Severe COVID-19 GWAS Group cohort) lead to increased risk of severe COVID-19 illness. No significant causal association of tPA, PAI-1, D-dimer, FVII, PT, FVIII, FXI, aPTT, FX or ETP with COVID-19 severity was observed. In addition, as an independent factor, VWF PRS explains a 31% higher risk of severe COVID-19 illness in the UKBB cohort (P = 0.047, OR per SD increase = 1.31, 95% CI: 1.00-1.71). In combination with age, sex, BMI and several pre-existing disease statues, our model can predict severity risks with an AUC of 0.70.\n\nConclusionTogether with the supporting evidence of recent retrospective cohort studies and independent validation based on UKBB data, our results suggest that the associations between coagulation factors VWF/ADAMTS13 and COVID-19 severity are essentially causal, which illuminates one of possible mechanisms underlying COVID-19 severity. This study also highlights the importance of dynamically monitoring the plasma levels of VWF/ADAMTS13 after SARS-CoV-2 infection, and facilitates the development of treatment strategy for controlling COVID-19 severity and associated thrombotic complication.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Yao Zhou",
+        "author_inst": "Tianjin Medical University"
+      },
+      {
+        "author_name": "Zipeng Liu",
+        "author_inst": "The University of Hong Kong"
+      },
+      {
+        "author_name": "Hongxi Yang",
+        "author_inst": "Tianjin Medical University"
+      },
+      {
+        "author_name": "Jianhua Wang",
+        "author_inst": "Tianjin Medical University"
+      },
+      {
+        "author_name": "Tong Liu",
+        "author_inst": "Tianjin Medical University"
+      },
+      {
+        "author_name": "Kexin Chen",
+        "author_inst": "Tianjin Medical University"
+      },
+      {
+        "author_name": "Yaogang Wang",
+        "author_inst": "Tianjin Medical University"
+      },
+      {
+        "author_name": "Pak Chung Sham",
+        "author_inst": "The University of Hong Kong"
+      },
+      {
+        "author_name": "Ying Yu",
+        "author_inst": "Tianjin Medical University"
+      },
+      {
+        "author_name": "Mulin Jun Li",
+        "author_inst": "Tianjin Medical University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "genetic and genomic medicine"
+  },
   {
     "rel_doi": "10.1101/2020.11.20.20227355",
     "rel_title": "Single cell profiling of COVID-19 patients: an international data resource from multiple tissues",
@@ -1055519,89 +1054542,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.11.18.20234211",
-    "rel_title": "Incidence of SARS-CoV-2 infection among asymptomatic frontline health workers in Los Angeles County, California",
-    "rel_date": "2020-11-21",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.18.20234211",
-    "rel_abs": "Beginning April 8, 2020, we enrolled 1787 frontline heath workers who were asymptomatic for COVID-19 into a longitudinal surveillance study. During that time 4 healthcare workers and 6 first responders tested positive for SARS-CoV-2 by RT-PCR. Additionally, 43 healthcare workers and 55 first responders had detectable IgG antibodies to SARS-CoV-2.",
-    "rel_num_authors": 17,
-    "rel_authors": [
-      {
-        "author_name": "Megan Halbrook",
-        "author_inst": "UCLA"
-      },
-      {
-        "author_name": "Adva Gadoth",
-        "author_inst": "Department of Epidemiology, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, USA"
-      },
-      {
-        "author_name": "Rachel Martin-Blais",
-        "author_inst": "Department of Pediatrics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA"
-      },
-      {
-        "author_name": "Ashley Grey",
-        "author_inst": "Division of Pediatric Hematology/Oncology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA"
-      },
-      {
-        "author_name": "Deisy Contreras",
-        "author_inst": "David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA"
-      },
-      {
-        "author_name": "Saman Kashani",
-        "author_inst": "Los Angeles County Fire Department, Los Angeles CA, USA"
-      },
-      {
-        "author_name": "Clayton Kazan",
-        "author_inst": "Los Angeles County Fire Department, Los Angeles CA, USA"
-      },
-      {
-        "author_name": "Brian Kane",
-        "author_inst": "Los Angeles County Fire Department, Los Angeles CA, USA"
-      },
-      {
-        "author_name": "Nicole H Tobin",
-        "author_inst": "Department of Pediatrics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA"
-      },
-      {
-        "author_name": "Jennifer A Fulcher",
-        "author_inst": "Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA"
-      },
-      {
-        "author_name": "Sarah L Brooker",
-        "author_inst": "Department of Pediatrics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA"
-      },
-      {
-        "author_name": "Scott G Kitchen",
-        "author_inst": "Division of Hematology/Oncology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA"
-      },
-      {
-        "author_name": "Emmanuelle Faure-Kumar",
-        "author_inst": "Department of Medicine, Division of Digestives Diseases, University of California, Los Angeles, Los Angeles, CA, USA"
-      },
-      {
-        "author_name": "Otto O Yang",
-        "author_inst": "Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA"
-      },
-      {
-        "author_name": "Kathie G Ferbas",
-        "author_inst": "David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA"
-      },
-      {
-        "author_name": "Grace M Aldrovandi",
-        "author_inst": "David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA"
-      },
-      {
-        "author_name": "Anne W Rimoin",
-        "author_inst": "Department of Epidemiology, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, USA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.11.20.20234013",
     "rel_title": "Prevention of severe COVID-19 in the elderly by early high-titer plasma",
@@ -1056520,6 +1055460,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.11.17.20231290",
+    "rel_title": "Secondary Attack Rate (SAR) in household contacts of expired primary cases of COVID-19: A study from Western India",
+    "rel_date": "2020-11-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.17.20231290",
+    "rel_abs": "Secondary attack rate (SAR) in household contacts of expired primary COVID-19 cases is not well studied yet. Based on our previous pilot study conducted in Gandhinagar district of Gujarat state, we developed a new research protocol to understand SAR statistics in household contacts of COVID-19 cases that died/expired. The details of expired COVID positive primary cases were obtained from Government records and the details of secondary cases were retrieved using telephonic interviews of the household members. Forty-nine expired cases were registered between March to August, 2020. Out of 49 deaths, 28 families could be reached on phone. Rest were not reachable or refused to give information. These were interviewed after taking verbal consent. The study reported 25% SAR in household contact of expired primary cases with 7.4% of mortality in secondary cases. Though this is representative data only from a single district, it was observed that 75% of the household contacts were still not infected in spite of repeated contact with the sever cases. More such studies in various regions are needed to understand disease transmission.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Komal Shah",
+        "author_inst": "Indian Institute of Public Health Gandhinagar"
+      },
+      {
+        "author_name": "Nupur Desai",
+        "author_inst": "Newyork university"
+      },
+      {
+        "author_name": "Dileep Mavalankar",
+        "author_inst": "Indian Institute of Public Health Gandhinagar"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.11.18.20230599",
     "rel_title": "Remdesivir induced viral RNA and subgenomic RNA suppression, and evolution of viral variants in SARS-CoV-2 infected patients.",
@@ -1058073,49 +1057040,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2020.11.19.389916",
-    "rel_title": "Natural deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape",
-    "rel_date": "2020-11-19",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.19.389916",
-    "rel_abs": "Zoonotic pandemics, like that caused by SARS-CoV-2, can follow the spillover of animal viruses into highly susceptible human populations. Their descendants have adapted to the human host and evolved to evade immune pressure. Coronaviruses acquire substitutions more slowly than other RNA viruses, due to a proofreading polymerase. In the spike glycoprotein, we find recurrent deletions overcome this slow substitution rate. Deletion variants arise in diverse genetic and geographic backgrounds, transmit efficiently, and are present in novel lineages, including those of current global concern. They frequently occupy recurrent deletion regions (RDRs), which map to defined antibody epitopes. Deletions in RDRs confer resistance to neutralizing antibodies. By altering stretches of amino acids, deletions appear to accelerate SARS-CoV-2 antigenic evolution and may, more generally, drive adaptive evolution.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Kevin R McCarthy",
-        "author_inst": "University of Pittsburgh School of Medicine"
-      },
-      {
-        "author_name": "Linda J Rennick",
-        "author_inst": "University of Pittsburgh School of Medicine"
-      },
-      {
-        "author_name": "Sham Nambulli",
-        "author_inst": "University of Pittsburgh School of Medicine"
-      },
-      {
-        "author_name": "Lindsey R Robinson-McCarthy",
-        "author_inst": "Harvard Medical School"
-      },
-      {
-        "author_name": "William G Bain",
-        "author_inst": "UPMC"
-      },
-      {
-        "author_name": "Ghady Haidar",
-        "author_inst": "University of Pittsburgh"
-      },
-      {
-        "author_name": "W. Paul Duprex",
-        "author_inst": "University of Pittsburgh School of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.11.18.20234369",
     "rel_title": "Antibodies to SARS-CoV-2 are associated with protection against reinfection",
@@ -1058454,6 +1057378,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.11.19.20234716",
+    "rel_title": "A precise measure of the impact of the first wave of Covid-19 on life expectancy. Regional differentials in Switzerland",
+    "rel_date": "2020-11-19",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.19.20234716",
+    "rel_abs": "Based on publicly available data supplied by the Swiss Federal Statistical Office (FSO), we calculated life tables by sex and by week for seven major regions of Switzerland in 2020, up to October 26th. These life tables provide information on the trends of life expectancy at birth and at the age of 65 years during the first wave of the coronavirus disease 2019 (COVID-19) epidemic.\n\nThe results show a strong cyclical decrease in life expectancy, particularly in Ticino, where this variable has decreased by almost 6 years compared to the 2019 life expectancy, and in the Lake Geneva region. The other regions of Switzerland observed more modest decreases during the first wave, generally not exceeding a 2-year reduction. This decrease can be explained to some extent by seasonal variations in this indicator.\n\nIn conclusion, the very sharp decrease in the average lifespan observed in the two regions mentioned above suggests that the first wave of the epidemic had a significant impact. It also reflects an unfavourable health situation. The life expectancy at the age of 65 years observed at the end of March 2020 in Ticino corresponded to the average life expectancy observed in Switzerland forty years ago.\n\nThe calculated indicators have the advantage of accounting for the age structures of the respective populations. They therefore demonstrate their usefulness in monitoring during a pandemic, such as the one occurring currently.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Philippe Wanner",
+        "author_inst": "University of Geneva"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.11.17.20233312",
     "rel_title": "Temporal Associations between Community Incidence of COVID-19 and Nursing Home Outbreaks in Ontario, Canada",
@@ -1059635,69 +1058578,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
-  {
-    "rel_doi": "10.1101/2020.11.16.20232967",
-    "rel_title": "Immune memory in mild COVID-19 patients and unexposed donors from India reveals persistent T cell responses after SARS-CoV-2 infection",
-    "rel_date": "2020-11-18",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.16.20232967",
-    "rel_abs": "Understanding the causes of the diverse outcome of COVID-19 pandemic in different geographical locations is important for the worldwide vaccine implementation and pandemic control responses. We analyzed 42 unexposed healthy donors and 28 mild COVID-19 subjects up to 5 months from the recovery for SARS-CoV-2 specific immunological memory. Using HLA class II predicted peptide megapools, we identified SARS-CoV-2 cross-reactive CD4+ T cells in around 66% of the unexposed individuals. Moreover, we found detectable immune memory in mild COVID-19 patients several months after recovery in the crucial arms of protective adaptive immunity; CD4+ T cells and B cells, with a minimal contribution from CD8+ T cells. Interestingly, the persistent immune memory in COVID-19 patients is predominantly targeted towards the Spike glycoprotein of the SARS-CoV-2. This study provides the evidence of both high magnitude pre-existing and persistent immune memory in Indian population. By providing the knowledge on cellular immune responses to SARS-CoV-2, our work has implication for the development and implementation of vaccines against COVID-19.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Asgar Ansari",
-        "author_inst": "National Institute of Immunology, New Delhi, 110067, India"
-      },
-      {
-        "author_name": "Rakesh Arya",
-        "author_inst": "All India Institute of Medical Sciences, New Delhi, 110029, India"
-      },
-      {
-        "author_name": "Shilpa Sachan",
-        "author_inst": "National Institute of Immunology, New Delhi, 110067, India"
-      },
-      {
-        "author_name": "Someshwar Nath Jha",
-        "author_inst": "National Institute of Immunology, New Delhi, 110067, India"
-      },
-      {
-        "author_name": "Anurag Kalia",
-        "author_inst": "National Institute of Immunology, New Delhi, 110067, India"
-      },
-      {
-        "author_name": "Anupam Lall",
-        "author_inst": "All India Institute of Medical Sciences, New Delhi, 110029, India"
-      },
-      {
-        "author_name": "Alessandro Sette",
-        "author_inst": "La Jolla Institute for Immunology, La Jolla, CA, 92037, USA"
-      },
-      {
-        "author_name": "Alba Grifoni",
-        "author_inst": "La Jolla Institute for Immunology, La Jolla, CA, 92037, USA"
-      },
-      {
-        "author_name": "Daniela Weiskopf",
-        "author_inst": "La Jolla Institute for Immunology, La Jolla, CA, 92037, USA"
-      },
-      {
-        "author_name": "Poonam Coshic",
-        "author_inst": "All India Institute of Medical Sciences, New Delhi, 110029, India"
-      },
-      {
-        "author_name": "Ashok Sharma",
-        "author_inst": "All India Institute of Medical Sciences, New Delhi, 110029, India"
-      },
-      {
-        "author_name": "Nimesh Gupta",
-        "author_inst": "National Institute of Immunology, New Delhi, 110067, India"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.11.17.20232827",
     "rel_title": "Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 transmission identifies community social distancing as the dominant intervention reducing outbreaks",
@@ -1060152,6 +1059032,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "cardiovascular medicine"
   },
+  {
+    "rel_doi": "10.1101/2020.11.17.20220681",
+    "rel_title": "An efficient distributed algorithm with application to COVID-19 data from heterogeneous clinical sites",
+    "rel_date": "2020-11-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.17.20220681",
+    "rel_abs": "ObjectivesIntegrating electronic health records (EHR) data from several clinical sites offers great opportunities to improve estimation with a more general population compared to analyses based on a single clinical site. However, sharing patient-level data across sites is practically challenging due to concerns about maintaining patient privacy. The objective of this study is to develop a novel distributed algorithm to integrate heterogeneous EHR data from multiple clinical sites without sharing patient-level data.\n\nMaterials and MethodsThe proposed distributed algorithm for binary regression can effectively account for between-site heterogeneity and is communication-efficient. Our method is built on a pairwise likelihood function in the extended Mantel-Haenszel regression, which is known to be statistically highly efficient. We construct a surrogate pairwise likelihood function through approximating the target pairwise likelihood by its surrogate. We show that the proposed surrogate pairwise likelihood leads to a consistent and asymptotically normal estimator by effective communication without sharing individual patient-level data. We study the empirical performance of the proposed method through a systematic simulation study and an application with data of 14,215 COVID-19 patients from 230 clinical sites at UnitedHealth Group Clinical Research Database.\n\nResultsThe proposed method was shown to perform close to the gold standard approach under extensive simulation settings. When the event rate is <5%, the relative bias of the proposed estimator is 30% smaller than that of the meta-analysis estimator. The proposed method retained high accuracy across different sample sizes and event rates compared with meta-analysis. In the data evaluation, the proposed estimate has a relative bias <9% when the event rate is <1%, whereas the meta-analysis estimate has a relative bias at least 10% higher than that of the proposed method.\n\nConclusionsOur simulation study and data application demonstrate that the proposed distributed algorithm provides an estimator that is robust to heterogeneity in event rates when effectively integrating data from multiple clinical sites. Our algorithm is therefore an effective alternative to both meta-analysis and existing distributed algorithms for modeling heterogeneous multi-site binary outcomes.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Jiayi Tong",
+        "author_inst": "University of Pennsylvania"
+      },
+      {
+        "author_name": "Chongliang Luo",
+        "author_inst": "University of Pennsylvania"
+      },
+      {
+        "author_name": "Md Nazmul Islam",
+        "author_inst": "UnitedHealth Group"
+      },
+      {
+        "author_name": "Natalie Sheils",
+        "author_inst": "UnitedHealth Group"
+      },
+      {
+        "author_name": "John Buresh",
+        "author_inst": "UnitedHealth Group"
+      },
+      {
+        "author_name": "Mackenzie Edmondson",
+        "author_inst": "University of Pennsylvania"
+      },
+      {
+        "author_name": "Peter A. Merkel",
+        "author_inst": "University of Pennsylvania"
+      },
+      {
+        "author_name": "Ebbing Lautenbach",
+        "author_inst": "University of Pennsylvania"
+      },
+      {
+        "author_name": "Rui Duan",
+        "author_inst": "Harvard University"
+      },
+      {
+        "author_name": "Yong Chen",
+        "author_inst": "University of Pennsylvania"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.11.17.20231548",
     "rel_title": "Meta-analysis of the SARS-CoV-2 serial interval and the impact of parameter uncertainty on the COVID-19 reproduction number",
@@ -1061089,69 +1060024,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.11.17.20233668",
-    "rel_title": "Sustained expression of inflammatory monocytes and activated T cells in COVID-19 patients and recovered convalescent plasma donors",
-    "rel_date": "2020-11-18",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.17.20233668",
-    "rel_abs": "Intense monocyte activation and infiltration into the target tissues is the main mechanism of lung injury in SARS CoV2 infection. A reduction in the degree and nature of such cellular responses is expected following recovery. We aimed to investigate the immune responses in severe Covid-19 patients and recovered patients.\n\nMethodsSevere COVID-19 patients (n=34) at Lok Nayak Hospital, New Delhi and COVID-19 recovered patients (n=15) from mild disease and considered for convalescent plasma (COPLA) donation at Institute of Liver and Biliary Sciences (ILBS), New Delhi were recruited. We performed a multiplex cytokine bead assay in plasma and detailed multicolour flow cytometric analysis in peripheral blood of both groups and outcomes were compared in both groups and with healthy controls (n=10).\n\nResultsA significant increase in inflammatory markers [MIP1-a, MIP3a, MCP1, MIF, MMP12, ITAC, VEGF-A, and leptin] was observed in severe patients. Non-survivors additionally showed increased IL-6 levels. Despite the sustained expression of MIPs, the recovered patients showed a surge in MCSF and IL-18 levels. Both the groups had increased CCR2, CX3CR1 positive monocytes, low CD8 T cells, APRIL and BAFFR+ve B cells compared with healthy subjects. In conclusion, patients who have recovered and considered for COPLA donations still have compromised immunity with sustained expression of inflammatory monocytes and activated T cells.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Nirupama Trehanpati Sr.",
-        "author_inst": "ILBS"
-      },
-      {
-        "author_name": "Ravinder Singh Jr.",
-        "author_inst": "ILBS"
-      },
-      {
-        "author_name": "Meenu Bajpai Sr.",
-        "author_inst": "ILBS"
-      },
-      {
-        "author_name": "Pushpa Yadav Jr.",
-        "author_inst": "ILBS"
-      },
-      {
-        "author_name": "Ashish Maheshwari",
-        "author_inst": "Institute of Liver and Biliary Sciences"
-      },
-      {
-        "author_name": "Suresh Kumar",
-        "author_inst": "Lok Nayak Jaiparkash Hospital"
-      },
-      {
-        "author_name": "Sonal Agrawal",
-        "author_inst": "ILBS"
-      },
-      {
-        "author_name": "Jayesh Kumar",
-        "author_inst": "ILBS"
-      },
-      {
-        "author_name": "Mojahidul Islam",
-        "author_inst": "ILBS"
-      },
-      {
-        "author_name": "Jaswinder Singh Maras",
-        "author_inst": "Institute of Liver and Biliary Sciences"
-      },
-      {
-        "author_name": "Gayatri Ramakrishna",
-        "author_inst": "ILBS"
-      },
-      {
-        "author_name": "Shiv K Sarin",
-        "author_inst": "Institute of Liver and Biliary Sciences (ILBS)"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.11.17.20233262",
     "rel_title": "COVID-19 critical care simulations: An international cross-sectional survey",
@@ -1061386,6 +1060258,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.11.16.20232900",
+    "rel_title": "High throughput wastewater SARS-CoV-2 detection enables forecasting of community infection dynamics in San Diego county",
+    "rel_date": "2020-11-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.16.20232900",
+    "rel_abs": "Large-scale wastewater surveillance has the ability to greatly augment the tracking of infection dynamics especially in communities where the prevalence rates far exceed the testing capacity. However, current methods for viral detection in wastewater are severely lacking in terms of scaling up for high throughput. In the present study, we employed an automated magnetic-bead based concentration approach for viral detection in sewage that can effectively be scaled up for processing 24 samples in a single 40-minute run. The method compared favorably to conventionally used methods for viral wastewater concentrations with higher recovery efficiencies from input sample volumes as low as 10ml and can enable the processing of over 100 wastewater samples in a day. The sensitivity of the high-throughput protocol was shown to detect cases as low as 2 in a hospital building with a known COVID-19 caseload. Using the high throughput pipeline, samples from the influent stream of the primary wastewater treatment plant of San Diego county (serving 2.3 million residents) were processed for a period of 13 weeks. Wastewater estimates of SARS-CoV-2 viral genome copies in raw untreated wastewater correlated strongly with clinically reported cases by the county, and when used alongside past reported case numbers and temporal information in an autoregressive integrated moving average (ARIMA) model enabled prediction of new reported cases up to 3 weeks in advance. Taken together, the results show that the high-throughput surveillance could greatly ameliorate comprehensive community prevalence assessments by providing robust, rapid estimates.\n\nImportanceWastewater monitoring has a lot of potential for revealing COVID-19 outbreaks before they happen because the virus is found in the wastewater before people have clinical symptoms. However, application of wastewater-based surveillance has been limited by long processing times specifically at the concentration step. Here we introduce a much faster method of processing the samples, and show that its robustness by demonstrating direct comparisons with existing methods and showing that we can predict cases in San Diego by a week with excellent accuracy, and three weeks with fair accuracy, using city sewage. The automated viral concentration method will greatly alleviate the major bottleneck in wastewater processing by reducing the turnaround time during epidemics.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Smruthi Karthikeyan",
+        "author_inst": "University of California - San Diego School of Medicine"
+      },
+      {
+        "author_name": "Nancy Ronquillo",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Pedro Belda-Ferre",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Destiny Alvarado",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Tara Javidi",
+        "author_inst": "University of California, San Diego"
+      },
+      {
+        "author_name": "Christopher A. Longhurst",
+        "author_inst": "UCSD"
+      },
+      {
+        "author_name": "Rob Knight",
+        "author_inst": "University of California, San Diego"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.11.18.20233957",
     "rel_title": "Early impact of school closure and social distancing for COVID-19 on the number of inpatients with childhood non-COVID-19 acute infections in Japan",
@@ -1062695,45 +1061610,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.11.16.20232181",
-    "rel_title": "The impact of the coronavirus disease 2019 (COVID-19) outbreak on hospital admissions for alcohol-related liver disease and pancreatitis: a time-series analysis",
-    "rel_date": "2020-11-17",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.16.20232181",
-    "rel_abs": "BackgroundDuring the coronavirus disease 2019 (COVID-19) pandemic, there have been health concerns related to alcohol use and misuse. Therefore, the World Health Organization cautioned that alcohol consumption during the pandemic might have a negative impact. The aim of this study was to examine the population-level change in cases of alcohol-related liver disease and pancreatitis that required admission during the COVID-19 outbreak.\n\nMethodsWe included patients aged 18 years or older who were hospitalized between July 2018 and June 2020 using Diagnostic Procedure Combination data, an administrative database in Japan, and counted the admission cases whose primary diagnosis was alcohol-related liver disease or pancreatitis. We defined the period from April 2020, when the Japanese government declared a state of emergency, as the beginning of the COVID-19 outbreak. The rate ratio (RR) of admissions with alcohol-related liver disease or pancreatitis per 1,000 admissions was tested using interrupted time series analysis. In addition, excess admissions for alcohol-related liver disease or pancreatitis were calculated.\n\nResultsOverall admissions were 3,026,389 cases, and a total of 10,242 admissions for alcohol-related liver disease or pancreatitis occurred from 257 hospitals. The rate of admissions per 1,000 admissions during the COVID-19 outbreak period (April 2020 to June 2020) had a 1.2 times increase compared with the pre-outbreak period (July 2018 to March 2020) for cases of alcohol-related liver disease or pancreatitis (RR: 1.22, 95%Confidence interval [CI]: 1.12 to 1.33). The COVID-19 pandemic caused about 214.75 (95%CI: 178.78 to 249.72) excess admissions for alcohol-related liver disease or pancreatitis based on predictions from our model.\n\nConclusionThe COVID-19 outbreak might have resulted in increased hospital admissions for alcohol-related liver disease or pancreatitis.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Hisashi Itoshima",
-        "author_inst": "Kyoto University Graduate School of Medicine"
-      },
-      {
-        "author_name": "Jung-ho Shin",
-        "author_inst": "Kyoto University Graduate School of Medicine"
-      },
-      {
-        "author_name": "Daisuke Takada",
-        "author_inst": "Kyoto University Graduate School of Medicine"
-      },
-      {
-        "author_name": "Tetsuji Morishita",
-        "author_inst": "Kyoto University Graduate School of Medicine"
-      },
-      {
-        "author_name": "Susumu Kunisawa",
-        "author_inst": "Kyoto University Graduate School of Medicine"
-      },
-      {
-        "author_name": "Yuichi Imanaka",
-        "author_inst": "Kyoto University Graduate School of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.11.16.20232397",
     "rel_title": "Effect of Vitamin D3 Supplementation vs Placebo on Hospital Length of Stay in Patients with Severe COVID-19: A Multicenter, Double-blind, Randomized Controlled Trial.",
@@ -1063136,6 +1062012,25 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2020.11.16.20149377",
+    "rel_title": "The effects of hypertension as an existing comorbidity on mortality rate in patients with COVID-19: a systematic review and meta-analysis.",
+    "rel_date": "2020-11-17",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.16.20149377",
+    "rel_abs": "IntroductionCoronavirus has spread throughout the world rapidly, and there is a growing need to identify host risk factors to identify those most at risk. There is a growing body of evidence suggesting a close link exists between an increased risk of infection and an increased severity of lung injury and mortality, in patients infected with COVID-19 who have existing hypertension. This is thought to be due to the possible involvement of the virus target receptor, ACE2, in the renin-angiotensin-aldosterone blood pressure management system.\n\nObjectiveTo investigate the association between hypertension as an existing comorbidity and mortality in hospitalized patients with confirmed coronavirus disease 2019 (COVID-19).\n\nMethodsA systematic literature search in several databases was performed to identify studies that comment on hypertension as an existing comorbidity, and its effect on mortality in hospitalized patients with confirmed COVID-19 infection. The results of these studies were then pooled, and a meta-analysis was peformed to assess the overall effect of hypertension as an existing comorbidity on risk of mortality in hospitalized COVID-19 positive patients.\n\nResultsA total of 12243 hospitalised patients were pooled from 19 studies. All studies demonstrated a higher fatality rate in hypertensive COVID-19 patients when compared to non-hypertensive patients. Meta-analysis of the pooled studies also demonstrated that hypertension was associated with increased mortality in hospitalized patients with confirmed COVID-19 infection (risk ratio (RR) 2.57 (95% confidence interval (CI) 2.10, 3.14), p < 0.001; I2 =74.98%).\n\nConclusionHypertension is associated with 157% increased risk of mortality in hospitalized COVID-19 positive patients. These results have not been adjusted for age, and a meta-regression of covariates including age is required to make these findings more conclusive.\n\nSummaryRisk of mortality is considerably higher in hospitalised COVID-19 patients who have hypertension as an existing comorbidity prior to admission.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Elena Whiteman",
+        "author_inst": "University of Warwick"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.11.17.387068",
     "rel_title": "Assessment of protein-protein interfaces in cryo-EM derived assemblies",
@@ -1064905,101 +1063800,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.11.12.20230763",
-    "rel_title": "Serological responses to SARS-CoV-2 following non-hospitalised infection: clinical and ethnodemographic features associated with the magnitude of the antibody response",
-    "rel_date": "2020-11-16",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.12.20230763",
-    "rel_abs": "ObjectiveTo determine clinical and ethnodemographic correlates of serological responses against the SARS-CoV-2 spike glycoprotein following mild-to-moderate COVID-19.\n\nDesignA retrospective cohort study of healthcare workers who had self-isolated due to COVID-19.\n\nSettingUniversity Hospitals Birmingham NHS Foundation Trust, UK (UHBFT).\n\nParticipants956 health care workers were recruited by open invitation via UHBFT trust email and social media.\n\nInterventionParticipants volunteered a venous blood sample that was tested for the presence of anti-SARS-CoV-2 spike glycoprotein antibodies. Results were interpreted in the context of the symptoms of their original illness and ethnodemographic variables.\n\nResultsUsing an assay that simultaneously measures the combined IgG, IgA and IgM response against the spike glycoprotein (IgGAM), the overall seroprevalence within this cohort was 46.2% (n=442/956). The seroprevalence of immunoglobulin isotypes was 36.3%, 18.7% and 8.1% for IgG, IgA and IgM respectively. IgGAM identified serological responses in 40.6% (n=52/128) of symptomatic individuals who reported a negative SARS-CoV-2 PCR test. Increasing age, non-white ethnicity and obesity were independently associated with greater IgG antibody response against the spike glycoprotein. Self-reported fever and fatigue were associated with greater IgG and IgA responses against the spike glycoprotein. The combination of fever and/or cough and/or anosmia had a positive predictive value of 92.3% for seropositivity.\n\nConclusions and relevanceAssays employing combined antibody detection demonstrate enhanced seroepidemiological sensitivity and can detect prior viral exposure even when PCR swabs have been negative. We demonstrate an association between known ethnodemographic risk factors associated with mortality from COVID-19 and the magnitude of serological responses in mild-to-moderate disease. The combination of cough, and/or fever and/or anosmia identifies the majority of individuals who should self-isolate for COVID-19.",
-    "rel_num_authors": 20,
-    "rel_authors": [
-      {
-        "author_name": "Adrian M Shields",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Sian E Faustini",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Marisol Perez-Toledo",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Sian Jossi",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Joel D Allen",
-        "author_inst": "University of Southampton"
-      },
-      {
-        "author_name": "Saly Al-Taei",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Claire Backhouse",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Lynsey Dunbar",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Daniel Ebanks",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Beena Emmanuel",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Aduragbemi A Faniyi",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Mark A Garvey",
-        "author_inst": "University Hospitals Birmingham NHS Foundation Trust"
-      },
-      {
-        "author_name": "Annabel Grinbergs",
-        "author_inst": "University Hospitals Birmingham NHS Foundation Trust"
-      },
-      {
-        "author_name": "Golaleh McGinnell",
-        "author_inst": "University Hospitals Birmingham NHS Foundation Trust"
-      },
-      {
-        "author_name": "Yasunori Watanabe",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Max Crispin",
-        "author_inst": "University of Southampton"
-      },
-      {
-        "author_name": "David C Wraith",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Adam F Cunningham",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Mark T Drayson",
-        "author_inst": "University of Birmingham"
-      },
-      {
-        "author_name": "Alex G Richter",
-        "author_inst": "University of Birmingham"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "allergy and immunology"
-  },
   {
     "rel_doi": "10.1101/2020.11.13.20231266",
     "rel_title": "Estimating the cumulative incidence of SARS-CoV-2 infection and the infection fatality ratio in light of waning antibodies",
@@ -1065262,6 +1064062,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
+  {
+    "rel_doi": "10.1101/2020.11.14.20231142",
+    "rel_title": "Capability impacts of the Covid-19 lockdown in association with mental well-being, social connections and existing vulnerabilities: an Austrian survey study",
+    "rel_date": "2020-11-16",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.14.20231142",
+    "rel_abs": "BackgroundImpacts of the Covid-19 pandemic and its public health measures go beyond physical and mental health and incorporate wider well-being impacts in terms of what people are free to do or be. We explored these capability impacts of the Covid-19 lockdown in association with peoples mental well-being, social support and existing vulnerabilities in Austria.\n\nMethodsAdult Austrian residents (n=560) provided responses to a cross-sectional online survey about their experiences during Covid-19 lockdown (15 March-15 April 2020). Instruments measuring capabilities (OxCAP-MH), depression and anxiety (HADS), social support (MSPSS) and mental well-being (WHO-5) were used in association with six pre-defined vulnerabilities using multivariable linear regression.\n\nResults31% of the participants reported low mental well-being and only 30% of those with a history of mental health treatment received treatment during lockdown. Past mental health treatment had a significant negative effect across all outcome measures with an associated capability well-being score reduction of -6.54 (95%CI: -9.26,-3.82). Direct Covid-19 experience and being  at risk due to age and/or physical health conditions were also associated with significant capability deprivations. When adjusted for vulnerabilities, significant capability reductions were observed in association with increased levels of depression (-1.79) and anxiety (-1.50), and significantly higher capability levels (+3.77) were associated with higher levels of social support. Compared to the cohort average, individual capability impacts varied between -9% for those reporting past mental health treatment and +5% for those reporting one score higher on the social support scale.\n\nConclusionsOur study is the first to assess the capability limiting aspects of a lockdown in association with specific vulnerabilities. The negative impacts of the Covid-19 lockdown were strongest for people with a history of mental health treatment. In future public health policies, special attention should be also paid to improving social support levels to increase public resilience.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Judit Simon",
+        "author_inst": "Department of Health Economics, Center for Public Health, Medical University of Vienna, Kinderspitalgasse 15, 1090 Vienna, Austria"
+      },
+      {
+        "author_name": "Timea M Helter",
+        "author_inst": "Department of Health Economics, Center for Public Health, Medical University of Vienna, Kinderspitalgasse 15, 1090 Vienna, Austria"
+      },
+      {
+        "author_name": "Ross G White",
+        "author_inst": "Primary Care and Mental Health, Institute of Population Health, University of Liverpool, School of Psychology, Brownlow Hill, Liverpool, L69 3GB, UK"
+      },
+      {
+        "author_name": "Catharina van der Boor",
+        "author_inst": "Primary Care and Mental Health, Institute of Population Health, University of Liverpool, School of Psychology, Brownlow Hill, Liverpool, L69 3GB, UK"
+      },
+      {
+        "author_name": "Agata Laszewska",
+        "author_inst": "Department of Health Economics, Center for Public Health, Medical University of Vienna, Kinderspitalgasse 15, 1090 Vienna, Austria"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.11.14.20231886",
     "rel_title": "Modeling the Effect of Lockdown Timing as a COVID-19 Control Measure in Countries with Differing Social Contacts",
@@ -1066475,25 +1065310,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.11.14.383075",
-    "rel_title": "COVATOR: A Software for Chimeric Coronavirus Identification",
-    "rel_date": "2020-11-16",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.14.383075",
-    "rel_abs": "The term chimeric virus was not popular in the last decades. Recently, according to current sequencing efforts in discovering COVID-19 Secrets, the generated information assumed the presence of 6 Coronavirus main strains, but coronavirus diverges into hundreds of sub-strains. the bottleneck is the mutation rate. With two mutation/month, humanity will meet a new sub-strain every month. Tracking new sequenced viruses is urgently needed because of the pathogenic effect of the new substrains. here we introduce COVATOR, A user-friendly and python-based software that identifies viral chimerism. COVATOR aligns input genome and protein that has no known source, against genomes and protein with known source, then gives the user a graphical summary.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Peter Habib",
-        "author_inst": "Bioimformatics Specialist, Colors Medical Laboratories"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "bioinformatics"
-  },
   {
     "rel_doi": "10.1101/2020.11.14.382770",
     "rel_title": "Discovery of rhodomyrtone as a broad-spectrum antiviral inhibitor with anti-SARS-CoV-2 activity",
@@ -1066932,6 +1065748,37 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2020.11.16.385468",
+    "rel_title": "Examining the Persistence of Human Coronaviruses on Fresh Produce",
+    "rel_date": "2020-11-16",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.16.385468",
+    "rel_abs": "Human coronaviruses (HCoVs) are mainly associated with respiratory infections. However, there is evidence that highly pathogenic HCoVs, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Middle East Respiratory Syndrome (MERS-CoV), infect the gastrointestinal (GI) tract and are shed in the fecal matter of the infected individuals. These observations have raised questions regarding the possibility of fecal-oral route as well as foodborne transmission of SARS-CoV-2 and MERS-CoV. Studies regarding the survival of HCoVs on inanimate surfaces demonstrate that these viruses can remain infectious for hours to days, however, to date, there is no data regarding the viral survival on fresh produce, which is usually consumed raw or with minimal heat processing. To address this knowledge gap, we examined the persistence of HCoV-229E, as a surrogate for highly pathogenic HCoVs, on the surface of commonly consumed fresh produce, including: apples, tomatoes and cucumbers. Herein, we demonstrated that viral infectivity declines within a few hours post-inoculation (p.i) on apples and tomatoes, and no infectious virus was detected at 24h p.i, while the virus persists in infectious form for 72h p.i on cucumbers. The stability of viral RNA was examined by droplet-digital RT-PCR (ddRT-PCR), and it was observed that there is no considerable reduction in viral RNA within 72h p.i.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Madeleine Blondin-Brosseau",
+        "author_inst": "Health Canada"
+      },
+      {
+        "author_name": "Jennifer Harlow",
+        "author_inst": "Health Canada"
+      },
+      {
+        "author_name": "Tanushka Doctor",
+        "author_inst": "Health Canada"
+      },
+      {
+        "author_name": "Neda Nasheri",
+        "author_inst": "Health Canada"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2020.11.14.382697",
     "rel_title": "Gene Expression Meta-Analysis Identifies Molecular Changes Associated with SARS-CoV Infection in Lungs",
@@ -1068473,65 +1067320,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.11.11.20223800",
-    "rel_title": "The Use of Saliva as a Diagnostic Specimen for SARS CoV-2 Molecular Diagnostic Testing for Pediatric Patients",
-    "rel_date": "2020-11-13",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.11.20223800",
-    "rel_abs": "BackgroundChildren are an important population to test for COVID-19 infection, particularly because they may shed the virus without displaying symptoms. Testing children for COVID-19 via sensitive molecular methods is important, although collecting nasopharyngeal (NP) specimens can be challenging. A less invasive mode of specimen collection that yields test results comparable to those from NP specimens would be beneficial to simplify sample collection.\n\nMethodsTo demonstrate that saliva is a suitable specimen for collection from children, the clinical usability/acceptability and the analytic performance of saliva were compared to NP specimens suspended in viral transport medium. Four different FDA EUA-approved real-time RT-PCR assays and one EUA approved saliva collection device were investigated.\n\nResultsThe study population included 526 patients between the ages of 3 and 61 years, 461 (88%) were <18 years, 425 were asymptomatic (81.1%), 92 were symptomatic (17.6%). Saliva mixed with saliva stabilizing buffer was found to yield comparable sensitivity to NP specimens when tested on the AllPlex SARS-CoV-2 molecular test (Seegene Inc). The analytic sensitivity of the AllPlex assay during testing of spiked saliva mixed with SpectrumDNA saliva stabilizer was found to be 250 genomic copies/mL.\n\nConclusionsOf the four FDA EUA-approved SARS-CoV-2 PCR assays studied, we found the AllPlex assay to be best suited for testing saliva specimens collected from children 5 years of age or older. The sensitivity of viral detection was equivalent to NP specimens when saliva specimens were mixed with the saliva stabilizer.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Meghan Delaney",
-        "author_inst": "Children's National Hospital"
-      },
-      {
-        "author_name": "Bobbe Thomas",
-        "author_inst": "Children's National Hospital"
-      },
-      {
-        "author_name": "Christal J Ralph",
-        "author_inst": "Children's National Hospital"
-      },
-      {
-        "author_name": "Kyah Draper",
-        "author_inst": "Children's National Hospital"
-      },
-      {
-        "author_name": "Mahdi Moshgriz",
-        "author_inst": "Children's National Hospital"
-      },
-      {
-        "author_name": "Joyce Granados",
-        "author_inst": "Children's National Hospital"
-      },
-      {
-        "author_name": "Michael Evangelista",
-        "author_inst": "Children's National Hospital"
-      },
-      {
-        "author_name": "Mark McGuire",
-        "author_inst": "Children's National Hospital"
-      },
-      {
-        "author_name": "Roberta L DeBiasi",
-        "author_inst": "Children's National Hospital"
-      },
-      {
-        "author_name": "Joelle Simpson",
-        "author_inst": "Children's National Hospital"
-      },
-      {
-        "author_name": "Joseph Campos",
-        "author_inst": "Children's National Hospital"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.11.11.20229500",
     "rel_title": "Association of social distancing and masking with risk of COVID-19",
@@ -1068958,6 +1067746,97 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.11.12.20145318",
+    "rel_title": "Critical care workers have lower seroprevalence of SARS-CoV-2 IgG compared with non-patient facing staff in first wave of COVID19.",
+    "rel_date": "2020-11-13",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.12.20145318",
+    "rel_abs": "With the first 2020 surge of the COVID-19 pandemic, many health care workers (HCW) were re-deployed to critical care environments to support intensive care teams to look after high numbers of patients with severe COVID-19. There was considerable anxiety of increased risk of COVID19 for staff working in these environments.\n\nUsing a multiplex platform to assess serum IgG responses to SARS-CoV-2 N, S and RBD proteins, and detailed symptom reporting, we screened over 500 HCW (25% of the total workforce) in a quaternary level hospital to explore the relationship between workplace and evidence of exposure to SARS-CoV-2.\n\nWhilst 45% of the cohort reported symptoms that they consider may have represented COVID-19, overall seroprevalence was 14% with anosmia and fever being the most discriminating symptoms for seropositive status. There was a significant difference in seropositive status between staff working in clinical and non-clinical roles (9% patient facing critical care, 15% patient facing non-critical care, 22% nonpatient facing). In the seropositive cohort, symptom severity increased with age for men and not for women. In contrast, there was no relationship between symptom severity and age or sex in the seronegative cohort reporting possible COVID-19 symptoms. Of the 12 staff screened PCR positive (10 symptomatic), 3 showed no evidence of seroconversion in convalescence.\n\nConclusionThe current approach to Personal Protective Equipment (PPE) appears highly effective in protecting staff from patient acquired infection in the critical care environment including protecting staff managing interhospital transfers of COVID-19 patients. The relationship between seroconversion and disease severity in different demographics warrants further investigation. Longitudinally paired virological and serological surveillance, with symptom reporting are urgently required to better understand the role of antibody in the outcome of HCW exposure during subsequent waves of COVID-19 in health care environments.",
+    "rel_num_authors": 19,
+    "rel_authors": [
+      {
+        "author_name": "Dr HE Baxendale",
+        "author_inst": "Royal Papworth Hospital NHS Foundation Trust"
+      },
+      {
+        "author_name": "Rainer Doffinger",
+        "author_inst": "Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK"
+      },
+      {
+        "author_name": "Jonathan Luke Heeney",
+        "author_inst": "Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom."
+      },
+      {
+        "author_name": "David Wells",
+        "author_inst": "Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom."
+      },
+      {
+        "author_name": "Jessica Gronlund",
+        "author_inst": "Royal Papworth NHS Trust, Cambridge, CB2 0AY, United Kingdom"
+      },
+      {
+        "author_name": "George Carnell",
+        "author_inst": "Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom"
+      },
+      {
+        "author_name": "Minna Paloniemi",
+        "author_inst": "Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom"
+      },
+      {
+        "author_name": "Paul Tonks",
+        "author_inst": "Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom"
+      },
+      {
+        "author_name": "Lourdes CeronGutierrez",
+        "author_inst": "Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK"
+      },
+      {
+        "author_name": "Ashleigh Sayer",
+        "author_inst": "Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK"
+      },
+      {
+        "author_name": "James Nathan",
+        "author_inst": "Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, United Kingdom"
+      },
+      {
+        "author_name": "Leo James",
+        "author_inst": "Protein and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom"
+      },
+      {
+        "author_name": "Jakob luptak",
+        "author_inst": "Protein and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom"
+      },
+      {
+        "author_name": "Guinevere L Grice",
+        "author_inst": "Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, United Kingdom"
+      },
+      {
+        "author_name": "Soraya Ebrahimi",
+        "author_inst": "Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK"
+      },
+      {
+        "author_name": "Xiaoli Xiong",
+        "author_inst": "Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, CB2 0QH, United Kingdom"
+      },
+      {
+        "author_name": "John AG Briggs",
+        "author_inst": "Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, CB2 0QH, United Kingdom"
+      },
+      {
+        "author_name": "Sumita Pai",
+        "author_inst": "ROYAL PAPWORTH HOSPITAL NHS FOUNDATION TRUST"
+      },
+      {
+        "author_name": "angalee nadesalingham",
+        "author_inst": "Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.11.13.381194",
     "rel_title": "In Vitro Activity of Itraconazole Against SARS-CoV-2",
@@ -1070183,57 +1069062,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.11.10.20228908",
-    "rel_title": "Evaluation of the disease outcome in Covid-19 infected patients by disease symptoms: a retrospective cross-sectional study in Ilam Province, Iran",
-    "rel_date": "2020-11-13",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.10.20228908",
-    "rel_abs": "Backgroundnovel coronavirus disease-19 (COVID-19) announced as a global pandemic in the year 2020. With the spread of the disease, a better understanding of patient outcomes associated with their symptoms in diverse geographic levels is vital. We aimed to analysis clinical outcomes of COVID-19 patients by disease symptoms in Ilam province of Iran.\n\nMethodsThis is a retrospective study. Data were collected from integrated health system records for all hospitals affiliated to Ilam University of Medical Sciences between 26 Jan 2020 and 02 May 2020. All patients with definite positive test were enrolled in this study. We used descriptive analyses, chi-square test and binary logistic regression to analyze the data using SPSS version 22.\n\nResultsThe mean age was 46.47{+/-}18.24 years. Of 3608 patients, 3477 (96.1%) were discharged and 129 (3.9%) were died. 54.2% of the patients were male and were in the age group of 30-40 years old age. Cough, sore throat, shortness of breath or difficulty breathing and fever or chills were the most common symptoms. People with symptoms of shortness of breath, abnormal radiographic findings of the chest, and chest pain and pressure were relatively more likely to die. Based on the findings of binary logistic regression probability of death in people who showed shortness of breath, abnormal chest radiographic findings and chest pain was 1.34, 1.24 and 1.32 times higher than those who did not show these symptoms, respectively.\n\nConclusionOur study provides evidence that presentation of some symptoms does significantly impact on outcomes of patients infected with SARS-CoV-2. Early detection of symptoms and proper management of outcomes can reduce mortality in patients with COVID-19.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Jamil Sadeghifar",
-        "author_inst": "Ilam University of Medical Sciences"
-      },
-      {
-        "author_name": "Habib Jalilian",
-        "author_inst": "Ahvaz Jundishapur University of medical sciences"
-      },
-      {
-        "author_name": "Khalil Momeni",
-        "author_inst": "Ilam University of Medical Sciences"
-      },
-      {
-        "author_name": "Hamed Delam",
-        "author_inst": "Larestan University of Medical Sciences"
-      },
-      {
-        "author_name": "Tadesse Sheleme",
-        "author_inst": "Mettu University"
-      },
-      {
-        "author_name": "Ayoub Rashidi",
-        "author_inst": "Ilam University of Medical Sciences"
-      },
-      {
-        "author_name": "Fariba Hemmati",
-        "author_inst": "Ilam University of Medical Sciences"
-      },
-      {
-        "author_name": "Shahab Falahi",
-        "author_inst": "Ilam University of Medical Sciences"
-      },
-      {
-        "author_name": "Morteza Arab-Zozani",
-        "author_inst": "Birjand University of Medical Sciences"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.11.10.20215145",
     "rel_title": "The Change in Seroprevalence in the US plus Puerto Rico between May and September of SARS-CoV-2 Antibody in the Asymptomatic Population",
@@ -1070396,6 +1069224,93 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health systems and quality improvement"
   },
+  {
+    "rel_doi": "10.1101/2020.11.10.20229401",
+    "rel_title": "Using Real World Data to Understand HIV and COVID-19 in the U.S.A. and Spain: Characterizing Co-Infected Patients Across the Care Cascade",
+    "rel_date": "2020-11-13",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.10.20229401",
+    "rel_abs": "ObjectiveMost patients severely affected by COVID-19 have been elderly and patients with underlying chronic disease such as diabetes, cardiovascular disease, or respiratory disease. People living with HIV (PLHIV) may have greater risk of contracting or developing severe COVID-19 due to the underlying HIV infection or higher prevalence of comorbidities.\n\nDesignThis is a cohort study, including PLHIV diagnosed, hospitalized, or requiring intensive services for COVID-19.\n\nMethodsData sources include routine electronic medical record or claims data from the U.S. and Spain. Patient demographics, comorbidities, and medication history are described.\n\nResultFour data sources had a population of HIV/COVID-19 coinfected patients ranging from 288 to 4606 lives. PLHIV diagnosed with COVID-19 were younger than HIV-negative patients diagnosed with COVID-19. PLHIV diagnosed with COVID-19 diagnosis had similar comorbidities as HIV-negative COVID-19 patients with higher prevalence of those comorbidities and history of severe disease. Treatment regimens were similar between PLHIV diagnosed with COVID-19 or PLHIV requiring intensive services.\n\nConclusionsOur study uses routine practice data to explore HIV impact on COVID-19, providing insight into patient history prior to COVID-19. We found that HIV and COVID-19 coinfected patients have higher prevalence of underlying comorbidities such as cardiovascular and respiratory disease as compared to HIV-negative COVID-19 infected patients. We also found that, across the care cascade, co-infected patients who received intensive services were more likely to have more serious underlying disease or a history of more serious events as compared to PLHIV who were diagnosed with COVID-19.",
+    "rel_num_authors": 18,
+    "rel_authors": [
+      {
+        "author_name": "Julianna Kohler",
+        "author_inst": "United States Agency for International Development"
+      },
+      {
+        "author_name": "Kristin M Kostka",
+        "author_inst": "IQVIA"
+      },
+      {
+        "author_name": "Rupa Makadia",
+        "author_inst": "Janssen Research and Development, Titusville, NJ, US"
+      },
+      {
+        "author_name": "Roger Paredes",
+        "author_inst": "IrsiCaixa AIDS Research Institute"
+      },
+      {
+        "author_name": "Talita Duarte-Salles",
+        "author_inst": "Fundacio Institut Universitari per a la recerca a l'Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain"
+      },
+      {
+        "author_name": "Scott L Duvall",
+        "author_inst": "VINCI Resource Center, VA Salt Lake City Health Care System, Salt Lake City, UT;  Division of Epidemiology, University of Utah, Salt Lake City, UT"
+      },
+      {
+        "author_name": "Michael Matheny",
+        "author_inst": "VINCI Resource Center, Tennessee Valley Healthcare System VA, Nashville, TN; Departments of Biomedical Informatics, Biostatistics, and Medicine, Vanderbilt Univ"
+      },
+      {
+        "author_name": "Kristine E Lynch",
+        "author_inst": "VINCI Resource Center, VA Salt Lake City Health Care System, Salt Lake City, UT; Division of Epidemiology, University of Utah, Salt Lake City, UT"
+      },
+      {
+        "author_name": "Alison Cheng",
+        "author_inst": "United States Agency for International Development"
+      },
+      {
+        "author_name": "Asieh Golozar",
+        "author_inst": "Johns Hopkins Bloomberg School of Public Health, Baltimore, MD US; Regeneron Pharmaceuticals, NY USA"
+      },
+      {
+        "author_name": "Jennifer C E Lane",
+        "author_inst": "Centre for Statistics in Medicine, NDORMS, University of Oxford"
+      },
+      {
+        "author_name": "Anthony G Sena",
+        "author_inst": "Janssen Research and Development, Titusville, NJ, US; Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands"
+      },
+      {
+        "author_name": "Peter J Rijnbeek",
+        "author_inst": "Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands"
+      },
+      {
+        "author_name": "Daniel R Morales",
+        "author_inst": "University of Dundee"
+      },
+      {
+        "author_name": "Patrick B Ryan",
+        "author_inst": "Janssen Research and Development, Titusville, NJ, US; Department of Biomedical Informatics, Columbia University, New York, New York, US"
+      },
+      {
+        "author_name": "Christian G Reich",
+        "author_inst": "Real World Solutions, IQVIA, Cambridge, MA, US"
+      },
+      {
+        "author_name": "George Siberry",
+        "author_inst": "United States Agency for International Development"
+      },
+      {
+        "author_name": "Daniel Prieto-Alhambra",
+        "author_inst": "University of Oxford"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "hiv aids"
+  },
   {
     "rel_doi": "10.1101/2020.11.11.20228692",
     "rel_title": "Impact of the COVID-19 nonpharmaceutical interventions on influenza and other respiratory viral infections in New Zealand",
@@ -1071921,41 +1070836,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
-  {
-    "rel_doi": "10.1101/2020.11.08.20224915",
-    "rel_title": "State- and County-Level COVID-19 Public Health Orders in California: Constructing a Dataset and Describing Their Timing, Content, and Stricture",
-    "rel_date": "2020-11-12",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.08.20224915",
-    "rel_abs": "Without vaccines, non-pharmaceutical interventions have been the most widely used approach to controlling the spread of COVID-19 epidemics. Various jurisdictions have implemented public health orders as a means of reducing effective contacts and controlling their local epidemics. Multiple studies have examined the effectiveness of various orders (e.g. use of face masks) for epidemic control. However, orders occur at different timings across jurisdictions and some orders on the same topic are stricter than others. We constructed a county-level longitudinal data set of more than 2,400 public health orders issues by California and its 58 counties pertaining to its 40 million residents. First, we describe methods used to construct the dataset that enables the characterization of the evolution over time of California state- and county-level public health orders dealing with COVID-19 from January 1, 2020 through June 30, 2021. Public health orders are both an interesting and important outcome in their own right and also a key input into analyses looking at how such orders may impact COVID-19 epidemics. To construct the dataset, we developed and executed a search strategy to identify COVID-19 public health orders over this time period for all relevant jurisdictions. We characterized each identified public health order in terms of the timing of when it was announced, went into effect and (potentially) expired. We also adapted an existing schema to describe the topic(s) each public health order dealt with and the level of stricture each imposed, applying it to all identified orders. Finally, as an initial assessment, we examined the patterns of public health orders within and across counties, focusing on the timing of orders, the rate of increase and decrease in stricture, and on variation and convergence of orders within regions.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Jeremy D Goldhaber-Fiebert",
-        "author_inst": "Stanford University"
-      },
-      {
-        "author_name": "Alexander F Holsinger",
-        "author_inst": "University of Texas at Austin"
-      },
-      {
-        "author_name": "Erin Holsinger",
-        "author_inst": "Stanford University"
-      },
-      {
-        "author_name": "Elizabeth Long",
-        "author_inst": "Stanford University"
-      },
-      {
-        "author_name": "- SC-COSMO Modeling Consortium",
-        "author_inst": ""
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health policy"
-  },
   {
     "rel_doi": "10.1101/2020.11.06.20223040",
     "rel_title": "Innovation of Audio-Visual Triage system in Combating the Spread of COVID-19 Infection and its efficacy: A Novel Strategy",
@@ -1072326,6 +1071206,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "cardiovascular medicine"
   },
+  {
+    "rel_doi": "10.1101/2020.11.09.20228007",
+    "rel_title": "Analysis of mitigation of Covid-19 outbreaks in workplaces and schools by hybrid telecommuting",
+    "rel_date": "2020-11-12",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.09.20228007",
+    "rel_abs": "The COVID-19 outbreak has forced most countries to impose new contact-limiting restrictions at workplaces, universities, schools, and more broadly in our societies. Yet, the power and limitations of these unprecedented strategies for containing virus spread within the populations remain unquantified. Here, we develop a simulation study to analyze COVID-19 outbreak magnitudes on three real-life contact networks stemming from a workplace, a primary school and a high school in France.\n\nOur study provides the first fine-grained analysis of the impact of contact-limiting strategies at work-places, schools and high schools, including (1) Rotating, in which workers are evenly split into two shifts that alternate on a daily or weekly basis; and (2) On-Off, where the whole group alternates periods of normal work interactions with complete telecommuting. We model epidemics spread in these different setups using an SEIR transmission model enriched with the coronavirus most salient specificities: super-spreaders, infectious asymptomatic individuals, and pre-symptomatic infectious periods. Our study yields clear results: The ranking of the strategies based on their ability to mitigate epidemic propagation in the network from a first index case is the same for all network topologies (work place, primary school and high school). Namely, from best to worst: Rotating week-by-week, Rotating day-by-day, On-Off week-by-week, and On-Off day-by-day. Moreover, our results show that when the baseline reproduction number R0 within the network is < 1.38, all four strategies efficiently control outbreak by decreasing effective Re to {inverted exclamation}1. These results can support public health decisions and telecommuting organization locally.\n\nO_TEXTBOXSignificance statement\n\nWe take advantage of available individual-level contact data for school and workplace social networks, to simulate COVID-19 epidemics on real-life networks. This framework enable us to compare and rank natural prevention strategies that require hybrid telecommuting, either for everyone synchronously (On-Off) or periodically switching between two groups of people (Rotating): weekly or daily Rotating, weekly or daily On-Off, and full telecommuting. All strategies have a significant impact when the reproduction number within the network is moderately high (< 1.3). These results can inform public health decisions and telecommuting organization at the local scale.\n\nC_TEXTBOX",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Simon Mauras",
+        "author_inst": "IRIF"
+      },
+      {
+        "author_name": "Vincent Cohen-Addad",
+        "author_inst": "Google Research"
+      },
+      {
+        "author_name": "Guillaume Duboc",
+        "author_inst": "IRIF"
+      },
+      {
+        "author_name": "Max Dupre la Tour",
+        "author_inst": "IRIF"
+      },
+      {
+        "author_name": "Paolo Frasca",
+        "author_inst": "Univ. Grenoble Alpes, CNRS, Inria, Grenoble INP, Gipsa-lab"
+      },
+      {
+        "author_name": "Claire Mathieu",
+        "author_inst": "CNRS, IRIF"
+      },
+      {
+        "author_name": "Lulla Opatowski",
+        "author_inst": "Univ Versailles Saint Quentin / Institut pasteur / Inserm"
+      },
+      {
+        "author_name": "Laurent Viennot",
+        "author_inst": "INRIA, IRIF"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.11.08.20227322",
     "rel_title": "COVID-19 pandemic risk analytics: Data mining with reliability engineering methods for analyzing spreading behavior and comparison with infectious diseases",
@@ -1074039,49 +1072966,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.11.09.20228452",
-    "rel_title": "Impact of public and private sector COVID-19 diagnostics and treatments on US healthcare resource utilization",
-    "rel_date": "2020-11-12",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.09.20228452",
-    "rel_abs": "IntroductionCoronavirus disease 2019 (COVID-19) has imposed a considerable burden on the United States (US) health system, with particular concern over healthcare capacity constraints.\n\nMethodsWe modeled the impact of public and private sector contributions to developing diagnostic testing and treatments on COVID-19-related healthcare resource use.\n\nResultsWe estimated that public sector contributions lead to [&ge;]30% reductions in COVID-19-related healthcare resource utilization. Private sector contributions to expanded diagnostic testing and treatments lead to further reductions in mortality (-44%), intensive care unit (ICU) and non-ICU hospital beds (-30% and -28%, respectively), and ventilator use (-29%). The combination of lower diagnostic test sensitivity and proportions of patients self-isolating may exacerbate case numbers, and policies that encourage self-isolating should be considered.\n\nConclusionWhile mechanisms exist to facilitate research, development, and patient access to diagnostic testing, future policies should focus on ensuring equitable patient access to both diagnostic testing and treatments which, in turn, will alleviate COVID-19-related resource constraints.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Daniel Sheinson",
-        "author_inst": "Genentech"
-      },
-      {
-        "author_name": "William Wong",
-        "author_inst": "Genentech"
-      },
-      {
-        "author_name": "Caroline Solon",
-        "author_inst": "Genentech"
-      },
-      {
-        "author_name": "Mindy Cheng",
-        "author_inst": "Roche Molecular Systems"
-      },
-      {
-        "author_name": "David Elsea",
-        "author_inst": "Bresmed"
-      },
-      {
-        "author_name": "Yang Meng",
-        "author_inst": "Bresmed"
-      },
-      {
-        "author_name": "Anuj Shah",
-        "author_inst": "Genentech"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.11.09.20223792",
     "rel_title": "The Individual and Social Determinants of COVID-19 in Ontario, Canada: A Population-Wide Study",
@@ -1074352,6 +1073236,89 @@
     "type": "new results",
     "category": "pharmacology and toxicology"
   },
+  {
+    "rel_doi": "10.1101/2020.11.11.375972",
+    "rel_title": "ACE2-Targeting Monoclonal Antibody As A \"Pan\" Coronavirus Blocker In Vitro and In A Mouse Model",
+    "rel_date": "2020-11-12",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.11.375972",
+    "rel_abs": "The evolution of coronaviruses, such as SARS-CoV-2, makes broad-spectrum coronavirus preventional or therapeutical strategies highly sought after. Here we report a human angiotensin-converting enzyme 2 (ACE2)-targeting monoclonal antibody, 3E8, blocked the S1-subunits and pseudo-typed virus constructs from multiple coronaviruses including SARS-CoV-2, SARS-CoV-2 mutant variants (SARS-CoV-2-D614G, B.1.1.7, B.1.351, B.1.617.1 and P.1), SARS-CoV and HCoV-NL63, without markedly affecting the physiological activities of ACE2 or causing severe toxicity in ACE2 \"knock-in\" mice. 3E8 also blocked live SARS-CoV-2 infection in vitro and in a prophylactic mouse model of COVID-19. Cryo-EM and \"alanine walk\" studies revealed the key binding residues on ACE2 interacting with the CDR3 domain of 3E8 heavy chain. Although full evaluation of safety in non-human primates is necessary before clinical development of 3E8, we provided a potentially potent and \"broad-spectrum\" management strategy against all coronaviruses that utilize ACE2 as entry receptors and disclosed an anti-coronavirus epitope on human ACE2.",
+    "rel_num_authors": 17,
+    "rel_authors": [
+      {
+        "author_name": "Yuning Chen",
+        "author_inst": "Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 200126, China."
+      },
+      {
+        "author_name": "Yanan Zhang",
+        "author_inst": "Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei 430"
+      },
+      {
+        "author_name": "Renhong Yan",
+        "author_inst": "Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School "
+      },
+      {
+        "author_name": "Guifeng Wang",
+        "author_inst": "Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 200126, China."
+      },
+      {
+        "author_name": "Yuanyuan Zhang",
+        "author_inst": "Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School "
+      },
+      {
+        "author_name": "Zherui Zhang",
+        "author_inst": "Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei 430"
+      },
+      {
+        "author_name": "Yaning Li",
+        "author_inst": "Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing"
+      },
+      {
+        "author_name": "jianxia ou",
+        "author_inst": "School of Chinese Materia Medica, Nanjing University of Chinese Medicine"
+      },
+      {
+        "author_name": "Wendi Chu",
+        "author_inst": "Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 200126, China."
+      },
+      {
+        "author_name": "Zhijuan Liang",
+        "author_inst": "Shanghai Institute of Materia Medica"
+      },
+      {
+        "author_name": "yongmei wang",
+        "author_inst": "Shanghai Institute of Materia Medica"
+      },
+      {
+        "author_name": "Yili Chen",
+        "author_inst": "Dartsbio Pharmaceuticals, Zhongshan, Guangdong 528400, China"
+      },
+      {
+        "author_name": "Ganjun Chen",
+        "author_inst": "Dartsbio Pharmaceuticals, Zhongshan, Guangdong 528400, China"
+      },
+      {
+        "author_name": "Qi Wang",
+        "author_inst": "Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 200126, China."
+      },
+      {
+        "author_name": "Qiang Zhou",
+        "author_inst": "Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School "
+      },
+      {
+        "author_name": "Bo Zhang",
+        "author_inst": "Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei 430"
+      },
+      {
+        "author_name": "Chunhe Wang",
+        "author_inst": "Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 200126, China."
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2020.11.12.379115",
     "rel_title": "Neuraminidase inhibitors rewire neutrophil function in murine sepsis and COVID-19 patient cells",
@@ -1076121,53 +1075088,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.11.07.20227504",
-    "rel_title": "Challenges of Deep Learning Methods for COVID-19 Detection Using Public Datasets",
-    "rel_date": "2020-11-10",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.07.20227504",
-    "rel_abs": "A large number of studies in the past months have proposed deep learning-based Artificial Intelligence (AI) tools for automated detection of COVID-19 using publicly available datasets of Chest X-rays (CXRs) or CT scans for training and evaluation. Most of these studies report high accuracy when classifying COVID-19 patients from normal or other commonly occurring pneumonia cases. However, these results are often obtained on cross-validation studies without an independent test set coming from a separate dataset and have biases such as the two classes to be predicted come from two completely different datasets. In this work, we investigate potential overfitting and biases in such studies by designing different experimental setups within the available public data constraints and highlight the challenges and limitations of developing deep learning models with such datasets. We propose a deep learning architecture for COVID-19 classification that combines two very popular classification networks, ResNet and Xception, and use it to carry out the experiments to investigate challenges and limitations. The results show that the deep learning models can overestimate their performance due to biases in the experimental design and overfitting to the training dataset. We compare the proposed architecture to state-of-the-art methods utilizing an independent test set for evaluation, where some of the identified bias and overfitting issues are reduced. Although our proposed deep learning architecture gives the best performance with our best possible setup, we highlight the challenges in comparing and interpreting various deep learning algorithms results. While the deep learning-based methods using chest imaging data show promise in being helpful for clinical management and triage of COVID-19 patients, our experiments suggest that a larger, more comprehensive database with less bias is necessary for developing tools applicable in real clinical settings.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Md. Kamrul Hasan",
-        "author_inst": "Khulna University of Engineering & Technology"
-      },
-      {
-        "author_name": "Md. Ashraful Alam",
-        "author_inst": "Khulna University of Engineering & Technology"
-      },
-      {
-        "author_name": "Lavsen Dahal",
-        "author_inst": "Nepal Applied Mathematics and Informatics Institute for Research"
-      },
-      {
-        "author_name": "Md. Toufick E Elahi",
-        "author_inst": "Khulna University of Engineering & Technology"
-      },
-      {
-        "author_name": "Shidhartho Roy",
-        "author_inst": "Khulna University of Engineering & Technology"
-      },
-      {
-        "author_name": "Sifat Redwan Wahid",
-        "author_inst": "Khulna University of Engineering & Technology"
-      },
-      {
-        "author_name": "Robert Marti",
-        "author_inst": "University of Girona"
-      },
-      {
-        "author_name": "Bishesh Khanal",
-        "author_inst": "Nepal Applied Mathematics and Informatics Institute for Research"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "radiology and imaging"
-  },
   {
     "rel_doi": "10.1101/2020.11.06.20227314",
     "rel_title": "Asymptomatic Employee Screening for SARS-CoV-2: Implementation of and Reactions to an Employer-Based Testing Program.",
@@ -1076382,6 +1075302,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.11.07.20227082",
+    "rel_title": "A saliva-based RNA extraction-free workflow integrated with Cas13a for SARS-CoV-2 detection",
+    "rel_date": "2020-11-10",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.07.20227082",
+    "rel_abs": "A major bottleneck in scaling-up COVID-19 testing is the need for sophisticated instruments and well-trained healthcare professionals, which are already overwhelmed due to the pandemic. Moreover, the high-sensitive SARS-CoV-2 diagnostics are contingent on an RNA extraction step, which, in turn, is restricted by constraints in the supply chain. Here, we present CASSPIT (Cas13 Assisted Saliva-based & Smartphone Integrated Testing), which will allow direct use of saliva samples without the need for an extra RNA extraction step for SARS-CoV-2 detection. CASSPIT utilizes CRISPR-Cas13a based SARS-CoV-2 RNA detection, and lateral-flow assay (LFA) readout of the test results. The sample preparation workflow includes an optimized chemical treatment and heat inactivation method, which, when applied to COVID-19 clinical samples, showed a 97% positive agreement with the RNA extraction method. With CASSPIT, LFA based visual limit of detection (LoD) for a given SARS-CoV-2 RNA spiked into the saliva samples was [~]200 copies; image analysis-based quantification further improved the analytical sensitivity to [~]100 copies. Upon validation of clinical sensitivity on RNA extraction-free saliva samples (n=76), a 98% agreement between the lateral-flow readout and RT-qPCR data was found (Ct<35). To enable user-friendly test results with provision for data storage and online consultation, we subsequently integrated lateral-flow strips with a smartphone application. We believe CASSPIT will eliminate our reliance on RT-qPCR by providing comparable sensitivity and will be a step toward establishing nucleic acid-based point-of-care (POC) testing for COVID-19.",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Iqbal Azmi",
+        "author_inst": "Jamia Millia Islamia"
+      },
+      {
+        "author_name": "Md Imama Faizan",
+        "author_inst": "Jamia Millia Islamia"
+      },
+      {
+        "author_name": "Rohit Kumar",
+        "author_inst": "Safdarjung Hospital"
+      },
+      {
+        "author_name": "Siddharth Raj Yadav",
+        "author_inst": "Safdarjung Hospital"
+      },
+      {
+        "author_name": "Nisha Chaudhary",
+        "author_inst": "Jamia Millia Islamia"
+      },
+      {
+        "author_name": "Deepak Kumar Singh",
+        "author_inst": "Jamia Millia Islamia"
+      },
+      {
+        "author_name": "Ruchika Butola",
+        "author_inst": "360 Diagnostic and Health Services"
+      },
+      {
+        "author_name": "Aryan Ganotra",
+        "author_inst": "Delhi Technological University"
+      },
+      {
+        "author_name": "Gopal Datt Joshi",
+        "author_inst": "Noodle Analytics Pvt Ltd"
+      },
+      {
+        "author_name": "Gagan Deep Jhingan",
+        "author_inst": "Vallerian Chem Pvt. Ltd. K37A, Ground Floor, Green Park MAIN, New Delhi 110016, India"
+      },
+      {
+        "author_name": "Jawed Iqbal",
+        "author_inst": "Jamia Millia Islamia"
+      },
+      {
+        "author_name": "Mohan C Joshi",
+        "author_inst": "Jamia Millia Islamia"
+      },
+      {
+        "author_name": "Tanveer Ahmad",
+        "author_inst": "Jamia Millia Islamia"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.11.09.20228171",
     "rel_title": "Risk factors for mortality of residents in nursing homes with Covid-19: a retrospective cohort study",
@@ -1077711,53 +1076698,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.11.06.20222398",
-    "rel_title": "Optimal test-assisted quarantine strategies for COVID-19",
-    "rel_date": "2020-11-09",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.06.20222398",
-    "rel_abs": "ObjectiveTo evaluate the effectiveness of SARS-CoV-2 testing on shortening the duration of quarantines for COVID-19 and to identify the most effective choices of testing schedules.\n\nDesignWe performed extensive simulations to evaluate the performance of quarantine strategies when one or more SARS-CoV-2 tests were administered during the quarantine. Simulations were based on statistical models for the transmissibility and viral loads of SARS-CoV-2 infections and the sensitivities of available testing methods. Sensitivity analyses were performed to evaluate the impact of perturbations in model assumptions on the outcomes of optimal strategies.\n\nResultsWe found that SARS-CoV-2 testing can effectively reduce the length of a quarantine without compromising safety. A single RT-PCR test performed before the end of quarantine can reduce quarantine duration to 10 days. Two tests can reduce the duration to 8 days, and three highly sensitive RT-PCR tests can justify a 6-day quarantine. More strategic testing schedules and longer quarantines are needed if tests are administered with less sensitive RT-PCR tests or antigen tests. Shorter quarantines can be utilized for applications that tolerate a residual post-quarantine transmission risk comparable to a 10-day quarantine.\n\nConclusionsTesting could substantially reduce the length of isolation, reducing the physical and mental stress caused by lengthy quarantines. With increasing capacity and lowered costs of SARS-CoV-2 tests, test-assisted quarantines could be safer and more cost-effective than 14-day quarantines and warrant more widespread use.\n\nRESEARCH IN CONTEXTO_ST_ABSWhat is already known on this topic?C_ST_ABSO_LIRecommendations for quarantining individuals who could have been infected with COVID-19 are based on limited evidence.\nC_LIO_LIDespite recent theoretical and case studies of test-assisted quarantines, there has been no substantive investigation to quantify the safety and efficacy of, nor an exhaustive search for, optimal test-assisted quarantine strategies.\nC_LI\n\nWhat this study addsO_LIOur simulations indicate that the 14-day quarantine approach is overly conservative and can be safely shortened if testing is performed.\nC_LIO_LIOur recommendations include testing schedules that could be immediately adopted and implemented as government and industry policies.\nC_LI\n\nRole of the Funding SourceA major technology company asked that we perform simulations to understand the optimal strategy for managing personnel quarantining before forming cohorts of individuals who would work closely together. The funding entity did not influence the scope or output of the study but requested that we include antigen testing as a component of the quarantining process. Patrick Yu and Peter Matos are employees of Corporate Medical Advisors, and International S.O.S employs Julie McCashin. Other funding sources are research grants and did not influence the investigation.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Bo Peng",
-        "author_inst": "Baylor College of Medicine"
-      },
-      {
-        "author_name": "Wen Zhou",
-        "author_inst": "Baylor College of Medicine"
-      },
-      {
-        "author_name": "Rowland W Pettit",
-        "author_inst": "Baylor College of Medicine"
-      },
-      {
-        "author_name": "Patrick Yu",
-        "author_inst": "Corporate Medical Advisors, Houston, TX"
-      },
-      {
-        "author_name": "Peter Matos",
-        "author_inst": "Corporate Medical Advisors, Houston, TX"
-      },
-      {
-        "author_name": "Alex Greninger",
-        "author_inst": "Laboratory Medicine, University of Washington"
-      },
-      {
-        "author_name": "Julie McCashin",
-        "author_inst": "International SOS, Houston,TX"
-      },
-      {
-        "author_name": "Christopher Ian Amos",
-        "author_inst": "Baylor College of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health systems and quality improvement"
-  },
   {
     "rel_doi": "10.1101/2020.11.05.20225052",
     "rel_title": "Symptomatic SARS-CoV-2 re-infection of a health care worker in a Belgian nosocomial outbreak despite primary neutralizing antibody response.",
@@ -1078004,6 +1076944,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.11.07.20201335",
+    "rel_title": "Socio-economic disparities in social distancing during the COVID-19 pandemic in the United States",
+    "rel_date": "2020-11-09",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.07.20201335",
+    "rel_abs": "ImportanceEliminating disparities in the burden of COVID-19 requires equitable access to control measures across socio-economic groups. Limited research on socio-economic differences in mobility hampers our ability to understand whether inequalities in social distancing are occurring during the SARS-CoV-2 pandemic.\n\nObjectiveTo assess how mobility patterns have varied across the United States during the COVID-19 pandemic, and identify associations with socio-economic factors of populations.\n\nDesign, Setting, and ParticipantsWe used anonymized mobility data from tens of millions of devices to measure the speed and depth of social distancing at the county level between February and May 2020. Using linear mixed models, we assessed the associations between social distancing and socio-economic variables, including the proportion of people below the poverty level, the proportion of Black people, the proportion of essential workers, and the population density.\n\nMain outcomes and ResultsWe find that the speed, depth, and duration of social distancing in the United States is heterogeneous. We particularly show that social distancing is slower and less intense in counties with higher proportions of people below the poverty level and essential workers; and in contrast, that social distancing is intense in counties with higher population densities and larger Black populations.\n\nConclusions and relevanceSocio-economic inequalities appear to be associated with the levels of adoption of social distancing, potentially resulting in wide-ranging differences in the impact of COVID-19 in communities across the United States. This is likely to amplify existing health disparities, and needs to be addressed to ensure the success of ongoing pandemic mitigation efforts.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Romain Garnier",
+        "author_inst": "Georgetown University"
+      },
+      {
+        "author_name": "Jan R Benetka",
+        "author_inst": "Unacast"
+      },
+      {
+        "author_name": "John Kraemer",
+        "author_inst": "Georgetown University"
+      },
+      {
+        "author_name": "Shweta Bansal",
+        "author_inst": "Georgetown University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.11.06.20227405",
     "rel_title": "Gout, rheumatoid arthritis and the risk of death from COVID-19: an analysis of the UK Biobank",
@@ -1079556,41 +1078527,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.11.05.20226555",
-    "rel_title": "Analytical assessment of Beckman Coulter Access anti-SARS-CoV-2 IgG immunoassay",
-    "rel_date": "2020-11-07",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.05.20226555",
-    "rel_abs": "BackgroundThe approach to diagnosing, treating and monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection relies strongly on laboratory resources, with serological testing representing the mainstay for studying the onset, nature and persistence of humoral immune response. This study was aimed at evaluating the analytical performance of the novel Beckman Coulter anti-SARS-CoV-2 IgG chemiluminescent immunoassay.\n\nMethodsThis analytical assessment encompassed the calculation of intra-assay, inter-assay and total imprecision, linearity, limit of blank (LOB), limit of detection (LOD), functional sensitivity, and comparison of anti-SARS-CoV-2 antibodies values obtained on paired serum samples using DiaSorin Liaison SARS-CoV-2 S1/S2 IgG and Roche Elecsys Anti-SARS-CoV-2 total antibodies. Diagnostic performance was also tested against results of molecular testing on nasopharyngeal swabs, collected over the previous 4 months.\n\nResultsIntra-assay, inter-assay and total imprecision of Beckman Coulter anti-SARS-CoV-2 IgG were between 4.3-4.8%, 2.3-3.9% and 4.9-6.2%, respectively. The linearity of the assay was excellent between 0.11-18.8 antibody titers. The LOB, LOD and functional sensitivity were 0.02, 0.02 and 0.05, respectively. The diagnostic accuracy (area under the curve; AUC) of Beckman Coulter anti-SARS-CoV-2 IgG compared to molecular testing was 0.87 (95% CI, 0.84-0.91; p<0.001) using manufacturers cut-off, and increased to 0.90 (95% CI, 0.86-0.94; p<0.001) with antibody titers. The AUC was non-significantly different from that of Roche Elecsys Anti-SARS-CoV-2, but was always higher than that of DiaSorin Liaison SARS-CoV-2 S1/S2 IgG. The correlation of Beckman Coulter Access SARS-CoV-2 IgG was 0.80 (95% CI, 0.75-0.84; p<0.001) with Roche Elecsys Anti-SARS-CoV-2 and 0.72 (95% CI, 0.66-0.77; p<0.001) with DiaSorin Liaison SARS-CoV-2 S1/S2 IgG, respectively.\n\nConclusionsThe results of this analytical evaluation of Beckman Coulter Access anti-SARS-CoV-2 IgG suggests that this fully-automated chemiluminescent immunoassay represents a valuable resource for large and accurate seroprevalence surveys.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Maurizio Ruscio",
-        "author_inst": "Division of Laboratory Medicine, University Hospital Giuliano Isontina (ASU GI), Trieste, Italy"
-      },
-      {
-        "author_name": "Elisa D'Agnolo",
-        "author_inst": "Division of Laboratory Medicine, University Hospital Giuliano Isontina (ASU GI), Trieste, Italy"
-      },
-      {
-        "author_name": "Anna Belgrano",
-        "author_inst": "Division of Laboratory Medicine, University Hospital Giuliano Isontina (ASU GI), Trieste, Italy"
-      },
-      {
-        "author_name": "Mario Plebani",
-        "author_inst": "University of Padova"
-      },
-      {
-        "author_name": "Giuseppe Lippi",
-        "author_inst": "University of Verona"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.11.06.20149690",
     "rel_title": "Healthcare strain and intensive care during the COVID-19 outbreak in the Lombardy region: a retrospective observational study on 43,538 hospitalized patients",
@@ -1079993,6 +1078929,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.11.06.20227017",
+    "rel_title": "Predicting the impact of disruptions in lymphatic filariasis elimination programmes due to the outbreak of coronavirus disease (COVID-19) and possible mitigation strategies",
+    "rel_date": "2020-11-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.06.20227017",
+    "rel_abs": "BackgroundIn view of the current global COVID-19 pandemic, mass drug administration interventions for neglected tropical diseases, including lymphatic filariasis, have been halted. We used mathematical modelling to estimate the impact of delaying or cancelling treatment rounds and explore possible mitigation strategies.\n\nMethodsWe used three established lymphatic filariasis transmission models to simulate infection trends in settings with annual treatment rounds and programme delays in 2020 of 6, 12, 18 or 24 months. We then evaluated the impact of various mitigation strategies upon resuming activities.\n\nResultsThe delay in achieving the elimination goals is on average similar to the number of years the treatment rounds are missed. Enhanced interventions implemented for as little as one year can allow catch-up on the progress lost, and if maintained throughout the programme can lead to acceleration of up to 3 years.\n\nConclusionsIn general, a short delay in the programme does not cause major delay in achieving the goals. Impact is strongest in high endemicity areas. Mitigation strategies such as biannual treatment or increased coverage are key to minimizing the impact of the disruption once the programme resumes; and lead to potential acceleration, should these enhanced strategies be maintained.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Joaquin M Prada",
+        "author_inst": "School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey"
+      },
+      {
+        "author_name": "Wilma A Stolk",
+        "author_inst": "Department of Public Health, Erasmus MC, University Medical Center Rotterdam"
+      },
+      {
+        "author_name": "Emma L Davis",
+        "author_inst": "Big Data Institute, Li Ka Shing Center for Health Information and Discovery, University of Oxford"
+      },
+      {
+        "author_name": "Panayiota Touloupou",
+        "author_inst": "Department of Statistics, University of Warwick"
+      },
+      {
+        "author_name": "Swarnali Sharma",
+        "author_inst": "College of Public Health, University of South Florida"
+      },
+      {
+        "author_name": "Johanna Munoz",
+        "author_inst": "Department of Public Health, Erasmus MC, University Medical Center Rotterdam"
+      },
+      {
+        "author_name": "Rocio M Caja Rivera",
+        "author_inst": "College of Public Health, University of South Florida"
+      },
+      {
+        "author_name": "Lisa J Reimer",
+        "author_inst": "Department of Vector Biology, Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Edwin Michael",
+        "author_inst": "College of Public Health, University of South Florida"
+      },
+      {
+        "author_name": "Sake J de Vlas",
+        "author_inst": "Department of Public Health, Erasmus MC, University Medical Center Rotterdam"
+      },
+      {
+        "author_name": "Deirdre Hollingsworth",
+        "author_inst": "Big Data Institute, Li Ka Shing Center for Health Information and Discovery, University of Oxford"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.11.06.20220087",
     "rel_title": "Seroprevalence of Anti-SARS-CoV-2 Antibodies in a Cohort of New York City Metro Blood Donors using Multiple SARS-CoV-2 Serological Assays: Implications for Controlling the Epidemic and Reopening.",
@@ -1081282,117 +1080277,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.11.05.20225003",
-    "rel_title": "Characteristics of three different chemiluminescence assays for testing for SARS-CoV-2 antibodies",
-    "rel_date": "2020-11-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.05.20225003",
-    "rel_abs": "Several tests based on chemiluminescence immunoassay techniques have become available to test for SARS-CoV-2 antibodies. There is currently insufficient data on serology assay performance beyond 35 days after symptoms onset. We aimed to evaluate SARS-CoV-2 antibody tests on three widely used platforms. A chemiluminescent microparticle immunoassay (CMIA; Abbott Diagnostics, USA), a luminescence immunoassay (LIA; Diasorin, Italy), and an electrochemiluminescence immunoassay (ECLIA; Roche Diagnostics, Switzerland) were investigated. In a multi-group study, sensitivity was assessed in a group of participants with confirmed SARS-CoV-2 (n=145), whereas specificity was determined in two groups of participants without evidence of COVID-19 (i.e. healthy blood donors, n=191, and healthcare workers, n=1002). Receiver operating characteristic (ROC) curves, multilevel likelihood ratios (LR), and positive (PPV) and negative (NPV) predictive values were characterized. Finally, analytical specificity was characterized in samples with evidence of Epstein-Barr virus (EBV) (n=9), cytomegalovirus (CMV) (n=7) and endemic common cold coronavirus infections (n=12) taken prior to the current SARS-CoV-2 pandemic. The diagnostic accuracy was comparable in all three assays (AUC 0.98). Using the manufacturers cut-offs, the sensitivities were 90%, 95% confidence interval,[84,94] (LIA), 93% [88,96] (CMIA), and 96% [91,98] (ECLIA). The specificities were 99.5% [98.9,99.8](CMIA) 99.7% [99.3,99,9] (LIA) and 99.9% [99.5,99.98] (ECLIA). The LR at half of the manufacturers cut-offs were 60 (CMIA), 82 (LIA), and 575 (ECLIA) for positive and 0.043 (CMIA) and 0.035 (LIA, ECLIA) for negative results. ECLIA had higher PPV at low pretest probabilities than CMIA and LIA. No interference with EBV or CMV infection was observed, whereas endemic coronavirus in some cases provided signals in LIA and/or CMIA. Although the diagnostic accuracy of the three investigated assays is comparable, their performance in low-prevalence settings is different. Introducing gray zones at half of the manufacturers cut-offs is suggested, especially for orthogonal testing approaches that use a second assay for confirmation.",
-    "rel_num_authors": 24,
-    "rel_authors": [
-      {
-        "author_name": "Myriam Weber",
-        "author_inst": "Landesspital Liechtenstein, Heiligkreuz, 9490 Vaduz, Liechtenstein"
-      },
-      {
-        "author_name": "Martin Risch",
-        "author_inst": "Central laboratory, Kantonsspital Graubuenden, Loesstrasse 170, 7000 Chur, Switzerland"
-      },
-      {
-        "author_name": "Sarah Thiel",
-        "author_inst": "Landesspital Liechtenstein, Heiligkreuz, 9490 Vaduz, Liechtenstein"
-      },
-      {
-        "author_name": "Kirsten Grossmann",
-        "author_inst": "Labormedizinisches zentrum Dr Risch, Wuhrstrasse 14, 9490 Vaduz, Liechtenstein, Switzerland"
-      },
-      {
-        "author_name": "Susanne Nigg",
-        "author_inst": "Department of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, Rohrschacherstrasse 95 9007 St Gallen, Switzerland"
-      },
-      {
-        "author_name": "Nadia Wohlwend",
-        "author_inst": "Labormedizinisches zentrum Dr Risch, Wuhrstrasse 14, 9490 Vaduz, Liechtenstein, Switzerland"
-      },
-      {
-        "author_name": "Thomas Lung",
-        "author_inst": "Labormedizinisches zentrum Dr Risch, Wuhrstrasse 14, 9490 Vaduz, Liechtenstein, Switzerland"
-      },
-      {
-        "author_name": "Dorothea Hillmann",
-        "author_inst": "Labormedizinisches zentrum Dr Risch, Wuhrstrasse 14, 9490 Vaduz, Liechtenstein,"
-      },
-      {
-        "author_name": "Michael Ritzler",
-        "author_inst": "Labormedizinisches zentrum Dr Risch, Wuhrstrasse 14, 9490 Vaduz, Liechtenstein"
-      },
-      {
-        "author_name": "Francesca Ferrara",
-        "author_inst": "Labormedizinisches zentrum Dr Risch, Wuhrstrasse 14, 9490 Vaduz, Liechtenstein"
-      },
-      {
-        "author_name": "Susanna Bigler",
-        "author_inst": "Labormedizinisches zentrum Dr Risch, Waldeggstrasse 37, 3097 Liebefeld, Switzerland"
-      },
-      {
-        "author_name": "Konrad Egli",
-        "author_inst": "Labormedizinisches zentrum Dr Risch, Waldeggstrasse 37, 3097 Liebefeld, Switzerland"
-      },
-      {
-        "author_name": "Thomas Bodmer",
-        "author_inst": "Labormedizinisches zentrum Dr Risch, Waldeggstrasse 37, 3097 Liebefeld, Switzerland"
-      },
-      {
-        "author_name": "Mauro Imperiali",
-        "author_inst": "Centro medicina di laboratorio Dr Risch, Via Arbostra 2, 6963 Pregassona, Switzerland"
-      },
-      {
-        "author_name": "Yacir Salimi",
-        "author_inst": "Clm Dr Risch arc lemanique SA, Chemin de l'Esparcette 10, 1023 Crissier, Switzerland"
-      },
-      {
-        "author_name": "Felix Fleisch",
-        "author_inst": "Division of Infectious Diseases, Kantonsspital Graubuenden, Loesstrasse 170, 7000 Chur, Switzerland"
-      },
-      {
-        "author_name": "Alexia Cusini",
-        "author_inst": "Division of Infectious Diseases, Kantonsspital Graubuenden, Loesstrasse 170, 7000 Chur, Switzerland"
-      },
-      {
-        "author_name": "Sonja Heer",
-        "author_inst": "Blutspendedienst Graubuenden, Loesstrasse 170, 7000 Chur, Switzerland"
-      },
-      {
-        "author_name": "Harald Renz",
-        "author_inst": "Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Philipps University Marburg, University Hospital Giessen and Marburg, Baldingerst"
-      },
-      {
-        "author_name": "Matthias Paprotny",
-        "author_inst": "Landesspital Liechtenstein, Heiligkreuz, 9490 Vaduz, Liechtenstein"
-      },
-      {
-        "author_name": "Philipp Kohler",
-        "author_inst": "Department of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, Rohrschacherstrasse 95 9007 St Gallen, Switzerland"
-      },
-      {
-        "author_name": "Pietro Vernazza",
-        "author_inst": "Department of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, Rohrschacherstrasse 95 9007 St Gallen, Switzerland"
-      },
-      {
-        "author_name": "Lorenz Risch",
-        "author_inst": "Labormedizinisches zentrum Dr Risch, Wuhrstrasse 14, 9490 Vaduz, Liechtenstein"
-      },
-      {
-        "author_name": "Christian R. Kahlert",
-        "author_inst": "Department of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, Rohrschacherstrasse 95 9007 St Gallen, Switzerland"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.11.05.20223289",
     "rel_title": "Longitudinal proteomic profiling of high-risk patients with COVID-19 reveals markers of severity and predictors of fatal disease",
@@ -1081911,6 +1080795,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.11.04.20226092",
+    "rel_title": "Nowcasting and forecasting provincial-level SARS-CoV-2 case positivity using google search data in South Africa",
+    "rel_date": "2020-11-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.04.20226092",
+    "rel_abs": "Data from non-traditional data sources, such as social media, search engines, and remote sensing, have previously demonstrated utility for disease surveillance. Few studies, however, have focused on countries in Africa, particularly during the SARS-CoV-2 pandemic. In this study, we use searches of COVID-19 symptoms, questions, and at-home remedies submitted to Google to model COVID-19 in South Africa, and assess how well the Google search data forecast short-term COVID-19 trends. Our findings suggest that information seeking trends on COVID-19 could guide models for anticipating COVID-19 trends and coordinating appropriate response measures.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Elaine O. Nsoesie",
+        "author_inst": "Boston University School of Public Health"
+      },
+      {
+        "author_name": "Karla Therese L. Sy",
+        "author_inst": "Boston University School of Public Health"
+      },
+      {
+        "author_name": "Olubusola Oladeji",
+        "author_inst": "Boston University School of Public Health"
+      },
+      {
+        "author_name": "Raesetje Sefala",
+        "author_inst": "University of the Witwatersrand"
+      },
+      {
+        "author_name": "Brooke E. Nichols",
+        "author_inst": "Boston University School of Public Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.11.05.20225300",
     "rel_title": "Children hospitalized for COVID-19 during first winter of the pandemic in Buenos Aires, Argentina",
@@ -1083384,77 +1082303,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2020.11.03.367375",
-    "rel_title": "Immunodominant T-cell epitopes from the SARS-CoV-2 spike antigen reveal robust pre-existing T-cell immunity in unexposed individuals",
-    "rel_date": "2020-11-05",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.03.367375",
-    "rel_abs": "The COVID-19 pandemic has revealed a range of disease phenotypes in infected patients with asymptomatic, mild or severe clinical outcomes, but the mechanisms that determine such variable outcomes remain unresolved. In this study, we identified immunodominant CD8 T-cell epitopes in the RBD and the non-RBD domain of the spike antigen using a novel TCR-binding algorithm. A selected pool of 11 predicted epitopes induced robust T-cell activation in unexposed donors demonstrating pre-existing CD4 and CD8 T-cell immunity to SARS-CoV-2 antigen. The T-cell reactivity to the predicted epitopes was higher than the Spike-S1 and S2 peptide pools containing 157 and 158 peptides both in unexposed donors and in convalescent patients suggesting that strong T-cell epitopes are likely to be missed when larger peptide pools are used in assays. A key finding of our study is that pre-existing T-cell immunity to SARS-CoV-2 is contributed by TCRs that recognize common viral antigens such as Influenza and CMV, even though the viral epitopes lack sequence identity to the SARS-CoV-2 epitopes. This finding is in contrast to multiple published studies in which pre-existing T-cell immunity is suggested to arise from shared epitopes between SARS-CoV-2 and other common cold-causing coronaviruses. Whether the presence of pre-existing T-cell immunity provides protection against COVID-19 or contributes to severe disease phenotype remains to be determined in a larger cohort. However, our findings raise the expectation that a significant majority of the global population is likely to have SARS-CoV-2 reactive T-cells because of prior exposure to flu and CMV viruses, in addition to common cold-causing coronaviruses.",
-    "rel_num_authors": 14,
-    "rel_authors": [
-      {
-        "author_name": "Swapnil Mahajan",
-        "author_inst": "MedGenome Inc."
-      },
-      {
-        "author_name": "Keshav Bhojak",
-        "author_inst": "MedGenome Inc."
-      },
-      {
-        "author_name": "Vasumathi Kode",
-        "author_inst": "MedGenome Inc."
-      },
-      {
-        "author_name": "Coral M Magdalene",
-        "author_inst": "MedGenome Inc."
-      },
-      {
-        "author_name": "Malini Manoharan",
-        "author_inst": "MedGenome Inc."
-      },
-      {
-        "author_name": "Kayla Lee",
-        "author_inst": "MedGenome Inc."
-      },
-      {
-        "author_name": "Athulya Ramesh",
-        "author_inst": "MedGenome Inc."
-      },
-      {
-        "author_name": "Sudheendra H V",
-        "author_inst": "MedGenome Inc."
-      },
-      {
-        "author_name": "Ankita Srivastava",
-        "author_inst": "MedGenome Inc."
-      },
-      {
-        "author_name": "Rekha Sathian",
-        "author_inst": "MedGenome Inc."
-      },
-      {
-        "author_name": "Prasanna Kumar",
-        "author_inst": "MedGenome Inc."
-      },
-      {
-        "author_name": "Tahira Khan",
-        "author_inst": "MedGenome Inc."
-      },
-      {
-        "author_name": "Papia Chakraborty",
-        "author_inst": "MedGenome Inc."
-      },
-      {
-        "author_name": "Amitabha Chaudhuri",
-        "author_inst": "MedGenome Inc."
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2020.11.04.364315",
     "rel_title": "SARS-CoV-2 Infects Human Engineered Heart Tissues and Models COVID-19 Myocarditis",
@@ -1083796,6 +1082644,25 @@
     "type": "new results",
     "category": "bioinformatics"
   },
+  {
+    "rel_doi": "10.1101/2020.11.03.20225425",
+    "rel_title": "Per capita COVID-19 Case Rates are Lower in U.S. Counties Voting more Heavily Democratic in the 2016 Presidential Election, except not in States with a Republican Governor and Legislature",
+    "rel_date": "2020-11-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.03.20225425",
+    "rel_abs": "In our recent paper Why do per capita COVID-19 Case Rates Differ Between U.S. States? we established that U.S. states with a Democratic governor and a Democratic legislature have lower COVID-19 per capita case rates than states with a Republican governor and a Republican legislature, and case rates of states with a mixed government fall between the two. This difference remained after accounting for differences between states in several demographic and socio-economic variables. In a recent working paper The Changing Political Geographies of COVID-19 in the U.S. it was found that that early in the pandemic U.S. counties at higher levels of percentage Democratic vote in the 2016 presidential election had higher weekly per capita COVID-19 rates, but that the situation was in the opposite direction by August 2020. We show here that counties with a higher percentage of Democratic vote in the 2016 presidential election have a lower mean cumulative per capita rate of COVID-19 cases and of COVID-19 deaths, adjusted for county demographic and socio-economic characteristics, but only for counties in states that currently have a Democratic governor and both chambers of the legislature Democratic or in states that have a mixed government, but not for states that currently have a Republican governor and both chambers in the legislature Republican. One possible contributor to this difference is that some state Republican governments have restricted local action to fight the spread of COVID-19.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Lloyd Chambless",
+        "author_inst": "Retired"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.11.03.20225326",
     "rel_title": "Coronavirus Disease 2019 (COVID-19) Candidate Chest CT Features: A Systematic Review of Extracted Imaging Features from 7571 Individuals",
@@ -1085845,41 +1084712,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.11.04.367896",
-    "rel_title": "Risk perceptions and preventive practices of COVID-19 among healthcare professionals in public hospitals in Ethiopia",
-    "rel_date": "2020-11-04",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.04.367896",
-    "rel_abs": "Healthcare professionals are at higher risk of contracting the novel coronavirus due to their work exposure in the healthcare settings. Practicing appropriate preventive measures to control COVID-19 infection is one of the most important interventions that healthcare workers are expected to use. The aim of this study was to assess the level of risk perception and practices of preventive measures of COVID-19 among health workers in Addis Ababa, Ethiopia. A hospital-based cross-sectional study was conducted from 9th to 26th June 2020 among healthcare professionals working at six public hospitals in Addis Ababa. Data were collected using a self-administered structured questionnaire. Frequency, percentage, and mean were used to summarize the data. A binary logistic regression analyses were performed to identify factors associated with risk perception about COVID-19. A total of 1,134 participants were surveyed. Wearing facemask (93%), hand washing for at least 20 seconds (93%), covering mouth and nose while coughing or sneezing (91%), and avoiding touching eyes, nose, and mouth (91%) were the commonly self-reported preventive practices. About 88% perceived that they were worried about the risk of becoming infected with coronavirus, and majority (91%) worried about the risk of infection to their family. The mean score of overall fear and worry of COVID-19 was 2.37 on a scale of 1 to 3. Respondents who ever provided clinical care to COVID-19 patients were more likely to report fear and worry (adjusted OR=1.34, 95% CI:1.02-1.91), however those who ever participated in Ebola or SARS outbreaks were less likely to report fear and worry due to COVID-19 crisis (adjusted OR=0.66, 95% CI:0.48-0.90). This study has revealed widespread practices of preventive measures and the highest perceived risk of COVID-19 among healthcare workers. Therefore, an effective risk communication intervention should be implemented to ensure the maintenance of appropriate practices during the current COVID-19 pandemic.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Wakgari Deressa",
-        "author_inst": "Addis Ababa University"
-      },
-      {
-        "author_name": "Alemayehu Worku",
-        "author_inst": "Addis Ababa University School of Public Health"
-      },
-      {
-        "author_name": "Workeabeba Abebe",
-        "author_inst": "Addis Ababa University Faculty of Medicine: Addis Ababa University School of Medicine"
-      },
-      {
-        "author_name": "Muluken Gizaw",
-        "author_inst": "Addis Ababa University School of Public Health"
-      },
-      {
-        "author_name": "Wondwossen Amogne",
-        "author_inst": "Addis Ababa University School of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "scientific communication and education"
-  },
   {
     "rel_doi": "10.1101/2020.10.30.20223461",
     "rel_title": "SARS-CoV-2 Infection Hospitalization Rate and Infection Fatality Rate among the Non-Congregant Population in Connecticut",
@@ -1086146,6 +1084978,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "sports medicine"
   },
+  {
+    "rel_doi": "10.1101/2020.11.01.20217943",
+    "rel_title": "CovidSIMVL - Agent-Based Modeling of Localized Transmission within a Heterogeneous Array of Locations: Motivation, Configuration and Calibration",
+    "rel_date": "2020-11-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.01.20217943",
+    "rel_abs": "CovidSIMVL is an agent-based infectious disease modeling tool that is designed specifically to simulate localized spread of infectious disease. It is intended to support tactical decision-making around localized/staged re-institution of pre-pandemic levels and patterns of social/economic/health service delivery activity, following an initial stage of pan-societal closures of social/economic institutions and broad-based reductions in services.\n\nBy design, CovidSIMVL supports the generation of dynamic models that reflect heterogeneity within and between a network of interacting localized contexts. This heterogeneity is embodied in a hierarchically organized set of rules. Primary rules reflect the pathophysiology of transmission. Secondary rules (\"HazardRadius\" and \"Mingle Factor\" in CovidSIMVL) relate transmission to proximity and movement within physically demarcated and relatively contained spaces (\"Universes\"). Tertiary rules (\"Schedules\") relate probabilities of transmission to movement of people between a network of localized contexts (a CovidSIMVL \"Multiverse\").\n\nThis report focuses mainly on calibration of secondary rules. To calibrate the HazardRadius and MingleFactor parameters, growth curves were generated with CovidSIMVL by setting different configurations of values on those two proximal determinants of viral transmission. These were compared to the characteristic shapes of curves generated by equation-based compartmental models (e.g., SEIR models) that fit different real-world datasets embodying different reproduction numbers (R0).\n\nBy operating with parameter values in CovidSIMVL that generate \"real-world\" growth curves, the tool can be used to produce plausible simulations of localized chains of transmission. These include transmission among different groups of persons (e.g., staff, patients) who are co-located within a single setting such as a long-term care facility. The Multiverse version of CovidSIMVL can be used to simulate localized cross-over transmission among arrays consisting of both unaffected and impacted contexts and associated sub-populations, via agents who interact within and across arrays of contexts such as schools, multigenerational families, recreational facilities, places of work, emergency shelters for homeless persons, or other settings in which people are in close physical proximity.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Kenneth Andrew Moselle",
+        "author_inst": "Island Health (Vancouver Island Health Authority)"
+      },
+      {
+        "author_name": "Ernie Chang",
+        "author_inst": "Contractor"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.11.01.20220475",
     "rel_title": "Hospital based contact tracing of COVID-19 patients and health care workers and risk stratification of exposed health care workers during the COVID-19 Pandemic in Eastern India",
@@ -1087335,53 +1086190,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
-  {
-    "rel_doi": "10.1101/2020.11.02.20224550",
-    "rel_title": "Understanding COVID-19 testing pathways in English care homes to identify the role of point-of-care testing: an interview-based process mapping study",
-    "rel_date": "2020-11-04",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.02.20224550",
-    "rel_abs": "IntroductionCare home residents are at high risk of dying from COVID-19. Regular testing producing rapid and reliable results is important in this population because infections spread quickly and presentations are often atypical or asymptomatic. This study evaluated current testing pathways in care homes to explore the role of point-of-care tests (POCTs).\n\nMethodsTen staff from eight care homes, purposively sampled to reflect care organisational attributes that influence outbreak severity, underwent a semi-structured remote videoconference interview. Transcripts were analysed using process mapping tools and framework analysis focussing on perceptions about, gaps within, and needs arising from, current pathways.\n\nResultsFour main steps were identified in testing: infection prevention, preparatory steps, swabbing procedure, and management of residents. Infection prevention was particularly challenging for mobile residents with cognitive impairment. Swabbing and preparatory steps were resource-intensive, requiring additional staff resource. Swabbing required flexibility and staff who were familiar to the resident. Frequent approaches to residents were needed to ensure they would participate at a suitable time. After-test management varied between sites. Several homes reported deviating from government guidance to take more cautious approaches, which they perceived to be more robust.\n\nConclusionSwab-based testing is organisationally complex and resource-intensive in care homes. It needs to be flexible to meet the needs of residents and provide care homes with rapid information to support care decisions. POCT could help address gaps but the complexity of the setting means that each technology must be evaluated in context before widespread adoption in care homes.\n\nKey-pointsO_LITesting for COVID-19 in care homes is complex and requires reconfiguration of staffing and environment.\nC_LIO_LIIsolation and testing procedures are challenged when providing person-centred care to people with dementia.\nC_LIO_LIPoint-of-care testing results could give care homes greater flexibility to test in person-centred ways.\nC_LIO_LIThere was evidence that care home staff interpret testing guidance, rather than follow it verbatim.\nC_LIO_LIEach POCT must be evaluated in the context of care homes to understand its effect on care home processes.\nC_LI",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Massimo Micocci",
-        "author_inst": "Imperial College London; NIHR London In Vitro Diagnostics Co-operative, London, UK"
-      },
-      {
-        "author_name": "Adam Gordon",
-        "author_inst": "Division of Medical Sciences and Graduate Entry Medicine, University of Nottingham, UK; NIHR Applied Research Collaboration East Midlands (ARC-EM), Nottingham U"
-      },
-      {
-        "author_name": "Joy Allen",
-        "author_inst": "NIHR Newcastle In Vitro Diagnostics Co-operative, Newcastle University, UK"
-      },
-      {
-        "author_name": "Timothy Hicks",
-        "author_inst": "NIHR Newcastle In Vitro Diagnostics Co-operative, Newcastle upon Tyne Hospitals NHS Foundation Trust, UK"
-      },
-      {
-        "author_name": "Patrick Kierkegaard",
-        "author_inst": "Imperial College London, NIHR London In Vitro Diagnostics Co-operative, London, UK"
-      },
-      {
-        "author_name": "Anna McLister",
-        "author_inst": "Imperial College London, NIHR London In Vitro Diagnostics Co-operative, London, UK"
-      },
-      {
-        "author_name": "Simon Walne",
-        "author_inst": "Imperial College London, NIHR London In Vitro Diagnostics Co-operative, London, UK"
-      },
-      {
-        "author_name": "Peter Buckle",
-        "author_inst": "Imperial College London, NIHR London In Vitro Diagnostics Co-operative, London, UK"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health systems and quality improvement"
-  },
   {
     "rel_doi": "10.1101/2020.11.01.20194233",
     "rel_title": "Cohorting of Non-Critically Ill COVID-19 Patients: A Multicenter Survey Study (COVID-COHORT)",
@@ -1087648,6 +1086456,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.10.31.20223776",
+    "rel_title": "Cell phone mobility data reveals heterogeneity in stay-at-home behavior during the SARS-CoV-2 pandemic",
+    "rel_date": "2020-11-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.31.20223776",
+    "rel_abs": "As COVID-19 cases resurge in the United States, understanding the complex interplay between human behavior, disease transmission, and non-pharmaceutical interventions during the pandemic could provide valuable insights to focus future public health efforts. Cell-phone mobility data offers a modern measurement instrument to investigate human mobility and behavior at an unprecedented scale. We investigate mobility data collected, aggregated, and anonymized by SafeGraph Inc. which measures how populations at the census-block-group geographic scale stayed at home in California, Georgia, Texas, and Washington since the beginning of the pandemic. Using manifold learning techniques, we find patterns of mobility behavior that align with stay-at-home orders, correlate with socioeconomic factors, cluster geographically, and reveal sub-populations that likely migrated out of urban areas. The analysis and approach provides policy makers a framework for interpreting mobility data and behavior to inform actions aimed at curbing the spread of COVID-19.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Roman Levin",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Dennis L Chao",
+        "author_inst": "Institute for Disease Modeling, Bill and Melinda Gates Foundation"
+      },
+      {
+        "author_name": "Edward A. Wenger",
+        "author_inst": "Institute for Disease Modeling, Bill and Melinda Gates Foundation"
+      },
+      {
+        "author_name": "Joshua L Proctor",
+        "author_inst": "Institute for Disease Modeling, Bill and Melinda Gates Foundation"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.11.02.20222778",
     "rel_title": "SARS-CoV-2 responsive T cell numbers are associated with protection from COVID-19: A prospective cohort study in keyworkers",
@@ -1088953,65 +1087792,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.11.02.20224667",
-    "rel_title": "The impact of lockdown during the COVID-19 pandemic on mental and social health of children and adolescents",
-    "rel_date": "2020-11-04",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.02.20224667",
-    "rel_abs": "ImportanceIt is unknown how a lockdown during the COVID-19 pandemic impacts childrens and adolescents mental and social health.\n\nObjectiveTo compare mental and social health of children and adolescents during the COVID-19 lockdown versus before, identify associated factors, describe the change in atmosphere at home and qualitatively assess the impact of COVID-19 regulations on daily life.\n\nDesignCross-sectional study comparing two Dutch representative samples of children and adolescents (8-18 years); before COVID-19 (Dec2017-July2018) and during the COVID-19 lockdown (April/May 2020).\n\nSettingPopulation-based\n\nParticipantsChildren and adolescents aged 8-18 years (M=13.4, 47.4% male), representative of the Dutch population on key demographics.\n\nExposure(s)COVID-19 pandemic lockdown\n\nMain Outcome(s) and Measure(s)Patient-Reported Outcomes Measurement Information System (PROMIS(R)) domains: Global Health, Peer Relationships, Anxiety, Depressive Symptoms, Anger and Sleep-Related Impairment. Single item on atmosphere at home and open question regarding the impact of the regulations on the child/adolescents daily life\n\nResultsChildren and adolescents reported significantly worse PROMIS T-scores on all domains (absolute mean difference range, 2.1-7.1; absolute 95% CI range, 1.3-7.9) during the COVID-19 lockdown as compared to before COVID-19. More children reported severe Anxiety (during 16.7% vs. before 8.6%; relative risk 1.95; 95% CI 1.55-2.46) and Sleep-Related Impairment (during 11.5% vs. before 6.1%; relative risk 1.89; 95% CI 1.29-2.78). Fewer children reported poor Global Health (during 1.7 vs. before 4.6%; relative risk 0.36; 95% CI 0.20-0.65). More mental and social health complaints during the COVID-19 lockdown were found in children and adolescents growing up in a single-parent family, having [&ge;]three children in the family, a negative change in work situation of parents due to COVID-19 regulations, and having a relative/friend infected with COVID-19. A small effect was found on atmosphere at home during the lockdown compared to before (mean difference, -3.1; 95% CI, -4.1 --2.1). A large majority (>90%) reported a negative impact of the COVID-19 regulations on their daily life.\n\nConclusions and RelevanceThis study showed that governmental regulations regarding lockdown pose a serious mental and social health threat on children and adolescents that should be brought to the forefront of political decision making and mental health care policy, intervention and prevention.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSWhat is the impact of lockdown during the COVID-19 pandemic on mental and social health in children and adolescents compared to before COVID-19?\n\nFindingsThis population-based study shows that during the COVID-19 lockdown children and adolescents report lower mental and social health, especially on anxiety and depressive symptoms.\n\nMeaningIn proposing new COVID regulations (e.g., closing schools) governments should be mindful of the negative impact of a lockdown on mental and social health of children and adolescents.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Michiel A.J. Luijten",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Maud M. van Muilekom",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Lorynn Teela",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Hedy A. van Oers",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Caroline B. Terwee",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Josjan Zijlmans",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Leonie Klaufus",
-        "author_inst": "Public Health Service Amsterdam"
-      },
-      {
-        "author_name": "Arne Popma",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Kim J. Oostrom",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Tinca J.C. Polderman",
-        "author_inst": "Amsterdam UMC"
-      },
-      {
-        "author_name": "Lotte Haverman",
-        "author_inst": "Amsterdam UMC"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "pediatrics"
-  },
   {
     "rel_doi": "10.1101/2020.11.02.20221622",
     "rel_title": "Reproducibility and sensitivity of 36 methods to quantify the SARS-CoV-2 genetic signal in raw wastewater: findings from an interlaboratory methods evaluation in the U.S.",
@@ -1089366,6 +1088146,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.10.30.20221440",
+    "rel_title": "The relationship between anxiety, health, and potential stressors among adults in the United States during the COVID-19 pandemic",
+    "rel_date": "2020-11-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.30.20221440",
+    "rel_abs": "ObjectiveTo estimate the prevalence of anxiety symptoms and the association between moderate or severe anxiety symptoms and health and potential stressors among adults in the U.S. during the COVID-19 pandemic\n\nMethodsThis analysis includes data from 5,250 adults in the Communities, Households and SARS/CoV-2 Epidemiology (CHASING) COVID Cohort Study surveyed in April 2020. Poisson models were used to estimate the association between moderate or severe anxiety symptoms and health and potential stressors among U.S. adults during the COVID-19 pandemic.\n\nResultsGreater than one-third (35%) of participants reported moderate or severe anxiety symptoms. Having lost income due to COVID-19 (adjusted prevalence ratio [aPR] 1.27 (95% CI 1.16, 1.30), having recent COVID-like symptoms (aPR 1.17 (95% CI 1.05, 1,31), and having been previously diagnosed with depression (aPR 1.49, (95% CI 1.35, 1.64) were positively associated with anxiety symptoms.\n\nConclusionsAnxiety symptoms were common among adults in the U.S. during the COVID-19 pandemic. Strategies to screen and treat individuals at increased risk of anxiety, such as individuals experiencing financial hardship and individuals with prior diagnoses of depression, should be developed and implemented.",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Angela Parcesepe",
+        "author_inst": "University of North Carolina at Chapel Hill"
+      },
+      {
+        "author_name": "McKaylee Robertson",
+        "author_inst": "CUNY ISPH"
+      },
+      {
+        "author_name": "Amanda Berry",
+        "author_inst": "CUNY ISPH"
+      },
+      {
+        "author_name": "Andrew R Maroko",
+        "author_inst": "CUNY ISPH; CUNY Graduate School of Public Health and Health Policy, Department of Environmental, Occupational, and Geospatial Health Sciences"
+      },
+      {
+        "author_name": "Rebecca Zimba",
+        "author_inst": "CUNY ISPH"
+      },
+      {
+        "author_name": "Christian Grov",
+        "author_inst": "CUNY ISPH; Department of Community Health and Social Services, Graduate School of Public Health and Health Policy, City University of New York"
+      },
+      {
+        "author_name": "Drew Westmoreland",
+        "author_inst": "CUNY ISPH"
+      },
+      {
+        "author_name": "Sarah Kulkarni",
+        "author_inst": "CUNY ISPH"
+      },
+      {
+        "author_name": "Madhura Rane",
+        "author_inst": "CUNY ISPH"
+      },
+      {
+        "author_name": "William Salgado-You",
+        "author_inst": "CUNY ISPH"
+      },
+      {
+        "author_name": "Chloe Mirzayi",
+        "author_inst": "CUNY ISPH; CUNY Graduate School of Public Health and Health Policy, Department of Epidemiology and Biostatistics"
+      },
+      {
+        "author_name": "Levi Waldron",
+        "author_inst": "CUNY ISPH; CUNY Graduate School of Public Health and Health Policy, Department of Epidemiology"
+      },
+      {
+        "author_name": "Denis Nash",
+        "author_inst": "CUNY ISPH; CUNY Graduate School of Public Health and Health Policy; Department of Epidemiology and Biostatistics"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.11.03.20225466",
     "rel_title": "Delirium and Post-Discharge Neuropsychological Outcomes in Critically Ill Patients with COVID-19: an Institutional Case Series",
@@ -1090575,41 +1089422,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.10.28.20221630",
-    "rel_title": "Phase II Clinical trial for Evaluation of BCG as potential therapy for COVID-19",
-    "rel_date": "2020-11-03",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.28.20221630",
-    "rel_abs": "Bacillus Calmette-Guerin (BCG) is widely used in national vaccination programs worldwide. It is accepted that BCG alleviates both pathogen and allergy induced respiratory diseases that could also include Covid-19. To investigate this possibility, we randomly assigned 60 Covid-19 patients, after admission to the hospital with pneumonia and requirement for oxygen therapy in a 1:1 ratio to receive either a single adult dose of intradermal BCG or normal saline with concomitant standard of care (SoC) medications. Primary endpoints were favorable prognosis of Covid-19 as deduced from resolution of pneumonia, viremia and secondary outcome were enumeration of ICU admissions, duration thereof and mortalities.\n\nResultsBoth primary and secondary endpoints were significantly improved in the BCG+SoC group. This could be seen from reduction in oxygen requirement due to Covid-19 associated pneumonia decreasing from day 3-4, improved radiological resolution from day 7-15. There were a total of 6 (10%) adverse events in the study of which 2 deaths and 4 ICU admissions were in SoC group (1 ICU admission culminated in death of the subject) and in contrast only 1 ICU admission in the BCG+SoC group. While there was an increase in Covid-19 specific IgG levels in the BCG+SoC group, there was no evidence of BCG induced cytokine storm in this group. Four patients showed localized inflammatory response at the injection site in the BCG+SoC group.\n\nConclusionsBCG+SoC administration resulted in a significantly higher percentage of patients with favorable outcomes than did SoC. A third of the patients were naive for childhood BCG vaccination. This mimicked elderly patients in countries with no universal vaccination policy for BCG. No BCG related adversity was seen in this group. The study shows that BCG is a safe, cost-effective treatment that can be introduced as a standard of care in patients with moderate Covid-19 that can reduce requirement of oxygen supplemented beds and disease burden in low resource countries, with additional long-term benefits of reducing risk for tuberculosis.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Usha Padmanabhan",
-        "author_inst": "Haffkine Institute for Training, Research & Testing"
-      },
-      {
-        "author_name": "Sanjay Mukherjee",
-        "author_inst": "Medical Education & drugs Department, Govt. of Maharashtra"
-      },
-      {
-        "author_name": "Rohidas Borse",
-        "author_inst": "BJ Medical College & Sassoon general hospital"
-      },
-      {
-        "author_name": "Samir Joshi",
-        "author_inst": "BJ Medical College & Sassoon General Hospital"
-      },
-      {
-        "author_name": "Rajesh Deshmukh",
-        "author_inst": "Haffkine Institute for Training, Research & Testing"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.10.28.20221879",
     "rel_title": "Surveillance study of acute neurological manifestations among 439 Egyptian patients with COVID-19 in Assiut and Aswan university hospitals",
@@ -1090844,6 +1089656,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "gastroenterology"
   },
+  {
+    "rel_doi": "10.1101/2020.10.29.20215996",
+    "rel_title": "''Necessity is the mother of invention'': Specialist palliative care service innovation and practice change in response to COVID-19. Results from a multi-national survey (CovPall)",
+    "rel_date": "2020-11-03",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.29.20215996",
+    "rel_abs": "BackgroundSpecialist palliative care services have a key role in a whole system response to COVID-19. There is a need to understand service response to share good practice and prepare for future care.\n\nAimTo map and understand specialist palliative care services innovations and practice changes in response to COVID-19 (CovPall).\n\nDesignOnline survey of specialist palliative care providers, disseminated via key stakeholders. Data collected on service characteristics, innovations and changes in response to COVID-19. Statistical analysis included frequencies, proportions and means, and free-text comments were analysed using a qualitative framework approach.\n\nSetting/participantsInpatient palliative care units, home nursing services, hospital and home palliative care teams from any country.\n\nResults458 respondents: 277 UK, 85 Europe (except UK), 95 World (except UK and Europe), 1 missing country. 54.8% provided care across 2+ settings; 47.4% hospital palliative care teams, 57% in-patient palliative care units, and 57% home palliative care teams. The crisis context meant services implemented rapid changes. Changes involved streamlining, extending and increasing outreach of services, using technology to facilitate communication, and implementing staff wellbeing innovations. Barriers included; fear and anxiety, duplication of effort, information overload, funding, and IT infrastructure issues. Enablers included; collaborative teamwork, pooling of staffing resources, staff flexibility, a pre-existing IT infrastructure and strong leadership.\n\nConclusionsSpecialist palliative care services have been flexible, highly adaptive and have adopted a  frugal innovation model in response to COVID-19. In addition to financial support, greater collaboration is essential to minimise duplication of effort and optimise resource use.\n\nISRCTN16561225https://doi.org/10.1186/ISRCTN16561225\n\nKey StatementsO_ST_ABSWhat is already known about the topic?C_ST_ABSO_LISpecialist palliative care is part of a whole healthcare system response to COVID-19.\nC_LIO_LIServices need to make practice changes in response to the global pandemic.\nC_LI\n\nWhat this paper addsO_LISpecialist palliative care services responded rapidly to COVID-19 in both planning for change and then adapting to needs and requirements.\nC_LIO_LIServices often relied on  improvisation,  quick fixes and  making do when responding to the COVID-19 crisis.\nC_LI\n\nImplications for practice, theory or policyO_LIIn addition to financial support, greater collaboration is essential to build organisational resilience and drive forward innovation, by minimising duplication of effort and optimising resource use.\nC_LIO_LIThe effectiveness and sustainability of any changes made during the crisis needs further evaluation.\nC_LI",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Lesley Dunleavy",
+        "author_inst": "Lancaster University"
+      },
+      {
+        "author_name": "Nancy Preston",
+        "author_inst": "Lancaster University"
+      },
+      {
+        "author_name": "Sabrina Bajwah",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Andy Bradshaw",
+        "author_inst": "University of Hull"
+      },
+      {
+        "author_name": "Rachel Cripps",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Lorna K Fraser",
+        "author_inst": "University of York"
+      },
+      {
+        "author_name": "Matthew Maddocks",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Mevhibe Hocaoglu",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Fliss EM Murtagh",
+        "author_inst": "University of Hull"
+      },
+      {
+        "author_name": "Adejoke Oluyase",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Katherine E Sleeman",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Irene Higginson",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Catherine Walshe",
+        "author_inst": "Lancaster University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "palliative medicine"
+  },
   {
     "rel_doi": "10.1101/2020.10.29.20222430",
     "rel_title": "The prevalence of common mental disorders among health care professionals during the COVID-19 pandemic at a tertiary Hospital in East Africa",
@@ -1092501,20 +1091380,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.10.29.20222513",
-    "rel_title": "Estimation of the severeness rate, death rate, household attack rate and the total number of COVID-19 cases based on 16 115 Polish surveillance records",
-    "rel_date": "2020-11-03",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.29.20222513",
-    "rel_abs": "BackgroundEstimating the actual number of COVID-19 infections is crucial for steering through the COVID-19 pandemic crisis. It is, however, notoriously difficult, as many cases have no or only mild symptoms. Surveillance data for in-household secondary infections offers unbiased samples for COVID-19 prevalence estimation.\n\nMethodsWe analyse 16 115 Polish surveillance records to obtain key figures of the COVID-19 pandemic. We propose conservative upper and lower bound estimators for the number of SARS-CoV-2 infections. Further, we estimate age-dependent bounds on the severe case rate, death rate, and the in-household attack rate.\n\nResultsBy maximum likelihood estimates, the total number of COVID-19 cases in Poland as of July 22nd, 2020, is at most around 13 times larger and at least 1.6 times larger than the recorded number. The lower bound on the severeness rate ranges between 0.2% for the 0-39 year-old to 5.7% for older than 80, while the upper bound is between 2.6% and 34.1%. The lower bound on the death rate is between 0.04% for the age group 40-59 to 1.34% for the oldest. Overall, the severeness and death rates grow exponentially with age. The in-household attack ratio is 8.18% for the youngest group and 16.88% for the oldest.\n\nConclusionsThe proposed approach derives highly relevant figures on the COVID-19 pandemic from routine surveillance data, under assumption that household members of detected infected are tested and all severe cases are diagnosed.\n\nMOCOSThe MOCOS (MOdelling COrona Spread) international research group is an interdisciplinary scientific consortium. The following authors are MOCOS members: Barbara Adamik, Marek Bawiec, Viktor Bezborodov, Przemyslaw Biecek, Wolfgang Bock, Marcin Bodych, Jan Pablo Burgard, Tyll Krueger, Agata Migalska, Tomasz O[z]a[n]ski, Barbara Pabjan, Magdalena Rosi[n]ska, Piotr Sobczyk and Ewa Szczurek",
-    "rel_num_authors": 0,
-    "rel_authors": null,
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.10.30.20221465",
     "rel_title": "The challenges of caring for people dying from COVID-19: a multinational,observational study of palliative and hospice services (CovPall)",
@@ -1092937,6 +1091802,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.10.30.20222604",
+    "rel_title": "Growth of respiratory droplets in cold and humid air",
+    "rel_date": "2020-11-03",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.30.20222604",
+    "rel_abs": "The ambient conditions surrounding liquid droplets determine their growth or shrinkage. However, the precise fate of a liquid droplet expelled from a respiratory puff as dictated by its surroundings and the puff itself has not yet been fully quantified. From the view of airborne disease transmission, such as SARS-CoV-2, knowledge of such dependencies are critical. Here we employ direct numerical simulations (DNS) of a turbulent respiratory vapour puff and account for the mass and temperature exchange with respiratory droplets and aerosols. In particular, we investigate how droplets respond to different ambient temperatures and relative humidity (RH) by tracking their Lagrangian statistics. We reveal and quantify that in cold and humid environments, as there the respiratory puff is supersaturated, expelled droplets can first experience significant growth, and only later followed by shrinkage, in contrast to the monotonic shrinkage of droplets as expected from the classical view by William F. Wells (1934). Indeed, cold and humid environments diminish the ability of air to hold water vapour, thus causing the respiratory vapour puff to super-saturate. Consequently, the super-saturated vapour field drives the growth of droplets that are caught and transported within the humid puff. To analytically predict the likelihood for droplet growth, we propose a model for the axial RH based on the assumption of a quasi-stationary jet. Our model correctly predicts super-saturated RH conditions and is in good quantitative agreement with our DNS. Our results culminate in a temperature-RH map that can be employed as an indicator for droplet growth or shrinkage.\n\nSignificance StatementInfluence of environmental conditions on airborne diseases transmission is an important issue, especially during the pandemic of COVID-19. Human-to-human transmission is mediated by the transport of virus-laden respiratory droplets. Here we investigate the problem from a fluid mechanics perspective by conducting numerical simulations to quantify the fate of respiratory droplets in a warm humid coughing puff under different ambient conditions. We reveal a non-intuitive regime with considerable growth of respiratory droplets, dominated by a super-saturated vapour field, preferentially occurring in cold and humid environments. We further propose a theoretical model that accurately predicts the condition for droplet growth. Our work should inform socializing policies and ventilation strategies for controlling indoor ambient conditions to mitigate dispersion of droplets from asymptomatic individuals.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Chong Shen Ng",
+        "author_inst": "University of Twente"
+      },
+      {
+        "author_name": "Kai Leong Chong",
+        "author_inst": "University of Twente"
+      },
+      {
+        "author_name": "Rui Yang",
+        "author_inst": "University of Twente"
+      },
+      {
+        "author_name": "Mogeng Li",
+        "author_inst": "University of Twente"
+      },
+      {
+        "author_name": "Roberto Verzicco",
+        "author_inst": "University of Rome 'Tor Vergata'"
+      },
+      {
+        "author_name": "Detlef Lohse",
+        "author_inst": "University of Twente"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.10.30.20222877",
     "rel_title": "Quantification of occupational and community risk factors for SARS-CoV-2 seropositivity among healthcare workers in a large U.S. healthcare system",
@@ -1094154,189 +1093058,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2020.11.02.365536",
-    "rel_title": "Plasma proteomics reveals tissue-specific cell death and mediators of cell-cell interactions in severe COVID-19 patients",
-    "rel_date": "2020-11-03",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.02.365536",
-    "rel_abs": "COVID-19 has caused over 1 million deaths globally, yet the cellular mechanisms underlying severe disease remain poorly understood. By analyzing several thousand plasma proteins in 306 COVID-19 patients and 78 symptomatic controls over serial timepoints using two complementary approaches, we uncover COVID-19 host immune and non-immune proteins not previously linked to this disease. Integration of plasma proteomics with nine published scRNAseq datasets shows that SARS-CoV-2 infection upregulates monocyte/macrophage, plasmablast, and T cell effector proteins. By comparing patients who died to severely ill patients who survived, we identify dynamic immunomodulatory and tissue-associated proteins associated with survival, providing insights into which host responses are beneficial and which are detrimental to survival. We identify intracellular death signatures from specific tissues and cell types, and by associating these with angiotensin converting enzyme 2 (ACE2) expression, we map tissue damage associated with severe disease and propose which damage results from direct viral infection rather than from indirect effects of illness. We find that disease severity in lung tissue is driven by myeloid cell phenotypes and cell-cell interactions with lung epithelial cells and T cells. Based on these results, we propose a model of immune and epithelial cell interactions that drive cell-type specific and tissue-specific damage in severe COVID-19.",
-    "rel_num_authors": 42,
-    "rel_authors": [
-      {
-        "author_name": "Michael R. Filbin",
-        "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Arnav Mehta",
-        "author_inst": "Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Alexis M. Schneider",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA"
-      },
-      {
-        "author_name": "Kyle R. Kays",
-        "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Jamey R. Guess",
-        "author_inst": "Olink Proteomics, Inc, Watertown, MA, USA"
-      },
-      {
-        "author_name": "Matteo Gentili",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA"
-      },
-      {
-        "author_name": "B\u00e1nk G. Fenyves",
-        "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Nicole C. Charland",
-        "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Anna L. K. Gonye",
-        "author_inst": "Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Irena Gushterova",
-        "author_inst": "Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Hargun K. Khanna",
-        "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Thomas J. LaSalle",
-        "author_inst": "Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Kendall M. Lavin-Parsons",
-        "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Brendan M. Lilley",
-        "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Carl L. Lodenstein",
-        "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Kasidet Manakongtreecheep",
-        "author_inst": "Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Justin D. Margolin",
-        "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Brenna N. McKaig",
-        "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Maricarmen Rojas-Lopez",
-        "author_inst": "Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Brian C. Russo",
-        "author_inst": "Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Nihaarika Sharma",
-        "author_inst": "Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Jessica Tantivit",
-        "author_inst": "Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Molly F. Thomas",
-        "author_inst": "Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Robert E. Gerszten",
-        "author_inst": "CardioVascular Institute, Department of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA"
-      },
-      {
-        "author_name": "Graham S. Heimberg",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA"
-      },
-      {
-        "author_name": "David J. Lieb",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA"
-      },
-      {
-        "author_name": "Brian Lin",
-        "author_inst": "Center for Regenerative Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Debby Ngo",
-        "author_inst": "Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA"
-      },
-      {
-        "author_name": "Karin Pelka",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA"
-      },
-      {
-        "author_name": "Miguel Reyes",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA"
-      },
-      {
-        "author_name": "Christopher S. Smillie",
-        "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA"
-      },
-      {
-        "author_name": "Avinash Waghray",
-        "author_inst": "Center for Regenerative Medicine, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Thomas E. Wood",
-        "author_inst": "Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Amanda S. Zajac",
-        "author_inst": "Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Lori J. Jennings",
-        "author_inst": "Novartis Institutes for BioMedical Research, Cambridge, MA, USA"
-      },
-      {
-        "author_name": "Ida Grundberg",
-        "author_inst": "Olink Proteomics, Inc, Watertown, MA, USA"
-      },
-      {
-        "author_name": "Roby P. Bhattacharyya",
-        "author_inst": "Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Blair Alden Parry",
-        "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Alexandra-Chlo\u00e9 Villani",
-        "author_inst": "Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Moshe Sade-Feldman",
-        "author_inst": "Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Nir Hacohen",
-        "author_inst": "Massachusetts General Hospital Cancer Center, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      },
-      {
-        "author_name": "Marcia B. Goldberg",
-        "author_inst": "Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "systems biology"
-  },
   {
     "rel_doi": "10.1101/2020.11.02.365833",
     "rel_title": "Zinc-embedded fabrics inactivate SARS-CoV-2 and influenza A virus",
@@ -1094667,6 +1093388,121 @@
     "type": "new results",
     "category": "genomics"
   },
+  {
+    "rel_doi": "10.1101/2020.11.01.363812",
+    "rel_title": "Structural basis for repurpose and design of nucleoside drugs for treating COVID-19",
+    "rel_date": "2020-11-02",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.01.363812",
+    "rel_abs": "SARS-CoV-2 has caused a global pandemic of COVID-19 that urgently needs an effective treatment. Nucleoside analog drugs including favipiravir have been repurposed for COVID-19 despite of unclear mechanism of their inhibition of the viral RNA polymerase (RdRp). Here we report the cryo-EM structures of the viral RdRp in complex with favipiravir and two other nucleoside inhibitor drugs ribavirin and penciclovir. Ribavirin and the ribosylated form of favipiravir share a similar ribose scaffold that is distinct from penciclovir. However, the structures reveal that all three inhibitors are covalently linked to the primer strand in a monophosphate form despite the different chemical scaffolds between favipiravir and penciclovir. Surprisingly, the base moieties of these inhibitors can form mismatched pairs with the template strand. Moreover, in view of the clinical disadvantages of remdesivir mainly associated with its prodrug form, we designed several orally-available remdesivir parent nucleoside derivatives, including VV16 that showed 5-fold more potent than remdesivir in inhibition of viral replication. Together, these results demonstrate an unexpected promiscuity of the viral RNA polymerase and provide a basis for repurpose and design of nucleotide analog drugs for COVID-19.\n\nOne Sentence SummaryCryo-EM structures of the RNA polymerase of SARS-CoV-2 reveals the basis for repurposing of old nucleotide drugs to treat COVID-19.",
+    "rel_num_authors": 25,
+    "rel_authors": [
+      {
+        "author_name": "Wanchao Yin",
+        "author_inst": "Shanghai Institute of Materia Medica"
+      },
+      {
+        "author_name": "Xiaodong Luan",
+        "author_inst": "School of Medicine, Tsinghua University, Haidian District, Beijing, China"
+      },
+      {
+        "author_name": "Zhihai Li",
+        "author_inst": "The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China"
+      },
+      {
+        "author_name": "Yuanchao Xie",
+        "author_inst": "The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China"
+      },
+      {
+        "author_name": "Ziwei Zhou",
+        "author_inst": "Shanghai Institute of Materia Medica"
+      },
+      {
+        "author_name": "Jia Liu",
+        "author_inst": "Shanghai Institute of Materia Medica"
+      },
+      {
+        "author_name": "Minqi Gao",
+        "author_inst": "WuxiBiortus Biosciences Co. Ltd"
+      },
+      {
+        "author_name": "Xiaoxi Wang",
+        "author_inst": "Shanghai Institute of Materia Medica Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Fulai Zhou",
+        "author_inst": "Shanghai Institute of Materia Medica, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Qingxia Wang",
+        "author_inst": "Shanghai Institute of Materia Medica, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Qingxing Wang",
+        "author_inst": "Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Dandan Shen",
+        "author_inst": "Zhejiang University School of Medicine"
+      },
+      {
+        "author_name": "Yan Zhang",
+        "author_inst": "Zhejiang University School of Medicine"
+      },
+      {
+        "author_name": "Guanghui Tian",
+        "author_inst": "Vigonvita Life Science Co., Ltd."
+      },
+      {
+        "author_name": "Haji A. Aisa",
+        "author_inst": "Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Tianwen Hu",
+        "author_inst": "Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Daibao Wei",
+        "author_inst": "Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Yi Jiang",
+        "author_inst": "Shanghai Institute of Materia Medica Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Gengfu Xiao",
+        "author_inst": "Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Hualiang Jiang",
+        "author_inst": "Shanghai Institute of Materia Medica, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Leike Zhang",
+        "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Xuekui Yu",
+        "author_inst": "Shanghai Institute of Materia Medica, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Jingshan Shen",
+        "author_inst": "Shanghai Institute of Materia Medica, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Shuyang Zhang",
+        "author_inst": "Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijin"
+      },
+      {
+        "author_name": "H. Eric Xu",
+        "author_inst": "Shanghai Institute of Materia Medica, Chinese Academy of Sciences"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "biophysics"
+  },
   {
     "rel_doi": "10.1101/2020.11.02.364497",
     "rel_title": "The SARS-CoV-2 RNA interactome",
@@ -1095912,37 +1094748,6 @@
     "type": "new results",
     "category": "biochemistry"
   },
-  {
-    "rel_doi": "10.1101/2020.10.30.363002",
-    "rel_title": "An insight into SARS-CoV-2 Membrane protein interaction with Spike, Envelope, and Nucleocapsid proteins",
-    "rel_date": "2020-11-01",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.30.363002",
-    "rel_abs": "Intraviral protein-protein interactions are crucial for replication, pathogenicity, and viral assembly. Among these, virus assembly is a critical step as it regulates the arrangements of viral structural proteins and helps in the encapsulation of genomic material. SARS-CoV-2 structural proteins play an essential role in the self-rearrangement, RNA encapsulation, and mature virus particle formation. In SARS-CoV, the membrane protein interacts with the envelope and spike protein in Endoplasmic Reticulum Golgi Intermediate Complex (ERGIC) to form an assembly in the lipid bilayer, followed by membrane-ribonucleoprotein (nucleocapsid) interaction. In this study, we tried to understand the interaction of membrane proteins interaction with envelope, spike, and nucleocapsid proteins using protein-protein docking. Further, simulation studies performed up to 100 ns to examine the stability of protein-protein complexes of Membrane-Envelope, Membrane-Spike, and Membrane-Nucleocapsid. Prime MM-GBSA showed high binding energy calculations than the docked complex. The interactions identified in our study will be of great importance, as it provides valuable insight into the protein-protein complex, which could be the potential drug targets for future studies.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Prateek Kumar",
-        "author_inst": "Indian Institute of Technology Mandi"
-      },
-      {
-        "author_name": "Amit Kumar",
-        "author_inst": "Indian Institute of Technology Mandi"
-      },
-      {
-        "author_name": "Neha Garg",
-        "author_inst": "Banaras Hindu University, Varanasi, Uttar Pradesh"
-      },
-      {
-        "author_name": "Rajanish Giri",
-        "author_inst": "Indian Institute of Technology Mandi"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "new results",
-    "category": "bioinformatics"
-  },
   {
     "rel_doi": "10.1101/2020.10.31.363309",
     "rel_title": "Molecular dynamics and in silico mutagenesis on the reversible inhibitor-bound SARS-CoV-2 Main Protease complexes reveal the role of lateral pocket in enhancing the ligand affinity",
@@ -1096265,6 +1095070,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.11.01.363788",
+    "rel_title": "Discovery of five HIV nucleoside analog reverse-transcriptase inhibitors (NRTIs) as potent inhibitors against the RNA-dependent RNA polymerase (RdRp) of SARS-CoV and 2019-nCoV",
+    "rel_date": "2020-11-01",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.01.363788",
+    "rel_abs": "The outbreak of SARS in 2002-2003 caused by SARS-CoV, and the pandemic of COVID-19 in 2020 caused by 2019-nCoV (SARS-CoV-2), have threatened human health globally and raised the urgency to develop effective antivirals against the viruses. In this study, we expressed and purified the RNA-dependent RNA polymerase (RdRp) nsp12 of SARS-CoV and developed a primer extension assay for the evaluation of nsp12 activity. We found that nsp12 could efficiently extend single-stranded RNA, while having low activity towards double-stranded RNA. Nsp12 required a catalytic metal (Mg2+ or Mn2+) for polymerase activity and the activity was also K+-dependent, while Na+ promoted pyrophosphorylation, the reverse process of polymerization. To identify antivirals against nsp12, a competitive assay was developed containing 4 natural rNTPs and a nucleotide analog, and the inhibitory effects of 24 FDA-approved nucleotide analogs were evaluated in their corresponding active triphosphate forms. Ten of the analogs, including 2 HIV NRTIs, could inhibit the RNA extension of nsp12 by more than 40%. The 10 hits were verified which showed dose-dependent inhibition. In addition, the 24 nucleotide analogs were screened on SARS-CoV primase nsp8 which revealed stavudine and remdesivir were specific inhibitors to nsp12. Furthermore, the 2 HIV NRTIs were evaluated on 2019-nCoV nsp12 which showed inhibition as well. Then we expanded the evaluation to all 8 FDA-approved HIV NRTIs and discovered 5 of them, tenofovir, stavudine, abacavir, zidovudine and zalcitabine, could inhibit the RNA extension by nsp12 of SARS-CoV and 2019-nCoV. In conclusion, 5 FDA-approved HIV NRTIs inhibited the RNA extension by nsp12 and were promising candidates for the treatment of SARS and COVID-19.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Jialei Sun",
+        "author_inst": "Global Health Drug Discovery Institute"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2020.10.26.20220160",
     "rel_title": "Features of C-reactive protein in COVID-19 patients with different ages, clinical types and outcomes: a cohort study",
@@ -1097678,37 +1096502,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.10.28.20221705",
-    "rel_title": "Association of County-Wide Mask Ordinances with Reductions in Daily CoVID-19 Incident Case Growth in a Midwestern Region Over 12 Weeks",
-    "rel_date": "2020-10-30",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.28.20221705",
-    "rel_abs": "ImportanceThis study assessed the longitudinal impact of new COVID-19 cases when a mask ordinance was implemented in 2 of a 5-county Midwestern U.S. metropolitan region over a 3-month period of time. Reduction in case growth was significant and reduced infection inequities by race and population density.\n\nObjectiveThe objective of this study was to assess the impact that a mandatory mask wearing requirement had on the rate of COVID-19 infections by comparing counties with a mandatory policy with those neighboring counties without a mandatory masking policy.\n\nDesignThis was a quasi-experimental longitudinal study conducted over the period of June 12-September 25, 2020.\n\nSettingThis study was a population-based study. Data were abstracted from local health department reports of COVID-19 cases.\n\nParticipantsRaw cases reported to the county health departments and abstracted for this study; census-level data were synthesized to address county-level population, income and race.\n\nIntervention(s) (for clinical trials) or Exposure(s) (for observational studies)The essential features of this intervention was an instituted mask mandate that occurred in St. Louis City and St. Louis County over a 12 week period.\n\nMain Outcome(s) and Measure(s)The primary study outcome measurement was daily COVID-19 infection growth rate. The mask mandate was hypothesized to lower daily infection growth rate.\n\nResultsOver the 15-week period, the average daily percent growth of reported COVID-19 cases across all five counties was 1.81% ({+/-}1.62%). The average daily percent growth in incident COVID-19 cases was similar between M+ and M- counties in the 3 weeks prior to implementation of mandatory mask policies (0.90% [{+/-}0.68] vs. 1.27% [{+/-}1.23%], respectively, p=0.269). Crude modeling with a difference-in-difference indicator showed that after 3 weeks of mask mandate implementation, M+ counties had a daily percent COVID-19 growth rate that was 1.32 times lower, or a 32% decrease. At 12 weeks post-mask policy implementation, the average daily COVID-19 case growth among M- was 2.42% ({+/-}1.92), and was significantly higher than the average daily COVID case growth among M+ counties (1.36% ({+/-}0.96%)) (p<0.001). A significant negative association was identified among counties between percent growth of COVID-19 cases and percent racial minorities per county (p<0.001), as well as population density (p<0.001).\n\nConclusions and RelevanceThese data demonstrate that county-level mask mandates were associated with significantly lower incident COVID-19 case growth over time, compared to neighboring counties that did not implement a mask mandate. The results highlight the swiftness of how a mask ordinance can impact the trajectory of infection rate growth. Another notable finding was that following implementation of mask mandates, the disparity of infection rate by race and population density was no longer significant, suggesting that regional-level policies can not only slow the spread of COVID-19, but simultaneously create more equal environment.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSHow are local mask ordinances associated with growth of COVID-19 cases among adjacent counties?\n\nFindingsEcological longitudinal analysis reveals a significant slowing of daily COVID-19 case growth after mask ordinance implementation among counties.\n\nMeaningLocal-level policy of mask ordinances are shown to be an effective COVID-19 mitigation strategy even within locations of diverse populations.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Enbal Shacham",
-        "author_inst": "Saint Louis University"
-      },
-      {
-        "author_name": "Stephen Scroggins",
-        "author_inst": "Saint Louis University"
-      },
-      {
-        "author_name": "Matthew Ellis",
-        "author_inst": "Saint Louis University"
-      },
-      {
-        "author_name": "Alexander Garza",
-        "author_inst": "SSM Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.10.27.20220723",
     "rel_title": "The psychological impact of coronavirus on university students and its socio-economic determinants in Malaysia",
@@ -1098051,6 +1096844,29 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2020.10.30.352914",
+    "rel_title": "Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses",
+    "rel_date": "2020-10-30",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.30.352914",
+    "rel_abs": "Seasonal coronaviruses (OC43, 229E, NL63 and HKU1) are endemic to the human population, regularly infecting and reinfecting humans while typically causing asymptomatic to mild respiratory infections. It is not known to what extent reinfection by these viruses is due to waning immune memory or antigenic drift of the viruses. Here, we address the influence of antigenic drift on immune evasion of seasonal coronaviruses. We provide evidence that at least two of these viruses, OC43 and 229E, are undergoing adaptive evolution in regions of the viral spike protein that are exposed to human humoral immunity. This suggests that reinfection may be due, in part, to positively-selected genetic changes in these viruses that enable them to escape recognition by the immune system. It is possible that, as with seasonal influenza, these adaptive changes in antigenic regions of the virus would necessitate continual reformulation of a vaccine made against them.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Kathryn Kistler",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      },
+      {
+        "author_name": "Trevor Bedford",
+        "author_inst": "Fred Hutchinson Cancer Research Center"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "evolutionary biology"
+  },
   {
     "rel_doi": "10.1101/2020.10.27.20221085",
     "rel_title": "How Emergency Care Congestion Increases Covid-19 Mortality: Evidence from Lombardy, Italy",
@@ -1100504,65 +1099320,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.10.28.359042",
-    "rel_title": "Ethacridine inhibits SARS-CoV-2 by inactivating viral particles in cellular models",
-    "rel_date": "2020-10-28",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.28.359042",
-    "rel_abs": "SARS-CoV-2 is the coronavirus that causes the respiratory disease COVID-19, which is now the third-leading cause of death in the United States. The FDA has recently approved remdesivir, an inhibitor of SARS-CoV-2 replication, to treat COVID-19, though recent data from the WHO shows little to no benefit with use of this anti-viral agent. Here we report the discovery of ethacridine, a safe antiseptic use in humans, as a potent drug for use against SARS-CoV-2 (EC50 ~ 0.08 M). Ethacridine was identified via high-throughput screening of an FDA-approved drug library in living cells using a fluorescent assay. Interestingly, the main mode of action of ethacridine is through inactivation of viral particles, preventing their binding to the host cells. Indeed, ethacridine is effective in various cell types, including primary human nasal epithelial cells. Taken together, these data identify a promising, potent, and new use of the old drug possessing a distinct mode of action for inhibiting SARS-CoV-2.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Xiaoquan Li",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Petr Lidsky",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Yinghong Xiao",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Chien-Ting Wu",
-        "author_inst": "Stanford"
-      },
-      {
-        "author_name": "Miguel Garcia-Knight",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Junjiao Yang",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Tsuguhisa Nakayama",
-        "author_inst": "Stanford"
-      },
-      {
-        "author_name": "Jayakar V. Nayak",
-        "author_inst": "Stanford"
-      },
-      {
-        "author_name": "Peter K. Jackson",
-        "author_inst": "Stanford"
-      },
-      {
-        "author_name": "Raul Andino",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Xiaokun Shu",
-        "author_inst": "UCSF"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.10.27.20220665",
     "rel_title": "ACE2 Netlas: In-silico functional characterization and drug-gene interactions of ACE2 gene network to understand its potential involvement in COVID-19 susceptibility",
@@ -1100845,6 +1099602,197 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.10.27.20219436",
+    "rel_title": "Childhood asthma outcomes during the COVID-19 pandemic: Findings from the PeARL multi-national cohort.",
+    "rel_date": "2020-10-28",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.27.20219436",
+    "rel_abs": "ImportanceImportance: The interplay between COVID-19 pandemic and asthma in children is still unclear.\n\nObjectiveWe evaluated the impact of COVID-19 pandemic on childhood asthma outcomes.\n\nDesignThe PeARL multinational cohort included children with asthma and non-asthmatic controls recruited during the COVID-19 pandemic and compared current disease activity with data available from the previous year.\n\nSettingPediatric outpatient clinics.\n\nParticipantsThe study included 1,054 children with asthma and 505 non-asthmatic controls, aged between 4-18 years, from 25 pediatric departments, from 15 countries globally.\n\nExposuresCOVID-19 pandemic first wave, starting from the date of the first fatality in the respective country.\n\nMain outcomes and measuresWe assessed the pandemics impact on the frequency of respiratory infections, emergency presentations and hospital admissions in asthmatic versus non-asthmatic participants, controlling for confounding factors including the pandemics duration and the frequency of such acute events during 2019. Using paired analyses, we evaluated the impact of the pandemic on the annualized frequency of asthma attacks and the previously mentioned acute events, asthma control, and pulmonary function in children with asthma, compared to their baseline disease activity, during the preceding year.\n\nResultsDuring the pandemic, children with asthma experienced fewer upper respiratory tract infections, episodes of pyrexia, emergency visits, hospital admissions, asthma attacks and hospitalizations due to asthma, in comparison to the preceding year. Sixty-six percent of asthmatic children had improved asthma control while in 33% the improvement exceeded the minimally clinically important difference. Pre-bronchodilatation FEV1 and peak expiratory flow rate were also improved during the pandemic.\n\nWhen compared to non-asthmatic controls, children with asthma were not found to be at increased risk of LRTIs, episodes of pyrexia, emergency visits or hospitalizations during the pandemic. However, an increased risk of URTIs emerged.\n\nConclusions and relevanceChildhood asthma outcomes, including control, were improved during the first wave of the COVID-19 pandemic, probably because of reduced exposure to asthma triggers and increased treatment adherence. The decreased frequency of acute episodes does not support the notion that childhood asthma may be a risk factor for COVID-19. Furthermore, the potential for improving childhood asthma outcomes through environmental control becomes apparent.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhat was the impact of COVID-19 pandemic on childhood asthma outcomes?\n\nFindingsDuring the first wave of the pandemic, children with asthma have experienced improved outcomes, as evidenced by fewer asthma attachks, hospitalizations, improved scores in validated asthma control measures and improved pulmonary function.\n\nMeaningThis is the first study to show a positive impact of COVID-19 pandemic on childhood asthma activity. This is probably the result of reduced exposure to asthma triggers and increased treatment adherence. The decreased frequency of acute episodes does not support the hypothesis that childhood asthma may be a risk factor for COVID-19.",
+    "rel_num_authors": 44,
+    "rel_authors": [
+      {
+        "author_name": "Nikolaos G. Papadopoulos",
+        "author_inst": "Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester, UK.  Allergy Department, 2nd "
+      },
+      {
+        "author_name": "Alexander G. Mathioudakis",
+        "author_inst": "Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester, UK. North West Lung Centre, W"
+      },
+      {
+        "author_name": "Adnan Custovic",
+        "author_inst": "Imperial College London, London, UK."
+      },
+      {
+        "author_name": "Antoine Deschildre",
+        "author_inst": "Univ. Lille, INSERM Unit  1019, CNRS UMR 8204, Institut Pasteur de Lille, Center for infection and immunity of Lille, 59019 Lille cedex, France."
+      },
+      {
+        "author_name": "Wanda Phipatanakul",
+        "author_inst": "Department of Allergy and Immunology, Boston Children Hospital, Boston, Massachusetts, USA."
+      },
+      {
+        "author_name": "Gary Wong",
+        "author_inst": "Department of Pediatrics, Faculty of Medicine, The Chinese University of Hong Kong, Sha Tin, Hong Kong."
+      },
+      {
+        "author_name": "Paraskevi Xepapadaki",
+        "author_inst": "Allergy Department, 2nd Paediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece"
+      },
+      {
+        "author_name": "Rola Abou-Taam",
+        "author_inst": "Pediatric Pulmonology and Allergy Department Hospital Necker-Enfants Malades, Paris, France."
+      },
+      {
+        "author_name": "Ioana Agache",
+        "author_inst": "Allergy & Clinical Immunology, Transylvania University, Brasov, Romania."
+      },
+      {
+        "author_name": "Jose A. Castro-Rodriguez",
+        "author_inst": "Department of Pediatric Pulmonology, School of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile."
+      },
+      {
+        "author_name": "Zhimin Chen",
+        "author_inst": "Department of pulmonology, the children hospital, Zhejiang University school of medicine, national clinical research center for child health, Hangzhou, Zhejiang"
+      },
+      {
+        "author_name": "Pierrick Cros",
+        "author_inst": "Department of Pediatrics, University Hospital Morvan, Brest, France."
+      },
+      {
+        "author_name": "Jean-Christop Dubus",
+        "author_inst": "Centre de Ressources et de Competences pour la Mucoviscidose Pneumo-Allergologie, Ventilation, Maladies Respiratoires Rares de l Enfant CHU Timone-Enfants, Mars"
+      },
+      {
+        "author_name": "Zeinab Awad El-Sayed",
+        "author_inst": "Pediatric Allergy and Immunology Unit, Children's Hospital, Ain Shams University, Cairo, Egypt."
+      },
+      {
+        "author_name": "Rasha El-Owaidy",
+        "author_inst": "Pediatric Allergy and Immunology Unit, Children's Hospital, Ain Shams University, Cairo, Egypt."
+      },
+      {
+        "author_name": "Wojciech Feleszko",
+        "author_inst": "Department of Pediatric Pneumonology and Allergy, The Medical University of Warsaw, Warsaw, Poland."
+      },
+      {
+        "author_name": "Vincenzo Fierro",
+        "author_inst": "Allergy Department, Bambino Gesu Children  Hospital IRCCS, Roma, Italy."
+      },
+      {
+        "author_name": "Alessandro Fiocchi",
+        "author_inst": "Allergy Department, Bambino Gesu Children Hospital IRCCS, Roma, Italy."
+      },
+      {
+        "author_name": "Luis Garcia-Marcos",
+        "author_inst": "Pediatric Respiratory and Allergy Units, Virgen de la Arrixaca Children University Clinical Hospital, University of Murcia, Murcia, Spain.  Institute for Biomed"
+      },
+      {
+        "author_name": "Anne Goh",
+        "author_inst": "Department of Internal Medicine, Rush Medical College, Chicago."
+      },
+      {
+        "author_name": "Elham M. Hossny",
+        "author_inst": "Pediatric Allergy and Immunology Unit, Children's Hospital, Ain Shams University, Cairo, Egypt"
+      },
+      {
+        "author_name": "Yunuen R. Huerta Villalobos",
+        "author_inst": "Hospital General Regional 1 Dr. Carlos Mac Gregor Sanchez Navarro IMSS, Mexico."
+      },
+      {
+        "author_name": "Tuomas Jartti",
+        "author_inst": "Department of Pediatrics and Adolescent Medicine, Oulu University Hospital and University of Oulu, Oulu, Finland."
+      },
+      {
+        "author_name": "Pascal Le Roux",
+        "author_inst": "Department of pediatrics, Groupe hospitalier Le Havre, France."
+      },
+      {
+        "author_name": "Julia Levina",
+        "author_inst": "Pediatric and Child Health Research Institute of the Central Clinical Hospital of the Russian Academy of Sciences, Russia."
+      },
+      {
+        "author_name": "Aida Ines Lopez Garcia",
+        "author_inst": "Allergy and Clinical Immunology Service of the University Hospital of Puebla, Mexico."
+      },
+      {
+        "author_name": "Angel Mazon Ramos",
+        "author_inst": "Pediatric Pulmonology & Allergy Unit Children Hospital la Fe, Valencia, Spain."
+      },
+      {
+        "author_name": "Mario Morais Almeida",
+        "author_inst": "Allergy Center, CUF Descobertas Hospital, Lisbon, Portugal."
+      },
+      {
+        "author_name": "Clare Murray",
+        "author_inst": "Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester, UK."
+      },
+      {
+        "author_name": "Karthik Nagaraju",
+        "author_inst": "VN Allergy & Asthma Research Centre, Chennai, Tamilnadu, India."
+      },
+      {
+        "author_name": "Major K. Nagaraju",
+        "author_inst": "Professor & Head, Department of Allergy & Clinical Immunology, Saveetha Medical College, Chennai, India."
+      },
+      {
+        "author_name": "Elsy Maureen Navarrete Rodriguez",
+        "author_inst": "Pediatric Allergy and Clinical Immunology Service, Hospital Infantil, til de Mexico Federico Gomez, Mexico."
+      },
+      {
+        "author_name": "Leyla Namazova-Baranova",
+        "author_inst": "Pediatric and Child Health Research Institute of the Central Clinical Hospital of the Russian Academy of Sciences, Russia. Pirogov Russian National Research Med"
+      },
+      {
+        "author_name": "Antonio Nieto Garcia",
+        "author_inst": "Pediatric Pulmonology & Allergy Unit Children Hospital la Fe, Valencia, Spain."
+      },
+      {
+        "author_name": "Cesar Fireth Pozo Beltran",
+        "author_inst": "Teaching and Research Department and Paediatric Allergy department, Hospital with Specialties Juan Maria de Salvatierra, La Paz, Baja California Sur Mexico.  Al"
+      },
+      {
+        "author_name": "Thanaporn Ratchataswan",
+        "author_inst": "Department of Allergy and Immunology, Boston Children Hospital, Boston, Massachusetts, USA."
+      },
+      {
+        "author_name": "Daniela Rivero Yeverino",
+        "author_inst": "Allergy and Clinical Immunology Department, Hospital Universitario de Puebla, Puebla, Mexico."
+      },
+      {
+        "author_name": "Erendira Rodriguez Zagal",
+        "author_inst": "Hospital General Regional 1 Dr. Carlos Mac Gregor Sanchez Navarro IMSS, Mexico."
+      },
+      {
+        "author_name": "Cyril E Schweitzer",
+        "author_inst": "CHRU de Nancy, Hopital d Enfants, Rue du Morvan, 54511 Vandoeuvre, France."
+      },
+      {
+        "author_name": "Marleena Tulkki",
+        "author_inst": "Department of Pediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland."
+      },
+      {
+        "author_name": "Katarzyna Wasilczuk",
+        "author_inst": "Department of Pediatric Pneumonology and Allergy, The Medical University of Warsaw, Warsaw, Poland"
+      },
+      {
+        "author_name": "Dan XU",
+        "author_inst": "Department of pulmonology, the children hospital, Zhejiang University school of medicine, national clinical research center for child health, Hangzhou, Zhejiang"
+      },
+      {
+        "author_name": "- PeARL Collaborators",
+        "author_inst": ""
+      },
+      {
+        "author_name": "- PeARL Think Tank",
+        "author_inst": ""
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "pediatrics"
+  },
   {
     "rel_doi": "10.1101/2020.10.27.20219618",
     "rel_title": "Modelling trachoma post 2020: Opportunities for mitigating the impact of COVID-19 and accelerating progress towards elimination.",
@@ -1101954,41 +1100902,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.10.23.20218289",
-    "rel_title": "Seroprevalence of SARS-CoV-2 antibodies and associated factors in health care workers: a systematic review and meta-analysis",
-    "rel_date": "2020-10-27",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.23.20218289",
-    "rel_abs": "BackgroundHealth care workers (HCWs) represent a high risk population for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection.\n\nAimTo determine the seroprevalence of SARS-CoV-2 antibodies among HCWs, and to find out the factors that are associated with this seroprevalence.\n\nMethodsThe Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines were applied for this systematic review and meta-analysis. Databases including PubMed/MEDLINE and pre-print services (medR{chi}iv and bioR{chi}iv) were searched from inception up to August 24, 2020.\n\nFindingsForty-nine studies, including 127,480 HCWs met the inclusion criteria. The estimated overall seroprevalence of SARS-CoV-2 antibodies among HCWs was 8.7% (95% CI: 6.7-10.9%). Seroprevalence was higher in studies that were conducted in North America (12.7%) compared to those in Europe (8.5%), Africa (8.2), and Asia (4%). Meta-regression showed that increased sensitivity of antibodies test was associated with increased seroprevalence. The following factors were associated with seropositivity: male gender, Black, Asian, and Hispanic HCWs, work in a coronavirus disease 2019 (COVID-19) unit, patient-related work, frontline health care workers, health care assistants, personal protective equipment shortage, self-reported belief for previous SARS-CoV-2 infection, previous positive polymerase chain reaction test, and household contact with suspected or confirmed COVID-19 patients.\n\nConclusionThe seroprevalence of SARS-CoV-2 antibodies among HCWs is high. Excellent adherence to infection prevention and control measures, sufficient and adequate personal protective equipment, and early recognition, identification and isolation of HCWs that are infected with SARS-CoV-2 are imperative to decrease the risk of SARS-CoV-2 infection.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Petros A Galanis",
-        "author_inst": "National and Kapodistrian University of Athens"
-      },
-      {
-        "author_name": "Irene Vraka",
-        "author_inst": "Children's Hospital \"Panayiotis & Aglaia Kyriakou\""
-      },
-      {
-        "author_name": "Despoina Fragkou",
-        "author_inst": "National and Kapodistrian University of Athens"
-      },
-      {
-        "author_name": "Angeliki Bilali",
-        "author_inst": "Children's Hospital \"Panayiotis & Aglaia Kyriakou\""
-      },
-      {
-        "author_name": "Daphne Kaitelidou",
-        "author_inst": "National and Kapodistrian University of Athens"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.10.23.20218230",
     "rel_title": "Abnormal liver tests in admitted patients with SARS-Cov-2 or other respiratory viruses- prognostic similarities and temporal disparities",
@@ -1102183,6 +1101096,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
+  {
+    "rel_doi": "10.1101/2020.10.24.20218727",
+    "rel_title": "DNA methylation and gene expression pattern of ACE2 and TMPRSS2 genes in saliva samples of patients with SARS-CoV-2 infection",
+    "rel_date": "2020-10-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.24.20218727",
+    "rel_abs": "COVID-19 caused by SARS-CoV-2 became a pandemic affecting the health and economy of the world. Although it was known that this virus uses ACE2 protein along with TMPRSS2 to enter the host cell, the methylation pattern and gene expression of ACE2 and TMPRSS2 genes are not explored in saliva samples of patients infected with COVID-19. The study aimed to quantify promoter methylation of ACE2 and TMPRSS2 along with its mRNA expression in saliva samples of COVID-19 patients in order to understand the regulatory mechanism of these genes in SARS-CoV-2 infection. Saliva samples were collected from thirty male patients with SARS-CoV-2 infection and thirty age-matched healthy control male subjects. Q MS PCR and qRT PCR was performed to quantify the promoter DNA methylation and mRNA expression of ACE2 and TMPRSS2 respectively. Our study didnt find any significant difference between methylation and expression of these two genes in cases compared to control subjects. However there was significant positive correlation between DNA methylation of ACE2 and its gene expression. Among cases, the sample collected [&ge;]7 days after appearance of symptoms showed higher amount of methylation in both ACE2 and TMPRSS2 genes when compared to sample collected before 7 days. In conclusion, we found that ACE2 and TMPRSS2 methylation plays a role in COVID-19.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Pratibha Misra",
+        "author_inst": "AFMC, Pune"
+      },
+      {
+        "author_name": "Bhasker Mukherjee",
+        "author_inst": "AFMC, Pune"
+      },
+      {
+        "author_name": "Rakhi Negi",
+        "author_inst": "AFMC, Pune"
+      },
+      {
+        "author_name": "Vikas Marwah",
+        "author_inst": "Army Institute of Cardio thoracic sciences, Pune"
+      },
+      {
+        "author_name": "Arijit Kumar Ghosh",
+        "author_inst": "Army Institute of Cardio thoracic sciences, Pune"
+      },
+      {
+        "author_name": "Prashant Jindamwar",
+        "author_inst": "Army Institute of Cardio thoracic sciences, Pune"
+      },
+      {
+        "author_name": "Mukesh U Singh",
+        "author_inst": "AFMC, Pune"
+      },
+      {
+        "author_name": "Yaongamphi Vashum",
+        "author_inst": "AFMC, Pune"
+      },
+      {
+        "author_name": "Syamraj R",
+        "author_inst": "AFMC, Pune"
+      },
+      {
+        "author_name": "Bala Chandra G",
+        "author_inst": "AFMC, Pune"
+      },
+      {
+        "author_name": "Sibin M K",
+        "author_inst": "Armed forces medical college"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.10.23.20218511",
     "rel_title": "Large-scale population analysis of SARS-CoV2 whole genome sequences reveals host-mediated viral evolution with emergence of mutations in the viral Spike protein associated with elevated mortality rates",
@@ -1103472,41 +1102444,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.10.24.20218909",
-    "rel_title": "Finding the real COVID-19 case-fatality rates for SAARC countries",
-    "rel_date": "2020-10-27",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.24.20218909",
-    "rel_abs": "Crude case fatality rate (CFR) is the most accurate when the pandemic is over. Adjustments to the crude CFR measure can better explain the pandemic situation by improving the CFR estimation. However, no study has thoroughly investigated COVID-19 adjusted CFR of the South Asian Association for Regional Cooperation (SAARC) countries. In this study, we estimated both survival interval and underreporting adjusted CFR of COVID-19 for the SAARC countries and observed the CFR changes due to the imposition of fees on COVID-19 tests in Bangladesh. Using the daily records up to 9th October, we implemented a statistical method to remove both the bias in crude CFR, i.e., the delay between disease onset and outcome bias and due to asymptomatic or mild symptomatic cases, reporting rates lower than 50% (95% CI: 10%-50%) bias. According to our findings, Afghanistan had the highest CFR, followed by Pakistan, India, Bangladesh, Nepal, Maldives, and Sri Lanka. Our estimated crude CFR varied from 3.71% to 0.29%, survival interval adjusted CFR varied from 3.77% to 0.3% and further underreporting adjusted CFR varied from 1.1% to 0.08%. We have also found that crude CFR increased from 1.261% to 1.572% after imposing the COVID-19 test fees in Bangladesh. Therefore, the authorities of countries with higher CFR should be looking for strategic counsel from the countries with lower CFR to equip themselves with the necessary knowledge to combat the pandemic. Moreover, caution is needed to report the CFR.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Md. Rafil Tazir Shah",
-        "author_inst": "Shahjalal University of Science and Technology, Sylhet-3114, Bangladesh"
-      },
-      {
-        "author_name": "Tanvir Ahammed",
-        "author_inst": "Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh"
-      },
-      {
-        "author_name": "Aniqua Anjum",
-        "author_inst": "Shahjalal University of Science and Technology, Sylhet-3114, Bangladesh"
-      },
-      {
-        "author_name": "Anisa Ahmed Chowdhury",
-        "author_inst": "Shahjalal University of Science and Technology, Sylhet-3114, Bangladesh"
-      },
-      {
-        "author_name": "Afroza Jannat Suchana",
-        "author_inst": "Shahjalal University of Science and Technology, Sylhet-3114, Bangladesh"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.10.24.20218321",
     "rel_title": "COVID-19 Infections Following Physical School Reopening",
@@ -1103701,6 +1102638,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "otolaryngology"
   },
+  {
+    "rel_doi": "10.1101/2020.10.25.20219212",
+    "rel_title": "Economic Losses Associated with COVID-19 Deaths in the United States",
+    "rel_date": "2020-10-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.25.20219212",
+    "rel_abs": "In addition to the overwhelming health effects of COVID-19, the disease has inflicted unprecedented economic damage. Vast resources have been directed at COVID-19 testing and health care while economic activity has been substantially curtailed due to disruptions resulting from individual choices and government policies. This study estimates the economic loss associated with COVID-19 deaths in the U.S. from February 1, 2020 through July 11, 2020. We use estimates of years of life lost that are based on the age and gender of decedents. Using a value of life year estimate of $66,759, we calculate economic losses of roughly $66 billion. The losses are concentrated in New York and New Jersey, which account for 17.5% of the total losses. Our analysis of per capita losses by state indicates that the highest values are located in the northeastern region of the country, while the values in the western states are relatively low. While economic losses associate with COVID-19 deaths is just one aspect of the pandemic, our estimates can provide context to the value of prevention and mitigation efforts.\n\nJEL codesI12, I18, J17",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Troy Quast",
+        "author_inst": "University of South Florida, College of Public Health"
+      },
+      {
+        "author_name": "Ross Andel",
+        "author_inst": "University of South Florida, School of Aging"
+      },
+      {
+        "author_name": "Sean Gregory",
+        "author_inst": "Northern Arizona University, Department of Politics & International Affairs"
+      },
+      {
+        "author_name": "Eric A. Storch",
+        "author_inst": "Baylor College of Medicine, Menninger Department of Psychiatry & Behavioral Sciences"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health economics"
+  },
   {
     "rel_doi": "10.1101/2020.10.25.20219337",
     "rel_title": "Efficacy of Convalescent Plasma Therapy compared to Fresh Frozen Plasma in Severely ill COVID-19 Patients: A Pilot Randomized Controlled Trial",
@@ -1104922,173 +1103890,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.10.26.20219642",
-    "rel_title": "A2B-COVID: A method for evaluating potential SARS-CoV-2 transmission events",
-    "rel_date": "2020-10-27",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.26.20219642",
-    "rel_abs": "Identifying linked cases of infection is a key part of the public health response to viral infectious disease. Viral genome sequence data is of great value in this task, but requires careful analysis, and may need to be complemented by additional types of data. The Covid-19 pandemic has highlighted the urgent need for analytical methods which bring together sources of data to inform epidemiological investigations. We here describe A2B-COVID, an approach for the rapid identification of linked cases of coronavirus infection. Our method combines knowledge about infection dynamics, data describing the movements of individuals, and novel approaches to genome sequence data to assess whether or not cases of infection are consistent or inconsistent with linkage via transmission. We apply our method to analyse and compare data collected from two wards at Cambridge University Hospitals, showing qualitatively different patterns of linkage between cases on designated Covid-19 and non-Covid-19 wards. Our method is suitable for the rapid analysis of data from clinical or other potential outbreak settings.",
-    "rel_num_authors": 38,
-    "rel_authors": [
-      {
-        "author_name": "Christopher J R Illingworth",
-        "author_inst": "MRC Biostatistics Unit, University of Cambridge"
-      },
-      {
-        "author_name": "William L Hamilton",
-        "author_inst": "Department of Medicine, University of Cambridge"
-      },
-      {
-        "author_name": "Christopher H Jackson",
-        "author_inst": "MRC Biostatistics Unit, University of Cambridge"
-      },
-      {
-        "author_name": "Ashley Popay",
-        "author_inst": "Public Health England Field Epidemiology Unit, Cambridge"
-      },
-      {
-        "author_name": "Luke Meredith",
-        "author_inst": "Department of Pathology, University of Cambridge"
-      },
-      {
-        "author_name": "Charlotte J Houldcroft",
-        "author_inst": "Department of Medicine, University of Cambridge"
-      },
-      {
-        "author_name": "Myra Hosmillo",
-        "author_inst": "Department of Pathology, University of Cambridge"
-      },
-      {
-        "author_name": "Aminu Jahun",
-        "author_inst": "Department of Pathology, University of Cambridge"
-      },
-      {
-        "author_name": "Matthew Routledge",
-        "author_inst": "Cambridge University Hospitals NHS Foundation Trust, Cambridge"
-      },
-      {
-        "author_name": "Ben Warne",
-        "author_inst": "Department of Medicine, University of Cambridge"
-      },
-      {
-        "author_name": "Laura Caller",
-        "author_inst": "Francis Crick Institute"
-      },
-      {
-        "author_name": "Sarah Caddy",
-        "author_inst": "Cambridge Institute for Therapeutic Immunology and Infectious Disease"
-      },
-      {
-        "author_name": "Anna Yakovleva",
-        "author_inst": "Department of Pathology, University of Cambridge"
-      },
-      {
-        "author_name": "Grant Hall",
-        "author_inst": "Department of Pathology, University of Cambridge"
-      },
-      {
-        "author_name": "Fahad A Khokhar",
-        "author_inst": "Department of Pathology, University of Cambridge"
-      },
-      {
-        "author_name": "Theresa Feltwell",
-        "author_inst": "Department of Medicine, University of Cambridge"
-      },
-      {
-        "author_name": "Malte Pinckert",
-        "author_inst": "Department of Pathology, University of Cambridge"
-      },
-      {
-        "author_name": "Iliana Georgana",
-        "author_inst": "Department of Pathology, University of Cambridge"
-      },
-      {
-        "author_name": "Yasmin Chaudhry",
-        "author_inst": "Department of Pathology, University of Cambridge"
-      },
-      {
-        "author_name": "Martin Curran",
-        "author_inst": "Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge"
-      },
-      {
-        "author_name": "Surendra Parmar",
-        "author_inst": "Public Health England Clinical Microbiology and Public Health Laboratory, Cambridge"
-      },
-      {
-        "author_name": "Dominic Sparkes",
-        "author_inst": "Cambridge University Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Lucy Rivett",
-        "author_inst": "Cambridge University Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Nick K Jones",
-        "author_inst": "Cambridge University Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Sushmita Sridhar",
-        "author_inst": "Department of Medicine, University of Cambridge"
-      },
-      {
-        "author_name": "Sally Forest",
-        "author_inst": "Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge"
-      },
-      {
-        "author_name": "Tom Dymond",
-        "author_inst": "Cambridge University Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Kayleigh Grainger",
-        "author_inst": "Cambridge University Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Chris Workman",
-        "author_inst": "Cambridge University Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Effrossyni Gkrania-Klotsas",
-        "author_inst": "Cambridge University Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Nicholas M Brown",
-        "author_inst": "Cambridge University Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Michael Weekes",
-        "author_inst": "Cambridge University"
-      },
-      {
-        "author_name": "Stephen Baker",
-        "author_inst": "Cambridge University"
-      },
-      {
-        "author_name": "Sharon J Peacock",
-        "author_inst": "Department of Medicine, University of Cambridge"
-      },
-      {
-        "author_name": "Theodore Gouliouris",
-        "author_inst": "Cambridge University Hospitals NHS Foundation Trust"
-      },
-      {
-        "author_name": "Ian G. Goodfellow",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Daniela de Angelis",
-        "author_inst": "MRC Biostatistics Unit, University of Cambridge"
-      },
-      {
-        "author_name": "M. Estee Torok",
-        "author_inst": "University of Cambridge"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.10.26.20219543",
     "rel_title": "Disruptions to schistosomiasis programmes due to COVID-19: an analysis of potential impact and mitigation strategies",
@@ -1105403,6 +1104204,101 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.10.27.20220541",
+    "rel_title": "A Scalable Saliva-based, Extraction-free RT-LAMP Protocol for SARS-Cov-2 Diagnosis",
+    "rel_date": "2020-10-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.27.20220541",
+    "rel_abs": "I.Scalable, cost-effective screening methods are an essential tool to control SARS-CoV-2 spread. We have developed a straight saliva-based, RNA extraction-free, RT-LAMP test that is comparable to current nasopharyngeal swab RT-PCR tests in both sensitivity and specificity. Using a 2-step readout of fluorescence and melting-point curve analysis, the test is scalable to more than 30,000 tests per day with average turnaround time of less than 3 hours. The test was validated using samples from 244 symptomatic patients, and showed sensitivity of 78.9% (vs. 85.5% for nasopharyngeal swabs RT-PCR) and specificity of 100% (vs. 100% for nasopharyngeal swabs RT-PCR). Our method is therefore accurate, robust, time and cost effective and therefore can be used for screening of SARS-CoV-2.",
+    "rel_num_authors": 20,
+    "rel_authors": [
+      {
+        "author_name": "Paula Asprino",
+        "author_inst": "Hospital Sirio-Libanes, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "Fabiana Bettoni",
+        "author_inst": "Hospital Sirio-Libanes, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "Anamaria Camargo",
+        "author_inst": "Hospital Sirio-Libanes, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "Diego Coelho",
+        "author_inst": "Mendelics Analise Genomica, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "Guilherme Coppini",
+        "author_inst": "Mendelics Analise Genomica, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "Igor Correa",
+        "author_inst": "Mendelics Analise Genomica, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "Erika Freitas",
+        "author_inst": "Mendelics Analise Genomica, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "Lilian Inoue",
+        "author_inst": "Hospital Sirio-Libanes, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "Joao Paulo Kitajima",
+        "author_inst": "Mendelics Analise Genomica, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "Mayra Kuroki",
+        "author_inst": "Hospital Sirio-Libanes, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "Cibele Masotti",
+        "author_inst": "Hospital Sirio-Libanes, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "Tatiana Marques",
+        "author_inst": "Hospital Sirio-Libanes, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "Alice Reis",
+        "author_inst": "Hospital Sirio-Libanes, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "Luiz Fernando Reis",
+        "author_inst": "Hospital Sirio-Libanes, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "Bibiana Santos",
+        "author_inst": "Mendelics Analise Genomica, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "Ernande dos Santos",
+        "author_inst": "Hospital Sirio-Libanes, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "David Schlesinger",
+        "author_inst": "Mendelics"
+      },
+      {
+        "author_name": "Cecilia Sena",
+        "author_inst": "Mendelics Analise Genomica, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "Talita Spadaccini",
+        "author_inst": "Mendelics Analise Genomica, Sao Paulo, Brazil"
+      },
+      {
+        "author_name": "Lucas Taniguti",
+        "author_inst": "Mendelics Analise Genomica, Sao Paulo, Brazil"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.10.26.20220244",
     "rel_title": "Age-adjusted Charlson comorbidity index score is the best predictor for severe clinical outcome in the hospitalized patients with COVID-19 infection: a result from nationwide database of 5,621 Korean patients",
@@ -1107176,93 +1106072,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.10.26.356279",
-    "rel_title": "Genetic determinants of COVID-19 drug efficacy revealed by genome-wide CRISPR screens",
-    "rel_date": "2020-10-27",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.26.356279",
-    "rel_abs": "Immunomodulatory agents dexamethasone and colchicine, antiviral drugs remdesivir, favipiravir and ribavirin, as well as antimalarial drugs chloroquine phosphate and hydroxychloroquine are currently used in the combat against COVID-191-16. However, whether some of these drugs have clinical efficacy for COVID-19 is under debate. Moreover, these drugs are applied in COVID-19 patients with little knowledge of genetic biomarkers, which will hurt patient outcome. To answer these questions, we designed a screen approach that could employ genome-wide sgRNA libraries to systematically uncover genes crucial for these drugs action. Here we present our findings, including genes crucial for the import, export, metabolic activation and inactivation of remdesivir, as well as genes that regulate colchicine and dexamethasones immunosuppressive effects. Our findings provide preliminary information for developing urgently needed genetic biomarkers for these drugs. Such biomarkers will help better interpret COVID-19 clinical trial data and point to how to stratify COVID-19 patients for proper treatment with these drugs.",
-    "rel_num_authors": 18,
-    "rel_authors": [
-      {
-        "author_name": "Wei Jiang",
-        "author_inst": "Shanghai Institute of Biochemistry and Cell Biology"
-      },
-      {
-        "author_name": "Ailing Yang",
-        "author_inst": "Shanghai Institute of Biochemistry and Cell Biology"
-      },
-      {
-        "author_name": "Jingchuan Ma",
-        "author_inst": "Shanghai Institute of Biochemistry and Cell Biology"
-      },
-      {
-        "author_name": "Dawei Lv",
-        "author_inst": "Institut Pasteur of Shanghai,Chinese Academy of Sciences; University of Chinese Academy of Sciences"
-      },
-      {
-        "author_name": "Mingxian Liu",
-        "author_inst": "Shanghai Institute of Biochemistry and Cell Biology"
-      },
-      {
-        "author_name": "Liang Xu",
-        "author_inst": "Shanghai Institute of Biochemistry and Cell Biology"
-      },
-      {
-        "author_name": "Chao Wang",
-        "author_inst": "Shanghai Institute of Biochemistry and Cell Biology"
-      },
-      {
-        "author_name": "Zhengjin He",
-        "author_inst": "Shanghai Institute of Biochemistry and Cell Biology"
-      },
-      {
-        "author_name": "Shuo Chen",
-        "author_inst": "Shanghai Institute of Biochemistry and Cell Biology"
-      },
-      {
-        "author_name": "Jie Zhao",
-        "author_inst": "Shanghai Institute of Biochemistry and Cell Biology"
-      },
-      {
-        "author_name": "Shishuang Chen",
-        "author_inst": "Shanghai Institute of Biochemistry and Cell Biology"
-      },
-      {
-        "author_name": "Qi Jiang",
-        "author_inst": "Shanghai Institute of Biochemistry and Cell Biology"
-      },
-      {
-        "author_name": "Yankai Chu",
-        "author_inst": "Shanghai Institute of Biochemistry and Cell Biology"
-      },
-      {
-        "author_name": "Lin Shan",
-        "author_inst": "Shanghai Institute of Biochemistry and Cell Biology"
-      },
-      {
-        "author_name": "Zhaocai Zhou",
-        "author_inst": "Fudan University"
-      },
-      {
-        "author_name": "Yun Zhao",
-        "author_inst": "Shanghai Institute of Biochemistry and Cell Biology"
-      },
-      {
-        "author_name": "Gang Long",
-        "author_inst": "Institut Pasteur of Shanghai"
-      },
-      {
-        "author_name": "Hai Jiang",
-        "author_inst": "Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "pharmacology and toxicology"
-  },
   {
     "rel_doi": "10.1101/2020.10.27.357350",
     "rel_title": "Binding Mode of SARS-CoV2 Fusion Peptide to Human Cellular Membrane",
@@ -1107577,6 +1106386,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
+  {
+    "rel_doi": "10.1101/2020.10.22.20217430",
+    "rel_title": "Covid-19 and Socioeconomic Factors: Cross-country Evidence",
+    "rel_date": "2020-10-26",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.22.20217430",
+    "rel_abs": "BackgroundCOVID-19 pandemic has affected all countries across the globe in varying intensity resulting in varied numbers for total cases and deaths.\n\nObjectivesThe paper aims to understand if different socioeconomic factors have a role to play in determining the intensity of COVID-19 impact.\n\nMethodsThe study uses a country-wise number of corona cases and deaths and analyse them in a cross-country multivariate regression framework. It uses gross domestic product per capita, average temperature, population density, and median age as independent variables. The study uses testing data as a control variable.\n\nResultsIn absence of the testing variable, higher-income countries have experienced a higher number of COVID cases. The population density, median age, climate do not have significant impact. The countries with higher population density have lower deaths. Each region shows different patterns of correlation between socioeconomic factors and COVID intensity.\n\nConclusionThe majority of the cross-country variation can be attributed to the number of tests done by a country. The countries with high population density would have applied strict lockdowns and proactive testing to curb the deaths. The study essentially refutes claims around corona being a high-income group disease, cold-climate disease, or a disease impacting old-age patients more.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Vishalkumar J Jani",
+        "author_inst": "Indian Institute of Public Health Gandhinagar"
+      },
+      {
+        "author_name": "Dileep V Mavalankar",
+        "author_inst": "Indian Institute of Public Health Gandhinagar"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health policy"
+  },
   {
     "rel_doi": "10.1101/2020.10.22.20215749",
     "rel_title": "An ultra-sensitive, ultra-fast whole blood monocyte CD169 assay for COVID-19 screening",
@@ -1108686,61 +1107518,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.10.20.20214718",
-    "rel_title": "Distinguishing non severe cases of dengue from COVID-19 in the context of co-epidemics: a cohort study in a SARS-CoV-2 testing center on Reunion island",
-    "rel_date": "2020-10-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.20.20214718",
-    "rel_abs": "BackgroundAs coronavirus 2019 (COVID-19) is spreading globally, several countries are handling dengue epidemics. As both infections are deemed to share similarities at presentation, it would be useful to distinguish COVID-19 from dengue in the context of co-epidemics. Hence, we performed a retrospective cohort study to identify predictors of both infections.\n\nMethodology/Principal FindingsAll the subjects suspected of COVID-19 between March 23 and May 10, 2020, were screened for COVID-19 within the testing center of the University hospital of Saint-Pierre, Reunion island. The screening consisted in a questionnaire surveyed in face-to-face, a nasopharyngeal swab specimen for the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) reverse transcription polymerase chain-reaction and a rapid diagnostic orientation test for dengue. Factors independently associated with COVID-19 or with dengue were sought using multinomial logistic regression models, taking other febrile illnesses (OFIs) as controls. Adjusted Odds ratios (OR) and 95% Confidence Intervals (95%CI) were assessed. Over a two-month study period, we diagnosed 80 COVID-19, 60 non-severe dengue and 872 OFIs cases. Among these, we identified delayed presentation (>3 days) since symptom onset (Odds ratio 1.91, 95% confidence interval 1.07-3.39), contact with a COVID-19 positive case (OR 3.81, 95%CI 2.21-6.55) and anosmia (OR 7.80, 95%CI 4.20-14.49) as independent predictors of COVID-19, body ache (OR 6.17, 95%CI 2.69-14.14), headache (OR 5.03, 95%CI 1.88-13.44) and retro-orbital pain (OR 5.55, 95%CI 2.51-12.28) as independent predictors of dengue, while smoking was less likely observed with COVID-19 (OR 0.27, 95%CI 0.09-0.79) and upper respiratory tract infection symptoms were associated with OFIs.\n\nConclusions/SignificanceAlthough prone to potential biases, these data suggest that non-severe dengue may be more symptomatic than COVID-19 in a co-epidemic setting with higher dengue attack rates. At clinical presentation, eight basic clinical and epidemiological indicators may help to distinguish COVID-19 or dengue from each other and other febrile illnesses.\n\nAuthor SummaryAs coronavirus 2019 (COVID-19) is spreading globally, several countries are facing dengue epidemics with the fear the two plagues might overburden their healthcare systems. On Reunion island, southwestern Indian ocean: dengue virus is circulating since 2004 under an endemo-epidemic pattern with yearly outbreaks peaking between March and May since 2015, whereas Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), the pathogen responsible of COVID-19, emerged in March 2020, imported from the Bahamas. COVID-19 and dengue are deemed two clinically similar entities, especially within the first two days from symptom onset. In this context, we conducted a cohort study between March 23 and May 10, 2020, within a SARS-CoV-2 testing center, aimed at identifying the factors discriminating both infections. Surprisingly, we found that non-severe dengue was more symptomatic than mild to moderate COVID-19. Indeed, we found body ache, headache and retro-orbital pain to be indicative of dengue, whereas contact with a COVID-19 positive case, anosmia, delayed presentation (>3 days post symptom onset) and absence of active smoking were indicative of COVID-19. These findings highlight the need for accurate diagnostic tools and not to jeopardize dengue control in areas wherever COVID-19 dengue co-epidemics have the potential to wrought havoc to the healthcare system.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Antoine Joubert",
-        "author_inst": "Centre Hospitalier Universitaire de la Reunion, Saint-Pierre, Reunion, France"
-      },
-      {
-        "author_name": "Fanny Andry",
-        "author_inst": "Centre Hospitalier Universitaire de la Reunion, Saint-Pierre, Reunion, France"
-      },
-      {
-        "author_name": "Antoine Bertolotti",
-        "author_inst": "Centre Hospitalier Universitaire de la Reunion, Saint-Pierre, Reunion, France"
-      },
-      {
-        "author_name": "Frederic Accot",
-        "author_inst": "Centre Hospitalier Universitaire de la Reunion, Saint-Pierre, Reunion, France"
-      },
-      {
-        "author_name": "Yatrika Koumar",
-        "author_inst": "Centre Hospitalier Universitaire de la Reunion, Saint-Pierre, Reunion, France"
-      },
-      {
-        "author_name": "Florian Legrand",
-        "author_inst": "Centre Hospitalier Universitaire de la Reunion, Saint-Pierre, Reunion, France"
-      },
-      {
-        "author_name": "Patrice Poubeau",
-        "author_inst": "Centre Hospitalier Universitaire de la Reunion, Saint-Pierre, Reunion, France"
-      },
-      {
-        "author_name": "Rodolphe Manaquin",
-        "author_inst": "Centre Hospitalier Universitaire de la Reunion, Saint-Pierre, Reunion, France"
-      },
-      {
-        "author_name": "Patrick Gerardin",
-        "author_inst": "Centre Hospitalier Universitaire de la Reunion, Saint-Pierre, Reunion, France"
-      },
-      {
-        "author_name": "Cecile Levin",
-        "author_inst": "Centre Hospitalier Universitaire de la Reunion, Saint-Pierre, Reunion, France"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.10.21.20215418",
     "rel_title": "COVID-19 in regions with low prevalence and low density of population. An uncertainty dynamic modeling approach.",
@@ -1108991,6 +1107768,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
+  {
+    "rel_doi": "10.1101/2020.10.21.20217406",
+    "rel_title": "Social and Psychiatric Effects of COVID-19 Pandemic and Distance Learning On High School Students: A Cross-Sectional Web-Based Survey Comparing Turkey and Denmark",
+    "rel_date": "2020-10-25",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20217406",
+    "rel_abs": "ObjectiveIn this study we investigated the socio-psychological effects of both the pandemic and distance learning on high school students in Turkey and Denmark. We aimed to assess whether there were any differences a) between students attending public or private schools in Turkey and b) between two countries having different approaches to pandemic and considerable socio-cultural and economic differences.\n\nMethodsWe conducted a web-based questionnaire study in a cross-sectional design using Survey Monkey platform and sent out via social media to high school students from Turkey and Denmark. The survey collected socio-demographic data, several variables associated with pandemic and distance education and their effects on social life and psychological status. Additionally, emotional status was assessed using positive (PA) and negative affects (NA) schedule (PANAS). The survey ran from July 3 and August 31 2020.\n\nResultsWe studied 565 (mean age: 16.5 {+/-} 1.0) Turkish and 92 (mean age:17.7 {+/-} 1.0) Danish students, of whom the majority were female adolescents (63% vs 76%). Students educated in public (47.6%) and private high schools (52.4%) were nearly similar in number in Turkish group, whereas in the Danish sample almost all students were from public school (98.9%). Turkish students were significantly more likely to be compliant with the pandemic related restrictions. Besides that, there were significant socio-economic disparities between Turkish and Danish students and also within Turkey between public and private school students. Turkish online education system was significantly less adequate and satisfactory compared to the Danish system. These were even worse for those who were attending public schools in Turkey. Regardless of the socio-economic differences, the majority of the students in both countries has been negatively affected by the pandemic and related restrictions and had a negative opinion about distance education. This was also true for the PANAS scores. The total scores of PANAS were similar between Turkish and Danish students (PA: 27.0 {+/-} 7.6 versus 25.8 {+/-} 5.6; NA: 24.8{+/-} 7.5 versus 24.5{+/-} 7.3) and also within Turkey between public and private school students (PA: 26.8 {+/-} 7.5 versus 27.1 {+/-} 7.6; NA: 24.7{+/-} 7.2 versus 25.0{+/-} 7.8). While female students were significantly more severely affected in the Turkish group, no such gender differences were observed in the Danish group. Additionally, considerable portion of the students in Turkey and Denmark expressed loneliness (55.2% vs 59.8%, p<0.706), boredom (71.2% vs 58.7%, p=0.019) and anxiety towards the future (61.4% vs 22.8%, p<0.001). Decreased physical activity, sleep problems, eating disorders and domestic abuse were other complaints.\n\nConclusionsAdolescents from both countries have been severely affected by the pandemic and its related restrictions and expressed negative views about distance education. Turkish online education system seemed to be less satisfactory when compared to Danish system and within Turkey, public school students had significantly more disadvantages compared to those attending private schools. Despite the fact that there were several socio-economic inequalities among students, in general, there were no robust significant differences regarding psychological status and opinion about distance learning, indicating a global worsening of emotional status during pandemic.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Lara Selin Seyahi",
+        "author_inst": "Robert college, Istanbul, Turkey"
+      },
+      {
+        "author_name": "Seyda Gul Ozcan",
+        "author_inst": "Cerrahpasa Medical Faculty, Department of Internal Medicine, Cerrahpasa Medical School, Istanbul University-Cerrahpasa, Istanbul, Turkey"
+      },
+      {
+        "author_name": "Necdet Sut",
+        "author_inst": "Department of Biostatistics and Medical Informatics, Trakya University Medical Faculty, Edirne, Turkey"
+      },
+      {
+        "author_name": "Ayumi Mayer",
+        "author_inst": "Aurehoj High School, Copenhagen, Denmark"
+      },
+      {
+        "author_name": "Burc Cagri Poyraz",
+        "author_inst": "Department of Psychiatry, Division of Geriatric Psychiatry, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpasa, Istanbul, Turkey"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.10.21.20217380",
     "rel_title": "Development of a predictive risk model for severe COVID-19 disease using population-based administrative data",
@@ -1110076,101 +1108888,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.10.21.20210203",
-    "rel_title": "Tocilizumab in nonventilated patients hospitalized with Covid-19 pneumonia",
-    "rel_date": "2020-10-23",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20210203",
-    "rel_abs": "BackgroundCoronavirus disease 2019 (Covid-19) pneumonia is often associated with hyperinflammation. Safety and efficacy of the anti-interleukin-6 receptor antibody tocilizumab was evaluated in patients hospitalized with Covid-19 pneumonia.\n\nMethodsNonventilated patients hospitalized with Covid-19 pneumonia were randomized (2:1) to tocilizumab (8 mg/kg intravenous) or placebo plus standard care. Sites enrolling high-risk and minority populations were emphasized. The primary endpoint was cumulative proportion of patients requiring mechanical ventilation or who had died by Day 28.\n\nResultsOf 389 randomized patients, 249 patients received tocilizumab and 128 received placebo in the modified intent-to-treat population (Hispanic/Latino, 56.0%; Black/African American, 14.9%; American Indian/Alaska Native, 12.7%; White, 12.7%; other/unknown, 3.7%). The cumulative proportion (95% confidence interval [CI]) of patients requiring mechanical ventilation or who had died by Day 28 was 12.0% (8.52% to 16.86%) and 19.3 % (13.34% to 27.36%) for the tocilizumab and placebo arms, respectively (log-rank P=0.0360; hazard ratio, 0.56 [95% CI, 0.33 to 0.97]). Median time to clinical failure up to Day 28 favored tocilizumab over placebo (hazard ratio 0.55 [95% CI, 0.33 to 0.93]). All-cause mortality by Day 28 was 10.4% with tocilizumab and 8.6% with placebo (weighted difference, 2.0% [95% CI, - 5.2% to 7.8%). In the safety population, serious adverse events occurred in 15.2% of tocilizumab patients (38/250 patients) and 19.7% of placebo patients (25/127).\n\nConclusionsThis trial demonstrated the efficacy and safety of tocilizumab over placebo in reducing the likelihood of progression to requiring mechanical ventilation or death in nonventilated patients hospitalized with Covid-19 pneumonia.\n\nTrial registrationClinicalTrials.gov NCT04372186",
-    "rel_num_authors": 20,
-    "rel_authors": [
-      {
-        "author_name": "Carlos Salama",
-        "author_inst": "Elmhurst Hospital Center, Icahn School of Medicine at the Mount Sinai Hospital, Elmhurst, NY, USA"
-      },
-      {
-        "author_name": "Jian Han",
-        "author_inst": "Genentech, South San Francisco, CA, USA"
-      },
-      {
-        "author_name": "Linda Yau",
-        "author_inst": "Genentech, South San Francisco, CA, USA"
-      },
-      {
-        "author_name": "William G. Reiss",
-        "author_inst": "Genentech, South San Francisco, CA, USA"
-      },
-      {
-        "author_name": "Benjamin Kramer",
-        "author_inst": "Genentech, South San Francisco, CA, USA"
-      },
-      {
-        "author_name": "Jeffrey D. Neidhart",
-        "author_inst": "San Juan Oncology Associates, Farmington, NM, USA"
-      },
-      {
-        "author_name": "Gerard J. Criner",
-        "author_inst": "Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA"
-      },
-      {
-        "author_name": "Emma Kaplan-Lewis",
-        "author_inst": "Elmhurst Hospital Center, New York City Health and Hospitals, Elmhurst, NY, USA"
-      },
-      {
-        "author_name": "Rachel Baden",
-        "author_inst": "Highland Hospital, Oakland, CA, USA"
-      },
-      {
-        "author_name": "Lavannya Pandit",
-        "author_inst": "Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX, USA"
-      },
-      {
-        "author_name": "Miriam L. Cameron",
-        "author_inst": "Holy Cross Health, Silver Spring, MD, USA"
-      },
-      {
-        "author_name": "Julia Garcia-Diaz",
-        "author_inst": "Ochsner Clinic Foundation, New Orleans, LA, USA"
-      },
-      {
-        "author_name": "Victoria Ch\u00e1vez",
-        "author_inst": "Central Military Hospital, Lima, Peru"
-      },
-      {
-        "author_name": "Martha Mekebeb-Reuter",
-        "author_inst": "Stellenbosch University, Cape Town, South Africa"
-      },
-      {
-        "author_name": "Ferdinando Lima Menezes",
-        "author_inst": "BR Trials, Pesquisa Cl\u00ednica, Sao Paulo, SP, Brazil"
-      },
-      {
-        "author_name": "Reena Shah",
-        "author_inst": "Aga Khan University Hospital, Nairobi, Kenya"
-      },
-      {
-        "author_name": "Maria F. Gonz\u00e1lez-Lara",
-        "author_inst": "Instituto Nacional de Ciencias M\u00e9dicas y Nutrici\u00f3n Salvador Zubir\u00e1n, Mexico City, Mexico"
-      },
-      {
-        "author_name": "Beverly Assman",
-        "author_inst": "Genentech, South San Francisco, CA, USA"
-      },
-      {
-        "author_name": "Jamie Freedman",
-        "author_inst": "Genentech, South San Francisco, CA, USA"
-      },
-      {
-        "author_name": "Shalini V. Mohan",
-        "author_inst": "Genentech, South San Francisco, CA, USA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.10.21.20217208",
     "rel_title": "Early use of nitazoxanide in mild Covid-19 disease: randomized, placebo-controlled trial",
@@ -1110581,6 +1109298,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.10.21.20216895",
+    "rel_title": "Superspreading Events Without Superspreaders: Using High Attack Rate Events to Estimate N o forAirborne Transmission of COVID-19",
+    "rel_date": "2020-10-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20216895",
+    "rel_abs": "We study transmission of COVID-19 using five well-documented case studies - a Washington state church choir, a Korean call center, a Korean exercise class, and two different Chinese bus trips. In all cases the likely index patients were pre-symptomatic or mildly symptomatic, which is when infective patients are most likely to interact with large groups of people. An estimate of N0, the characteristic number of COVID-19 virions needed to induce infection in each case, is found using a simple physical model of airborne transmission. We find that the N0 values are similar for five COVID-19 superspreading cases ([~]300-2,000 viral copies) and of the same order as influenza A. Consistent with the recent results of Goyal et al, these results suggest that viral loads relevant to infection from presymptomatic or mildly symptomatic individuals may fall into a narrow range, and that exceptionally high viral loads are not required to induce a superspreading event [1,2]. Rather, the accumulation of infective aerosols exhaled by a typical pre-symptomatic or mildly symptomatic patient in a confined, crowded space (amplified by poor ventilation, particularly activity like exercise or singing, or lack of masks) for exposure times as short as one hour are sufficient. We calculate that talking and breathing release [~]460N0 and [~]10N0 (quanta)/hour, respectively, providing a basis to estimate the risks of everyday activities. Finally, we provide a calculation which motivates the observation that fomites appear to account for a small percentage of total COVID-19 infection events.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "MARA G. PRENTISS",
+        "author_inst": "Harvard University"
+      },
+      {
+        "author_name": "Arthur Chu",
+        "author_inst": "QVT Family Office"
+      },
+      {
+        "author_name": "Karl K. Berggren",
+        "author_inst": "MIT"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.10.21.20217042",
     "rel_title": "Viral dynamics of SARS-CoV-2 infection and the predictive value of repeat testing",
@@ -1111806,81 +1110550,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.10.23.352666",
-    "rel_title": "Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19",
-    "rel_date": "2020-10-23",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.23.352666",
-    "rel_abs": "The novel SARS-CoV-2 virus emerged in December 2019 and has few effective treatments. We applied a computational drug repositioning pipeline to SARS-CoV-2 differential gene expression signatures derived from publicly available data. We utilized three independent published studies to acquire or generate lists of differentially expressed genes between control and SARS-CoV-2-infected samples. Using a rank-based pattern matching strategy based on the Kolmogorov-Smirnov Statistic, the signatures were queried against drug profiles from Connectivity Map (CMap). We validated sixteen of our top predicted hits in live SARS-CoV-2 antiviral assays in either Calu-3 or 293T-ACE2 cells. Validation experiments in human cell lines showed that 11 of the 16 compounds tested to date (including clofazimine, haloperidol and others) had measurable antiviral activity against SARS-CoV-2. These initial results are encouraging as we continue to work towards a further analysis of these predicted drugs as potential therapeutics for the treatment of COVID-19.",
-    "rel_num_authors": 15,
-    "rel_authors": [
-      {
-        "author_name": "Brian L Le",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Gaia Andreoletti",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Tomiko Oskotsky",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Albert Vallejo-Gracia",
-        "author_inst": "Gladstone Institutes"
-      },
-      {
-        "author_name": "Romel Rosales",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Katharine Z Yu",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Idit Kosti",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Kristoffer E Leon",
-        "author_inst": "Gladstone Institutes"
-      },
-      {
-        "author_name": "Daniel G Bunis",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Christine Li",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "G. Renuka Kumar",
-        "author_inst": "Gladstone Institutes"
-      },
-      {
-        "author_name": "Kris M. White",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Adolfo E Garc\u00eda-Sastre",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Melanie Ott",
-        "author_inst": "Gladstone Institutes"
-      },
-      {
-        "author_name": "Marina Sirota",
-        "author_inst": "UCSF"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "bioinformatics"
-  },
   {
     "rel_doi": "10.1101/2020.10.20.20216143",
     "rel_title": "The incubation period of COVID-19: A scoping review and meta-analysis to aid modelling and planning",
@@ -1112127,6 +1110796,49 @@
     "type": "new results",
     "category": "bioinformatics"
   },
+  {
+    "rel_doi": "10.1101/2020.10.22.349522",
+    "rel_title": "Analysis of SARS-CoV-2 ORF3a structure reveals chloride binding sites",
+    "rel_date": "2020-10-22",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.22.349522",
+    "rel_abs": "SARS-CoV-2 ORF3a is believed to form ion channels, which may be involved in the modulation of virus release, and has been implicated in various cellular processes like the up-regulation of fibrinogen expression in lung epithelial cells, downregulation of type 1 interferon receptor, caspase-dependent apoptosis, and increasing IFNAR1 ubiquitination. ORF3a assemblies as homotetramers, which are stabilized by residue C133. A recent cryoEM structure of a homodimeric complex of ORF3a has been released. A lower-resolution cryoEM map of the tetramer suggests two dimers form it, arranged side by side. The dimers cryoEM structure revealed that each protomer contains three transmembrane helices arranged in a clockwise configuration forming a six helices transmembrane domain. This domains potential permeation pathway has six constrictions narrowing to about 1 [A] in radius, suggesting the structure solved is in a closed or inactivated state. At the cytosol end, the permeation pathway encounters a large and polar cavity formed by multiple beta strands from both protomers, which opens to the cytosolic milieu. We modeled the tetramer following the arrangement suggested by the low-resolution tetramer cryoEM map. Molecular dynamics simulations of the tetramer embedded in a membrane and solvated with 0.5 M of KCl were performed. Our simulations show the cytosolic cavity is quickly populated by both K+ and Cl-, yet with different dynamics. K+ ions moved relatively free inside the cavity without forming proper coordination sites. In contrast, Cl- ions enter the cavity, and three of them can become stably coordinated near the intracellular entrance of the potential permeation pathway by an inter-subunit network of positively charged amino acids. Consequently, the central cavitys electrostatic potential changed from being entirely positive at the beginning of the simulation to more electronegative at the end.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Valeria Marquez-Miranda",
+        "author_inst": "Interdisciplinary Center of Neuroscience of Valparaiso, Faculty of Sciences, University of Valparaiso, Chile"
+      },
+      {
+        "author_name": "Maximiliano Rojas",
+        "author_inst": "Center for Bioinformatics and Integrative Biology, Universidad Andres Bello, Avenida Republica 330, Santiago, Chile"
+      },
+      {
+        "author_name": "Yorley Duarte",
+        "author_inst": "Center for Bioinformatics and Integrative Biology, Universidad Andres Bello, Avenida Republica 330, Santiago, Chile"
+      },
+      {
+        "author_name": "Ignacio Diaz-Franulic",
+        "author_inst": "Center for Bioinformatics and Integrative Biology, Universidad Andres Bello, Avenida Republica 330, Santiago, Chile"
+      },
+      {
+        "author_name": "Miguel Holmgren",
+        "author_inst": "Molecular Neurophysiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, MD, USA"
+      },
+      {
+        "author_name": "Raul Cachau",
+        "author_inst": "Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA"
+      },
+      {
+        "author_name": "Fernando Danilo Gonzalez-Nilo",
+        "author_inst": "Center for Bioinformatics and Integrative Biology, Universidad Andres Bello, Avenida Republica 330, Santiago, Chile"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "biophysics"
+  },
   {
     "rel_doi": "10.1101/2020.10.22.349951",
     "rel_title": "Immunogenicity of a new gorilla adenovirus vaccine candidate for COVID-19",
@@ -1113448,20 +1112160,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
-  {
-    "rel_doi": "10.1101/2020.10.19.20214395",
-    "rel_title": "Could nutrition modulate COVID-19 susceptibility and severity of disease? A systematic review",
-    "rel_date": "2020-10-21",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.19.20214395",
-    "rel_abs": "BackgroundMany nutrients have powerful immunomodulatory actions with the potential to alter susceptibility to COVID-19 infection, progression to symptoms, likelihood of severe disease and survival. The pandemic has fostered many nutrition-related theories, sometimes backed by a biased interpretation of evidence.\n\nObjectivesTo provide a systematic review of the latest evidence on how malnutrition across all its forms (under- and over-nutrition and micronutrient status) may influence both susceptibility to, and progression and severity of, COVID-19.\n\nMethodsWe synthesised information on 13 nutrition-related components and their potential interactions with COVID-19: overweight, obesity and diabetes; protein-energy malnutrition; anaemia; vitamins A, C, D, and E; poly-unsaturated fatty acids; iron; selenium; zinc; anti-oxidants, and nutritional support. For each section we provide: a) a landscape review of pertinent material; b) a systematic search of the literature in PubMed and EMBASE databases, including a systematic search of a wide range of pre-print servers; and c) a screen of six clinical trial registries. Two reviewers were assigned per section for data extraction. All original research was considered, without restriction to study design, and included if it covered: 1) SARS-CoV-2, MERS-CoV or SARS-CoV viruses and 2) disease susceptibility or 3) disease progression, and 4) the nutritional component of interest. Searches took place between 16th May and 11th August, 2020. PROSPERO registration CRD42020186194.\n\nResultsAcross the 13 searches, a total of 2732 articles from PubMed and EMBASE, 4164 articles from the pre-print servers, and 433 trials were returned. A total of 288 published articles and 278 pre-print articles were taken to full text screening. In the final narrative synthesis, we cover 22 published articles, 39 pre-print articles and 79 trials. The review highlights a range of mechanistic and observational evidence to highlight the role nutrition can play in susceptibility and progression of COVID-19. However, to date, there is limited evidence that high-dose supplements of micronutrients will either prevent severe disease or speed up recovery, although results of clinical trials are eagerly awaited.\n\nConclusionsTo date there is no conclusive evidence supporting adoption of novel nutritional therapies. However, given the known impacts of all forms of malnutrition on the immune system, public health strategies to reduce micronutrient deficiencies and undernutrition remain of critical importance. There is strong evidence that prevention of obesity, and its consequent type-2 diabetes, will reduce the risk of serious COVID-19 outcomes.",
-    "rel_num_authors": 0,
-    "rel_authors": null,
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "nutrition"
-  },
   {
     "rel_doi": "10.1101/2020.10.19.20215517",
     "rel_title": "An agent-based model of spread of a pandemic with validation using COVID-19 data from New York State",
@@ -1113808,6 +1112506,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.10.20.20215863",
+    "rel_title": "Cognitive deficits in people who have recovered from COVID-19 relative to controls: An N=84,285 online study",
+    "rel_date": "2020-10-21",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.20.20215863",
+    "rel_abs": "Case studies have revealed neurological problems in severely affected COVID-19 patients. However, there is little information regarding the nature and broader prevalence of cognitive problems post-infection or across the full spread of severity. We analysed cognitive test data from 84,285 Great British Intelligence Test participants who completed a questionnaire regarding suspected and biologically confirmed COVID-19 infection. People who had recovered, including those no longer reporting symptoms, exhibited significant cognitive deficits when controlling for age, gender, education level, income, racial-ethnic group and pre-existing medical disorders. They were of substantial effect size for people who had been hospitalised, but also for mild but biologically confirmed cases who reported no breathing difficulty. Finer grained analyses of performance support the hypothesis that COVID-19 has a multi-system impact on human cognition.\n\nSignificance statementThere is evidence that COVID-19 may cause long term health changes past acute symptoms, termed  long COVID. Our analyses of detailed cognitive assessment and questionnaire data from tens thousands of datasets, collected in collaboration with BBC2 Horizon, align with the view that there are chronic cognitive consequences of having COVID-19. Individuals who recovered from suspected or confirmed COVID-19 perform worse on cognitive tests in multiple domains than would be expected given their detailed age and demographic profiles. This deficit scales with symptom severity and is evident amongst those without hospital treatment. These results should act as a clarion call for more detailed research investigating the basis of cognitive deficits in people who have survived SARS-COV-2 infection.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Adam Hampshire",
+        "author_inst": "Imperial College London"
+      },
+      {
+        "author_name": "William Trender",
+        "author_inst": "Imperial College London"
+      },
+      {
+        "author_name": "Samuel Chamberlain",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Amy Jolly",
+        "author_inst": "Imperial College London"
+      },
+      {
+        "author_name": "Jon E Grant",
+        "author_inst": "University of Chicago"
+      },
+      {
+        "author_name": "Fiona Patrick",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Ndaba Mazibuko",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Steve Williams",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Joe M Barnby",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Peter Hellyer",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Mitul A Mehta",
+        "author_inst": "King's College London"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "psychiatry and clinical psychology"
+  },
   {
     "rel_doi": "10.1101/2020.10.19.20215079",
     "rel_title": "Epidemic Curve of Contamination in a Hospital That Served as Sentinel of the Spread of the SARS-Cov-2 Epidemic in the City of Rio de Janeiro",
@@ -1115001,33 +1113758,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.10.14.20212878",
-    "rel_title": "Integration of Kalman filter in the epidemiological model: a robust approach to predict COVID-19 outbreak in Bangladesh",
-    "rel_date": "2020-10-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.14.20212878",
-    "rel_abs": "As one of the most densely populated countries in the world, Bangladesh have been trying to contain the impact of a pandemic like COVID-19 since March, 2020. Although government announced an array of restricted measures to slow down the diffusion in the beginning of the pandemic, the lockdown has been lifted gradually by reopening all the industries, markets and offices with a notable exception of educational institutes. As the physical geography of Bangladesh is highly variable across the largest delta, the population of different regions and their lifestyle also differ in the country. Thus, to get the real scenario of the current pandemic across Bangladesh, it is essential to analyze the transmission dynamics over the individual districts. In this article, we propose to integrate the Unscented Kalman Filter (UKF) with classic SIRD model to explain the epidemic evolution of individual districts in the country. We show that UKF-SIRD model results in a robust prediction of the transmission dynamics for 1-4 months. Then we apply the robust UKF-SIRD model over different regions in Bangladesh to estimates the course of the epidemic. Our analysis demonstrate that in addition to the densely populated areas, industrial areas and popular tourist spots are in the risk of higher COVID-19 transmission. In the light of these outcomes, we provide a set of suggestions to contain the pandemic in Bangladesh. All the data and relevant codebase is available at https://mjonyh.github.io.\n\nHighlightsO_LIWe integrate the UKF with classic SIRD model for the better estimation of the COVID-19 diffusion of 64 districts in Bangladesh.\nC_LIO_LINationwide analysis show the strong correlation between population density and the number of COVID-19 positive cases in the country.\nC_LIO_LIIndustrial zones and popular tourists spots are at greater risk of spreading the Coronavirus.\nC_LIO_LIWith the better assessment of the COVID-19 cases dynamics, the Government will find effective policies to contain the current pandemic.\nC_LI",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Md. Shariful Islam",
-        "author_inst": "North South University, Dhaka - 1229, Bangladesh"
-      },
-      {
-        "author_name": "Md. Enamul Hoque",
-        "author_inst": "Shahjalal Unversity of Science and Technology, Sylhet - 3114, Bangladesh"
-      },
-      {
-        "author_name": "Mohammad Ruhul Amin",
-        "author_inst": "Fordham University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.10.15.20212712",
     "rel_title": "A Multiplexed, Next Generation Sequencing Platform for High-Throughput Detection of SARS-CoV-2",
@@ -1115322,6 +1114052,101 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.10.15.20213512",
+    "rel_title": "COVID-19 neutralizing antibodies predict disease severity and survival",
+    "rel_date": "2020-10-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.15.20213512",
+    "rel_abs": "COVID-19 exhibits variable symptom severity ranging from asymptomatic to life-threatening, yet the relationship between severity and the humoral immune response is poorly understood. We examined antibody responses in 113 COVID-19 patients and found that severe cases resulting in intubation or death exhibited increased inflammatory markers, lymphopenia, and high anti-RBD antibody levels. While anti-RBD IgG levels generally correlated with neutralization titer, quantitation of neutralization potency revealed that high potency was a predictor of survival. In addition to neutralization of wild-type SARS-CoV-2, patient sera were also able to neutralize the recently emerged SARS-CoV-2 mutant D614G, suggesting protection from reinfection by this strain. However, SARS-CoV-2 sera was unable to cross-neutralize a highly-homologous pre-emergent bat coronavirus, WIV1-CoV, that has not yet crossed the species barrier. These results highlight the importance of neutralizing humoral immunity on disease progression and the need to develop broadly protective interventions to prevent future coronavirus pandemics.",
+    "rel_num_authors": 20,
+    "rel_authors": [
+      {
+        "author_name": "Wilfredo F Garcia-Beltran",
+        "author_inst": "Massachusetts General Hospital, Department of Pathology"
+      },
+      {
+        "author_name": "Evan C Lam",
+        "author_inst": "Ragon Institute of MGH, MIT, and Harvard"
+      },
+      {
+        "author_name": "Michael G Astudillo",
+        "author_inst": "Massachusetts General Hospital, Department of Pathology"
+      },
+      {
+        "author_name": "Diane Yang",
+        "author_inst": "Massachusetts General Hospital, Department of Pathology"
+      },
+      {
+        "author_name": "Tyler E Miller",
+        "author_inst": "Massachusetts General Hospital, Department of Pathology"
+      },
+      {
+        "author_name": "Jared Feldman",
+        "author_inst": "Ragon Institute of MGH, MIT, and Harvard"
+      },
+      {
+        "author_name": "Blake M Hauser",
+        "author_inst": "Ragon Institute of MGH, MIT, and Harvard"
+      },
+      {
+        "author_name": "Timothy M Caradonna",
+        "author_inst": "Ragon Institute of MGH, MIT, and Harvard"
+      },
+      {
+        "author_name": "Kiera L Clayton",
+        "author_inst": "Ragon Institute of MGH, MIT, and Harvard"
+      },
+      {
+        "author_name": "Adam D Nitido",
+        "author_inst": "Ragon Institute of MGH, MIT, and Harvard"
+      },
+      {
+        "author_name": "Mandakolathur R Murali",
+        "author_inst": "Ragon Institute of MGH, MIT, and Harvard"
+      },
+      {
+        "author_name": "Galit Alter",
+        "author_inst": "Ragon Institute of MGH, MIT, and Harvard"
+      },
+      {
+        "author_name": "Richelle C Charles",
+        "author_inst": "Massachusetts General Hospital, Infectious Disease Unit"
+      },
+      {
+        "author_name": "Anand Dighe",
+        "author_inst": "Massachusetts General Hospital, Department of Pathology"
+      },
+      {
+        "author_name": "John A Branda",
+        "author_inst": "Massachusetts General Hospital, Department of Pathology"
+      },
+      {
+        "author_name": "Jochen K Lennerz",
+        "author_inst": "Massachusetts General Hospital, Department of Pathology"
+      },
+      {
+        "author_name": "Daniel Lingwood",
+        "author_inst": "Ragon Institute of MGH, MIT, and Harvard"
+      },
+      {
+        "author_name": "Aaron G Schmidt",
+        "author_inst": "Ragon Institute of MGH, MIT, and Harvard"
+      },
+      {
+        "author_name": "A. John Iafrate",
+        "author_inst": "Massassachusetts General Hospital, Department of Pathology"
+      },
+      {
+        "author_name": "Alejandro B Balazs",
+        "author_inst": "Ragon Institute of MGH, MIT, and Harvard"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.10.15.20213108",
     "rel_title": "FebriDx point-of-care test in patients with suspected COVID-19: a pooled diagnostic accuracy study",
@@ -1116719,53 +1115544,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.10.16.20214098",
-    "rel_title": "Dataset of COVID-19 outbreak and potential predictive features in the USA",
-    "rel_date": "2020-10-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.16.20214098",
-    "rel_abs": "This dataset provides information related to the outbreak of COVID-19 disease in the United States, including data from each of 3142 US counties from the beginning of the outbreak (January 2020) until September 2020. This data is collected from many public online databases and includes the daily number of COVID-19 confirmed cases and deaths, as well as 33 features that may be relevant to the pandemic dynamics: demographic, geographic, climatic, traffic, public-health, social-distancing-policy adherence, and political characteristics of each county. We anticipate many researchers will use this dataset to train models that can predict the spread of COVID-19 and to identify the key driving factors.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Arezoo Haratian",
-        "author_inst": "Isfahan University of Technology, Department of Electrical and Computer Engineering"
-      },
-      {
-        "author_name": "Hadi Fazelinia",
-        "author_inst": "Isfahan University of Technology, Department of Electrical and Computer Engineering"
-      },
-      {
-        "author_name": "Zeinab Maleki",
-        "author_inst": "Isfahan University of Technology, Department of Electrical and Computer Engineering"
-      },
-      {
-        "author_name": "pouria Ramazi",
-        "author_inst": "University of Alberta, Department of Mathematical and Statistical Sciences"
-      },
-      {
-        "author_name": "Hao Wang",
-        "author_inst": "University of Alberta, Department of Mathematical and Statistical Sciences"
-      },
-      {
-        "author_name": "Mark Lewis",
-        "author_inst": "University of Alberta, Department of Mathematical and Statistical Sciences"
-      },
-      {
-        "author_name": "Russell Greiner",
-        "author_inst": "University of Alberta, Department of Computing Science"
-      },
-      {
-        "author_name": "David Wishart",
-        "author_inst": "University of Alberta, Department of Computing Science"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.10.16.20213892",
     "rel_title": "Why do per capita COVID-19 Case Rates Differ Between U.S. States?",
@@ -1117020,6 +1115798,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "neurology"
   },
+  {
+    "rel_doi": "10.1101/2020.10.17.20214429",
+    "rel_title": "SARS-CoV-2 infection among patients with multiple sclerosis; A cross-sectional study",
+    "rel_date": "2020-10-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.17.20214429",
+    "rel_abs": "BackgroundNeurological disability associated with multiple sclerosis and immunosuppressive or immunomodulatory therapy which is administered for it may increases the risk of SARS-CoV-2 infection and its morbidity/mortality.\n\nObjectiveIn this study, we evaluated the infection rate and the severity of SARS-CoV-2 infection in patients with multiple sclerosis (MS)\n\nMethodsOne thousand and three hundred and sixty one MS patients from Fars province, south of Iran, were interviewed by phone from April 3 to June 20, 2020. Basic demographic data, information about MS disease and any symptoms or laboratory results relevant to COVID-19 were gathered and reviewed by treating neurologist and MS nurses. SPSS version 22 was used for data analysis.\n\nResults68 (5%) of MS patients were suspected cases and 8 (0.58%) of all patients with positive real-time reverse transcription polymerase chain reaction (RT-PCR) or chest CT were in the confirmed group. 5 cases of the confirmed group needed hospitalization. Two patients died while both of them had PPMS and were taking rituximab. The frequency rate of suspected cases with RRMS was 57 (87.7%), followed by PPMS 5 (7.7%) and CIS 2(3.1%). In the confirmed group 37.5% had RRMS, 50% had PPMS, 25% use corticosteroid drug, and 50% were on rituximab. 62.5% of confirmed cases had high disability level and need assistance to walk. 36.8% of suspected and 25% of the confirmed cases were on IFN-{beta}1; eventually all of them recovered well from COVID-19 infection.\n\nConclusionThe present study showed that rate of developing COVID-19 in MS patients are similar to the general population and the frequency of PPMS phenotype, rituximab therapy and corticosteroid therapy were higher in the confirmed group.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Mahnaz Bayat",
+        "author_inst": "Shiraz University of Medical Sciences"
+      },
+      {
+        "author_name": "Alireza Fayyazpoor",
+        "author_inst": "Shiraz Medical School, Shiraz University of Medical Sciences"
+      },
+      {
+        "author_name": "Afshin Borhani Haghighi",
+        "author_inst": "Shiraz University of Medical Sciences"
+      },
+      {
+        "author_name": "Daniyal Salehi",
+        "author_inst": "Shiraz University of Medical Sciences"
+      },
+      {
+        "author_name": "Hossein Molavi Vardanjan",
+        "author_inst": "Shiraz University of Medical Sciences"
+      },
+      {
+        "author_name": "Maryam Poursadeghfard",
+        "author_inst": "Shiraz University of Medical Sciences"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "neurology"
+  },
   {
     "rel_doi": "10.1101/2020.10.18.20213942",
     "rel_title": "LOCKDOWN FATIGUE AMONG COLLEGE STUDENTS DURING THE COVID-19 PANDEMIC: PREDICTIVE ROLE OF PERSONAL RESILIENCE, COPING BEHAVIOURS, AND HEALTH",
@@ -1118457,53 +1117274,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.10.19.345470",
-    "rel_title": "Structural basis of SARS-CoV-2 polymerase inhibition by Favipiravir",
-    "rel_date": "2020-10-19",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.19.345470",
-    "rel_abs": "The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has developed into an unprecedented global pandemic. Nucleoside analogues, such as Remdesivir and Favipiravir, can serve as the first-line broad-spectrum antiviral drugs against the newly emerging viral diseases. Recent clinical trials of these two drugs for SARS-CoV-2 treatment revealed antiviral efficacies as well as side effects with different extents1-4. As a pyrazine derivative, Favipiravir could be incorporated into the viral RNA products by mimicking both adenine and guanine nucleotides, which may further lead to mutations in progeny RNA copies due to the non-conserved base-pairing capacity5. Here, we determined the cryo-EM structure of Favipiravir bound to the replicating polymerase complex of SARS-CoV-2 in the pre-catalytic state. This structure provides a missing snapshot for visualizing the catalysis dynamics of coronavirus polymerase, and reveals an unexpected base-pairing pattern between Favipiravir and pyrimidine residues which may explain its capacity for mimicking both adenine and guanine nucleotides. These findings shed lights on the mechanism of coronavirus polymerase catalysis and provide a rational basis for developing antiviral drugs to combat the SARS-CoV-2 pandemic.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Qi Peng",
-        "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences"
-      },
-      {
-        "author_name": "Ruchao Peng",
-        "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences"
-      },
-      {
-        "author_name": "Bin Yuan",
-        "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences"
-      },
-      {
-        "author_name": "Min Wang",
-        "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences"
-      },
-      {
-        "author_name": "Jingru Zhao",
-        "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences"
-      },
-      {
-        "author_name": "Lifen Fu",
-        "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences"
-      },
-      {
-        "author_name": "Jianxun Qi",
-        "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences"
-      },
-      {
-        "author_name": "Yi Shi",
-        "author_inst": "Institute Of Microbiology Chinese Academy of Sciences"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.10.19.345363",
     "rel_title": "SARS-CoV and SARS-CoV-2 are transmitted through the air between ferrets over more than one meter distance",
@@ -1118722,6 +1117492,77 @@
     "type": "new results",
     "category": "biochemistry"
   },
+  {
+    "rel_doi": "10.1101/2020.10.19.343954",
+    "rel_title": "Single cell resolution of SARS-CoV-2 tropism, antiviral responses, and susceptibility to therapies in primary human airway epithelium",
+    "rel_date": "2020-10-19",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.19.343954",
+    "rel_abs": "The human airway epithelium is the initial site of SARS-CoV-2 infection. We used flow cytometry and single cell RNA-sequencing to understand how the heterogeneity of this diverse cell population contributes to elements of viral tropism and pathogenesis, antiviral immunity, and treatment response to remdesivir. We found that, while a variety of epithelial cell types are susceptible to infection, ciliated cells are the predominant cell target of SARS-CoV-2. The host protease TMPRSS2 was required for infection of these cells. Importantly, remdesivir treatment effectively inhibited viral replication across cell types, and blunted hyperinflammatory responses. Induction of interferon responses within infected cells was rare and there was significant heterogeneity in the antiviral gene signatures, varying with the burden of infection in each cell. We also found that heavily infected secretory cells expressed abundant IL-6, a potential mediator of COVID-19 pathogenesis.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Jessica K. Fiege",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Joshua M. Thiede",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Hezkiel Nanda",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "William E Matchett",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Patrick J. Moore",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Noe Rico Montanari",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Beth K Thielen",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Jerry Daniel",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Emma Stanley",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Ryan C Hunter",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Vineet D Menachery",
+        "author_inst": "University of Texas Medical Branch"
+      },
+      {
+        "author_name": "Steven S. Shen",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Tyler D. Bold",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Ryan A. Langlois",
+        "author_inst": "University of Minnesota"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2020.10.15.20213348",
     "rel_title": "COVID-19 In a Rural Health System in New York - Case Series and an Approach to Management",
@@ -1120006,65 +1118847,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.10.13.337212",
-    "rel_title": "SARS-CoV-2 S protein ACE2 interaction reveals novel allosteric targets",
-    "rel_date": "2020-10-16",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.13.337212",
-    "rel_abs": "The Spike (S) protein is the main handle for SARS-CoV-2 to enter host cells through surface ACE2 receptors. How ACE2 binding activates proteolysis of S protein is unknown. Here, we have mapped the S:ACE2 interface and uncovered long-range allosteric propagation of ACE2 binding to sites critical for viral host entry. Unexpectedly, ACE2 binding enhances dynamics at a distal S1/S2 cleavage site and flanking protease docking site ~27 [A] away while dampening dynamics of the stalk hinge (central helix and heptad repeat) regions ~ 130 [A] away. This highlights that the stalk and proteolysis sites of the S protein are dynamic hotspots in the pre-fusion state. Our findings provide a mechanistic basis for S:ACE2 complex formation, critical for proteolytic processing and viral-host membrane fusion and highlight protease docking sites flanking the S1/S2 cleavage site, fusion peptide and heptad repeat 1 (HR1) as allosterically exposed cryptic hotspots for potential therapeutic development.\n\nOne Sentence SummarySARS-CoV-2 spike protein binding to receptor ACE2 allosterically enhances furin proteolysis at distal S1/S2 cleavage sites",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Ganesh Srinivasan Anand",
-        "author_inst": "National University of Singapore"
-      },
-      {
-        "author_name": "Raghuvamsi Palur",
-        "author_inst": "National University of Singapore"
-      },
-      {
-        "author_name": "Nikhil Kumar Tulsian",
-        "author_inst": "National University of Singapore"
-      },
-      {
-        "author_name": "Firdaus Samsudin",
-        "author_inst": "A*STAR"
-      },
-      {
-        "author_name": "Xinlei Qian",
-        "author_inst": "National University of Singapore"
-      },
-      {
-        "author_name": "Kiren Purushotorman",
-        "author_inst": "National University of Singapore"
-      },
-      {
-        "author_name": "Gu Yue",
-        "author_inst": "National University of Singapore"
-      },
-      {
-        "author_name": "Mary Kozma McQueen",
-        "author_inst": "National University of Singapore"
-      },
-      {
-        "author_name": "Julien Lescar",
-        "author_inst": "Sorbonne Universit\u00e9s, UPMC Univ Paris 06, INSERM, CNRS"
-      },
-      {
-        "author_name": "Pete Bond",
-        "author_inst": "National University of Singapore"
-      },
-      {
-        "author_name": "Paul Anthony McAry",
-        "author_inst": "National University of Singapore"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "biochemistry"
-  },
   {
     "rel_doi": "10.1101/2020.10.14.20212571",
     "rel_title": "Novel Machine-Learned Approach for COVID-19 Resource Allocation: A Tool for EvaluatingCommunity Susceptibility",
@@ -1120311,6 +1119093,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.10.14.20212555",
+    "rel_title": "Multi-organ impairment in low-risk individuals with long COVID",
+    "rel_date": "2020-10-16",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.14.20212555",
+    "rel_abs": "BackgroundSevere acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) infection has disproportionately affected older individuals and those with underlying medical conditions. Research has focused on short-term outcomes in hospital, and single organ involvement. Consequently, impact of long COVID (persistent symptoms three months post-infection) across multiple organs in low-risk individuals is yet to be assessed.\n\nMethodsAn ongoing prospective, longitudinal, two-centre, observational study was performed in individuals symptomatic after recovery from acute SARS-CoV-2 infection. Symptoms and organ function (heart, lungs, kidneys, liver, pancreas, spleen) were assessed by standardised questionnaires (EQ-5D-5L, Dyspnoea-12), blood investigations and quantitative magnetic resonance imaging, defining single and multi-organ impairment by consensus definitions.\n\nFindingsBetween April and September 2020, 201 individuals (mean age 44 (SD 11.0) years, 70% female, 87% white, 31% healthcare workers) completed assessments following SARS-CoV-2 infection (median 140, IQR 105-160 days after initial symptoms). The prevalence of pre-existing conditions (obesity: 20%, hypertension: 6%; diabetes: 2%; heart disease: 4%) was low, and only 18% of individuals had been hospitalised with COVID-19. Fatigue (98%), muscle aches (88%), breathlessness (87%), and headaches (83%) were the most frequently reported symptoms. Ongoing cardiorespiratory (92%) and gastrointestinal (73%) symptoms were common, and 42% of individuals had ten or more symptoms.\n\nThere was evidence of mild organ impairment in heart (32%), lungs (33%), kidneys (12%), liver (10%), pancreas (17%), and spleen (6%). Single (66%) and multi-organ (25%) impairment was observed, and was significantly associated with risk of prior COVID-19 hospitalisation (p<0.05).\n\nInterpretationIn a young, low-risk population with ongoing symptoms, almost 70% of individuals have impairment in one or more organs four months after initial symptoms of SARS-CoV-2 infection. There are implications not only for burden of long COVID but also public health approaches which have assumed low risk in young people with no comorbidities.\n\nFundingThis work was supported by the UKs National Consortium of Intelligent Medical Imaging through the Industry Strategy Challenge Fund, Innovate UK Grant 104688, and also through the European Unions Horizon 2020 research and innovation programme under grant agreement No 719445.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Andrea Dennis",
+        "author_inst": "Perspectum"
+      },
+      {
+        "author_name": "Malgorzata Wamil",
+        "author_inst": "Great Western Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "Sandeep Kapur",
+        "author_inst": "Mayo Clinic Healthcare"
+      },
+      {
+        "author_name": "Johann Alberts",
+        "author_inst": "Alliance Medical"
+      },
+      {
+        "author_name": "Andrew Badley",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Gustav Anton Decker",
+        "author_inst": "Mayo Clinic International"
+      },
+      {
+        "author_name": "Stacey A Rizza",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Rajarshi Banerjee",
+        "author_inst": "Perspectum"
+      },
+      {
+        "author_name": "Amitava Banerjee",
+        "author_inst": "University College London"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health policy"
+  },
   {
     "rel_doi": "10.1101/2020.10.14.20207050",
     "rel_title": "A betacoronavirus multiplex microsphere immunoassay detects early SARS-CoV-2 seroconversion and controls for pre-existing seasonal human coronavirus antibody cross-reactivity",
@@ -1121656,65 +1120489,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.10.14.20212803",
-    "rel_title": "Characteristics and Factors Associated with COVID-19 Infection, Hospitalization, and Mortality Across Race and Ethnicity",
-    "rel_date": "2020-10-15",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.14.20212803",
-    "rel_abs": "BackgroundData on the characteristics of COVID-19 patients disaggregated by race/ethnicity remain limited. We evaluated the sociodemographic and clinical characteristics of patients across racial/ethnic groups and assessed their associations with COVID-19 outcomes.\n\nMethodsThis retrospective cohort study examined 629,953 patients tested for SARS-CoV-2 in a large health system spanning California, Oregon, and Washington between March 1 and December 31, 2020. Sociodemographic and clinical characteristics were obtained from electronic health records. Odds of SARS-CoV-2 infection, COVID-19 hospitalization, and in-hospital death were assessed with multivariate logistic regression.\n\nResults570,298 patients with known race/ethnicity were tested for SARS-CoV-2, of whom 27.8% were non-White minorities. 54,645 individuals tested positive, with minorities representing 50.1%. Hispanics represented 34.3% of infections but only 13.4% of tests. While generally younger than White patients, Hispanics had higher rates of diabetes but fewer other comorbidities. 8,536 patients were hospitalized and 1,246 died, of whom 56.1% and 54.4% were non-White, respectively. Racial/ethnic distributions of outcomes across the health system tracked with state-level statistics. Increased odds of testing positive and hospitalization were associated with all minority races/ethnicities. Hispanic patients also exhibited increased morbidity, and Hispanic race/ethnicity was associated with in-hospital mortality (OR: 1.39 [95% CI: 1.14-1.70]).\n\nConclusionMajor healthcare disparities were evident, especially among Hispanics who tested positive at a higher rate, required excess hospitalization and mechanical ventilation, and had higher odds of in-hospital mortality despite younger age. Targeted, culturally-responsive interventions and equitable vaccine development and distribution are needed to address the increased risk of poorer COVID-19 outcomes among minority populations.\n\nKey pointsRacial/ethnic disparities are evident in the disaggregated characteristics of COVID-19 patients. Minority patients experience increased odds of SARS-CoV-2 infection and COVID-19 hospitalization. Hospitalized Hispanic patients presented with more severe illness, experienced increased morbidity, and faced increased mortality.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Chengzhen L Dai",
-        "author_inst": "Institute for Systems Biology, Seattle, WA, USA"
-      },
-      {
-        "author_name": "Sergey A Kornilov",
-        "author_inst": "Institute for Systems Biology, Seattle, WA, USA"
-      },
-      {
-        "author_name": "Ryan T Roper",
-        "author_inst": "Institute for Systems Biology, Seattle, WA, USA"
-      },
-      {
-        "author_name": "Hannah Cohen-Cline",
-        "author_inst": "Providence Center for Outcomes Research and Education, Providence Health System, Renton, WA, USA"
-      },
-      {
-        "author_name": "Kathleen Jade",
-        "author_inst": "Institute for Systems Biology, Seattle, WA, USA"
-      },
-      {
-        "author_name": "Brett Smith",
-        "author_inst": "Institute for Systems Biology, Seattle, WA, USA"
-      },
-      {
-        "author_name": "James R Heath",
-        "author_inst": "Institute for Systems Biology, Seattle, WA, USA"
-      },
-      {
-        "author_name": "George Diaz",
-        "author_inst": "Providence Regional Medical Center, Everett, WA, USA"
-      },
-      {
-        "author_name": "Jason D Goldman",
-        "author_inst": "Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA, USA"
-      },
-      {
-        "author_name": "Andrew T Magis",
-        "author_inst": "Institute for Systems Biology, Seattle, WA, USA"
-      },
-      {
-        "author_name": "Jennifer J Hadlock",
-        "author_inst": "Institute for Systems Biology, Seattle, WA, USA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.10.13.20212258",
     "rel_title": "Development of a deep learning classifier to accurately distinguish COVID-19 from look-a-like pathology on lung ultrasound",
@@ -1122029,6 +1120803,69 @@
     "type": "new results",
     "category": "biochemistry"
   },
+  {
+    "rel_doi": "10.1101/2020.10.14.339952",
+    "rel_title": "Multiplexed proteomics and imaging of resolving and lethal SARS-CoV-2 infection in the lung",
+    "rel_date": "2020-10-15",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.14.339952",
+    "rel_abs": "Normal tissue physiology and repair depends on communication with the immune system. Understanding this communication at the molecular level in intact tissue requires new methods. The consequences of SARS-CoV-2 infection, which can result in acute respiratory distress, thrombosis and death, has been studied primarily in accessible liquid specimens such as blood, sputum and bronchoalveolar lavage, all of which are peripheral to the primary site of infection in the lung. Here, we describe the combined use of multiplexed deep proteomics with multiplexed imaging to profile infection and its sequelae directly in fixed lung tissue specimens obtained from necropsy of infected animals and autopsy of human decedents. We characterize multiple steps in disease response from cytokine accumulation and protein phosphorylation to activation of receptors, changes in signaling pathways, and crosslinking of fibrin to form clots. Our data reveal significant differences between naturally resolving SARS-CoV-2 infection in rhesus macaques and lethal COVID-19 in humans. The approach we describe is broadly applicable to other tissues and diseases.\n\nSummaryProteomics of infected tissue reveals differences in inflammatory and thrombotic responses between resolving and lethal COVID-19.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Marian Kalocsay",
+        "author_inst": "Harvard Medical School"
+      },
+      {
+        "author_name": "Zoltan Maliga",
+        "author_inst": "Harvard Medical School"
+      },
+      {
+        "author_name": "Ajit J Nirmal",
+        "author_inst": "Harvard Medical School"
+      },
+      {
+        "author_name": "Robyn J Eisert",
+        "author_inst": "Harvard Medical School"
+      },
+      {
+        "author_name": "Gary A Bradshaw",
+        "author_inst": "Harvard Medical School"
+      },
+      {
+        "author_name": "Yu-An Chen",
+        "author_inst": "Harvard Medical School"
+      },
+      {
+        "author_name": "Roxanne J Pelletier",
+        "author_inst": "Harvard Medical School"
+      },
+      {
+        "author_name": "Connor A Jacobson",
+        "author_inst": "Harvard Medical School"
+      },
+      {
+        "author_name": "Julian Mintseris",
+        "author_inst": "Harvard Medical School"
+      },
+      {
+        "author_name": "Amanda J Martinot",
+        "author_inst": "Tufts University"
+      },
+      {
+        "author_name": "Dan H Barouch",
+        "author_inst": "Beth Israel Deaconess Medical Center, Ragon Institute of MGH, MIT, and Harvard"
+      },
+      {
+        "author_name": "Peter Sorger",
+        "author_inst": "Harvard University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "pathology"
+  },
   {
     "rel_doi": "10.1101/2020.10.15.325050",
     "rel_title": "The Strand-biased Transcription of SARS-CoV-2 and Unbalanced Inhibition by Remdesivir",
@@ -1123150,41 +1121987,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.10.12.20210294",
-    "rel_title": "SARS-CoV-2 sequencing reveals rapid transmission from college student clusters resulting in morbidity and deaths in vulnerable populations",
-    "rel_date": "2020-10-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.12.20210294",
-    "rel_abs": "College reopening decisions during the SARS-CoV-2 pandemic represent a trade-off between competing risks to students, faculty and staff, and college finances. Additionally, risks taken in reopening colleges can impose significant burdens on individuals living in surrounding communities. Many colleges that reopened for in-person instruction have reported frequent SARS-CoV-2 outbreaks. La Crosse County, Wisconsin experienced a substantial SARS-CoV-2 outbreak (2,002 cases in September 2020) that coincided with the return to in-person instruction at three local academic institutions. Genomic sequencing of SARS-CoV-2 cases in La Crosse during that period found rapid expansion of two viral substrains. Although the majority of cases were among college-age individuals, from a total of 111 genomes sequenced we identified rapid transmission of the virus into more vulnerable populations. Eight sampled genomes represented two independent transmission events into two skilled nursing facilities, resulting in two fatalities. Our study highlights the very significant risks imposed by college administrator reopening decisions, not just on college-associated populations, but on vulnerable individuals in surrounding communities.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Craig S Richmond",
-        "author_inst": "Gundersen Medical Foundation"
-      },
-      {
-        "author_name": "Arick P Sabin",
-        "author_inst": "Gundersen Health System"
-      },
-      {
-        "author_name": "Dean A Jobe",
-        "author_inst": "Gundersen Medical Foundation"
-      },
-      {
-        "author_name": "Steven D Lovrich",
-        "author_inst": "Gundersen Medical Foundation"
-      },
-      {
-        "author_name": "Paraic A Kenny",
-        "author_inst": "Gundersen Medical Foundation"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.10.12.20211532",
     "rel_title": "Early Crowdfunding Response to the COVID-19 Pandemic",
@@ -1123415,6 +1122217,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pharmacology and therapeutics"
   },
+  {
+    "rel_doi": "10.1101/2020.10.13.20178483",
+    "rel_title": "Automated chest radiograph diagnosis: A Twofer for tuberculosis and Covid-19",
+    "rel_date": "2020-10-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.13.20178483",
+    "rel_abs": "Coronavirus disease (Covid 19) and Tuberculosis (TB) are two challenges the world is facing. TB is a pandemic which has challenged mankind for ages and Covid 19 is a recent onset fast spreading pandemic. We study these two conditions with focus on Artificial Intelligence (AI) based imaging, the role of digital chest x-ray and utility of end to end platform to improve turnaround times. Using artificial intelligence assisted technology for triage and creation of structured radiology reports using an end to end platform can ensure quick diagnosis. Changing dynamics of TB screening in the times of Covid 19 pandemic have resulted in bottlenecks for TB diagnosis. The paper tries to outline two types of use cases, one is COVID-19 screening in a hospital-based scenario and the other is TB screening project in mobile van setting and discusses the learning of these models which have both used AI for prescreening and generating structured radiology reports.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Mitusha Verma",
+        "author_inst": "Nanavati Hospital"
+      },
+      {
+        "author_name": "Deepak Patkar",
+        "author_inst": "Nanavati Hospital"
+      },
+      {
+        "author_name": "Madhura Ingalhalikar",
+        "author_inst": "Symbiosis Center for Medical Image Analysis, Symbiosis International University"
+      },
+      {
+        "author_name": "Amit Kharat",
+        "author_inst": "DeepTek Inc"
+      },
+      {
+        "author_name": "Pranav Ajmera",
+        "author_inst": "Dr D Y Patil Hospital and Medical College, D Y Patil University, Pune"
+      },
+      {
+        "author_name": "Viraj Kulkarni",
+        "author_inst": "Deeptek Inc"
+      },
+      {
+        "author_name": "Aniruddha Pant",
+        "author_inst": "Deeptek Inc"
+      },
+      {
+        "author_name": "Vaishnavi Thakker",
+        "author_inst": "Dr D Y Patil Medical College, Hospital and Research Centre, Dr D Y Patil University, Pune"
+      },
+      {
+        "author_name": "Gunjan Naik",
+        "author_inst": "Deeptek Inc"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.10.12.20211565",
     "rel_title": "Funding and COVID-19 Research Priorities - Are the research needs for Africa being met?",
@@ -1124884,33 +1123737,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "genetic and genomic medicine"
   },
-  {
-    "rel_doi": "10.1101/2020.10.13.20211425",
-    "rel_title": "Dynamic dysregulation of IL-6 and genes functional in NETosis, complement and coagulation in severe COVID-19 illness",
-    "rel_date": "2020-10-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.13.20211425",
-    "rel_abs": "Comprehensive and unbiased re-analysis of published blood transcriptome data from patients of COVID-19 reveals significant up-regulation of the gene set functional in NETosis, but no evidence of general \"cytokine storm\". In severe COVID-19 illness, there is significant up-regulation of complement and coagulation pathway, and negative correlation between NETosis and respiratory function (oxygen saturation). Interestingly, there is an early spike in the level of IL-6 gene expression in severe illness compared to moderate illness. With passing days post-onset, the level of IL-6 expression in severe illness approaches that in moderate illness. The data are consistent with IL-6 acting as a driver of NETosis in the early phase of severe COVID-19 illness, that results in a vicious cycle of NETosis-complement/coagulation-respiratory dysfunction. This has important consequence for timing of rational therapy with anti-IL-6 and NETosis inhibitors in severe COVID-19 illness.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Samanwoy Mukhopadhyay",
-        "author_inst": "National Institute of Biomedical Genomics, Kalyani, West Bengal - 741251, India"
-      },
-      {
-        "author_name": "Subrata Sinha",
-        "author_inst": "All India Institute of Medical Sciences, Ansari Nagar, New Delhi - 110029, India"
-      },
-      {
-        "author_name": "Saroj Kant Mohapatra",
-        "author_inst": "National Institute of Biomedical Genomics, Kalyani, West Bengal - 741251, India"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.10.13.20212035",
     "rel_title": "Virus detection and identification in minutes using single-particle imaging and deep learning",
@@ -1125277,6 +1124103,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.10.13.20211904",
+    "rel_title": "Background and concurrent factors predicting non-adherence to public health preventive measures during the chronic phase of the COVID-19 pandemic",
+    "rel_date": "2020-10-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.13.20211904",
+    "rel_abs": "To determine factors that predict non-adherence to preventive measures for COVID-19 during the chronic phase of the pandemic, a cross-sectional, general population survey was conducted in Israel. Sociodemographic, health-related, behavioral, and COVID-19-related characteristics were collected. Among 2055 participants, non-adherence was associated with male gender, young age, bachelorhood, being employed, lower decrease in income, low physical activity, psychological distress, ADHD symptoms, past risk-taking and anti-social behavior, low pro-sociality, perceived social norms favoring non-adherence, low perceived risk of COVID-19, low perceived efficacy of the preventive measures, and high perceived costs of adherence to the preventive measures. There appears to be a need for setting out and communicating preventive measures to specifically targeted at-risk populations.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Yehuda Pollak",
+        "author_inst": "The Hebrew University of Jerusalem"
+      },
+      {
+        "author_name": "Rachel Shoham",
+        "author_inst": "Talpiot College"
+      },
+      {
+        "author_name": "Haym Dayan",
+        "author_inst": "The Hebrew University of Jerusalem"
+      },
+      {
+        "author_name": "Ortal Gabrieli Seri",
+        "author_inst": "The Hebrew University of Jerusalem"
+      },
+      {
+        "author_name": "Itai Berger",
+        "author_inst": "The Hebrew University of Jerusalem"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.10.11.20210849",
     "rel_title": "Post mortem pathological findings in COVID-19 cases: A Systematic Review",
@@ -1126542,25 +1125403,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.10.09.20209866",
-    "rel_title": "Development and evaluation of a new IgM/IgG rapid diagnostic test for SARS-CoV-2",
-    "rel_date": "2020-10-13",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.09.20209866",
-    "rel_abs": "There is an urgent need in rapid diagnostic test (RDT) to detect antibodies against SARS-CoV-2. We have developed a rapid and simple point-of-care lateral flow immunoassay (LFIA) detecting IgM and IgG against SARS-CoV-2 in 10 minutes. The aim of this study is to evaluate the diagnostic performance of this RDT. RT-PCR positive plasma samples (n=35) for SARS-CoV-2 and 97 negative control samples were studied. Diagnostic performance of IgG/IgM RDT was assessed using both gold standard RT-PCR and Electro-chemiluminescence immunoassay (ECLIA) Elecsys(R) Anti-SARS-CoV-2 total Ig. Overall, RDT sensitivity was 100% (95% confidence interval [95%CI]: 88-100%) and specificity 93% (95% CI: 85-97%). This IgG/IgM RDT done in plasma displays a high diagnostic accuracy for SARS-CoV-2 IgG/IgM in high COVID-19 prevalence settings. Its use could be considered in the absence of routine diagnostic serology facilities for samples collected between 10 and 180 days after symptoms onset.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Percevent Jeremy Ducrest",
-        "author_inst": "GaDia SA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.10.10.20210096",
     "rel_title": "Extracorporeal Blood Purification in moderate and severe COVID-19 patients: a prospective cohort study",
@@ -1126854,6 +1125696,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.10.10.20210427",
+    "rel_title": "Mathematical Modeling of COVID-19 pandemic in the African continent",
+    "rel_date": "2020-10-13",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.10.20210427",
+    "rel_abs": "The present work aims to give a contribution to the understanding of the highly infectious pandemic caused by the COVID-19 in the African continent. The study focuses on the modelling and the forecasting of COVID-19 spread in the most affected African continent, namely: Morocco, Algeria, Tunisia, Egypt and South Africa and for the sake of comparison two of the most affected European country are also considered, namely: France and Italy. To this end, an epidemiological SEIQRDP model is presented, which is an adaptation of the classic SIR model widely used in mathematical epidemiology. In order to better coincide with the preventive measures taken by the governments to deal with the spread of COVID-19, this model considers the quarantine. For the identification of the models parameters, official data of the pandemic up to August 1st, 2020 are considered. The results show that the number of infections due to the use of quarantine is expected to be very low provided the isolation is effective. However, it is increasing in some countries with the early lifting of containment. Finally, the information provided by the SEIQRDP model could help to establish a realistic assessment of the short-term pandemic situation. Moreover, this will help maintain the most appropriate and necessary public health measures after the lockdown lifting.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Nawel ARIES",
+        "author_inst": "Centre de Developpement des Energies Renouvelables"
+      },
+      {
+        "author_name": "Houdayfa OUNIS",
+        "author_inst": "Institut de Recherche Dupuy de Lome,CNRS UMR 6027, IRDL, Lorient F-56100, France"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.10.09.20209429",
     "rel_title": "Robust test and trace strategies can prevent COVID-19 resurgences: a case study from New South Wales, Australia",
@@ -1128671,73 +1127536,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.10.09.20209858",
-    "rel_title": "COVID-19 serological survey using micro blood sampling",
-    "rel_date": "2020-10-13",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.09.20209858",
-    "rel_abs": "During August 2020, we carried out a serological survey among students and employees at the Okinawa Institute of Science and Technology Graduate University (OIST), Japan, testing for the presence of antibodies against SARS-CoV-2, the causative agent of COVID-19. We used a FDA-authorized 2-step ELISA protocol (1, 2) in combination with at-home self-collection of blood samples using a custom low-cost finger prick-based capillary blood collection kit. Although our survey did not find any COVID-19 seropositive individuals among the OIST cohort, it reliably detected all positive control samples obtained from a local hospital and excluded all negatives controls. We found that high serum antibody titers can persist for at least up to 6.5 months post infection. Among our controls, we found strong cross-reactivity of antibodies in samples from a serum pool from two MERS patients in the anti-SARS-CoV-2-S ELISA. Here we show that a centralized ELISA in combination with patient-based capillary blood collection using as little as one drop of blood can reliably assess the seroprevalence among communities. Anonymous sample tracking and an integrated website created a stream-lined procedure. Major parts of the workflow were automated on a liquid handler, demonstrating scalability. We anticipate this concept to serve as a prototype for reliable serological testing among larger populations.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Melissa M Matthews",
-        "author_inst": "Okinawa Institute of Science and Technology Graduate University"
-      },
-      {
-        "author_name": "Tae Gyun Kim",
-        "author_inst": "Okinawa Institute of Science and Technology Graduate University"
-      },
-      {
-        "author_name": "Satoshi Shibata",
-        "author_inst": "Okinawa Institute of Science and Technology Graduate University"
-      },
-      {
-        "author_name": "Noriko Shibata",
-        "author_inst": "Okinawa Institute of Science and Technology Graduate University"
-      },
-      {
-        "author_name": "Christian Butcher",
-        "author_inst": "Okinawa Institute of Science and Technology Graduate University"
-      },
-      {
-        "author_name": "Jaekyung Hyun",
-        "author_inst": "Okinawa Institute of Science and Technology Graduate University"
-      },
-      {
-        "author_name": "Keon Young Kim",
-        "author_inst": "Okinawa Institute of Science and Technology Graduate University"
-      },
-      {
-        "author_name": "Theodore Robb",
-        "author_inst": "Okinawa Institute of Science and Technology Graduate University"
-      },
-      {
-        "author_name": "Siang Sheng Jheng",
-        "author_inst": "Okinawa Institute of Science and Technology Graduate University"
-      },
-      {
-        "author_name": "Masashi Narita",
-        "author_inst": "Okinawa Chubu Hospital, Division of Infectious Diseases"
-      },
-      {
-        "author_name": "Tomoari Mori",
-        "author_inst": "Okinawa Institute of Science and Technology Graduate University"
-      },
-      {
-        "author_name": "Mary Collins",
-        "author_inst": "Okinawa Institute of Science and Technology Graduate University"
-      },
-      {
-        "author_name": "Matthias Wolf",
-        "author_inst": "Okinawa Institute of Science and Technology Graduate University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.10.08.20209684",
     "rel_title": "Examining Unit Costs for COVID-19 Case Management in Kenya",
@@ -1129204,6 +1128002,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.10.08.20208991",
+    "rel_title": "Covid Pandemic Analysis using Regression",
+    "rel_date": "2020-10-13",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.08.20208991",
+    "rel_abs": "Covid-19 is a pandemic which has affected all parts of the world. Covid-19 is a pandemic which can be controlled only by maintaining social distancing, proper hygiene, wearing mask, hand sanitation and to a extend by wearing face shield. Even though each state has followed their own ways of controlling the infection, awareness among citizens and behaving as responsible citizens is very important in controlling this disease. Contact tracing plays an important role in controlling this pandemic. This paper deals with the effect of Covid-19 in various states of India and also forecasts its effect using machine learning techniques. Regression analysis like Linear and polynomial have been used for analysis of Covid-19, where Kaggle dataset has been used. This helps in understanding the much-affected states in India and helps to understand the infrastructure requirements to handle this pandemic efficiently.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Raji P",
+        "author_inst": "NMIT"
+      },
+      {
+        "author_name": "Deeba Lakshmi G R",
+        "author_inst": "NMIT"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.10.09.20209981",
     "rel_title": "The risk for a new COVID-19 wave -- and how it depends on $R_0$, the current immunity level and current restrictions",
@@ -1130272,53 +1129093,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "medical education"
   },
-  {
-    "rel_doi": "10.1101/2020.10.08.20209304",
-    "rel_title": "Prevalence of COVID-19-related risk factors and risk of severe influenza outcomes in cancer survivors: a matched cohort study using linked English electronic health records data",
-    "rel_date": "2020-10-12",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.08.20209304",
-    "rel_abs": "BackgroundPeople with active cancer are recognised as at risk of COVID-19 complications, but it is unclear whether the much larger population of cancer survivors is at elevated risk. We aimed to address this by comparing cancer survivors and cancer-free controls for (i) prevalence of comorbidities considered risk factors for COVID-19; and (ii) risk of severe influenza, as a marker of susceptibility to severe outcomes from epidemic respiratory viruses.\n\nMethodsWe included survivors ([&ge;]1 year) of the 20 most common cancers, and age, sex and general practice-matched cancer-free controls, derived from UK primary care data linked to cancer registrations, hospital admissions and death registrations. Comorbidity prevalences were calculated 1 and 5 years from cancer diagnosis. Risk of hospitalisation or death due to influenza was compared using Cox models adjusted for baseline demographics and comorbidities.\n\nFindings108,215 cancer survivors and 523,541 cancer-free controls were included. Cancer survivors had more asthma, other respiratory, cardiac, diabetes, neurological, renal, and liver disease, and less obesity, compared with controls, but there was variation by cancer site. There were 205 influenza hospitalisations/deaths, with cancer survivors at higher risk than controls (adjusted HR 2.78, 95% CI 2.04-3.80). Haematological cancer survivors had large elevated risks persisting for >10 years (HR overall 15.17, 7.84-29.35; HR >10 years from cancer diagnosis 10.06, 2.47-40.93). Survivors of other cancers had evidence of raised risk up to 5 years from cancer diagnosis only (HR 2.22, 1.31-3.74).\n\nInterpretationRisks of severe COVID-19 outcomes are likely to be elevated in cancer survivors. This should be taken into account in policies targeted at clinical risk groups, and vaccination for both influenza, and, when available, COVID-19, should be encouraged in cancer survivors.\n\nFundingWellcome Trust, Royal Society, NIHR.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSFew data are available to date on how COVID-19 affects cancer survivors. We searched PubMed with the keywords \"influenza cancer survivors\" to identify studies that compared severe influenza outcomes in cancer survivors and in a control group. No study was identified.\n\nAdded value of this studyIn this matched cohort study of routinely collected electronic health records, we demonstrated raised risks of influenza hospitalisation or mortality in survivors from haematological malignancies for >10 years after diagnosis, and in survivors from solid cancers up to 5 years after diagnosis.\n\nImplications of all the available evidenceCancer survivorship appears to be an important risk factor for severe influenza outcomes, suggesting that cancer survivors may also be at raised risk of poor COVID-19 outcomes. This should be taken into account in public health policies targeted at protecting clinical risk groups. Influenza vaccination should be encouraged in this group, and may need to be extended to a wider population of medium- to long-term cancer survivors than currently recommended.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Helena Carreira",
-        "author_inst": "London School of Hygiene & Tropical Medicine"
-      },
-      {
-        "author_name": "Helen Strongman",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Maria Peppa",
-        "author_inst": "London School of Hygiene and Tropical Medicine; NIHR Health Protection Research Unit in Immunisation"
-      },
-      {
-        "author_name": "Helen I McDonald",
-        "author_inst": "London School of Medicine and Tropical Medicine, NIHR Health Protection Research Unit in Immunisation"
-      },
-      {
-        "author_name": "Isabel dos-Santos-Silva",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Susannah Stanway",
-        "author_inst": "The Royal Marsden NHS Foundation Trust"
-      },
-      {
-        "author_name": "Liam Smeeth",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Krishnan Bhaskaran",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "oncology"
-  },
   {
     "rel_doi": "10.1101/2020.10.08.20209593",
     "rel_title": "COVID-19 Susceptibility and Severity Risks in a Survey of Over 500,000 People",
@@ -1130649,6 +1129423,201 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.10.10.20210492",
+    "rel_title": "Transmission of SARS-CoV-2 from Children and Adolescents",
+    "rel_date": "2020-10-12",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.10.20210492",
+    "rel_abs": "A better understanding of SARS-CoV-2 transmission from children and adolescents is crucial for informing public health mitigation strategies. We conducted a retrospective cohort study among household contacts of primary cases defined as children and adolescents aged 719 years with laboratory evidence of SARS-CoV-2 infection acquired during an overnight camp outbreak. Among household contacts, we defined secondary cases using the Council of State and Territorial Epidemiologists definition. Among 526 household contacts of 224 primary cases, 48 secondary cases were identified, corresponding to a secondary attack rate of 9% (95% confidence interval [CI], 7%-12%). Our findings show that children and adolescents can transmit SARS-CoV-2 to adult contacts and other children in a household setting.",
+    "rel_num_authors": 45,
+    "rel_authors": [
+      {
+        "author_name": "Victoria T. Chu",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Anna R. Yousaf",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Karen Chang",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Noah Schwartz",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Clinton McDaniel",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Christine Szablewski",
+        "author_inst": "Georgia Department of Public Health"
+      },
+      {
+        "author_name": "Marie Brown",
+        "author_inst": "Georgia Department of Public Health"
+      },
+      {
+        "author_name": "Kathryn Winglee",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Scott Lee",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Zhaohui Cui",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Adebola Adebayo",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Tiffiany Aholou",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Minal Amin",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Peter Aryee",
+        "author_inst": "Georgia Department of Public Health"
+      },
+      {
+        "author_name": "Cindy Castaneda",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Trudy Chambers",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Amy Fleshman",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Christin Goodman",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Tony Holmes",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Asha Ivey-Stephenson",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Emiko Kamitani",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Susan Katz",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Jennifer Knapp",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Maureen Kolasa",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Maranda Lumsden",
+        "author_inst": "Georgia Department of Public Health"
+      },
+      {
+        "author_name": "Erin Mayweather",
+        "author_inst": "Georgia Department of Public Health"
+      },
+      {
+        "author_name": "Asfia Mohammed",
+        "author_inst": "Georgia Department of Public Health"
+      },
+      {
+        "author_name": "Anne Moorman",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Alpa Patel-Larson",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Lara Perinet",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Mark Pilgard",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Deirdre Pratt",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Shanica Railey",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Jaina Shah",
+        "author_inst": "Georgia Department of Public Health"
+      },
+      {
+        "author_name": "Dawn Tuckey",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Emilio Dirlikov",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Dale Rose",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Julie Villanueva",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Alicia Fry",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Aron Hall",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Hannah Kirking",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Jacqueline Tate",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Cherie Drenzek",
+        "author_inst": "Georgia Department of Public Health"
+      },
+      {
+        "author_name": "Tatiana Lanzieri",
+        "author_inst": "Centers for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Rebekah Stewart",
+        "author_inst": "Centers for Disease Control and Prevention"
+      }
+    ],
+    "version": "1",
+    "license": "cc0",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.10.11.20210773",
     "rel_title": "Summer School Holidays and the Growth Rate in Sars-CoV-2 Infections Across German Districts",
@@ -1131894,57 +1130863,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "respiratory medicine"
   },
-  {
-    "rel_doi": "10.1101/2020.10.09.20210237",
-    "rel_title": "Risk of death during the 2020 UK COVID-19 epidemic among people with rare autoimmune diseases compared to the general population. Preliminary results from the RECORDER project.",
-    "rel_date": "2020-10-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.09.20210237",
-    "rel_abs": "ObjectivesTo quantify the risk of death among people with rare autoimmune rheumatic diseases (RAIRD) during the UK 2020 COVID-19 pandemic compared to the general population, and compared to their pre-COVID risk.\n\nMethodsWe conducted a cohort study in Hospital Episode Statistics for England 2003 onwards, and linked data from the NHS Personal Demographics Service. We used ONS published data for general population mortality rates.\n\nResultsWe included 168,691 people with a recorded diagnosis of RAIRD alive on 01/03/2020. Their median age was 61.7 (IQR 41.5-75.4) years, and 118,379 (70.2%) were female. Our case ascertainment methods had a positive predictive value of 85%. 1,815 (1.1%) participants died during March and April 2020. The age-standardised mortality rate (ASMR) among people with RAIRD (3669.3, 95% CI 3500.4-3838.1 per 100,000 person-years) was 1.44 (95% CI 1.42-1.45) times higher than the average ASMR during the same months of the previous 5 years, whereas in the general population of England it was 1.38 times higher. Age-specific mortality rates in people with RAIRD compared to the pre-COVID rates were higher from the age of 35 upwards, whereas in the general population the increased risk began from age 55 upwards. Women had a greater increase in mortality rates during COVID-19 compared to men.\n\nConclusionThe risk of all-cause death is more prominently raised during COVID-19 among people with RAIRD than among the general population. We urgently need to quantify how much risk is due to COVID-19 infection and how much is due to disruption to healthcare services.\n\nKey messagesO_LIPeople with RAIRD had an increased risk of dying during COVID-19 from age 35 years onwards, whereas in the general population it increased from the age of 55 onwards.\nC_LIO_LIWomen had a greater increase in their risk of death during COVID-19 compared to men.\nC_LIO_LIThe risk of working age people with RAIRD dying during COVID-19 was similar to that of someone 20 years older in the general population.\nC_LI",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Emily J Peach",
-        "author_inst": "University of Nottingham"
-      },
-      {
-        "author_name": "Megan Rutter",
-        "author_inst": "University of Nottingham"
-      },
-      {
-        "author_name": "Peter C Lanyon",
-        "author_inst": "Nottingham University Hospitals NHS Trust"
-      },
-      {
-        "author_name": "Matthew J Grainge",
-        "author_inst": "University of Nottingham"
-      },
-      {
-        "author_name": "Richard B Hubbard",
-        "author_inst": "University of Nottingham"
-      },
-      {
-        "author_name": "Jeanette Aston",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Mary Bythell",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Sarah Stevens",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Fiona A Pearce",
-        "author_inst": "University of Nottingham"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "rheumatology"
-  },
   {
     "rel_doi": "10.1101/2020.10.06.20205369",
     "rel_title": "Extended laboratory panel testing in the Emergency Department for risk-stratification of patients with COVID-19: a single centre retrospective service evaluation",
@@ -1132411,6 +1131329,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.10.06.20208025",
+    "rel_title": "Enoxaparin is associated with lower rates of thrombosis, kidney injury, and mortality than Unfractionated Heparin in hospitalized COVID patients",
+    "rel_date": "2020-10-11",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.06.20208025",
+    "rel_abs": "Although anticoagulants such as unfractionated heparin and low molecular weight heparin (LMWH, e.g. enoxaparin) are both being used for therapeutic mitigation of COVID associated coagulopathy (CAC), differences in their clinical outcomes remain to be investigated. Here, we employ automated neural networks supplemented with expert curation ( augmented curation) for retrospectively analyzing the complete electronic health records (EHRs) of 671 hospitalized COVID-19 patients administered either enoxaparin or unfractionated heparin, but not both. We find that COVID-19 patients administered unfractionated heparin but not enoxaparin have higher rates of mortality (risk ratio: 2.6; 95% C.I.: [1.2-5.4]; p-value: 0.02; BH adjusted p-value: 0.09), thrombotic events (risk ratio: 5.7, 95% C.I.: [2.1, 33.9], p-value: 0.024), acute kidney injury (risk ratio: 5.5; 95% C.I.: [1.2-17.7]; p-value: 0.02; BH adjusted p-value: 0.10), and bacterial pneumonia (risk ratio undefined; 95% C.I.: [1.0, 292]; p-value:0.02; BH adjusted p-value:0.10), compared to patients administered enoxaparin but not unfractionated heparin. Notably, even after controlling for potential confounding factors such as demographics, comorbidities, admission diagnosis, initial ICU status, and initial level of oxygen support, the above differences between the enoxaparin and unfractionated heparin patient cohorts remain statistically significant. This study emphasizes the need for mechanistically investigating differential modulation of the COVID-associated coagulation cascades by enoxaparin versus unfractionated heparin.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Colin Pawlowski",
+        "author_inst": "nference"
+      },
+      {
+        "author_name": "AJ Venkatakrishnan",
+        "author_inst": "nference"
+      },
+      {
+        "author_name": "Christian Kirkup",
+        "author_inst": "nference"
+      },
+      {
+        "author_name": "Gabriela Berner",
+        "author_inst": "nference"
+      },
+      {
+        "author_name": "Arjun Puranik",
+        "author_inst": "nference"
+      },
+      {
+        "author_name": "John C O'Horo",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Andrew D Badley",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Venky Soundararajan",
+        "author_inst": "nference"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.10.09.20210302",
     "rel_title": "Polyester Nasal Swabs Collected in a Dry Tube are a Robust and Inexpensive, Minimal Self-Collection Kit for SARS-CoV-2 Testing",
@@ -1133764,85 +1132729,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.10.06.20205864",
-    "rel_title": "AncestryDNA COVID-19 Host Genetic Study Identifies Three Novel Loci",
-    "rel_date": "2020-10-09",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.06.20205864",
-    "rel_abs": "Human infection with SARS-CoV-2, the causative agent of COVID-19, leads to a remarkably diverse spectrum of outcomes, ranging from asymptomatic to fatal. Recent reports suggest that both clinical and genetic risk factors may contribute to COVID-19 susceptibility and severity. To investigate genetic risk factors, we collected over 500,000 COVID-19 survey responses between April and May 2020 with accompanying genetic data from the AncestryDNA database. We conducted sex-stratified and meta-analyzed genome-wide association studies (GWAS) for COVID-19 susceptibility (positive nasopharyngeal swab test, ncases=2,407) and severity (hospitalization, ncases=250). The severity GWAS replicated associations with severe COVID-19 near ABO and SLC6A20 (P<0.05). Furthermore, we identified three novel loci with P<5x10-8. The strongest association was near IVNS1ABP, a gene involved in influenza virus replication1, and was associated only in males. The other two novel loci harbor genes with established roles in viral replication or immunity: SRRM1 and the immunoglobulin lambda locus. We thus present new evidence that host genetic variation likely contributes to COVID-19 outcomes and demonstrate the value of large-scale, self-reported data as a mechanism to rapidly address a health crisis.",
-    "rel_num_authors": 16,
-    "rel_authors": [
-      {
-        "author_name": "Genevieve H.L. Roberts",
-        "author_inst": "AncestryDNA, Lehi Utah"
-      },
-      {
-        "author_name": "Danny S. Park",
-        "author_inst": "AncestryDNA, San Francisco, CA"
-      },
-      {
-        "author_name": "Marie V. Coignet",
-        "author_inst": "AncestryDNA, San Francisco, CA"
-      },
-      {
-        "author_name": "Shannon R. McCurdy",
-        "author_inst": "AncestryDNA, San Francisco, CA"
-      },
-      {
-        "author_name": "Spencer C. Knight",
-        "author_inst": "AncestryDNA, San Francisco, CA"
-      },
-      {
-        "author_name": "Raghavendran Partha",
-        "author_inst": "AncestryDNA, San Francisco, CA"
-      },
-      {
-        "author_name": "Brooke Rhead",
-        "author_inst": "AncestryDNA, San Francisco, CA"
-      },
-      {
-        "author_name": "Miao Zhang",
-        "author_inst": "AncestryDNA, San Francisco, CA"
-      },
-      {
-        "author_name": "Nathan Berkowitz",
-        "author_inst": "AncestryDNA, San Francisco, CA"
-      },
-      {
-        "author_name": "AncestryDNA Science Team",
-        "author_inst": "AncestryDNA, San Francisco, CA"
-      },
-      {
-        "author_name": "Asher K. Haug Baltzell",
-        "author_inst": "AncestryDNA, Lehi Utah"
-      },
-      {
-        "author_name": "Harendra Guturu",
-        "author_inst": "AncestryDNA, San Francisco, CA"
-      },
-      {
-        "author_name": "Ahna R. Girshick",
-        "author_inst": "AncestryDNA, San Francisco, CA"
-      },
-      {
-        "author_name": "Kristin A. Rand",
-        "author_inst": "AncestryDNA, San Francisco, CA"
-      },
-      {
-        "author_name": "Eurie L. Hong",
-        "author_inst": "AncestryDNA, San Francisco, CA"
-      },
-      {
-        "author_name": "Catherine A. Ball",
-        "author_inst": "AncestryDNA, San Francisco, CA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.10.07.20208819",
     "rel_title": "Modelling testing and response strategies for COVID-19 outbreaks in remote Australian Aboriginal communities",
@@ -1134085,6 +1132971,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.10.07.20208280",
+    "rel_title": "A high-throughput microfluidic nano-immunoassay for detecting anti-SARS-CoV-2 antibodies in serum or ultra-low volume dried blood samples",
+    "rel_date": "2020-10-09",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.07.20208280",
+    "rel_abs": "Novel technologies are needed to facilitate large-scale detection and quantification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) specific antibodies in human blood samples. Such technologies are essential to support seroprevalence studies, vaccine clinical trials, and to monitor quality and duration of immunity. We developed a microfluidic nano-immunnoassay for the detection of anti-SARS-CoV-2 IgG antibodies in 1024 samples per device. The method achieved a specificity of 100% and a sensitivity of 98% based on the analysis of 289 human serum samples. To eliminate the need for venipuncture, we developed low-cost, ultra-low volume whole blood sampling methods based on two commercial devices and repurposed a blood glucose test strip. The glucose test strip permits the collection, shipment, and analysis of 0.6 {micro}L whole blood easily obtainable from a simple fingerprick. The nano-immunoassay platform achieves high-throughput, high sensitivity and specificity, negligible reagent consumption, and a decentralized and simple approach to blood sample collection. We expect this technology to be immediately applicable to current and future SARS-CoV-2 related serological studies and to protein biomarker diagnostics in general.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Zoe Swank",
+        "author_inst": "Ecole Polytechnique Federale de Lausanne"
+      },
+      {
+        "author_name": "Gr\u00e9goire Michielin",
+        "author_inst": "Ecole Polytechnique Federale de Lausanne"
+      },
+      {
+        "author_name": "Hon Ming Yip",
+        "author_inst": "Ecole Polytechnique Federale de Lausanne"
+      },
+      {
+        "author_name": "Patrick Cohen",
+        "author_inst": "University of Geneva Hospitals"
+      },
+      {
+        "author_name": "Diego O. Andrey",
+        "author_inst": "University of Geneva Hospitals"
+      },
+      {
+        "author_name": "Nicolas Vuilleumier",
+        "author_inst": "University of Geneva Hospitals"
+      },
+      {
+        "author_name": "Laurent Kaiser",
+        "author_inst": "University of Geneva Hospitals"
+      },
+      {
+        "author_name": "Isabella Eckerle",
+        "author_inst": "University of Geneva Hospitals"
+      },
+      {
+        "author_name": "Benjamin Meyer",
+        "author_inst": "University of Geneva"
+      },
+      {
+        "author_name": "Sebastian J. Maerkl",
+        "author_inst": "Ecole Polytechnique Federale de Lausanne"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.10.09.333278",
     "rel_title": "Major role of IgM in the neutralizing activity of convalescent plasma against SARS-CoV-2",
@@ -1135301,49 +1134242,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2020.10.08.331751",
-    "rel_title": "Preferential recognition and antagonism of SARS-CoV-2 spike glycoprotein binding to 3-O-sulfated heparan sulfate",
-    "rel_date": "2020-10-08",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.08.331751",
-    "rel_abs": "The COVID-19 pandemic caused by SARS-CoV-2 is in immediate need of an effective antidote. Although the Spike glycoprotein (SgP) of SARS-CoV-2 has been shown to bind to heparins, the structural features of this interaction, the role of a plausible heparan sulfate proteoglycan (HSPG) receptor, and the antagonism of this pathway through small molecules remain unaddressed. Using an in vitro cellular assay, we demonstrate HSPGs modified by the 3-O-sulfotransferase isoform-3, but not isoform-5, preferentially increased SgP-mediated cell-to-cell fusion in comparison to control, unmodified, wild-type HSPGs. Computational studies support preferential recognition of the receptor-binding domain of SgP by 3-O-sulfated HS sequences. Competition with either fondaparinux, a 3-O-sulfated HS-binding oligopeptide, or a synthetic, non-sugar small molecule, blocked SgP-mediated cell-to-cell fusion. Finally, the synthetic, sulfated molecule inhibited fusion of GFP-tagged pseudo SARS-CoV-2 with human 293T cells with sub-micromolar potency. Overall, overexpression of 3-O-sulfated HSPGs contribute to fusion of SARS-CoV-2, which could be effectively antagonized by a synthetic, small molecule.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Vaibhav Tiwari",
-        "author_inst": "Midwestern University"
-      },
-      {
-        "author_name": "Ritesh Tandon",
-        "author_inst": "University of Mississippi Medical Center"
-      },
-      {
-        "author_name": "Nehru Viji Sankaranarayanan",
-        "author_inst": "Virginia Commonwealth University"
-      },
-      {
-        "author_name": "Jacob C Beer",
-        "author_inst": "Midwestern University"
-      },
-      {
-        "author_name": "Ellen K Kohlmeir",
-        "author_inst": "Midwestern University"
-      },
-      {
-        "author_name": "Michelle Swanson-Mungerson",
-        "author_inst": "Midwestern University"
-      },
-      {
-        "author_name": "Umesh R. Desai",
-        "author_inst": "Virginia Commonwealth University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "biochemistry"
-  },
   {
     "rel_doi": "10.1101/2020.10.07.326462",
     "rel_title": "Genome-scale identification of SARS-CoV-2 and pan-coronavirus host factor networks",
@@ -1135682,6 +1134580,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.10.02.20205674",
+    "rel_title": "Mental health symptoms in a cohort of hospital healthcare workers following the first peak of the Covid-19 pandemic in the United Kingdom.",
+    "rel_date": "2020-10-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.02.20205674",
+    "rel_abs": "BackgroundThe Covid-19 pandemic is likely to lead to a significant increase in mental health disorders amongst healthcare workers (HCW).\n\nAimsWe evaluated the prevalence of anxiety, depressive and post-traumatic stress disorder (PTSD) symptoms in a HCW population in the United Kingdom (UK), to identify subgroups most at risk.\n\nMethodsAn electronic survey was conducted between the 05/06/2020 and 31/07/2020 of all hospital HCW in the West Midlands, UK using clinically validated questionnaires: Patient Health Questionnaire-4 (PHQ-4) and the Impact of Event Scale-Revised (IES-R). Univariate analyses and adjusted logistic regression analyses were performed to estimate the strengths in associations.\n\nResultsThere were 2638 eligible participants who completed the survey (female: 79.5%, median age: 42 [IQR: 32-51] years). The prevalence rates of clinically significant symptoms of anxiety, depression and PTSD were 34.3%, 31.2% and 24.5% respectively. In adjusted analysis a history of mental health conditions was associated with clinically significant symptoms of anxiety (odds ratio 2.3 [95% CI 1.9-2.7]; p<0.001), depression (2.5 [2.1-3.0]; p<0.001) and PTSD (2.1 [1.7-2.5]; p<0.001). The availability of adequate personal protective equipment (PPE), wellbeing support and lower exposure to moral dilemmas at work demonstrated significant negative associations with former symptoms (p[&le;]0.001).\n\nConclusionsWe report a high prevalence of clinically significant symptoms of anxiety, depression and PTSD in hospital HCW following the initial Covid-19 pandemic peak in the UK. Those with a history of mental health conditions were most at risk. Adequate PPE availability, access to wellbeing support and reduced exposure to moral dilemmas may protect hospital HCW from mental health symptoms.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Kasun Wanigasooriya",
+        "author_inst": "University of Birmingham"
+      },
+      {
+        "author_name": "Priyanka Palimar",
+        "author_inst": "Forward Thinking Birmingham"
+      },
+      {
+        "author_name": "David Naumann",
+        "author_inst": "University Hospitals Birmingham NHS Foundation Trust"
+      },
+      {
+        "author_name": "Khalida Ismail",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Jodie L. Fellows",
+        "author_inst": "University Hospitals Birmingham NHS Foundation Trust"
+      },
+      {
+        "author_name": "Peter Logan",
+        "author_inst": "Walsall Healthcare NHS Trust"
+      },
+      {
+        "author_name": "Christopher V. Thompson",
+        "author_inst": "Sandwell and West Birmingham Hospitals NHS Trust"
+      },
+      {
+        "author_name": "Helen Bermingham",
+        "author_inst": "University Hospitals Birmingham NHS Foundation Trust"
+      },
+      {
+        "author_name": "Andrew D. Beggs",
+        "author_inst": "University of Birmingham"
+      },
+      {
+        "author_name": "Tariq Ismail",
+        "author_inst": "University Hospitals Birmingham NHS Foundation Trust"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "psychiatry and clinical psychology"
+  },
   {
     "rel_doi": "10.1101/2020.10.05.20207423",
     "rel_title": "Psychiatric side effects induced by chloroquine and hydroxychloroquine: a systematic review of case reports and population studies",
@@ -1137111,25 +1136064,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.10.05.20206839",
-    "rel_title": "A Numerical Study of the Current COVID-19 Spread Patterns in India, the USA and the World",
-    "rel_date": "2020-10-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.05.20206839",
-    "rel_abs": "In this article, we are going to study the current COVID-19 spread patterns in India and the United States. We are interested to show how the daily increase in the total number of cases in these two countries is affecting the COVID-19 spread pattern in the World. For the study, we have considered the cumulative total numbers of cases in India, the United States and the World. We have found that the situation in the United States is already on the threshold of a change towards retardation. In the World as a whole also we have observed that a similar conclusion can be made. In India, the situation can be expected to move towards betterment soon, and once that happens the situation in the World as a whole would start improving. We shall demonstrate that as long as the rate of change of the logarithm of the cumulative total number of cases with respect to time in a pandemic continues to reduce, the pattern of growth would continue to remain nearly exponential, and as soon as it is seen that the rate of change starts to become nearly constant the growth can be expected to start to change towards a nearly logarithmic pattern.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Hemanta Kumar Baruah",
-        "author_inst": "The Assam Royal Global University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.10.03.20206185",
     "rel_title": "Fractal and inertia moment analysis of SARS CoV-2 proliferation through replication",
@@ -1137352,6 +1136286,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health economics"
   },
+  {
+    "rel_doi": "10.1101/2020.10.05.20206920",
+    "rel_title": "Development of a customised data management system for a COVID-19-adapted colorectal cancer pathway",
+    "rel_date": "2020-10-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.05.20206920",
+    "rel_abs": "PurposeThe COVID-19 pandemic posed an unprecedented challenge to healthcare systems around the world. To mitigate the risks of those referred with possible colorectal cancer during the pandemic we implemented a clinical pathway which required a customised data management system for robust operation. Here, we describe the principal concepts and evaluation of the performance of a spreadsheet-based data management system.\n\nMethodsA system was developed using Microsoft Excel(R) 2007 aiming to retain the spreadsheets inherent intuitiveness of direct data entry. Data was itemised limiting entry errors. Visual Basic for Applications (VBA) was used to construct a user-friendly interface to enhance efficiency of data entry and segregate the data required for operational tasks. This was done with built-in loop-back data entry. Finally data derivation and analysis was performed to facilitate pathway monitoring.\n\nResultsFor a pathway which required rapid implementation and development of a customised data management system, the use of a spreadsheet was advantageous due to its user-friendly direct data entry capability. Its function was enhanced by UserForm and large data handling by data segregation using VBA macros. Data validation and conditional formatting minimised data entry errors. Computation by the COUNT function facilitated live data monitoring on a dashboard. During the three months the pathway ran for, the system processed 36 nodal data points for each of the included 837 patients. Data monitoring confirmed its accuracy.\n\nConclusionLarge volume data management using a spreadsheet system is possible with appropriate data definition and VBA programmed data segregation. Clinicians regular input and optimisation made the system adaptable for rapid implementation.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Frances Gunn",
+        "author_inst": "1.\tDepartment of Colorectal Surgery, Western General Hospital, Edinburgh, United Kingdom"
+      },
+      {
+        "author_name": "Janice Miller",
+        "author_inst": "1.\tDepartment of Colorectal Surgery, Western General Hospital, Edinburgh, United Kingdom, 2. Clinical Surgery, University of Edinburgh, Edinburgh, United Kingdo"
+      },
+      {
+        "author_name": "Malcolm G Dunlop",
+        "author_inst": "Institute of Genetics and Molecular Medicine"
+      },
+      {
+        "author_name": "Farhat V N Din",
+        "author_inst": "1.\tDepartment of Colorectal Surgery, Western General Hospital, Edinburgh, United Kingdom  2.\tClinical Surgery, University of Edinburgh, Edinburgh, United Kingdo"
+      },
+      {
+        "author_name": "Yasuko Maeda",
+        "author_inst": "Western General Hospital and University of Edinburgh"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health informatics"
+  },
   {
     "rel_doi": "10.1101/2020.10.04.20206516",
     "rel_title": "Rationale and prognosis of repurposed drugs with risk stratification of patients in oxygen support in COVID-19: A systematic review and meta-analysis",
@@ -1138357,61 +1137326,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.10.05.20206805",
-    "rel_title": "The impact of the COVID-19 pandemic on families in Germany",
-    "rel_date": "2020-10-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.05.20206805",
-    "rel_abs": "ObjectiveTo assess the impact of the COVID-19 pandemic on families with young children in two population-based childhood cohorts with a low and moderate COVID-19 prevalence, respectively.\n\nMethodsA cross-sectional study using online questionnaires in families from LIFE Child (n=306, Leipzig) and KUNO Kids (n=612, Regensburg) was performed at the end of the German lock-down period. Outcomes were parent-reported impact of the COVID-19 pandemic on family life, concerns and trust in political measures.\n\nResultsMost families were concerned about the COVID-19 pandemic and lock-down measures, with major concerns directed towards the economic situation (>70%), the health of close-ones (37%), but less towards their own health (<10%). Many concerns, seeking information and approval of federal measures were more pronounced in the more affected region. Approval of lockdown measures and concerns about economic recession were related to regional differences and not significantly dependent on educational status or being personally affected by the disease.\n\nConclusionRegional differences in approval of lockdown measures were observed and thus, measures to specifically support families according to the regional impact of the COVID-19 pandemic are needed.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Susanne Branstetter",
-        "author_inst": "University Children's Hospital Regensburg (KUNO), Hospital St. Hedwig of the Order of St. John, Steinmetzstr., 1-3, 93049 Regensburg, Germany"
-      },
-      {
-        "author_name": "Tanja Poulain",
-        "author_inst": "LIFE Child, LIFE Leipzig Research Center for Civilization Diseases, Leipzig University, Philipp-Rosenthal-Strasse 27, 04103 Leipzig, Germany"
-      },
-      {
-        "author_name": "Mandy Vogel",
-        "author_inst": "Department of Women and Child Health, University Hospital for Children and Adolescents, and Center for Pediatric Research, Leipzig University, Liebigstrasse 20a"
-      },
-      {
-        "author_name": "Christof Meigen",
-        "author_inst": "LIFE Child, LIFE Leipzig Research Center for Civilization Diseases, Leipzig University, Philipp-Rosenthal-Strasse 27, 04103 Leipzig, Germany"
-      },
-      {
-        "author_name": "Michael Melter",
-        "author_inst": "University Children's Hospital Regensburg (KUNO), Hospital St. Hedwig of the Order of St. John, Steinmetzstr., 1-3, 93049 Regensburg, Germany"
-      },
-      {
-        "author_name": "Birgit Seelbach-Goebel",
-        "author_inst": "Member of the Research and Development Campus Regensburg (WECARE) at the Hospital St. Hedwig of the Order of St. John, University of Regensburg, Regensburg, Ger"
-      },
-      {
-        "author_name": "Christian Apfelbacher",
-        "author_inst": "Member of the Research and Development Campus Regensburg (WECARE) at the Hospital St. Hedwig of the Order of St. John, University of Regensburg, Regensburg, Ger"
-      },
-      {
-        "author_name": "Wieland Kiess",
-        "author_inst": "Department of Women and Child Health, University Hospital for Children and Adolescents, and Center for Pediatric Research, Leipzig University, Liebigstrasse 20a"
-      },
-      {
-        "author_name": "Michael Kabesch",
-        "author_inst": "University Children's Hospital Regensburg (KUNO), Hospital St. Hedwig of the Order of St. John, Steinmetzstr., 1-3, 93049 Regensburg, Germany"
-      },
-      {
-        "author_name": "Antje Koerner",
-        "author_inst": "Department of Women and Child Health, University Hospital for Children and Adolescents, and Center for Pediatric Research, Leipzig University, Liebigstrasse 20a"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "pediatrics"
-  },
   {
     "rel_doi": "10.1101/2020.10.02.20206052",
     "rel_title": "Vulnerability and burden of all-cause mortality associated with particulate air pollution increased during COVID-19 pandemic: a nationwide observed study in Italy",
@@ -1138726,6 +1137640,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.10.06.20207662",
+    "rel_title": "Which factors should be included in triage? An online survey of the attitudes of the UK general public to pandemic triagedilemmas",
+    "rel_date": "2020-10-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.06.20207662",
+    "rel_abs": "ObjectiveAs cases of COVID-19 infections surge, concerns have renewed about intensive care units (ICU) being overwhelmed and the need for specific triage protocols over winter. This study aimed to help inform triage guidance by exploring the view of lay people about factors to include in triage decisions.\n\nDesign, setting and participantsOnline survey between 29th May and 22nd June 2020 based on hypothetical triage dilemmas. Participants recruited from existing market research panels, representative of the UK general population. Scenarios were presented in which a single ventilator is available, and two patients require ICU admission and ventilation. Patients differed in one of: chance of survival, life expectancy, age, expected length of treatment, disability, and degree of frailty. Respondents were given the option of choosing one patient to treat, or tossing a coin to decide.\n\nResultsSeven hundred and sixty-three participated. A majority of respondents prioritized patients who would have a higher chance of survival (72-93%), longer life expectancy (78-83%), required shorter duration of treatment (88-94%), were younger (71-79%), or had a lesser degree of frailty (60-69% all p< .001). Where there was a small difference between two patients, a larger proportion elected to toss a coin to decide which patient to treat. A majority (58-86%) were prepared to withdraw treatment from a patient in intensive care who had a lower chance of survival than another patient currently presenting with COVID-19. Respondents also indicated a willingness to give higher priority to healthcare workers and to patients with young children.\n\nConclusionMembers of the UK general public potentially support a broadly utilitarian approach to ICU triage in the face of overwhelming need. Survey respondents endorsed the relevance of patient factors currently included in triage guidance, but also factors not currently included. They supported the permissibility of reallocating treatment in a pandemic.\n\nBMJI, the Submitting Author has the right to grant and does grant on behalf of all authors of the Work (as defined in the below author licence), an exclusive licence and/or a non-exclusive licence for contributions from authors who are: i) UK Crown employees; ii) where BMJ has agreed a CC-BY licence shall apply, and/or iii) in accordance with the terms applicable for US Federal Government officers or employees acting as part of their official duties; on a worldwide, perpetual, irrevocable, royalty-free basis to BMJ Publishing Group Ltd (\"BMJ\") its licensees and where the relevant Journal is co-owned by BMJ to the co-owners of the Journal, to publish the Work in this journal and any other BMJ products and to exploit all rights, as set out in our licence.\n\nThe Submitting Author accepts and understands that any supply made under these terms is made by BMJ to the Submitting Author unless you are acting as an employee on behalf of your employer or a postgraduate student of an affiliated institution which is paying any applicable article publishing charge (\"APC\") for Open Access articles. Where the Submitting Author wishes to make the Work available on an Open Access basis (and intends to pay the relevant APC), the terms of reuse of such Open Access shall be governed by a Creative Commons licence - details of these licences and which Creative Commons licence will apply to this Work are set out in our licence referred to above.\n\nOther than as permitted in any relevant BMJ Authors Self Archiving Policies, I confirm this Work has not been accepted for publication elsewhere, is not being considered for publication elsewhere and does not duplicate material already published. I confirm all authors consent to publication of this Work and authorise the granting of this licence.\n\nArticle SummaryO_ST_ABSStrengths and Limitations of this studyC_ST_ABSO_LIFirst UK survey to investigate public attitudes to pandemic triage dilemmas\nC_LIO_LILarge survey, representative of the UK general population\nC_LIO_LIEnables comparison of ethical arguments and existing guidance with the views of the public\nC_LIO_LIIdentifies relevance of specific patient factors in concrete forced choice dilemmas: may be helpful in development or revision of triage policies\nC_LIO_LISurvey findings do not allow assessment of relative weight of different factors\nC_LI",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Dominic Wilkinson",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Hazem Zohny",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Andreas Kappes",
+        "author_inst": "City, University of London"
+      },
+      {
+        "author_name": "Walter Sinnott-Armstrong",
+        "author_inst": "Duke University"
+      },
+      {
+        "author_name": "Julian Savulescu",
+        "author_inst": "University of Oxford"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "medical ethics"
+  },
   {
     "rel_doi": "10.1101/2020.09.25.20199562",
     "rel_title": "Pathogenesis-based pre-exposure prophylaxis associated with low risk of SARS-CoV-2 infection in healthcare workers at a designated Covid-19 hospital",
@@ -1139983,37 +1138932,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.10.02.20204818",
-    "rel_title": "COVID-19 Outbreaks in Refugee Camps. A simulation study.",
-    "rel_date": "2020-10-05",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.02.20204818",
-    "rel_abs": "1We built a mathematical model for SARS-CoV-2 transmission and analyze it using both a deterministic and a stochastic approach. We used this model to project the burden of the disease in refugee camps characterized by peculiar demographic characteristics and a high level of deprivation, including lack of medical facilities and personnel, as well as limited possibility to implement containment and quarantine measures. Most of the parameters in our model were adapted from published literature but we used our own estimates of the basic reproduction number, R0 as well as the lethality by age group and gender. We projected the burden in terms of number of infections, number of deaths and number of bed-days in hospitalization and intensive care, among others. We conclude that the harsh conditions of refugee camps combined with a high share of young people leads to a relatively mild scenario for the burden of the disease.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "CARLOS M HERNANDEZ-SUAREZ",
-        "author_inst": "UNIVERSIDAD DE COLIMA"
-      },
-      {
-        "author_name": "Paolo Verme",
-        "author_inst": "World Bank Group"
-      },
-      {
-        "author_name": "Sergiy Radyakin",
-        "author_inst": "World Bank Group"
-      },
-      {
-        "author_name": "Efren Murillo-Zamora",
-        "author_inst": "Mexican Institute of Social Security"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.10.02.20205757",
     "rel_title": "Investigating the potential benefit that requiring travellers to self-isolate on arrival may have upon the reducing of case importations during international outbreaks of influenza, SARS, Ebola virus disease and COVID-19",
@@ -1140232,6 +1139150,65 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2020.10.03.20205278",
+    "rel_title": "Validation of self-collected buccal swab and saliva as a diagnostic tool for COVID-19",
+    "rel_date": "2020-10-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.03.20205278",
+    "rel_abs": "BackgroundEffective management of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) requires large-scale testing. Collection of nasopharyngeal swab (NPS) by healthcare workers (HCW) is currently used to diagnose SARS-CoV-2, which increases the risk of transmission to HCWs. Self-administered saliva and buccal swabs are convenient, painless and safe alternative sample collection methods.\n\nMethodsA cross-sectional single centre study was conducted on 42 participants who were tested positive for SARS-CoV-2 via NPS within the past 7 days. A self-collected saliva and buccal swab and a HCW-collected NPS were obtained. Real-time polymerase chain reaction (RT-PCR) was performed and cycle threshold (CT) values were obtained. Positive percent agreement (PPA), negative percent agreement (NPA) and overall agreement (OA) were calculated for saliva and buccal swabs, as compared with NPS.\n\nResultsAmong the 42 participants, 73.8% (31/42) tested positive via any one of the 3 tests. With reference to NPS, the saliva test had PPA 66.7%, NPA 91.7% and OA 69.0%. The buccal swab had PPA 56.7%, NPA 100% and OA 73.8%. Presence of symptoms improved diagnostic accuracy. There was no statistically significant association between CT values and duration of symptom onset within the first 12 days of symptoms for all three modalities.\n\nConclusionSelf-collected saliva tests and buccal swabs have only moderate agreement with HCW-collected NPS swabs. Primary screening for SARS-CoV-2 may be performed with a saliva test or buccal swab, with a negative test warranting a confirmatory NPS to avoid false negatives. This combined strategy minimizes discomfort and reduces the risk of spread to the community and HCWs.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Chee Wai Ku",
+        "author_inst": "KK Women's and Children's Hospital"
+      },
+      {
+        "author_name": "Shivani Durai",
+        "author_inst": "KK Women's and Children's Hospital"
+      },
+      {
+        "author_name": "Jacqueline Q T Kwan",
+        "author_inst": "National University Singapore"
+      },
+      {
+        "author_name": "See Ling Loy",
+        "author_inst": "Duke-NUS Medical School"
+      },
+      {
+        "author_name": "Christina Erwin",
+        "author_inst": "Duke-NUS Medical School"
+      },
+      {
+        "author_name": "Karrie K K Ko",
+        "author_inst": "Singapore General Hospital"
+      },
+      {
+        "author_name": "Xiang Wen Ng",
+        "author_inst": "KK Womens and Childrens Hospital"
+      },
+      {
+        "author_name": "Lynette Oon",
+        "author_inst": "Singapore General Hospital"
+      },
+      {
+        "author_name": "Koh Cheng Thoon",
+        "author_inst": "KK Women's and Children's Hospital"
+      },
+      {
+        "author_name": "Shirin Kalimuddin",
+        "author_inst": "Singapore General Hospital"
+      },
+      {
+        "author_name": "Jerry KY Chan",
+        "author_inst": "KK Women's and Children's Hospital"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.10.02.20205724",
     "rel_title": "COVID-19 severity in asthma patients: A multi-center matched cohort study",
@@ -1141589,33 +1140566,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.10.04.325423",
-    "rel_title": "GABA administration prevents severe illness and death following coronavirus infection in mice",
-    "rel_date": "2020-10-04",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.04.325423",
-    "rel_abs": "There is an urgent need for new treatments to prevent and ameliorate severe illness and death induced by SARS-CoV-2 infection in COVID-19 patients. The coronavirus mouse hepatitis virus (MHV)-1 causes pneumonitis in mice which shares many pathological characteristics with human SARS-CoV infection. Previous studies have shown that the amino acid gamma-aminobutyric acid (GABA) has anti-inflammatory effects. We tested whether oral treatment with GABA could modulate the MHV-1 induced pneumonitis in susceptible A/J mice. As expected, MHV-1-inoculated control mice became severely ill (as measured by weight loss, clinical score, and the ratio of lung weight to body weight) and >60% of them succumbed to the infection. In contrast, mice that received GABA immediately after MHV-1 inoculation became only mildly ill and all of them recovered. When GABA treatment was initiated after the appearance of illness (3 days post-MHV-1 infection), we again observed that GABA treatment significantly reduced the severity of illness and greatly increased the frequency of recovery. Therefore, the engagement of GABA receptors (GABA-Rs) prevented the MHV-1 infection-induced severe pneumonitis and death in mice. Given that GABA-R agonists, like GABA and homotaurine, are safe for human consumption, stable, inexpensive, and available worldwide, they are promising candidates to help prevent severe illness stemming from SARS-CoV-2 infection and other coronavirus strains.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Jide Tian",
-        "author_inst": "Univeristy of California, Los Angeles"
-      },
-      {
-        "author_name": "Blake Milddleton",
-        "author_inst": "University of California, Los Angeles"
-      },
-      {
-        "author_name": "Daniel L Kaufman",
-        "author_inst": "University of California, Los Angeles"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2020.10.04.325316",
     "rel_title": "Efficient culture of SARS-CoV-2 in human hepatoma cells enhances viability of the virus in human lung cancer cell lines permitting the screening of antiviral compounds",
@@ -1142170,6 +1141120,81 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.09.30.20204719",
+    "rel_title": "Corticosteroid pulses for hospitalized patients with COVID-19. Effects on mortality and in-hospital stay.",
+    "rel_date": "2020-10-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.30.20204719",
+    "rel_abs": "Background: COVID-19 has high mortality in hospitalized patients, and we need effective treatments. Our objective was to assess corticosteroid pulses influence on 60-days mortality in hospitalized patients with severe COVID-19, intensive care admission, and hospital stay. Methods: We designed a multicenter retrospective cohort study in three teaching hospitals of Castilla y Leon, Spain (865.096 people). We selected patients with confirmed COVID-19 and lung involvement with a pO2/FiO2 < 300, excluding those exposed to immunosuppressors before or during hospitalization, patients terminally ill at admission, or died the first 24 hours. We performed a propensity score matching (PSM) adjusting covariates that modify the probability of being treated. Then we used a Cox regression model in the PSM group to consider factors affecting mortality. Findings: From 2933 patients, 257 fulfilled the inclusion and exclusion criteria. One hundred and twenty-four patients were on corticosteroid pulses, and 133 were not. 30{middle dot}3% (37/122) of patients died in the corticosteroid pulses group and 42{middle dot}9% (57/133) in the non-exposed cohort. These differences (12{middle dot}6% CI95% [8{middle dot}54-16{middle dot}65]) were statically significant (log-rank 4{middle dot}72, p=0{middle dot}03). We performed PSM using the exact method. Mortality differences remained in the PSM group (log-rank 5{middle dot}31, p=0{middle dot}021) and were still significant after a Cox regression model (HR for corticosteroid pulses 0{middle dot}561, p= 0{middle dot}039). There were no significant differences in intensive care admission rate (p=0{middle dot}173). The hospital stay was longer in the corticosteroid group (p<0,001). Interpretation: This study provides evidence about treatment with corticosteroid pulses in severe COVID-19 that might significantly reduce mortality. Strict inclusion and exclusion criteria with that selection process set a reliable frame to compare mortality in both exposed and non-exposed groups. Funding: There was no funding provided.",
+    "rel_num_authors": 15,
+    "rel_authors": [
+      {
+        "author_name": "Ivan Cusacovich",
+        "author_inst": "Hospital Clinico Universitario de Valladolid"
+      },
+      {
+        "author_name": "Alvaro Aparisi",
+        "author_inst": "Hospital Clinico de Valladolid. Spain"
+      },
+      {
+        "author_name": "Miguel Marcos",
+        "author_inst": "University Hospital of Salamanca-IBSAL, University of Salamanca"
+      },
+      {
+        "author_name": "Cristina Ybarra-Falcon",
+        "author_inst": "Hospital Clinico de Valladolid"
+      },
+      {
+        "author_name": "Carolina Iglesias-Echevarria",
+        "author_inst": "Hospital Clinico de Valladolid"
+      },
+      {
+        "author_name": "Maria Lopez-Veloso",
+        "author_inst": "Hospital Universitario de Burgos"
+      },
+      {
+        "author_name": "Julio Barraza-Vengoechea",
+        "author_inst": "Hospital Universitario de Burgos"
+      },
+      {
+        "author_name": "carlos Duenas",
+        "author_inst": "Hospital Clinico de Valladolid"
+      },
+      {
+        "author_name": "Santiago Antonio Juarros Martinez",
+        "author_inst": "Hospital Clinico de Valladolid"
+      },
+      {
+        "author_name": "Beatriz Rodriguez-Alonso",
+        "author_inst": "Hospital Universitario de Salamanca"
+      },
+      {
+        "author_name": "Jose-Angel Martin-Oterino",
+        "author_inst": "Hospital Universitario de Salamanca"
+      },
+      {
+        "author_name": "Miguel Montero-Baladia",
+        "author_inst": "Hospital Universitario de Burgos"
+      },
+      {
+        "author_name": "Leticia Moralejo",
+        "author_inst": "Hospital Universitario de Salamanca"
+      },
+      {
+        "author_name": "David Andaluz-Ojeda",
+        "author_inst": "Hospital Clinico de Valladolid"
+      },
+      {
+        "author_name": "Roberto Gonzalez-Fuentes",
+        "author_inst": "Hospital Clinico de Valladolid"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.10.02.20199083",
     "rel_title": "Performance of a rapid SARS-COV-2 serology test in whole blood and separated plasma",
@@ -1143323,57 +1142348,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.10.01.323220",
-    "rel_title": "Potent mouse monoclonal antibodies that block SARS-CoV-2 infection",
-    "rel_date": "2020-10-02",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.01.323220",
-    "rel_abs": "Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has developed into a global pandemic since its first outbreak in the winter of 2019. An extensive investigation of SARS-CoV-2 is critical for disease control. Various recombinant monoclonal antibodies of human origin that neutralize SARS-CoV-2 infection have been isolated from convalescent patients and will be applied as therapies and prophylaxis. However, the need for dedicated monoclonal antibodies in molecular pathology research is not fully addressed. Here, we produced mouse anti-SARS-CoV-2 spike monoclonal antibodies that exhibit not only robust performance in immunoassays including western blotting, ELISA, immunofluorescence, and immunoprecipitation, but also neutralizing activity against SARS-CoV-2 infection in vitro. Our monoclonal antibodies are of mouse origin, making them compatible with the experimental immunoassay setups commonly used in basic molecular biology research laboratories, and large-scale production and easy distribution are guaranteed by conventional mouse hybridoma technology.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Youjia Guo",
-        "author_inst": "Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan"
-      },
-      {
-        "author_name": "Atsushi Kawaguchi",
-        "author_inst": "Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan"
-      },
-      {
-        "author_name": "Masaru Takeshita",
-        "author_inst": "Division of Rheumatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan"
-      },
-      {
-        "author_name": "Takeshi Sekiya",
-        "author_inst": "Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan"
-      },
-      {
-        "author_name": "Mikako Hirohama",
-        "author_inst": "Department of Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan"
-      },
-      {
-        "author_name": "Akio Yamashita",
-        "author_inst": "Department of Molecular Biology, Yokohama City University School of Medicine, Yokohama, Japan"
-      },
-      {
-        "author_name": "- the Keio Donner Project",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Haruhiko Siomi",
-        "author_inst": "Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan"
-      },
-      {
-        "author_name": "Kensaku Murano",
-        "author_inst": "Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.10.02.323519",
     "rel_title": "Transmission of SARS-COV-2 from China to Europe and West Africa: a detailed phylogenetic analysis.",
@@ -1143888,6 +1142862,49 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2020.09.30.320903",
+    "rel_title": "SARS-CoV-2 viral budding and entry can be modeled using virus-like particles",
+    "rel_date": "2020-10-01",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.30.320903",
+    "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first discovered in December 2019 in Wuhan, China and expeditiously spread across the globe causing a global pandemic. While a select agent designation has not been made for SARS-CoV-2, closely related SARS-CoV-1 and MERS coronaviruses are classified as Risk Group 3 select agents, which restricts use of the live viruses to BSL-3 facilities. Such BSL-3 classification make SARS-CoV-2 research inaccessible to the majority of functioning research laboratories in the US; this becomes problematic when the collective scientific effort needs to be focused on such in the face of a pandemic. In this work, we assessed the four structural proteins from SARS-CoV-2 for their ability to form viruslike particles (VLPs) from human cells to form a competent system for BSL-2 studies of SARS-CoV-2. Herein, we provide methods and resources of producing, purifying, fluorescently and APEX2-labeling of SARS-CoV-2 VLPs for the evaluation of mechanisms of viral budding and entry as well as assessment of drug inhibitors under BSL-2 conditions.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Caroline B. Plescia",
+        "author_inst": "Purdue University"
+      },
+      {
+        "author_name": "Emily A. David",
+        "author_inst": "Purdue University"
+      },
+      {
+        "author_name": "Dhabaleswar Patra",
+        "author_inst": "Purdue University"
+      },
+      {
+        "author_name": "Ranjan Sengupta",
+        "author_inst": "Purdue University"
+      },
+      {
+        "author_name": "Souad Amiar",
+        "author_inst": "Purdue University"
+      },
+      {
+        "author_name": "Yuan Su",
+        "author_inst": "Purdue University"
+      },
+      {
+        "author_name": "Robert V. Stahelin",
+        "author_inst": "Purdue University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2020.09.30.319863",
     "rel_title": "Thiopurines activate an antiviral unfolded protein response that blocks viral glycoprotein accumulation in cell culture infection model",
@@ -1145061,29 +1144078,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.09.28.20202911",
-    "rel_title": "Forecasting Covid-19 Infections and Deaths Horizon in Egypt",
-    "rel_date": "2020-09-30",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.28.20202911",
-    "rel_abs": "The coronavirus Covid-19 pandemic is defining a global health crisis, which is the hugest challenge the world has faced since World War II. Accordingly, the global economy as well is facing the worst economic catastrophe since the 1930s Great Depression. The case in Egypt is similar to the rest of the world. Despite being threatened by GDP decline and income losses; the Egyptian government has reacted early to restrain the pandemic outbreak. By mid-March, many measures had been undertaken to contain the spread of the virus. More than three months after imposing them, Egypt began lifting many of the restrictions put in place to curb the spread of coronavirus. Predictions of the potential spread of Covid-19 based on time series Auto Regressive Integrated Moving Average (ARIMA) and econometric Autoregressive-Distributed Lag (ARDL) forecasting models are utilized in this paper for designing and/or evaluating countermeasures. The aim of this study is threefold, first using the most recent available data to find the best prediction models for daily cases and death in Egypt and forecast them up to 7 November 2020. Second, to analyze the effect of mobility on the incidence of the pandemic using Google Community Mobility Reports (GCMR) to evaluate the results of easing lockdown restrictions. Finally, providing some recommendations that may help lessen the spread of the virus and eradicate new deaths as possible. The results revealed that mobility of population is affecting the incidence of new cases of Covid-19 significantly over the period of the study. Additionally, the total number of infections on November 7 2020 is expected to reach 102,352 cases, while the total death toll is predicted to be 5,938 according to the most accurate methods of forecasting. Accordingly, in order to sustain the predicted flat pandemic curve, many restrictions must be continued and emergency mechanisms need to be considered. For instance, adhering to the precautions of social distancing advised by the health minister and the declared hygiene rules to ensure that infection is prevented or transmitted is necessary. Besides, being prepared with re-imposing lockdown strategies and health system support are essential among others. It should also be noted that this expected pattern can shift, yet that depends on peoples actions.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Shereen Nosier",
-        "author_inst": "Bibliotheca Alexandrina"
-      },
-      {
-        "author_name": "Reham Salah Beram",
-        "author_inst": "Bibliotheca Alexandrina"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.09.30.20204230",
     "rel_title": "Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State",
@@ -1145602,6 +1144596,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.09.30.20201830",
+    "rel_title": "Geospatial Analysis of Individual and Community-Level Socioeconomic Factors Impacting SARS-CoV-2 Prevalence and Outcomes",
+    "rel_date": "2020-09-30",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.30.20201830",
+    "rel_abs": "BackgroundThe SARS-CoV-2 pandemic has disproportionately affected racial and ethnic minority communities across the United States. We sought to disentangle individual and census tract-level sociodemographic and economic factors associated with these disparities.\n\nMethods and FindingsAll adults tested for SARS-CoV-2 between February 1 and June 21, 2020 were geocoded to a census tract based on their address; hospital employees and individuals with invalid addresses were excluded. Individual (age, sex, race/ethnicity, preferred language, insurance) and census tract-level (demographics, insurance, income, education, employment, occupation, household crowding and occupancy, built home environment, and transportation) variables were analyzed using linear mixed models predicting infection, hospitalization, and death from SARS-CoV-2.\n\nAmong 57,865 individuals, per capita testing rates, individual (older age, male sex, non-White race, non-English preferred language, and non-private insurance), and census tract-level (increased population density, higher household occupancy, and lower education) measures were associated with likelihood of infection. Among those infected, individual age, sex, race, language, and insurance, and census tract-level measures of lower education, more multi-family homes, and extreme household crowding were associated with increased likelihood of hospitalization, while higher per capita testing rates were associated with decreased likelihood. Only individual-level variables (older age, male sex, Medicare insurance) were associated with increased mortality among those hospitalized.\n\nConclusionsThis study of the first wave of the SARS-CoV-2 pandemic in a major U.S. city presents the cascade of outcomes following SARS-CoV-2 infection within a large, multi-ethnic cohort. SARS-CoV-2 infection and hospitalization rates, but not death rates among those hospitalized, are related to census tract-level socioeconomic characteristics including lower educational attainment and higher household crowding and occupancy, but not neighborhood measures of race, independent of individual factors.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Sara J Cromer",
+        "author_inst": "Massachusetts General Hospital"
+      },
+      {
+        "author_name": "Chirag M Lakhani",
+        "author_inst": "Harvard Medical School"
+      },
+      {
+        "author_name": "Deborah J Wexler",
+        "author_inst": "Massachusetts General Hospital"
+      },
+      {
+        "author_name": "Sherri-Ann M Burnett-Bowie",
+        "author_inst": "Massachusetts General Hospital"
+      },
+      {
+        "author_name": "Miriam Udler",
+        "author_inst": "Massachusetts General Hospital"
+      },
+      {
+        "author_name": "Chirag J Patel",
+        "author_inst": "Harvard Medical School"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.09.29.20201368",
     "rel_title": "Seroprevalence of SARS-CoV-2 IgG antibodies, in Corsica (France), April and June 2020.",
@@ -1147023,41 +1146056,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "genetic and genomic medicine"
   },
-  {
-    "rel_doi": "10.1101/2020.09.28.20203406",
-    "rel_title": "Transfer transcriptomic signatures for infectious diseases",
-    "rel_date": "2020-09-29",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.28.20203406",
-    "rel_abs": "The modulation of the transcriptome is among the earliest responses to infection, and vaccination. However, defining transcriptome signatures of disease is challenging because logistic, technical and cost factors limit the size and representativeness of samples in clinical studies. These limitations lead to poor performance of signatures when applied to new datasets or varying study settings. Using a novel approach, we leverage existing transcriptomic signatures as classifiers in unseen datasets from prospective studies, with the goal of predicting individual outcomes. Machine learning allowed the identification of sets of genes, which we name transfer transcriptomic signatures, that are predictive across diverse datasets and/or species (rhesus to humans) and that are also suggestive of activated pathways and cell type composition. We demonstrate the usefulness of transfer signatures in two use cases: progression of latent to active tuberculosis, and severity of COVID-19 and influenza A H1N1 infection. The broad significance of our work lies in the concept that a small set of archetypal human immunophenotypes, captured by transfer signatures, can explain a larger set of responses to diverse diseases.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Julia di Iulio",
-        "author_inst": "Vir Biotechnology Inc."
-      },
-      {
-        "author_name": "Istvan Bartha",
-        "author_inst": "Vir Biotechnology Inc."
-      },
-      {
-        "author_name": "Roberto Spreafico",
-        "author_inst": "Vir Biotechnology Inc."
-      },
-      {
-        "author_name": "Herbert W Virgin",
-        "author_inst": "Vir Biotechnology Inc."
-      },
-      {
-        "author_name": "Amalio Telenti",
-        "author_inst": "The Scripps Research Institute"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.09.28.20202929",
     "rel_title": "T cell assays differentiate clinical and subclinical SARS-CoV-2 infections from cross-reactive antiviral responses",
@@ -1147636,6 +1146634,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.09.29.20203760",
+    "rel_title": "Which early indicator allows for a better understanding of the evolution of the COVID-19 epidemic in France?",
+    "rel_date": "2020-09-29",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.29.20203760",
+    "rel_abs": "We provide an explanation for the apparent discrepancy between the dynamic of the positive COVID-19 test rates and of the numbers of COVID-19-related hospital and intensive care admissions and deaths in France. We highlight the existence of a latency period of around 5 weeks between the infections of young individual (generally asymptomatic) to older individuals that may have a severe form of the disease and may be hospitalized. If the overall positive detection rate provided relevant information until the end of August, since the beginning of September the overall positive detection rate has reached a plateau and no longer provides relevant information on the current state of the epidemic. We show that the positive detection rate in the 70+ age group is a relevant and early indicator of the epidemic. Furthermore, we have shown an identical doubling time of around 16 days for the following indicators: the positive tests rate for the 70+ age group, the number of new admissions to hospital, intensive care unit admissions and deaths.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Patrice Loisel",
+        "author_inst": "INRAE"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.09.29.20203885",
     "rel_title": "Estimation of the Basic Reproduction Number of SARS-CoV-2 in Bangladesh Using Exponential Growth Method",
@@ -1148757,41 +1147774,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
-  {
-    "rel_doi": "10.1101/2020.09.29.20203612",
-    "rel_title": "Probabilistic analysis of COVID-19 patients' individual length of stay in Swiss intensive care units",
-    "rel_date": "2020-09-29",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.29.20203612",
-    "rel_abs": "RationaleThe COVID-19 pandemic induces considerable strain on intensive care unit resources.\n\nObjectivesWe aim to provide early predictions of individual patients intensive care unit length of stay, which might improve resource allocation and patient care during the on-going pandemic.\n\nMethodsWe developed a new semiparametric distributional index model depending on covariates which are available within 24h after intensive care unit admission. The model was trained on a large cohort of acute respiratory distress syndrome patients out of the Minimal Dataset of the Swiss Society of Intensive Care Medicine. Then, we predict individual length of stay of patients in the RISC-19-ICU registry.\n\nMeasurementsThe RISC-19-ICU Investigators for Switzerland collected data of 557 critically ill patients with COVID-19.\n\nMain ResultsThe model gives probabilistically and marginally calibrated predictions which are more informative than the empirical length of stay distribution of the training data. However, marginal calibration was worse after approximately 20 days in the whole cohort and in different subgroups. Long staying COVID-19 patients have shorter length of stay than regular acute respiratory distress syndrome patients. We found differences in LoS with respect to age categories and gender but not in regions of Switzerland with different stress of intensive care unit resources.\n\nConclusionA new probabilistic model permits calibrated and informative probabilistic prediction of LoS of individual patients with COVID-19. Long staying patients could be discovered early. The model may be the basis to simulate stochastic models for bed occupation in intensive care units under different casemix scenarios.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Alexander Henzi",
-        "author_inst": "Institute of Mathematical Statistics and Actuarial Science, University of Bern, Switzerland"
-      },
-      {
-        "author_name": "Gian-Reto Kleger",
-        "author_inst": "Division of Intensive Care Medicine, Cantonal Hospital, St.Gallen, Switzerland"
-      },
-      {
-        "author_name": "Matthias P. Hilty",
-        "author_inst": "The RISC-19-ICU registry board, University of Zurich, Switzerland and Institute of Intensive Care Medicine, University Hospital of Zurich, Switzerland"
-      },
-      {
-        "author_name": "Pedro D. Wendel Garcia",
-        "author_inst": "The RISC-19-ICU registry board, University of Zurich, Switzerland and Institute of Intensive Care Medicine, University Hospital of Zurich, Switzerland"
-      },
-      {
-        "author_name": "Johanna F. Ziegel",
-        "author_inst": "Institute of Mathematical Statistics and Actuarial Science, University of Bern, Switzerland"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.09.28.20203398",
     "rel_title": "Functional immunoparalysis characterized by elevated Interleukin-10 and Interleukin-10-to-Lymphocyte Count Ratio is associated with severe disease and poor outcomes in coronavirus disease 2019 (COVID-19)",
@@ -1149110,6 +1148092,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.09.26.20201814",
+    "rel_title": "Evolution of COVID-19 cases in selected low- and middle-income countries: past the herd immunity peak?",
+    "rel_date": "2020-09-28",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.26.20201814",
+    "rel_abs": "We have studied the evolution of COVID-19 in 12 low- and middle-income countries in which reported cases have peaked and declined rapidly in the past 2-3 months. In most of these countries the declines happened while control measures were consistent or even relaxing, and without signs of significant increases in cases that might indicate second waves. For the 12 countries we studied, the hypothesis that these countries have reached herd immunity warrants serious consideration. The Reed-Frost model, perhaps the simplest description for the evolution of cases in an epidemic, with only a few constant parameters, fits the observed case data remarkably well, and yields parameter values that are reasonable. The best-fitting curves suggest that the effective basic reproduction numberin these countries ranged between 1.5 and 2.0, indicating that the curve was \"flattened \"in some countries but not \"suppressed \"by pushing the reproduction number below 1. The results suggest that between 51 and 80% of the population in these countries have been infected, and that between 0.05% and 2.50% of cases have been detected - values which are consistent with findings from serological and T-cell immunity studies. The infection rates, combined with data and estimates for deaths from COVID-19, allow us to estimate overall infection fatality rates for three of the countries. The values are lower than expected from reported infection fatality rates by age, based on data from several high-income countries, and the countries   populations by age. COVID-19 may have a lower mortality risk in these three countries (to differing degrees in each country) than in high-income countries, due to differences in immune-response, prior exposure to coronaviruses, disease characteristics or other factors. We find that the herd immunity hypothesis would not have fit the evolution of reported cases in several European countries, even just after the initial peaks - and subsequent resurgences of cases obviously prove that those countries have infection rates well below herd immunity levels. Our hypothesis that the 12 countries we studied have reached herd immunity should now be tested further, through serological and T-cell-immunity studies.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Axel S Lexmond",
+        "author_inst": "University of Pretoria"
+      },
+      {
+        "author_name": "Carlijn JA Nouwen",
+        "author_inst": "Personal capacity"
+      },
+      {
+        "author_name": "Othmane Fourtassi",
+        "author_inst": "Personal capacity"
+      },
+      {
+        "author_name": "John Paul Callan",
+        "author_inst": "Personal capacity"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.09.26.20202325",
     "rel_title": "An optimal control policy for COVID-19 pandemic until a vaccine deployment",
@@ -1150495,41 +1149508,6 @@
     "type": "new results",
     "category": "genomics"
   },
-  {
-    "rel_doi": "10.1101/2020.09.28.316307",
-    "rel_title": "Fluorescence-detection size-exclusion chromatography utilizing nanobody technology for expression screening of membrane proteins",
-    "rel_date": "2020-09-28",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.28.316307",
-    "rel_abs": "Membrane proteins play numerous physiological roles and are thus of tremendous interest in pharmacology. Nevertheless, stable and homogeneous sample preparation is one of the bottlenecks in biophysical and pharmacological studies of membrane proteins because membrane proteins are typically unstable and poorly expressed. To overcome such obstacles, GFP fusion-based Fluorescence-detection Size-Exclusion Chromatography (FSEC) has been widely employed for membrane protein expression screening for over a decade. However, fused GFP itself may occasionally affect the expression and/or stability of the targeted membrane protein, leading to both false-positive and false-negative results in expression screening. Furthermore, GFP fusion technology is not well suited for some membrane proteins depending on their membrane topology. Here, we developed an FSEC assay utilizing nanobody (Nb) technology, named FSEC-Nb, in which targeted membrane proteins are fused to a small peptide tag and recombinantly expressed. The whole-cell extracts are solubilized, mixed with anti-peptide Nb fused to GFP and applied to a size-exclusion chromatography column attached to a fluorescence detector for FSEC analysis. FSEC-Nb enables one to evaluate the expression, monodispersity and thermostability of membrane proteins without the need of purification by utilizing the benefits of the GFP fusion-based FSEC method, but does not require direct GFP fusion to targeted proteins. We applied FSEC-Nb to screen zinc-activated ion channel (ZAC) family proteins in the Cys-loop superfamily and membrane proteins from SARS-CoV-2 as examples of the practical application of FSEC-Nb. We successfully identified a ZAC ortholog with high monodispersity but moderate expression levels that could not be identified with the previously developed GFP fusion-free FSEC method. Consistent with the results of FSEC-Nb screening, the purified ZAC ortholog showed monodispersed particles by both negative staining EM and cryo-EM. Furthermore, we identified two membrane proteins from SARS-CoV-2 with high monodispersity and expression level by FSEC-Nb, which may facilitate structural and functional studies of SARS-CoV-2. Overall, our results show FSEC-Nb as a powerful tool for membrane protein expression screening that can provide further opportunity to prepare well-behaved membrane proteins for structural and functional studies.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Fei Jin",
-        "author_inst": "Fudan University"
-      },
-      {
-        "author_name": "Yao Wang",
-        "author_inst": "Fudan University"
-      },
-      {
-        "author_name": "Mengqi Wang",
-        "author_inst": "Fudan University"
-      },
-      {
-        "author_name": "Minxuan Sun",
-        "author_inst": "Fudan University"
-      },
-      {
-        "author_name": "Motoyuki Hattori",
-        "author_inst": "Fudan University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "biophysics"
-  },
   {
     "rel_doi": "10.1101/2020.09.28.317206",
     "rel_title": "Exploring dynamics and network analysis of spike glycoprotein of SARS-COV-2",
@@ -1150744,6 +1149722,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
+  {
+    "rel_doi": "10.1101/2020.09.25.20201616",
+    "rel_title": "COVID-19 in Youth Soccer",
+    "rel_date": "2020-09-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.25.20201616",
+    "rel_abs": "PurposeThe purpose of this study was to determine the case and incidence rates of COVID-19 among youth soccer players and evaluate the relationship with background COVID-19 risk and phase of return to play.\n\nMethodsSurveys were distributed to soccer clubs throughout the country regarding their phase of return to soccer (individual only, group non-contact, group contact) and date of reinitiation, number of players, cases of COVID-19, and risk reduction procedures that were being implemented. Overall case and incidence rates were compared to national pediatric data and county data from the prior 10 weeks where available. Finally, a negative binomial regression model was developed to predict club COVID-19 cases with local incidence rate and phase of return as covariates and the log of club player-days as an offset.\n\nResults129 clubs responded, of whom 124 had reinitiated soccer, representing 91,007 players with a median duration of 73 days (IQR: 53-83 days) since restarting. Of the 119 that had progressed to group activities, 218 cases of COVID-19 were reported among 85,861 players. Youth soccer players had a lower case rate and incidence rate than the national rate for children in the US (254 v. 477 cases per 100,000; IRR = 0.511, 95% CI = [0.40-0.57], p<0.001) and the general population from the counties in which soccer clubs were based where data was available (268 v. 864 cases per 100,000; IRR = 0.202 [0.19-0.21], p<0.001). After adjusting for local COVID-19 incidence, there was no relationship between club COVID-19 incidence and phase of return (non-contact: {beta}=0.35{+/-}0.67, p=0.61; contact: {beta}=0.18{+/-}0.67, p=0.79). No cases were reported to have resulted in hospitalization or death. 100% of clubs reported having a plan in place to reduce the risk of COVID-19 and utilizing multiple different risk reduction procedures (median 8, IQR 6-10).\n\nConclusionsThe incidence of COVID-19 among youth soccer athletes is relatively low when compared to the background incidence among children in the United States and the local general population. No relationship was identified between club COVID-19 incidence and phase of return to soccer. Youth soccer clubs universally report implementing a number of risk reduction procedures.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Andrew Watson",
+        "author_inst": "University of Wisconsin School of Medicine and Public Health"
+      },
+      {
+        "author_name": "Kristin Haraldsdottir",
+        "author_inst": "University of Wisconsin School of Medicine and Public Health"
+      },
+      {
+        "author_name": "Kevin Biese",
+        "author_inst": "University of Wisconsin-Madison"
+      },
+      {
+        "author_name": "Leslie Goodavish",
+        "author_inst": "University of Wisconsin School of Medicine and Public Health"
+      },
+      {
+        "author_name": "Bethany Stevens",
+        "author_inst": "University of Wisconsin-Madison"
+      },
+      {
+        "author_name": "Timothy McGuine",
+        "author_inst": "University of Wisconsin School of Medicine and Public Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "sports medicine"
+  },
   {
     "rel_doi": "10.1101/2020.09.24.20200196",
     "rel_title": "Cost-effectiveness of remdesivir and dexamethasone for COVID-19 treatment in South Africa",
@@ -1151845,45 +1150862,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "radiology and imaging"
   },
-  {
-    "rel_doi": "10.1101/2020.09.24.20200857",
-    "rel_title": "The potential health and economic value of SARS-CoV-2 vaccination alongside physical distancing in the UK: transmission model-based future scenario analysis and economic evaluation",
-    "rel_date": "2020-09-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.24.20200857",
-    "rel_abs": "BackgroundIn response to the coronavirus disease 2019 (COVID-19), the UK adopted mandatory physical distancing measures in March 2020. Vaccines against the newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may become available as early as late 2020. We explored the health and economic value of introducing SARS-CoV-2 immunisation alongside physical distancing scenarios in the UK.\n\nMethodsWe used an age-structured dynamic-transmission and economic model to explore different scenarios of immunisation programmes over ten years. Assuming vaccines are effective in 5-64 year olds, we compared vaccinating 90% of individuals in this age group to no vaccination. We assumed either vaccine effectiveness of 25% and 1-year protection and 90% re-vaccinated annually, or 75% vaccine effectiveness and 10-year protection and 10% re-vaccinated annually. Natural immunity was assumed to last 45 weeks in the base case. We also explored the additional impact of physical distancing. We considered benefits from disease prevented in terms of quality-adjusted life-years (QALYs), and costs to the healthcare payer versus the national economy. We discounted at 3.5% annually and monetised health impact at {pound}20,000 per QALY to obtain the net monetary value, which we explored in sensitivity analyses.\n\nFindingsWithout vaccination and physical distancing, we estimated 147.9 million COVID-19 cases (95% uncertainty interval: 48.5 million, 198.7 million) and 2.8 million (770,000, 4.2 million) deaths in the UK over ten years. Vaccination with 75% vaccine effectiveness and 10-year protection may stop community transmission entirely for several years, whereas SARS-CoV-2 becomes endemic without highly effective vaccines. Introducing vaccination compared to no vaccination leads to economic gains (positive net monetary value) of {pound}0.37 billion to +{pound}1.33 billion across all physical distancing and vaccine effectiveness scenarios from the healthcare perspective, but net monetary values of physical distancing scenarios may be negative from societal perspective if the daily national economy losses are persistent and large.\n\nInterpretationOur model findings highlight the substantial health and economic value of introducing SARS-CoV-2 vaccination. Given uncertainty around both characteristics of the eventually licensed vaccines and long-term COVID-19 epidemiology, our study provides early insights about possible future scenarios in a post-vaccination era from an economic and epidemiological perspective.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed and medRxiv for economic evaluations of SARS-CoV-2 vaccines with the search string (coronavirus OR COVID OR SARS-CoV-2) AND (vaccin* OR immunisation) AND ((economic evaluation) OR (cost effectiveness analysis)) AND 2020[dp] on September 21, 2020, with no language restrictions. We found one pre-print that valued health outcomes in monetary terms and explored the additional impact of vaccines in a cost-benefit analysis of physical distancing for the USA; no study focused on vaccines in a full economic evaluation.\n\nAdded value of this studyWith a growing number of vaccine candidates under development and having entered clinical trials, our study is to our knowledge the first to explore the health and economic value of introducing a national SARS-CoV-2 immunisation programme. A programme with high vaccine effectiveness and long-lasting protection may stop the community transmission entirely for a couple of years, but even a vaccine with 25% vaccine effectiveness is worthwhile to use; even at short-lived natural and vaccine-induced protections. After an initial lockdown, voluntary physical distancing as a sole strategy risks a large second epidemic peak, unless accompanied by highly effective immunisation. Compared to no vaccination, introducing vaccination leads to positive net monetary value across physical distancing scenarios from the healthcare perspective, subject to the long-run vaccine price and cost-effectiveness of other treatments (e.g. new drugs). The net monetary value of immunisation decreases if vaccine introduction is delayed, natural immunity is long or vaccine-induced protection is short. Intermittent physical distancing leads to negative net benefits from the perspective of the wider economy if the daily national income losses are persistent and large.\n\nImplications of all the available evidenceOur model findings highlight the health and economic value of introducing SARS-CoV-2 vaccination to control the COVID-19 epidemic. Despite the many uncertainties, continued physical distancing may be needed to reduce community transmission until vaccines with sufficiently high vaccine effectiveness and long-lasting protection are available. Our study provides first broad health-economic insights rather than precise quantitative projections given the many uncertainties and unknown characteristics of the vaccine candidates and aspects of the long-term COVID-19 epidemiology, and the value of vaccines will ultimately depend on other socioeconomic and health-related policies and population behaviours.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Frank Sandmann",
-        "author_inst": "PHE/LSHTM"
-      },
-      {
-        "author_name": "Nicholas Davies",
-        "author_inst": "LSHTM"
-      },
-      {
-        "author_name": "- Centre for the Mathematical Modelling of Infectious Diseases COVID-19 working group",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Anna Vassall",
-        "author_inst": "LSHTM"
-      },
-      {
-        "author_name": "W John Edmunds",
-        "author_inst": "LSHTM"
-      },
-      {
-        "author_name": "Mark Jit",
-        "author_inst": "LSHTM"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health economics"
-  },
   {
     "rel_doi": "10.1101/2020.09.24.20191411",
     "rel_title": "Detection of SARS-CoV-2 within the healthcare environment: a multicentre study conducted during the first wave of the COVID-19 outbreak in England",
@@ -1152322,6 +1151300,81 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.09.23.20198713",
+    "rel_title": "Suitability of Two Rapid Lateral Flow Immunochromatographic Assays for Predicting SARS-CoV-2 Neutralizing Activity of Sera",
+    "rel_date": "2020-09-25",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.23.20198713",
+    "rel_abs": "PurposeAssessment of commercial SARS-CoV-2 immunoassays for their capacity to provide reliable information on sera neutralizing activity is an emerging need. We evaluated the performance of two commercially-available lateral flow immunochromatographic assays (LFIC) (Wondfo SARS-CoV-2 Antibody test and the INNOVITA 2019-nCoV Ab test) in comparison with a SARS-CoV-2 neutralization pseudotyped assay for COVID-19 diagnosis in hospitalized patients, and investigate whether the intensity of the test band in LFIC associates with neutralizing antibody (NtAb) titers.\n\nPatients and MethodsNinety sera were included from 51 patients with moderate to severe COVID-19. A green fluorescent protein (GFP) reporter-based pseudotyped neutralization assay (vesicular stomatitis virus coated with SARS-CoV-2 spike protein) was used. Test line intensity was scored using a 4-level scale (0 to 3+).\n\nResultsOverall sensitivity of LFIC assays was 91.1% for the Wondfo SARS-CoV-2 Antibody test, 72.2% for the INNOVITA 2019-nCoV IgG, 85.6% for the INNOVITA 2019-nCoV IgM and 92.2% for the NtAb assay. Sensitivity increased for all assays in sera collected beyond day 14 after symptoms onset (93.9%, 79.6%,93.9% and 93.9%, respectively). Reactivities equal to or more intense than the positive control line ([&ge;]2+) in the Wondfo assay had a negative predictive value of 100% and a positive predictive value of 96.4% for high NtAb50 titers ([&ge;]1/160).\n\nConclusionsOur findings support the use of LFIC assays evaluated herein, particularly the Wondfo test, for COVID-19 diagnosis. We also find evidence that these rapid immunoassays can be used to predict high SARS-CoV-2-S NtAb50 titers.",
+    "rel_num_authors": 15,
+    "rel_authors": [
+      {
+        "author_name": "Arantxa Valdivia",
+        "author_inst": "Clinic University Hospital, Valencia, Spain."
+      },
+      {
+        "author_name": "Ignacio Torres",
+        "author_inst": "Clinic University Hospital, Valencia, Spain."
+      },
+      {
+        "author_name": "Victor Latorre",
+        "author_inst": "Institute for Integrative System Biology, I2sysBio, Univeristat de Valencia-CSIC."
+      },
+      {
+        "author_name": "Clara Frances-Gomez",
+        "author_inst": "Institute for Integrative System Biology, I2sysBio, Univeristat de Valencia-CSIC."
+      },
+      {
+        "author_name": "Josep Ferrer",
+        "author_inst": "Clinic University Hospital, Valencia, Spain."
+      },
+      {
+        "author_name": "Lorena Forque",
+        "author_inst": "Clinic University Hospital, Valencia, Spain."
+      },
+      {
+        "author_name": "Rosa Costa",
+        "author_inst": "Clinic University Hospital, Valencia, Spain."
+      },
+      {
+        "author_name": "Carlos Solano de la Asuncion",
+        "author_inst": "Clinic University Hospital, Valencia, Spain."
+      },
+      {
+        "author_name": "Dixie Huntley",
+        "author_inst": "Clinic University Hospital, Valencia, Spain."
+      },
+      {
+        "author_name": "Roberto Gozalbo-Rovira",
+        "author_inst": "Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain"
+      },
+      {
+        "author_name": "Javier Buesa",
+        "author_inst": "Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain"
+      },
+      {
+        "author_name": "Estela Gimenez",
+        "author_inst": "Clinic University Hospital, Valencia, Spain."
+      },
+      {
+        "author_name": "Jesus Rodriguez-Diaz",
+        "author_inst": "Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain"
+      },
+      {
+        "author_name": "Ron Geller",
+        "author_inst": "Institute for Integrative System Biology, I2sysBio, Univeristat de Valencia-CSIC."
+      },
+      {
+        "author_name": "David Navarro",
+        "author_inst": "Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain."
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.09.24.20200048",
     "rel_title": "Genetic mechanisms of critical illness in Covid-19",
@@ -1153659,69 +1152712,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.09.24.20201285",
-    "rel_title": "CHARACTERISTICS, MANAGEMENT AND OUTCOMES OF CRITICALLY ILL COVID-19 PATIENTS ADMITTED TO ICU IN HOSPITALS IN BANGLADESH: A RETROSPECTIVE STUDY",
-    "rel_date": "2020-09-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.24.20201285",
-    "rel_abs": "ObjectivesThis study aimed to analyse the epidemiological and clinical characteristics of critical COVID-19 cases and investigate risk factors including comorbidities and age in relation with the clinical aftermath of COVID-19 in critical cases in Bangladesh.\n\nMethodsIn this retrospective study, epidemiological and clinical characteristics, complications, laboratory results, and clinical management of the patients were studied from data obtained from 168 individuals diagnosed with an advanced prognosis of COVID-19 admitted in two hospitals in Bangladesh.\n\nResultsIndividuals in the study sample contracted COVID-19 through community transmission. 56.5% (n = 95) cases died in intensive care units (ICU) during the study period. The median age was 56 years and 79.2% (n=134) were male. Typical clinical manifestation included Acute respiratory distress syndrome (ARDS) related complications (79.2%), fever (54.2%) and cough (25.6%) while diabetes mellitus (52.4%), hypertension (41.1%) and heart diseases (16.7%) were the conventional comorbidities. Clinical outcomes were detrimental due to comorbidities rather than age and comorbid individuals over 50 were at more risk. In the sample, oxygen saturation was low (< 95% SpO2) in 135 patients (80.4%) and 158 (93.4%) patients received supplemental oxygen. Identical biochemical parameters were found in both deceased and surviving cases. Administration of antiviral drug Remdesivir and the glucocorticoid, Dexamethasone increased the proportion of surviving patients slightly.\n\nConclusionsSusceptibility to developing critical illness due to COVID-19 was found more in comorbid males. These atypical patients require more clinical attention from the prospect of controlling mortality rate in Bangladesh.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Ayan Saha",
-        "author_inst": "Disease Biology and Molecular Epidemiology Research Group, Chattogram, Bangladesh"
-      },
-      {
-        "author_name": "Mohammad Moinul Ahsan",
-        "author_inst": "Intensive Care Unit, 250 Beded General Hospital Chittagong, Chattogram, Bangladesh"
-      },
-      {
-        "author_name": "Tarek-Ul Quader",
-        "author_inst": "Intensive Care Unit, Chittagong Medical College, Chattogram, Bangladesh"
-      },
-      {
-        "author_name": "Mohammad Umer Sharif Shohan",
-        "author_inst": "Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh"
-      },
-      {
-        "author_name": "Sabekun Naher",
-        "author_inst": "Department of Microbiology, University of Chittagong, Chattogram, Bangladesh"
-      },
-      {
-        "author_name": "Preya Dutta",
-        "author_inst": "Department of Pharmacy, BGC Trust University, Chattogram, Bangladesh"
-      },
-      {
-        "author_name": "Al-Shahriar Akash",
-        "author_inst": "Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh"
-      },
-      {
-        "author_name": "H M Hamidullah Mehedi",
-        "author_inst": "Department of Medicine, 250 Beded General Hospital Chittagong, Bangladesh"
-      },
-      {
-        "author_name": "A S M Arman Ullah Chowdhury",
-        "author_inst": "Intensive Care Unit, 250 Beded General Hospital Chittagong, Chattogram, Bangladesh"
-      },
-      {
-        "author_name": "Hasanul Karim",
-        "author_inst": "Intensive Care Unit, 250 Beded General Hospital Chittagong, Chattogram, Bangladesh"
-      },
-      {
-        "author_name": "Tazrina Rahman",
-        "author_inst": "Department of Microbiology, Chittagong Medical College, Chattogram, Bangladesh"
-      },
-      {
-        "author_name": "Ayesha Parvin",
-        "author_inst": "Department of Biochemistry, Chittagong Medical College, Chattogram, Bangladesh"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "intensive care and critical care medicine"
-  },
   {
     "rel_doi": "10.1101/2020.09.24.20197293",
     "rel_title": "Poor inhibitory control and stress as risk-factors for alcohol (mis)use during the COVID-19 pandemic in the UK: a national cross-sectional study across four generations",
@@ -1153988,6 +1152978,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "nursing"
   },
+  {
+    "rel_doi": "10.1101/2020.09.24.20201228",
+    "rel_title": "Outcomes associated with SARS-CoV-2 viral clades in COVID-19",
+    "rel_date": "2020-09-25",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.24.20201228",
+    "rel_abs": "BackgroundThe COVID-19 epidemic of 2019-20 is due to the novel coronavirus SARS-CoV-2. Following first case description in December, 2019 this virus has infected over 10 million individuals and resulted in at least 500,000 deaths world-wide. The virus is undergoing rapid mutation, with two major clades of sequence variants emerging. This study sought to determine whether SARS-CoV-2 sequence variants are associated with differing outcomes among COVID-19 patients in a single medical system.\n\nMethodsWhole genome SARS-CoV-2 RNA sequence was obtained from isolates collected from patients registered in the University of Washington Medicine health system between March 1 and April 15, 2020. Demographic and baseline medical data along with outcomes of hospitalization and death were collected. Statistical and machine learning models were applied to determine if viral genetic variants were associated with specific outcomes of hospitalization or death.\n\nFindingsFull length SARS-CoV-2 sequence was obtained 190 subjects with clinical outcome data. 35 (18.4%) were hospitalized and 14 (7.4%) died from complications of infection. A total of 289 single nucleotide variants were identified. Clustering methods demonstrated two major viral clades, which could be readily distinguished by 12 polymorphisms in 5 genes. A trend toward higher rates of hospitalization of patients with Clade 2 was observed (p=0.06). Machine learning models utilizing patient demographics and co-morbidities achieved area-under-the-curve (AUC) values of 0.93 for predicting hospitalization. Addition of viral clade or sequence information did not significantly improve models for outcome prediction.\n\nConclusionSARS-CoV-2 shows substantial sequence diversity in a community-based sample. Two dominant clades of virus are in circulation. Among patients sufficiently ill to warrant testing for virus, no significant difference in outcomes of hospitalization or death could be discerned between clades in this sample. Major risk factors for hospitalization and death for either major clade of virus include patient age and comorbid conditions.\n\nFundingSupported by NIH P30EY001730, the Mark J. Daily, MD Research Fund (RVG), the Alida and Christopher Latham Research Fund (RVG, AYL, CSL), NIH K23EY029246 (AYL), US Food and Drug Administration (QYL)",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Kenji Nakamichi",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Jolie Zhu Shen",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Cecilia S Lee",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Aaron Y Lee",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Emma Adaline Roberts",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Paul D Simonson",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Pavitra Roychoudhury",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Jessica G Andriesen",
+        "author_inst": "jandries@fredhutch.org"
+      },
+      {
+        "author_name": "April K Randhawa",
+        "author_inst": "arandhaw@fredhutch.org"
+      },
+      {
+        "author_name": "Patrick C Mathias",
+        "author_inst": "University of Washington School of Medicine"
+      },
+      {
+        "author_name": "Alex Greninger",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Keith R Jerome",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Russell N Van Gelder",
+        "author_inst": "University of Washington"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.09.22.20192443",
     "rel_title": "Reinfection with SARS-CoV-2 and Failure of Humoral Immunity: a case report.",
@@ -1155409,77 +1154466,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2020.09.24.311977",
-    "rel_title": "Hamster and ferret experimental infection with intranasal low dose of a single strain of SARS-CoV-2",
-    "rel_date": "2020-09-24",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.24.311977",
-    "rel_abs": "Understanding the pathogenesis of the SARS-CoV-2 infection is key to develop preventive and therapeutic strategies against COVID-19, in the case of severe illness but also when the disease is mild. The use of appropriate experimental animal models remains central in the in-vivo exploration of the physiopathology of infection and antiviral strategies. This study describes SARS-CoV-2 intra-nasal infection in ferrets and hamsters with low doses of low-passage SARS-CoV-2 clinical French isolate UCN19, describing infection levels, excretion, immune responses and pathological patterns in both animal species. Individual infection with 103 pfu SARS-CoV-2 induced a more severe disease in hamsters than in ferrets. Viral RNA was detected in the lungs of hamsters but not of ferrets and in the brain (olfactive and/or spinal bulbs) of both species. Overall, the clinical disease remained mild, with serological responses detected from 7 days and 10 days post inoculation in hamsters and ferrets respectively. Virus became undetectable and pathology resolved within 14 days. The kinetics and levels of infection can be used in ferrets and hamsters as experimental models for understanding the pathogenicity of SARS-CoV-2, and testing the protective effect of drugs.",
-    "rel_num_authors": 14,
-    "rel_authors": [
-      {
-        "author_name": "Elodie Monchatre-Leroy",
-        "author_inst": "Anses"
-      },
-      {
-        "author_name": "Sandrine Lesellier",
-        "author_inst": "Anses"
-      },
-      {
-        "author_name": "Marine Wasniewski",
-        "author_inst": "Anses Laboratoire de la rage et de la faune sauvage de Nancy"
-      },
-      {
-        "author_name": "Evelyne Picard-Meyer",
-        "author_inst": "Anses"
-      },
-      {
-        "author_name": "Celine Richomme",
-        "author_inst": "Anses"
-      },
-      {
-        "author_name": "Franck Boue",
-        "author_inst": "Anses"
-      },
-      {
-        "author_name": "Sandra Lacote",
-        "author_inst": "Anses"
-      },
-      {
-        "author_name": "Severine Murri",
-        "author_inst": "ANSES"
-      },
-      {
-        "author_name": "Coralie Pulido",
-        "author_inst": "ANSES"
-      },
-      {
-        "author_name": "Johann Vulin",
-        "author_inst": "ANSES"
-      },
-      {
-        "author_name": "Francisco J Salguero",
-        "author_inst": "PHE"
-      },
-      {
-        "author_name": "Meriadeg Ar Legouilh",
-        "author_inst": "Normandie Universite Chu de Caen"
-      },
-      {
-        "author_name": "Alexandre Servat",
-        "author_inst": "Anses"
-      },
-      {
-        "author_name": "Philippe Marianneau",
-        "author_inst": "Anses"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "confirmatory results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.09.24.285940",
     "rel_title": "Resveratrol And Pterostilbene Potently Inhibit SARS-CoV-2 Infection In Vitro",
@@ -1155822,6 +1154808,101 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2020.09.23.309948",
+    "rel_title": "Respiratory disease in cats associated with human-to-cat transmission of SARS-CoV-2 in the UK",
+    "rel_date": "2020-09-23",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.23.309948",
+    "rel_abs": "Two cats from different COVID-19-infected households in the UK were found to be infected with SARS-CoV-2 from humans, demonstrated by immunofluorescence, in situ hybridisation, reverse transcriptase quantitative PCR and viral genome sequencing. Lung tissue collected post-mortem from cat 1 displayed pathological and histological findings consistent with viral pneumonia and tested positive for SARS-CoV-2 antigens and RNA. SARS-CoV-2 RNA was detected in an oropharyngeal swab collected from cat 2 that presented with rhinitis and conjunctivitis. High throughput sequencing of the virus from cat 2 revealed that the feline viral genome contained five single nucleotide polymorphisms (SNPs) compared to the nearest UK human SARS-CoV-2 sequence. An analysis of cat 2s viral genome together with nine other feline-derived SARS-CoV-2 sequences from around the world revealed no shared catspecific mutations. These findings indicate that human-to-cat transmission of SARS-CoV-2 occurred during the COVID-19 pandemic in the UK, with the infected cats developing mild or severe respiratory disease. Given the versatility of the new coronavirus, it will be important to monitor for human-to-cat, cat-to-cat and cat-to-human transmission.",
+    "rel_num_authors": 20,
+    "rel_authors": [
+      {
+        "author_name": "Margaret J Hosie",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Ilaria Epifano",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Vanessa Herder",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Richard Orton",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Andrew Stevenson",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Natasha Johnson",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Emma MacDonald",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Dawn Dunbar",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Michael McDonald",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Fiona Howie",
+        "author_inst": "SRUC Veterinary Services"
+      },
+      {
+        "author_name": "Bryn Tennant",
+        "author_inst": "SRUC Veterinary Services"
+      },
+      {
+        "author_name": "Darcy Herrity",
+        "author_inst": "Fareham Creek Veterinary Surgery"
+      },
+      {
+        "author_name": "Ana C Filipe",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Daniel G Streicker",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Brian J Willett",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Pablo R Murcia",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Ruth F Jarrett",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "David L Robertson",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "William Weir",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "- COVID-19 Genomics UK Consortium",
+        "author_inst": "-"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2020.09.23.309849",
     "rel_title": "Establishment of a reverse genetics system for SARS-CoV-2 using circular polymerase extension reaction",
@@ -1157019,45 +1156100,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.09.23.20199927",
-    "rel_title": "Challenges and opportunities of the COVID-19 pandemic for perinatal mental health care: a mixed methods study of mental health care staff",
-    "rel_date": "2020-09-23",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.23.20199927",
-    "rel_abs": "Purposethe aim of this study was to explore staff perceptions of the impact of the COVID-19 pandemic on mental health service delivery and outcomes for women who were pregnant or in the first year after birth ( perinatal women).\n\nMethodssecondary analysis of an online mixed-methods survey open to all mental health care staff in the UK involving 363 staff working with women in the perinatal period.\n\nResultsstaff perceived the mental health of perinatal women to be particularly vulnerable to the impact of stressors associated with the pandemic such as social isolation (rated by 79.3% as relevant or extremely relevant; 288/363) and domestic violence and abuse (53.3%; 192/360). As a result of changes to mental health and other health and social care services, staff reported feeling less able to assess women, particularly their relationship with their baby (43.3%; 90/208), and to mobilise safeguarding procedures (29.4%; 62/211). While 42% of staff reported that some women engaged poorly with virtual appointments, they also found flexible remote consulting to be beneficial for some women and helped time management due to reductions in travel time.\n\nConclusionsdelivery of perinatal care needs to be tailored to the needs of women; virtual appointments are perceived not to be appropriate for assessments but may be helpful for some women in subsequent interactions. Safeguarding and other risk assessment procedures must remain robust in spite of modifications made to service delivery during pandemics.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Claire A Wilson",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Christian A Dalton-Locke",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Sonia Johnson",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Alan Simpson",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Sian Oram",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Louise M Howard",
-        "author_inst": "King's College London"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "psychiatry and clinical psychology"
-  },
   {
     "rel_doi": "10.1101/2020.09.22.20199455",
     "rel_title": "Norwich COVID-19 Testing Initiative: feasibility project evaluation",
@@ -1157500,6 +1156542,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.09.22.20198275",
+    "rel_title": "Knowledge, Attitude and Practice towards COVID-19 among people in Bangladesh during the pandemic: a cross-sectional study.",
+    "rel_date": "2020-09-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.22.20198275",
+    "rel_abs": "The world is grappling with Covid-19, a dire public health crisis. Preventive and control measures are adopted to reduce the spread of COVID-19. It is important to know the knowledge, attitude, and practice (KAP) of people towards this pandemic to suggest appropriate coping strategies. The aim of this study was to assess the KAP of Bangladeshi people towards Covid-19 and determinants of those KAPs. We conducted a cross-sectional survey of 492 Bangladeshi people aged above 18 years from May 7 to 29, 2020 throughout the country. Simple and multiple logistic regression analyses were conducted to identify the factors associated with KAP on COVID-19. About 45% of respondents had good knowledge, 49% of respondents expressed positive attitude towards controlling of COVID-19 and 24% of respondents had favorable practice towards COVID-19. Almost three fourths of the respondents went outside home during the lockdown period. Furthermore, the study found that good knowledge and attitude were associated with better practice of COVID-19 health measures. An evidence informed and context specific risk communication and community engagement, and a social and behavior change communication strategy against COVID-19 should be developed in Bangladesh, based on the findings of this study, targeting different socio-economic groups.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Md. Golam Rabbani",
+        "author_inst": "Public Health Foundation, Bangladesh"
+      },
+      {
+        "author_name": "Orin Akter",
+        "author_inst": "icddr,b"
+      },
+      {
+        "author_name": "Md. Zahid Hasan",
+        "author_inst": "icddr,b"
+      },
+      {
+        "author_name": "Nandeeta Samad",
+        "author_inst": "North South University, Dhaka, Bangladesh"
+      },
+      {
+        "author_name": "Shehrin Shaila Mahmood",
+        "author_inst": "icddr,b"
+      },
+      {
+        "author_name": "Taufique Joarder",
+        "author_inst": "Public Health Foundation, Bangladesh; Johns Hopkins Bloomberg School of Public Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.09.22.20199802",
     "rel_title": "Smoking is associated with worse outcomes of COVID-19 particularly among younger adults: A systematic review and meta-analysis",
@@ -1158925,41 +1158006,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.09.21.20166934",
-    "rel_title": "Potentials of constrained sliding mode control as an intervention guide to manage COVID19 spread",
-    "rel_date": "2020-09-23",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.21.20166934",
-    "rel_abs": "This work evaluates the potential of using sliding mode reference conditioning (SMRC) techniques as a guide for non-pharmaceutical interventions and population confinement to control the COVID-19 pandemic. SMRC technique allows robustly delimiting a given variable in dynamical systems. In particular, for the epidemio-logical problem addressed here, it can be used to compute day by day the contact rate reduction requirement in order to limit the intense care units occupancy to a given threshold. What is more, it could impose a given approaching rate to the health care system limits. Simulations are performed using the well-known SEIR model fitted to the Argentinian case to demonstrate what this control strategy sug-gests, while the effect of realistic period transitions between different confinement levels are also considered.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Sebastian Nu\u00f1ez",
-        "author_inst": "Universidad Nacional de La Plata - CONICET"
-      },
-      {
-        "author_name": "Fernando A. Inthamoussou",
-        "author_inst": "Universidad Nacional de La Plata - CONICET"
-      },
-      {
-        "author_name": "Fernando Valenciaga",
-        "author_inst": "Universidad Nacional de La Plata - CONICET"
-      },
-      {
-        "author_name": "Hernan De Battista",
-        "author_inst": "Universidad Nacional de La Plata - CONICET"
-      },
-      {
-        "author_name": "Fabricio Garelli",
-        "author_inst": "Universidad Nacional de La Plata - CONICET"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.09.18.20197228",
     "rel_title": "COVeAGE-DB: A database of age-structured COVID-19 cases and deaths.",
@@ -1159590,6 +1158636,33 @@
     "type": "new results",
     "category": "bioinformatics"
   },
+  {
+    "rel_doi": "10.1101/2020.09.18.20197582",
+    "rel_title": "Ruling In and Ruling Out COVID-19: Computing SARS-CoV-2 Infection Risk From Symptoms, Imaging and Test Data.",
+    "rel_date": "2020-09-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.18.20197582",
+    "rel_abs": "BackgroundAssigning meaningful probabilities of SARS-CoV-2 infection risk presents a diagnostic challenge across the continuum of care.\n\nMethodsWe integrated patient symptom and test data using machine learning and Bayesian inference to quantify individual patient risk of SARS-CoV-2 infection. We trained models with 100,000 simulated patient profiles based on thirteen symptoms, estimated local prevalence, imaging, and molecular diagnostic performance from published reports. We tested these models with consecutive patients who presented with a COVID-19 compatible illness at the University of California San Diego Medical Center over 14 days starting in March 2020.\n\nResultsWe included 55 consecutive patients with fever (78%) or cough (77%) presenting for ambulatory (n=11) or hospital care (n=44). 51% (n=28) were female, 49% were age <60. Common comorbidities included diabetes (22%), hypertension (27%), cancer (16%) and cardiovascular disease (13%). 69% of these (n=38) were RT-PCR confirmed positive for SARS-CoV-2 infection, 11 had repeated negative nucleic acid testing and an alternate diagnosis. Bayesian inference network, distance metric-learning, and ensemble models discriminated between patients with SARS-CoV-2 infection and alternate diagnoses with sensitivities of 81.6 - 84.2%, specificities of 58.8 - 70.6%, and accuracies of 61.4 - 71.8%. After integrating imaging and laboratory test statistics with the predictions of the Bayesian inference network, changes in diagnostic uncertainty at each step in the simulated clinical evaluation process were highly sensitive to location, symptom, and diagnostic test choices.\n\nConclusionsDecision support models that incorporate symptoms and available test results can help providers diagnose SARS-CoV-2 infection in real world settings.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Chistopher D'Ambrosia",
+        "author_inst": "University of California San Diego, Department of Computer Science and Engineering"
+      },
+      {
+        "author_name": "Henrik Christensen",
+        "author_inst": "University of California San Diego, Department of Computer Science and Engineering"
+      },
+      {
+        "author_name": "Eliah Aronoff-Spencer",
+        "author_inst": "UC San Diego"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health informatics"
+  },
   {
     "rel_doi": "10.1101/2020.09.20.20198150",
     "rel_title": "Forecasting daily COVID-19 confirmed, deaths and recovered cases using univariate time series models: A case of Pakistan study",
@@ -1160743,73 +1159816,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.09.21.20198838",
-    "rel_title": "Monitoring SARS-CoV-2 circulation and diversity through community wastewater sequencing",
-    "rel_date": "2020-09-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.21.20198838",
-    "rel_abs": "The current SARS-CoV-2 pandemic has rapidly become a major global health problem for which public health surveillance is crucial to monitor virus spread. Given the presence of viral RNA in feces in around 40% of infected persons, wastewater-based epidemiology has been proposed as an addition to disease-based surveillance to assess the spread of the virus at the community level. Here we have explored the possibility of using next-generation sequencing (NGS) of sewage samples to evaluate the diversity of SARS-CoV-2 at the community level from routine wastewater testing, and compared these results with the virus diversity in patients from the Netherlands and Belgium. Phylogenetic analysis revealed the presence of viruses belonging to the most prevalent clades (19A, 20A and 20B) in both countries. Clades 19B and 20C were not identified, while they were present in clinical samples during the same period. Low frequency variant (LFV) analysis showed that some known LFVs can be associated with particular clusters within a clade, different to those of their consensus sequences, suggesting the presence of at least 2 clades within a single sewage sample. Additionally, combining genome consensus and LFV analyses we found a total of 57 unique mutations in the SARS-CoV-2 genome which have not been described before. In conclusion, this work illustrates how NGS analysis of wastewater can be used to approximate the diversity of SARS-CoV-2 viruses circulating in a community.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Ray W. Izquierdo Lara",
-        "author_inst": "Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands."
-      },
-      {
-        "author_name": "Goffe Elsinga",
-        "author_inst": "KWR Water Research Institute, 3433 PE, Nieuwegein, The Netherlands."
-      },
-      {
-        "author_name": "Leo Heijnen",
-        "author_inst": "KWR Water Research Institute, 3433 PE, Nieuwegein, The Netherlands."
-      },
-      {
-        "author_name": "Bas B. Oude Munnink",
-        "author_inst": "Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands."
-      },
-      {
-        "author_name": "Claudia M. E. Schapendonk",
-        "author_inst": "Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands."
-      },
-      {
-        "author_name": "David Nieuwenhuijse",
-        "author_inst": "Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands."
-      },
-      {
-        "author_name": "Matthijs Kon",
-        "author_inst": "Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands."
-      },
-      {
-        "author_name": "Lu Lu",
-        "author_inst": "Usher Institute, University of Edinburgh, Edinburgh, UK."
-      },
-      {
-        "author_name": "Frank M. Aarestrup",
-        "author_inst": "National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark."
-      },
-      {
-        "author_name": "Samantha Lycett",
-        "author_inst": "The Roslin Institute, University of Edinburgh, Edinburgh, UK."
-      },
-      {
-        "author_name": "Gertjan Medema",
-        "author_inst": "KWR Water Research Institute, 3433 PE, Nieuwegein, The Netherlands."
-      },
-      {
-        "author_name": "Marion P.G. Koopmans",
-        "author_inst": "Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands."
-      },
-      {
-        "author_name": "Miranda de Graaf",
-        "author_inst": "Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands."
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.09.22.20199430",
     "rel_title": "Factors associated with drinking behaviour during COVID-19 social distancing and lockdown among adults in the UK",
@@ -1161168,6 +1160174,69 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2020.09.22.308023",
+    "rel_title": "Humoral response to SARS-CoV-2 by healthy and sick dogs during COVID-19 pandemic in Spain.",
+    "rel_date": "2020-09-22",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.22.308023",
+    "rel_abs": "COVID-19 is a zoonotic disease originated by SARS-CoV-2. Infection of animals with SARS-CoV-2 are being reported during last months, and also an increase of severe lung pathologies in domestic dogs has been detected by veterinarians in Spain. Therefore it is necessary to describe the pathological processes in those animals that show symptoms similar to those described in humans affected by COVID-19. The potential for companion animals contributing to the continued human-to-human disease, infectivity, and community spread is an urgent issue to be considered.\n\nForty animals with pulmonary pathologies were studied by chest X-ray, ultrasound study, and computed tomography. Nasopharyngeal and rectal swab were analyzed to detect canine pathogens, including SARS-CoV-2. Twenty healthy dogs living in SARS-CoV-2 positive households were included. Immunoglobulin detection by different immunoassays was performed. Our findings show that sick dogs presented severe alveolar or interstitial pattern, with pulmonary opacity, parenchymal abnormalities, and bilateral lesions. Forty dogs were negative for SARS-CoV-2 but Mycoplasma spp. was detected in 26 of 33 dogs. Five healthy and one pathological dog presented IgG against SARS-CoV-2.\n\nHere we report that despite detecting dogs with IgG -SARS-CoV-2, we never obtained a positive RT-qPCR, not even in dogs with severe pulmonary disease; suggesting that even in the case of a canine infection transmission would be unlikely. Moreover, dogs living in COVID-19 positive households could have been more exposed to be infected during outbreaks.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Ana Judith Perise-Barrios",
+        "author_inst": "Universidad Alfonso X el Sabio"
+      },
+      {
+        "author_name": "Beatriz Davinia Tomeo-Martin",
+        "author_inst": "Universidad Alfonso X el Sabio"
+      },
+      {
+        "author_name": "Pablo Gomez-Ochoa",
+        "author_inst": "Vetcorner"
+      },
+      {
+        "author_name": "Pablo Delgado-Bonet",
+        "author_inst": "Universidad Alfonso X el Sabio"
+      },
+      {
+        "author_name": "Pedro Plaza",
+        "author_inst": "ERVET-DIEZ BRU"
+      },
+      {
+        "author_name": "Paula Palau-Concejo",
+        "author_inst": "Universidad Alfonso X el Sabio"
+      },
+      {
+        "author_name": "Jorge Gonzalez",
+        "author_inst": "Micros Veterinaria SL"
+      },
+      {
+        "author_name": "Gustavo Ortiz-Diez",
+        "author_inst": "Universidad Alfonso X el Sabio"
+      },
+      {
+        "author_name": "Antonio Melendez-Lazo",
+        "author_inst": "Laboklin GmbH & Co. KG"
+      },
+      {
+        "author_name": "Michaela Gentil",
+        "author_inst": "Laboklin GmbH & Co. KG"
+      },
+      {
+        "author_name": "Javier Garcia-Castro",
+        "author_inst": "Instituto de Salud Carlos III"
+      },
+      {
+        "author_name": "Alicia Barbero-Fernandez",
+        "author_inst": "Universidad Alfonso X el Sabio"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2020.09.22.307751",
     "rel_title": "High prevalence of SARS-CoV-2 antibodies in pets from COVID-19+ households",
@@ -1162480,29 +1161549,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2020.09.18.20197723",
-    "rel_title": "Suppression of COVID-19 infection by isolation time control based on the SIR model and an analogy from nuclear fusion research",
-    "rel_date": "2020-09-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.18.20197723",
-    "rel_abs": "The coronavirus disease 2019 (COVID-19) has been damaging our daily life after declaration of pandemic. Therefore, we have started studying on the characteristics of Susceptible-Infectious-Recovered (SIR) model to know about the truth of infectious disease and our future.\n\nAfter detailed studies on the characteristics of the SIR model for the various parameter dependencies with respect to such as the outing restriction (lockdown) ratio and vaccination rate, we have finally noticed that the second term (isolation term) in the differential equation of the number of the infected is quite similar to the \"helium ash particle loss term\" in deuterium-tritium (D-T) nuclear fusion. Based on this analogy, we have found that isolation of the infected is not actively controlled in the SIR model. Then we introduce the isolation control time parameter q and have studied its effect on this pandemic. Required isolation time to terminate the COVID-19 can be estimated by this proposed method.\n\nTo show this isolation control effect, we choose Tokyo for the model calculation because of high population density. We determine the reproduction number and the isolation ratio in the initial uncontrolled phase, and then the future number of the infected is estimated under various conditions. If the confirmed case can be isolated in 3[~]8 days by widely performed testing, this pandemic could be suppressed without awaiting vaccination. If the mild outing restriction and vaccination are taken together, the isolation control time can be longer. We consider this isolation time control might be the only solution to overcome the pandemic when vaccine is not available.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Osamu Mitarai",
-        "author_inst": "Institute for Advanced Fusion & Physics Education"
-      },
-      {
-        "author_name": "Nagato Yanagi",
-        "author_inst": "National Institute for Fusion Science"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.09.18.20197590",
     "rel_title": "SARS-CoV-2 antigen and antibody prevalence among UK staff working with cancer patients during the COVID-19 pandemic.",
@@ -1162741,6 +1161787,29 @@
     "type": "new results",
     "category": "cell biology"
   },
+  {
+    "rel_doi": "10.1101/2020.09.18.304493",
+    "rel_title": "An immunodominance hierarchy exists in CD8+ T cell responses to HLA-A*02:01-restricted epitopes identified from the non-structural polyprotein 1a of SARS-CoV-2.",
+    "rel_date": "2020-09-19",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.18.304493",
+    "rel_abs": "COVID-19 vaccines are being rapidly developed and human trials are underway. Almost all of these vaccines have been designed to induce antibodies targeting spike protein of SARS-CoV-2 in expectation of neutralizing activities. However, non-neutralizing antibodies are at risk of causing antibody-dependent enhancement. Further, the longevity of SARS-CoV-2-specific antibodies is very short. Therefore, in addition to antibody-induced vaccines, novel vaccines on the basis of SARS-CoV-2-specific cytotoxic T lymphocytes (CTLs) should be considered in the vaccine development. Here, we attempted to identify HLA-A*02:01-restricted CTL epitopes derived from the non-structural polyprotein 1a of SARS-CoV-2. Eighty-two peptides were firstly predicted as epitope candidates on bioinformatics. Fifty-four in 82 peptides showed high or medium binding affinities to HLA-A*02:01. HLA-A*02:01 transgenic mice were then immunized with each of the 54 peptides encapsulated into liposomes. The intracellular cytokine staining assay revealed that 18 out of 54 peptides were CTL epitopes because of the induction of IFN-{gamma}-producing CD8+ T cells. In the 18 peptides, 10 peptides were chosen for the following analyses because of their high responses. To identify dominant CTL epitopes, mice were immunized with liposomes containing the mixture of the 10 peptides. Some peptides were shown to be statistically predominant over the other peptides. Surprisingly, all mice immunized with the liposomal 10 peptide mixture did not show the same reaction pattern to the 10 peptides. There were three pattern types that varied sequentially, suggesting the existence of an immunodominance hierarchy, which may provide us more variations in the epitope selection for designing CTL-based COVID-19 vaccines.\n\nImportanceFor the development of vaccines based on SARS-CoV-2-specific cytotoxic T lymphocytes (CTLs), we attempted to identify HLA-A*02:01-restricted CTL epitopes derived from the non-structural polyprotein 1a of SARS-CoV-2. Out of 82 peptides predicted on bioinformatics, 54 peptides showed good binding affinities to HLA-A*02:01. Using HLA-A*02:01 transgenic mice, 18 in 54 peptides were found to be CTL epitopes in the intracellular cytokine staining assay. Out of 18 peptides, 10 peptides were chosen for the following analyses because of their high responses. To identify dominant epitopes, mice were immunized with liposomes containing the mixture of the 10 peptides. Some peptides were shown to be statistically predominant. Surprisingly, all immunized mice did not show the same reaction pattern to the 10 peptides. There were three pattern types that varied sequentially, suggesting the existence of an immunodominance hierarchy, which may provide us more variations in the epitope selection for designing CTL-based COVID-19 vaccines.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Akira Takagi",
+        "author_inst": "Saitama Medical University"
+      },
+      {
+        "author_name": "Masanori Matsui",
+        "author_inst": "Saitama Medical University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2020.09.18.304139",
     "rel_title": "Antisense oligonucleotides target a nearly invariant structural element from the SARS-CoV-2 genome and drive RNA degradation",
@@ -1163902,25 +1162971,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.09.14.20193821",
-    "rel_title": "Prediction of Covid-19 Infections Through December 2020 for 10 US States Incorporating Outdoor Temperature and School Re-Opening Effects-August Update",
-    "rel_date": "2020-09-18",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.14.20193821",
-    "rel_abs": "End-of-August updates for Covid-19 infection case predictions for 10 US States (NY, WA, GA, IL, MN, FL, OH, MI, CA, and NC) are compared to actual data. Several states that experienced significant summer surges gained control of accelerating infection spread during August. The US as a whole and the 10 States investigated continue to follow periods of linear infection growth that defines a boundary separating accelerated infection growth and infection decay. August 31 predictions (initiated July 27, 2020) for four States (NY, WA, MI and MN) are within 10% of actual data. Predictions for four other States (GA, IL, CA, and OH) agree between 10 and 20% of actual data. Predictions for two States (FL and NC) are greater than 20% different from actual data. Systematic differences between predictions and actual data are related to the impact of the June-July summer surge, and human behavior reactions (ie, increased face mask usage and distancing) to accelerated infection growth. Outdoor temperature effects and school re-opening effects are not apparent nor expected for August. Human behavior parameters (Social Distance Index, SDI, and disease transmission efficiency, G, parameters) are adjusted to mirror August data. Comparisons of actual versus predicted daily new infection cases display the complexity of SARS-CoV-2 transmission.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Ty A Newell",
-        "author_inst": "University of Illinois"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.09.14.20193904",
     "rel_title": "A SARS-CoV-2 Reference Standard Quantified by Multi-digital PCR Platforms for Quality Assessment of Molecular Tests",
@@ -1164239,6 +1163289,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.09.15.20191957",
+    "rel_title": "Adherence to the test, trace and isolate system: results from a time series of 21 nationally representative surveys in the UK (the COVID-19 Rapid Survey of Adherence to Interventions and Responses  study)",
+    "rel_date": "2020-09-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.15.20191957",
+    "rel_abs": "Objectives: To investigate rates of adherence to the UKs test, trace and isolate system over time. Design: Time series of cross-sectional online surveys. Setting: Data were collected between 2 March and 5 August 2020. Participants: 42,127 responses from 31,787 people living in the UK, aged 16 years or over, are presented (21 survey waves, n{approx}2,000 per wave). Main outcome measures: Identification of the key symptoms of COVID-19 (cough, high temperature / fever, and loss of sense of smell or taste), self-reported adherence to self-isolation if symptomatic, requesting an antigen test if symptomatic, intention to share details of close contacts, self-reported adherence to quarantine if alerted that you had been in contact with a confirmed COVID-19 case. Results: Only 48.9% of participants (95% CI 48.2% to 49.7%) identified key symptoms of COVID-19. Self-reported adherence to test, trace and isolate behaviours was low (self-isolation 18.2%, 95% CI 16.4% to 19.9%; requesting an antigen test 11.9%, 95% CI 10.1% to 13.8%; intention to share details of close contacts 76.1%, 95% CI 75.4% to 76.8%; quarantining 10.9%, 95% CI 7.8% to 13.9%) and largely stable over time. By contrast, intention to adhere to protective measures was much higher. Non-adherence was associated with: men, younger age groups, having a dependent child in the household, lower socio-economic grade, greater hardship during the pandemic, and working in a key sector. Conclusions: Practical support and financial reimbursement is likely to improve adherence. Targeting messaging and policies to men, younger age groups, and key workers may also be necessary.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Louise E. Smith",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Henry W. W. Potts",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Richard Amlot",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Nicola T. Fear",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Susan Michie",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "James Rubin",
+        "author_inst": "King's College London"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.09.15.20195222",
     "rel_title": "Demand for Self-Managed Online Telemedicine Abortion in Eight European Countries During the COVID-19 Pandemic: A Regression Discontinuity Analysis",
@@ -1165792,73 +1164881,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
-  {
-    "rel_doi": "10.1101/2020.09.16.20191528",
-    "rel_title": "The case series of 34 patients with COVID-19 diagnosed with HIV infection from Central and Eastern European Countries - Euroguidelines in Central and Eastern Europe Network Group data",
-    "rel_date": "2020-09-18",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.16.20191528",
-    "rel_abs": "BackgroundA novel coronavirus (SARS-CoV-2) causing coronavirus disease (COVID-19) was detected at the end of 2019 in China. There are many COVID-19 studies in progress however, little is known about the course of COVID-19 in people living with HIV (PLWH). The aim of our study was to describe epidemiology and clinical characteristics of PLWH diagnosed with COVID-19 reported form Central and Eastern European Countries.\n\nMethodsOn-line survey was sent to Euroguidelines in Central and Eastern Europe (ECEE) Network Group. Analysis included all confirmed COVID-19 cases between March 11 and June 26 2020 among PLWH in 12 countries: Albania, Belarus, Bosnia and Herzegovina, Bulgaria, Czech Republic, Estonia, Hungary, Lithuania, Poland, Romania, Russia, and Serbia.\n\nResultsIn total 34 cases were reported. The mean age of those patients was 42.7 years (IQR = 35.8-48.5) and most of the patients were male (70.6% vs 29.4%). The mean CD4+ T-cell count prior COVID-19 diagnosis was 558 cells/mm3 (IQR = 312-719) and HIV RNA viral load (VL) was undetectable in 18 of 34 (53%) cases, the data about most recent HIV RNA VL was not available in three cases (8,8%). Comorbidities were observed in 19 (55.9%) patients, mostly cardiovascular disease (27,8%), and in 10 (29.4%) patients had coinfection, mostly chronic hepatitis C (87.5%). The clinical course of COVID-19 was asymptomatic in 4 (12%) cases, mild disease without hospitalization was reported in 11 (32%) cases. Stable patients with respiratory and/or systemic symptoms have been documented in 14 (41%) cases; 5 (15%) patients were clinically unstable with respiratory failure. Full recovery was reported in 31 (91%) cases, two patients died. In one case the data was not available.\n\nConclusionThis study from 12 countries in Central and Eastern Europe region indicates no alarming signals of increased morbidity or mortality from COVID-19 among HIV-positive persons there is a need for further research.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Kerstin Kase",
-        "author_inst": "West Tallinn Central Hospital, Estonia"
-      },
-      {
-        "author_name": "Agata Skrzat-Klapaczynska",
-        "author_inst": "Department of Adults Infectious Diseases, Hospital for Infectious Diseases, Medical University of Warsaw, Poland"
-      },
-      {
-        "author_name": "Anne Vassilenko",
-        "author_inst": "Belarusian State Medical University, Minsk, Belarus"
-      },
-      {
-        "author_name": "Arjan Harxhi",
-        "author_inst": "University Hospital Center of Tirana, Infectious Disease Service, Albania"
-      },
-      {
-        "author_name": "Botond Lakatos",
-        "author_inst": "National Institute of Hematology and Infectious Diseases, South-Pest Central Hospital, National Center of HIV, Hungary"
-      },
-      {
-        "author_name": "Gordana Dragovic Lukic",
-        "author_inst": "Department of Pharmacology, Clinical Pharmacology and Toxicology, School of Medicine; University of Belgrade, Serbia"
-      },
-      {
-        "author_name": "David Jilich",
-        "author_inst": "Department of Infectious Diseases, Charles University in Prague and Na Bulovce Hospital, Czech Republic"
-      },
-      {
-        "author_name": "Antonija Verhaz",
-        "author_inst": "Infection Diseases Clinic, University Clinical Centre of the Republic of Srpska, Centre for Biomedical Research, Faculty of Medicine, University of Banja Luka, "
-      },
-      {
-        "author_name": "Nina Yancheva",
-        "author_inst": "Department for AIDS. Specialized Hospital for Active Treatment of Infectious and Parasitic Disease Sofia, Bulgaria"
-      },
-      {
-        "author_name": "Florentina Dumitrescu",
-        "author_inst": "University of Medicine and Pharmacy Craiova, Victor Babes Clinical Hospital of Infectious Diseases and Pneumology, Craiova, Romania"
-      },
-      {
-        "author_name": "Raimonda Matulionyte",
-        "author_inst": "Vilnius University, Faculty of Medicine, Vilnius University Hospital Santaros Klinikos, Lithuania"
-      },
-      {
-        "author_name": "Andrzej Horban",
-        "author_inst": "Department of Adults Infectious Diseases, Hospital for Infectious Diseases, Medical University of Warsaw, Poland"
-      },
-      {
-        "author_name": "Justyna Dominika Kowalska",
-        "author_inst": "Department of Adults Infectious Diseases, Hospital for Infectious Diseases, Medical University of Warsaw, Poland"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "hiv aids"
-  },
   {
     "rel_doi": "10.1101/2020.09.17.20197020",
     "rel_title": "On Topological Properties of COVID-19: Predicting and Controling Pandemic Risk with Network Statistics",
@@ -1166289,6 +1165311,101 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.09.16.20195446",
+    "rel_title": "High-throughput quantitation of SARS-CoV-2 antibodies in a single-dilution homogeneous assay",
+    "rel_date": "2020-09-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.16.20195446",
+    "rel_abs": "SARS-CoV-2 emerged in late 2019 and has since spread around the world, causing a pandemic of the respiratory disease COVID-19. Detecting antibodies against the virus is an essential tool for tracking infections and developing vaccines. Such tests, primarily utilizing the enzyme-linked immunosorbent assay (ELISA) principle, can be either qualitative (reporting positive/negative results) or quantitative (reporting a value representing the quantity of specific antibodies). Quantitation is vital for determining stability or decline of antibody titers in convalescence, efficacy of different vaccination regimens, and detection of asymptomatic infections. Quantitation typically requires two-step ELISA testing, in which samples are first screened in a qualitative assay and positive samples are subsequently analyzed as a dilution series. To overcome the throughput limitations of this approach, we developed a simpler and faster system that is highly automatable and achieves quantitation in a single-dilution screening format with sensitivity and specificity comparable to those of ELISA.",
+    "rel_num_authors": 20,
+    "rel_authors": [
+      {
+        "author_name": "Markus H Kainulainen",
+        "author_inst": "Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA"
+      },
+      {
+        "author_name": "Eric Bergeron",
+        "author_inst": "Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA"
+      },
+      {
+        "author_name": "Payel Chatterjee",
+        "author_inst": "Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA"
+      },
+      {
+        "author_name": "Asheley P Chapman",
+        "author_inst": "School of Chemistry and Biochemistry, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA"
+      },
+      {
+        "author_name": "Joo Lee",
+        "author_inst": "Reagent and Diagnostic Services Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, USA"
+      },
+      {
+        "author_name": "Asiya Chida",
+        "author_inst": "Reagent and Diagnostic Services Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, USA"
+      },
+      {
+        "author_name": "Xiaoling Tang",
+        "author_inst": "Reagent and Diagnostic Services Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, USA"
+      },
+      {
+        "author_name": "Rebekah E Wharton",
+        "author_inst": "Emergency Response Branch, Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, GA, USA"
+      },
+      {
+        "author_name": "Kristina B Mercer",
+        "author_inst": "Newborn Screening & Molecular Biology Branch, Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, GA, USA"
+      },
+      {
+        "author_name": "Marla Petway",
+        "author_inst": "Reagent and Diagnostic Services Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, USA"
+      },
+      {
+        "author_name": "Harley M Jenks",
+        "author_inst": "Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA"
+      },
+      {
+        "author_name": "Timothy D Flietstra",
+        "author_inst": "Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA"
+      },
+      {
+        "author_name": "Amy J Schuh",
+        "author_inst": "Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA"
+      },
+      {
+        "author_name": "Panayampalli S Satheshkumar",
+        "author_inst": "Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA"
+      },
+      {
+        "author_name": "Jasmine M Chaitram",
+        "author_inst": "Division of Laboratory Systems, Centers for Disease Control and Prevention, Atlanta, GA, USA"
+      },
+      {
+        "author_name": "S Michele Owen",
+        "author_inst": "National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA"
+      },
+      {
+        "author_name": "M G Finn",
+        "author_inst": "School of Chemistry and Biochemistry, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA"
+      },
+      {
+        "author_name": "Jason M Goldstein",
+        "author_inst": "Reagent and Diagnostic Services Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, USA"
+      },
+      {
+        "author_name": "Joel M Montgomery",
+        "author_inst": "Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA"
+      },
+      {
+        "author_name": "Christina F Spiropoulou",
+        "author_inst": "Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA"
+      }
+    ],
+    "version": "1",
+    "license": "cc0",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.09.16.20193466",
     "rel_title": "Inexpensive, versatile and open-source methods for SARS-CoV-2 detection",
@@ -1167578,33 +1166695,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.09.16.20196295",
-    "rel_title": "Ranking the relative importance of COVID-19 immunisation strategies: a survey of expert stakeholders in Canada",
-    "rel_date": "2020-09-18",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.16.20196295",
-    "rel_abs": "BackgroundIn the face of anticipated limited COVID-19 vaccine supply necessitating the vaccination of certain groups earlier than others, the assessment of values and preferences of stakeholders is an important component of an ethically sound vaccine prioritisation framework.\n\nObjectiveTo establish a preliminary expert stakeholder perspective on the relative importance of pandemic immunisation strategies for different COVID-19 pandemic scenarios at the time of initial COVID-19 vaccine availability.\n\nMethodsA survey was conducted by an email process from July 22 to August 14, 2020. Stakeholders included clinical and public health expert groups, provincial and territorial committees and national Indigenous groups, patient and community advocacy representatives and experts, health professional associations, and federal government departments in Canada. Survey results were analysed using descriptive statistics.\n\nResultsOf 156 stakeholders contacted, 74 surveys were completed for a participation rate of 47.4%. During an anticipated period of initial vaccine scarcity for all pandemic scenarios, stakeholders generally considered the most important immunisation strategy to be protecting those who are most vulnerable to severe illness and death from COVID-19. This was followed in importance by the strategies to protect healthcare capacity, and to minimise transmission of COVID-19. In this supply constrained context, an immunisation strategy to protect critical infrastructure was considered the least important.\n\nConclusionThe findings of this study provide a timely, preliminary Canadian expert perspective on priority COVID-19 pandemic immunisation strategies to guide early public health planning for an eventual COVID-19 immunisation program. These results fill a gap in the literature and could help advisory groups around the world in their assessment of values and preferences for ethical guidelines for COVID-19 vaccine allocation.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Linlu Zhao",
-        "author_inst": "Public Health Agency of Canada"
-      },
-      {
-        "author_name": "Shainoor J Ismail",
-        "author_inst": "Public Health Agency of Canada"
-      },
-      {
-        "author_name": "Matthew C Tunis",
-        "author_inst": "Public Health Agency of Canada"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.09.16.20195917",
     "rel_title": "Meta-analysis of the clinical performance of commercial SARS-CoV-2 nucleic acid, antigen and antibody tests up to 22 August 2020",
@@ -1167919,6 +1167009,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.09.18.20195669",
+    "rel_title": "How do the general population behave with facemasks to prevent COVID-19 in the community?",
+    "rel_date": "2020-09-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.18.20195669",
+    "rel_abs": "IMPORTANCE The appropriate use of facemasks, recommended or mandated by authorities, is critical to protect the community and prevent the spread of COVID-19. OBJECTIVE To evaluate the frequency and quality of facemask use in general populations of different socio-spatial backgrounds. DESIGN A multi-site observational study carried out from 25 June 2020 to 21 July 2020. SETTING The observations were carried out in 43 different locations in a region in the west of France, representing various areas: rural and urban, indoor and outdoor, and in areas where masks were mandated or not. An observer was positioned at a predetermined place, facing a landmark, and collected information about the use of facemasks and socio-demographic data. PARTICIPANTS All individual passing between the observer and the landmark were included. EXPOSURE The observer collected information on whether a mask was worn, the type of mask used, the quality of the positioning, gender, and the age category of each individual. MAIN OUTCOMES AND MEASURES The main outcomes were the use of a facemask and the quality of the positioning. Factors associated with these outcomes were identified. RESULTS A total of 3354 observations were recorded. A facemask was worn by 56.4% (n=1892) of individuals, varying from 49% (n=1359) in non-mandatory areas and 91.7% (n=533) in mandatory areas, including surgical facemasks (56.8%, n=1075) and cloth masks (43.2%, n=817). The facemask was correctly positioned in 75.2% (n=1422) of cases. The factors independently associated with wearing a facemask were being indoors (adjusted odds ratio [aOR], 0.37; 95% confidence interval [CI], 0.31-0.44), being in a mandatory area (aOR, 0.14; 95%CI, 0.10-0.20), female gender (aOR, 0.57; 95%CI, 0.49-0.66), and age >40 years (aOR, 0.54; 95%CI, 0.46-0.63). The factors independently associated with correct mask position were rural location (aOR, 0.76; 95%CI, 0.97-0.98), being in an indoor area (aOR, 0.49; 95%CI, 0.38-0.65), use of a cloth mask (aOR, 0.65; 95%CI, 0.52-0.81), and age >40 years (aOR, 0.61; 95%CI 0.49-0.76). CONCLUSIONS AND RELEVANCE Information campaigns should promote the use of cloth masks. Young people in general and men in particular are the priority targets. Simplifying the rules to require universal mandatory masking seems to be the best approach for health authorities.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Colin DESCHANVRES",
+        "author_inst": "CHU de Nantes"
+      },
+      {
+        "author_name": "Thomas HAUDEBOURG",
+        "author_inst": "CHU de Nantes"
+      },
+      {
+        "author_name": "Nathan PEIFFER-SMADJA",
+        "author_inst": "Hopital Bichat Claude Bernard"
+      },
+      {
+        "author_name": "Karine BLANCKAERT",
+        "author_inst": "CHU de Nantes"
+      },
+      {
+        "author_name": "David BOUTOILLE",
+        "author_inst": "CHU de Nantes"
+      },
+      {
+        "author_name": "Jean-Christophe LUCET",
+        "author_inst": "Hopital Bichat Claude Bernard"
+      },
+      {
+        "author_name": "Gabriel BIRGAND",
+        "author_inst": "CHU de Nantes"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.09.16.20195750",
     "rel_title": "Association between corticosteroids and intubation or death among patients with COVID-19 pneumonia in non-ICU settings: an observational study using of real-world data from 51 hospitals in France and Luxembourg",
@@ -1169468,253 +1168601,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.09.17.301093",
-    "rel_title": "Comparison of Rhesus and Cynomolgus macaques as an authentic model for COVID-19.",
-    "rel_date": "2020-09-17",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.17.301093",
-    "rel_abs": "A novel coronavirus, SARS-CoV-2, has been identified as the causative agent of the current COVID-19 pandemic. Animal models, and in particular non-human primates, are essential to understand the pathogenesis of emerging diseases and to the safety and efficacy of novel vaccines and therapeutics. Here, we show that SARS-CoV-2 replicates in the upper and lower respiratory tract and causes pulmonary lesions in both rhesus and cynomolgus macaques, resembling the mild clinical cases of COVID-19 in humans. Immune responses against SARS-CoV-2 were also similar in both species and equivalent to those reported in milder infections and convalescent human patients. Importantly, we have devised a new method for lung histopathology scoring that will provide a metric to enable clearer decision making for this key endpoint. In contrast to prior publications, in which rhesus are accepted to be the optimal study species, we provide convincing evidence that both macaque species authentically represent mild to moderate forms of COVID-19 observed in the majority of the human population and both species should be used to evaluate the safety and efficacy of novel and repurposed interventions against SARS-CoV-2. Accessing cynomolgus macaques will greatly alleviate the pressures on current rhesus stocks.",
-    "rel_num_authors": 58,
-    "rel_authors": [
-      {
-        "author_name": "Francisco J Salguero",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Andrew D White",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Gillian S Slack",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Susan A Fotheringham",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Kevin R Bewley",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Karen E Gooch",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Stephanie Longet",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Holly E Humphries",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Robert J Watson",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Laura Hunter",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Kathryn A Ryan",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Yper Hall",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Laura Sibley",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Charlotte Sarfas",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Lauren Allen",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Marilyn Aram",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Emily Brunt",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Phillip Brown",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Karen R Buttigieg",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Breeze E Cavell",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Rebecca Cobb",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Naomi S Coombes",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Owen Daykin-Pont",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Michael J Elmore",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Konstantinos Gkolfinos",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Kerry J Godwin",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Jade Gouriet",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Rachel Halkerston",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Debbie J Harris",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Thomas Hender",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Catherine M.K. Ho",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Chelsea L Kennard",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Daniel Knott",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Stephanie Leung",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Vanessa Lucas",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Adam Mabbutt",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Alexandra L Morrison",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Didier Ngabo",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Jemma Paterson",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Elizabeth J Penn",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Steve Pullan",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Irene Taylor",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Tom Tipton",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Stephen Thomas",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Julia A Tree",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Carrie Turner",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Nadina Wand",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Nathan R Wiblin",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Sue Charlton",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Bassam Hallis",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Geoffrey Pearson",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Emma L Rayner",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Andrew G Nicholson",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Simon G Funnell",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Mike J Dennis",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Fergus V Gleeson",
-        "author_inst": "National Heart and Lung Institute"
-      },
-      {
-        "author_name": "Sally Sharpe",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Miles W Carroll",
-        "author_inst": "Public Health England"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.09.17.301861",
     "rel_title": "Discovery of human ACE2 variants with altered recognition by the SARS-CoV-2 spike protein",
@@ -1170025,6 +1168911,65 @@
     "type": "new results",
     "category": "biophysics"
   },
+  {
+    "rel_doi": "10.1101/2020.09.16.299537",
+    "rel_title": "Mouse model for testing SARS-CoV-2 antivirals: Pharmacokinetics",
+    "rel_date": "2020-09-16",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.16.299537",
+    "rel_abs": "Background and ObjectivesRemdesivir and hydroxychloroquine are or were among the most promising therapeutic options to tackle the current SARS-CoV-2 pandemic. Besides the use of the prodrug remdesivir itself, the direct administration of GS-441 524, the resulting main metabolite of remdesivir, could be advantageous and even more effective. All substances were not originally developed for the treatment of COVID-19 and especially for GS-441 524 little is known about its pharmacokinetic and physical-chemical properties. To justify the application of new or repurposed drugs in humans, pre-clinical in vivo animal models are mandatory to investigate relevant PK and PD properties and their relationship to each other. In this study, an adapted mouse model was chosen to demonstrate its suitability to provide sufficient information on the model substances GS-441 524 and HCQ regarding plasma concentration and distribution into relevant tissues a prerequisite for treatment effectiveness.\n\nMethodsGS-441 524 and HCQ were administered intravenously as a single injection to male mice. Blood and organ samples were taken at several time points and drug concentrations were quantified in plasma and tissue homogenates by two liquid chromatography/tandem mass spectrometry methods. In vitro experiments were conducted to investigate the degradation of remdesivir in human plasma and blood. All pharmacokinetic analyses were performed with R Studio using non-compartmental analysis.\n\nResultsHigh tissue to plasma ratios for GS-441 524 and HCQ were found, indicating a significant distribution into the examined tissue, except for the central nervous system and fat. For GS-441 524, measured tissue concentrations exceeded the reported in vitro EC50 values by more than 10-fold and in consideration of its high efficacy against feline infectious peritonitis, GS-441 524 could indeed be effective against SARS-CoV-2 in vivo. For HCQ, relatively high in vitro EC50 values are reported, which were not reached in all tissues. Facing its slow tissue distribution, HCQ might not lead to sufficient tissue saturation for a reliable antiviral effect.\n\nConclusionThe mouse model was able to characterise the PK and tissue distribution of both model substances and is a suitable tool to investigate early drug candidates against SARS-CoV-2. Furthermore, we could demonstrate a high tissue distribution of GS-441 524 even if not administered as the prodrug remdesivir.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Oliver Scherf-Clavel",
+        "author_inst": "University of Wuerzburg"
+      },
+      {
+        "author_name": "Edith Kaczmarek",
+        "author_inst": "University of Veterinary Medicine Hannover"
+      },
+      {
+        "author_name": "Martina Kinzig",
+        "author_inst": "Institute for Biomedical and Pharmaceutical Research"
+      },
+      {
+        "author_name": "Bettina Friedl",
+        "author_inst": "University of Wuerzburg"
+      },
+      {
+        "author_name": "Malte Feja",
+        "author_inst": "University of Veterinary Medicine Hannover"
+      },
+      {
+        "author_name": "Rainer Hoehl",
+        "author_inst": "Paracelsus Medical Private University"
+      },
+      {
+        "author_name": "Roland Nau",
+        "author_inst": "University Medical Center Goettingen"
+      },
+      {
+        "author_name": "Ulrike Holzgrabe",
+        "author_inst": "University of Wuerzburg"
+      },
+      {
+        "author_name": "Manuela Gernert",
+        "author_inst": "University of Veterinary Medicine Hannover"
+      },
+      {
+        "author_name": "Franziska Richter",
+        "author_inst": "University of Veterinary Medicine Hannover"
+      },
+      {
+        "author_name": "Fritz Soergel",
+        "author_inst": "Institute for Biomedical and Pharmaceutical Research, Paul-Ehrlich-Strasse 19, D-90562 Nuernberg-Heroldsberg"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "systems biology"
+  },
   {
     "rel_doi": "10.1101/2020.09.16.297945",
     "rel_title": "Characterisation of protease activity during SARS-CoV-2 infection identifies novel viral cleavage sites and cellular targets for drug repurposing",
@@ -1171246,49 +1170191,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.09.14.20194407",
-    "rel_title": "Flushing of stagnant premise water systems after theCOVID-19 shutdown can reduce infection risk byLegionella and Mycobacterium spp.",
-    "rel_date": "2020-09-15",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.14.20194407",
-    "rel_abs": "The unprecedented widespread closing of buildings due to the COVID-19 pandemic has allowed water to stagnate in premise plumbing systems, creating conditions that may facilitate the growth of opportunistic pathogens. In this study, we flushed and collected samples from showers in buildings that had been unoccupied for approximately two months and quantified Legionella pneumophila using a commercial cultivation-based assay. In addition, all bacteria, Legionella spp., L. pneumophila, L. pneumophila serogroup 1, non-tuberculous mycobacteria (NTM), and Mycobacterium avium complex (MAC) were analyzed using quantitative PCR (qPCR). Despite low or negligible total chlorine in the stagnant pre-flush water samples, L. pneumophila were not detected by either method; Legionella spp., NTM, and MAC, however, were widespread. Using quantitative microbial risk assessment (QMRA), estimated risks of clinical illness from exposure to legionella and MAC via showering were generally low, but the risk of subclinical infection via Legionella spp. could exceed a 10-7 daily risk threshold if just a small fraction ([&ge;]0.1 %) of those legionellae detected by qPCR are highly infectious. Flushing cold and hot water lines rapidly restored a total chlorine (as chloramine) residual and decreased all bacterial gene targets to building inlet water levels within 30 min. Following flushing, the chlorine residual rapidly dissipated and bacterial gene targets rebounded, approaching pre-flush concentrations after 6 to 7 days of stagnation. These results suggest that stagnant water in premise plumbing may contain elevated levels of opportunistic pathogens; flushing, however, can rapidly improve water quality and reduce the health risk but the improvement will be short-lived if building disuse persists.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Raymond M Hozalski",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Timothy M LaPara",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Xiaotian Zhao",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Taegyu Kim",
-        "author_inst": "University of Minnesota"
-      },
-      {
-        "author_name": "Michael B Waak",
-        "author_inst": "Norwegian University of Science and Technology & SINTEF Community"
-      },
-      {
-        "author_name": "Tucker Burch",
-        "author_inst": "U.S. Department of Agriculture"
-      },
-      {
-        "author_name": "Michael McCarty",
-        "author_inst": "University of Minnesota"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.09.14.20191106",
     "rel_title": "Impact of SARS-CoV-2 antibodies at delivery in women, partners and newborns",
@@ -1171739,6 +1170641,97 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.09.14.20191759",
+    "rel_title": "SARS-CoV-2 N-antigenemia: A new alternative to nucleic acid amplification techniques",
+    "rel_date": "2020-09-15",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.14.20191759",
+    "rel_abs": "Background. Molecular assays on nasopharyngeal swabs remain the cornerstone of COVID-19 diagnostic. Despite massive worldwide efforts, the high technicalities of nasopharyngeal sampling and molecular assays, as well as scarce resources of reagents, limit our testing capabilities. Several strategies failed, to date, to fully alleviate this testing process (e.g. saliva sampling or antigen testing on nasopharyngeal samples). We assessed the performances of a new ELISA microplate assay quantifying SARS-CoV-2 nucleocapsid antigen (N-antigen) in serum or plasma. Methods. The specificity of the assay, determined on 63 non-COVID patients, was 98.4% (95% confidence interval [CI], 85.3 to 100). Performances were determined on 227 serum samples from 165 patients with RT-PCR confirmed SARS-CoV-2 infection included in the French COVID and CoV-CONTACT cohorts. Findings. Sensitivity was 132/142, 93.0% (95% CI, 84.7 to 100), within the first two weeks after symptoms onset. A subset of 73 COVID-19 patients had a serum collected within 24 hours following or preceding a positive nasopharyngeal swab. Among patients with high nasopharyngeal viral loads, Ct value below 30 and 33, only 1/50 and 4/67 tested negative for N-antigenemia, respectively. Among patients with a negative nasopharyngeal RT-PCR, 8/12 presented positive N-antigenemia. The lower respiratory tract was explored for 6/8 patients, showing positive PCR in 5 cases. Interpretation. This is the first demonstration of the N-antigen antigenemia during COVID-19. Its detection presented a robust sensitivity, especially within the first 14 days after symptoms onset and high nasopharyngeal viral loads. These findings have to be confirmed with higher representation of outpatients. This approach could provide a valuable new option for COVID-19 diagnosis, only requiring a blood draw and easily scalable in all clinical laboratories.",
+    "rel_num_authors": 19,
+    "rel_authors": [
+      {
+        "author_name": "Quentin Le Hingrat",
+        "author_inst": "Universite de Paris, Virology, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France"
+      },
+      {
+        "author_name": "Benoit Visseaux",
+        "author_inst": "Universite de Paris, Virology, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France"
+      },
+      {
+        "author_name": "Cedric Laouenan",
+        "author_inst": "Universite de Paris, Center for Clinical Investigation, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France"
+      },
+      {
+        "author_name": "Sarah Tubiana",
+        "author_inst": "Universite de Paris, Center for Clinical Investigation, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France"
+      },
+      {
+        "author_name": "Lila Bouadma",
+        "author_inst": "Universite de Paris, Medical and Infectious Diseases Intensive Care Unit, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Pari"
+      },
+      {
+        "author_name": "Yazdan Yazdanpanah",
+        "author_inst": "Universite de Paris, Tropical and infectious diseases Department, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, Franc"
+      },
+      {
+        "author_name": "Xavier Duval",
+        "author_inst": "Universite de Paris, Center for Clinical Investigation, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France"
+      },
+      {
+        "author_name": "Houria Ichou",
+        "author_inst": "Virology, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France"
+      },
+      {
+        "author_name": "Florence Damond",
+        "author_inst": "Virology, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France"
+      },
+      {
+        "author_name": "Melanie Bertine",
+        "author_inst": "Virology, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France"
+      },
+      {
+        "author_name": "Nabil Benmalek",
+        "author_inst": "Virology, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France"
+      },
+      {
+        "author_name": "- French COVID cohort management committee",
+        "author_inst": ""
+      },
+      {
+        "author_name": "- CoV-CONTACT study group",
+        "author_inst": ""
+      },
+      {
+        "author_name": "Christophe Choquet",
+        "author_inst": "Emergency Department, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital Paris, France"
+      },
+      {
+        "author_name": "Jean-Francois Timsit",
+        "author_inst": "Universite de Paris, Medical and Infectious Diseases Intensive Care Unit, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Pari"
+      },
+      {
+        "author_name": "Jade Ghosn",
+        "author_inst": "Universite de Paris, Tropical and infectious diseases Department, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, Franc"
+      },
+      {
+        "author_name": "Charlotte Charpentier",
+        "author_inst": "Universite de Paris, Virology, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France"
+      },
+      {
+        "author_name": "Diane Descamps",
+        "author_inst": "Universite de Paris, Virology, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France"
+      },
+      {
+        "author_name": "Nadhira Houhou-Fidouh",
+        "author_inst": "Virology, Assistance Publique-Hopitaux de Paris, Bichat-Claude Bernard University Hospital, Paris, France"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.09.14.20194001",
     "rel_title": "Predictors of characteristics associated with negative SARS-CoV-2 PCR test despite proven disease and association with treatment and outcomes.The COVID-19 RT-PCR Study.",
@@ -1173004,25 +1171997,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.09.13.20193599",
-    "rel_title": "A full-scale agent-based model of Lombardy COVID-19 dynamics to explore social networks connectivity and vaccine impact on epidemic",
-    "rel_date": "2020-09-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.13.20193599",
-    "rel_abs": "COVID-19 outbreak is an awful event. However it gives to the scientists the possibility to test theories about epidemic. The aim of this contribution is to propose a individual-based model of Lombardy COVID-19 outbreak at full-scale, where full-scale means that will be simulated all the 10 millions inhabitant population of Lombardy person by person, in a commercial computer. All this to test the impact of our daily actions in epidemic, investigate social networks connectivity and in the end have an insight on the impact of an hypothetical vaccine.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Giuseppe Giacopelli",
-        "author_inst": "University of Palermo"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.09.12.20193433",
     "rel_title": "The impact of natural disasters on the spread of COVID-19: a geospatial, agent based epidemiology model",
@@ -1173389,6 +1172363,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "genetic and genomic medicine"
   },
+  {
+    "rel_doi": "10.1101/2020.09.13.20193722",
+    "rel_title": "Sensing of COVID-19 Antibodies in Seconds via Aerosol Jet Printed Three Dimensional Electrodes",
+    "rel_date": "2020-09-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.13.20193722",
+    "rel_abs": "Rapid diagnosis is critical for the treatment and prevention of diseases. In this research, we report sensing of antibodies specific to SARS-CoV-2 virus in seconds via an electrochemical platform consisting of gold micropillar array electrodes decorated with reduced graphene oxide and functionalized with recombinant viral antigens. The array electrodes are fabricated by Aerosol Jet (AJ) nanoparticle 3D printing, where gold nanoparticles (3-5nm) are assembled in 3D space, sintered, and integrated with a microfluidic device. The device is shown to detect antibodies to SARS-CoV-2 spike S1 protein and its receptor-binding-domain (RBD) at concentrations down to 1pM via electrochemical impedance spectroscopy and read by a smartphone-based user interface. In addition, the sensor can be regenerated within a minute by introducing a low-pH chemistry that elutes the antibodies from the antigens, allowing successive testing of multiple antibody samples using the same sensor. The detection time for the two antibodies tested in this work is 11.5 seconds. S1 protein sensing of its antibodies is specific, which cross-reacts neither with other antibodies nor with proteins such as Nucleocapsid antibody and Interleukin-6 protein. The proposed sensing platform is generic and can also be used for the rapid detection of biomarkers for other infectious agents such as Ebola, HIV, and Zika, which will benefit the public health.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Md Azahar Ali",
+        "author_inst": "Carnegie Mellon University"
+      },
+      {
+        "author_name": "Chunshan Hu",
+        "author_inst": "Carnegie Mellon University"
+      },
+      {
+        "author_name": "Sanjida Jahan",
+        "author_inst": "Carnegie Mellon University"
+      },
+      {
+        "author_name": "Bin Yuan",
+        "author_inst": "Carnegie Mellon University"
+      },
+      {
+        "author_name": "Mohammad Sadeq Saleh",
+        "author_inst": "Carnegie Mellon University"
+      },
+      {
+        "author_name": "Enguo Ju",
+        "author_inst": "University of Pittsburgh Medical Center"
+      },
+      {
+        "author_name": "Shou-Jiang Gao",
+        "author_inst": "University of Pittsburgh Medical Center"
+      },
+      {
+        "author_name": "Rahul P Panat",
+        "author_inst": "Carnegie Mellon University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.09.13.20193805",
     "rel_title": "Genome sequencing of sewage detects regionally prevalent SARS-CoV-2 variants",
@@ -1174602,69 +1173623,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.09.11.20192773",
-    "rel_title": "Serological evidence of human infection with SARS-CoV-2: a systematic review and meta-analysis",
-    "rel_date": "2020-09-13",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.11.20192773",
-    "rel_abs": "BackgroundA rapidly increasing number of serological surveys for anti-SARS-CoV-2 antibodies have been reported worldwide. A synthesis of this large corpus of data is needed.\n\nPurposeTo evaluate the quality of serological studies and provide a global picture of seroprevalence across demographic and occupational groups, and to provide guidance for conducting better serosurveys.\n\nData sourcesWe searched PubMed, Embase, Web of Science, and 4 pre-print servers for English-language papers published from December 1, 2019 to September 25, 2020.\n\nStudy selectionSerological studies evaluating SARS-CoV-2 seroprevalence in humans.\n\nData extractionTwo investigators independently extracted data from studies.\n\nData SynthesisMost of 230 serological studies, representing tests in >1,400,000 individuals, identified were of low quality based on a standardized study quality scale. In the 51 studies of higher quality, high-risk healthcare workers had higher seroprevalence of 17.1% (95% CI: 9.9-24.4%), compared to low-risk healthcare workers and general population of 5.4% (0.7-10.1%) and 5.3% (4.2-6.4%). Seroprevalence varied hugely across WHO regions, with lowest seroprevalence of general population in Western Pacific region (1.7%, 0.0-5.0%). Generally, the young (<20 years) and the old ([&ge;]65 years) were less likely to be seropositive compared to middle-aged (20-64 years) populations.\n\nSeroprevalence correlated with clinical COVID-19 reports, with pooled average of 7.7 (range: 2.0 to 23.1) serologically-detected-infections per confirmed COVID-19 case.\n\nLimitationsSome heterogeneity cannot be well explained quantitatively.\n\nConclusionsThe overall quality of seroprevalence studies examined was low. The relatively low seroprevalence among general populations suggest that in most settings, antibody-mediated herd immunity is far from being reached. Given the relatively narrow range of estimates of the ratio of serologically-detected infections to confirmed cases across different locales, reported case counts may help provide insights into the true proportion of the population infected.\n\nPrimary Funding sourceNational Science Fund for Distinguished Young Scholars (PROSPERO: CRD42020198253).",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Xinhua Chen",
-        "author_inst": "1.\tSchool of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China"
-      },
-      {
-        "author_name": "Zhiyuan Chen",
-        "author_inst": "1.\tSchool of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China"
-      },
-      {
-        "author_name": "Andrew S Azman",
-        "author_inst": "1.\tDepartment of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA  2.\tUnit of Population Epidemiology, Division of Primary Care"
-      },
-      {
-        "author_name": "Xiaowei Deng",
-        "author_inst": "1.\tSchool of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China"
-      },
-      {
-        "author_name": "Xinghui Chen",
-        "author_inst": "1.\tSchool of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China"
-      },
-      {
-        "author_name": "Wanying Lu",
-        "author_inst": "1.\tSchool of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China"
-      },
-      {
-        "author_name": "Zeyao Zhao",
-        "author_inst": "1.\tSchool of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China"
-      },
-      {
-        "author_name": "Juan Yang",
-        "author_inst": "1.\tSchool of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China"
-      },
-      {
-        "author_name": "Cecile Viboud",
-        "author_inst": "Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA"
-      },
-      {
-        "author_name": "Marco Ajelli",
-        "author_inst": "Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA"
-      },
-      {
-        "author_name": "Daniel T Leung",
-        "author_inst": "Division of Infectious Diseases, University of Utah School of Medicine, Salt Lake City, UT, USA"
-      },
-      {
-        "author_name": "Hongjie Yu",
-        "author_inst": "1.\tSchool of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.09.08.20190876",
     "rel_title": "Automatic Contact Tracing for Outbreak Detection UsingHospital Electronic Medical Record Data",
@@ -1174827,6 +1173785,77 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.09.11.20192401",
+    "rel_title": "Anakinra and Intravenous IgG versus Tocilizumab in the Treatment of COVID-19 Pneumonia",
+    "rel_date": "2020-09-13",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.11.20192401",
+    "rel_abs": "Background: COVID-19 can lead to acute respiratory failure and an exaggerated inflammatory response. Studies have suggested promising outcomes using monoclonal antibodies targeting IL-1{beta} (Anakinra) or IL6 (Tocilizumab), however no head to head comparison was done between the two treatments. Herein, we report our experience in treating COVID-19 pneumonia associated with cytokine storm with either subcutaneous Anakinra given concomitantly with intravenous immunoglobulin (IVIG), or intravenous Tocilizumab. Methods: Comprehensive clinical and laboratory data from patients with COVID-19 pneumonia admitted at our hospital between March and May 2020 were collected. Patients who received either Anakinra/ IVIG or Tocilizumab were selected. Baseline characteristics including oxygen therapy, respiratory status evaluation using ROX index, clinical assessment using NEWS score and laboratory data were collected. Outcomes included mortality, intubation, ICU admission and length of stay. In addition, we compared the change in ROX index, NEWS score and inflammatory markers at days 7 and 14 post initiation of therapy. Results: 84 consecutive patients who received either treatment (51 in the Anakinra/ IVIG group and 33 in the Tocilizumab group) were retrospectively studied. Baseline inflammatory markers were similar in both groups. There was no significant difference regarding to death (21.6% vs 15.2%, p 0.464), intubation (15.7% vs 24.2%, p 0.329), ICU need (57.1% vs 48.5%, p 0.475) or length of stay (13+9.6 vs 14.9+11.6, p 0.512) in the Anakinra/IVIG and Tocilizumab, respectively. Additionally, the rate of improvement in ROX index, NEWS score and inflammatory markers was similar in both groups at days 7 and 14. Furthermore, there was no difference in the incidence of superinfection in both groups. Conclusion: Treating COVID-19 pneumonia associated with cytokine storm features with either subcutaneous Anakinra/IVIG or intravenous Tocilizumab is associated with improved clinical outcomes in most subjects. The choice of treatment does not appear to affect morbidity or mortality. Randomized controlled trials are needed to confirm our study findings. Funding: None.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Massa Zantah",
+        "author_inst": "Lewis Katz School of Medicine at Temple University"
+      },
+      {
+        "author_name": "Eduardo Dominguez Castillo",
+        "author_inst": "Lewis Katz School of Medicine at Temple University"
+      },
+      {
+        "author_name": "Andrew J. Gangemi",
+        "author_inst": "Lewis Katz School of Medicine at Temple University"
+      },
+      {
+        "author_name": "Maulin Patel",
+        "author_inst": "Lewis Katz School of Medicine at Temple University"
+      },
+      {
+        "author_name": "Junad Chowdhury",
+        "author_inst": "Lewis Katz School of Medicine at Temple University"
+      },
+      {
+        "author_name": "Steven Verga",
+        "author_inst": "Lewis Katz School of Medicine at Temple University"
+      },
+      {
+        "author_name": "Osheen Abramian",
+        "author_inst": "Lewis Katz School of Medicine at Temple University"
+      },
+      {
+        "author_name": "Mattew Zheng",
+        "author_inst": "Lewis Katz School of Medicine at Temple University"
+      },
+      {
+        "author_name": "Kevin Lu",
+        "author_inst": "Lewis Katz School of Medicine at Temple University"
+      },
+      {
+        "author_name": "Arthur Lau",
+        "author_inst": "Lewis Katz School of Medicine at Temple University"
+      },
+      {
+        "author_name": "Justin Levinson",
+        "author_inst": "Lewis Katz School of Medicine at Temple University"
+      },
+      {
+        "author_name": "Hauquing Zhao",
+        "author_inst": "Lewis Katz School of Medicine at Temple University"
+      },
+      {
+        "author_name": "Gerard J. Criner",
+        "author_inst": "Lewis Katz School of Medicine at Temple University"
+      },
+      {
+        "author_name": "Roberto Caricchio",
+        "author_inst": "Lewis Katz School of Medicine at Temple University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.09.11.20193011",
     "rel_title": "Clinical effectiveness of drugs in hospitalized patients with COVID-19 infection: a systematic review and meta-analysis.",
@@ -1176288,33 +1175317,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "dentistry and oral medicine"
   },
-  {
-    "rel_doi": "10.1101/2020.09.09.20191494",
-    "rel_title": "Analysis of twenty-week time-series of confirmed cases of New Coronavirus COVID-19 and their simple short-term prediction for Georgia and Neighboring Countries (Armenia, Azerbaijan, Turkey, Russia) in amid of a global pandemic",
-    "rel_date": "2020-09-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.09.20191494",
-    "rel_abs": "Results of a comparative statistical analysis of the daily data associated with New coronavirus COVID-19 infection of confirmed cases ([C]) of the population in Georgia (GEO), Armenia (ARM), Azerbaijan (AZE), Turkey (TUR) and Russia (RUS) amid a global pandemic (WLD) in the period from March 14 to July 31, 2020 are presented.\n\nThe analysis of data is carried out with the use of the standard statistical analysis methods of random events and methods of mathematical statistics for the non-accidental time-series of observations.\n\nIn particular, a correlation and autocorrelation analysis of the observational data was carried out, the periodicity in the time- series of [C] were revealed, the calculation of the interval prediction values of [C] taking into account the periodicity in the time-series of observations from August 1 to 31, 2020 (ARM, AZE) and from August 1 to September 11, 2020 (WLD, GEO, TUR, RUS) were carried out.\n\nComparison of real and calculated predictions data on [C] in the study sites from August 1 to August 31, 2020 is carried out. It was found that daily, monthly and mean weekly real values of [C] for all the studied locations practically fall into the 99% confidence interval of the predicted values of [C] for the specified time period.\n\nA dangerous situation with the spread of coronavirus infection may arise when the mean weekly values of [C] of the 99% upper level of the forecast confidence interval are exceeded within 1-2 weeks. Favorable - when the mean weekly values of [C] decrease below 99% of the lower level of the forecast confidence interval.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Avtandil G. Amiranashvili",
-        "author_inst": "Mikheil Nodia Institute of Geophysics of Ivane Javakhishvili Tbilisi State University"
-      },
-      {
-        "author_name": "Ketevan R. Khazaradze",
-        "author_inst": "Georgian State Teaching University of Physical Education and Sport, Tbilisi, Georgia  Ministry of Internally Displaced Persons from Occupied Territories, Labour"
-      },
-      {
-        "author_name": "Nino D. Japaridze",
-        "author_inst": "Ministry of Internally Displaced Persons from Occupied Territories, Labour, Health and Social Affair of Georgia, Tbilisi, Georgia"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.09.10.20192138",
     "rel_title": "Socio-economic disparities and COVID-19 in the USA",
@@ -1176553,6 +1175555,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.09.10.20191841",
+    "rel_title": "The King's College London Coronavirus Health and Experiences of Colleagues at King's Study: SARS-CoV-2 antibody response in an occupational sample",
+    "rel_date": "2020-09-11",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.10.20191841",
+    "rel_abs": "We report test results for SARS-CoV-2 antibodies in an occupational group of postgraduate research students and current members of staff at Kings College London. Between June and July 2020, antibody testing kits were sent to n=2296 participants; n=2004 (86.3%) responded, of whom n=1882 (93.9%) returned valid test results. Of those that returned valid results, n=124 (6.6%) tested positive for SARS-CoV-2 antibodies, with initial comparisons showing variation by age group and clinical exposure.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Daniel Leightley",
+        "author_inst": "Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London."
+      },
+      {
+        "author_name": "Valentina Vitiello",
+        "author_inst": "The School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and   Medicine, King's College London, London, UK."
+      },
+      {
+        "author_name": "Gabriella Bergin-Cartwright",
+        "author_inst": "Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London."
+      },
+      {
+        "author_name": "Alice Wickersham",
+        "author_inst": "Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London"
+      },
+      {
+        "author_name": "Katrina A S Davis",
+        "author_inst": "Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London."
+      },
+      {
+        "author_name": "Sharon Stevelink",
+        "author_inst": "Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London"
+      },
+      {
+        "author_name": "Matthew Hotopf",
+        "author_inst": "Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London"
+      },
+      {
+        "author_name": "Reza Razavi",
+        "author_inst": "The School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King's College London"
+      },
+      {
+        "author_name": "- On behalf of the KCL CHECK research team",
+        "author_inst": ""
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.09.09.20191643",
     "rel_title": "Spatial and temporal trends in social vulnerability and COVID-19 incidence and death rates in the United States",
@@ -1177862,61 +1176915,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.09.11.20191783",
-    "rel_title": "No association between circulating levels of testosterone and sex hormone-binding globulin and risk of COVID-19 mortality in UK biobank",
-    "rel_date": "2020-09-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.11.20191783",
-    "rel_abs": "Background: Sex-disaggregated data suggest that men with coronavirus disease 2019 (COVID-19) are more likely to die than women. Whether circulating testosterone or sex hormone-binding globulin (SHBG) contributes to such sex differences remains unknown. Objective: To evaluate the associations of circulating total testosterone (TT), free testosterone (FT), and SHBG with COVID-19 mortality. Design: Prospective analysis. Setting: UK Biobank. Participants: We included 1306 COVID-19 patients (678 men and 628 women) who had serum TT and SHBG measurements and were free of cardiovascular disease or cancer at baseline (2006-2010). Main outcome measures: The death cases of COVID-19 were identified from National Health Service death records updated at 31 July 2020. Unconditional logistic regression was performed to estimate the odds ratio (OR) and 95% confidence intervals (CI) for mortality. Results: We documented 315 deaths of COVID-19 (194 men and 121 women). After adjusting for potential confounders, we did not find any statistically significant associations for TT (OR per 1-SD increase = 1.03, 95% CI: 0.85-1.25), FT (OR per 1-SD increase = 0.95, 95% CI: 0.77-1.17), or SHBG (OR per 1-SD increase = 1.09, 95% CI: 0.87-1.37) with COVID-19 mortality in men. Similar null results were observed in women (TT: OR per 1-SD increase = 1.10, 95% CI: 0.85-1.42; FT: OR per 1-SD increase = 1.10, 95% CI: 0.82-1.46; SHBG: OR per 1-SD increase = 1.16, 95% CI: 0.89-1.53). Conclusions: Our findings do not support a significant role of circulating testosterone or SHBG in COVID-19 prognosis.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Xikang Fan",
-        "author_inst": "Nanjing Medical University"
-      },
-      {
-        "author_name": "Jing Yang",
-        "author_inst": "Nanjing Medical University"
-      },
-      {
-        "author_name": "Jiayu Wang",
-        "author_inst": "Nanjing Medical University"
-      },
-      {
-        "author_name": "Cheng Yin",
-        "author_inst": "Jiangning Hospital Affiliated to Nanjing Medical University"
-      },
-      {
-        "author_name": "Meng Zhu",
-        "author_inst": "Nanjing Medical University"
-      },
-      {
-        "author_name": "Hongxia Ma",
-        "author_inst": "Nanjing Medical University"
-      },
-      {
-        "author_name": "Guangfu Jin",
-        "author_inst": "Nanjing Medical University"
-      },
-      {
-        "author_name": "Zhibin Hu",
-        "author_inst": "Nanjing Medical University"
-      },
-      {
-        "author_name": "Hongbing Shen",
-        "author_inst": "Nanjing Medical University"
-      },
-      {
-        "author_name": "Dong Hang",
-        "author_inst": "Nanjing Medical University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.09.10.20191817",
     "rel_title": "COVID-19: Mechanistic model calibration subject to active and varying non-pharmaceutical interventions",
@@ -1178219,6 +1177217,93 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.09.10.20192260",
+    "rel_title": "Evaluating ten commercially-available SARS-CoV-2 rapid serological tests using the STARD (Standards for Reporting of Diagnostic Accuracy Studies) method.",
+    "rel_date": "2020-09-11",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.10.20192260",
+    "rel_abs": "Numerous SARS-CoV-2 rapid serological tests have been developed, but their accuracy has usually been assessed using very few samples, and rigorous comparisons between these tests are scarce. In this study, we evaluated and compared 10 commercially-available SARS-CoV-2 rapid serological tests using the STARD methodology (Standards for Reporting of Diagnostic Accuracy Studies). 250 sera from 159 PCR-confirmed SARS-CoV-2 patients (collected from 0 to 32 days after onset of symptoms) were tested with rapid serological tests. Control sera (N=254) were retrieved from pre-COVID periods from patients with other coronavirus infections (N=11), positive rheumatoid factors (N=3), IgG/IgM hyperglobulinemia (N=9), malaria (n=5), or no documented viral infection (N=226). All samples were tested using rapid lateral flow immunoassays (LFIA) from ten manufacturers. Only four tests achieved [&ge;]98% specificity, with other tests ranging from 75.7%-99.2%. Sensitivities varied by the day of sample collection, from 31.7%-55.4% (Days 0-9), 65.9%-92.9% (Days 10-14), and 81.0%-95.2% (>14 days) after the onset of symptoms, respectively. Only three tests evaluated met French Health Authorities' thresholds for SARS-CoV-2 serological tests ([&ge;]90% sensitivity + [&ge;]98% specificity). Overall, the performances between tests varied greatly, with only a third meeting acceptable specificity and sensitivity thresholds. Knowing the analytical performance of these tests will allow clinicians to use them with more confidence, could help determine the general population's immunological status, and may diagnose some patients with false-negative RT-PCR results.",
+    "rel_num_authors": 18,
+    "rel_authors": [
+      {
+        "author_name": "Laurent Dortet",
+        "author_inst": "Hopital de Bicetre"
+      },
+      {
+        "author_name": "Jean-Baptiste Ronat",
+        "author_inst": "MSF France"
+      },
+      {
+        "author_name": "Christelle Vauloup-Fellous",
+        "author_inst": "Service de Virologie, H\u00f4pital Paul-Brousse, Inserm U 1193 ; Universit\u00e9 Paris-Saclay Villejuif, APHP Paris-Saclay"
+      },
+      {
+        "author_name": "C\u00e9line Langendorf",
+        "author_inst": "Epicentre (South Africa)"
+      },
+      {
+        "author_name": "David-Alexis Mendels",
+        "author_inst": "xrapid-group"
+      },
+      {
+        "author_name": "C\u00e9cile Emeraud",
+        "author_inst": "Hopital de Bicetre"
+      },
+      {
+        "author_name": "Saoussen Oueslati",
+        "author_inst": "INSERM U914"
+      },
+      {
+        "author_name": "Delphine Girlich",
+        "author_inst": "Service de Bacteriologie"
+      },
+      {
+        "author_name": "Anthony Chauvin",
+        "author_inst": "APHP, H\u00f4pitaux universitaires Lariboisi\u00e8re-Saint Louis-Fernand-WIdal"
+      },
+      {
+        "author_name": "Ali Afdjei",
+        "author_inst": "Emergency Department, H\u00f4pital Parly-2,"
+      },
+      {
+        "author_name": "Sandrine Bernabeu",
+        "author_inst": "Paris-Sud University, LabEx Lermit, Faculty of Medecine"
+      },
+      {
+        "author_name": "Samuel Le Pape",
+        "author_inst": "Service de Virologie, H\u00f4pital Paul-Brousse, Inserm U 1193 ; Universit\u00e9 Paris-Saclay Villejuif, APHP Paris-Saclay"
+      },
+      {
+        "author_name": "Rim Kallala",
+        "author_inst": "Service de Virologie, H\u00f4pital Paul-Brousse"
+      },
+      {
+        "author_name": "Alice Rochard",
+        "author_inst": "APHP, Hopital de Bicetre"
+      },
+      {
+        "author_name": "Celine Verstuyft",
+        "author_inst": "Facult\u00e9 de M\u00e9decine Paris-Sud, Univ Paris-Sud, Universit\u00e9 Paris-Saclay; INSERM U1184; Service de G\u00e9n\u00e9tique mol\u00e9culaire, Pharmacog\u00e9n\u00e9tique et H"
+      },
+      {
+        "author_name": "Nicolas Fortineau",
+        "author_inst": "APHP"
+      },
+      {
+        "author_name": "Anne-Marie Roque-Afonso",
+        "author_inst": "Service de Virologie, H\u00f4pital Paul-Brousse, Inserm U 1193 ; Universit\u00e9 Paris-Saclay Villejuif, APHP Paris-Saclay"
+      },
+      {
+        "author_name": "Thierry Naas",
+        "author_inst": "APHP"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.09.10.20189696",
     "rel_title": "High COVID-19 transmission potential associated with re-opening universities can be mitigated with layered interventions",
@@ -1179352,49 +1178437,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.09.09.20178764",
-    "rel_title": "Metagenomic sequencing to detect respiratory viruses in persons under investigation for COVID-19",
-    "rel_date": "2020-09-10",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.09.20178764",
-    "rel_abs": "We used metagenomic next-generation sequencing (mNGS) to assess the frequencies of alternative viral infections in SARS-CoV-2 RT-PCR negative persons under investigations (PUIs) (n=30) and viral co-infections in SARS-CoV-2 RT-PCR positive PUIs (n=45). mNGS identified both co-infections and alternative viral infections that were not detected by routine clinical workup.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Ahmed Babiker",
-        "author_inst": "Emory University"
-      },
-      {
-        "author_name": "Heath Bradley",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Victoria Stittleburg",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Autum Key",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Colleen Suzanne Kraft",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Jesse Waggoner",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Anne Piantadosi",
-        "author_inst": "Emory University School of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.09.03.20187526",
     "rel_title": "Safety and Efficacy of Antiviral Drugs for the Treatment of Patients with SARS-CoV-2 Infection: A Systematic Review and Meta-analyses",
@@ -1179701,6 +1178743,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.09.09.20188482",
+    "rel_title": "Adherence to COVID-19 pandemic prescribed recommendations, source of information and lockdown psychological impact of Nigeria social media users",
+    "rel_date": "2020-09-10",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.09.20188482",
+    "rel_abs": "BackgroundCOVID-19 is a highly infectious viral disease that has spread to over one hundred and eight countries, including Nigeria. Countries across the globe have been implementing preventive measures towards curbing the spread and impact of the virus. Thus, the present study was aimed at assessing compliance to prescribe preventive recommendations, the psychological effect of lockdown, and the source of information among Nigeria social media users.\n\nMethodsThis research implemented an online cross-sectional survey using an unidentified online Google based questionnaire to elicit required information from potential respondents via social media channels such as WhatsApp, Twitter, Instagram, Telegram and Facebook. On these forums, an external link with google based questionnaire was shared with Nigerians social media users to participate from 1st to 31st April 2020 and we had 1,131 respondents who participated in the survey.\n\nResultsAge and respondents scientific or non-scientific backgrounds were the socio-demographic variables associated with respondents having psychological challenges as P<0.05. However, none of the socio-demographic variables of the respondents were associated with compliance with the recommendations as P>0.05. Also, most (63.4%) of the respondents were stressed by the feelings associated with the COVID-19 pandemic, as the expected majority (80.1%) sources information about the epidemics through social media platforms.\n\nConclusionGiven numerous uncertainties surrounding the global COVID-19 pandemics, there is a need to continuously increase awareness through various media and ensure that people are highly complying with the preventive measures being put in place by relevant authorities. Also, palliative measures should be put in place to reduce the psychological impact of the pandemic.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Obasanjo Afolabi Bolarinwa",
+        "author_inst": "University of Kwazulu-Natal, Durban, South Africa; Obafemi Awolowo University, Nigeria"
+      },
+      {
+        "author_name": "Olalekan Seun Olagunju",
+        "author_inst": "Obafemi Awolowo University, Nigeria"
+      },
+      {
+        "author_name": "Tesleem Babalola",
+        "author_inst": "University of KwaZulu-Natal, South Africa"
+      },
+      {
+        "author_name": "Balsam Qubais",
+        "author_inst": "University of Sharjah"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.09.09.20182592",
     "rel_title": "Is there a correlation between pulmonary inflammation index with COVID-19 disease severity and outcome?",
@@ -1180874,81 +1179947,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.09.07.20164947",
-    "rel_title": "Effectiveness of digital interventions to improve household and community infection prevention and control behaviours and to reduce incidence of respiratory and/or gastro-intestinal infections: A rapid systematic review",
-    "rel_date": "2020-09-09",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.07.20164947",
-    "rel_abs": "BackgroundDigital interventions have potential to efficiently support improved hygiene practices to reduce transmission of COVID-19.\n\nObjectiveTo evaluate the evidence for digital interventions to improve hygiene practices within the community.\n\nMethodsWe reviewed articles published between 01 January 2000 and 26 May 2019 that presented a controlled trial of a digital intervention to improve hygiene behaviours in the community. We searched MEDLINE, Embase, PsycINFO, Cochrane Controlled Register of Trials (CENTRAL), China National Knowledge Infrastructure and grey literature. Trials in hospitals were excluded, as were trials aiming at prevention of sexually transmitted infections; only target diseases with transmission mechanisms similar to COVID-19 (e.g. respiratory and gastrointestinal infections) were included. Trials had to evaluate a uniquely digital component of an intervention. Study designs were limited to randomised controlled trials, controlled before-and-after trials, and interrupted time series analyses. Outcomes could be either incidence of infections or change in hygiene behaviours. The Risk of Bias 2 tool was used to assess study quality.\n\nResultsWe found seven studies that met the inclusion criteria. Six studies reported successfully improving self-reported hygiene behaviour or health outcomes, but only one of these six trials confirmed improvements using objective measures (reduced consultations and antibiotic prescriptions), Germ Defence. Settings included kindergartens, workplaces, and service station restrooms. Modes of delivery were diverse: WeChat, website, text messages, audio messages to mobiles, electronic billboards, and electronic personal care records. Four interventions targeted parents of young children with educational materials. Two targeted the general population; these also used behaviour change techniques or theory to inform the intervention. Only one trial had low risk of bias, Germ Defence; the most common concerns were lack of information about the randomisation, possible bias in reporting of behavioural outcomes, and lack of an analysis plan and possible selective reporting of results.\n\nConclusionThere was only one intervention that was judged to be at low risk of bias, Germ Defence, which reduced incidence and severity of illness, as confirmed by objective measures. Further evaluation is required to determine the effectiveness of the other interventions reviewed.",
-    "rel_num_authors": 15,
-    "rel_authors": [
-      {
-        "author_name": "Natalie Gold",
-        "author_inst": "Public Health England Behavioural Insights, Public Health England, UK; Faculty of Philosophy, University of Oxford, UK"
-      },
-      {
-        "author_name": "Xiao-Yang Hu",
-        "author_inst": "Primary Care Population Sciences and Medical Education, University of Southampton, UK"
-      },
-      {
-        "author_name": "Sarah Denford",
-        "author_inst": "Bristol Medical School (PHS), Faculty of Health Sciences, University of Bristol; School of Psychological Science, University of Bristol, UK"
-      },
-      {
-        "author_name": "Ru-Yu Xia",
-        "author_inst": "Centre for Evidence-Based Chinese Medicine, Beijing University of Chinese Medicine, China"
-      },
-      {
-        "author_name": "Lauren Towler",
-        "author_inst": "School of Psychology, University of Southampton, UK"
-      },
-      {
-        "author_name": "Julia Groot",
-        "author_inst": "Department of Psychology, University of Bath, UK"
-      },
-      {
-        "author_name": "Rachel Gledhill",
-        "author_inst": "Public Health England Behavioural Insights, Public Health England, UK"
-      },
-      {
-        "author_name": "Merlin Willcox",
-        "author_inst": "Primary Care Population Sciences and Medical Education, University of Southampton, UK"
-      },
-      {
-        "author_name": "Ben Ainsworth",
-        "author_inst": "Department of Psychology, University of Bath, UK"
-      },
-      {
-        "author_name": "Sascha Miller",
-        "author_inst": "School of Psychology, University of Southampton, UK"
-      },
-      {
-        "author_name": "Michael Moore",
-        "author_inst": "Primary Care Population Sciences and Medical Education, University of Southampton, UK"
-      },
-      {
-        "author_name": "Paul Little",
-        "author_inst": "Primary Care Population Sciences and Medical Education, University of Southampton, UK"
-      },
-      {
-        "author_name": "Richard Aml\u00f4t",
-        "author_inst": "Public Health England Behavioural Insights, Public Health England, UK"
-      },
-      {
-        "author_name": "Tim Chadborn",
-        "author_inst": "Public Health England Behavioural Insights, Public Health England, UK"
-      },
-      {
-        "author_name": "Lucy Yardley",
-        "author_inst": "School of Psychology, University of Southampton, UK; School of Psychological Science, University of Bristol, UK"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.09.07.20189449",
     "rel_title": "Mitigation Strategies and Compliance in the Covid-19 Fight; How Much Compliance is Enough?",
@@ -1181515,6 +1180513,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.09.07.20189597",
+    "rel_title": "COVID-19 control across urban-rural gradients",
+    "rel_date": "2020-09-09",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.07.20189597",
+    "rel_abs": "Controlling the regional re-emergence of SARS-CoV-2 after its initial spread in ever-changing personal contact networks and disease landscapes is a challenging task. In a landscape context, contact opportunities within and between populations are changing rapidly as lockdown measures are relaxed and a number of social activities re-activated. Using an individual-based metapopulation model, we explored the efficacy of different control strategies across an urban-rural gradient in Wales, UK. Our model shows that isolation of symptomatic cases, or regional lockdowns in response to local outbreaks, have limited efficacy unless the overall transmission rate is kept persistently low. Additional isolation of non-symptomatic infected individuals, who may be detected by effective test and trace strategies, is pivotal to reduce the overall epidemic size over a wider range of transmission scenarios. We define an  urban-rural gradient in epidemic size as a correlation between regional epidemic size and connectivity within the region, with more highly connected urban populations experiencing relatively larger outbreaks. For interventions focused on regional lockdowns, the strength of such gradients in epidemic size increased with higher travel frequencies, indicating a reduced efficacy of the control measure in the urban regions under these conditions. When both non-symptomatic and symptomatic individuals are isolated or regional lockdown strategies are enforced, we further found the strongest urban-rural epidemic gradients at high transmission rates. This effect was reversed for strategies targeted at symptomatics only. Our results emphasise the importance of test-and-tracing strategies and maintaining low transmission rates for efficiently controlling COVID19 spread, both at landscape scale and in urban areas.\n\nAuthor summaryThe spread of infectious diseases is the outcome of contact patterns and involves source-sink dynamics of how infectious individuals spread the disease through pools of susceptible individuals. Control strategies that aim to reduce disease spread often need to accept ongoing transmission chains and therefore, may not work equally well in different scenarios of how individuals and populations are connected to each other. To understand the efficacy of different control strategies to contain the spread of COVID19 across gradients of urban and rural populations, we simulated a large range of different control strategies in response to regional COVID19 outbreaks, involving regional lockdown and the isolation individuals that express symptoms and those that developed not symptoms but may contribute to disease transmission. Our results suggest that isolation of asymptomatic individuals through intensive test-and-tracing is important for efficiently reducing the epidemic size. Regional lockdowns and the isolation of symptomatic cases only are of limited efficacy for reducing the epidemic size, unless overall transmission rate is kept persistently low. Moreover, we found high overall transmission rates to result in relatively larger epidemics in urban than in rural communities for these control strategies, emphasising the importance of keeping transmission rates constantly low in addition to regional measures to avoid the disease spread at large scale.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Konstans Wells",
+        "author_inst": "Swansea University"
+      },
+      {
+        "author_name": "Miguel Lurgi",
+        "author_inst": "Swansea University"
+      },
+      {
+        "author_name": "Brendan Collins",
+        "author_inst": "Department of Public Health and Policy, University of Liverpool, Liverpool L69 3GB, UK"
+      },
+      {
+        "author_name": "Biagio Lucini",
+        "author_inst": "Department of Mathematics, Swansea University, Swansea SA2 8PP, Wales, UK"
+      },
+      {
+        "author_name": "Rowland Raymond Kao",
+        "author_inst": "University of Edinburgh"
+      },
+      {
+        "author_name": "Alun L. Lloyd",
+        "author_inst": "Biomathematics Graduate Program and Department of Mathematics, North Carolina State University, Raleigh, NC 27695, USA"
+      },
+      {
+        "author_name": "Simon D.W. Frost",
+        "author_inst": "Microsoft Research Lab, Redmond, Washington, WA 98052, USA and London School of Hygiene and Tropical Medicine, London, WC1E 7HT"
+      },
+      {
+        "author_name": "Mike B. Gravenor",
+        "author_inst": "Swansea University Medical School, Swansea University, Swansea SA2 8PP, Wales, UK"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.09.07.20184887",
     "rel_title": "Age-structured SIR model and resource growth dynamics: A preliminary COVID-19 study",
@@ -1182484,53 +1181529,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.09.09.20191247",
-    "rel_title": "Early indirect impact of COVID-19 pandemic on utilization and outcomes of reproductive, maternal, newborn, child and adolescent health services in Kenya",
-    "rel_date": "2020-09-09",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.09.20191247",
-    "rel_abs": "BackgroundThe COVID-19 global pandemic is expected to result in 8.3-38.6% additional maternal deaths in many low-income countries. The objective of this paper was to determine the initial impact of COVID-19 pandemic on reproductive, maternal, newborn, child and adolescent health (RMNCAH) services in Kenya.\n\nMethodsData for the first four months (March-June) of the pandemic and the equivalent period in 2019 were extracted from Kenya Health Information System. Two-sample test of proportions for hospital attendance for select RMNCAH services between the two periods were computed.\n\nResultsThere were no differences in monthly mean ({+/-}SD) attendance between March-June 2019 vs 2020 for antenatal care (400,191.2{+/-}12,700.0 vs 384,697.3{+/-}20,838.6), hospital births (98,713.0{+/-}4,117.0 vs 99,634.5{+/-}3,215.5), family planning attendance (431,930.5{+/-}19,059.9 vs 448,168.3{+/-}31,559.8), post-abortion care (3,206.5{+/-}111.7 vs 448,168.3{+/-}31,559.8) and pentavalent 1 immunisation (114,701.0{+/-}3,701.1 vs 110,915.8{+/-}7,209.4), p>0.05. However, there were increasing trends for adolescent pregnancy rate, significant increases in FP utilization among young people (25.7% to 27.0%), injectable (short-term) FP method uptake (58.2% to 62.3%), caesarean section rate (14.6% to 15.8%), adolescent maternal deaths (6.2% to 10.9%) and fresh stillbirths (0.9% to 1.0%) with a reduction in implants (long-term) uptake (16.5% to 13.0%) (p< 0.05). No significant change in maternal mortality ratio between the two periods (96.6 vs 105.8/100,000 live births, p = 0.1023) although the trend was increasing.\n\nConclusionCOVID-19 may have contributed to increased adolescent pregnancy, adolescent maternal death and stillbirth rates in Kenya. If this trend persists, recent gains achieved in maternal and perinatal health in Kenya will be lost. With uncertainty around the duration of the pandemic, strategies to mitigate against catastrophic indirect maternal health outcomes are urgently needed.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "DUNCAN N SHIKUKU",
-        "author_inst": "LIVERPOOL SCHOOL OF TROPICAL MEDICINE"
-      },
-      {
-        "author_name": "Irene Nyaoke",
-        "author_inst": "Liverpool School of Tropical Medicine (Kenya)"
-      },
-      {
-        "author_name": "Sylvia Gichuru",
-        "author_inst": "Liverpool School of Tropical Medicine (Kenya)"
-      },
-      {
-        "author_name": "Onesmus Maina",
-        "author_inst": "Liverpool School of Tropical Medicine (Kenya)"
-      },
-      {
-        "author_name": "Martin Eyinda",
-        "author_inst": "Liverpool School of Tropical Medicine (Kenya)"
-      },
-      {
-        "author_name": "Pamela Godia",
-        "author_inst": "Liverpool School of Tropical Medicine (Kenya) and University of Nairobi (School of Public Health)"
-      },
-      {
-        "author_name": "Lucy Nyaga",
-        "author_inst": "Liverpool School of Tropical Medicine (Kenya)"
-      },
-      {
-        "author_name": "Charles Ameh",
-        "author_inst": "Liverpool School of Tropical Medicine (UK) and University of Nairobi (Department of Obstetrics and Gynaecology)"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "sexual and reproductive health"
-  },
   {
     "rel_doi": "10.1101/2020.09.08.20190272",
     "rel_title": "Functional myeloid-derived suppressor cells expand in blood but not airways of COVID-19 patients and predict disease severity",
@@ -1182985,6 +1181983,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.09.09.20191239",
+    "rel_title": "COVID-19 Transmission Within Danish Households: A Nationwide Study from Lockdown to Reopening",
+    "rel_date": "2020-09-09",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.09.20191239",
+    "rel_abs": "BackgroundThe Covid-19 pandemic is one of the most serious global public health threats in recent times. Understanding transmission of SARS-CoV-2 is of utmost importance to be able to respond to outbreaks and take action against spread of the disease. Transmission within the household is a concern, especially because infection control is difficult to apply within the household domain.\n\nMethodsWe used comprehensive administrative register data from Denmark, comprising the full population and all COVID-19 tests, to estimate household transmission risk and attack rate.\n\nResultsWe studied the testing dynamics for COVID-19 and found that the day after receiving a positive test result within the household, 35% of potential secondary cases were tested and 13% of these were positive. After a primary case in 6,782 households, 82% of potential secondary cases were tested within 14 days, of which 17% tested positive as secondary cases, implying an attack rate of 17%. Among primary cases, those aged 0-24 were underrepresented when compared with the total population. We found an approximately linearly increasing relationship between attack rate and age. We investigated the transmission risk from primary cases by age, and found an increasing risk with age of primary cases for adults, while the risk seems to decrease with age for children.\n\nConclusionsAlthough there is an increasing attack rate and transmission risk of SARS-CoV-2 with age, children are also able to transmit SARS-CoV-2 within the household.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Frederik Plesner Lyngse",
+        "author_inst": "University of Copenhagen"
+      },
+      {
+        "author_name": "Carsten Thure Kirkeby",
+        "author_inst": "University of Copenhagen"
+      },
+      {
+        "author_name": "Tariq Halasa",
+        "author_inst": "University of Copenhagen"
+      },
+      {
+        "author_name": "Viggo Andreasen",
+        "author_inst": "Roskilde University"
+      },
+      {
+        "author_name": "Robert Leo Skov",
+        "author_inst": "Statens Serum Institut"
+      },
+      {
+        "author_name": "Frederik Trier M\u00f8ller",
+        "author_inst": "Statens Serum Institut"
+      },
+      {
+        "author_name": "Tyra Grove Krause",
+        "author_inst": "Statens Serum Institut"
+      },
+      {
+        "author_name": "K\u00e5re M\u00f8lbak",
+        "author_inst": "Statens Serum Institut"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.09.09.20188961",
     "rel_title": "Effect of Screen time on Glycaemic control of Type 2 Diabetes patients during COVID-19 Outbreak: A Survey based Study",
@@ -1184554,101 +1183599,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.09.05.20184655",
-    "rel_title": "Activin/Follistatin-axis deregulation is independently associated with COVID-19 in-hospital mortality",
-    "rel_date": "2020-09-08",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.05.20184655",
-    "rel_abs": "RationaleActivins are inflammatory and tissue-repair-related members of the TGF{beta}-superfamily that have been implicated in the pathogenesis of several immuno-inflammatory disorders including sepsis/acute respiratory distress syndrome (ARDS). We hypothesized that they might be of particular relevance to COVID-19 pathophysiology.\n\nObjectivesTo assess the involvement of the Activin-Follistatin-axis in COVID-19 pathophysiology.\n\nMethodsLevels of Activins -A, -B and their physiological inhibitor Follistatin, were retrospectively analyzed in 314 serum samples from 117 COVID-19 patients derived from two independent centers and compared with common demographic, clinical and laboratory parameters. Optimal-scaling with ridge-regression was used to screen variables and establish a prediction model.\n\nMain ResultsThe Activin/Follistatin-axis was significantly deregulated during the course of COVID-19 and was independently associated with severity and in-hospital mortality. FACT-CLINYCoD, a novel disease scoring system, adding one point for each of Follistatin >6235 pg/ml, Activin-A >591 pg/ml, Activin-B >249 pg/ml, CRP >10.3 mg/dL, LDH >427 U/L, Intensive Care Unit (ICU) admission, Neutrophil/Lymphocyte-Ratio >5.6, Years of Age >61, Comorbidities >1 and D-dimers >1097 ng/ml, efficiently predicted and monitored fatal outcome independently of multiplicity and timing of sampling (AUC: 0.951{+/-}0.032, p<10-6). Validation in 35 samples derived from a third hospital indicated comparable AUC (0.958{+/-}0.086, p=0.032).\n\nConclusionThis study unravels the link between Activin/Folistatin-axis and COVID-19 mortality and introduces FACT-CLINYCoD, a novel pathophysiology-based tool that copes with the dynamic and heterogeneous nature of COCVID-19, predicts disease outcome and supports clinical decision making. Prospective large-scale validation of this calculator, as well as investigation of the mechanisms linking Activin/Folistatin-axis to COVID-19 pathogenesis is warranted.",
-    "rel_num_authors": 20,
-    "rel_authors": [
-      {
-        "author_name": "Evgenia Synolaki",
-        "author_inst": "Biomedical Research Foundation Academy of Athens, Athens, Greece"
-      },
-      {
-        "author_name": "Vasileios Papadopoulos",
-        "author_inst": "First Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece."
-      },
-      {
-        "author_name": "Georgios Divolis",
-        "author_inst": "Biomedical Research Foundation Academy of Athens, Athens, Greece"
-      },
-      {
-        "author_name": "Olga Tsachouridou",
-        "author_inst": "First Department of Internal Medicine , AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece"
-      },
-      {
-        "author_name": "Efstratios Gavriilidis",
-        "author_inst": "First Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece."
-      },
-      {
-        "author_name": "Georgia Loli",
-        "author_inst": "First Department of Internal Medicine , AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece"
-      },
-      {
-        "author_name": "Arriana Gavriil",
-        "author_inst": "Biomedical Research Foundation Academy of Athens, Athens, Greece"
-      },
-      {
-        "author_name": "Christina Tsigalou",
-        "author_inst": "Laboratory of Microbiology, University Hospital of Alexandroupolis, Democritus University of Thrace,  Alexandroupolis, Greece"
-      },
-      {
-        "author_name": "Nikolaos R Tziolos",
-        "author_inst": "5Fourth Department of Internal Medicine, Attikon University Hospital, National and Kapodistrian University of Athens Medical School, Athens, Greece"
-      },
-      {
-        "author_name": "Eleni Sertaridou",
-        "author_inst": "Intensive Care Unit, University Hospital of Alexandroupolis, Alexandroupolis, Greece."
-      },
-      {
-        "author_name": "Bhanu Kalra",
-        "author_inst": "AnshLabs, Webster, Texas, USA"
-      },
-      {
-        "author_name": "Ajay Kumar",
-        "author_inst": "AnshLabs, Webster, Texas, USA"
-      },
-      {
-        "author_name": "Petros Rafailidis",
-        "author_inst": "Second Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece."
-      },
-      {
-        "author_name": "Arja Pasternack",
-        "author_inst": "Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland"
-      },
-      {
-        "author_name": "Dimitrios Boumpas",
-        "author_inst": "4th Department of Medicine, \"Attikon\" University Hospital, National and Kapodistrian University of Athens, Athens, Greece"
-      },
-      {
-        "author_name": "Georgios Germanidis",
-        "author_inst": "First Department of Internal Medicine , AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece"
-      },
-      {
-        "author_name": "Olli Ritvos",
-        "author_inst": "Department of Physiology, Faculty of Medicine, University of Helsinki, Helsinki, Finland"
-      },
-      {
-        "author_name": "Symeon Metalidis",
-        "author_inst": "First Department of Internal Medicine , AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece"
-      },
-      {
-        "author_name": "Panagiotis Skendros",
-        "author_inst": "First Department of Internal Medicine, University Hospital of Alexandroupolis, Democritus University of Thrace, Alexandroupolis, Greece"
-      },
-      {
-        "author_name": "Paschalis Sideras",
-        "author_inst": "Biomedical Research Foundation Academy of Athens, Athens, Greece"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.09.05.20188912",
     "rel_title": "Beneficial and Harmful Outcomes of Tocilizumab in Severe COVID-19: A Systematic Review and Meta-Analysis",
@@ -1184863,6 +1183813,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.09.04.20188110",
+    "rel_title": "Modelling the transmission of infectious diseases inside hospital bays: implications for Covid-19",
+    "rel_date": "2020-09-08",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.04.20188110",
+    "rel_abs": "Healthcare associated transmission of viral infections is a major problem that has significant economic costs and can lead to loss of life. Infections with the highly contagious SARS-CoV-2 virus have been shown to have a high prevalence in hospitals around the world. The spread of this virus might be impacted by the density of patients inside hospital bays. To investigate this aspect, in this study we consider a mathematical modelling and computational approach to describe the spread of SARS-CoV-2 among hospitalised patients. We focus on 4-bed bays and 6-bed bays, which are commonly used to accommodate various non-Covid-19 patients in many hospitals across UK. We use this mathematical model to investigate the spread of SARS-CoV-2 infections among patients in non-Covid bays, in the context of various scenarios: changes in the number of contacts with infected patients and staff, having symptomatic vs. asymptomatic patients, removing infected individuals from these hospital bays once they are known to be infected, and the role of periodic testing of hospitalised patients. Our results show that 4-bed bays reduce the spread of SARS-CoV-2 compared to 6-bed bays. Moreover, we show that the position of a new (not infected) patient in specific beds in a 6-bed bay might also slow the spread of the disease. Finally, we propose that regular SARS-CoV-2 testing of hospitalised patients would allow appropriate placement of infected patients in specific (Covid-only) hospital bays.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "David Moreno Martos",
+        "author_inst": "University of Dundee"
+      },
+      {
+        "author_name": "Benjamin Parcell",
+        "author_inst": "NHS Tayside"
+      },
+      {
+        "author_name": "Raluca Eftimie",
+        "author_inst": "University of Dundee"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.09.05.20189142",
     "rel_title": "Development and Validation of the Patient History COVID-19 (PH-Covid19) Scoring System: A Multivariable Prediction Model of Death in Mexican Patients with COVID-19",
@@ -1187552,29 +1186529,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.09.04.20188631",
-    "rel_title": "Contact tracing efficiency, transmission heterogeneity, and accelerating COVID-19 epidemics",
-    "rel_date": "2020-09-07",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.04.20188631",
-    "rel_abs": "Simultaneously controlling COVID-19 epidemics and limiting economic and societal impacts presents a difficult challenge, especially with limited public health budgets. Testing, contact tracing, and isolating/quarantining is a key strategy that has been used to reduce transmission of SARS-CoV-2, the virus that causes COVID-19. However, manual contact tracing is a time-consuming process and as case numbers increase it takes longer to reach each cases contacts, leading to additional virus spread. Delays between symptom onset and being tested (and receiving results), and a low fraction of symptomatic cases being tested can also reduce the impact of contact tracing on transmission. We examined the relationship between cases, delays, and participation and the pathogen reproductive number Rt. We also examined implications for infection dynamics using a stochastic compartment model of SARS-CoV-2. We found that Rt increases sigmoidally with the number of cases due to decreasing contact tracing efficacy. This relationship results in accelerating epidemics because Rt increases, rather than declines, as infections increase. Shifting contact tracers from locations with high and low case burdens relative to capacity to locations with intermediate case burdens maximizes their impact in reducing Rt (but minimizing total infections is more complicated). We also found that contact tracing quickly becomes ineffective in reducing Rt with increasing delays between symptom onset and tracing and with lower fraction of symptomatic infections being tested. Finally, we found that when cases are low, testing and tracing reductions in Rt can sometimes greatly delay epidemics due to the highly heterogeneous transmission dynamics of SARS-CoV-2, in which a small fraction of infections often give rise to most of transmission. These results demonstrate the importance of having an expandable or mobile team of contact tracers that can be used to control surges in cases. They also emphasize the value of easy access, high testing capacity and rapid turn-around of testing results, as well as outreach efforts to encourage symptomatic infections to be tested immediately after symptom onset. An efficient and adaptive public health capacity strategy can allow for increased economic activity and should be employed in the current and future pandemics.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Billy J Gardner",
-        "author_inst": "University of California, Santa Cruz"
-      },
-      {
-        "author_name": "A. Marm Kilpatrick",
-        "author_inst": "University of California, Santa Cruz"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.09.04.20188318",
     "rel_title": "Trans-ethnic analysis reveals genetic and non-genetic associations with COVID-19 susceptibility and severity",
@@ -1187817,6 +1186771,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.09.04.20188359",
+    "rel_title": "COVID-19 superspreading in cities versus the countryside",
+    "rel_date": "2020-09-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.04.20188359",
+    "rel_abs": "So far, the COVID-19 pandemic has been characterised by an initial rapid rise in new cases followed by a peak and a more erratic behaviour that varies between regions. This is not easy to reproduce with traditional SIR models, which predict a more symmetric epidemic. Here, we argue that superspreaders and population heterogeneity are the core factors explaining this discrepancy. We do so through an agent-based lattice model of a disease spreading in a heterogeneous population. We predict that an epidemic driven by superspreaders will spread rapidly in cities, but not in the countryside where the sparse population limits the maximal number of secondary infections. This suggests that mitigation strategies should include restrictions on venues where people meet a large number of strangers. Furthermore, mitigating the epidemic in cities and in the countryside may require different levels of restrictions.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Andreas Eilersen",
+        "author_inst": "University of Copenhagen"
+      },
+      {
+        "author_name": "Kim Sneppen",
+        "author_inst": "University of Copenhagen"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.09.04.20188680",
     "rel_title": "CAN EDUCATIONAL INSTITUTIONS REOPEN FOR IN-PERSON CLASSES SAFELY AMID THE COVID-19 PANDEMIC?",
@@ -1189182,57 +1188159,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.09.04.20187724",
-    "rel_title": "Switched and unswitched memory B cells detected during SARS-CoV-2 convalescence correlate with limited symptom duration",
-    "rel_date": "2020-09-05",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.04.20187724",
-    "rel_abs": "Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of the pandemic human respiratory illness COVID-19, is a global health emergency. While severe acute disease has been linked to an expansion of antibody-secreting plasmablasts, we sought to identify B cell responses that correlated with positive clinical outcomes in convalescent patients. We characterized the peripheral blood B cell immunophenotype and plasma antibody responses in 40 recovered non-hospitalized COVID-19 subjects that were enrolled as donors in a convalescent plasma treatment study. We observed a significant negative correlation between the frequency of peripheral blood memory B cells and the duration of symptoms for convalescent subjects. Memory B cell subsets in convalescent subjects were composed of classical CD24+ class-switched memory B cells, but also activated CD24-negative and natural unswitched CD27+ IgD+ IgM+ subsets. Memory B cell frequency was significantly correlated with both IgG1 and IgM responses to the SARS-CoV-2 spike protein receptor binding domain (RBD).\n\nIgM+ memory, but not switched memory, directly correlated with virus-specific antibody responses, and remained stable over time. Our findings suggest that the frequency of memory B cells is a critical indicator of disease resolution, and that IgM+ memory B cells play an important role in SARS-CoV-2 immunity.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Krista L Newell",
-        "author_inst": "SUNY Upstate Medical University"
-      },
-      {
-        "author_name": "Deanna C Clemmer",
-        "author_inst": "SUNY Upstate Medical University"
-      },
-      {
-        "author_name": "Justin B Cox",
-        "author_inst": "SUNY Upstate Medical University"
-      },
-      {
-        "author_name": "Yetunde I Kayode",
-        "author_inst": "SUNY Upstate Medical University"
-      },
-      {
-        "author_name": "Victoria Zoccoli-Rodriguez",
-        "author_inst": "SUNY Upstate Medical University"
-      },
-      {
-        "author_name": "Harry E Taylor",
-        "author_inst": "SUNY Upstate Medical University"
-      },
-      {
-        "author_name": "Timothy P Endy",
-        "author_inst": "SUNY Upstate Medical University"
-      },
-      {
-        "author_name": "Joel R Wilmore",
-        "author_inst": "SUNY Upstate Medical University"
-      },
-      {
-        "author_name": "Gary Winslow",
-        "author_inst": "Upstate Medical University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "allergy and immunology"
-  },
   {
     "rel_doi": "10.1101/2020.09.04.20187948",
     "rel_title": "Long, thin transmission chains of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) may go undetected for several weeks at low to moderate reproductive numbers: Implications for containment and elimination strategy",
@@ -1189431,6 +1188357,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.09.03.20187336",
+    "rel_title": "Household Secondary Attack Rate in Gandhinagar district of Gujarat state from Western India",
+    "rel_date": "2020-09-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.03.20187336",
+    "rel_abs": "Objectives: Current retrospective study aims to evaluate household Secondary Attack Rate (SAR) of COVID-19 in Gandhinagar (rural) district of Gujarat, India. Methods: Line-listing of 486 laboratory-confirmed patients, tested between 28th March to 2nd July was collected, out of them 80 (15% of overall sample) cases were randomly selected. Demographic, clinical and household details of cases were collected through telephonic interview. During interview 28 more patients were identified from the same household and were added accordingly. So, study included 74 unrelated cluster of households with 74 primary cases and 386 close contacts. Results: SAR in household contacts of COVID-19 in Gandhinagar was 8.8%. Out of 108, 8 patients expired (7.4%), where higher mortality was observed in primary cases (9.5%) as compared to secondary cases (3%). Occupational analysis showed that majority of the secondary cases (88%) were not working and hence had higher contact time with patient. No out-of-pocket expenditure occurred in 94% of the patients, in remaining 6% average expenditure of 1,49,633INR (2027 USD) was recorded. Conclusions: Key observations from the study are 1) SAR of 8.8% is relatively low and hence home isolation of the cases can be continued 2) Primary case is more susceptible to fatal outcome as compared to secondary cases 3) Government has covered huge population of the COVID-19 patients under cost protection. However, more robust studies with larger datasets are needed to further validate the findings.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Komal Shah",
+        "author_inst": "Indian Institute of Public Health Gandhinagar"
+      },
+      {
+        "author_name": "Nupur Desai",
+        "author_inst": "New York University, USA"
+      },
+      {
+        "author_name": "Deepak Saxena",
+        "author_inst": "Indian Institute of Public Health Gandhinagar"
+      },
+      {
+        "author_name": "Dileep Mavalankar",
+        "author_inst": "Indian Institute of Public Health Gandhinagar"
+      },
+      {
+        "author_name": "Umang Mishra",
+        "author_inst": "Epidemic, Commissioner (Health, Medical Services and Medical Education), Gandhinagar"
+      },
+      {
+        "author_name": "G C Patel",
+        "author_inst": "Epidemic Branch, Commissionerate of Health, Gandhinagar, Gujarat"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.09.03.20183947",
     "rel_title": "SARS-CoV-2-specific IgA and limited inflammatory cytokines are present in the stool of select patients with acute COVID-19",
@@ -1190716,33 +1189681,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "rheumatology"
   },
-  {
-    "rel_doi": "10.1101/2020.09.01.20185876",
-    "rel_title": "Dark matter, second waves and epidemiological modelling",
-    "rel_date": "2020-09-03",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.01.20185876",
-    "rel_abs": "BackgroundRecent reports based on conventional SEIR models suggest that the next wave of the COVID-19 pandemic in the UK could overwhelm health services, with fatalities that far exceed the first wave. These models suggest non-pharmaceutical interventions would have limited impact without intermittent national lockdowns and consequent economic and health impacts. We used Bayesian model comparison to revisit these conclusions, when allowing for heterogeneity of exposure, susceptibility, and viral transmission.\n\nMethodsWe used dynamic causal modelling to estimate the parameters of epidemiological models and, crucially, the evidence for alternative models of the same data. We compared SEIR models of immune status that were equipped with latent factors generating data; namely, location, symptom, and testing status. We analysed daily cases and deaths from the US, UK, Brazil, Italy, France, Spain, Mexico, Belgium, Germany, and Canada over the period 25-Jan-20 to 15-Jun-20. These data were used to estimate the composition of each countrys population in terms of the proportions of people (i) not exposed to the virus, (ii) not susceptible to infection when exposed, and (iii) not infectious when susceptible to infection.\n\nFindingsBayesian model comparison found overwhelming evidence for heterogeneity of exposure, susceptibility, and transmission. Furthermore, both lockdown and the build-up of population immunity contributed to viral transmission in all but one country. Small variations in heterogeneity were sufficient to explain the large differences in mortality rates across countries. The best model of UK data predicts a second surge of fatalities will be much less than the first peak (31 vs. 998 deaths per day. 95% CI: 24-37)--substantially less than conventional model predictions. The size of the second wave depends sensitively upon the loss of immunity and the efficacy of find-test-trace-isolate-support (FTTIS) programmes.\n\nInterpretationA dynamic causal model that incorporates heterogeneity of exposure, susceptibility and transmission suggests that the next wave of the SARS-CoV-2 pandemic will be much smaller than conventional models predict, with less economic and health disruption. This heterogeneity means that seroprevalence underestimates effective herd immunity and, crucially, the potential of public health programmes.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSHundreds of modelling papers have been published recently, offering predictions and projections of the current coronavirus outbreak. These range from peer-reviewed publications to rapid reports from learned societies. Many, if not most, of these modelling initiatives commit to a particular kind of epidemiological model that precludes heterogeneity in viral exposure, susceptibility, and transmission. The ensuing projections can be fantastical in terms of fatalities and ensuing public health responses.\n\nAdded value of this studyThis study revisits the evidence for conventional epidemiological modelling assumptions using dynamic causal modelling and Bayesian model comparison. It provides overwhelming evidence for heterogeneity, and the interaction between lockdown and herd immunity in suppressing viral transmission.\n\nImplications of all the available evidenceHeterogeneity of this sort means that low seroprevalence (<20%) is consistent with levels of population immunity that play a substantive role in attenuating viral transmission and, crucially, facilitating public health measures.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Karl Friston",
-        "author_inst": "UCL"
-      },
-      {
-        "author_name": "Anthony Costello",
-        "author_inst": "UCL"
-      },
-      {
-        "author_name": "Deenan Pillay",
-        "author_inst": "UCL"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health informatics"
-  },
   {
     "rel_doi": "10.1101/2020.09.01.20182220",
     "rel_title": "Cross-reactive antibody responses against SARS-CoV-2 and seasonal common cold coronaviruses",
@@ -1191013,6 +1189951,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.09.01.20185280",
+    "rel_title": "SARS-CoV-2 Protein in Wastewater Mirrors COVID-19 Prevalence.",
+    "rel_date": "2020-09-03",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.01.20185280",
+    "rel_abs": "The COVID-19 pandemic has given rise to diverse approaches to track infections. The causative agent, SARS-CoV-2, is a fecally-shed RNA virus, and many groups have assayed wastewater for viral RNA fragments by quantitative reverse transcription polymerase chain reaction (qRT-PCR) as a proxy for COVID-19 prevalence in the community. Most groups report low levels of viral RNA that often skirt the methods theoretical limits of detection and quantitation. Here, we demonstrate the presence of SARS-CoV-2 structural proteins in wastewater using traditional immunoblotting and quantitate them from wastewater solids using an immuno-linked PCR method called Multiplex Paired-antibody Amplified Detection (MPAD). MPAD demonstrated facile detection of SARS-CoV-2 proteins compared with SARS-CoV-2 RNA via qRT-PCR in wastewater. In this longitudinal study, we corrected for stochastic variability inherent to wastewater-based epidemiology using multiple fecal content protein biomarkers. These normalized SARS-CoV-2 protein data correlated well with public health metrics. Our method of assaying SARS-CoV-2 protein from wastewater represents a promising and sensitive epidemiological tool to assess prevalence of fecally-shed pathogens in the community.",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Nafisa Neault",
+        "author_inst": "Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada, K1H 8L1"
+      },
+      {
+        "author_name": "Aiman T. Baig",
+        "author_inst": "Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada, K1H 8L1"
+      },
+      {
+        "author_name": "Tyson E. Graber",
+        "author_inst": "Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada, K1H 8L1"
+      },
+      {
+        "author_name": "Patrick M. D'Aoust",
+        "author_inst": "Department of Civil Engineering, University of Ottawa, Ottawa, Canada, K1N 6N5"
+      },
+      {
+        "author_name": "Elisabeth Mercier",
+        "author_inst": "Department of Civil Engineering, University of Ottawa, Ottawa, Canada, K1N 6N5"
+      },
+      {
+        "author_name": "Ilya Alexandrov",
+        "author_inst": "ActivSignal LLC., Natick, MA, United States, 01760"
+      },
+      {
+        "author_name": "Daniel Crosby",
+        "author_inst": "ActivSignal LLC., Natick, MA, United States, 01760"
+      },
+      {
+        "author_name": "Janice Mayne",
+        "author_inst": "Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada, K1H 8M5"
+      },
+      {
+        "author_name": "Thomas Pounds",
+        "author_inst": "ActivSignal LLC., Natick, MA, United States, 01760"
+      },
+      {
+        "author_name": "Malcolm MacKenzie",
+        "author_inst": "ActivSignal LLC., Natick, MA, United States, 01760"
+      },
+      {
+        "author_name": "Daniel Figeys",
+        "author_inst": "Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Canada, K1H 8M5; Department of Chemistry and Biomolecular Sciences, Unive"
+      },
+      {
+        "author_name": "Alex E. MacKenzie",
+        "author_inst": "Children's Hospital of Eastern Ontario Research Institute, Ottawa, Canada, K1H 8L1"
+      },
+      {
+        "author_name": "Robert Delatolla",
+        "author_inst": "Department of Civil Engineering, University of Ottawa, Ottawa, Canada, K1N 6N5"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.09.01.20186049",
     "rel_title": "App-based symptom tracking to optimize SARS-CoV-2 testing strategy using machine learning",
@@ -1192082,125 +1191087,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.09.02.20186817",
-    "rel_title": "Revealing the extent of the COVID-19 pandemic in Kenya based on serological and PCR-test data",
-    "rel_date": "2020-09-03",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.02.20186817",
-    "rel_abs": "Policy makers in Africa need robust estimates of the current and future spread of SARS-CoV-2. Data suitable for this purpose are scant. We used national surveillance PCR test, serological survey and mobility data to develop and fit a county-specific transmission model for Kenya. We estimate that the SARS-CoV-2 pandemic peaked before the end of July 2020 in the major urban counties, with 34 - 41% of residents infected, and will peak elsewhere in the country within 2-3 months. Despite this penetration, reported severe cases and deaths are low. Our analysis suggests the COVID-19 disease burden in Kenya may be far less than initially feared. A similar scenario across sub-Saharan Africa would have implications for balancing the consequences of restrictions with those of COVID-19.",
-    "rel_num_authors": 26,
-    "rel_authors": [
-      {
-        "author_name": "John Ojal",
-        "author_inst": "Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya and London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Samuel PC Brand",
-        "author_inst": "The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, UK."
-      },
-      {
-        "author_name": "Vincent Were",
-        "author_inst": "Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya"
-      },
-      {
-        "author_name": "Emelda A Okiro",
-        "author_inst": "Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya"
-      },
-      {
-        "author_name": "Ivy Kadzo Kombe",
-        "author_inst": "KEMRI-Wellcome Trust Research Programme"
-      },
-      {
-        "author_name": "Caroline Mburu",
-        "author_inst": "Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya"
-      },
-      {
-        "author_name": "Rabia Aziza",
-        "author_inst": "The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, UK."
-      },
-      {
-        "author_name": "Morris Ogero",
-        "author_inst": "Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya"
-      },
-      {
-        "author_name": "Ambrose Agweyu",
-        "author_inst": "Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya"
-      },
-      {
-        "author_name": "George M Warimwe",
-        "author_inst": "KEMRI-Wellcome Trust Research Programme"
-      },
-      {
-        "author_name": "Sophie Uyoga",
-        "author_inst": "KEMRI Wellcome Trust Research Programme"
-      },
-      {
-        "author_name": "Ifedayo M. O Adetifa",
-        "author_inst": "KEMRI-Wellcome Trust Research Programme"
-      },
-      {
-        "author_name": "John Anthony Scott",
-        "author_inst": "London School of Hygiene & Tropical Medicine"
-      },
-      {
-        "author_name": "Edward Otieno",
-        "author_inst": "Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya"
-      },
-      {
-        "author_name": "Lynette I Ochola-Oyier",
-        "author_inst": "Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya"
-      },
-      {
-        "author_name": "Charles Nyaigoti Agoti",
-        "author_inst": "Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya"
-      },
-      {
-        "author_name": "Kadondi Kasera",
-        "author_inst": "Ministry of Health, Government of Kenya, Kenya"
-      },
-      {
-        "author_name": "Patrick Amoth",
-        "author_inst": "Ministry of Health, Government of Kenya, Kenya"
-      },
-      {
-        "author_name": "Mercy Mwangangi",
-        "author_inst": "Ministry of Health, Government of Kenya, Kenya"
-      },
-      {
-        "author_name": "Rashid Aman",
-        "author_inst": "Ministry of Health, Government of Kenya, Kenya"
-      },
-      {
-        "author_name": "Wangari Ng'ang'a",
-        "author_inst": "Presidential Policy & Strategy Unit, The Presidency, Government of Kenya"
-      },
-      {
-        "author_name": "Benjamin Tsofa",
-        "author_inst": "Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya"
-      },
-      {
-        "author_name": "Philip Bejon",
-        "author_inst": "Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya"
-      },
-      {
-        "author_name": "Edwine Barasa",
-        "author_inst": "KEMRI-Wellcome Trust Research Programme"
-      },
-      {
-        "author_name": "Matt J Keeling",
-        "author_inst": "The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, UK"
-      },
-      {
-        "author_name": "D James Nokes",
-        "author_inst": "KEMRI-Wellcome Trust Research Programme, Kenya and School of Life Sciences, University of Warwick, UK"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.09.02.20185173",
     "rel_title": "Characteristics and outcomes of 627 044 COVID-19 patients with and without obesity in the United States, Spain, and the United Kingdom",
@@ -1192547,6 +1191433,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.09.01.20182873",
+    "rel_title": "Effects of Public Health Interventions on the Epidemiological Spread During the First Wave of the COVID-19 Outbreak in Thailand",
+    "rel_date": "2020-09-03",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.01.20182873",
+    "rel_abs": "A novel infectious respiratory disease was recognized in Wuhan (Hubei Province, China) in December 2019. In February 2020, the disease was named \"coronavirus disease 2019\" (COVID-19). COVID-19 became a pandemic in March 2020, and, since then, different countries have implemented a broad spectrum of policies. Thailand is considered to be among the top countries in handling its first wave of the outbreak -- 12 January to 31 July 2020. Here, we illustrate how Thailand tackled the COVID-19 outbreak, particularly the effects of public health interventions on the epidemiologic spread. This study shows how the available data from the outbreak can be analyzed and visualized to quantify the severity of the outbreak, the effectiveness of the interventions, and the level of risk of allowed activities during an easing of a \"lockdown.\" This study shows how a well-organized governmental apparatus can overcome the havoc caused by a pandemic.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Sipat Dr. Triukose",
+        "author_inst": "Research group on Applied Digital Technology in Medicine (ATM) and Chulalongkorn University Big Data Analytics and IoT Center (CUBIC), Chulalongkorn University"
+      },
+      {
+        "author_name": "Sirin Dr. Nitinawarat",
+        "author_inst": "International School of Engineering, Faculty of Engineering and Research group on Applied Digital Technology in Medicine (ATM), Chulalongkorn University"
+      },
+      {
+        "author_name": "Ponlapat Satian",
+        "author_inst": "Lansaka Hospital, Office of the permanent secretary, Ministry of Public Health, Thailand"
+      },
+      {
+        "author_name": "Anupap Dr. Somboonsavatdee",
+        "author_inst": "Greater Data Science Lab, Department of Statistics, Chulalongkorn Business School, 15 Chulalongkorn University, Bangkok, Thailand"
+      },
+      {
+        "author_name": "Ponlachart Dr. Chotikarn",
+        "author_inst": "Marine and Coastal Resources Institute, Faculty of Environmental Management, Coastal Oceanography and Climate Change Research Center, Prince of Songkla Universi"
+      },
+      {
+        "author_name": "Thunchanok Thammasanya",
+        "author_inst": "TrueEye Company Limited, Bangkok, Thailand"
+      },
+      {
+        "author_name": "Nasamon Wanlapakorn",
+        "author_inst": "Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, 22 Chulalongkorn University, Bangkok, Thailand"
+      },
+      {
+        "author_name": "Natthinee Dr. Sudhinaraset",
+        "author_inst": "Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand"
+      },
+      {
+        "author_name": "Pitakpol Dr. Boonyamalik",
+        "author_inst": "Office of the Permanent Secretary, Ministry of Public Health, Bangkok, Thailand"
+      },
+      {
+        "author_name": "Bancha Kakhong",
+        "author_inst": "Department of Health, Ministry of Public Health, Bangkok, Thailand"
+      },
+      {
+        "author_name": "Yong Poovorawan",
+        "author_inst": "Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.09.02.20186577",
     "rel_title": "COVID-19: Impact on the health and wellbeing of ex-serving personnel (Veterans-CHECK) protocol paper",
@@ -1193792,33 +1192737,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.08.30.20184697",
-    "rel_title": "Prevalence and predictors of depression, anxiety and stress symptoms among pregnant women during COVID-19-related lockdown in Abakaliki, Nigeria",
-    "rel_date": "2020-09-02",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.30.20184697",
-    "rel_abs": "IntroductionSeveral studies on COVID-19 and pregnancy have been published recently, but few studies have evaluated the impact of this pandemic on maternal mental health particularly in low-resource setting.\n\nAimTo determine the prevalence and predictors of COVID-19-related depression, anxiety and stress symptoms among pregnant women.\n\nMaterials and methodsThis was a questionnaire-based cross-sectional study conducted among 456 pregnant women attending prenatal care at Abakaliki, Nigeria during COVID-19-related lockdown. They were screened for psychological morbidities using DASS 21 (Depression, Anxiety and Stress Scale).\n\nResultsSevere and extremely severe depression were reported in 33 (7.2%) and 29 (6.4%) participants respectively. 15 (3.3%) and 35 (7.7%) women had severe and extremely severe anxiety respectively. 105 (23%) had severe anxiety whereas 76 (16.7%) reported extremely severe stress. Multiparity (2 - 4) and occupations such as trading and farming were predictors of depression whereas grandmultiparity, urban residence and trading were identified as predictors of anxiety and stress.\n\nConclusionDepression, anxiety and stress symptoms were relatively common among pregnant women during COVID-19-related lockdown in Abakaliki, Nigeria. There is a need to integrate screening for depression, anxiety and stress in existing antenatal care programs so as to identify and prevent long term adverse psychological outcome related to COVID-19 pandemic.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Johnbosco Ifunanya Nwafor",
-        "author_inst": "Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Ebonyi State, Nigeria"
-      },
-      {
-        "author_name": "Ijeoma Nkem Okedo-Alex",
-        "author_inst": "Department of Community Medicine, Alex Ekwueme Federal University Teaching Hospital"
-      },
-      {
-        "author_name": "Arinze Chidiebere Ikeotuonye",
-        "author_inst": "Department of Obstetrics and Gynaecology, Alex Ekwueme Federal University Teaching Hospital"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "obstetrics and gynecology"
-  },
   {
     "rel_doi": "10.1101/2020.08.30.20184739",
     "rel_title": "Test Sensitivity for Infection versus Infectiousness of SARS-CoV-2",
@@ -1194037,6 +1192955,89 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.08.29.20184135",
+    "rel_title": "Modeling the combined effect of digital exposure notification and non-pharmaceutical interventions on the COVID-19 epidemic in Washington state",
+    "rel_date": "2020-09-02",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.29.20184135",
+    "rel_abs": "Contact tracing is increasingly being used to combat COVID-19, and digital implementations are now being deployed, many of them based on Apple and Googles Exposure Notification System. These systems are new and are based on smartphone technology that has not traditionally been used for this purpose, presenting challenges in understanding possible outcomes. In this work, we use individual-based computational models to explore how digital exposure notifications can be used in conjunction with non-pharmaceutical interventions, such as traditional contact tracing and social distancing, to influence COVID-19 disease spread in a population. Specifically, we use a representative model of the household and occupational structure of three counties in the state of Washington together with a proposed digital exposure notifications deployment to quantify impacts under a range of scenarios of adoption, compliance, and mobility. In a model in which 15% of the population participated, we found that digital exposure notification systems could reduce infections and deaths by approximately 8% and 6%, effectively complementing traditional contact tracing. We believe this can serve as guidance to health authorities in Washington state and beyond on how exposure notification systems can complement traditional public health interventions to suppress the spread of COVID-19.",
+    "rel_num_authors": 17,
+    "rel_authors": [
+      {
+        "author_name": "Matthew Abueg",
+        "author_inst": "Google Research"
+      },
+      {
+        "author_name": "Robert Hinch",
+        "author_inst": "Nuffield Department of Medicine, University of Oxford"
+      },
+      {
+        "author_name": "Neo Wu",
+        "author_inst": "Google Research"
+      },
+      {
+        "author_name": "Luyang Liu",
+        "author_inst": "Google Research"
+      },
+      {
+        "author_name": "William J M Probert",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Austin Wu",
+        "author_inst": "Google LLC"
+      },
+      {
+        "author_name": "Paul Eastham",
+        "author_inst": "Google Research"
+      },
+      {
+        "author_name": "Yusef Shafi",
+        "author_inst": "Google Research"
+      },
+      {
+        "author_name": "Matt Rosencrantz",
+        "author_inst": "Google Research"
+      },
+      {
+        "author_name": "Michael Dikovsky",
+        "author_inst": "Google Research"
+      },
+      {
+        "author_name": "Zhao Cheng",
+        "author_inst": "Google Research"
+      },
+      {
+        "author_name": "Anel Nurtay",
+        "author_inst": "Nuffield Department of Medicine, University of Oxford"
+      },
+      {
+        "author_name": "Lucie Abeler-D\u00f6rner",
+        "author_inst": "Nuffield Department of Medicine, University of Oxford"
+      },
+      {
+        "author_name": "David G Bonsall",
+        "author_inst": "Big Data Institute"
+      },
+      {
+        "author_name": "Michael V McConnell",
+        "author_inst": "Google LLC"
+      },
+      {
+        "author_name": "Shawn O'Banion",
+        "author_inst": "Google Research"
+      },
+      {
+        "author_name": "Christophe Fraser",
+        "author_inst": "University of Oxford"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.08.29.20184465",
     "rel_title": "One Study of COVID-19 Spreading at The United States - Brazil - Colombia",
@@ -1195478,37 +1194479,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pediatrics"
   },
-  {
-    "rel_doi": "10.1101/2020.08.31.20185215",
-    "rel_title": "Dealing with Covid-19 infections in Kolkata, India: A GIS based risk analysis and implications for future scenarios",
-    "rel_date": "2020-09-02",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.31.20185215",
-    "rel_abs": "The Covid-19 pandemic has inherently affected daily lives of people around the world. We, the people, have already started to live in a new-normal way, such as wearing masks, keeping a safe distance from others and maintaining higher level of health & hygiene standards. However, because of this pandemic, the global economy has taken a major blow. Many people have lost their livelihood, and now facing challenges in getting better healthcare facilities and food for survival. Given the serious challenges to the problem, this paper analyzes demographic data to predict vulnerable areas in Kolkata metropolitan city that houses nearly one-third of its population in slums and one-fifth below poverty level, under compromised living conditions. The analysis revealed that the highest risk areas are located in the east and west of the city, the area to a great extent overlapped with wards containing larger share of population below poverty level and are also living in slums. The analysis of publicly accessible Covid-19 case records and containment zones data indicate the hardest hit areas lies in the central Kolkata and several wards along the eastern and northeastern border of the Kolkata Municipal Corporation. The data further revealed that the virus infections have extended to the south Kolkata with increasing number of  broad-based containment zones with heightened cases. The analysis of demographic characteristics of the hardest hit wards revealed that not a single variables are directly associated with the increase in the number of containments for a particular ward. The ranking of wards based on four intervention criterion have suggested that the  lack of social awareness along with  lack of social distancing have dominantly contributed to the increasing number of containments of Covid-19 cases in Kolkata. Determination of optimized ranking and Spearmans rank correlation coefficient of the wards based on four intervention criterion provided a basis for the policy makers to assess ward-based interventions criterion to control further spread of the disease and/or prevent second wave of infections. Given that the effective antiviral drugs is far away from common publics reach, the application of our study approach would benefit saving lives of many vulnerable populations.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Bibhash Nath",
-        "author_inst": "Hunter College of the City University of New York"
-      },
-      {
-        "author_name": "Santanu Majumder",
-        "author_inst": "Texas A&M University"
-      },
-      {
-        "author_name": "Mohammad Mahmudur Rahman",
-        "author_inst": "The University of Newcastle"
-      },
-      {
-        "author_name": "Jayanta Sen",
-        "author_inst": "West Bengal State University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.08.30.20184168",
     "rel_title": "Suicide during the COVID-19 pandemic in Japan",
@@ -1195891,6 +1194861,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.08.31.20185587",
+    "rel_title": "Health and economic effects of COVID-19 control in Australia: Modelling and quantifying the payoffs of hard versus soft lockdown",
+    "rel_date": "2020-09-02",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.31.20185587",
+    "rel_abs": "Objective(s)Australia requires high quality evidence to optimise likely health and economy outcomes to effectively manage the current resurgence of COVID-19. We hypothesise that the most stringent social distancing (SD) measures (100% of level in Australia in April 2020) deliver better public health and economy outcomes.\n\nDesign Fit-for-purpose (individual-based and compartment) models were used to simulate the effects of different SD and detection strategies on Australian COVID-19 infections and the economy from March to July 2020. Public reported COVID-19 data were used to estimate model parameters.\n\nMain outcome measuresPublic health and economy outcomes for multiple social distancing levels were evaluated, assessing \"hard\" versus \"soft\" lockdowns, and for early versus later relaxation of social distancing. Outcomes included costs and the timing and magnitude of observed COVID-19 cases and cumulative deaths in Australia from March to June 2020.\n\nResultsHigher levels of social distancing achieve zero community transmission with 100% probability and lower economy cost while low levels of social distancing result in uncontrolled outbreaks and higher economy costs. High social distancing total economy costs were $17.4B versus $41.2B for 0.7 social distancing. Early relaxation of suppression results in worse public health outcomes and higher economy costs.\n\nConclusion(s)Better public health outcomes (reduced COVID-19 fatalities) are positively associated with lower economy costs and higher levels of social distancing; achieving zero community transmission lowers both public health and economy costs compared to allowing community transmission to continue; and early relaxation of social distancing increases both public health and economy costs.\n\nSignificanceThe known is that COVID-19 infections can be suppressed with social distancing (SD) measures of sufficient stringency and duration.\n\nThe new is we find highest levels of SD (100% SD that prevailed in April 2020) generate much lower COVID-9 deaths; reduced SD days; increased economic activity; and much higher probability of elimination over a subsequent 12-month period than lower levels of SD.\n\nThe implications are that greater levels of SD are preferred to lower SD because they deliver both better public health and lower economy costs.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Quentin Grafton",
+        "author_inst": "Australian National University"
+      },
+      {
+        "author_name": "Tom Kompas",
+        "author_inst": "University of Melbourne"
+      },
+      {
+        "author_name": "John Parslow",
+        "author_inst": "CSIRO"
+      },
+      {
+        "author_name": "Kathryn Glass",
+        "author_inst": "Australian National University"
+      },
+      {
+        "author_name": "Emily Banks",
+        "author_inst": "Australian National University"
+      },
+      {
+        "author_name": "Kamalini Lokuge",
+        "author_inst": "Australian National University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.08.31.20185033",
     "rel_title": "Asymptomatic cases and limited transmission of SARS-CoV-2 in residents and healthcare workers in three Dutch nursing homes",
@@ -1197240,41 +1196249,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
-  {
-    "rel_doi": "10.1101/2020.08.31.20185439",
-    "rel_title": "Towards Improved Social Distancing Guidelines: Space and Time Dependence of Virus Transmission from Speech-driven Aerosol Transport Between Two Individuals",
-    "rel_date": "2020-09-02",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.31.20185439",
-    "rel_abs": "It is now recognized that aerosol transport contributes to the transmission of the SARS-CoV-2. Existing social distancing guidelines are given in terms of distance, with vague statements about contact times. Also, estimates of inhalation of virus in a contaminated space typically assume a well-mixed environment, which is realistic for some, but not all, situations. We consider a local casual interaction of an infected individual and a susceptible individual, both maskless, account for the air flow and aerosol transport characteristics of speaking and breathing, and propose guidelines that involve both space and contact time, based on a conservative model of the interactions.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Fan Yang",
-        "author_inst": "Princeton University"
-      },
-      {
-        "author_name": "Amir A. Pahlavan",
-        "author_inst": "Princeton University"
-      },
-      {
-        "author_name": "Simon Mendez",
-        "author_inst": "University of Montpellier"
-      },
-      {
-        "author_name": "Manouk Abkarian",
-        "author_inst": "University of Montpellier"
-      },
-      {
-        "author_name": "Howard A. Stone",
-        "author_inst": "Princeton University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.09.01.20185447",
     "rel_title": "Rapid evaluation of neutralizing antibodies in COVID-19 patients",
@@ -1197697,6 +1196671,33 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2020.09.01.278366",
+    "rel_title": "An intestinal cell type in zebrafish is the nexus for the SARS-CoV-2 receptor and the Renin-Angiotensin-Aldosterone System that contributes to COVID-19 comorbidities",
+    "rel_date": "2020-09-02",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.01.278366",
+    "rel_abs": "People with underlying conditions, including hypertension, obesity, and diabetes, are especially susceptible to negative outcomes after infection with the coronavirus SARS-CoV-2. These COVID-19 comorbidities are exacerbated by the Renin-Angiotensin-Aldosterone System (RAAS), which normally protects from rapidly dropping blood pressure or dehydration via the peptide Angiotensin II (Ang II) produced by the enzyme Ace. The Ace paralog Ace2 degrades Ang II, thus counteracting its chronic effects. Ace2 is also the SARS-CoV-2 receptor. Ace, the coronavirus, and COVID-19 comorbidities all regulate Ace2, but we dont yet understand how. To exploit zebrafish (Danio rerio) as a disease model to understand mechanisms regulating the RAAS and its relationship to COVID-19 comorbidities, we must first identify zebrafish orthologs and co-orthologs of human RAAS genes, and second, understand where and when these genes are expressed in specific cells in zebrafish development. To achieve these goals, we conducted genomic analyses and investigated single cell transcriptomes. Results showed that most human RAAS genes have an ortholog in zebrafish and some have two or more co-orthologs. Results further identified a specific intestinal cell type in zebrafish larvae as the site of expression for key RAAS components, including Ace, Ace2, the coronavirus co-receptor Slc6a19, and the Angiotensin-related peptide cleaving enzymes Anpep and Enpep. Results also identified specific vascular cell subtypes as expressing Ang II receptors, apelin, and apelin receptor genes. These results identify specific genes and cell types to exploit zebrafish as a disease model for understanding the mechanisms leading to COVID-19 comorbidities.\n\nSUMMARY STATEMENTGenomic analyses identify zebrafish orthologs of the Renin-Angiotensin-Aldosterone System that contribute to COVID-19 comorbidities and single-cell transcriptomics show that they act in a specialized intestinal cell type.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "John Postlethwait",
+        "author_inst": "University of Oregon"
+      },
+      {
+        "author_name": "Dylan R Farnsworth",
+        "author_inst": "University of Oregon"
+      },
+      {
+        "author_name": "Adam C Miller",
+        "author_inst": "University of Oregon"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "developmental biology"
+  },
   {
     "rel_doi": "10.1101/2020.09.01.278952",
     "rel_title": "Structural Variants in SARS-CoV-2 Occur at Template-Switching Hotspots",
@@ -1199262,45 +1198263,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.08.26.20182709",
-    "rel_title": "Cardiometabolic Risk Factors for COVID-19 Susceptibility and Severity: A Mendelian Randomization Analysis",
-    "rel_date": "2020-09-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.26.20182709",
-    "rel_abs": "ImportanceEarly epidemiological studies report associations of diverse cardiometabolic conditions especially body mass index (BMI), with COVID-19 susceptibility and severity, but causality has not been established. Identifying causal risk factors is critical to inform preventive strategies aimed at modifying disease risk.\n\nObjectiveWe sought to evaluate the causal associations of cardiometabolic conditions with COVID-19 susceptibility and severity.\n\nDesignTwo-sample Mendelian Randomization (MR) Study.\n\nSettingPopulation-based cohorts that contributed to the genome-wide association study (GWAS) meta-analysis by the COVID-19 Host Genetics Initiative.\n\nParticipantsPatients hospitalized with COVID-19 diagnosed by RNA PCR, serologic testing, or clinician diagnosis. Population controls defined as anyone who was not a case in the cohorts.\n\nExposuresSelected genetic variants associated with 17 cardiometabolic diseases, including diabetes, coronary artery disease, stroke, chronic kidney disease, and BMI, at p<5x10-8 from published largescale GWAS.\n\nMain outcomesWe performed an inverse-variance weighted averages of variant-specific causal estimates for susceptibility, defined as people who tested positive for COVID-19 vs. population controls, and severity, defined as patients hospitalized with COVID-19 vs. population controls, and repeated the analysis for BMI using effect estimates from UKBB. To estimate direct and indirect causal effects of BMI through obesity-related cardiometabolic diseases, we performed pairwise multivariable MR. We used p<0.05/17 exposure/2 outcomes=0.0015 to declare statistical significance.\n\nResultsGenetically increased BMI was causally associated with testing positive for COVID-19 [6,696 cases / 1,073,072 controls; p=6.7x10-4, odds ratio and 95% confidence interval 1.08 (1.03, 1.13) per kg/m2] and a higher risk of COVID-19 hospitalization [3,199 cases/897,488 controls; p=8.7x10-4, 1.12 (1.04, 1.21) per kg/m2]. In the multivariable MR, the direct effect of BMI was abolished upon conditioning on the effect on type 2 diabetes but persisted when conditioning on the effects on coronary artery disease, stroke, chronic kidney disease, and c-reactive protein. No other cardiometabolic exposures tested were associated with a higher risk of poorer COVID-19 outcomes.\n\nConclusions and RelevanceGenetic evidence supports BMI as a causal risk factor for COVID-19 susceptibility and severity. This relationship may be mediated via type 2 diabetes. Obesity may have amplified the disease burden of the COVID-19 pandemic either single-handedly or through its metabolic consequences.\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSIs there a causal association between cardiometabolic conditions and COVID-19 susceptibility or severity?\n\nFindingsUsing two-sample Mendelian randomization of 17 cardiometabolic diseases and traits, only body mass index was found to be causally associated with testing positive for COVID-19 (6,696 cases/ 1,073,072 controls; p=6.7x10-4) and a higher risk of COVID-19 (3,199 cases/897,488 controls; p=8.7x10-4).\n\nMeaningGenetic evidence supports BMI as a causal risk factor for COVID-19 susceptibility and severity.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Aaron Leong",
-        "author_inst": "MASSACHUSETTS GENERAL HOSPITAL"
-      },
-      {
-        "author_name": "Joanne Cole",
-        "author_inst": "Broad Institute"
-      },
-      {
-        "author_name": "Laura N. Brenner",
-        "author_inst": "Massachusetts General Hospital"
-      },
-      {
-        "author_name": "James B. Meigs",
-        "author_inst": "Massachusetts General Hospital"
-      },
-      {
-        "author_name": "Jose C. Florez",
-        "author_inst": "Massachusetts General Hospital"
-      },
-      {
-        "author_name": "Josep M. Mercader",
-        "author_inst": "Broad Institute"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.08.26.20157297",
     "rel_title": "Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: A guide and case study in setting up an emergency-use, laboratory-developed molecular assay",
@@ -1199643,6 +1198605,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.08.26.20182584",
+    "rel_title": "A multipurpose machine learning approach to predict COVID-19 negative prognosis in Sao Paulo, Brazil",
+    "rel_date": "2020-09-01",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.26.20182584",
+    "rel_abs": "IntroductionThe new coronavirus disease (COVID-19) is a challenge for clinical decision-making and the effective allocation of healthcare resources. An accurate prognostic assessment is necessary to improve survival of patients, especially in developing countries. This study proposes to predict the risk of developing critical conditions in COVID-19 patients by training multipurpose algorithms.\n\nMethodsA total of 1,040 patients with a positive RT-PCR diagnosis for COVID-19 from a large hospital from Sao Paulo, Brazil, were followed from March to June 2020, of which 288 (28%) presented a severe prognosis, i.e. Intensive Care Unit (ICU) admission, use of mechanical ventilation or death. Routinely-collected laboratory, clinical and demographic data was used to train five machine learning algorithms (artificial neural networks, extra trees, random forests, catboost, and extreme gradient boosting). A random sample of 70% of patients was used to train the algorithms and 30% were left for performance assessment, simulating new unseen data. In order to assess if the algorithms could capture general severe prognostic patterns, each model was trained by combining two out of three outcomes to predict the other.\n\nResultsAll algorithms presented very high predictive performance (average AUROC of 0.92, sensitivity of 0.92, and specificity of 0.82). The three most important variables for the multipurpose algorithms were ratio of lymphocyte per C-reactive protein, C-reactive protein and Braden Scale.\n\nConclusionThe results highlight the possibility that machine learning algorithms are able to predict unspecific negative COVID-19 outcomes from routinely-collected data.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Fernando Timoteo Fernandes",
+        "author_inst": "Fundacentro"
+      },
+      {
+        "author_name": "Tiago Almeida de Oliveira",
+        "author_inst": "Paraiba State University"
+      },
+      {
+        "author_name": "Cristiane Esteves Teixeira",
+        "author_inst": "National Cancer Institute"
+      },
+      {
+        "author_name": "Andre Filipe de Moraes Batista",
+        "author_inst": "University of Sao Paulo"
+      },
+      {
+        "author_name": "Gabriel Dalla Costa",
+        "author_inst": "BP - A Beneficencia Portuguesa de Sao Paulo"
+      },
+      {
+        "author_name": "Alexandre Chiavegatto Filho",
+        "author_inst": "University of Sao Paulo"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.08.26.20182618",
     "rel_title": "Post-COVID-19 Functional Status: Relation to age, smoking, hospitalization and comorbidities",
@@ -1200724,33 +1199725,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
-  {
-    "rel_doi": "10.1101/2020.08.27.20182980",
-    "rel_title": "The impact of the COVID-19 pandemic on mental health in the general population: a comparison between Germany and the UK",
-    "rel_date": "2020-09-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.27.20182980",
-    "rel_abs": "BackgroundThe COVID-19 pandemic has led to dramatic social and economic changes in daily life. First studies report an impact on mental health of the general population showing increased levels of anxiety, stress and depression. In this study, we compared the impact of the pandemic on two culturally and economically similar European countries: the UK and Germany.\n\nMethodsParticipants (UK=241, German=541) completed an online-survey assessing COVID-19 exposure, impact on financial situation and work, substance and media consumption, mental health using the tSymptom-Check-List-27 (SCL-27) and the Schizotypal Personality Questionnaire.\n\nResultsWe found distinct differences between the two countries. UK responders reported a stronger direct impact on health, financial situation and families. UK responders had higher clinical scores on the SCL-27, and higher prevalence. Interestingly, German responders were less hopeful for an end of the pandemic and more concerned about their life-stability.\n\nConclusionAs 25% of both German and UK responders reported a subjective worsening of the general psychological symptoms and 20-50% of German and UK responders reached the clinical cut-off for depressive and dysthymic symptoms as well as anxieties, it specifically shows the need for tailored intervention systems to support large proportions of the general public.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Franziska Knolle",
-        "author_inst": "Technical University Munich"
-      },
-      {
-        "author_name": "Lisa Ronan",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Graham K Murray",
-        "author_inst": "University of Cambridge"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "psychiatry and clinical psychology"
-  },
   {
     "rel_doi": "10.1101/2020.08.28.20183814",
     "rel_title": "Host-to-Host Airborne Transmission As a Multiphase Flow Problem For Science-Based Social Distance Guidelines",
@@ -1201065,6 +1200039,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "neurology"
   },
+  {
+    "rel_doi": "10.1101/2020.08.27.20183277",
+    "rel_title": "DeepSOCIAL: Social Distancing Monitoring and Infection Risk Assessment in COVID-19 Pandemic",
+    "rel_date": "2020-09-01",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.27.20183277",
+    "rel_abs": "Social distancing is a recommended solution by the World Health Organisation (WHO) to minimise the spread of COVID-19 in public places. The majority of governments and national health authorities have set the 2-meter physical distancing as a mandatory safety measure in shopping centres, schools and other covered areas. In this research, we develop a generic Deep Neural Network-Based model for automated people detection, tracking, and inter-people distances estimation in the crowd, using common CCTV security cameras. The proposed model includes a YOLOv4-based framework and inverse perspective mapping for accurate people detection and social distancing monitoring in challenging conditions, including people occlusion, partial visibility, and lighting variations. We also provide an online risk assessment scheme by statistical analysis of the Spatio-temporal data from the moving trajectories and the rate of social distancing violations. We identify high-risk zones with the highest possibility of virus spread and infections. This may help authorities to redesign the layout of a public place or to take precaution actions to mitigate high-risk zones. The efficiency of the proposed methodology is evaluated on the Oxford Town Centre dataset, with superior performance in terms of accuracy and speed compared to three state-of-the-art methods.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Mahdi Rezaei",
+        "author_inst": "The University of Leeds"
+      },
+      {
+        "author_name": "Mohsen Azarmi",
+        "author_inst": "Qazvin Azad University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health informatics"
+  },
   {
     "rel_doi": "10.1101/2020.08.28.20183863",
     "rel_title": "Unmasking the conversation on masks: Natural language processing for topical sentiment analysis of COVID-19 Twitter discourse",
@@ -1202466,53 +1201463,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pathology"
   },
-  {
-    "rel_doi": "10.1101/2020.08.27.20183434",
-    "rel_title": "Risk factors for severe outcomes of COVID-19: a rapid review",
-    "rel_date": "2020-09-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.27.20183434",
-    "rel_abs": "BackgroundIdentification of high-risk groups is needed to inform COVID-19 vaccine prioritization strategies in Canada. A rapid review was conducted to determine the magnitude of association between potential risk factors and risk of severe outcomes of COVID-19.\n\nMethodsMethods, inclusion criteria, and outcomes were prespecified in a protocol that is publicly available. Ovid MEDLINE(R) ALL, Epistemonikos COVID-19 in L{middle dot}OVE Platform, and McMaster COVID-19 Evidence Alerts, and select websites were searched to 15 June 2020. Studies needed to be conducted in Organisation for Economic Co-operation and Development countries and have used multivariate analyses to adjust for potential confounders. After piloting, screening, data extraction, and quality appraisal were all performed by a single reviewer. Authors collaborated to synthesize the findings narratively and appraise the certainty of the evidence for each risk factor-outcome association.\n\nResultsOf 3,740 unique records identified, 34 were included in the review. The studies included median 596 (range 44 to 418,794) participants with a mean age between 42 and 84 years. Half of the studies (17/34) were conducted in the United States and 19/34 (56%) were rated as good quality. There was low or moderate certainty evidence for a large ([&ge;]2-fold) association with increased risk of hospitalization in people having confirmed COVID-19, for the following risk factors: obesity class III, heart failure, diabetes, chronic kidney disease, dementia, age over 45 years (vs. younger), male gender, Black race/ethnicity (vs. non-Hispanic white), homelessness, and low income (vs. above average). Age over 60 and 70 years may be associated with large increases in the rate of mechanical ventilation and severe disease, respectively. For mortality, a large association with increased risk may exist for liver disease, Bangladeshi ethnicity (vs. British white), age over 45 years (vs. <45 years), age over 80 years (vs. 65-69 years), and male gender in those 20-64 years (but not older). Associations with hospitalization and mortality may be very large ([&ge;]5-fold increased risk) for those aged over 60 years.\n\nConclusionAmong other factors, increasing age (especially >60 years) appears to be the most important risk factor for severe outcomes among those with COVID-19. There is a need for high quality primary research (accounting for multiple confounders) to better understand the level of risk that might be associated with immigration or refugee status, religion or belief system, social capital, substance use disorders, pregnancy, Indigenous identity, living with a disability, and differing levels of risk among children.\n\nPROSPERO registrationCRD42020198001\n\nO_LSTWhat is already knownC_LSTO_LIThe novel nature of COVID-19 means that in many countries there are currently no pre-determined priority groups for the receipt of the eventual COVID-19 vaccine(s).\nC_LIO_LIPrimary research is rapidly emerging, but consensus on who might be at increased risk of severe outcomes from COVID-19 has not been established.\nC_LI\n\nO_LSTWhat this study addsC_LSTO_LIThis rapid review shows that advancing age (>45 years and especially >60 years) may be the most important risk factor for hospitalization and mortality from COVID-19.\nOther important risk factors for severe disease identified by this review include several pre-existing chronic conditions (class III obesity, heart failure, diabetes, chronic kidney disease, liver disease, dementia), male gender, Black race/ethnicity (vs. non-Hispanic white), Bangladeshi ethnicity (vs. British white), low income (vs. high), and homelessness.\nC_LI",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Aireen Wingert",
-        "author_inst": "University of Alberta"
-      },
-      {
-        "author_name": "Jennifer Pillay",
-        "author_inst": "University of Alberta"
-      },
-      {
-        "author_name": "Michelle Gates",
-        "author_inst": "University of Alberta"
-      },
-      {
-        "author_name": "Samantha Guitard",
-        "author_inst": "University of Alberta"
-      },
-      {
-        "author_name": "Sholeh Rahman",
-        "author_inst": "University of Alberta"
-      },
-      {
-        "author_name": "Andrew Beck",
-        "author_inst": "University of Alberta"
-      },
-      {
-        "author_name": "Ben Vandermeer",
-        "author_inst": "University of Alberta"
-      },
-      {
-        "author_name": "Lisa Hartling",
-        "author_inst": "University of Alberta"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.08.28.20183921",
     "rel_title": "The importance of saturating density dependence for predicting SARS-CoV-2 resurgence",
@@ -1203039,6 +1201989,25 @@
     "type": "new results",
     "category": "scientific communication and education"
   },
+  {
+    "rel_doi": "10.1101/2020.08.25.20181347",
+    "rel_title": "Correction of Daily Positivity Rates for contribution of various test protocols being used in a pandemic.",
+    "rel_date": "2020-08-31",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.25.20181347",
+    "rel_abs": "Daily positivity rate (DPR) is a popular metric to judge the prevalence of an infection in the population and the testing response to it as a single number. It has been widely implicated in predicting future course of the SARS CoV-2 pandemic in India. With increasing use of multiple testing protocols with varying sensitivity and specificity in various proportions, the naive calculation loses meaning particularly during comparison between states/countries with large daily variations in contribution of different testing protocols to the testing response. We propose an adjustment to the naive DPR based on the testing parameters and the relative proportional use of each such protocol. Such a correction has become essential for comparing testing response of Indian states from Jun 2020 - Aug 2020 because of steep variations in testing protocol in certain states.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Bhavik Bansal",
+        "author_inst": "All India Institute of Medical Sciences, New Delhi"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.08.24.20180752",
     "rel_title": "Disease-dependent interaction policies to support health and economic outcomes during the COVID-19 epidemic",
@@ -1204632,101 +1203601,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.08.25.20181909",
-    "rel_title": "ICU Outcomes and Survival in Patients with Severe COVID-19 in the Largest Health Care System in Central Florida",
-    "rel_date": "2020-08-31",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.25.20181909",
-    "rel_abs": "BackgroundObservational studies have consistently described poor clinical outcomes and increased ICU mortality in patients with severe coronavirus disease 2019 (COVID-19) who require mechanical ventilation (MV). Our study describes the clinical characteristics and outcomes of patients with severe COVID-19 admitted to ICU in the largest health care system in the state of Florida, United States.\n\nMethodsRetrospective cohort study of patients admitted to ICU due to severe COVID-19 in AdventHealth health system in Orlando, Florida from March 11th until May 18th, 2020. Patients were characterized based on demographics, baseline comorbidities, severity of illness, medical management including experimental therapies, laboratory markers and ventilator parameters. Major clinical outcomes analyzed at the end of the study period were: hospital and ICU length of stay, MV-related mortality and overall hospital mortality of ICU patients.\n\nResultsOut of total of 1283 patients with COVID-19, 131 (10.2%) met criteria for ICU admission (median age: 61 years [interquartile range {IQR}, 49.5-71.5]; 35.1% female). Common comorbidities were hypertension (84; 64.1%), and diabetes (54; 41.2%). Of the 131 ICU patients, 109 (83.2%) required MV and 9 (6.9%) received ECMO. Lower positive end expiratory pressure (PEEP) were observed in survivors [9.2 (7.7-10.4)] vs non-survivors [10 (9.1-12.9] p= 0.004]. Compared to non-survivors, survivors had a longer MV length of stay (LOS) [14 (IQR 8-22) vs 8.5 (IQR 5-10.8) p< 0.001], Hospital LOS [21 (IQR 13-31) vs 10 (7-1) p< 0.001] and ICU LOS [14 (IQR 7-24) vs 9.5 (IQR 6-11), p < 0.001]. The overall hospital mortality and MV-related mortality were 19.8% and 23.8% respectively. After exclusion of hospitalized patients, the hospital and MV-related mortality rates were 21.6% and 26.5% respectively.\n\nConclusionsOur study demonstrates an important improvement in mortality of patients with severe COVID-19 who required ICU admission and MV in comparison to previous observational reports and emphasize the importance of standard of care measures in the management of COVID-19.",
-    "rel_num_authors": 20,
-    "rel_authors": [
-      {
-        "author_name": "Eduardo Oliveira",
-        "author_inst": "AdventHealth Orlando"
-      },
-      {
-        "author_name": "Amay Parikh",
-        "author_inst": "AdventHealth Orlando"
-      },
-      {
-        "author_name": "Arnaldo Lopez-Ruiz",
-        "author_inst": "AdventHealth Orlando"
-      },
-      {
-        "author_name": "Maria Carrillo",
-        "author_inst": "AdventHealth Orlando"
-      },
-      {
-        "author_name": "Joshua Goldberg",
-        "author_inst": "AdventHealth Orlando"
-      },
-      {
-        "author_name": "Martin Cearras",
-        "author_inst": "AdventHealth Orlando"
-      },
-      {
-        "author_name": "Khaled Fernainy",
-        "author_inst": "AdventHealth Orlando"
-      },
-      {
-        "author_name": "Sonja Andersen",
-        "author_inst": "AdventHealth Orlando"
-      },
-      {
-        "author_name": "Luis Mercado",
-        "author_inst": "AdventHealth Orlando"
-      },
-      {
-        "author_name": "Jian Guan",
-        "author_inst": "AdventHealth Orlando"
-      },
-      {
-        "author_name": "Hammad Zafar",
-        "author_inst": "AdventHealth Orlando"
-      },
-      {
-        "author_name": "Patricia Louzon",
-        "author_inst": "AdventHealth Orlando"
-      },
-      {
-        "author_name": "Amy Carr",
-        "author_inst": "AdventHealth Orlando"
-      },
-      {
-        "author_name": "Natasha Baloch",
-        "author_inst": "AdventHealth Orlando"
-      },
-      {
-        "author_name": "Richard Pratley",
-        "author_inst": "AdventHealth Orlando"
-      },
-      {
-        "author_name": "Scott Silvestry",
-        "author_inst": "AdventHealth Orlando"
-      },
-      {
-        "author_name": "Vincent Hsu",
-        "author_inst": "AdventHealth Orlando"
-      },
-      {
-        "author_name": "Jason Sniffen",
-        "author_inst": "AdventHealth Orlando"
-      },
-      {
-        "author_name": "Victor Herrera",
-        "author_inst": "Adventhealth Orlando"
-      },
-      {
-        "author_name": "Neil Finkler",
-        "author_inst": "AdventHealth Orlando"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "intensive care and critical care medicine"
-  },
   {
     "rel_doi": "10.1101/2020.08.25.20181792",
     "rel_title": "Mortality & COVID-19: A Snapshot of a Tertiary Care Facility in Pakistan",
@@ -1205001,6 +1203875,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.08.25.20182113",
+    "rel_title": "Post-infection depression, anxiety and PTSD: a retrospective cohort study with mild COVID-19 patients",
+    "rel_date": "2020-08-31",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.25.20182113",
+    "rel_abs": "BackgroundIt remains unclear whether COVID-19 is associated with psychiatric symptoms during or after the acute illness phase. Being affected by the disease exposes the individual to an uncertain prognosis and a state of quarantine. These factors can predispose individuals to the development of mental symptoms during or after the acute phase of the disease. There is a need for prospective studies assessing mental health symptoms in COVID-19 patients in the post-infection period.\n\nMethodsIn this retrospective cohort study, nasopharyngeal swabs for COVID-19 tests were collected at patients homes under the supervision of trained healthcare personnel. Patients who tested positive for COVID-19 and were classified as mild cases (N=895) at treatment intake were further assessed for the presence of mental health disorders (on average, 56.6 days after the intake). We investigated the association between the number of COVID-19 symptoms at intake and depression, anxiety and PTSD, adjusting for previous mental health status, time between baseline and outcome, and other confounders. Multivariate logistic regression and generalized linear models were employed for categorical and continuous outcomes, respectively.\n\nFindingsDepression, anxiety and PTSD were reported by 26.2% (N=235), 22.4% (N=201), and 17.3% (N=155) of the sample. Reporting an increased number of COVID-related symptoms was associated with depression (aOR=1.059;95%CI=1.002-1.119), anxiety (aOR=1.072;95%CI=1.012-1.134), and PTSD (aOR=1.092;95%CI=1.024-1.166). Sensitivity analyses supported findings for both continuous and categorical measures.\n\nInterpretationExposure to an increased number of COVID-19 symptoms may predispose individuals to depression, anxiety and PTSD after the acute phase of the disease. These patients should be monitored for the development of mental health disorders after COVID-19 treatment discharge. Early interventions, such as brief interventions of psychoeducation on coping strategies, could benefit these individuals.\n\nFundingThe city health department of Sao Caetano do Sul (Secretaria Municipal de Saude da Prefeitura de Sao Caetano do Sul) funded the establishment and implementation of the COVID-19 platform.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Flavia Ismael",
+        "author_inst": "Universidade Municipal de Sao Caetano do Sul, Sao Caetano do Sul, SP, Brazil"
+      },
+      {
+        "author_name": "Joao C. S. Bizario",
+        "author_inst": "Faculdade de Medicina de Olinda, Olinda, PE, Brazil"
+      },
+      {
+        "author_name": "Tatiane Battagin",
+        "author_inst": "Universidade Municipal de Sao Caetano do Sul, Sao Caetano do Sul, SP, Brazil"
+      },
+      {
+        "author_name": "Beatriz Zaramella",
+        "author_inst": "Universidade Municipal de Sao Caetano do Sul, Sao Caetano do Sul, SP, Brazil"
+      },
+      {
+        "author_name": "Fabio E Leal",
+        "author_inst": "Universidade Municipal de Sao Caetano do Sul, Sao Caetano do Sul, SP, Brazil"
+      },
+      {
+        "author_name": "Julio Torales",
+        "author_inst": "Department of Psychiatry, School of Medical Sciences, National University of Asuncion, Asuncion, Paraguay"
+      },
+      {
+        "author_name": "Antonio Ventriglio",
+        "author_inst": "Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy"
+      },
+      {
+        "author_name": "Megan E. Marziali",
+        "author_inst": "Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, U.S."
+      },
+      {
+        "author_name": "Silvia S. Martins",
+        "author_inst": "Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, U.S."
+      },
+      {
+        "author_name": "Joao M. Castaldelli-Maia",
+        "author_inst": "Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, U.S."
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "psychiatry and clinical psychology"
+  },
   {
     "rel_doi": "10.1101/2020.08.25.20181420",
     "rel_title": "The Role of Air Conditioning in the Diffusion of Sars-CoV-2 in Indoor Environments: a First Computational Fluid Dynamic Model, based on Investigations performed at the Vatican State Childrens Hospital.",
@@ -1206566,37 +1205495,6 @@
     "type": "new results",
     "category": "developmental biology"
   },
-  {
-    "rel_doi": "10.1101/2020.08.29.272963",
-    "rel_title": "Establishment of murine hybridoma cells producing antibodies against spike protein of SARS-CoV-2",
-    "rel_date": "2020-08-29",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.29.272963",
-    "rel_abs": "In 2020 the world faced the pandemic of COVID-19 - severe acute respiratory syndrome caused by a new type of coronavirus named SARS-CoV-2. To stop the spread of the disease, it is crucial to create molecular tools allowing to investigate, diagnose and treat COVID-19. One of such tools are monoclonal antibodies (mAbs). In this study we describe the development of hybridoma cells that can produce mouse mAbs against receptor binding domain of SARS-CoV-2 spike (S) protein. These mAbs are able to specifically detect native and denaturized S protein in all tested applications including immunoblotting, immunofluorescence staining and enzyme-linked immunosorbent assay. In addition, we showed that the obtained mAbs decreased infection rate of human cells by SARS-CoV-2 pseudovirus particles in in vitro experiments. Finally, we determined the amino acid sequence of light and heavy chains of the mAbs. This information will allow to use the corresponding peptides to establish genetically engineered therapeutic antibodies. To date multiple mAbs against SARS-CoV-2 proteins have been established, however due to the restrictions caused by pandemic, it is imperative to have a local source of the antibodies suitable for researches and diagnostics of COVID-19. Moreover, as each mAb has a unique binding sequence, bigger sets of various antibodies will allow to detect SARS-CoV-2 proteins even if the virus acquires novel mutations.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Nadezhda V Antipova",
-        "author_inst": "Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry"
-      },
-      {
-        "author_name": "Tatyana D Larionova",
-        "author_inst": "Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry"
-      },
-      {
-        "author_name": "Michail I Shakhparonov",
-        "author_inst": "Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry"
-      },
-      {
-        "author_name": "Marat S Pavlyukov",
-        "author_inst": "Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "biochemistry"
-  },
   {
     "rel_doi": "10.1101/2020.08.28.272955",
     "rel_title": "Global BioID-based SARS-CoV-2 proteins proximal interactome unveils novel ties between viral polypeptides and host factors involved in multiple COVID19-associated mechanisms",
@@ -1207063,6 +1205961,25 @@
     "type": "new results",
     "category": "genetics"
   },
+  {
+    "rel_doi": "10.1101/2020.08.26.269118",
+    "rel_title": "Fractal signatures of SARS-CoV2 coronavirus, the indicator matrix, the fractal dimension and the 2D directional wavelet transform: A comparative study with SARS-CoV, MERS-CoV and SARS-like coronavirus.",
+    "rel_date": "2020-08-28",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.26.269118",
+    "rel_abs": "The main goal of this paper is to show the 2D fractal signatures of SARS-CoV2 coronavirus, indicator matrixes maps showing the concentration of nucleotide acids are built form the RNA sequences, and then the fractal dimension and 2D Directional Wavelet Transform (DCWT) are calculated. Analysis of 21 RNA sequences downloaded from NCBI database shows that indicator matrixes and 2D DCWT exhibit the same patterns with different positions, while the fractal dimensions are oscillating around 1.60. A comparison with SARS-CoV, MERS-CoV and SARS-like Coronavirus shows slightly different fractal dimensions, however the indicator matrix and 2D DCWT exhibit the same patterns for the couple (SARS-CoV2, SARS-CoV) and (MERS-CoV, SARS-like) Coronavirus. Obtained results show that SARS-CoV2 is probably a result of SARS-CoV mutation process.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Sid-Ali Ouadfeul",
+        "author_inst": "Algerian Petroleum Institute"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "new results",
+    "category": "genomics"
+  },
   {
     "rel_doi": "10.1101/2020.08.27.270835",
     "rel_title": "Secondary analysis of transcriptomes of SARS-CoV-2 infection models to characterize COVID-19",
@@ -1208299,33 +1207216,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.08.24.20180745",
-    "rel_title": "Anxiety and media exposure during COVID-19 outbreak in Kuwait",
-    "rel_date": "2020-08-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.24.20180745",
-    "rel_abs": "BackgroundRising fear and panic among public during COVID19 pandemic increase concern regarding anxiety cases in Kuwait. Media capture our attention during this period looking for daily virus update lead to more fear. Our purpose of this study to examine the relationship between anxiety and media exposure among Kuwaiti during COVID19 outbreak\n\nMethodcross sectional study among Kuwaiti citizen between age23-55yrs old was conducted from April,21,2020 to May,15,2020 using online survey. Total of 1230 participants involve in the current study after exclusion criteria removed. Beside demographic data and media exposure anxiety was assessed using generalized anxiety disorder scale GAD-7, multivariable regression was used to identify the correlation between anxiety and media exposure\n\nResultthe result show that there is positive correlation between media exposure and anxiety during COVID19 outbreak in Kuwait (p<.001), furthermore it revealed that there is significant relationship between the frequency of exposure and anxiety(<.001)\n\nConclusionfrom this study we can understand that during COVID19 pandemic exposure to media can cause anxiety therefore measures should be taken by the governments to fight misinformation and physician should pay more attention to mental health disease during this period.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "lulua falah alasousi",
-        "author_inst": "KIMS"
-      },
-      {
-        "author_name": "sara alhammouri",
-        "author_inst": "KIMS"
-      },
-      {
-        "author_name": "sara alabdulhadi",
-        "author_inst": "KIMS"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "primary care research"
-  },
   {
     "rel_doi": "10.1101/2020.08.24.20180729",
     "rel_title": "Convalescent Plasma in treatment of COVID-19: A review of evidence for a living systematic benefit-risk assessment",
@@ -1208560,6 +1207450,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.08.24.20170175",
+    "rel_title": "Evidence of SARS-CoV-2 transcriptional activity in cardiomyocytes of COVID-19 patients without clinical signs of cardiac involvement",
+    "rel_date": "2020-08-26",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.24.20170175",
+    "rel_abs": "BackgroundCardiovascular complication in patients affected by novel Coronavirus respiratory disease (COVID-19) are increasingly recognized. However, although a cardiac tropism of SARS-CoV-2 for inflammatory cells in autopsy heart samples of COVID-19 patients has been reported, the presence of the virus in cardiomyocytes has not been documented yet.\n\nMethodsWe investigated for SARS-CoV-2 presence in heart tissue autopsies of 6 consecutive COVID-19 patients deceased for respiratory failure showing no signs of cardiac involvement and with no history of heart disease. Cardiac autopsy samples were analysed by digital PCR, Western blot, immunohistochemistry, immunofluorescence, RNAScope, and transmission electron microscopy assays.\n\nResultsThe presence of SARS-CoV-2 into cardiomyocytes was invariably detected. A variable pattern of cardiomyocytes injury was observed, spanning from the absence of cell death and subcellular alterations hallmarks to the intracellular oedema and sarcomere ruptures. In addition, we found active viral transcription in cardiomyocytes, by detecting both sense and antisense SARS-CoV-2 spike RNA.\n\nConclusionsIn this analysis of autopsy cases, the presence of SARS-CoV-2 into cardiomyocytes, determining variable patterns of intracellular involvement, has been documented. All these findings suggest the need of a cardiologic surveillance even in survived COVID-19 patients not displaying a cardiac phenotype, in order to monitor potential long-term cardiac sequelae.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Gaetano Pietro Bulfamante",
+        "author_inst": "University of Milan"
+      },
+      {
+        "author_name": "Gianluca Lorenzo Perrucci",
+        "author_inst": "Centro Cardiologico Monzino-IRRCS"
+      },
+      {
+        "author_name": "Monica Falleni",
+        "author_inst": "University of Milan"
+      },
+      {
+        "author_name": "Elena Sommariva",
+        "author_inst": "Centro Cardiologico Monzino-IRCCS"
+      },
+      {
+        "author_name": "Delfina Tosi",
+        "author_inst": "University of Milan"
+      },
+      {
+        "author_name": "Carla Martinelli",
+        "author_inst": "University of Milan"
+      },
+      {
+        "author_name": "Paola Songia",
+        "author_inst": "Centro Cardiologico Monzino-IRCCS"
+      },
+      {
+        "author_name": "Paolo Poggio",
+        "author_inst": "Centro Cardiologico Monzino-IRCCS"
+      },
+      {
+        "author_name": "Stefano Carugo",
+        "author_inst": "University of Milan"
+      },
+      {
+        "author_name": "Giulio Pompilio",
+        "author_inst": "Centro Cardiologico Monzino-IRCCS"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "cardiovascular medicine"
+  },
   {
     "rel_doi": "10.1101/2020.08.24.20174367",
     "rel_title": "COVID-19 and heart medications: What's the connection?",
@@ -1210057,69 +1209002,6 @@
     "type": "new results",
     "category": "molecular biology"
   },
-  {
-    "rel_doi": "10.1101/2020.08.26.267997",
-    "rel_title": "AI aided design of epitope-based vaccine for the induction of cellular immune responses against SARS-CoV-2",
-    "rel_date": "2020-08-26",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.26.267997",
-    "rel_abs": "The heavy burden imposed by the COVID-19 pandemic on our society triggered the race towards the development of therapies or preventive strategies. Among these, antibodies and vaccines are particularly attractive because of their high specificity, low probability of drug-drug interaction, and potentially long-standing protective effects. While the threat at hand justifies the pace of research, the implementation of therapeutic strategies cannot be exempted from safety considerations. There are several potential adverse events reported after the vaccination or antibody therapy, but two are of utmost importance: antibody-dependent enhancement (ADE) and cytokine storm syndrome (CSS). On the other hand, the depletion or exhaustion of T-cells has been reported to be associated with worse prognosis in COVID-19 patients. This observation suggests a potential role of vaccines eliciting cellular immunity, which might simultaneously limit the risk of ADE and CSS. Such risk was proposed to be associated with FcR-induced activation of proinflammatory macrophages (M1) by Fu et al. 2020 and Iwasaki et al. 2020. All aspects of the newly developed vaccine (including the route of administration, delivery system, and adjuvant selection) may affect its effectiveness and safety. In this work we use a novel in silico approach (based on AI and bioinformatics methods) developed to support the design of epitope-based vaccines. We evaluated the capabilities of our method for predicting the immunogenicity of epitopes. Next, the results of our approach were compared with other vaccine-design strategies reported in the literature. The risk of immuno-toxicity was also assessed. The analysis of epitope conservation among other Coronaviridae was carried out in order to facilitate the selection of peptides shared across different SARS-CoV-2 strains and which might be conserved in emerging zootic coronavirus strains. Finally, the potential applicability of the selected epitopes for the development of a vaccine eliciting cellular immunity for COVID-19 was discussed, highlighting the benefits and challenges of such an approach.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Giovanni Mazzocco",
-        "author_inst": "Ardigen, Krakow, Poland"
-      },
-      {
-        "author_name": "Iga Niemiec",
-        "author_inst": "Ardigen, Krakow, Poland"
-      },
-      {
-        "author_name": "Alexander Myronov",
-        "author_inst": "Ardigen, Krakow, Poland; Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland"
-      },
-      {
-        "author_name": "Piotr Skoczylas",
-        "author_inst": "Ardigen, Krakow, Poland"
-      },
-      {
-        "author_name": "Jan Kaczmarczyk",
-        "author_inst": "Ardigen, Krakow, Poland"
-      },
-      {
-        "author_name": "Anna Sanecka-Duin",
-        "author_inst": "Ardigen, Krakow, Poland"
-      },
-      {
-        "author_name": "Katarzyna Gruba",
-        "author_inst": "Ardigen, Krakow, Poland; Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland"
-      },
-      {
-        "author_name": "Paulina Kr\u00f3l",
-        "author_inst": "Ardigen, Krakow, Poland"
-      },
-      {
-        "author_name": "Micha\u0142 Drwal",
-        "author_inst": "Ardigen, Krakow, Poland"
-      },
-      {
-        "author_name": "Marian Szczepanik",
-        "author_inst": "Department of Medical Biology, Faculty of Health Sciences, Jagiellonian University Medical College, Krakow, Poland"
-      },
-      {
-        "author_name": "Krzysztof Pyr\u0107",
-        "author_inst": "Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland"
-      },
-      {
-        "author_name": "Piotr St\u0119pniak",
-        "author_inst": "Ardigen"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "bioinformatics"
-  },
   {
     "rel_doi": "10.1101/2020.08.26.267724",
     "rel_title": "Epitopes targeted by T cells in convalescent COVID-19 patients",
@@ -1210458,6 +1209340,97 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2020.08.22.20179754",
+    "rel_title": "Monitoring COVID-19 transmission risks by RT-PCR tracing of droplets in hospital and living environments",
+    "rel_date": "2020-08-25",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.22.20179754",
+    "rel_abs": "SARS-CoV-2 environmental contamination occurs through droplets and biological fluids released in the surroundings from patients or asymptomatic carriers. Surfaces and objects contaminated by saliva or nose secretions represent a risk for indirect transmission of COVID-19. We assayed surfaces from hospital and living spaces to identify the presence of viral RNA and the spread of fomites in the environment. Anthropic contamination by droplets and biological fluids was monitored by detecting the microbiota signature using multiplex RT-PCR on selected species and massive sequencing on 16S-amplicons.\n\nA total of 92 samples (flocked swab) were collected from critical areas during the pandemic, including indoor (3 hospitals and 3 public buildings) and outdoor surfaces exposed to anthropic contamination (handles and handrails, playgrounds). Traces of biological fluids were frequently detected in spaces open to the public and on objects that are touched with the hands (>80%). However, viral RNA was not detected in hospital wards or other indoor and outdoor surfaces either in the air system of a COVID-hospital, but only in the surroundings of an infected patient, in consistent association with droplets traces and fomites. Handled objects accumulated the highest level of multiple contaminations by saliva, nose secretions and faecal traces, further supporting the priority role of handwashing in prevention.\n\nIn conclusion, anthropic contamination by droplets and biological fluids is widespread in spaces open to the public and can be traced by RT-PCR. Monitoring fomites can support evaluation of indirect transmission risks for Coronavirus or other flu-like viruses in the environment.\n\nImportanceSeveral studies searched for SARS-CoV-2 in the environment because saliva and nasopharyngeal droplets can land on objects and surfaces creating fomites. However, the ideal indicator would be the detection of the biofluid. This approach was not yet considered, but follows a traditional principle in hygiene, using indicators rather than pathogens. We searched for viral RNA but also for droplets on surfaces at risk. For the first time, we propose to monitor droplets thorugh their microbiota, by RT-PCR or NGS.\n\nEven if performed during the pandemic, SARS-CoV-2 wasnt largely spread on surfaces, unless in proximity of an infectious patient. However, anthropic contamination was frequently at high level, suggesting a putative marker for indirect transmission and risk assessment. Moreover, all SARS-CoV-2-contaminated surfaces showed the droplets microbiota.\n\nFomites detection may have an impact on public health, supporting prevention of indirect transmission also for other communicable diseases such as Flu and Flu-like infections.\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC=\"FIGDIR/small/20179754v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (30K):\norg.highwire.dtl.DTLVardef@b15c11org.highwire.dtl.DTLVardef@1398ddorg.highwire.dtl.DTLVardef@98f501org.highwire.dtl.DTLVardef@1fd5282_HPS_FORMAT_FIGEXP  M_FIG C_FIG",
+    "rel_num_authors": 19,
+    "rel_authors": [
+      {
+        "author_name": "Andrea Piana",
+        "author_inst": "Department of Medical, Surgical and Experimental Sciences, University of Sassari"
+      },
+      {
+        "author_name": "Maria Eugenia Colucci",
+        "author_inst": "Department of Medicine and Surgery, University Hospital, University of Parma"
+      },
+      {
+        "author_name": "Federica Valeriani",
+        "author_inst": "Department of Movement, Human and Health Sciences, Unit of Public Health-Laboratory of Epidemiology and Biotechnologies, University of Rome Foro Italico"
+      },
+      {
+        "author_name": "Adriano Marcolongo",
+        "author_inst": "Sant Andrea Hospital, Sapienza University of Rome"
+      },
+      {
+        "author_name": "Giovanni Sotgiu",
+        "author_inst": "Department of Medical, Surgical and Experimental Sciences, University of Sassari"
+      },
+      {
+        "author_name": "Cesira Pasquarella",
+        "author_inst": "Department of Medicine and Surgery, University Hospital, University of Parma"
+      },
+      {
+        "author_name": "Lory Marika Margarucci",
+        "author_inst": "Department of Movement, Human and Health Sciences, Unit of Public Health-Laboratory of Epidemiology and Biotechnologies, University of Rome Foro Italico"
+      },
+      {
+        "author_name": "Andrea Petrucca",
+        "author_inst": "Sant Andrea Hospital, Sapienza University of Rome"
+      },
+      {
+        "author_name": "Gianluca Gianfranceschi",
+        "author_inst": "Department of Movement, Human and Health Sciences, Unit of Public Health-Laboratory of Epidemiology and Biotechnologies, University of Rome Foro Italico"
+      },
+      {
+        "author_name": "Sergio Babudieri",
+        "author_inst": "Department of Medical, Surgical and Experimental Sciences, University of Sassari"
+      },
+      {
+        "author_name": "Pietro Vitali",
+        "author_inst": "Department of Medicine and Surgery, University Hospital, University of Parma"
+      },
+      {
+        "author_name": "Giuseppe D'Ermo",
+        "author_inst": "Department of Surgery, Sapienza University of Rome"
+      },
+      {
+        "author_name": "Assunta Bizzarro",
+        "author_inst": "Department of Medicine and Surgery, University Hospital, University of Parma"
+      },
+      {
+        "author_name": "Flavio De Maio",
+        "author_inst": "Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie-Sezione di Microbiologia, Universita Cattolica del Sacro Cuore"
+      },
+      {
+        "author_name": "Matteo Vitali",
+        "author_inst": "Department of Public Health and Infectious Diseases, University of Rome La Sapienza"
+      },
+      {
+        "author_name": "Antonio Azara",
+        "author_inst": "Department of Medical, Surgical and Experimental Sciences, University of Sassari"
+      },
+      {
+        "author_name": "Ferdinando Romano",
+        "author_inst": "Department of Public Health and Infectious Diseases, University of Rome La Sapienza"
+      },
+      {
+        "author_name": "Maurizio Simmaco",
+        "author_inst": "Sant Andrea Hospital, Sapienza University of Rome"
+      },
+      {
+        "author_name": "Vincenzo Romano Spica",
+        "author_inst": "University of Rome \"Foro Italico\""
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.08.22.20179960",
     "rel_title": "Impacts of K-12 school reopening on the COVID-19 epidemic in Indiana, USA",
@@ -1211791,37 +1210764,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "occupational and environmental health"
   },
-  {
-    "rel_doi": "10.1101/2020.08.23.20180299",
-    "rel_title": "The health sector cost of different policy responses to COVID-19 in low- and middle- income countries",
-    "rel_date": "2020-08-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.23.20180299",
-    "rel_abs": "Much attention has focussed in recent months on the impact that COVID-19 has on health sector capacity, including critical care bed capacity and resources such as personal protective equipment. However, much less attention has focussed on the overall cost to health sectors, including the full human resource costs and the health system costs to address the pandemic. Here we present estimates of the total costs of COVID-19 response in low- and middle-income countries for different scenarios of COVID-19 mitigation over a one year period. We find costs vary substantially by setting, but in some settings even mitigation scenarios place a substantial fiscal impact on the health system. We conclude that the choices facing many low- and middle-income countries, without further rapid emergency financial support, are stark, between fully funding an effective COVID-19 reponse or other core essential health services.\n\nO_TEXTBOXThis is preliminary report that has not yet been peer reviewed. These estimates should not yet guide policy in specific countries nor be reported as established information. We are placing these in the public domain to inform those who are estimaing Covid costs in low- and middle-income countries about the methods and assumptions required; higlight the broad level of fiscal impact and to invite comments for others working in this field, prior to submission to peer review publication.\n\nThese estimates have been subjected to a detailed validation and error checking process internally. Nevertheless, given the dearth of data to inform Covid cost estimates at this time, our results depend on a range of assumptions. Comments and suggestions to improve this work are welcomed and can be sent to the authors below\n\nC_TEXTBOX",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Sergio Torres Rueda",
-        "author_inst": "London School of Hygiene andTropical Medicine"
-      },
-      {
-        "author_name": "Sedona Sweeney",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Fiammetta Bozzani",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Anna Vassall",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health economics"
-  },
   {
     "rel_doi": "10.1101/2020.08.23.20180497",
     "rel_title": "Bayesian Estimation of the Seroprevalence of Antibodies to SARS-CoV-2",
@@ -1212048,6 +1210990,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.08.23.20177501",
+    "rel_title": "Therapeutic Prospects for Th-17 Cell Immune Storm Syndrome and Neurological Symptoms in COVID-19: Thiamine Efficacy and Safety, In-vitro Evidence and Pharmacokinetic Profile",
+    "rel_date": "2020-08-25",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.23.20177501",
+    "rel_abs": "IntroductionEmerging infectious diseases, especially the coronavirus disease identified in 2019 (COVID-19), can be complicated by a severe exacerbation in the Th17 cell-mediated IL-17 proinflammatory immune storm. This enhanced immune response plays a major role in mortality and morbidity, including neurological symptoms. We hypothesized that countering the cytokine storm with thiamine may have therapeutic efficacy in lowering the Th17 cell proinflammatory response. We used an in vitro study and corroborated those results in disease controls (DC). We developed an effective dose range and model for key pharmacokinetic measures with the potential of targeting the cytokine storm and neurological symptoms of COVID-19.\n\nStudy Participants and MethodsWe investigated the effect of a three-week 200 mg dose of thiamine in lowering the Th17 response in sixteen DC (proinflammatory origin due to heavy alcohol drinking) patients; and eight healthy control/volunteers (HV) as a pilot clinical-translational investigation. To further investigate, we performed an in vitro study evaluating the effectiveness of thiamine treatment in lowering the Th17 proinflammatory response in a mouse macrophage cell line (RAW264.7) treated with ethanol. In this in vitro study, 100 mg/day equivalent (0.01 {micro}g/ml) thiamine was used. Based on recent publications, we compared the results of the IL-17 response from our clinical and in vitro study to those found in other proinflammatory disease conditions (metabolic conditions, septic shock, viral infections and COVID-19), including symptoms, and dose ranges of effective and safe administration of thiamine. We developed a dose range and pharmacokinetic profile for thiamine as a novel intervention strategy in COVID-19 to alleviate the effects of the cytokine storm and neurological symptoms.\n\nResultsThe DC group showed significantly elevated proinflammatory cytokines compared to HV. Three-week of 200 mg daily thiamine treatment significantly lowered the baseline IL-17 levels while increased IL-22 levels (anti-inflammatory response). This was validated by an in vitro macrophage response using a lower thiamine dose equivalent (100 mg), which resulted in attenuation of IL-17 and elevation of IL-22 at the mRNA level compared to the ethanol-only treated group. In humans, a range of 79-474 mg daily of thiamine was estimated to be effective and safe as an intervention for the COVID-19 cytokine storm. A literature review showed that several neurological symptoms of COVID-19 (which exist in 45.5% of the severe cases) occur in other viral infections and neuroinflammatory states that may also respond to thiamine treatment.\n\nDiscussionThe Th17 mediated IL-17 proinflammatory response can potentially be attenuated by thiamine. Thiamine, a very safe drug even at very high doses, could be repurposed for treating the cytokine/immune storm of COVID-19 and the subsequent neurological symptoms observed in COVID-19 patients. Further studies using thiamine as an interventional/prevention strategy in severe COVID-19 patients could identify its precise anti-inflammatory role.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Vatsalya Vatsalya",
+        "author_inst": "University of Louisville"
+      },
+      {
+        "author_name": "Fengyuan Li",
+        "author_inst": "University of Louisville"
+      },
+      {
+        "author_name": "Jane C Frimodig",
+        "author_inst": "University of Louisville"
+      },
+      {
+        "author_name": "Khushboo S Gala",
+        "author_inst": "University of Louisville"
+      },
+      {
+        "author_name": "Shweta Srivastava",
+        "author_inst": "University of Louisville"
+      },
+      {
+        "author_name": "Maiying Kong",
+        "author_inst": "University of Louisville"
+      },
+      {
+        "author_name": "Vijay A Ramchandani",
+        "author_inst": "National Institute on Alcohol Abuse and Alcoholism"
+      },
+      {
+        "author_name": "Wenke Feng",
+        "author_inst": "University of Louisville"
+      },
+      {
+        "author_name": "Xiang Zhang",
+        "author_inst": "University of Louisville"
+      },
+      {
+        "author_name": "Craig J McClain",
+        "author_inst": "University of Louisville"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.08.24.20176792",
     "rel_title": "Temporal increase in D614G mutation of SARS-CoV-2 in the Middle East and North Africa: Phylogenetic and mutation analysis study",
@@ -1213640,61 +1212637,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.08.24.264564",
-    "rel_title": "Flagellin from Pseudomonas aeruginosa increases the expression of the SARS-CoV2 entry protease TMPRSS2 in airway epithelial cells",
-    "rel_date": "2020-08-24",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.24.264564",
-    "rel_abs": "The major challenge of the COVID-19 health crisis is to identify the factors of susceptibility to SARS-Cov2 in order to adapt the recommendations to the populations and to reduce the risk of getting COVID-19 to the most vulnerable people especially those having chronic respiratory diseases including cystic fibrosis (CF). Airway epithelial cells (AEC) are playing a critical role in the immune response and in COVID-19 severity. SARS-CoV-2 infects the airways through ACE2 receptor and the host protease TMPRSS2 was shown to play a major role in SARS-CoV-2 infectivity. Here, we show that the main component of P. aeruginosa flagella, ie. flagellin is able to increase TMPRSS2 expression in AEC, and even more in those deficient for CFTR. Importantly, this increased TMPRSS2 expression is associated with an increase in the level of SARS-CoV-2 infection. Considering the urgency of the health situation, this result is of major significance for patients with CF which are frequently infected and colonized by P. aeruginosa during the course of the disease.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Manon Ruffin",
-        "author_inst": "Inserm"
-      },
-      {
-        "author_name": "Jeanne Bigot",
-        "author_inst": "Inserm"
-      },
-      {
-        "author_name": "Claire Calmel",
-        "author_inst": "Inserm"
-      },
-      {
-        "author_name": "Julia Mercier",
-        "author_inst": "Inserm"
-      },
-      {
-        "author_name": "Andres Pizzorno",
-        "author_inst": "Centre International de Recherche en Infectiologie (CIRI)"
-      },
-      {
-        "author_name": "Manuel Rosa-Calatrava",
-        "author_inst": "Centre International de Recherche en Infectiologie (CIRI)"
-      },
-      {
-        "author_name": "Harriet Corvol",
-        "author_inst": "AP-HP"
-      },
-      {
-        "author_name": "Viviane Balloy",
-        "author_inst": "Inserm"
-      },
-      {
-        "author_name": "Olivier Terrier",
-        "author_inst": "Centre International de Recherche en Infectiologie"
-      },
-      {
-        "author_name": "Loic Guillot",
-        "author_inst": "Inserm"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "pathology"
-  },
   {
     "rel_doi": "10.1101/2020.08.24.265090",
     "rel_title": "Induction of SARS-CoV-2 protein S-specific CD8+ T cells in the lungs of gp96-Ig-S vaccinated mice",
@@ -1214009,6 +1212951,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "hematology"
   },
+  {
+    "rel_doi": "10.1101/2020.08.21.20177923",
+    "rel_title": "Prevalence and outcome of Covid-19 infection in cancer patients: a national VA study",
+    "rel_date": "2020-08-24",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.21.20177923",
+    "rel_abs": "BackgroundEmerging data suggest variability in susceptibility and outcome to Covid-19 infection. Identifying the risk-factors associated with infection and outcomes in cancer patients is necessary to develop healthcare recommendations.\n\nMethodsWe analyzed electronic health records of the US National Veterans Administration healthcare system and assessed the prevalence of Covid-19 infection in cancer patients. We evaluated the proportion of cancer patients tested for Covid-19 and their confirmed positivity, with clinical characteristics, and outcome, and stratified by demographics, comorbidities, cancer treatment and cancer type.\n\nResultsOf 22914 cancer patients tested for Covid-19, 1794 (7.8%) were positive. The prevalence of Covid-19 was similar across all ages. Higher prevalence was observed in African-American (AA) (15%) compared to white (5.5%; P<.001), in Hispanic vs non-Hispanic population and in patients with hematologic malignancy compared to those with solid tumors (10.9% vs 7.7%; P<.001). Conversely, prevalence was lower in current smoker patients, patients with other co-morbidities and having recently received cancer therapy (< 6 months). The Covid-19 attributable mortality was 10.9%. Highest mortality rates were observed in older patients, those with renal dysfunction, higher Charlson co-morbidity score and with certain cancer types. Recent (< 6 months) or past treatment did not influence mortality. Importantly, AA patients had 3.5-fold higher Covid-19 attributable hospitalization, however had similar mortality rate as white patients.\n\nConclusionPre-existence of cancer affects both susceptibility to Covid-19 infection and eventual outcome. The overall Covid-19 attributable mortality in cancer patients is affected by age, co-morbidity and specific cancer types, however, race or recent treatment including immunotherapy does not impact outcome.\n\nFundingsVA Office of Research and Development and National Institutes of Health.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Nathanael R Fillmore",
+        "author_inst": "VA Boston Healthcare System, Harvard Medical School, Dana-Farber Cancer Institute"
+      },
+      {
+        "author_name": "Jennifer La",
+        "author_inst": "VA Boston Healthcare System"
+      },
+      {
+        "author_name": "Raphael E Szalat",
+        "author_inst": "VA Boston Healthcare System, Dana-Farber Cancer Institute, Boston University School of Medicine"
+      },
+      {
+        "author_name": "David P Tuck",
+        "author_inst": "VA Boston Healthcare System, Boston University School of Medicine"
+      },
+      {
+        "author_name": "Vinh Nguyen",
+        "author_inst": "VA Boston Healthcare System"
+      },
+      {
+        "author_name": "Cenk Yildirim",
+        "author_inst": "VA Boston Healthcare System"
+      },
+      {
+        "author_name": "Nhan V Do",
+        "author_inst": "VA Boston Healthcare System, Boston University School of Medicine"
+      },
+      {
+        "author_name": "Mary T Brophy",
+        "author_inst": "VA Boston Healthcare System, Boston University School of Medicine"
+      },
+      {
+        "author_name": "Nikhil C Munshi",
+        "author_inst": "VA Boston Healthcare System, Harvard Medical School, Dana-Farber Cancer Institute"
+      }
+    ],
+    "version": "1",
+    "license": "cc0",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.08.21.20178863",
     "rel_title": "Next generation sequencing of SARS-CoV-2 from patient specimens of Nevada reveals occurrence of specific nucleotide variants at high frequency",
@@ -1215182,49 +1214175,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.08.20.20174169",
-    "rel_title": "Associations of comorbidities and medications with COVID-19 outcome: A retrospective analysis of real-world evidence data",
-    "rel_date": "2020-08-23",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.20.20174169",
-    "rel_abs": "BackgroundHundreds of thousands of deaths have already been recorded for patients with the severe acute respiratory syndrome coronavirus (SARS-CoV-2; aka COVID-19). Understanding whether there is a relationship between comorbidities and COVID-19 positivity will not only impact clinical decisions, it will also allow an understanding of how better to define the long-term complications in the groups at risk. In turn informing national policy on who may benefit from more stringent social distancing and shielding strategies. Furthermore, understanding the associations between medications and certain outcomes may also further our understanding of indicators of vulnerability in people with COVID-19 and co-morbidities.\n\nMethodsElectronic healthcare records (EHR) from two London hospitals were analysed between 1st January and 27th May 2020. 5294 patients presented to the hospitals in whom COVID status was formally assessed; 1253 were positive for COVID-19 and 4041 were negative. This dataset was analysed to identify associations between comorbidities and medications, separately and two outcomes: (1) presentation with a COVID-19 positive diagnosis, and (2) inpatient death following COVID-19 positive diagnosis. Medications were analysed in different time windows of prescription to differentiate between short-term and long-term medications. All analyses were done with controls (without co-morbidity) matched for age, sex, and number of admissions, and a robustness approach was conducted to only accept results that consistently appear when the analysis is repeated with different proportions of the data.\n\nResultsWe observed higher COVID-19 positive presentation for patients with hypertension (1.7 [1.3-2.1]) and diabetes (1.6 [1.2-2.1]). We observed higher inpatient COVID-19 mortality for patients with hypertension (odds ratio 2.7 [95% CI 1.9-3.9]), diabetes (2.2 [1.4-3.5]), congestive heart failure (3.1 [1.5-6.4]), and renal disease (2.6 [1.4-5.1]). We also observed an association with reduced COVID-19 mortality for diabetic patients for whom anticoagulants (0.11 [0.03-0.50]), lipid-regulating drugs (0.15 [0.04-0.58]), penicillins (0.20 [0.06-0.63]), or biguanides (0.19 [0.05-0.70]) were administered within 21 days after their positive COVID-19 test with no evidence that they were on them before, and for hypertensive patients for whom anticoagulants (0.08 [0.02-0.35]), antiplatelet drugs (0.10 [0.02-0.59]), lipid-regulating drugs (0.15 [0.05-0.46]), penicillins (0.14 [0.05-0.45]), or angiotensin-converting enzyme inhibitors (ARBs) (0.06 [0.01-0.53]) were administered within 21 days post-COVID-19-positive testing with no evidence that they were on them before. Moreover, long-term antidiabetic drugs were associated with reduced COVID-19 mortality in diabetic patients (0.26 [0.10-0.67]).\n\nConclusionsWe provided real-world evidence for observed associations between COVID-19 outcomes and a number of comorbidities and medications. These results require further investigation and replication in other data sets.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Basel Abu-Jamous",
-        "author_inst": "Sensyne Health plc"
-      },
-      {
-        "author_name": "Arseni Anisimovich",
-        "author_inst": "Sensyne Health plc"
-      },
-      {
-        "author_name": "Janie Baxter",
-        "author_inst": "Sensyne Health plc"
-      },
-      {
-        "author_name": "Lucy Mackillop",
-        "author_inst": "Sensyne Health plc"
-      },
-      {
-        "author_name": "Marcela P Vizcaychipi",
-        "author_inst": "Chelsea and Westminster Hospital NHS Foundation Trust"
-      },
-      {
-        "author_name": "Alex McCarthy",
-        "author_inst": "Chelsea and Westminster Hospital NHS Foundation Trust"
-      },
-      {
-        "author_name": "Rabia T Khan",
-        "author_inst": "Sensyne Health plc"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.08.20.20178699",
     "rel_title": "Systematic review and patient-level meta-analysis of SARS-CoV-2 viral dynamics to model response to antiviral therapies",
@@ -1215463,6 +1214413,101 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.08.20.20178970",
+    "rel_title": "Poor knowledge of COVID-19 and unfavourable perception of the response to the pandemic by healthcare workers at the Bafoussam Regional Hospital (West Region - Cameroon)",
+    "rel_date": "2020-08-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.20.20178970",
+    "rel_abs": "BackgroundThe World Health Organization has warned against a dramatic impact of COVID-19 in sub-Saharan Africa unless adequate response strategies are implemented. Whatever the strategy, the role of health care workers is pivotal. We undertook this study to assess knowledge of COVID-19 and perception of the response to the pandemic among the staff of a regional hospital in charge of COVID-19 patients in West Cameroon.\n\nMethodsWe used a convenience non probabilistic sampling method to carry out a survey with a self-administered questionnaire from April 14, 2020 to April 29, 2020 at the Bafoussam Regional Hospital (BRH). All the staff was invited to participate. Statistical analyses were done using Microsoft Excel 2010 and Epi-lnfo version 7.1.5.2 software.\n\nResultsResponse rate was 76.1% (464/610). Mean age (SD) and average work experience (SD) were 35.0 (8.9) and 8.4 (7.4) years respectively. Sex ratio (M/F) was 101/356. Nursing and midwifery staff (56.8%) and in-patients units (49.94%) were predominant. Knowledge on origin and transmission of SARS-CoV-2 was poor but knowledge of clinical signs and the role of laboratory tests were good. 53.2% of respondents said all therapeutic regimens are only supportive and only a third of them trusted drugs recommended by health authorities. For 36.9% of respondents, herbal remedies can prevent/cure COVID-19. 70% of staffs felt they were not knowledgeable enough to handle COVID-19 cases. 85.6% of respondents thought the BRH had insufficient resources to adequately respond to COVID-19 and 55.6% were dissatisfied with its response to the pandemic (weaknesses: medicines/technologies (74.5%), service delivery (28.1%), human resource (10.9%)). 68% of staff felt insufficiently protected on duty and 76.5% reported that the pandemic significantly reduced non-COVID-19 services. 85.5% said they complied with preventive measures while in the community. For 44% of respondents Cameroonian regulations on COVID-19 corpses should be made more culture-sensitive. 51.2% of respondents were against vaccine trial in their community.\n\nConclusionKnowledge of COVID-19 was poor and perception of the response to the pandemic was unfavorable.",
+    "rel_num_authors": 20,
+    "rel_authors": [
+      {
+        "author_name": "JOVANNY TSUALA FOUOGUE",
+        "author_inst": "Faculty of Medicine and pharmaceutical sciences_ university of Dschang"
+      },
+      {
+        "author_name": "MICHEL NOUBOM",
+        "author_inst": "Faculty of Medicine and Pharmaceutical sciences _ University of Dschang"
+      },
+      {
+        "author_name": "BRUNO KENFACK",
+        "author_inst": "Faculty of Medicine and Pharmaceutical Sciences _ University of Dschang"
+      },
+      {
+        "author_name": "NORBERT TANKE DONGMO",
+        "author_inst": "Cameroon Society of Epidemiology"
+      },
+      {
+        "author_name": "MAXIME TABEU",
+        "author_inst": "Bafoussam Regional Hospital"
+      },
+      {
+        "author_name": "LINDA MEGOZEU",
+        "author_inst": "Bafoussam Regional Hospital"
+      },
+      {
+        "author_name": "JEAN MARIE ALIMA",
+        "author_inst": "Bafoussam Regional Hospital"
+      },
+      {
+        "author_name": "YANNICK FOGOUM FOGANG",
+        "author_inst": "Faculty of Medicine and Pharmaceutical Sciences_ University of Dschang"
+      },
+      {
+        "author_name": "LANDRY  CHARLES A  NYAM RIM",
+        "author_inst": "Bafoussam Regional Hospital"
+      },
+      {
+        "author_name": "FLORENT YMELE FOUELIFACK",
+        "author_inst": "Institut Superieur de Technologies Medicales, Yaounde"
+      },
+      {
+        "author_name": "JEANNE HORTENCE FOUEDJIO",
+        "author_inst": "Faculty of Medicine and Biomedical Sciences, University of Yaounde 1"
+      },
+      {
+        "author_name": "PAMELA LEONIE NZOGNING FOUOGUE MANEBOU",
+        "author_inst": "Freelance translator, Bafoussam, Cameroon"
+      },
+      {
+        "author_name": "CLOTAIRE DAMIEN BIBOU ZE",
+        "author_inst": "Yagoua Health District, Yagoua"
+      },
+      {
+        "author_name": "BRICE FOUBI KOUAM",
+        "author_inst": "Bafoussam Regional Hospital"
+      },
+      {
+        "author_name": "LAURIANE NOMENE FOMETE",
+        "author_inst": "Agence Nationale de Recherche sur le Sida et les Hepatite virales - Site Cameroun,"
+      },
+      {
+        "author_name": "PIERRE MARIE TEBEU",
+        "author_inst": "Faculty of Medicine and Biomedical Sciences, University of Yaounde 1"
+      },
+      {
+        "author_name": "JEAN DUPONT NGOWA KEMFANG",
+        "author_inst": "Faculty of Medicine and Biomedical Sciences, University of Yaounde 1"
+      },
+      {
+        "author_name": "PASCAL FOUMANE",
+        "author_inst": "Faculty of Medicine and Biomedical Sciences, University of Yaounde 1"
+      },
+      {
+        "author_name": "ZACHARIE SANDO",
+        "author_inst": "Faculty of Medicine and Biomedical Sciences, University of Yaounde 1"
+      },
+      {
+        "author_name": "GEORGE ENOW ENOWNCHONG OROCK",
+        "author_inst": "Bafoussam Regional Hospital"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health systems and quality improvement"
+  },
   {
     "rel_doi": "10.1101/2020.08.20.20178889",
     "rel_title": "Impact of Duration of Cessation of Mass BCG Vaccination Programs on Covid -19 Mortality",
@@ -1216764,69 +1215809,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.08.19.20178285",
-    "rel_title": "Potential interruptions in HIV prevention and treatment services for gay, bisexual, and other men who have sex with men associated with COVID-19",
-    "rel_date": "2020-08-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.19.20178285",
-    "rel_abs": "BackgroundGlobally, the coronavirus pandemic has necessitated a range of population-based measures in order to stem the spread of infection and reduce COVID-19-related morbidity and mortality. These measures may be associated with disruptions to other health services including for gay, bisexual, and other men who have sex with men (MSM) at risk for or living with HIV. Here, we assess the relationship between stringency of COVID-19 mitigation strategies and interruptions to HIV prevention and treatment services for MSM.\n\nMethodsData for this study were collected as part of a COVID-19 Disparities Survey implemented by the gay social networking app Hornet, with data collected between April 16th, 2020 and May 24th, 2020. Data were assessed for countries where at least 50 participants completed the survey, to best evaluate country-level heterogeneity. We used a modified Poisson regression model, with clustering at the country-level, to assess the association between stringency of pandemic control measures and access to HIV services. Pandemic control measures were quantified using the Oxford Government Response Tracker Stringency Index; each country received a score (0-100) based on the number and strictness of nine indicators related to school and workplace closures and travel bans.\n\nResultsA total of 10,654 MSM across 20 countries were included in these analyses. The mean age was 34.2 (standard deviation: 10.8), and 12% (1264/10540) of participants reported living with HIV. The median stringency score was 82.31 (Range:[19.44, Belarus]-[92.59, Ukraine]). For every ten-point increase in stringency, there was a 3% reduction in the prevalence of access to in-person testing (aPR: 0.97, 95% Cl:[0.96, 0.98]), a 6% reduction in the prevalence of access to self-testing (aPR: 0.94, 95% Cl:[0.93, 0.95]), and a 5% reduction in access to PrEP (aPR: 0.95, 95% Cl:[0.95, 0.97]). Among those living with HIV, close to one in five (n = 218/1105) participants reported being unable to access their provider either in-person or via telemedicine during the COVID-19 pandemic, with a greater proportion of interruptions to treatment services reported in Belarus and Mexico. Almost half (n = 820/1254) reported being unable to refill their HIV medicine prescription remotely.\n\nConclusionsMore stringent government responses were associated with decreased access to HIV diagnostic, prevention, and treatment services. To minimize increases in HIV-related morbidity and mortality, innovative strategies are needed to facilitate minimize service interruptions to MSM communities during this and potential future waves of COVID-19.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Amrita Rao",
-        "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore USA"
-      },
-      {
-        "author_name": "Katherine Rucinski",
-        "author_inst": "Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore USA"
-      },
-      {
-        "author_name": "Brooke Jarrett",
-        "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore USA"
-      },
-      {
-        "author_name": "Benjamin Ackerman",
-        "author_inst": "Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore USA"
-      },
-      {
-        "author_name": "Sara Wallach",
-        "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore USA"
-      },
-      {
-        "author_name": "Julia Marcus",
-        "author_inst": "Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston USA; Fenway Institute, Boston USA"
-      },
-      {
-        "author_name": "Tyler Adamson",
-        "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore USA"
-      },
-      {
-        "author_name": "Alex Garner",
-        "author_inst": "Hornet, San Francisco, USA"
-      },
-      {
-        "author_name": "Glenn-Milo Santos",
-        "author_inst": "Community Health Systems Department, University of California San Francisco, San Francisco, USA; Center of Public Health Research, San Francisco Department of P"
-      },
-      {
-        "author_name": "Chris Beyrer",
-        "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore USA"
-      },
-      {
-        "author_name": "Sean Howell",
-        "author_inst": "Hornet, San Francisco, USA"
-      },
-      {
-        "author_name": "Stefan Baral",
-        "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore USA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.08.19.20178228",
     "rel_title": "COVID19 epidemic growth rates have declined since early March in U.S. regions with active hospitalized case surveillance",
@@ -1217025,6 +1216007,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.08.20.20176529",
+    "rel_title": "Preventing within household transmission of COVID-19: Is self-isolation outside the home feasible and acceptable?",
+    "rel_date": "2020-08-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.20.20176529",
+    "rel_abs": "BackgroundWithin-household transmission of COVID-19 is responsible for a significant number of infections. The risk of within-household infection is greatly increased among those from Black Asian and minority ethnic (BAME) and low income communities. Efforts to protect these communities are urgently needed. The aim of this study is to explore the acceptability of the availability of accommodation to support isolation among at risk populations.\n\nMethodsOur study used a mixed methods design structured in two phases. In phase 1, we conducted a survey study of a sample of volunteers from our existing database of 300 individuals who had provided consent to be contacted about ongoing research projects into infection control. In phase 2, we conducted semi-structured interviews with 19 participants from BAME communities and low income communities recruited through social media.\n\nResultsParticipants from the survey and interview phase of the study viewed the provision of accommodation as important and necessary. Factors influencing likely uptake of accommodation included perceived 1) vulnerability of household 2) exposure to the virus and 3) options for isolation at home. Barriers to accepting the offer of accommodation included 1) being able to isolate at home 2) wanting to be with family 3) caring responsibilities 4) concerns about mental wellbeing 5) upheaval of moving when ill and 6) concerns about infection control. Participants raised a series of issues that should be addressed before accommodation is offered. These included questions regarding who should use temporary accommodation and at what stage to effectively reduce transmission in the home, and how infection control in temporary accommodation would be managed.\n\nConclusionThis research provides evidence that the provision of accommodation to prevent within household transmission of the virus is viewed as acceptable, feasible and necessary by many people who are concerned about infection transmission in the home. We explore ways in which accommodation might be offered. In particular, vulnerable members of the household could be protected if accommodation is offered to individuals who are informed through test trace and isolate that they have been in contact with the virus.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Sarah Denford",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Kate S Morton",
+        "author_inst": "University of Southampton"
+      },
+      {
+        "author_name": "Jeremy Horwood",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Rachel de Garang",
+        "author_inst": "Public Contributor"
+      },
+      {
+        "author_name": "Lucy Yardley",
+        "author_inst": "University of Bristol, University of Southampton"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.08.19.20178186",
     "rel_title": "Self assessment overestimates historical COVID-19 disease relative to sensitive serological assays: cross sectional study in UK key workers",
@@ -1218294,33 +1217311,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "surgery"
   },
-  {
-    "rel_doi": "10.1101/2020.08.17.20176909",
-    "rel_title": "On COVID-19-safety ranking of seats in intercontinental commercial aircrafts: A preliminary multiphysics computational perspective",
-    "rel_date": "2020-08-21",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.17.20176909",
-    "rel_abs": "The evolution of coronavirus disease (COVID-19) into a pandemic has severely hampered the usage of public transit systems. In a post-COVID-19 world, we may see an increased reliance on autonomous cars and personal rapid transit (PRT) systems, with inherent physical distancing, over buses, trains and aircraft for intracity, intercity, and interstate travel. However, air travel would continue to be the dominant mode of intercontinental transportation for humans. In this study, we perform a comprehensive computational analysis of typical intercontinental aircraft ventilation systems to determine the seat where environmental factors are most conducive to human comfort with regards to air quality, protection from orally or nasally released pollutants such as CO2 and coronavirus, and thermal comfort levels. Air velocity, temperature, and air pollutant concentration emitted from the nose/mouth of fellow travelers are considered for both Boeing and Airbus planes. In each plane, first class, business class, and economy class sections were analyzed. We present conclusions as to which is the optimum seat in each section of each plane and provide the data of the environmental conditions to support our inferences. The findings may be used by the general public to decide which seat to occupy for their next intercontinental flight. Alternatively, the commercial airliners can use such a model to plan the occupancy of the aircraft on long-duration intercontinental flights (viz., Airbus A380 and Boeing B747).",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Prathamesh S Desai",
-        "author_inst": "W. M. Rice University"
-      },
-      {
-        "author_name": "Nihar Sawant",
-        "author_inst": "Courant Institute of Mathematical Sciences"
-      },
-      {
-        "author_name": "Andrew Keene",
-        "author_inst": "MPR"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "occupational and environmental health"
-  },
   {
     "rel_doi": "10.1101/2020.08.18.20167270",
     "rel_title": "Keep calm and carry on: safety, feasibility and early outcomes of head and neck cancer treatment during the COVID-19 pandemic",
@@ -1218763,6 +1217753,121 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.08.18.20174623",
+    "rel_title": "Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom",
+    "rel_date": "2020-08-21",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.18.20174623",
+    "rel_abs": "In the early phases of the SARS coronavirus type 2 (SARS-CoV-2) pandemic, testing focused on individuals fitting a strict case definition involving a limited set of symptoms together with an identified epidemiological risk, such as contact with an infected individual or travel to a high-risk area. To assess whether this impaired our ability to detect and control early introductions of the virus into the UK, we PCR-tested archival specimens collected on admission to a large UK teaching hospital who retrospectively were identified as having a clinical presentation compatible with COVID-19. In addition, we screened available archival specimens submitted for respiratory virus diagnosis, and dating back to early January 2020, for the presence of SARS-CoV-2 RNA. Our data provides evidence for widespread community circulation of SARS-CoV2 in early February 2020 and into March that was undetected at the time due to restrictive case definitions informing testing policy. Genome sequence data showed that many of these early cases were infected with a distinct lineage of the virus. Sequences obtained from the first officially recorded case in Nottinghamshire - a traveller returning from Daegu, South Korea - also clustered with these early UK sequences suggesting acquisition of the virus occurred in the UK and not Daegu. Analysis of a larger sample of sequences obtained in the Nottinghamshire area revealed multiple viral introductions, mainly in late February and through March. These data highlight the importance of timely and extensive community testing to prevent future widespread transmission of the virus.",
+    "rel_num_authors": 25,
+    "rel_authors": [
+      {
+        "author_name": "Joseph G Chappell",
+        "author_inst": "University of Nottingham"
+      },
+      {
+        "author_name": "Theocharis Tsoleridis",
+        "author_inst": "University of Nottingham"
+      },
+      {
+        "author_name": "Gemma Clark",
+        "author_inst": "Nottingham University Hospitals"
+      },
+      {
+        "author_name": "Louise Berry",
+        "author_inst": "Nottingham University Hospitals"
+      },
+      {
+        "author_name": "Nadine Holmes",
+        "author_inst": "University of Nottingham"
+      },
+      {
+        "author_name": "Christopher Moore",
+        "author_inst": "University of Nottingham"
+      },
+      {
+        "author_name": "Matthew Carlile",
+        "author_inst": "University of Nottingham"
+      },
+      {
+        "author_name": "Fei Sang",
+        "author_inst": "University of Nottingham"
+      },
+      {
+        "author_name": "Johnny Debebe",
+        "author_inst": "University of Nottingham"
+      },
+      {
+        "author_name": "Victoria Wright",
+        "author_inst": "University of Nottingham"
+      },
+      {
+        "author_name": "William Irving",
+        "author_inst": "University of Nottingham"
+      },
+      {
+        "author_name": "Brian J Thomson",
+        "author_inst": "Nottingham University Hospitals"
+      },
+      {
+        "author_name": "Timothy C.J. Boswell",
+        "author_inst": "Nottingham University Hospitals"
+      },
+      {
+        "author_name": "Iona Willingham",
+        "author_inst": "Nottingham University Hospitals"
+      },
+      {
+        "author_name": "Amelia Joseph",
+        "author_inst": "Nottingham University Hospitals"
+      },
+      {
+        "author_name": "Wendy Smith",
+        "author_inst": "Nottingham University Hopsitals"
+      },
+      {
+        "author_name": "Manjinder Khakh",
+        "author_inst": "Nottingham University Hospitals"
+      },
+      {
+        "author_name": "Vicki M. Fleming",
+        "author_inst": "Nottingham University Hospitals"
+      },
+      {
+        "author_name": "Michelle M. Lister",
+        "author_inst": "Nottingham University Hospitals"
+      },
+      {
+        "author_name": "Hannah C. Howson-Wells",
+        "author_inst": "Nottingham University Hospitals"
+      },
+      {
+        "author_name": "Edward C Holmes",
+        "author_inst": "University of Sydney"
+      },
+      {
+        "author_name": "Matthew W. Loose",
+        "author_inst": "University of Nottingham"
+      },
+      {
+        "author_name": "Jonathan K. Ball",
+        "author_inst": "University of Nottingham"
+      },
+      {
+        "author_name": "C. Patrick McClure",
+        "author_inst": "University of Nottingham"
+      },
+      {
+        "author_name": "- The COVID-19 Genomics UK consortium study group",
+        "author_inst": ""
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.08.18.20159608",
     "rel_title": "Severity-stratified and longitudinal analysis of VWF/ADAMTS13 imbalance, altered fibrin crosslinking and inhibition of fibrinolysis as contributors to COVID-19 coagulopathy",
@@ -1219832,121 +1218937,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health economics"
   },
-  {
-    "rel_doi": "10.1101/2020.08.18.20172874",
-    "rel_title": "The Prognostic Value of Eosinophil Recovery in COVID-19: A Multicentre, Retrospective Cohort Study on Patients Hospitalised in Spanish Hospitals.",
-    "rel_date": "2020-08-21",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.18.20172874",
-    "rel_abs": "ObjectivesA decrease in blood cell counts, especially lymphocytes and eosinophils, has been described in patients with severe SARS-CoV-2 (COVID-19), but there is no knowledge of the potential role of their recovery in these patients prognosis. This article aims to analyse the effect of blood cell depletion and blood cell recovery on mortality due to COVID-19.\n\nDesignThis work is a multicentre, retrospective, cohort study of 9,644 hospitalised patients with confirmed COVID-19 from the Spanish Society of Internal Medicines SEMI-COVID-19 Registry.\n\nSettingThis study examined patients hospitalised in 147 hospitals throughout Spain.\n\nParticipantsThis work analysed 9,644 patients (57.12% male) out of a cohort of 12,826 patients [&ge;]18 years of age hospitalised with COVID-19 in Spain included in the SEMI-COVID-19 Registry as of 29 May 2020.\n\nMain outcome measuresThe main outcome measure of this work is the effect of blood cell depletion and blood cell recovery on mortality due to COVID-19. Univariate analysis was performed to determine possible predictors of death and then multivariate analysis was carried out to control for potential confounders.\n\nResultsAn increase in the eosinophil count on the seventh day of hospitalisation was associated with a better prognosis, including lower mortality rates (5.2% vs 22.6% in non-recoverers, OR 0.234 [95% CI, 0.154 to 0.354]) and lower complication rates, especially regarding to development of acute respiratory distress syndrome (8% vs 20.1%, p=0.000) and ICU admission (5.4% vs 10.8%, p=0.000). Lymphocyte recovery was found to have no effect on prognosis. Treatment with inhaled or systemic glucocorticoids was not found to be a confounding factor.\n\nConclusionEosinophil recovery in patients with COVID-19 is a reliable marker of a good prognosis that is independent of prior treatment. This finding could be used to guide discharge decisions.",
-    "rel_num_authors": 25,
-    "rel_authors": [
-      {
-        "author_name": "Maria Mateos Gonzalez",
-        "author_inst": "Internal Medicine Department, Infanta Cristina University Hospital, Parla, Madrid, Spain."
-      },
-      {
-        "author_name": "Elena Sierra Gonzalo",
-        "author_inst": "Pathology Department, Infanta Cristina University Hospital, Parla, Madrid, Spain"
-      },
-      {
-        "author_name": "Irene Casado Lopez",
-        "author_inst": "Internal Medicine Department, Infanta Cristina University Hospital, Parla, Madrid, Spain"
-      },
-      {
-        "author_name": "Francisco Arnalich Fernandez",
-        "author_inst": "Internal Medicine Department, La Paz University Hospital, Madrid, Spain"
-      },
-      {
-        "author_name": "Jose Luis Beato Perez",
-        "author_inst": "Internal Medicine Department, Albacete University Hospital Complex, Albacete, Spain."
-      },
-      {
-        "author_name": "Daniel Monge Monge",
-        "author_inst": "Internal Medicine Department, Segovia Hospital Complex, Segovia, Spain."
-      },
-      {
-        "author_name": "Juan Antonio Vargas Nunez",
-        "author_inst": "Internal Medicine Department, Puerta de Hierro University Hospital, Majadahonda, Madrid, Spain"
-      },
-      {
-        "author_name": "Rosa Garcia Fenoll",
-        "author_inst": "Internal Medicine Department, Miguel Servet Hospital, Zaragoza, Spain."
-      },
-      {
-        "author_name": "Carmen Suarez Fernandez",
-        "author_inst": "Internal Medicine Department, La Princesa University Hospital, Madrid, Spain."
-      },
-      {
-        "author_name": "Santiago Jesus Freire Castro",
-        "author_inst": "Internal Medicine Department, A Coruna University Hospital, A Coruna, Spain."
-      },
-      {
-        "author_name": "Manuel Mendez Bailon",
-        "author_inst": "Internal Medicine Department, Clinico San Carlos Hospital, Madrid, Spain."
-      },
-      {
-        "author_name": "Isabel Perales Fraile",
-        "author_inst": "Internal Medicine Department, Infanta Sofia Hospital, San Sebastian de los Reyes, Madrid, Spain."
-      },
-      {
-        "author_name": "Manuel Madrazo",
-        "author_inst": "Internal Medicine Department, Dr. Peset University Hospital, Valencia, Spain."
-      },
-      {
-        "author_name": "Paula Maria Pesqueira Fontan",
-        "author_inst": "Internal Medicine Department, Santiago Clinical Hospital, Santiago de Compostela, A Coruna, Spain."
-      },
-      {
-        "author_name": "Jeffrey Oskar Magallanes Gamboa",
-        "author_inst": "Internal Medicine Department, Nuestra Senora del Prado Hospital, Talavera de la Reina, Toledo, Spain."
-      },
-      {
-        "author_name": "Andres Gonzalez Garcia",
-        "author_inst": "Internal Medicine Department, Ramon y Cajal University Hospital, Madrid, Spain"
-      },
-      {
-        "author_name": "Anxela Crestelo Vieitez",
-        "author_inst": "Internal Medicine Department, Royo Villanova Hospital, Zaragoza, Spain."
-      },
-      {
-        "author_name": "Eva Maria Fonseca Aizpuru",
-        "author_inst": "Internal Medicine Department, Cabuenes Hospital, Gijon, Asturias, Spain."
-      },
-      {
-        "author_name": "Asier Aranguren Arostegui",
-        "author_inst": "Internal Medicine Department, Urduliz Alfredo Espinosa Hospital, Urduliz, Vizcaya, Spain"
-      },
-      {
-        "author_name": "Ainara Coduras Erdozain",
-        "author_inst": "Internal Medicine Department, Santa Marina Hospital, Bilbao, Spain"
-      },
-      {
-        "author_name": "Carmen Martinez Cilleros",
-        "author_inst": "Internal Medicine Department, HLA Moncloa Hospital, Madrid, Spain."
-      },
-      {
-        "author_name": "Jose Loureiro Amigo",
-        "author_inst": "Internal Medicine Department, Moises Broggi Hospital, Sant Joan Despi, Barcelona, Spain"
-      },
-      {
-        "author_name": "Francisco Epelde",
-        "author_inst": "Internal Medicine Department, Parc Tauli Hospital, Sabadell, Barcelona, Spain"
-      },
-      {
-        "author_name": "Carlos Lumbreras Bermejo",
-        "author_inst": "Internal Medicine Department, 12 de Octubre University Hospital, Madrid, Spain"
-      },
-      {
-        "author_name": "Juan Miguel Anton Santos",
-        "author_inst": "Internal Medicine Department, Infanta Cristina University Hospital, Parla, Madrid, Spain"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.08.17.20176925",
     "rel_title": "Engineering luminescent biosensors for point-of-care SARS-CoV-2 antibody detection",
@@ -1220321,6 +1219311,69 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "allergy and immunology"
   },
+  {
+    "rel_doi": "10.1101/2020.08.17.20177022",
+    "rel_title": "Decontaminating N95 respirators during the Covid-19 pandemic: simple and practical approaches to increase decontamination capacity, speed, safety and ease of use.",
+    "rel_date": "2020-08-21",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.17.20177022",
+    "rel_abs": "BackgroundThe COVID-19 pandemic has caused a severe shortage of personal protective equipment (PPE), especially N95 respirators. Efficient, effective and economically feasible methods for large-scale PPE decontamination are urgently needed.\n\nAims(1) to develop protocols for effectively decontaminating PPE using vaporized hydrogen peroxide (VHP); (2) to develop novel approaches that decrease set up and take down time while also increasing decontamination capacity (3) to test decontamination efficiency for N95 respirators heavily contaminated by makeup or moisturizers.\n\nMethodsWe converted a decommissioned Biosafety Level 3 laboratory into a facility that could be used to decontaminate N95 respirators. N95 respirators were hung on metal racks, stacked in piles, placed in paper bags or covered with makeup or moisturizer. A VHP(R)VICTORYTM unit from STERIS was used to inject VHP into the facility. Biological and chemical indicators were used to validate the decontamination process.\n\nFindingsN95 respirators individually hung on metal racks were successfully decontaminated using VHP. N95 respirators were also successfully decontaminated when placed in closed paper bags or if stacked in piles of up to six. Stacking reduced the time needed to arrange N95 respirators for decontamination by approximately two-thirds while almost tripling facility capacity. Makeup and moisturizer creams did not interfere with the decontamination process.\n\nConclusionsRespirator stacking can reduce the hands-on time and increase decontamination capacity. When personalization is needed, respirators can be decontaminated in labeled paper bags. Make up or moisturizers do not appear to interfere with VHP decontamination.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "RICCARDO RUSSO",
+        "author_inst": "Rutgers, The State University of New Jersey"
+      },
+      {
+        "author_name": "Carly Levine",
+        "author_inst": "Rutgers, The State University of New Jersey"
+      },
+      {
+        "author_name": "Courtney Veilleux",
+        "author_inst": "Rutgers, The State University of New Jersey"
+      },
+      {
+        "author_name": "Blas Peixoto",
+        "author_inst": "Rutgers, The State University of New Jersey"
+      },
+      {
+        "author_name": "Jessica McCormick-Ell",
+        "author_inst": "National Institutes of Health"
+      },
+      {
+        "author_name": "Thomas Block",
+        "author_inst": "Rutgers, The State University of New Jersey"
+      },
+      {
+        "author_name": "Anthony Gresko",
+        "author_inst": "Rutgers, The State University of New Jersey"
+      },
+      {
+        "author_name": "Guillaume Delmas",
+        "author_inst": "Rutgers, The State University of New Jersey"
+      },
+      {
+        "author_name": "Poonam Chitale",
+        "author_inst": "Rutgers, The State University of New Jersey"
+      },
+      {
+        "author_name": "Alexis Frees",
+        "author_inst": "Rutgers, The State University of New Jersey"
+      },
+      {
+        "author_name": "Alejandro Ruiz",
+        "author_inst": "Rutgers, The State University of New Jersey"
+      },
+      {
+        "author_name": "David Alland",
+        "author_inst": "Rutgers, The State University of New Jersey"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.08.18.20171074",
     "rel_title": "Bayesian Spatio-Temporal Modeling of COVID-19: Inequalities on Case-Fatality Risk",
@@ -1221594,69 +1220647,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2020.08.19.251249",
-    "rel_title": "A Human-Immune-System mouse model for COVID-19 research(DRAGA mouse: HLA-A2.HLA-DR4.Rag1KO.IL-2R\u03b3c KO.NOD)",
-    "rel_date": "2020-08-20",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.19.251249",
-    "rel_abs": "We report the first Human Immune System (HIS)-humanized mouse model (\"DRAGA\": HLA-A2.HLA-DR4.Rag1KO.IL-2R{gamma}cKO.NOD) for COVID-19 research. This mouse is reconstituted with human cord blood-derived, HLA-matched hematopoietic stem cells. It engrafts human epi/endothelial cells expressing the human ACE2 receptor for SARS-CoV-2 and TMPRSS2 serine protease co-localized on lung epithelia. HIS-DRAGA mice sustained SARS-CoV-2 infection, showing deteriorated clinical condition, replicating virus in the lungs, and human-like lung immunopathology including T-cell infiltrates, microthrombi and pulmonary sequelae. Among T-cell infiltrates, lung-resident (CD103+) CD8+ T cells were sequestered in epithelial (CD326+) lung niches and secreted granzyme B and perforin, indicating cytotoxic potential. Infected mice also developed antibodies against the SARS-CoV-2 viral proteins. Hence, HIS-DRAGA mice showed unique advantages as a surrogate in vivo human model for studying SARS-CoV-2 immunopathology and for testing the safety and efficacy of candidate vaccines and therapeutics.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Teodor-Doru Brumeanu",
-        "author_inst": "Uniformed Services University of the Health Sciences, Department of Medicine, Bethesda, MD 20814, U.S.A."
-      },
-      {
-        "author_name": "Pooja Vir",
-        "author_inst": "Uniformed Services University of the Health Sciences, Department of Medicine, Bethesda, MD 20814, U.S.A."
-      },
-      {
-        "author_name": "Ahmad Faisal Karim",
-        "author_inst": "Uniformed Services University of the Health Sciences, Department of Medicine, Bethesda, MD 20814, U.S.A."
-      },
-      {
-        "author_name": "Swagata Kar",
-        "author_inst": "Bioqual Inc., Rockville, MD 20852, U.S.A."
-      },
-      {
-        "author_name": "Dalia Benetiene",
-        "author_inst": "Bioqual, Inc."
-      },
-      {
-        "author_name": "Megan Lok",
-        "author_inst": "Bioqual, Inc."
-      },
-      {
-        "author_name": "Jack Greenhouse",
-        "author_inst": "Bioqual, Inc."
-      },
-      {
-        "author_name": "Tammy Putmon-Taylor",
-        "author_inst": "Bioqual, Inc."
-      },
-      {
-        "author_name": "Christopher Kitajewski",
-        "author_inst": "Bioqual, Inc."
-      },
-      {
-        "author_name": "Kevin K. Chung",
-        "author_inst": "Uniformed Services University of the Health Sciences, Department of Medicine, Bethesda, MD 20814, U.S.A"
-      },
-      {
-        "author_name": "Kathleen P. Pratt",
-        "author_inst": "Uniformed Services University of the Health Sciences, Department of Medicine, Bethesda, MD 20814, U.S.A"
-      },
-      {
-        "author_name": "Sofia A. Casares",
-        "author_inst": "Naval Medical Research Center/Walter Reed Army Institute of Research, Infectious Diseases Directorate, Silver Spring, MD 20910, U.S.A."
-      }
-    ],
-    "version": "1",
-    "license": "cc0",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2020.08.19.258244",
     "rel_title": "An effective, safe and cost-effective cell-based chimeric vaccine against SARS-CoV2",
@@ -1222175,6 +1221165,33 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2020.08.20.258772",
+    "rel_title": "What if we perceive SARS-CoV-2 genomes as documents? Topic modelling using Latent Dirichlet Allocation to identify mutation signatures and classify SARS-CoV-2 genomes",
+    "rel_date": "2020-08-20",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.20.258772",
+    "rel_abs": "Topic modeling is frequently employed for discovering structures (or patterns) in a corpus of documents. Its utility in text-mining and document retrieval tasks in various fields of scientific research is rather well known. An unsupervised machine learning approach, Latent Dirichlet Allocation (LDA) has particularly been utilized for identifying latent (or hidden) topics in document collections and for deciphering the words that define one or more topics using a generative statistical model. Here we describe how SARS-CoV-2 genomic mutation profiles can be structured into a  Bag of Words to enable identification of signatures (topics) and their probabilistic distribution across various genomes using LDA. Topic models were generated using ~47000 novel corona virus genomes (considered as documents), leading to identification of 16 amino acid mutation signatures and 18 nucleotide mutation signatures (equivalent to topics) in the corpus of chosen genomes through coherence optimization. The document assumption for genomes also helped in identification of contextual nucleotide mutation signatures in the form of conventional N-grams (e.g. bi-grams and tri-grams). We validated the signatures obtained using LDA driven method against the previously reported recurrent mutations and phylogenetic clades for genomes. Additionally, we report the geographical distribution of the identified mutation signatures in SARS-CoV-2 genomes on the global map. Use of the non-phylogenetic albeit classical approaches like topic modeling and other data centric pattern mining algorithms is therefore proposed for supplementing the efforts towards understanding the genomic diversity of the evolving SARS-CoV-2 genomes (and other pathogens/microbes).",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Sunil Nagpal",
+        "author_inst": "BioSciences R&D, TCS Research, Tata Consultancy Services Ltd. Pune, India"
+      },
+      {
+        "author_name": "Divyanshu Srivastava",
+        "author_inst": "BioSciences R&D, TCS Research, Tata Consultancy Services Ltd, Pune, India."
+      },
+      {
+        "author_name": "Sharmila S Mande",
+        "author_inst": "BioSciences R&D, TCS Research, Tata Consultancy Services Ltd, Pune, India."
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "confirmatory results",
+    "category": "bioinformatics"
+  },
   {
     "rel_doi": "10.1101/2020.08.16.20176065",
     "rel_title": "Multi-organ Proteomic Landscape of COVID-19 Autopsies",
@@ -1223592,29 +1222609,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.08.15.20175810",
-    "rel_title": "Study of Coronavirus Impact on Parisian Population from April to June using Twitter and Text Mining Approach",
-    "rel_date": "2020-08-18",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.15.20175810",
-    "rel_abs": "The fast spreading of coronavirus name covid19, generated the actual pandemic forcing to change daily activities. Health Councils of each country promote health policies, close borders and start a partial or total lockdown. One of the first countries in Europe with high impact was Italy. Besides at the end of April, one country with a shared border was on the top of 10 countries with more total cases, then France started with its own battle to beat coronavirus. This paper studies the impact of coronavirus in the poopulation of Paris, France from April 23 to June 18, using Text Mining approach, processing data collected from Social Network and using trends related of searching. First finding is a decreasing pattern of publications/interest, and second is related to health crisis and economical impact generated by coronavirus.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Josimar E. Chire Saire",
-        "author_inst": "University of Sao Paulo"
-      },
-      {
-        "author_name": "Jimmy Frank Oblitas Cruz",
-        "author_inst": "Universidad Privada del Norte"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.08.16.20176081",
     "rel_title": "Protection Level and Reusability of a Modified Full-Face Snorkel Mask as Alternative Personal Protective Equipment for Healthcare Workers During the COVID-19 Pandemic",
@@ -1223985,6 +1222979,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "intensive care and critical care medicine"
   },
+  {
+    "rel_doi": "10.1101/2020.08.16.20176073",
+    "rel_title": "Impacts on Surgery Resident Education at a first wave COVID-19 epicenter",
+    "rel_date": "2020-08-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.16.20176073",
+    "rel_abs": "BackgroundThis study aims to identify the effects of the COVID-19 pandemic on surgical resident training and education at Danbury Hospital.\n\nMethodsWe conducted an observational study at a Western Connecticut hospital heavily affected by the first wave of the COVID-19 pandemic to assess its effects on surgical residents, focusing on surgical education, clinical experience, and operative skills development. Objective data was available through recorded work hours, case logs, and formal didactics. In addition, we created an anonymous survey to assess resident perception of their residency experience during the pandemic.\n\nResultsThere are 22 surgical residents at our institution; all were included in the study. Resident weekly duty hours decreased by 23.9 hours with the majority of clinical time redirected to caring for COVID-19 patients. Independent studying increased by 1.6 hours (26.2%) while weekly didactics decreased by 2.1 hours (35.6%). The operative volume per resident decreased by 65.7% from 35.0 to 12.0 cases for the period of interest, with a disproportionately high effect on junior residents, who experienced a 76.2% decrease. Unsurprisingly, 70% of residents reported a negative effect of the pandemic on their surgical skills.\n\nConclusionsDuring the first wave of the COVID-19 pandemic, surgical residents usual workflows changed dramatically, as much of their time was dedicated to the critical care of patients with COVID-19. However, the consequent opportunity cost was to surgery-specific training; there was a significant decrease in operative cases and time spent in surgical didactics, along with elevated concern about overall preparedness for their intended career.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Alexander Ostapenko",
+        "author_inst": "Danbury Hospital"
+      },
+      {
+        "author_name": "Samantha McPeck",
+        "author_inst": "University of Connecticut"
+      },
+      {
+        "author_name": "Shawn Liechty",
+        "author_inst": "Danbury Hospital"
+      },
+      {
+        "author_name": "Daniel Kleiner",
+        "author_inst": "Danbury Hospital"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "surgery"
+  },
   {
     "rel_doi": "10.1101/2020.08.16.20176057",
     "rel_title": "On the use of growth models for forecasting epidemic outbreaks with application to COVID-19 data",
@@ -1225534,41 +1224559,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.08.15.20175844",
-    "rel_title": "IL-6 and IL-10 as predictors of disease severity in COVID 19 patients: Results from Meta-analysis and Regression",
-    "rel_date": "2020-08-17",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.15.20175844",
-    "rel_abs": "AimsSARS-CoV-2, an infectious agent behind the ongoing COVID-19 pandemic, induces high levels of cytokines such as IL-1, IL-2, IL-4, IL-6, IL-10, TNF-, IFN-{gamma} etc in infected individuals which contribute towards the underlying disease patho-physiology. Nonetheless, exact association and contribution of every cytokine towards COVID-19 pathology remains poorly understood. Delineation of the role of the cytokines during COVID-19 holds the key of efficient patient management in clinics. This study performed a comprehensive meta-analysis to establish association between induced cytokines and COVID-19 disease severity to help in prognosis and clinical care.\n\nMain methodsScientific literature was searched to identify 13 cytokines (IL-1{beta}, IL-2, IL-2R, IL-4, IL-5, IL-6, IL-7, IL-8, IL-10, IL-12, IL-17, TNF- and IFN-{gamma}) from 18 clinical studies. Standardized mean difference (SMD) for selected 6 cytokines IL-2, IL-4, IL-6, IL-10, TNF- and IFN-{gamma} between severe and non-severe COVID-19 patient groups were summarized using random effects model. A classifier was built using logistic regression model with cytokines having significant SMD as covariates.\n\nKey findingsOut of 13 cytokines, IL-6 and IL-10 showed statistically significant SMD across the studies synthesized. Classifier with mean values of both IL-6 and IL-10 as covariates performed well with accuracy of ~ 92% that was significantly higher than accuracy reported in literature with IL-6 and IL-10 as individual covariates.\n\nSignificanceSimple panel proposed by us with only two cytokine markers can be used as predictors for fast diagnosis of patients with higher risk of COVID-19 disease deterioration and thus can be managed well for a favourable prognosis.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Sujan K Dhar",
-        "author_inst": "Beyond Antibody"
-      },
-      {
-        "author_name": "Vishnupriyan K",
-        "author_inst": "Mazumdar Shaw Medical Foundation"
-      },
-      {
-        "author_name": "Sharat Damodar",
-        "author_inst": "Mazumdar Shaw Medical Center"
-      },
-      {
-        "author_name": "Shashi Gujar",
-        "author_inst": "Dalhousie University"
-      },
-      {
-        "author_name": "Manjula Das",
-        "author_inst": "Mazumdar Shaw Medical Foundation"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.08.15.20172080",
     "rel_title": "Evaluation of commercially available immuno-magnetic agglutination and enzyme-linked immunosorbent assays for rapid point-of-care diagnostics of COVID-19",
@@ -1225843,6 +1224833,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
+  {
+    "rel_doi": "10.1101/2020.08.14.20170290",
+    "rel_title": "Efficient Deep Network Architecture for COVID-19 Detection Using Computed Tomography Images",
+    "rel_date": "2020-08-17",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.14.20170290",
+    "rel_abs": "Globally the devastating consequence of COVID-19 or Severe Acute Respiratory Syndrome-Coronavirus (SARS-CoV-2) has posed danger on the life of living beings. Doctors and scientists throughout the world are working day and night to combat the proliferation or transmission of this deadly disease in terms of technology, finances, data repositories, protective equipment, and many other services. Rapid and efficient detection of COVID-19 reduces the rate of spreading this deadly disease and early treatment improve the recovery rate. In this paper, we proposed a new framework to exploit powerful features extracted from the autoencoder and Gray Level Co-occurence Matrix (GLCM), combined with random forest algorithm for the efficient and fast detection of COVID-19 using computed tomographic images. The models performance is evident from its 97.78% accuracy, 96.78% recall, and 98.77% specificity.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Chirag Goel",
+        "author_inst": "Thapar Institute of Engineering and Technology"
+      },
+      {
+        "author_name": "Abhimanyu Kumar",
+        "author_inst": "Thapar Institute of Engineering and Technology"
+      },
+      {
+        "author_name": "Satish Kumar Dubey",
+        "author_inst": "Indian Institute of Technology Delhi"
+      },
+      {
+        "author_name": "Vishal Srivastava",
+        "author_inst": "Thapar Institute of Engineering and Technology"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "radiology and imaging"
+  },
   {
     "rel_doi": "10.1101/2020.08.15.20175869",
     "rel_title": "Pulmonary cavitation; an under-recognized late complication of severe COVID-19 lung disease",
@@ -1227060,121 +1226081,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.08.14.20172429",
-    "rel_title": "Knowledge, Practice and associated factors towards the Prevention of COVID-19 among high-risk groups: A cross-sectional study in Addis Ababa, Ethiopia",
-    "rel_date": "2020-08-16",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.14.20172429",
-    "rel_abs": "BackgroundCoronavirus disease (COVID-19) is a highly transmittable virus that continues to disrupt livelihoods, particularly those of low income segments of society, around the world. In Ethiopia, more specifically in the capital city of Addis Ababa, a sudden increase in the number of confirmed positive cases in high-risk groups of the community has been observed over the last few weeks of the first case. Therefore, this study aims to assess knowledge, practices and associated factors that can contribute to the prevention of COVID-19 among high-risk groups in Addis Ababa.\n\nMethodsA cross-sectional in person survey (n=6007) was conducted from 14-30 April, 2020 following a prioritization within high-risk groups in Addis Ababa. The study area targeted bus stations, public transport drivers, air transport infrastructure, health facilities, public and private pharmacies, hotels, government-owned and private banks, telecom centers, trade centers, orphanages, elderly centers, prison, prisons and selected slum areas where the people live in a crowed. A questionnaire comprised of four sections (demographics, knowledge, practice and reported symptoms) was used for data collection. The outcomes (knowledge on the transmission and prevention of COVID-19 and practices) were measured using four items. A multi variable logistic regression was applied with adjustment for potential confounding.\n\nResultsAbout half (48%, 95% CI: 46-49) of the study participants had poor knowledge on the transmission mode of COVID-19 whereas six out of ten (60%, 95% CI: 58-61) had good knowledge on prevention methods for COVID-19. The practice of preventive measures towards COVID-19 was found to be low (49%, 95% CI: 48-50). Factors that influence knowledge on COVID-19 transmission mechanisms were female gender, older age, occupation (health care and grocery worker), lower income and the use of the 8335 free call centre. Older age, occupation (being a health worker), middle income, experience of respiratory illness and religion were significantly associated with being knowledgeable about the prevention methods for COVID-19. The study found that occupation, religion, income, knowledge on the transmission and prevention of COVID-19 were associated with the practice of precautionary measures towards COVID-19.\n\nConclusionThe study highlighted that there was moderate knowledge about transmission modes and prevention mechanism. Similarly, there was moderate practice of measures that contribute towards the prevention of COVID-19 among these priority high risk communities of Addis Ababa. There is an urgent need to fill the knowledge gap in terms of transmission mode and prevention methods of COVID-19 to improve preventions practices and control the spread of COVID-19. Use of female public figures and religious leaders could support the effort towards the increase in awareness.",
-    "rel_num_authors": 25,
-    "rel_authors": [
-      {
-        "author_name": "ATKURE DEFAR",
-        "author_inst": "Ethiopian Public Health Institute"
-      },
-      {
-        "author_name": "Gebeyaw Molla",
-        "author_inst": "Ethiopian Public Health Institute, Addis Ababa, Ethiopia"
-      },
-      {
-        "author_name": "Saro Abdella",
-        "author_inst": "Ethiopian Public Health Institute, Addis Ababa, Ethiopia"
-      },
-      {
-        "author_name": "Masresha Tessema",
-        "author_inst": "Ethiopian Public Health Institute, Addis Ababa, Ethiopia"
-      },
-      {
-        "author_name": "Muhammed Ahmed",
-        "author_inst": "Ethiopian Public Health Institute, Addis Ababa, Ethiopia"
-      },
-      {
-        "author_name": "Ashenif Tadele",
-        "author_inst": "Ethiopian Public Health Institute, Addis Ababa, Ethiopia"
-      },
-      {
-        "author_name": "Fikresilassie Getachew",
-        "author_inst": "Ethiopian Public Health Institute, Addis Ababa, Ethiopia"
-      },
-      {
-        "author_name": "Bezawit Hailegiorgis",
-        "author_inst": "Ethiopian Public Health Institute, Addis Ababa, Ethiopia"
-      },
-      {
-        "author_name": "Eyasu Tigabu",
-        "author_inst": "Ethiopian Public Health Institute, Addis Ababa, Ethiopia"
-      },
-      {
-        "author_name": "Sabit Ababor Sr.",
-        "author_inst": "Ethiopian Public Health Institute, Addis Ababa, Ethiopia"
-      },
-      {
-        "author_name": "Ketema Bizuwork",
-        "author_inst": "Ethiopian Public Health Institute, Addis Ababa, Ethiopia"
-      },
-      {
-        "author_name": "Assefa Deressa",
-        "author_inst": "Ethiopian Public Health Institute, Addis Ababa, Ethiopia"
-      },
-      {
-        "author_name": "Geremew Tasew",
-        "author_inst": "Ethiopian Public Health Institute, Addis Ababa, Ethiopia"
-      },
-      {
-        "author_name": "Addisu kebede",
-        "author_inst": "Ethiopian Public Health Institute, Addis Ababa, Ethiopia"
-      },
-      {
-        "author_name": "Daniel Melese",
-        "author_inst": "Ethiopian Public Health Institute, Addis Ababa, Ethiopia"
-      },
-      {
-        "author_name": "Andargachew Gashu",
-        "author_inst": "Ethiopian Public Health Institute, Addis Ababa, Ethiopia"
-      },
-      {
-        "author_name": "Kirubel Eshetu",
-        "author_inst": "Ethiopian Public Health Institute, Addis Ababa, Ethiopia"
-      },
-      {
-        "author_name": "Adamu Tayachew",
-        "author_inst": "Ethiopian Public Health Institute, Addis Ababa, Ethiopia"
-      },
-      {
-        "author_name": "Mesfin Wossen",
-        "author_inst": "mesfinwossen@gmail.com"
-      },
-      {
-        "author_name": "Abduilhafiz Hassen",
-        "author_inst": "Ethiopian Public Health Institute, Addis Ababa, Ethiopia"
-      },
-      {
-        "author_name": "Shambel Habebe",
-        "author_inst": "Ethiopian Public Health Institute, Addis Ababa, Ethiopia"
-      },
-      {
-        "author_name": "Zewdu Assefa",
-        "author_inst": "Ethiopian Public Health Institute, Addis Ababa, Ethiopia"
-      },
-      {
-        "author_name": "Aschalew Abayneh",
-        "author_inst": "Ethiopian Public Health Institute"
-      },
-      {
-        "author_name": "Ebba Abate",
-        "author_inst": "Ethiopian Public Health Institute, Addis Ababa, Ethiopia"
-      },
-      {
-        "author_name": "Getachew Tollera",
-        "author_inst": "Ethiopian Public Health Institute"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.08.14.20174649",
     "rel_title": "Widespread testing, case isolation and contact tracing may allow safe school reopening with continued moderate physical distancing: a modeling analysis of King County, WA data",
@@ -1227657,6 +1226563,81 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2020.08.15.252395",
+    "rel_title": "Susceptibility of swine cells and domestic pigs to SARS-CoV-2",
+    "rel_date": "2020-08-16",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.15.252395",
+    "rel_abs": "The emergence of SARS-CoV-2 has resulted in an ongoing global pandemic with significant morbidity, mortality, and economic consequences. The susceptibility of different animal species to SARS-CoV-2 is of concern due to the potential for interspecies transmission, and the requirement for pre-clinical animal models to develop effective countermeasures. In the current study, we determined the ability of SARS-CoV-2 to (i) replicate in porcine cell lines, (ii) establish infection in domestic pigs via experimental oral/intranasal/intratracheal inoculation, and (iii) transmit to co-housed naive sentinel pigs. SARS-CoV-2 was able to replicate in two different porcine cell lines with cytopathic effects. Interestingly, none of the SARS-CoV-2-inoculated pigs showed evidence of clinical signs, viral replication or SARS-CoV-2-specific antibody responses. Moreover, none of the sentinel pigs displayed markers of SARS-CoV-2 infection. These data indicate that although different porcine cell lines are permissive to SARS-CoV-2, five-week old pigs are not susceptible to infection via oral/intranasal/intratracheal challenge. Pigs are therefore unlikely to be significant carriers of SARS-CoV-2 and are not a suitable pre-clinical animal model to study SARS-CoV-2 pathogenesis or efficacy of respective vaccines or therapeutics.",
+    "rel_num_authors": 15,
+    "rel_authors": [
+      {
+        "author_name": "David A Meekins",
+        "author_inst": "Center of Excellence for Emerging and Zoonotic Animal Diseases, Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State Uni"
+      },
+      {
+        "author_name": "Igor Morozov",
+        "author_inst": "Center of Excellence for Emerging and Zoonotic Animal Diseases, Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State Uni"
+      },
+      {
+        "author_name": "Jessie D Trujillo",
+        "author_inst": "Center of Excellence for Emerging and Zoonotic Animal Diseases, Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State Uni"
+      },
+      {
+        "author_name": "Natasha N Gaudreault",
+        "author_inst": "Center of Excellence for Emerging and Zoonotic Animal Diseases, Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State Uni"
+      },
+      {
+        "author_name": "Dashzeveg Bold",
+        "author_inst": "Center of Excellence for Emerging and Zoonotic Animal Diseases, Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State Uni"
+      },
+      {
+        "author_name": "Bianca L Artiaga",
+        "author_inst": "Center of Excellence for Emerging and Zoonotic Animal Diseases, Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State Uni"
+      },
+      {
+        "author_name": "Sabarish V Indran",
+        "author_inst": "Center of Excellence for Emerging and Zoonotic Animal Diseases, Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State Uni"
+      },
+      {
+        "author_name": "Taeyong Kwon",
+        "author_inst": "Center of Excellence for Emerging and Zoonotic Animal Diseases, Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State Uni"
+      },
+      {
+        "author_name": "Velmurugan Balaraman",
+        "author_inst": "Center of Excellence for Emerging and Zoonotic Animal Diseases, Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State Uni"
+      },
+      {
+        "author_name": "Daniel W Madden",
+        "author_inst": "Center of Excellence for Emerging and Zoonotic Animal Diseases, Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State Uni"
+      },
+      {
+        "author_name": "Heinz Feldmann",
+        "author_inst": "Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA"
+      },
+      {
+        "author_name": "Jamie Henningson",
+        "author_inst": "Center of Excellence for Emerging and Zoonotic Animal Diseases, Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State Uni"
+      },
+      {
+        "author_name": "Wenjun Ma",
+        "author_inst": "Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA and Department of Veterinary Pathobi"
+      },
+      {
+        "author_name": "Udeni B.R. Balasuriya",
+        "author_inst": "Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Roug"
+      },
+      {
+        "author_name": "Juergen A Richt",
+        "author_inst": "Center of Excellence for Emerging and Zoonotic Animal Diseases, Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State Uni"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2020.08.15.252353",
     "rel_title": "High titers of multiple antibody isotypes against the SARS-CoV-2 spike receptor-binding domain and nucleoprotein associate with better neutralization.",
@@ -1229150,73 +1228131,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "respiratory medicine"
   },
-  {
-    "rel_doi": "10.1101/2020.08.13.20174565",
-    "rel_title": "The Effect of Neutropenia and Filgrastim (G-CSF) in Cancer Patients With COVID-19 Infection",
-    "rel_date": "2020-08-15",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.13.20174565",
-    "rel_abs": "BackgroundNeutropenia is commonly encountered in cancer patients, and recombinant human granulocyte colony-stimulating factor (G-CSF, filgrastim) is widely given to oncology patients to counteract neutropenia and prevent infection. G-CSF is both a growth factor and cytokine that initiates proliferation and differentiation of mature granulocytes. However, the clinical impact of neutropenia and G-CSF use in cancer patients, who are also afflicted with coronavirus disease 2019 (COVID-19), remains unknown.\n\nMethodsAn observational cohort of 304 hospitalized patients with COVID-19 at Memorial Sloan Kettering Cancer Center was assembled to investigate links between concurrent neutropenia (N=55) and G-CSF administration (N=16) on COVID-19-associated respiratory failure and death. These factors were assessed as time-dependent predictors using an extended Cox model, controlling for age and underlying cancer diagnosis. To determine whether the degree of granulocyte response to G-CSF affected outcomes, a similar model was constructed with patients that received G-CSF, categorized into \"high\"- and \"low\"- response, based on the level of absolute neutrophil count (ANC) rise 24 hours after growth factor administration.\n\nResultsNeutropenia (ANC < 1 K/mcL) during COVID-19 course was not independently associated with severe respiratory failure or death (HR: 0.71, 95% Cl: 0.34-1.50, P value: 0.367) in hospitalized COVID-19 patients. When controlling for neutropenia, G-CSF administration was associated with increased need for high oxygen supplementation and death (HR: 2.97, 95% CI: 1.06-8.28, P value: 0.038). This effect was predominantly seen in patients that exhibited a \"high\" response to G-CSF based on their ANC increase post-G-CSF administration (HR: 5.18, 95% CI: 1.61-16.64, P value: 0.006).\n\nConclusionPossible risks versus benefits of G-CSF administration should be weighed in neutropenic cancer patients with COVID-19 infection, as G-CSF may lead to worsening clinical and respiratory status in this setting.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Sejal Morjaria",
-        "author_inst": "Memorial Sloan Kettering Cancer Center"
-      },
-      {
-        "author_name": "Allen Zhang",
-        "author_inst": "University of British Columbia"
-      },
-      {
-        "author_name": "Anna Kaltsas MD",
-        "author_inst": "Memorial Sloan Kettering Cancer Center"
-      },
-      {
-        "author_name": "Rekha Parameswaran",
-        "author_inst": "Memorial Sloan Kettering Cancer Center"
-      },
-      {
-        "author_name": "Dhruvkumar Patel",
-        "author_inst": "Memorial Sloan Kettering Cancer Center"
-      },
-      {
-        "author_name": "Wei Zhou",
-        "author_inst": "Memorial Sloan Kettering Cancer Center"
-      },
-      {
-        "author_name": "Jacqueline Predmore",
-        "author_inst": "Memorial Sloan Kettering Cancer Center"
-      },
-      {
-        "author_name": "Rocio Perez Johnston",
-        "author_inst": "Memorial Sloan Kettering Cancer Center"
-      },
-      {
-        "author_name": "Justin Jee",
-        "author_inst": "MSKCC"
-      },
-      {
-        "author_name": "Miguel Perales",
-        "author_inst": "Memorial Sloan Kettering Cancer Center"
-      },
-      {
-        "author_name": "Anthony Daniyan",
-        "author_inst": "Memorial Sloan Kettering Cancer Center"
-      },
-      {
-        "author_name": "Ying Taur",
-        "author_inst": "Memorial Sloan Kettering Cancer Center"
-      },
-      {
-        "author_name": "Sham Mailankody",
-        "author_inst": "Memorial Sloan Kettering Cancer Center"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.08.13.20174524",
     "rel_title": "Mortality Associated With Intubation and Mechanical Ventilation in Patients with COVID-19",
@@ -1229419,6 +1228333,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.08.13.249847",
+    "rel_title": "Open Science Saves Lives: Lessons from the COVID-19 Pandemic",
+    "rel_date": "2020-08-14",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.13.249847",
+    "rel_abs": "In the last decade Open Science principles have been successfully advocated for and are being slowly adopted in different research communities. In response to the COVID-19 pandemic many publishers and researchers have sped up their adoption of Open Science practices, sometimes embracing them fully and sometimes partially or in a sub-optimal manner. In this article, we express concerns about the violation of some of the Open Science principles and its potential impact on the quality of research output. We provide evidence of the misuses of these principles at different stages of the scientific process. We call for a wider adoption of Open Science practices in the hope that this work will encourage a broader endorsement of Open Science principles and serve as a reminder that science should always be a rigorous process, reliable and transparent, especially in the context of a pandemic where research findings are being translated into practice even more rapidly. We provide all data and scripts at https://osf.io/renxy/.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Lonni Besan\u00e7on",
+        "author_inst": "Faculty of Information Technology, Monash University, Melbourne, Australia"
+      },
+      {
+        "author_name": "Nathan Peiffer-Smadja",
+        "author_inst": "Universite de Paris, IAME, INSERM, F-75018 Paris, France"
+      },
+      {
+        "author_name": "Corentin Segalas",
+        "author_inst": "Department of Medical Statistics, London School of Hygiene and Tropical Medicine, London, United Kingdom"
+      },
+      {
+        "author_name": "Haiting Jiang",
+        "author_inst": "School of Health Policy and Management, Nanjing Medical University, No.101 Longmian Avenue, Nanjing 211166, P.R.China"
+      },
+      {
+        "author_name": "Paola Masuzzo",
+        "author_inst": "IGDORE, Institute for Globally Distributed Open Research and Education"
+      },
+      {
+        "author_name": "Cooper A Smout",
+        "author_inst": "The University of Queensland"
+      },
+      {
+        "author_name": "Eric Billy",
+        "author_inst": "Immuno-oncology researcher, Strasbourg, France"
+      },
+      {
+        "author_name": "Maxime Deforet",
+        "author_inst": "Sorbonne Universite, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), F-75005, Paris, France"
+      },
+      {
+        "author_name": "Cl\u00e9mence Leyrat",
+        "author_inst": "Department of Medical Statistics, London School of Hygiene and Tropical Medicine, London, United Kingdom"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "new results",
+    "category": "scientific communication and education"
+  },
   {
     "rel_doi": "10.1101/2020.08.11.245415",
     "rel_title": "Extensive Genetic Diversity and Host Range of Rodent-borne Coronaviruses",
@@ -1230656,33 +1229621,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.08.13.20174144",
-    "rel_title": "Precise Prediction of COVID-19 in Chest X-Ray Images Using KE Sieve Algorithm",
-    "rel_date": "2020-08-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.13.20174144",
-    "rel_abs": "The novel coronavirus (COVID-19) pandemic is pressurizing the healthcare systems across the globe and few of them are on the verge of failing. The detection of this virus as early as possible will help in contaminating the spread of it as the virus is mutating itself as fast as possible and currently there are about 4,300 strains of the virus according to the reports. Clinical studies have shown that most of the COVID-19 patients suffer from a lung infection similar to influenza. So, it is possible to diagnose lung infection using imaging techniques. Although a chest computed tomography (CT) scan has been shown to be an effective imaging technique for lung-related disease diagnosis, chest X-ray is more widely available across the hospitals due to its considerably lower cost and faster imaging time than CT scan. The advancements in the area of machine learning and pattern recognition has resulted in intelligent systems that analyze CT Scans or X-ray images and classify between pneumonia and normal patients. This paper proposes KE Sieve Neural Network architecture, which helps in the rapid diagnosis of COVID-19 using chest X-ray images. This architecture is achieving an accuracy of 98.49%. This noninvasive prediction method can assist the doctors in this pandemic and reduce the stress on health care systems.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "S Sai Thejeshwar",
-        "author_inst": "Alpes.ai"
-      },
-      {
-        "author_name": "Chaitanya Chokkareddy",
-        "author_inst": "ALPES.ai"
-      },
-      {
-        "author_name": "K Eswaran",
-        "author_inst": "Sreenidhi Institute Of Science and Technology"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "radiology and imaging"
-  },
   {
     "rel_doi": "10.1101/2020.08.11.20171967",
     "rel_title": "Lower respiratory tract myeloid cells harbor SARS-CoV-2 and display an inflammatory phenotype",
@@ -1231045,6 +1229983,113 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.08.11.20171843",
+    "rel_title": "Functional SARS-CoV-2-specific immune memory persists after mild COVID-19",
+    "rel_date": "2020-08-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.11.20171843",
+    "rel_abs": "The recently emerged SARS-CoV-2 virus is currently causing a global pandemic and cases continue to rise. The majority of infected individuals experience mildly symptomatic coronavirus disease 2019 (COVID-19), but it is unknown whether this can induce persistent immune memory that might contribute to herd immunity. Thus, we performed a longitudinal assessment of individuals recovered from mildly symptomatic COVID-19 to determine if they develop and sustain immunological memory against the virus. We found that recovered individuals developed SARS-CoV-2-specific IgG antibody and neutralizing plasma, as well as virus-specific memory B and T cells that not only persisted, but in some cases increased numerically over three months following symptom onset. Furthermore, the SARS-CoV-2-specific memory lymphocytes exhibited characteristics associated with potent antiviral immunity: memory T cells secreted IFN-{gamma} and expanded upon antigen re-encounter, while memory B cells expressed receptors capable of neutralizing virus when expressed as antibodies. These findings demonstrate that mild COVID-19 elicits memory lymphocytes that persist and display functional hallmarks associated with antiviral protective immunity.",
+    "rel_num_authors": 23,
+    "rel_authors": [
+      {
+        "author_name": "Lauren B Rodda",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Jason Netland",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Laila Shehata",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Kurt B Pruner",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Peter M Morawski",
+        "author_inst": "Benaroya Research Institute"
+      },
+      {
+        "author_name": "Christopher Thouvenel",
+        "author_inst": "Seattle Children's Research Institute"
+      },
+      {
+        "author_name": "Kennidy K Takehara",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Julie Eggenberger",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Emily A Hemann",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Hayley R Waterman",
+        "author_inst": "Benaroya Research Institute"
+      },
+      {
+        "author_name": "Mitchell L Fahning",
+        "author_inst": "Benaroya Research Institute"
+      },
+      {
+        "author_name": "Yu Chen",
+        "author_inst": "Seattle Children's Research Institute"
+      },
+      {
+        "author_name": "Jennifer Rathe",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Caleb Stokes",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Samuel Wrenn",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Brooke Fiala",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Lauren P Carter",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Jessica A Hamerman",
+        "author_inst": "Benaroya Research Institute"
+      },
+      {
+        "author_name": "Neil P King",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Michael Gale",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Daniel J Campbell",
+        "author_inst": "Benaroya Research Institute"
+      },
+      {
+        "author_name": "David Rawlings",
+        "author_inst": "Seattle Children's Research Institute"
+      },
+      {
+        "author_name": "Marion Pepper",
+        "author_inst": "University of Washington"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.08.12.20156257",
     "rel_title": "Obesity, old age and frailty are the true risk factors for COVID-19 mortality and not chronic disease or ethnicity in Croydon.",
@@ -1232314,29 +1231359,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.08.12.20173617",
-    "rel_title": "Comprehensive analysis of the key epidemiological parameters to evaluate the impact of BCG vaccination on COVID-19 pandemic",
-    "rel_date": "2020-08-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.12.20173617",
-    "rel_abs": "Globally, the heterogenous coronavirus disease 2019 (COVID-19) case fatality rate (CFR) could be influenced by various epidemiological parameters. Identifying these could help formulate effective public health strategies. Incidence and mortality of COVID-19 for each of the 220 countries as on July 30, 2020 were evaluated against key epidemiological variables, namely - BCG vaccination (ongoing vs. discontinued/never undertaken), %population aged [&ge;]65 years, incidences of ischemic heart disease (IHD), hypertensive heart disease (HHD), cancer, malaria, and diabetes; human development index (HDI) and population density. These were retrieved from the public domains of WHO, UN, World Bank and published reports. The COVID-19 CFRs ranged between 0.0% and 28.3% (mean {+/-} SD: 3.05% {+/-} 3.48). The influence of the individual epidemiological parameters on CFR were evaluated through the event rate estimations. A significantly lower event rate was observed in countries with ongoing BCG vaccination program (ER: with vs without ongoing BCG vaccination: 0.020 vs 0.034, p<0.001). The type of BCG strains used also influenced the ER; this being 0.018, 0.031 and 0.019 for early, late and mixed strains respectively (p=0.008). The epidemiological variables significantly associated with higher COVID-19 event rate were countries with higher %population aged [&ge;]65 years (p<0.001), greater incidence of IHD (p<0.001) and cancer (p=0.003) and better HDI (p=0.003). Incidences of malaria, HHD and diabetes along with population density had no significant impact on COVID-19 CFR. Further, BCG vaccination significantly lowered the COVID-19 ER in each of the high-risk population subgroups - countries with >7.1% population aged [&ge;]65 years (p=0.008), >0.737 HDI (p=0.001), IHD >1171/105 population (p=0.004) and cancer incidence >15726 (p<0.001). The results supports BCG induced \"trained immunity\" leading to heterologous immunoprotection against COVID-19. Thus BCG vaccination with early strains could provide a cost-effective prophylaxis, especially in high-risk individuals and bridge the gap till an effective vaccine against SARS-CoV-2 is freely available globally.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Niloy R Datta",
-        "author_inst": "Kantonsspital Aarau"
-      },
-      {
-        "author_name": "Sneha Datta",
-        "author_inst": "Independent Researcher"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.08.12.20173849",
     "rel_title": "Obesity and Smoking as Risk Factors for Invasive Mechanical Ventilation in COVID-19: a Retrospective, Observational Cohort Study",
@@ -1232575,6 +1231597,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.08.13.20173997",
+    "rel_title": "Deep Learning for Automated Recognition of Covid-19 from Chest X-ray Images",
+    "rel_date": "2020-08-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.13.20173997",
+    "rel_abs": "BackgroundThe pandemic caused by coronavirus in recent months is having a devastating global effect, which puts the world under the most ever unprecedented emergency. Currently, since there are not effective antiviral treatments for Covid-19 yet, it is crucial to early detect and monitor the progression of the disease, thus helping to reduce mortality. While a corresponding vaccine is being developed, and different measures are being used to combat the virus, medical imaging techniques have also been investigated to assist doctors in diagnosing this disease.\n\nObjectiveThis paper presents a practical solution for the detection of Covid-19 from chest X-ray (CXR) images, exploiting cutting-edge Machine Learning techniques.\n\nMethodsWe employ EfficientNet and MixNet, two recently developed families of deep neural networks, as the main classification engine. Furthermore, we also apply different transfer learning strategies, aiming at making the training process more accurate and efficient. The proposed approach has been validated by means of two real datasets, the former consists of 13,511 training images and 1,489 testing images, the latter has 14,324 and 3,581 images for training and testing, respectively.\n\nResultsThe results are promising: by all the experimental configurations considered in the evaluation, our approach always yields an accuracy larger than 95.0%, with the maximum accuracy obtained being 96.64%.\n\nConclusionsAs a comparison with various existing studies, we can thus conclude that our performance improvement is significant.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Phuong Nguyen",
+        "author_inst": "University of L'Aquila"
+      },
+      {
+        "author_name": "Ludovico Iovino",
+        "author_inst": "Gran Sasso Science Institute, Italy"
+      },
+      {
+        "author_name": "Michele Flammini",
+        "author_inst": "Gran Sasso Science Institute, Italy"
+      },
+      {
+        "author_name": "Linh Tuan Linh",
+        "author_inst": "Duy Tan University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "radiology and imaging"
+  },
   {
     "rel_doi": "10.1101/2020.08.11.20172551",
     "rel_title": "Results and Impact of Intensive SARS-CoV-2 Testing in a High Volume, Outpatient Radiation Oncology Clinic in a Pandemic Hotspot",
@@ -1233676,33 +1232729,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.08.12.20173328",
-    "rel_title": "Hospital preparedness in epidemics by using simulation. The case of COVID-19",
-    "rel_date": "2020-08-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.12.20173328",
-    "rel_abs": "This paper presents a discrete event simulation model to support the decision-making concerned with the short-term planning of the necessary hospital resources, especially Intensive Care Unit (ICU) beds, to face outbreaks, as the SARS-CoV-2. Being used as a short-term forecasting tool, the simulation model requires an accurate representation of the current system state and high fidelity in mimicking the system dynamics from that state. The two main components of the simulation model are the stochastic modeling of the admission of new patients and the patient flow through the hospital facilities. For the patient arrival process, we analyze different models based on growth curves of the twenty most affected countries (until June 15) and propose the use of the Gompertz curve. The length of stay is divided into several stages, each one modeled separately. We analyze the starting of the simulation model, which requires different procedures depending on the information available about the patients currently hospitalized. We also report the use of this simulation model during the COVID-19 outbreak in the Autonomous Community of Navarre, in Spain. Every day, the research team informed the regional logistic team in charge of planning the health resources, who programmed the ward and ICU beds based on the resulting predictions.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Daniel Garcia-Vicuna",
-        "author_inst": "Public University of Navarre"
-      },
-      {
-        "author_name": "Laida Esparza",
-        "author_inst": "Hospital Compound of Navarre"
-      },
-      {
-        "author_name": "Fermin Mallor",
-        "author_inst": "Public University of Navarre"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.08.13.20174045",
     "rel_title": "COVID-19 vaccination intention in the UK: Results from the COVID-19 Vaccination Acceptability Study (CoVAccS), a nationally representative cross-sectional survey",
@@ -1234117,6 +1233143,29 @@
     "type": "new results",
     "category": "genomics"
   },
+  {
+    "rel_doi": "10.1101/2020.08.13.250076",
+    "rel_title": "In Silico Design of siRNAs Targeting Existing and Future Respiratory Viruses with VirusSi",
+    "rel_date": "2020-08-14",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.13.250076",
+    "rel_abs": "The COVID-19 pandemic has exposed global inadequacies in therapeutic options against both the COVID-19-causing SARS-CoV-2 virus and other newly emerged respiratory viruses. In this study, we present the VirusSi computational pipeline, which facilitates the rational design of siRNAs to target existing and future respiratory viruses. Mode A of VirusSi designs siRNAs against an existing virus, incorporating considerations on siRNA properties, off-target effects, viral RNA structure and viral mutations. It designs multiple siRNAs out of which the top candidate targets >99% of SARS-CoV-2 strains, and the combination of the top four siRNAs is predicted to target all SARS-CoV-2 strains. Additionally, we develop Greedy Algorithm with Redundancy (GAR) and Similarity-weighted Greedy Algorithm with Redundancy (SGAR) to support the Mode B of VirusSi, which pre-designs siRNAs against future emerging viruses based on existing viral sequences. Time-simulations using known coronavirus genomes as early as 10 years prior to the COVID-19 outbreak show that at least three SARS-CoV-2-targeting siRNAs are among the top 30 pre-designed siRNAs. Before-the-outbreak pre-design is also possible against the MERS-CoV virus and the 2009-H1N1 swine flu virus. Our data support the feasibility of pre-designing anti-viral siRNA therapeutics prior to viral outbreaks. We propose the development of a collection of pre-designed, safety-tested, and off-the-shelf siRNAs that could accelerate responses toward future viral diseases.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Dingyao Zhang",
+        "author_inst": "Yale University"
+      },
+      {
+        "author_name": "Jun Lu",
+        "author_inst": "Yale University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "bioinformatics"
+  },
   {
     "rel_doi": "10.1101/2020.08.14.251496",
     "rel_title": "Rational Design of SARS-CoV-2 Spike Glycoproteins To Increase Immunogenicity By T Cell Epitope Engineering",
@@ -1235574,29 +1234623,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.08.09.20171181",
-    "rel_title": "The impact of COVID-19 on Italy web users: a quantitative analysis of regional hygiene interest and emotional response",
-    "rel_date": "2020-08-13",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.09.20171181",
-    "rel_abs": "BackgroundBetween the end of February and the beginning of June 2020, Italy was certainly one of the worst affected countries in the world by the COVID-19 pandemic. During this period, Web interest in the novel coronavirus underwent a drastic surge.\n\nObjectiveThe aim of this study was to quantitatively analyze the impact of COVID-19 on Web searches related to hygiene-preventive measures and emotional-psychological aspects as well as to estimate the effectiveness and limits of online information during an epidemic. We looked for significant correlations between COVID-19 relative search volumes and cases per region to understand the interest of the average Italian Web user during international, national, and regional COVID-19 situations. By doing so, from the analysis of Web searches, it will be possible to deduce the mental and physical health of the population.\n\nMethodsTo conduct this research, we used the \"Google Trends\" tool, which returns normalized values, called \"relative search volumes\" (RSVs), ranging from 0 to 100 according to the Web popularity of a group of queries. By comparing the RSVs in periods before and after the outbreak of the novel coronavirus in Italy, we derived the impact of COVID-19 on the activity of Italian netizens towards novel coronavirus itself, specifically regarding hygiene, prevention, and psychological well-being. Furthermore, we calculated Pearsons correlations{rho} between all these queries and COVID-19 cases for each region. We chose a p-value (p) threshold  = .1.\n\nResultsAfter the two initial spikes that occurred on February 23 and March 9, 2020, the general Web interest in COVID-19 in Italy waned, as did the correlation with the official number of cases per region (p < .1 only until March 14, 2020). However, Web interest was similarly distributed across the regions (ASV = 92, SD = 6). We also found that all trends depend significantly on the number of COVID-19 cases at the national but not international or regional levels. Between February 20 and June 10, 2020, Web interest relating to hygiene and prevention increased by 116 and, 901% respectively, compared to those from January 1 to February 19, 2020 (95% CIs: [115.3, 116.3], [850.3, 952,2]). Significant correlations between regional cumulative Web searches and COVID-19 cases were found only between February 26 and March 7, 2020 ({rho}best = .43, 95% CI: [.42, .44],p = .07). During the COVID-19 pandemic until June 10, 2020, national Web searches of the generic terms \"fear\" and \"anxiety\" grew by 8% and 21%, respectively (95% CIs: [8.0,8.2], [20.4,20.6]), compared to those of the period of January 1, 2018 - December 29, 2019. We found cyclically significant correlations between negative emotions related to the novel coronavirus and COVID-19 official data.\n\nConclusionsItalian netizens showed a marked interest in the COVID-19 pandemic only when this became a direct national problem. In general, Web searches have rarely been correlated with the number of cases per region; we conclude that the danger, once it arrived in the country, was perceived similarly in all regions. We can state that the period of maximum effectiveness of online information in relation to this type of situation is limited to 3-4 days from a specific key event. If such a scenario were to occur again, we suggest that all government agencies focus their Web disclosure efforts over that time. Despite this, we found cyclical correlations with Web searches related to negative feelings such as anxiety, depression, fear, and stress. Therefore, to identify mental and physical health problems among the population, it suffices to observe slight variations in the trend of related Web queries.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Alessandro Rovetta",
-        "author_inst": "Mensana srls; Redeev srl"
-      },
-      {
-        "author_name": "Lucia Castaldo",
-        "author_inst": "Redeev srl, Mensana srls"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.08.10.20167247",
     "rel_title": "Fine-tuned Forecasting Techniques for COVID-19 Prediction in India",
@@ -1235867,6 +1234893,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.08.10.20171629",
+    "rel_title": "Risk of fomite-mediated transmission of SARS-CoV-2 in child daycares, schools, and offices: a modeling study",
+    "rel_date": "2020-08-13",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20171629",
+    "rel_abs": "SARS-CoV-2 can persist on surfaces, suggesting that surface-based transmission might be important for this pathogen. We find that fomites may be a substantial source of risk, particularly in schools and child daycares. Combining surface cleaning and decontamination with strategies to reduce pathogen shedding on surfaces can help mitigate this risk.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Alicia Nicole Mullis Kraay",
+        "author_inst": "Emory University"
+      },
+      {
+        "author_name": "Michael A L Hayashi",
+        "author_inst": "University of Michigan, Ann Arbor"
+      },
+      {
+        "author_name": "David M Berendes",
+        "author_inst": "Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Pr"
+      },
+      {
+        "author_name": "Julia S Sobolik",
+        "author_inst": "Emory University"
+      },
+      {
+        "author_name": "Juan S Leon",
+        "author_inst": "Emory University"
+      },
+      {
+        "author_name": "Benjamin A Lopman",
+        "author_inst": "Emory University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.08.10.20169649",
     "rel_title": "The COVID-19 Pandemic Vulnerability Index (PVI) Dashboard: monitoring county level vulnerability",
@@ -1237072,77 +1236137,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.08.10.20171942",
-    "rel_title": "High prevalence of symptoms among Brazilian subjects with antibodies against SARS-CoV-2: a nationwide household survey",
-    "rel_date": "2020-08-12",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20171942",
-    "rel_abs": "Since the beginning of the pandemic of COVID-19, there has been a widespread assumption that most infected persons are asymptomatic. A frequently-cited early study from China suggested that 86% of all infections were undocumented, which was used as indirect evidence that patients were asymptomatic.\n\nUsing data from the most recent wave of the EPICOVID19 study, a nationwide household-based survey including 133 cities from all states of Brazil, we estimated the proportion of people with and without antibodies for SARS-CoV-2 who were asymptomatic, which symptoms were most frequently reported, the number of symptoms reported and the association between symptomatology and socio-demographic characteristics. We were able to test 33,205 subjects using a rapid antibody test that was previously validated. Information on symptoms was collected before participants received the test result. Out of 849 (2.7%) participants who tested positive for SARS-CoV-2 antibodies, only 12.1% (95%CI 10.1-14.5) reported no symptoms since the start of the pandemic, compared to 42.2% (95%CI 41.7-42.8) among those who tested negative. The largest difference between the two groups was observed for changes in smell or taste (56.5% versus 9.1%, a 6.2-fold difference). Symptoms change in smell or taste, fever and myalgia were most likely to predict positive test results as suggested by recursive partitioning tree analysis.\n\nAmong individuals without any of these three symptoms (74.2% of the sample), only 0.8% tested positive, compared to 18.3% of those with both fever and changes in smell or taste. Most subjects with antibodies against SARS-CoV-2 in Brazil are symptomatic, even though most present only mild symptoms.",
-    "rel_num_authors": 14,
-    "rel_authors": [
-      {
-        "author_name": "Ana Maria Baptista Menezes",
-        "author_inst": "Universidade Federal de Pelotas"
-      },
-      {
-        "author_name": "Cesar G Victora",
-        "author_inst": "Universidade Federal de Pelotas"
-      },
-      {
-        "author_name": "Fernando P Hartwig",
-        "author_inst": "Universidade Federal de Pelotas"
-      },
-      {
-        "author_name": "Mariangela F Silveira",
-        "author_inst": "Universidade Federal de Pelotas"
-      },
-      {
-        "author_name": "Bernardo L Horta",
-        "author_inst": "Universidade Federal de Pelotas"
-      },
-      {
-        "author_name": "Aluisio J D Barros",
-        "author_inst": "Universidade Federal de Pelotas"
-      },
-      {
-        "author_name": "Fernando C Whermeister",
-        "author_inst": "Universidade Federal de Pelotas"
-      },
-      {
-        "author_name": "Marilia A Mesenburg",
-        "author_inst": "Universidade Federal de Pelotas"
-      },
-      {
-        "author_name": "Lucia C Pellanda",
-        "author_inst": "Fundacao Universidade Federal de Ciencias de Saude de Porto Alegre"
-      },
-      {
-        "author_name": "Odir A Dellagostin",
-        "author_inst": "Universidade Federal de Pelotas"
-      },
-      {
-        "author_name": "Claudio J Struchiner",
-        "author_inst": "Fundacao Getulio Vargas"
-      },
-      {
-        "author_name": "Marcelo N Burattini",
-        "author_inst": "Universidade de Sao Paulo"
-      },
-      {
-        "author_name": "Fernando C Barros",
-        "author_inst": "Universidade Federal de Pelotas"
-      },
-      {
-        "author_name": "Pedro C Hallal",
-        "author_inst": "Universidade Federal de Pelotas"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.08.11.20173005",
     "rel_title": "Histopathology of Third Trimester Placenta from SARS-CoV-2-Positive Women",
@@ -1237453,6 +1236447,181 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.08.11.247395",
+    "rel_title": "Elicitation of potent neutralizing antibody responses by designed protein nanoparticle vaccines for SARS-CoV-2",
+    "rel_date": "2020-08-12",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.11.247395",
+    "rel_abs": "A safe, effective, and scalable vaccine is urgently needed to halt the ongoing SARS-CoV-2 pandemic. Here, we describe the structure-based design of self-assembling protein nanoparticle immunogens that elicit potent and protective antibody responses against SARS-CoV-2 in mice. The nanoparticle vaccines display 60 copies of the SARS-CoV-2 spike (S) glycoprotein receptor-binding domain (RBD) in a highly immunogenic array and induce neutralizing antibody titers roughly ten-fold higher than the prefusion-stabilized S ectodomain trimer despite a more than five-fold lower dose. Antibodies elicited by the nanoparticle immunogens target multiple distinct epitopes on the RBD, suggesting that they may not be easily susceptible to escape mutations, and exhibit a significantly lower binding:neutralizing ratio than convalescent human sera, which may minimize the risk of vaccine-associated enhanced respiratory disease. The high yield and stability of the protein components and assembled nanoparticles, especially compared to the SARS-CoV-2 prefusion-stabilized S trimer, suggest that manufacture of the nanoparticle vaccines will be highly scalable. These results highlight the utility of robust antigen display platforms for inducing potent neutralizing antibody responses and have launched cGMP manufacturing efforts to advance the lead RBD nanoparticle vaccine into the clinic.",
+    "rel_num_authors": 40,
+    "rel_authors": [
+      {
+        "author_name": "Alexandra C Walls",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Brooke Fiala",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Alexandra Schaefer",
+        "author_inst": "University of North Carolina Chapel Hill"
+      },
+      {
+        "author_name": "Samuel Wrenn",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Minh N Pham",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Michael Murphy",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Longping V Tse",
+        "author_inst": "University of North Carolina Chapel Hill"
+      },
+      {
+        "author_name": "Laila Shehata",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Chengbo Chen",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Mary Jane Navarro",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Marcos C Miranda",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Deleah Pettie",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Rashmi Ravichandran",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "John C Kraft",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Cassandra Ogohara",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Anne Palser",
+        "author_inst": "Kymab Ltd"
+      },
+      {
+        "author_name": "Sara Chalk",
+        "author_inst": "Kymab Ltd"
+      },
+      {
+        "author_name": "E-Chiang Lee",
+        "author_inst": "Kymab Ltd"
+      },
+      {
+        "author_name": "Elizabeth Kepl",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Cameron M Chow",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Claire Sydeman",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Edgar A Hodge",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Brieann Brown",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Jim T Fuller",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Kenneth Dinnon III",
+        "author_inst": "University of North Carolina at Chapel Hill"
+      },
+      {
+        "author_name": "Lisa Gralinski",
+        "author_inst": "University of North Carolina at Chapel Hill"
+      },
+      {
+        "author_name": "Sarah R Leist",
+        "author_inst": "University of North Carolina"
+      },
+      {
+        "author_name": "Kendra L Gully",
+        "author_inst": "University of North Carolina at Chapel Hill"
+      },
+      {
+        "author_name": "Thomas B Lewis",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Miklos Guttman",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Helen Y Chu",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Kelly K Lee",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Deborah H Fuller",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Ralph S. Baric",
+        "author_inst": "University of North Carolina at Chapel Hill"
+      },
+      {
+        "author_name": "Paul Kellam",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Lauren Carter",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Marion Pepper",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Timothy P Sheahan",
+        "author_inst": "University of North Carolina at Chapel Hill"
+      },
+      {
+        "author_name": "David Veesler",
+        "author_inst": "University of Washington"
+      },
+      {
+        "author_name": "Neil P King",
+        "author_inst": "University of Washington"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2020.08.11.247320",
     "rel_title": "Efficacy of Targeting SARS-CoV-2 by CAR-NK Cells",
@@ -1238810,53 +1237979,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.08.07.20170001",
-    "rel_title": "Switching from algorithm-based to universal admission screening for COVID-19 in hospital settings",
-    "rel_date": "2020-08-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.07.20170001",
-    "rel_abs": "Detection of COVID-19 positive cases on admission to hospitals is crucial to protect patients and staff at the same time. While universal admission screening can prevent more undetected introductions than the algorithm-based screening, which preselects patient based on their symptoms and exposure, it is a more costly strategy as it involves testing a large number of patients.\n\nWe construct a simple tool to help determine when the benefit of additionally found cases outweighs the cost of the additionally tested patients, based on the numbers of patients to be screened in an acceptable time span to find an additional case when screening all admitted patients.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Tjibbe Donker",
-        "author_inst": "University Hospital Freiburg"
-      },
-      {
-        "author_name": "Hajo Grundmann",
-        "author_inst": "University Hospital Freiburg"
-      },
-      {
-        "author_name": "Fabian B\u00fcrkin",
-        "author_inst": "University Hospital Freiburg"
-      },
-      {
-        "author_name": "Hartmut Hengel",
-        "author_inst": "University Hospital Freiburg"
-      },
-      {
-        "author_name": "Hartmut B\u00fcrkle",
-        "author_inst": "University Hospital Freiburg"
-      },
-      {
-        "author_name": "Thorsten Hammer",
-        "author_inst": "University Hospital Freiburg"
-      },
-      {
-        "author_name": "Frederik Wenz",
-        "author_inst": "University Hospital Freiburg"
-      },
-      {
-        "author_name": "Winfried Kern",
-        "author_inst": "University Hospital Freiburg"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.08.07.20160275",
     "rel_title": "Severe COVID-19 and Diabetes: A Retrospective Cohort Study from Three London Teaching Hospitals",
@@ -1239167,6 +1238289,77 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.08.07.20170449",
+    "rel_title": "Outcomes of COVID-19 related hospitalisation among people with HIV in the ISARIC WHO Clinical Characterisation Protocol UK Protocol: prospective observational study",
+    "rel_date": "2020-08-11",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.07.20170449",
+    "rel_abs": "Background.There is conflicting evidence about how HIV infection influences COVID-19. We compared the presentation characteristics and outcomes of people with and without HIV hospitalised with COVID-19 at 207 centres across the United Kingdom.\n\nMethods.We analysed data from people with laboratory confirmed or highly likely COVID-19 enrolled into the ISARIC CCP-UK study. The primary endpoint was day-28 mortality after presentation. We used Kaplan-Meier methods and Cox regression to describe the association with HIV status after adjustment for sex, ethnicity, age, indeterminate/probable hospital acquisition of COVID-19 (definite hospital acquisition excluded), presentation date, and presence/absence of ten comorbidities. We additionally adjusted for disease severity at presentation as defined by hypoxia/oxygen therapy.\n\nFindings.Among 47,539 patients, 115 (0{middle dot}24%) had confirmed HIV-positive status and 103/115 (89{middle dot}6%) had a record of antiretroviral therapy. At presentation, relative to the HIV-negative group, HIV-positive people were younger (median 55 versus 74 years; p<0{middle dot}001), had a higher prevalence of obesity and moderate/severe liver disease, higher lymphocyte counts and C-reactive protein, and more systemic symptoms. The cumulative incidence of day-28 mortality was 25{middle dot}2% in the HIV-positive group versus 32{middle dot}1% in the HIV-negative group (p=0{middle dot}12); however, stratification for age revealed a higher mortality among HIV-positive people aged below 60 years. The effect of HIV-positive status was confirmed in adjusted analyses (adjusted hazard ratio [HR] 1{middle dot}49, 95% confidence interval [CI] 0{middle dot}99-2{middle dot}25; p=0{middle dot}06). Following additional adjustment for disease severity at presentation, mortality was higher in HIV-positive people (adjusted HR 1{middle dot}63; 95% CI 1{middle dot}07-2{middle dot}48; p=0{middle dot}02). In the HIV-positive group, mortality was more common among those who were slightly older and among people with obesity and diabetes with complications.\n\nInterpretation.HIV-positive status may be associated with an increased risk of day-28 mortality following a COVID-19 related hospitalisation.\n\nFunding.NIHR, MRC, Wellcome Trust, Department for International Development, Bill and Melinda Gates Foundation.\n\nStudy registrationISRCTN66726260\n\nRESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed for articles in all languages containing the words \"COVID*\", \"coronavirus\", \"SARS CoV-2\" AND \"HIV\". After screening on 23rd July 2020, we found 51 articles reporting outcomes of COVID-19 in HIV-positive people. Of these, 2 were systematic reviews, 24 were single case reports or case series of under 10 participants, and 12 were larger case series or retrospective cohorts without matched controls. There were two cohort studies that matched HIV-positive people diagnosed with COVID-19 to the general population attending for HIV care in the same area, and three studies that matched HIV-positive people diagnosed with COVID-19 to HIV-negative controls. Some of the evidence from the United States and Europe to date suggests that people with HIV experience a similar disease course and outcomes of COVID-19 compared to the general population. However, many of the studies are limited by small sample size, lack of comparator group and lack of adjustment for potential confounding. In contrast, preliminary results from a cohort study of over 20,000 participants in South Africa indicate that HIV-positive status more than doubles the risk of COVID-19 related mortality. Currently, the evidence from the United Kingdom is limited to two case series comprising a total of 21 patients.\n\nAdded value of this studyThis study analysed data collected from 207 sites across the United Kingdom as part of ISARIC CCP, the largest prospective cohort of patients hospitalised with COVID-19, to evaluate the association between HIV-positive status and day-28 mortality. The study has the benefit of a relatively large number of participants with HIV (n=115, almost all receiving antiretroviral therapy) and importantly, the ability to direct compare their presenting characteristics and outcomes to those of 47,424 HIV-negative controls within the same dataset. This includes the ability to assess the influence of gender, ethnicity and age, as well as the effect of key comorbidities including chronic cardiac, pulmonary, renal and haematological disease, diabetes, obesity, chronic neurological disorder, dementia, liver disease, and malignancy. Unlike some of the other evidence to date, but in line with the data from South Africa, this study indicates that HIV-positive status may increase the risk of mortality with COVID-19 compared to the general population, with an effect that was especially evident among people with HIV aged below 60 years and was independent of gender or ethnicity. Although we detected an association between mortality among people with HIV and occurrence of obesity and diabetes with complication, the effect of HIV-positive status persisted after adjusting for comorbidities.\n\nImplications of all the available evidencePeople with HIV may be at increased risk of severe outcomes from COVID-19 compared to the general population. Ongoing data collection is needed to confirm this association. Linkage of hospital outcome data to the HIV history will be paramount to establishing the determinants of the increased risk. COVID-19 related hospitalisation should pursue systematic recording of HIV status to ensure optimal management and gathering of evidence.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Anna Maria Geretti",
+        "author_inst": "University of Liverpool"
+      },
+      {
+        "author_name": "Alexander Stockdale",
+        "author_inst": "University of Liverpool"
+      },
+      {
+        "author_name": "Sophie Kelly",
+        "author_inst": "University of Liverpool"
+      },
+      {
+        "author_name": "Muge Cevik",
+        "author_inst": "University of St Andrews"
+      },
+      {
+        "author_name": "Simon Collins",
+        "author_inst": "HIV i-Base"
+      },
+      {
+        "author_name": "Laura Waters",
+        "author_inst": "Central and North West London NHS Foundation Trust, British HIV Association"
+      },
+      {
+        "author_name": "Giovanni Villa",
+        "author_inst": "University of Sussex"
+      },
+      {
+        "author_name": "Annemarie B Docherty",
+        "author_inst": "University of Edinburgh"
+      },
+      {
+        "author_name": "Ewen M Harrison",
+        "author_inst": "University of Edinburgh"
+      },
+      {
+        "author_name": "Lance Turtle",
+        "author_inst": "University of Liverpool"
+      },
+      {
+        "author_name": "Peter JM Openshaw",
+        "author_inst": "Imperial College London"
+      },
+      {
+        "author_name": "Kenneth Baillie",
+        "author_inst": "Royal Infirmary Edinburgh, University of Edinburgh"
+      },
+      {
+        "author_name": "Caroline Sabin",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Malcolm Gracie Semple",
+        "author_inst": "University of Liverpool"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "hiv aids"
+  },
   {
     "rel_doi": "10.1101/2020.08.05.20169060",
     "rel_title": "Tocilizumab in hospitalized patients with COVID-19: Clinical outcomes, inflammatory marker kinetics, safety, and a review of the literature",
@@ -1240528,69 +1239721,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.08.10.20172163",
-    "rel_title": "The impact of COVID-19 on the reproductive health of people living in Australia: findings from an online survey",
-    "rel_date": "2020-08-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20172163",
-    "rel_abs": "IntroductionAustralia introduced  lockdown measures to control COVID-19 on 22 March 2020. For two months, Australians were asked to remain at home and only leave for essential activities. We investigate the impact this had on sexual and reproductive health (SRH).\n\nMethodsAustralians aged 18+ were eligible to participate in an online survey from 23 April-11 May 2020. Questions included contraceptive use, pregnancy intentions and access to SRH services. We report on the experiences of 518 female participants aged <50 years. Pregnancy intentions and contraceptive use were analysed using descriptive statistics. Odds ratios and 95% confidence intervals were calculated to investigate difficulty accessing SRH products and services. Qualitative data were analysed using descriptive thematic analysis.\n\nResultsMost participants (55.4%, 287/518) were aged 18-24 years. Most (76.1%, 379/498) indicated they were trying to avoid pregnancy. The oral contraceptive pill was the most common single method used (20.8%; 107/514). Nearly 20% (101/514) reported they were not using contraception. Older women (OR=0.4; 95%CI: 0.1, 0.9 for 25-34 vs 18-24 years) and those employed (OR=0.4; 95%CI: 0.2, 0.7) had less trouble accessing contraception during lockdown. Women aged 25-34 (OR=0.4; 95%CI: 0.3, 0.7) or 35-49 years (OR=0.3; 95%CI: 0.1, 0.6) were less likely to experience difficulty accessing feminine hygiene products. Qualitative analysis suggested that COVID-19 affected pregnancy plans, with participants delaying childbearing, or deciding to remain childfree.\n\nConclusionCOVID-19 lockdown impacted the SRH of Australian women. Findings highlight the importance of continued access to SRH services and products during global emergencies.\n\nKEY MESSAGESO_LINearly a third of participants reported difficulties accessing their usual feminine hygiene products during lockdown in Australia.\nC_LIO_LIParticipants reported delaying childbearing or deciding to remain childfree due to the COVID-19 pandemic.\nC_LIO_LIEnsuring continued access to sexual and reproductive health services and products for all who require them during global emergencies is essential.\nC_LI",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Jacqueline Coombe",
-        "author_inst": "The University of Melbourne"
-      },
-      {
-        "author_name": "Fabian Kong",
-        "author_inst": "The University of Melbourne"
-      },
-      {
-        "author_name": "Helen Bittleston",
-        "author_inst": "The University of Melbourne"
-      },
-      {
-        "author_name": "Hennie Williams",
-        "author_inst": "Melbourne Sexual Health Centre & The University of Melbourne"
-      },
-      {
-        "author_name": "Jane Tomnay",
-        "author_inst": "The University of Melbourne"
-      },
-      {
-        "author_name": "Alaina Vaisey",
-        "author_inst": "The University of Melbourne"
-      },
-      {
-        "author_name": "Sue Malta",
-        "author_inst": "National Ageing Research Institute & The University of Melbourne"
-      },
-      {
-        "author_name": "Jane Goller",
-        "author_inst": "The University of Melbourne"
-      },
-      {
-        "author_name": "Meredith Temple-Smith",
-        "author_inst": "The University of Melbourne"
-      },
-      {
-        "author_name": "Louise Bourchier",
-        "author_inst": "The University of Melbourne"
-      },
-      {
-        "author_name": "Andrew Lau",
-        "author_inst": "The University of Melbourne"
-      },
-      {
-        "author_name": "Jane S Hocking",
-        "author_inst": "The University of Melbourne"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "sexual and reproductive health"
-  },
   {
     "rel_doi": "10.1101/2020.08.11.244863",
     "rel_title": "Cryo-EM Structures of the SARS-CoV-2 Endoribonuclease Nsp15",
@@ -1240849,6 +1239979,109 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.08.10.20171033",
+    "rel_title": "Post-exertion oxygen saturation as a prognostic factor for adverse outcome in patients attending the emergency department with suspected COVID-19: Observational cohort study",
+    "rel_date": "2020-08-11",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20171033",
+    "rel_abs": "BackgroundMeasurement of post-exertion oxygen saturation has been proposed to assess illness severity in suspected COVID-19 infection. We aimed to determine the accuracy of post-exertional oxygen saturation for predicting adverse outcome in suspected COVID-19.\n\nMethodsWe undertook an observational cohort study across 70 emergency departments during first wave of the COVID-19 pandemic in the United Kingdom. We collected data prospectively, using a standardised assessment form, and retrospectively, using hospital records, from patients with suspected COVID-19, and reviewed hospital records at 30 days for adverse outcome (death or receiving organ support). Patients with post-exertion oxygen saturation recorded were selected for this analysis.\n\nResultsWe analysed data from 817 patients with post-exertion oxygen saturation recorded after excluding 54 in whom measurement appeared unfeasible. The c-statistic for post-exertion change in oxygen saturation was 0.589 (95% confidence interval 0.465 to 0.713), and the positive and negative likelihood ratios of a 3% or more desaturation were respectively 1.78 (1.25 to 2.53) and 0.67 (0.46 to 0.98). Multivariable analysis showed that post-exertion oxygen saturation was not a significant predictor of adverse outcome when baseline clinical assessment was taken into account (p=0.368). Secondary analysis excluding patients in whom post-exertion measurement appeared inappropriate resulted in a c-statistic of 0.699 (0.581 to 0.817), likelihood ratios of 1.98 (1.26 to 3.10) and 0.61 (0.35 to 1.07), and some evidence of additional prognostic value on multivariable analysis (p=0.019).\n\nConclusionsPost-exertion oxygen saturation provides modest prognostic information in the assessment of patients attending the emergency department with suspected COVID-19.\n\nRegistrationISRCTN registry, ISRCTN56149622, http://www.isrctn.com/ISRCTN28342533\n\nKey messagesWhat is already known on this subject?\n\nO_LIPost exertional decrease in oxygen saturation can be used to predict prognosis in chronic lung diseases\nC_LIO_LIPost exertional desaturation has been proposed as a way of predicting adverse outcome in people with suspected COVID-19\nC_LI\n\nWhat this study adds:\n\nO_LIPost-exertion oxygen saturation provides modest prognostic information in the assessment of patients attending the emergency department with suspected COVID-19\nC_LI",
+    "rel_num_authors": 22,
+    "rel_authors": [
+      {
+        "author_name": "Steve Goodacre",
+        "author_inst": "University of Sheffield"
+      },
+      {
+        "author_name": "Ben Thomas",
+        "author_inst": "University of Sheffield"
+      },
+      {
+        "author_name": "Ellen Lee",
+        "author_inst": "University of Sheffield"
+      },
+      {
+        "author_name": "Laura Sutton",
+        "author_inst": "University of Sheffield"
+      },
+      {
+        "author_name": "Katie Biggs",
+        "author_inst": "University of Sheffield"
+      },
+      {
+        "author_name": "Carl Marincowitz",
+        "author_inst": "University of Sheffield"
+      },
+      {
+        "author_name": "Amanda Loban",
+        "author_inst": "University of Sheffield"
+      },
+      {
+        "author_name": "Simon Waterhouse",
+        "author_inst": "University of Sheffield"
+      },
+      {
+        "author_name": "Richard Simmonds",
+        "author_inst": "University of Sheffield"
+      },
+      {
+        "author_name": "Jose Schutter",
+        "author_inst": "University of Sheffield"
+      },
+      {
+        "author_name": "Sarah Connelly",
+        "author_inst": "University of Sheffield"
+      },
+      {
+        "author_name": "Elena Sheldon",
+        "author_inst": "University of Sheffield"
+      },
+      {
+        "author_name": "Jamie Hall",
+        "author_inst": "University of Sheffield"
+      },
+      {
+        "author_name": "Emma Young",
+        "author_inst": "University of Sheffield"
+      },
+      {
+        "author_name": "Andrew Bentley",
+        "author_inst": "Manchester University NHS Foundation Trust, Wythenshawe Hospital"
+      },
+      {
+        "author_name": "Kirsty Challen",
+        "author_inst": "Lancashire Teaching Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "Chris Fitzsimmons",
+        "author_inst": "Sheffield Children's NHS Foundation Trust"
+      },
+      {
+        "author_name": "Tim Harris",
+        "author_inst": "Barts Health NHS Trust"
+      },
+      {
+        "author_name": "Fiona Lecky",
+        "author_inst": "University of Sheffield"
+      },
+      {
+        "author_name": "Andrew Lee",
+        "author_inst": "University of Sheffield"
+      },
+      {
+        "author_name": "Ian Maconochie",
+        "author_inst": "Imperial College Healthcare NHS Trust"
+      },
+      {
+        "author_name": "Darren Walter",
+        "author_inst": "Manchester University NHS Foundation Trust"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "emergency medicine"
+  },
   {
     "rel_doi": "10.1101/2020.08.11.244996",
     "rel_title": "Pleiotropic effect of Lactoferrin in the prevention and treatment of COVID-19 infection: in vivo, in silico and in vitro preliminary evidences",
@@ -1242662,65 +1241895,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.08.07.242073",
-    "rel_title": "K18-hACE2 Mice for Studies of COVID-19 Treatments and Pathogenesis Including Anosmia",
-    "rel_date": "2020-08-10",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.07.242073",
-    "rel_abs": "The ongoing COVID-19 pandemic is associated with substantial morbidity and mortality. While much has been learned in the first months of the pandemic, many features of COVID-19 pathogenesis remain to be determined. For example, anosmia is a common presentation and many patients with this finding show no or only minor respiratory signs. Studies in animals experimentally infected with SARS-CoV-2, the cause of COVID-19, provide opportunities to study aspects of the disease not easily investigated in human patients. COVID-19 severity ranges from asymptomatic to lethal. Most experimental infections provide insights into mild disease. Here, using K18-hACE2 mice that we originally developed for SARS studies, we show that infection with SARS-CoV-2 causes severe disease in the lung, and in some mice, the brain. Evidence of thrombosis and vasculitis was detected in mice with severe pneumonia. Further, we show that infusion of convalescent plasma (CP) from a recovered COVID-19 patient provided protection against lethal disease. Mice developed anosmia at early times after infection. Notably, while treatment with CP prevented significant clinical disease, it did not prevent anosmia. Thus K18-hACE2 mice provide a useful model for studying the pathological underpinnings of both mild and lethal COVID-19 and for assessing therapeutic interventions.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Stanley Perlman",
-        "author_inst": "University of Iowa"
-      },
-      {
-        "author_name": "Jian Zheng",
-        "author_inst": "University of Iowa"
-      },
-      {
-        "author_name": "LOK YIN ROY WONG",
-        "author_inst": "University of Iowa"
-      },
-      {
-        "author_name": "Kun Li",
-        "author_inst": "University of Iowa"
-      },
-      {
-        "author_name": "Abhishek K Verma",
-        "author_inst": "University of Iowa"
-      },
-      {
-        "author_name": "Miguel E Ortiz Bezara",
-        "author_inst": "University of Iowa"
-      },
-      {
-        "author_name": "Christine Wohlford-Lenane",
-        "author_inst": "University of Iowa"
-      },
-      {
-        "author_name": "Mariah R. Leidinger",
-        "author_inst": "University of Iowa"
-      },
-      {
-        "author_name": "Michael C. Kundson",
-        "author_inst": "University of Iowa"
-      },
-      {
-        "author_name": "David K. Meyerholz",
-        "author_inst": "University of Iowa"
-      },
-      {
-        "author_name": "Paul B McCray Jr.",
-        "author_inst": "University of Iowa"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.08.07.241653",
     "rel_title": "Characterization of SARS-CoV-2 ORF6 deletion variants detected in a nosocomial cluster during routine genomic surveillance, Lyon, France",
@@ -1242939,6 +1242113,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.08.06.20155804",
+    "rel_title": "Characterization of Israeli COVID-19 Outbreak Drivers and Forecasting Using a Versatile Web App",
+    "rel_date": "2020-08-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.06.20155804",
+    "rel_abs": "BackgroundNo versatile web app exists that allows epidemiologists and managers around the world to fully analyze the impacts of COVID-19 mitigation. The NMB-DASA web app presented here fills this gap.\n\nMethodsOur web app uses a model that explicitly identifies a contact class of individuals, symptomatic and asymptomatic classes and a parallel set of response class, subject to lower contact pathogen contact rates. The user inputs a CSV file containing incidence and mortality time series. A default set of parameters is available that can be overwritten through input or online entry, and a subset of these can be fitted to the model using an MLE algorithm. The end of model-fitting and forecasting intervals are specifiable and changes to parameters allows counterfactual and forecasted scenarios to be explored.\n\nFindingsWe illustrate the app in the context of the current COVID-19 outbreak in Israel, which can be divided into four distinct phases: an initial outbreak; a social distancing, a social relaxation, and a second wave mitigation phase. Our projections beyond the relaxation phase indicate that an 85% drop in social relaxation rates are needed just to stabilize the current incidence rate and that at least a 95% drop is needed to quell the outbreak.\n\nInterpretationOur analysis uses only incidence and mortality rates. In the hands of policy makers and health officers, we believe our web app provides an invaluable tool for evaluating the impacts of different outbreak mitigation policies and measures.\n\nFundingThis research was funded by NSF Grant 2032264.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Wayne M. Getz",
+        "author_inst": "University of California, Berkeley"
+      },
+      {
+        "author_name": "Richard Salter",
+        "author_inst": "Oberlin College"
+      },
+      {
+        "author_name": "Ludovica Luisa Vissat",
+        "author_inst": "University of California, Berkeley"
+      },
+      {
+        "author_name": "Nir Horvitz",
+        "author_inst": "University of California, Berkeley"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.07.29.20164558",
     "rel_title": "Clinical and intestinal histopathological findings in SARS-CoV-2/COVID-19 patients with hematochezia",
@@ -1244576,53 +1243781,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.08.06.20169599",
-    "rel_title": "Characteristics and outcomes of patients admitted to Swedish intensive care units for COVID-19 during the first 60 days of the 2020 pandemic: a registry-based, multicenter, observational study.",
-    "rel_date": "2020-08-07",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.06.20169599",
-    "rel_abs": "BackgroundThe mortality of patients admitted to the intensive care unit (ICU) with COVID-19 is unclear due to variable censoring and substantial proportions of undischarged patients at follow-up. Nationwide data have not been previously reported. We studied the outcomes of Swedish patients at 30 days after ICU admission.\n\nMethodsWe conducted a registry-based cohort study of all adult patients admitted to Swedish ICUs from 6 March-6 May, 2020 with laboratory confirmed COVID-19 disease and complete 30-day follow-up. Data including baseline characteristics, comorbidities, intensive care treatments, organ failures and outcomes were collected. The primary outcome was 30-day all-cause mortality. A multivariable model was used to determine the independent association between potential predictor variables and the primary outcome.\n\nResultsA total of 1563 patients were identified. Median ICU length of stay was 12 (5-21) days, and fifteen patients remained in ICU at the time of follow-up. Median age was 61 (52-69), median Simplified Acute Physiology Score III (SAPS III) was 53 (46-59), and 66{middle dot}8% had at least one comorbidity. Median PaO2/FiO2 on admission was 97{middle dot}5 (75{middle dot}0-140{middle dot}6) mmHg, 74{middle dot}7% suffered from moderate to severe acute respiratory distress syndrome (ARDS). The 30-day all-cause mortality was 26{middle dot}7%. The majority of deaths occurred during ICU admission. Age, male sex (adjusted odds ratio [aOR] 1{middle dot}5 [1{middle dot}1-2{middle dot}1]), SAPS III score (aOR 1{middle dot}3 [1{middle dot}2-1{middle dot}4]), severe ARDS (aOR 3{middle dot}1 [2{middle dot}0-4{middle dot}8], specific COVID-19 pharmacotherapy (aOR 1{middle dot}4 [1{middle dot}0-1{middle dot}9]), and CRRT (aOR 2{middle dot}2 [1{middle dot}6-3{middle dot}0]), were associated with increased mortality. With the exception of chronic lung disease, the presence of comorbidities was not independently associated with mortality.\n\nConclusionsThirty-day mortality rate in COVID-19 patients admitted to Swedish intensive care units is generally lower than previously reported. Mortality appears to be driven by age, baseline disease severity, the degree of organ failure and ICU treatment, rather than preexisting comorbidities.\n\nFundingRegion Ostergotland County Council and Linkoping University; number 30320008.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSIn previous studies reporting outcomes for COVID-19 patients admitted to intensive care units (ICUs), none reported 30-day mortality rates, many were censored after short observation periods, and most had substantial proportions of undischarged patients at the time of follow-up. Incomplete data may cause bias in reported mortality rates. Further, national data on critically ill patients have not been previously published.\n\nAdded value of this studyOur study provides complete 30-day follow up in a nationwide population of 1563 unselected patients admitted to intensive care units in Sweden. All but 15 patients had been discharged from ICU at follow-up thus the study also provides an accurate reflection of ICU mortality. We also provide age-stratified mortality rates and information on ICU treatment and outcomes. This cohort also differs from previous studies in so far as directed antiviral therapy for COVID-19 disease was infrequently used. Adjusted risk estimates for the effect of baseline factors, ICU complications and treatment demonstrate that age, the severity of respiratory failure and need for continuous renal replacement therapy were the most important risk factors for death.\n\nImplications of all the available evidenceMortality rates of COVID-19 patients in Swedish ICUs are lower than those previously reported, despite the high incidence of comorbidities, an ageing population and a high proportion of patients with severe ARDS. Directed antiviral pharmacotherapy was given only to a minority of patients suggesting that survival from COVID-19 in ICU is achievable with good supportive care. Our analysis also suggests that unaccounted factors eg. process and organizational, may be important in determining the outcome of critically ill patients with COVID-19. Our results may be of interest since Sweden has a very limited number of ICU beds and has adopted a unique response to the pandemic compared to other countries. Despite limited numbers of ICU beds per capita, Sweden was able to increase its ICU capacity during the first 2 months of the COVID-19 pandemic and provide essential care to the critically ill with encouraging results.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Michelle S Chew",
-        "author_inst": "Department of Biomedical and Clinical Sciences, Anaesthesiology and Intensive Care, Linkoping University Hospital"
-      },
-      {
-        "author_name": "Patrik Blixt",
-        "author_inst": "Department of Biomedical and Clinical Sciences, Anaesthesiology and Intensive Care, Linkoping University Hospital"
-      },
-      {
-        "author_name": "Rasmus Ahman",
-        "author_inst": "Department of Biomedical and Clinical Sciences, Anaesthesiology and Intensive Care, Linkoping University Hospital"
-      },
-      {
-        "author_name": "Lars Engerstrom",
-        "author_inst": "Department of Anaesthesia and Intensive Care, Vrinnevi Hospital, Norrkoping, Department of Thoracic and Vascular Surgery, Medical and Health Sciences, Linkoping"
-      },
-      {
-        "author_name": "Henrik Andersson",
-        "author_inst": "Department of Biomedical and Clinical Sciences, Anaesthesiology and Intensive Care, Linkoping University Hospital"
-      },
-      {
-        "author_name": "Ritva Kiiski Berggren",
-        "author_inst": "Department of Anaesthesia, Intensive Care and Perioperative Services, Umea University Hospital"
-      },
-      {
-        "author_name": "Anders Tegnell",
-        "author_inst": "Department of Public Health Reporting, Public Health Agency of Sweden"
-      },
-      {
-        "author_name": "Sarah McIntyre",
-        "author_inst": "Department of Biomedical and Clinical Sciences, Center for Social and Affective Neuroscience, Linkoping University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "intensive care and critical care medicine"
-  },
   {
     "rel_doi": "10.1101/2020.08.06.20169797",
     "rel_title": "The effect of school closures and reopening strategies on COVID-19 infection dynamics in the San Francisco Bay Area: a cross-sectional survey and modeling analysis",
@@ -1244973,6 +1244131,101 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.08.06.20169722",
+    "rel_title": "SARS-CoV-2 infection fatality risk in a nationwide seroepidemiological study",
+    "rel_date": "2020-08-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.06.20169722",
+    "rel_abs": "ObjectiveTo estimate the range of the age- and sex-specific infection fatality risk (IFR) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) based on confirmed coronavirus disease 2019 (COVID-19) deaths and excess all-cause deaths.\n\nDesignNationwide population-based seroepidemiological study combined with two national surveillance systems.\n\nSetting and participantsNon-institutionalized Spanish population of all ages.\n\nMain outcome measuresThe range of IFR was calculated as the observed number of COVID-19 deaths and excess deaths divided by the estimated number of SARS-CoV-2 infections in the non-institutionalized Spanish population. Laboratory-confirmed COVID-19 deaths were obtained from the National Epidemiological Surveillance Network (RENAVE) and excess all-cause deaths from the Monitoring Mortality System (MoMo) up to July 15, 2020. SARS-CoV-2 infections were derived from the estimated seroprevalence by a chemiluminiscent microparticle immunoassay for IgG antibodies in 61,092 participants in the ENE-COVID nationwide serosurvey between April 27 and June 22, 2020.\n\nResultsThe overall IFR (95% confidence interval) was 0.8% (0.8% to 0.9%) for confirmed COVID-19 deaths and 1.1% (1.0% to 1.2%) for excess deaths. The IFR ranged between 1.1% (1.0% to 1.2%) and 1.4% (1.3% to 1.5%) in men and between 0.6% (0.5% to 0.6%) and 0.8% (0.7% to 0.8%) in women. The IFR increased sharply after age 50, ranging between 11.6% (8.1% to 16.5%) and 16.4% (11.4% to 23.2%) in men [&ge;]80 years and between 4.6% (3.4% to 6.3%) and 6.5% (4.7% to 8.8%) in women [&ge;]80 years.\n\nConclusionThe sharp increase in SARS-CoV-2 IFR after age 50 was more marked in men than in women. Fatality from COVID-19 is substantially greater than that reported for other common respiratory diseases such as seasonal influenza.\n\nWHAT IS ALREADY KNOWN ON THIS TOPICInfection fatality risk (IFR) for SARS-CoV-2 is a key indicator for policy decision making, but its magnitude remains under debate. Case fatality risk, which accounts for deaths among confirmed COVID-19 cases, overestimates SARS-CoV-2 fatality as it excludes a large proportion of asymptomatic and mild-symptomatic infections. Population-based seroepidemiological studies are a valuable tool to properly estimate the number of infected individuals, regardless of symptoms. Also, because ascertainment of deaths due to COVID-19 is often incomplete, the calculation of the IFR should be complemented with data on excess all-cause mortality. In addition, data on age- and sex-specific IFR are scarce, even though age and sex are well known modifiers of the clinical evolution of COVID-19.\n\nWHAT THIS STUDY ADDSUsing the ENE-COVID nationwide serosurvey and two national surveillance systems in Spain, this study provides a range of age- and sex-specific IFR estimates for SARS-CoV-2 based on laboratory-confirmed COVID-19 deaths and excess all-cause deaths. The risk of death was very low among infected individuals younger than 50 years, but it increased sharply with age, particularly among men. In the oldest age group ([&ge;]80 years), it was estimated that 12% to 16% of infected men and 5% to 6% of infected women died during the first epidemic wave.",
+    "rel_num_authors": 20,
+    "rel_authors": [
+      {
+        "author_name": "Roberto Pastor-Barriuso",
+        "author_inst": "Instituto de Salud Carlos III"
+      },
+      {
+        "author_name": "Beatriz Perez-Gomez",
+        "author_inst": "Instituto de Salud Carlos III"
+      },
+      {
+        "author_name": "Miguel A Hernan",
+        "author_inst": "Chan School of Public Health, Harvard"
+      },
+      {
+        "author_name": "Mayte Perez-Olmeda",
+        "author_inst": "Instituto de Salud Carlos III"
+      },
+      {
+        "author_name": "Raquel Yotti",
+        "author_inst": "Instituto de Salud Carlos III"
+      },
+      {
+        "author_name": "Jesus Oteo",
+        "author_inst": "Instituto de Salud Carlos III"
+      },
+      {
+        "author_name": "Jose Luis Sanmartin",
+        "author_inst": "Ministerio de Sanidad"
+      },
+      {
+        "author_name": "Inmaculada Leon-Gomez",
+        "author_inst": "Instituto de Salud Carlos III"
+      },
+      {
+        "author_name": "Aurora Fernandez-Garcia",
+        "author_inst": "Instituto de Salud Carlos III"
+      },
+      {
+        "author_name": "Pablo Fernandez-Navarro",
+        "author_inst": "Instituto de Salud Carlos III"
+      },
+      {
+        "author_name": "Israel Cruz",
+        "author_inst": "Instituto de Salud Carlos III"
+      },
+      {
+        "author_name": "Mariano Martin",
+        "author_inst": "Ministerio de Sanidad"
+      },
+      {
+        "author_name": "Concepcion Delgado-Sanz",
+        "author_inst": "Instituto de Salud Carlos III"
+      },
+      {
+        "author_name": "Nerea Fernandez de Larrea",
+        "author_inst": "Instituto de Salud Carlos III"
+      },
+      {
+        "author_name": "Jose Leon Paniagua",
+        "author_inst": "Instituto de Salud Carlos III"
+      },
+      {
+        "author_name": "Juan Fernando Munoz-Montalvo",
+        "author_inst": "Ministerio de Sanidad"
+      },
+      {
+        "author_name": "Faustino Blanco",
+        "author_inst": "Ministerio de Sanidad"
+      },
+      {
+        "author_name": "Amparo Larrauri",
+        "author_inst": "Instituto de Salud Carlos III"
+      },
+      {
+        "author_name": "Marina Pollan",
+        "author_inst": "Instituto de Salud Carlos III"
+      },
+      {
+        "author_name": "Marina Pollan",
+        "author_inst": "Instituto de Salud Carlos III"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.08.06.20169813",
     "rel_title": "Outcome of Conservative Therapy in COVID-19 Patients Presenting with Gastrointestinal Bleeding",
@@ -1246242,33 +1245495,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.08.04.20164061",
-    "rel_title": "Is Higher Viral Load in SARS-CoV-2 Associated With Death?",
-    "rel_date": "2020-08-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.04.20164061",
-    "rel_abs": "BackgroundThere is no proven prognostic marker or adequate number of studies in patients hospitalized for coronavirus disease 2019 (COVID-19).\n\nMethodsWe conducted a retrospective cohort study of patients hospitalized with COVID-19 from March 14 to June 17, 2020, at Sao Paulo Hospital. SARS-CoV-2 viral load was assessed using the cycle threshold (Ct) values obtained from an RT-PCR assay applied to the nasopharyngeal swab samples. Disease severity and patient outcomes were compared.\n\nResultsAmong the 875 patients, 50.1% (439/875) had mild, 30.4% (266/875) moderate, and 19.5% (170/875) severe disease. A Ct value of <25 (472/875) indicated a high viral load, which was independently associated with mortality (OR: 0,34; 95% CI: 0,217-0,533; p < 0.0001).\n\nConclusionsAdmission SARS-CoV-2 viral load is an important surrogate biomarker of infectivity and is independently associated with mortality among patients hospitalized with COVID-19.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Klinger Soares Faico-Filho",
-        "author_inst": "Federal University of Sao Paulo"
-      },
-      {
-        "author_name": "Victor Cabelho Passarelli",
-        "author_inst": "Federal University of Sao Paulo"
-      },
-      {
-        "author_name": "Nancy Bellei",
-        "author_inst": "Federal University of Sao Paulo"
-      }
-    ],
-    "version": "2",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.08.05.20168682",
     "rel_title": "The Trend of Neutralizing Antibody Response Against SARS-CoV-2 and the Cytokine/Chemokine Release in Patients with Differing Severities of COVID-19: All Individuals Infected with SARS-CoV-2 Obtained Neutralizing Antibody",
@@ -1246607,6 +1245833,89 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.08.05.20168948",
+    "rel_title": "Development of mass spectrometry-based targeted assay for direct detection of novel SARS-CoV-2 coronavirus from clinical specimens",
+    "rel_date": "2020-08-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.05.20168948",
+    "rel_abs": "The COVID-19 pandemic caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) has overwhelmed health systems worldwide and highlighted limitations of diagnostic testing. Several types of diagnostics including RT-PCR-based assays, antigen detection by lateral flow assays and antibody-based assays have been developed and deployed in a short time. However, many of these assays are lacking in sensitivity and/or specificity. Here, we describe an immunoaffinity purification followed by high resolution mass spectrometry-based targeted assay capable of detecting viral antigen in nasopharyngeal swab samples of SARS-CoV-2 infected individuals. Based on our discovery experiments using purified virus, recombinant viral protein and nasopharyngeal swab samples from COVID-19 positive patients, nucleocapsid protein was selected as a target antigen. We then developed an automated antibody capture-based workflow coupled to targeted high-field asymmetric ion mobility spectrometry (FAIMS) - parallel reaction monitoring (PRM) assays on an Orbitrap Exploris 480 mass spectrometer. An ensemble machine learning-based model for determining COVID-19 positive samples was created using fragment ion intensities in the PRM data. This resulted in 97.8% sensitivity and 100% specificity with RT-PCR-based molecular testing as the gold standard. Our results demonstrate that direct detection of infectious agents from clinical samples by mass spectrometry-based assays have potential to be deployed as diagnostic assays in clinical laboratories.",
+    "rel_num_authors": 17,
+    "rel_authors": [
+      {
+        "author_name": "Santosh Renuse",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Patrick M Vanderboom",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Anthony D. Maus",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Jennifer V. Kemp",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Kari M. Gurtner",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Anil K. Madugundu",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Sandip Chavan",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Jane A. Peterson",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Benjamin J. Madden",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Kiran K. Mangalaparthi",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Dong-Gi Mun",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Smrita Singh",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Benjamin R. Kipp",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Surendra Dasari",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Ravinder J. Singh",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Stefan K. Grebe",
+        "author_inst": "Mayo Clinic"
+      },
+      {
+        "author_name": "Akhilesh Pandey",
+        "author_inst": "Mayo Clinic"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.08.05.20168146",
     "rel_title": "Clinical Mortality Review in a Large COVID-19 Cohort",
@@ -1248096,105 +1247405,6 @@
     "type": "new results",
     "category": "bioengineering"
   },
-  {
-    "rel_doi": "10.1101/2020.08.06.240192",
-    "rel_title": "Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors",
-    "rel_date": "2020-08-06",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.06.240192",
-    "rel_abs": "The number of new cases world-wide for the COVID-19 disease is increasing dramatically, while efforts to contain Severe Acute Respiratory Syndrome Coronavirus 2 is producing varied results in different countries. There are three key SARS-CoV-2 enzymes potentially targetable with antivirals: papain-like protease (PLpro), main protease (Mpro), and RNA-dependent RNA polymerase. Of these, PLpro is an especially attractive target because it plays an essential role in several viral replication processes, including cleavage and maturation of viral polyproteins, assembly of the replicase-transcriptase complex (RTC), and disruption of host viral response machinery to facilitate viral proliferation and replication. Moreover, this enzyme is conserved across different coronaviruses and promising inhibitors have already been discovered for its SARS-CoV variant. Here we report a substantive body of structural, biochemical, and virus replication studies that identify several inhibitors of the enzyme from SARS-CoV-2 in both wild-type and mutant forms. These efforts include the first structures of wild-type PLpro, the active site C111S mutant, and their complexes with inhibitors, determined at 1.60-2.70 Angstroms. This collection of structures provides fundamental molecular and mechanistic insight to PLpro, and critically, illustrates details for inhibitors recognition and interactions. All presented compounds inhibit the peptidase activity of PLpro in vitro, and some molecules block SARS-CoV-2 replication in cell culture assays. These collated findings will accelerate further structure-based drug design efforts targeting PLpro, with the ultimate goal of identifying high-affinity inhibitors of clinical value for SARS-CoV-2.",
-    "rel_num_authors": 21,
-    "rel_authors": [
-      {
-        "author_name": "Jerzy Osipiuk",
-        "author_inst": "UChicago/ANL"
-      },
-      {
-        "author_name": "Saara-Anne Azizi",
-        "author_inst": "UChicago"
-      },
-      {
-        "author_name": "Steve Dvorkin",
-        "author_inst": "UChicago"
-      },
-      {
-        "author_name": "Michael Endres",
-        "author_inst": "UChicago/ANL"
-      },
-      {
-        "author_name": "Robert Jedrzejczak",
-        "author_inst": "UChicago/ANL"
-      },
-      {
-        "author_name": "Krysten A. Jones",
-        "author_inst": "UChicago"
-      },
-      {
-        "author_name": "Soowon Kang",
-        "author_inst": "UChicago"
-      },
-      {
-        "author_name": "Rahul S. Kathayat",
-        "author_inst": "UChicago"
-      },
-      {
-        "author_name": "Youngchang Kim",
-        "author_inst": "UChicago/ANL"
-      },
-      {
-        "author_name": "Vladislav G. Lisnyak",
-        "author_inst": "UChicago"
-      },
-      {
-        "author_name": "Samantha L. Maki",
-        "author_inst": "UChicago"
-      },
-      {
-        "author_name": "Vlad Nicolaescu",
-        "author_inst": "UChicago"
-      },
-      {
-        "author_name": "Cooper A. Taylor",
-        "author_inst": "UChicago"
-      },
-      {
-        "author_name": "Christine Tesar",
-        "author_inst": "UChicago/ANL"
-      },
-      {
-        "author_name": "Yu-An Zhang",
-        "author_inst": "UChicago"
-      },
-      {
-        "author_name": "Zhiyao Zhou",
-        "author_inst": "UChicago"
-      },
-      {
-        "author_name": "Glenn Randall",
-        "author_inst": "UChicago"
-      },
-      {
-        "author_name": "Karolina Michalska",
-        "author_inst": "UChicago/ANL"
-      },
-      {
-        "author_name": "Scott A. Snyder",
-        "author_inst": "UChicago"
-      },
-      {
-        "author_name": "Bryan C. Dickinson",
-        "author_inst": "UChicago"
-      },
-      {
-        "author_name": "Andrzej Joachimiak",
-        "author_inst": "UChicago/ANL"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "molecular biology"
-  },
   {
     "rel_doi": "10.1101/2020.08.06.234674",
     "rel_title": "Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate",
@@ -1248557,6 +1247767,33 @@
     "type": "new results",
     "category": "evolutionary biology"
   },
+  {
+    "rel_doi": "10.1101/2020.08.05.237404",
+    "rel_title": "Analysis of single nucleotide polymorphisms between 2019-nCoV genomes and its impact on codon usage",
+    "rel_date": "2020-08-05",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.05.237404",
+    "rel_abs": "The spread of COVID-19 is a global concern that has taken a toll on entire human health. Researchers across the globe has been working in devising the strategies to combat this dreadful disease. Studies focused on genetic variability helps design effective drugs and vaccines. Considering this, the present study entails the information regarding the genome-wide mutations detected in the 108 SARS CoV-2 genomes worldwide. We identified a few hypervariable regions localized in orf1ab, spike, and nucleocapsid gene. These nucleotide polymorphisms demonstrated their effect on both codon usage as well as amino acid usage pattern. Altogether the present study provides valuable information that would be helpful to ongoing research on 2019-nCoV vaccine development.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Suruchi Gupta",
+        "author_inst": "CSIR- Indian Institute of Integrative Medicine"
+      },
+      {
+        "author_name": "Ravail Singh",
+        "author_inst": "CSIR- Indian Institute of Integrative Medicine"
+      },
+      {
+        "author_name": "Prosenjit Paul",
+        "author_inst": "Negenome Bio Solutions"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "confirmatory results",
+    "category": "genomics"
+  },
   {
     "rel_doi": "10.1101/2020.08.04.20168112",
     "rel_title": "Seroprevalence of COVID-19 in Niger State",
@@ -1250198,245 +1249435,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.07.31.20165647",
-    "rel_title": "Magnitude and Dynamics of the T-Cell Response to SARS-CoV-2 Infection at Both Individual and Population Levels",
-    "rel_date": "2020-08-04",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.31.20165647",
-    "rel_abs": "T cells are involved in the early identification and clearance of viral infections and also support the development of antibodies by B cells. This central role for T cells makes them a desirable target for assessing the immune response to SARS-CoV-2 infection. Here, we combined two high-throughput immune profiling methods to create a quantitative picture of the T-cell response to SARS-CoV-2. First, at the individual level, we deeply characterized 3 acutely infected and 58 recovered COVID-19 subjects by experimentally mapping their CD8 T-cell response through antigen stimulation to 545 Human Leukocyte Antigen (HLA) class I presented viral peptides (class II data in a forthcoming study). Then, at the population level, we performed T-cell repertoire sequencing on 1,815 samples (from 1,521 COVID-19 subjects) as well as 3,500 controls to identify shared \"public\" T-cell receptors (TCRs) associated with SARS-CoV-2 infection from both CD8 and CD4 T cells. Collectively, our data reveal that CD8 T-cell responses are often driven by a few immunodominant, HLA-restricted epitopes. As expected, the T-cell response to SARS-CoV-2 peaks about one to two weeks after infection and is detectable for at least several months after recovery. As an application of these data, we trained a classifier to diagnose SARSCoV-2 infection based solely on TCR sequencing from blood samples, and observed, at 99.8% specificity, high early sensitivity soon after diagnosis (Day 3-7 = 85.1% [95% CI = 79.9-89.7]; Day 8-14 = 94.8% [90.7-98.4]) as well as lasting sensitivity after recovery (Day 29+/convalescent = 95.4% [92.1-98.3]). These results demonstrate an approach to reliably assess the adaptive immune response both soon after viral antigenic exposure (before antibodies are typically detectable) as well as at later time points. This blood-based molecular approach to characterizing the cellular immune response has applications in clinical diagnostics as well as in vaccine development and monitoring.",
-    "rel_num_authors": 56,
-    "rel_authors": [
-      {
-        "author_name": "Thomas M Snyder",
-        "author_inst": "Adaptive Biotechnologies"
-      },
-      {
-        "author_name": "Rachel M Gittelman",
-        "author_inst": "Adaptive Biotechnologies"
-      },
-      {
-        "author_name": "Mark Klinger",
-        "author_inst": "Adaptive Biotechnologies"
-      },
-      {
-        "author_name": "Damon H May",
-        "author_inst": "Adaptive Biotechnologies"
-      },
-      {
-        "author_name": "Edward J Osborne",
-        "author_inst": "Adaptive Biotechnologies"
-      },
-      {
-        "author_name": "Ruth Taniguchi",
-        "author_inst": "Adaptive Biotechnologies"
-      },
-      {
-        "author_name": "H Jabran Zahid",
-        "author_inst": "Microsoft Research"
-      },
-      {
-        "author_name": "Ian M Kaplan",
-        "author_inst": "Adaptive Biotechnologies"
-      },
-      {
-        "author_name": "Jennifer N Dines",
-        "author_inst": "Adaptive Biotechnologies"
-      },
-      {
-        "author_name": "Matthew N Noakes",
-        "author_inst": "Adaptive Biotechnologies"
-      },
-      {
-        "author_name": "Ravi Pandya",
-        "author_inst": "Microsoft Research"
-      },
-      {
-        "author_name": "Xiaoyu Chen",
-        "author_inst": "Adaptive Biotechnologies"
-      },
-      {
-        "author_name": "Summer Elasady",
-        "author_inst": "Adaptive Biotechnologies"
-      },
-      {
-        "author_name": "Emily Svejnoha",
-        "author_inst": "Adaptive Biotechnologies"
-      },
-      {
-        "author_name": "Peter Ebert",
-        "author_inst": "Adaptive Biotechnologies"
-      },
-      {
-        "author_name": "Mitchell W Pesesky",
-        "author_inst": "Adaptive Biotechnologies"
-      },
-      {
-        "author_name": "Patricia De Almeida",
-        "author_inst": "Adaptive Biotechnologies"
-      },
-      {
-        "author_name": "Hope O'Donnell",
-        "author_inst": "Adaptive Biotechnologies"
-      },
-      {
-        "author_name": "Quinn DeGottardi",
-        "author_inst": "Adaptive Biotechnologies"
-      },
-      {
-        "author_name": "Gladys Keitany",
-        "author_inst": "Adaptive Biotechnologies"
-      },
-      {
-        "author_name": "Jennifer Lu",
-        "author_inst": "Adaptive Biotechnologies"
-      },
-      {
-        "author_name": "Allen Vong",
-        "author_inst": "Adaptive Biotechnologies"
-      },
-      {
-        "author_name": "Rebecca Elyanow",
-        "author_inst": "Adaptive Biotechnologies"
-      },
-      {
-        "author_name": "Paul Fields",
-        "author_inst": "Adaptive Biotechnologies"
-      },
-      {
-        "author_name": "Julia Greissl",
-        "author_inst": "Microsoft Research"
-      },
-      {
-        "author_name": "Lance Baldo",
-        "author_inst": "Adaptive Biotechnologies"
-      },
-      {
-        "author_name": "Simona Semprini",
-        "author_inst": "University of Bologna"
-      },
-      {
-        "author_name": "Claudio Cerchione",
-        "author_inst": "Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS"
-      },
-      {
-        "author_name": "Fabio Nicolini",
-        "author_inst": "Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS"
-      },
-      {
-        "author_name": "Massimiliano Mazza",
-        "author_inst": "Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS"
-      },
-      {
-        "author_name": "Ottavia M Delmonte",
-        "author_inst": "National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Kerry Dobbs",
-        "author_inst": "National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Rocio Laguna-Goya",
-        "author_inst": "Hospital 12 de Octubre, i+12, CNIO, Complutense University"
-      },
-      {
-        "author_name": "Gonzalo Carre\u00f1o-Tarragona",
-        "author_inst": "Hospital 12 de Octubre, i+12, CNIO, Complutense University"
-      },
-      {
-        "author_name": "Santiago Barrio",
-        "author_inst": "Hospital 12 de Octubre, i+12, CNIO, Complutense University"
-      },
-      {
-        "author_name": "Luisa Imberti",
-        "author_inst": "ASST Spedali Civili di Brescia and University of Brescia"
-      },
-      {
-        "author_name": "Alessandra Sottini",
-        "author_inst": "ASST Spedali Civili di Brescia and University of Brescia"
-      },
-      {
-        "author_name": "Eugenia Quiros-Roldan",
-        "author_inst": "ASST Spedali Civili di Brescia and University of Brescia"
-      },
-      {
-        "author_name": "Camillo Rossi",
-        "author_inst": "ASST Spedali Civili di Brescia and University of Brescia"
-      },
-      {
-        "author_name": "Andrea Biondi",
-        "author_inst": "MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo"
-      },
-      {
-        "author_name": "Laura Rachele Bettini",
-        "author_inst": "MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo"
-      },
-      {
-        "author_name": "Mariella D'Angio",
-        "author_inst": "MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo"
-      },
-      {
-        "author_name": "Paolo Bonfanti",
-        "author_inst": "University of Milano-Bicocca-Ospedale San Gerardo"
-      },
-      {
-        "author_name": "Miranda F Tompkins",
-        "author_inst": "Uniformed Services University of the Health Sciences"
-      },
-      {
-        "author_name": "Camille Alba",
-        "author_inst": "Uniformed Services University of the Health Sciences"
-      },
-      {
-        "author_name": "Clifton Dalgard",
-        "author_inst": "Uniformed Services University of the Health Sciences"
-      },
-      {
-        "author_name": "Vittorio Sambri",
-        "author_inst": "University of Bologna"
-      },
-      {
-        "author_name": "Giovanni Martinelli",
-        "author_inst": "Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS"
-      },
-      {
-        "author_name": "Jason D Goldman",
-        "author_inst": "Swedish Medical Center, and University of Washington"
-      },
-      {
-        "author_name": "James R Heath",
-        "author_inst": "Institute for Systems Biology"
-      },
-      {
-        "author_name": "Helen C Su",
-        "author_inst": "National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Luigi D Notarangelo",
-        "author_inst": "National Institute of Allergy and Infectious Diseases, National Institutes of Health"
-      },
-      {
-        "author_name": "Estela Paz-Artal",
-        "author_inst": "Hospital 12 de Octubre, i+12, CNIO, Complutense University"
-      },
-      {
-        "author_name": "Joaquin Martinez-Lopez",
-        "author_inst": "Hospital 12 de Octubre, i+12, CNIO, Complutense University"
-      },
-      {
-        "author_name": "Jonathan M Carlson",
-        "author_inst": "Microsoft Research"
-      },
-      {
-        "author_name": "Harlan S Robins",
-        "author_inst": "Adaptive Biotechnologies"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.07.30.20165563",
     "rel_title": "Making cotton face masks extra-protective by use of impervious cloth as the front layer to restrict flow of aerosols and droplets",
@@ -1250811,6 +1249809,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.07.31.20165480",
+    "rel_title": "Clinical course and severity outcome indicators among COVID 19 hospitalized patients in relation to comorbidities distribution Mexican cohort",
+    "rel_date": "2020-08-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.31.20165480",
+    "rel_abs": "IntroductionCOVID-19 affected worldwide, causing to date, around 500,000 deaths. In Mexico, by April 29, the general case fatality was 6.52%, with 11.1% confirmed case mortality and hospital recovery rate around 72%. Once hospitalized, the odds for recovery and hospital death rates depend mainly on the patients comorbidities and age. In Mexico, triage guidelines use algorithms and risk estimation tools for severity assessment and decision-making. The studys objective is to analyze the underlying conditions of patients hospitalized for COVID-19 in Mexico concerning four severity outcomes.\n\nMaterials and MethodsRetrospective cohort based on registries of all laboratory-confirmed patients with the COVID-19 infection that required hospitalization in Mexico. Independent variables were comorbidities and clinical manifestations.\n\nDependent variables were four possible severity outcomes(a) pneumonia, (b) mechanical ventilation (c) intensive care unit, and (d) death; all of them were coded as binary Results: We included 69,334 hospitalizations of laboratory-confirmed and hospitalized patients to June 30, 2020. Patients were 55.29 years, and 62.61% were male. Hospital mortality among patients aged<15 was 9.11%, 51.99% of those aged >65 died. Male gender and increasing age predicted every severity outcome. Diabetes and hypertension predicted every severity outcome significantly. Obesity did not predict mortality, but CKD, respiratory diseases, cardiopathies were significant predictors.\n\nConclusionObesity increased the risk for pneumonia, mechanical ventilation, and intensive care admittance, but it was not a predictor of in-hospital death. Patients with respiratory diseases were less prone to develop pneumonia, to receive mechanical ventilation and intensive care unit assistance, but they were at higher risk of in-hospital death.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Genny Carrillo",
+        "author_inst": "Texas A&M University"
+      },
+      {
+        "author_name": "Nina Mendez Dominguez",
+        "author_inst": "Universidad Marista, School of Medicina, Merida, Yucatan, Mexico"
+      },
+      {
+        "author_name": "Kassandra D Santos Zaldivar",
+        "author_inst": "Universidad Marista de Merida, Yucatan, Mexico"
+      },
+      {
+        "author_name": "Andrea Rochel Perez",
+        "author_inst": "Universidad Marista de Merida, Yucatan, Mexico"
+      },
+      {
+        "author_name": "Mario Azuela Morales",
+        "author_inst": "Universidad Marista de Merida, Yucatan, Mexico"
+      },
+      {
+        "author_name": "Osman Cuevas Koh",
+        "author_inst": "Universidad Marista de Merida, Yucatan,Mexico"
+      },
+      {
+        "author_name": "Alberto Alvarez Baeza",
+        "author_inst": "Universidad Marista de Merida, Yucatan, Mexico"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.07.31.20166264",
     "rel_title": "Risk stratification as a tool to rationalize quarantine among health care workers exposed to COVID-19 cases - Evidence from a tertiary healthcare centre in India",
@@ -1251936,61 +1250977,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.08.01.20166546",
-    "rel_title": "Analytical and clinical performances of five immunoassays for the detection of SARS-CoV-2 antibodies in comparison with neutralization activity",
-    "rel_date": "2020-08-04",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.01.20166546",
-    "rel_abs": "BackgroundReliable high-throughput serological assays for SARS-CoV-2 antibodies (Abs) are urgently needed for the effective containment of the COVID-19 pandemic, as it is of crucial importance to understand the strength and duration of immunity after infection, and to make informed decisions concerning the activation or discontinuation of physical distancing restrictions.\n\nMethodsIn 184 serum samples from 130 COVID-19 patients and 54 SARS-CoV-2 negative subjects, the analytical and clinical performances of four commercially available chemiluminescent assays (Abbott SARS-Cov-2 IgG, Roche Elecsys anti-SARS-CoV-2, Ortho SARS-CoV-2 total and IgG) and one enzyme-linked immunosorbent assay (Diesse ENZY-WELL SARS-CoV-2 IgG) were evaluated and compared with the neutralization activity achieved using the plaque reduction neutralization test (PRNT).\n\nFindingsPrecision results ranged from 0.9% to 11.8% for all assays. Elecsys anti-SARS-CoV-2 demonstrated linearity of results at concentrations within the cut-off value. Overall, sensitivity ranged from 78.5 to 87.8%, and specificity, from 97.6 to 100%. On limiting the analysis to samples collected 12 days after onset of symptoms, the sensitivity of all assays increased, the highest value (95.2%) being obtained with VITRO Anti-SARS-CoV-2 Total and Architect SARS-CoV-2 IgG. The strongest PRNT50 correlation with antibody levels was obtained with ENZY-Well SARS-CoV-2 IgG (rho = 0.541, p < 0.001).\n\nInterpretationThe results confirmed that all immunoassays had an excellent specificity, whereas sensitivity varied across immunoassays, depending strongly on the time interval between symptoms onset and sample collection. Further studies should be conducted to achieve a stronger correlation between antibody measurement and PRNT50 in order to obtain useful information for providing effective passive antibody therapy, and developing a vaccine against the SARS-CoV-2 virus.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Mario Plebani",
-        "author_inst": "University of Padova"
-      },
-      {
-        "author_name": "Andrea Padoan",
-        "author_inst": "university of padova"
-      },
-      {
-        "author_name": "Laura Sciacovelli",
-        "author_inst": "Azienda Ospedale Universita di Padova"
-      },
-      {
-        "author_name": "Francesco Bonfante",
-        "author_inst": "Istituto Zooprofilattico Veneto"
-      },
-      {
-        "author_name": "Matteo Pagliari",
-        "author_inst": "Zooprofilattico Veneto"
-      },
-      {
-        "author_name": "Dania Bozzato",
-        "author_inst": "Universita di Padova"
-      },
-      {
-        "author_name": "Chiara Cosma",
-        "author_inst": "Azienda Ospedale Universita di Padova"
-      },
-      {
-        "author_name": "Alessio Bortolami",
-        "author_inst": "Zooprofilattico Veneto"
-      },
-      {
-        "author_name": "Davide Negrini",
-        "author_inst": "Universita di Padova"
-      },
-      {
-        "author_name": "Silvia Zuin",
-        "author_inst": "Universita di padova"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.08.01.20166595",
     "rel_title": "Implication of backward contact tracing in the presence of overdispersed transmission in COVID-19 outbreak",
@@ -1252241,6 +1251227,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.08.03.20167189",
+    "rel_title": "Evaluating Data-Driven Forecasting Methods for Predicting SARS-CoV2 Cases: Evidence From 173 Countries",
+    "rel_date": "2020-08-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.03.20167189",
+    "rel_abs": "The WHO announced the epidemic of SARS-CoV2 as a public health emergency of international concern on 30th January 2020. To date, it has spread to more than 200 countries, and has been declared as a global pandemic. For appropriate preparedness, containment, and mitigation response, the stakeholders and policymakers require prior guidance on the propagation of SARS-CoV2. This study aims to provide such guidance by forecasting the cumulative COVID-19 cases up to 4 weeks ahead for 173 countries, using four data-driven methodologies; autoregressive integrated moving average (ARIMA), exponential smoothing model (ETS), random walk forecasts (RWF) with and without drift. We also evaluate the accuracy of these forecasts using the Mean Absolute Percentage Error (MAPE). The results show that the ARIMA and ETS methods outperform the other two forecasting methods. Additionally, using these forecasts, we generated heat maps to provide a pictorial representation of the countries at risk of having an increase in cases in the coming 4 weeks for June. Due to limited data availability during the ongoing pandemic, less data-hungry forecasting models like ARIMA and ETS can help in anticipating the future burden of SARS-CoV2 on healthcare systems.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Ghufran Ahmad",
+        "author_inst": "National University of Sciences and Technology (NUST), Islamabad, Pakistan"
+      },
+      {
+        "author_name": "Furqan Ahmed",
+        "author_inst": "Leibniz Institute for Prevention Research and Epidemiology, Bremen, Germany"
+      },
+      {
+        "author_name": "Muhammad Suhail Rizwan",
+        "author_inst": "National University of Sciences and Technology (NUST), Islamabad, Pakistan"
+      },
+      {
+        "author_name": "Javed Muhammad",
+        "author_inst": "University of Swabi, Pakistan"
+      },
+      {
+        "author_name": "Hira Fatima",
+        "author_inst": "University of Adelaide, Australia"
+      },
+      {
+        "author_name": "Aamer Ikram",
+        "author_inst": "National Institute of Health, Pakistan"
+      },
+      {
+        "author_name": "Hajo Zeeb",
+        "author_inst": "Leibniz Institute for Prevention Research and Epidemiology, Bremen, Germany"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.08.03.20167197",
     "rel_title": "Spreading of COVID-19 in Italy as the spreading of a wave packet",
@@ -1253510,89 +1252539,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.08.03.20164897",
-    "rel_title": "Risk of hospitalisation with coronavirus disease 2019 in healthcare workers and their households:a nationwide linkage cohort study",
-    "rel_date": "2020-08-04",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.03.20164897",
-    "rel_abs": "ObjectiveMany healthcare staff work in high-risk settings for contracting and transmitting Severe Acute Respiratory Syndrome Coronavirus 2. Their risk of hospitalisation for coronavirus disease 2019 (COVID-19), and that of their households, is poorly understood.\n\nDesign and settings and participantsDuring the peak period for COVID-19 infection in Scotland (1st March 2020 to 6th June 2020) we conducted a national record linkage study to compare the risk of COVID-19 hospitalisation among healthcare workers (age: 18-65 years), their households and other members of the general population.\n\nMain outcomeHospitalisation with COVID-19\n\nResultsThe cohort comprised 158,445 healthcare workers, the majority being patient facing (90,733 / 158,445; 57.3%), and 229,905 household members. Of all COVID-19 hospitalisations in the working age population (18-65-year-old), 17.2% (360 / 2,097) were in healthcare workers or their households. Adjusting for age, sex, ethnicity, socio-economic deprivation and comorbidity, the risk of COVID-19 hospitalisation in non-patient facing healthcare workers and their households was similar to the risk in the general population (hazards ratio [HR] 0.81; 95%CI 0.52-1.26 and 0.86; 95%CI 0.49-1.51 respectively). In models adjusting for the same covariates however, patient facing healthcare workers, compared to non-patient facing healthcare workers, were at higher risk (HR 3.30; 95%CI 2.13-5.13); so too were household members of patient facing healthcare workers (HR 1.79; 95%CI 1.10-2.91). On sub-dividing patient-facing healthcare workers into those who worked in front-door, intensive care and non-intensive care aerosol generating settings and other, those in  front door roles were at higher risk (HR 2.09; 95%CI 1.49-2.94). For most patient facing healthcare workers and their households, the estimated absolute risk of COVID-19 hospitalisation was less than 0.5% but was 1% and above in older men with comorbidity.\n\nConclusionsHealthcare workers and their households contribute a sixth of hospitalised COVID-19 cases. Whilst the absolute risk of hospitalisation was low overall, patient facing healthcare workers and their households had 3- and 2-fold increased risks of COVID-19 hospitalisation.",
-    "rel_num_authors": 17,
-    "rel_authors": [
-      {
-        "author_name": "Anoop SV Shah",
-        "author_inst": "London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Rachael Wood",
-        "author_inst": "Public Health Scotland"
-      },
-      {
-        "author_name": "Ciara Gribben",
-        "author_inst": "Public health scotland"
-      },
-      {
-        "author_name": "David Caldwell",
-        "author_inst": "Public health scotland"
-      },
-      {
-        "author_name": "Jennifer Bishop",
-        "author_inst": "Public health scotland"
-      },
-      {
-        "author_name": "Amanda Weir",
-        "author_inst": "Public health scotland"
-      },
-      {
-        "author_name": "Sharon Kennedy",
-        "author_inst": "Public health scotland"
-      },
-      {
-        "author_name": "Martin Reid",
-        "author_inst": "Public health scotland"
-      },
-      {
-        "author_name": "Alison Smith-Palmer",
-        "author_inst": "Public health scotland"
-      },
-      {
-        "author_name": "David Goldberg",
-        "author_inst": "Health protection scotland"
-      },
-      {
-        "author_name": "Jim McMenamin",
-        "author_inst": "Public health scotland"
-      },
-      {
-        "author_name": "Colin Fischbacher",
-        "author_inst": "Public health scotland"
-      },
-      {
-        "author_name": "Chris Robertson",
-        "author_inst": "Public health scotland"
-      },
-      {
-        "author_name": "Sharon Hutchinson",
-        "author_inst": "Public health scotland"
-      },
-      {
-        "author_name": "Paul M McKeigue",
-        "author_inst": "University of Edinburgh"
-      },
-      {
-        "author_name": "Helen M Colhoun",
-        "author_inst": "University of Edinburgh"
-      },
-      {
-        "author_name": "David McAllister",
-        "author_inst": "University of Glasgow"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.08.03.20167122",
     "rel_title": "Ethnic minority groups in England and Wales - factors affecting the size and timing of elevated COVID-19 mortality: a retrospective cohort study linking Census and death records",
@@ -1253883,6 +1252829,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.08.03.20167403",
+    "rel_title": "The mental health and experiences of discrimination of LGBTQ+ people during the COVID-19 pandemic: Initial findings from the Queerantine Study",
+    "rel_date": "2020-08-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.03.20167403",
+    "rel_abs": "ObjectiveTo assess mental health status and experiences of discrimination amongst a sample of Lesbian, Gay, Bisexual, Transgender, Queer people (LGBTQ+, the \"plus\" including those who dont identify with any such label) during the COVID-19 pandemic.\n\nDesignCross-sectional web-based survey.\n\nSettingResponses were collected during the COVID-19 pandemic between April 27thand July 13th.\n\nParticipants398 LGBTQ+ respondents forming an analytical sample of 310 in the main models.\n\nMethodsWe used a combined measure of gender identity or expression and sexual orientation as the main explanatory variable. We assessed mental health with the 4-item Perceived Stress Scale (PSS-4), and with the 10-item Center for Epidemiological Studies Depression scale (CES-D-10). We measured experiences of discrimination with a battery of questions that asked respondents whether they had experienced a set of discriminatory experiences because of their LGBTQ+ identity during the coronavirus pandemic. Experiences of discrimination was considered a mediating factor and examined both as an outcome as well as an explanatory variable. Models were adjusted for a range of demographic and socioeconomic variables.\n\nResultsThe prevalence of depression and stress were both high, with the majority of the sample exhibiting significant depressive symptomology (69%). Around one-in-six respondents reported some form of discrimination since the start of the pandemic because they were LGBTQ+ (16.7%). In regression models, the average score for perceived stress increased by 1.44 (95% Confidence Interval (CI): 0.517-2.354) for those who had experienced an instance of homophobic or transphobic harassment, compared to respondents who had not. Similarly, the odds of exhibiting significant depressive symptomology (CES-D-10 scores of 10 or more) increased three-fold among those who had experienced harassment based on their gender or sexuality compared to those who had not (OR: 3.251; 95% CI: 1.168-9.052). These marked associations remained after adjustment for a number of socioeconomic and demographic covariates. Cis-female respondents who identify as gay or lesbian had the lowest scores for perceived social or depressive symptoms; conversely transgender and gender diverse individuals had the highest scores.\n\nConclusionsWe found high levels of stress and depressive symptoms, particularly among younger and transgender and gender diverse respondents. These associations were partially explained by experiences of discrimination which had a large, consistent and pernicious impact on stress and mental health.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Dylan Kneale",
+        "author_inst": "University College London"
+      },
+      {
+        "author_name": "Laia Becares",
+        "author_inst": "University of Sussex"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.07.31.20166082",
     "rel_title": "Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity",
@@ -1255347,109 +1254316,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.07.30.20149567",
-    "rel_title": "Detection of asymptomatic SARS-CoV-2 infections among healthcare workers: results from a large-scale screening program based on rapid serological testing.",
-    "rel_date": "2020-08-04",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20149567",
-    "rel_abs": "ObjectiveTo evaluate the performance of two available rapid immunological tests for identification of severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) antibodies and their subsequent application to a regional screening of health care workers (HCW) in Tuscany (Italy).\n\nDesignmeasures of accuracy and HCW serological surveillance\n\nSetting6 major health facilities in Tuscany, Italy.\n\nParticipants17,098 HCW of the Tuscany Region. Measures of accuracy were estimated to assess sensitivity in 176 hospitalized Covid-19 clinical subjects at least 14 days after a diagnostic PCR-positive assay result. Specificity was assessed in 295 sera biobanked in the pre-Covid-19 era in winter or summer 2013-14\n\nMain outcome measuresSensitivity and specificity, and 95% confidence intervals, were measured using two serological tests, named T-1 and T-2. Positive and Negative predictive values were estimated at different levels of prevalence. HCW of the health centers were tested using the serological tests, with a follow-up nasopharyngeal PCR-test swab in positive tested cases.\n\nResultsSensitivity was estimated as 99% (95%CI: 95%-100%) and 97% (95% CI: 90%-100%), whereas specificity was the 95% and 92%, for Test T-1 and T-2 respectively. In the historical samples IgM cross-reactions were detected in sera collected during the winter period, probably linked to other human coronaviruses. Out of the 17,098 tested, 3.1% have shown the presence of SARS-CoV-2 IgG antibodies, among them 6.8% were positive at PCR follow-up test on nasopharyngeal swabs.\n\nConclusionBased on the low prevalence estimate observed in this survey, the use of serological test as a stand-alone test is not justified to assess the individual immunity status. Serological tests showed good performance and might be useful in an integrated surveillance, for identification of infected subjects and their contacts as required by the policy of contact tracing, with the aim to reduce the risk of dissemination, especially in health service facilities.",
-    "rel_num_authors": 22,
-    "rel_authors": [
-      {
-        "author_name": "Francesca Maria Carozzi",
-        "author_inst": "Regional Laboratory of Cancer Prevention, Institute for prevention, research and oncological network (ISPRO)"
-      },
-      {
-        "author_name": "Maria Grazia Cusi",
-        "author_inst": "Department of Medical Biotechnologies, University of Siena, Siena"
-      },
-      {
-        "author_name": "Mauro Pistello",
-        "author_inst": "Virology Unit, Pisa University Hospital, Pisa, Italy"
-      },
-      {
-        "author_name": "Luisa Galli",
-        "author_inst": "Department of Health Sciences, University of Florence, Florence, Italy  and Pediatric Infectious Diseases Unit, Meyer Children's University, Hospital, Florence,"
-      },
-      {
-        "author_name": "Alessandro Bartoloni",
-        "author_inst": "Infectious and Tropical Diseases Unit, Careggi Hospital, Florence, Italy  and Department of Experimental and Clinical Medicine, University of Florence, Florence"
-      },
-      {
-        "author_name": "Gabriele Anichini",
-        "author_inst": "Department of Translational Research, University of Pisa, Pisa, Italy"
-      },
-      {
-        "author_name": "Chiara Azzari",
-        "author_inst": "Department of Health Sciences, University of Florence, Florence, Italy and Pediatric Immunology Unit, Meyer Children's University Hospital, Florence, Italy"
-      },
-      {
-        "author_name": "Michele Emdin",
-        "author_inst": "Fondazione Toscana G. Monasterio, Pisa and Massa, Italy"
-      },
-      {
-        "author_name": "Claudia Gandolfo",
-        "author_inst": "Department of Translational Research, University of Pisa, Pisa, Italy"
-      },
-      {
-        "author_name": "Fabrizio Maggi",
-        "author_inst": "Virology Unit, Pisa University Hospital, Pisa, Italy  and Department of Translational Research, University of Pisa, Pisa, Italy"
-      },
-      {
-        "author_name": "Elisabetta Mantengoli",
-        "author_inst": "Infectious and Tropical Diseases Unit, Careggi Hospital, Florence, Italy"
-      },
-      {
-        "author_name": "Maria Moriondo",
-        "author_inst": "Department of Health Sciences, University of Florence, Florence, Italy and  Pediatric Immunology Unit, Meyer Children's University Hospital, Florence, Italy"
-      },
-      {
-        "author_name": "Giovanna Moscato",
-        "author_inst": "Department of Laboratory Medicine, Pisa University Cisanello Hospital, Pisa, Italy"
-      },
-      {
-        "author_name": "Irene Paganini",
-        "author_inst": "Regional Laboratory of Cancer Prevention, Institute for prevention, research and oncological network (ISPRO)"
-      },
-      {
-        "author_name": "Claudio Passino",
-        "author_inst": "Fondazione Toscana G. Monasterio, Pisa and Massa, Italy"
-      },
-      {
-        "author_name": "Francesco Profili",
-        "author_inst": "Epidemiology Unit, Regional Health Agency of Tuscany, Florence, Italy"
-      },
-      {
-        "author_name": "Fabio Voller",
-        "author_inst": "Epidemiology Unit, Regional Health Agency of Tuscany, Florence, Italy"
-      },
-      {
-        "author_name": "Marco Zappa",
-        "author_inst": "Unit of Clinical and Descriptive Epidemiology, Institute for prevention, research and oncological network (ISPRO), Florence, Italy"
-      },
-      {
-        "author_name": "Filippo Quattrone",
-        "author_inst": "Fondazione Toscana G. Monasterio, Pisa and Massa, Italy"
-      },
-      {
-        "author_name": "Gian Maria Rossolini",
-        "author_inst": "Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy and Department of Experimental and Clinical Medicine, University of Fl"
-      },
-      {
-        "author_name": "Paolo Francesconi",
-        "author_inst": "Epidemiology Unit, Regional Health Agency of Tuscany, Florence, Italy"
-      },
-      {
-        "author_name": "- SARS-CoV-2 Serosurvey Tuscan Working Group",
-        "author_inst": ""
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.08.04.234153",
     "rel_title": "SARS-CoV-2 genome analysis of strains in Pakistan reveals GH, S and L clade strains at the start of the pandemic",
@@ -1255772,6 +1254638,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.08.02.233510",
+    "rel_title": "Mechanism of duplex unwinding by coronavirus nsp13 helicases",
+    "rel_date": "2020-08-03",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.02.233510",
+    "rel_abs": "The current COVID-19 pandemic urges in-depth investigation into proteins encoded with coronavirus (CoV), especially conserved CoV replicases. The nsp13 of highly pathogenic MERS-CoV, SARS-CoV-2, and SARS-CoV exhibit the most conserved CoV replicases. Using single-molecule FRET, we observed that MERS-CoV nsp13 unwound DNA in discrete steps of approximately 9 bp when ATP was used. If another NTP was used, then the steps were only 4 to 5 bp. In dwell time analysis, we detected 3 or 4 hidden steps in each unwinding process, which indicated the hydrolysis of 3 or 4 dTTP. Based on crystallographic and biochemical studies of CoV nsp13 helicases, we modeled an unwinding mechanism similar to the spring-loaded mechanism of HCV NS3 helicase, although our model proposes that flexible 1B and stalk domains, by allowing a lag greater than 4 bp during unwinding, cause the accumulated tension on the nsp13-DNA complex. The hinge region between two RecA-like domains in SARS-CoV-2 nsp13 is intrinsically more flexible than in MERS-CoV nsp13 due to the difference of a single amino acid, which causes the former to induce significantly greater NTP hydrolysis. Our findings thus establish a blueprint for determining the unwinding mechanism of a unique helicase family.\n\nO_LIWhen dTTP was used as the energy source, 4 hidden steps in each individual unwinding step after 3 - 4 NTP hydrolysis were observed.\nC_LIO_LIAn unwinding model of MERS-CoV-nsp13 which is similar to the spring-loaded mechanism of HCV NS3 helicase, except the accumulation of tension on nsp13/DNA complex is caused by the flexible 1B and stalk domains that allow a lag of 4-bp in unwinding.\nC_LIO_LIComparing to MERS-CoV nsp13, the hinge region between two RecA-like domains in SARS-CoV-2 nsp13 is intrinsically more flexible due to a single amino acid difference, which contributes to the significantly higher NTP hydrolysis by SARS-CoV-2 nsp13.\nC_LI",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Xiao Hu",
+        "author_inst": "University of Cincinnati College of Medicine"
+      },
+      {
+        "author_name": "Wei Hao",
+        "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College"
+      },
+      {
+        "author_name": "Bo Qin",
+        "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College"
+      },
+      {
+        "author_name": "Zhiqi Tian",
+        "author_inst": "University of Cincinnati College of Medicine"
+      },
+      {
+        "author_name": "Ziheng Li",
+        "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College"
+      },
+      {
+        "author_name": "Pengjiao Hou",
+        "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College"
+      },
+      {
+        "author_name": "Rong Zhao",
+        "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College"
+      },
+      {
+        "author_name": "Sheng Cui",
+        "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College"
+      },
+      {
+        "author_name": "Jiajie Diao",
+        "author_inst": "University of Cincinnati College of Medicine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "biophysics"
+  },
   {
     "rel_doi": "10.1101/2020.08.02.230839",
     "rel_title": "Natural Killer cell activation, reduced ACE2, TMPRSS2, cytokines G-CSF, M-CSF and SARS-CoV-2-S pseudovirus infectivity by MEK inhibitor treatment of human cells",
@@ -1257577,81 +1256494,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.07.31.231282",
-    "rel_title": "Purification of recombinant SARS-CoV-2 spike, its receptor binding domain, and CR3022 mAb for serological assay",
-    "rel_date": "2020-08-02",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.31.231282",
-    "rel_abs": "Serology testing for COVID-19 is highly attractive because of the relatively short diagnosis time and the ability to test for an active immune response against the SARS-CoV-2. In many types of serology tests, the sensitivity and the specificity are directly influenced by the quality of the antigens manufactured. Protein purification of these recombinantly expressed viral antigens [e.g., spike and its receptor binding domain (RBD)] is an important step in the manufacturing process. Simple and high-capacity protein purification schemes for spike, RBD, and CR3022 mAb, recombinantly expressed in CHO and HEK293 cells, are reported in this article. The schemes consist of an affinity chromatography step and a desalting step. Purified proteins were validated in ELISA-based serological tests. Interestingly, extracellular matrix proteins [most notably heparan sulfate proteoglycan (HSPG)] were co-purified from spike-expressing CHO culture with a long cultivation time. HSPG-spike interaction could play a functional role in the pathology and the pathogenesis of SARS-CoV-2 and other coronaviruses.",
-    "rel_num_authors": 15,
-    "rel_authors": [
-      {
-        "author_name": "Kang Lan Tee",
-        "author_inst": "The University of Sheffield"
-      },
-      {
-        "author_name": "Philip J Jackson",
-        "author_inst": "The University of Sheffield"
-      },
-      {
-        "author_name": "Joseph M Scarrott",
-        "author_inst": "The University of Sheffield"
-      },
-      {
-        "author_name": "Stephen RP Jaffe",
-        "author_inst": "The University of Sheffield"
-      },
-      {
-        "author_name": "Abayomi O Johnson",
-        "author_inst": "The University of Sheffield"
-      },
-      {
-        "author_name": "Yusuf Johari",
-        "author_inst": "The University of Sheffield"
-      },
-      {
-        "author_name": "Thilo H Pohle",
-        "author_inst": "The University of Sheffield"
-      },
-      {
-        "author_name": "Theo Mozzanino",
-        "author_inst": "The University of Sheffield"
-      },
-      {
-        "author_name": "Joseph Price",
-        "author_inst": "The University of Sheffield"
-      },
-      {
-        "author_name": "James Grinham",
-        "author_inst": "The University of Sheffield"
-      },
-      {
-        "author_name": "Adam Brown",
-        "author_inst": "The University of Sheffield"
-      },
-      {
-        "author_name": "Martin J Nicklin",
-        "author_inst": "The University of Sheffield"
-      },
-      {
-        "author_name": "David C James",
-        "author_inst": "The University of Sheffield"
-      },
-      {
-        "author_name": "Mark J Dickman",
-        "author_inst": "The University of Sheffield"
-      },
-      {
-        "author_name": "Tuck Seng Wong",
-        "author_inst": "The University of Sheffield"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "biochemistry"
-  },
   {
     "rel_doi": "10.1101/2020.08.02.233023",
     "rel_title": "A Systemic and Molecular Study of Subcellular Localization of SARS-CoV-2 Proteins",
@@ -1257938,6 +1256780,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "endocrinology"
   },
+  {
+    "rel_doi": "10.1101/2020.07.30.20165282",
+    "rel_title": "A Compartmental Epidemic Model Incorporating Probable Cases to Model COVID-19 Outbreak in Regions with Limited Testing Capacity",
+    "rel_date": "2020-08-02",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20165282",
+    "rel_abs": "We propose a new compartmental epidemic model taking into account people who has symptoms with no confirmatory laboratory testing (probable cases). We prove well-posedness of the model and provide an explicit expression for the basic reproduction number ([R]0). We use the model together with an extended Kalman filter (EKF) to estimate the time-varying effective reproduction number ([R]t) of COVID-19 in West Java province, Indonesia, where laboratory testing capacity is limited. Based on our estimation, the value of [R]t is higher when the probable cases are taken into account. This correction can be used by decision and policy makers when considering re-opening policy and evaluation of measures.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Agus Hasan",
+        "author_inst": "University of Southern Denmark"
+      },
+      {
+        "author_name": "Yuki Nasution",
+        "author_inst": "Universitas Mulawarman"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.07.30.20165100",
     "rel_title": "Clinical manifestations of patients with Coronavirus Disease 2019 (COVID- 19) attending at hospitals in Bangladesh",
@@ -1259367,109 +1258232,6 @@
     "type": "new results",
     "category": "genomics"
   },
-  {
-    "rel_doi": "10.1101/2020.07.30.20164970",
-    "rel_title": "High SARS-CoV-2 seroprevalence in Health Care Workers but relatively low numbers of deaths in urban Malawi",
-    "rel_date": "2020-08-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20164970",
-    "rel_abs": "BackgroundIn low-income countries, like Malawi, important public health measures including social distancing or a lockdown, have been challenging to implement owing to socioeconomic constraints, leading to predictions that the COVID-19 pandemic would progress rapidly. However, due to limited capacity to test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, there are no reliable estimates of the true burden of infection and death. We, therefore, conducted a SARS-CoV-2 serosurvey amongst health care workers (HCW) in Blantyre city to estimate the cumulative incidence of SARS-CoV-2 infection in urban Malawi.\n\nMethodsFive hundred otherwise asymptomatic HCWs were recruited from Blantyre City (Malawi) from 22nd May 2020 to 19th June 2020 and serum samples were collected all participants. A commercial ELISA was used to measure SARS-CoV-2 IgG antibodies in serum. We run local negative samples (2018 - 2019) to verify the specificity of the assay. To estimate the seroprevalence of SARS CoV-2 antibodies, we adjusted the proportion of positive results based on local specificity of the assay.\n\nResultsEighty-four participants tested positive for SARS-CoV-2 antibodies. The HCW with a positive SARS-CoV-2 antibody result came from different parts of the city. The adjusted seroprevalence of SARS-CoV-2 antibodies was 12.3% [CI 9.0-15.7]. Using age-stratified infection fatality estimates reported from elsewhere, we found that at the observed adjusted seroprevalence, the number of predicted deaths was 8 times the number of reported deaths.\n\nConclusionThe high seroprevalence of SARS-CoV-2 antibodies among HCW and the discrepancy in the predicted versus reported deaths, suggests that there was early exposure but slow progression of COVID-19 epidemic in urban Malawi. This highlights the urgent need for development of locally parameterised mathematical models to more accurately predict the trajectory of the epidemic in sub-Saharan Africa for better evidence-based policy decisions and public health response planning.",
-    "rel_num_authors": 22,
-    "rel_authors": [
-      {
-        "author_name": "Marah Grace Chibwana",
-        "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research programme"
-      },
-      {
-        "author_name": "Khuzwayo Chidiwa Jere",
-        "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research programme"
-      },
-      {
-        "author_name": "Jonathan Mandolo",
-        "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme"
-      },
-      {
-        "author_name": "Vincent Katunga-Phiri",
-        "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme"
-      },
-      {
-        "author_name": "Dumizulu Tembo",
-        "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme"
-      },
-      {
-        "author_name": "Ndaona Mitole",
-        "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme"
-      },
-      {
-        "author_name": "Samantha Musasa",
-        "author_inst": "College of Medicine, University of Malawi"
-      },
-      {
-        "author_name": "Simon Sichone",
-        "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme"
-      },
-      {
-        "author_name": "Agness Lakudzala",
-        "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme"
-      },
-      {
-        "author_name": "Lusako Sibale",
-        "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme"
-      },
-      {
-        "author_name": "Prisca Matambo",
-        "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme"
-      },
-      {
-        "author_name": "Innocent Kadwala",
-        "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme"
-      },
-      {
-        "author_name": "Rachel Louise Byrne",
-        "author_inst": "Liverpool School of Tropical Medicine"
-      },
-      {
-        "author_name": "Alice Mbewe",
-        "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme"
-      },
-      {
-        "author_name": "Marc Y.R. Henrion",
-        "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research programme"
-      },
-      {
-        "author_name": "Ben Morton",
-        "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme"
-      },
-      {
-        "author_name": "Chimota Phiri",
-        "author_inst": "Ministry of Health, Queen Elizabeth Central Hospital"
-      },
-      {
-        "author_name": "Jane Mallewa",
-        "author_inst": "College of Medicine, University of Malawi"
-      },
-      {
-        "author_name": "Henry C Mwandumba",
-        "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme"
-      },
-      {
-        "author_name": "Emily R Adams",
-        "author_inst": "Liverpool School of Tropical Medicine"
-      },
-      {
-        "author_name": "Stephen B Gordon",
-        "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme"
-      },
-      {
-        "author_name": "Kondwani Charles Jambo",
-        "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Programme"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.07.30.20164921",
     "rel_title": "Estrogen and COVID-19 symptoms: associations in women from the COVID Symptom Study",
@@ -1259856,6 +1258618,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.07.30.20165050",
+    "rel_title": "Quantification of the association between predisposing health conditions, demographic, and behavioural factors with hospitalisation, intensive care unit admission, and death from COVID-19: a systematic review and meta-analysis",
+    "rel_date": "2020-08-01",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20165050",
+    "rel_abs": "BackgroundComprehensive evidence synthesis on the associations between comorbidities and behavioural factors with hospitalisation, Intensive Care Unit (ICU) admission, and death due to COVID-19 is lacking leading to inconsistent national and international recommendations on who should be targeted for non-pharmaceutical interventions and vaccination strategies.\n\nMethodsWe performed a systematic review and meta-analysis on studies and publicly available data to quantify the association between predisposing health conditions, demographics, and behavioural factors with hospitalisation, ICU admission, and death from COVID-19. We provided ranges of reported and calculated effect estimates and pooled relative risks derived from a meta-analysis and meta-regression.\n\nResults75 studies were included into qualitative and 74 into quantitative synthesis, with study populations ranging from 19 - 44,672 COVID-19 cases. The risk of dying from COVID-19 was significantly associated with cerebrovascular [pooled RR 2.7 (95% CI 1.7-4.1)] and cardiovascular [RR 3.2 (CI 2.3-4.5)] diseases, hypertension [RR 2.6 (CI 2.0-3.4)], and renal disease [RR 2.5 (CI 1.8-3.4)]. Health care workers had lower risk for death and severe outcomes of disease (RR 0.1 (CI 0.1-0.3). Our meta-regression showed a decrease of the effect of some comorbidities on severity of disease with higher median age of study populations. Associations between comorbidities and hospitalisation and ICU admission were less strong than for death.\n\nConclusionsWe obtained robust estimates on the magnitude of risk for COVID-19 hospitalisation, ICU admission, and death associated with comorbidities, demographic, and behavioural risk factors. We identified and confirmed population groups that are vulnerable and that require targeted prevention approaches.\n\nSummaryComorbidities such as cardiovascular disease or hypertension are less strongly associated with hospitalization and ICU admission than with death in COVID-19 patients. Increasing age is associated with a lower effect on comorbidities on disease severity.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Nathalie Veronica Fernandez Villalobos",
+        "author_inst": "Helmholtz Centre for Infection Research"
+      },
+      {
+        "author_name": "Joerdis Jennifer Ott",
+        "author_inst": "Helmholtz Centre for Infection Research, Hannover Medical School, German Centre for Infection Research"
+      },
+      {
+        "author_name": "Carolina Judith Klett-Tammen",
+        "author_inst": "Helmholtz Centre for Infection Research"
+      },
+      {
+        "author_name": "Annabelle Bockey",
+        "author_inst": "Helmholtz Centre for Infection Research, University Hospital Freiburg"
+      },
+      {
+        "author_name": "Patrizio Vanella",
+        "author_inst": "Helmholtz Centre for Infection Research"
+      },
+      {
+        "author_name": "Gerard Krause",
+        "author_inst": "Helmholtz Centre for Infection Research, Hannover Medical School, German Centre for Infection Research, Twincore"
+      },
+      {
+        "author_name": "Berit Lange",
+        "author_inst": "Helmholtz Centre for Infection Research, German Centre for Infection Research"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.07.30.20164608",
     "rel_title": "Visualizing and Assessing US County-Level COVID19 Vulnerability",
@@ -1261101,49 +1259906,6 @@
     "type": "new results",
     "category": "molecular biology"
   },
-  {
-    "rel_doi": "10.1101/2020.07.29.20164244",
-    "rel_title": "Changes in the behavioural determinants of health during the coronavirus (COVID-19) pandemic: gender, socioeconomic and ethnic inequalities in 5 British cohort studies",
-    "rel_date": "2020-07-31",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.29.20164244",
-    "rel_abs": "BackgroundThe coronavirus (COVID-19) pandemic and consequent physical distancing measures are expected to have far-reaching consequences on population health, particularly in already disadvantaged groups. These consequences include changes in health impacting behaviours (such as exercise, sleep, diet and alcohol use) which are arguably important drivers of health inequalities. We sought to add to the rapidly developing empirical evidence base investigating the impacts of the pandemic on such behavioural outcomes.\n\nMethodsUsing data from five nationally representative British cohort studies (born 2001, 1990, 1970, 1958, and 1946), we investigated sleep, physical activity (exercise), diet, and alcohol intake (N=14,297). Using measures of each behaviour reported before and during lockdown, we investigated change in each behaviour, and whether such changes differed by age/cohort, gender, ethnicity, and socioeconomic position (SEP; childhood social class, education attainment, and adult reporting of financial difficulties). Binary or ordered logistic regression models were used, adjusting for prior measures of each health behaviour and accounting for study design and non-response weights. Meta-analyses were used to pool cohort-specific estimates and formally test for heterogeneity across cohorts.\n\nResultsChanges in these outcomes occurred in in both directions ie, shifts from the middle part of the distribution to both declines and increases in sleep, exercise, and alcohol use. For all outcomes, older cohorts were less likely to report changes in behaviours compared with younger cohorts. In the youngest cohort (born 2001), the following shifts were more evident: increases in exercise, fruit and vegetable intake, sleep, and less frequent alcohol consumption. After adjustment for prior behaviour levels, during lockdown females were less likely to sleep within the typical range (6-9 hours) yet exercised more frequently; lower SEP was associated with lower odds of sleeping within the typical range (6-9 hours), lower exercise participation, and lower consumption of fruit and vegetables; and ethnic minorities were less likely than White participants to sleep within the typical range (6-9 hours), exercise less frequently, yet reported less frequent alcohol consumption.\n\nConclusionsOur findings highlight the multiple changes to behavioural outcomes that may have occurred due to COVID-19 lockdown, and the differential impacts across generation, gender, SEP and ethnicity. Such changes require further monitoring given their possible implications to population health and the widening of health inequalities.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "David Bann",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Aase Villadsen",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Jane Maddock",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Alun Hughes",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "George Ploubidis",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Richard Silverwood",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Praveetha Patalay",
-        "author_inst": "University College London"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.07.28.20163915",
     "rel_title": "Converting Microwave Ovens into Plasma-Generating Decontamination Units for N-95 Respirators",
@@ -1261442,6 +1260204,125 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.07.29.20164293",
+    "rel_title": "Persistent fatigue following SARS-CoV-2 infection is common and independent of severity of initial infection",
+    "rel_date": "2020-07-30",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.29.20164293",
+    "rel_abs": "Fatigue is a common symptom in those presenting with symptomatic COVID-19 infection. However, it is unknown if COVID-19 results in persistent fatigue in those recovered from acute infection. We examined the prevalence of fatigue in individuals recovered from the acute phase of COVID-19 illness using the Chalder Fatigue Score (CFQ-11). We further examined potential predictors of fatigue following COVID-19 infection, evaluating indicators of COVID-19 severity, markers of peripheral immune activation and circulating pro-inflammatory cytokines. Of 128 participants (49.5 {+/-} 15 years; 54% female), more than half reported persistent fatigue (52.3%; 45/128) at 10 weeks (median) after initial COVID-19 symptoms. There was no association between COVID-19 severity (need for inpatient admission, supplemental oxygen or critical care) and fatigue following COVID-19. Additionally, there was no association between routine laboratory markers of inflammation and cell turnover (leukocyte, neutrophil or lymphocyte counts, neutrophil-to-lymphocyte ratio, lactate dehydrogenase, C-reactive protein) or pro-inflammatory molecules (IL-6 or sCD25) and fatigue post COVID-19. Female gender and those with a pre-existing diagnosis of depression/anxiety were over-represented in those with fatigue. Our findings demonstrate a significant burden of post-viral fatigue in individuals with previous SARS-CoV-2 infection after the acute phase of COVID-19 illness. This study highlights the importance of assessing those recovering from COVID-19 for symptoms of severe fatigue, irrespective of severity of initial illness, and may identify a group worthy of further study and early intervention.",
+    "rel_num_authors": 26,
+    "rel_authors": [
+      {
+        "author_name": "Liam Townsend",
+        "author_inst": "St James's Hospital"
+      },
+      {
+        "author_name": "Adam H Dyer",
+        "author_inst": "St James's Hospital"
+      },
+      {
+        "author_name": "Karen Jones",
+        "author_inst": "St James's Hospital"
+      },
+      {
+        "author_name": "Jean Dunne",
+        "author_inst": "St James's Hospital"
+      },
+      {
+        "author_name": "Rachel Kiersey",
+        "author_inst": "St James's Hospital"
+      },
+      {
+        "author_name": "Fiona Gaffney",
+        "author_inst": "St James's Hospital"
+      },
+      {
+        "author_name": "Laura O'Connor",
+        "author_inst": "St James's Hospital"
+      },
+      {
+        "author_name": "Aoife Mooney",
+        "author_inst": "St James's Hospital"
+      },
+      {
+        "author_name": "Deirdre Leavy",
+        "author_inst": "St James's Hospital"
+      },
+      {
+        "author_name": "Katie Ridge",
+        "author_inst": "St James's Hospital"
+      },
+      {
+        "author_name": "Catherine King",
+        "author_inst": "St James's Hospital"
+      },
+      {
+        "author_name": "Fionnuala Cox",
+        "author_inst": "St James's Hospital"
+      },
+      {
+        "author_name": "Kate O'Brien",
+        "author_inst": "St James's Hospital"
+      },
+      {
+        "author_name": "Joanne Dowds",
+        "author_inst": "St James's Hospital"
+      },
+      {
+        "author_name": "Jamie Sugrue",
+        "author_inst": "Trinity College Dublin"
+      },
+      {
+        "author_name": "David Hopkins",
+        "author_inst": "Trinity College Dublin"
+      },
+      {
+        "author_name": "Patricia Byrne",
+        "author_inst": "St James's Hospital"
+      },
+      {
+        "author_name": "Tara Kingston",
+        "author_inst": "St James's Hospital"
+      },
+      {
+        "author_name": "Cliona Ni Cheallaigh",
+        "author_inst": "St James's Hospital"
+      },
+      {
+        "author_name": "Parthiban Nadarajan",
+        "author_inst": "St James's Hospital"
+      },
+      {
+        "author_name": "Anne Marie McLaughlin",
+        "author_inst": "St James's Hospital"
+      },
+      {
+        "author_name": "Nollaig M Bourke",
+        "author_inst": "Trinity College Dublin"
+      },
+      {
+        "author_name": "Colm Bergin",
+        "author_inst": "St James's Hospital"
+      },
+      {
+        "author_name": "Cliona O'Farrelly",
+        "author_inst": "Trinity College Dublin"
+      },
+      {
+        "author_name": "Ciaran Bannan",
+        "author_inst": "St James's Hospital"
+      },
+      {
+        "author_name": "Niall Conlon",
+        "author_inst": "St James's Hospital"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.07.29.20164160",
     "rel_title": "Tocilizumab shortens time on mechanical ventilation and length of hospital stay in patients with severe COVID-19: a retrospective cohort study.",
@@ -1262583,37 +1261464,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.07.28.20163154",
-    "rel_title": "Reduced susceptibility to SARS-CoV-2 in metropolitan regions",
-    "rel_date": "2020-07-30",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.28.20163154",
-    "rel_abs": "The coronavirus pandemic is wreaking public health, social, and economic havoc across the globe, and to date a variety of strategies have been implemented to attempt to control the spread of disease [1, 2]. A critical unknown for policy planning is the number of people who have been infected and are no longer susceptible [3]. Tests for active SARS-CoV-2 infection or antibody presence can provide an indication, but both are prone to selection bias, under-representative population sampling and insufficient reliability [4, 5]. Here, we present an alternative to determine residual susceptibilities based on the analysis of observed population-wide disease dynamics data. For four highly-affected countries, we directly compared the dynamics in the largest metropolitan regions with the rest of the countries. We show that substantial susceptibility reductions are measurable in the metropolitan regions, which all continued in a phase of exponential growth of case numbers for a relatively longer time before public health interventions were introduced. Compared to these interventions, the reduction in metropolitan region susceptibility had a substantial role in the post-growth decline in infection rates. Reduced population susceptibility has far reaching consequences on future policy responses and disease forecasts including vaccine trial planning and, in the case of a second epidemic wave, higher population-normalised mortality rates for non-metropolitan regions.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Thomas J. Barrett",
-        "author_inst": "University of Sussex"
-      },
-      {
-        "author_name": "Karen C. Patterson",
-        "author_inst": "Brighton & Sussex Medical School"
-      },
-      {
-        "author_name": "Timothy M. James",
-        "author_inst": "University of Sussex"
-      },
-      {
-        "author_name": "Peter Kruger",
-        "author_inst": "University of Sussex"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.07.29.20164152",
     "rel_title": "The Role of Weather Conditions in COVID-19 Transmission: A Study of a Global Panel of 1236 Regions",
@@ -1262924,6 +1261774,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "hematology"
   },
+  {
+    "rel_doi": "10.1101/2020.07.29.20159442",
+    "rel_title": "Early Clinical Factors Predicting the Development of Critical Disease in Japanese Patients with COVID-19: A Single-Center Retrospective, Observational Study",
+    "rel_date": "2020-07-30",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.29.20159442",
+    "rel_abs": "BackgroundInsufficient evidence of factors predicting the COVID-19 progression from mild to moderate to critical has been established. We retrospectively evaluated risk factors for critical progression in Japanese COVID-19 patients.\n\nMethodSeventy-four laboratory-confirmed COVID-19 patients were hospitalized in our hospital between February 20, 2020, and June 10, 2020. We excluded asymptomatic, non-Japanese, and child patients. We divided patients into the stable group (SG) and the progression group (PG) (patients requiring mechanical ventilation). We compared the clinical factors in both groups. We established the cutoff values (COVs) for significantly different factors via receiver operating characteristic (ROC) curve analysis and evaluated risk factors by univariate regression.\n\nResultsWe enrolled 57 COVID-19 patients (median age 52 years, 56.1% male). The median progression time from symptom onset was eight days. Seven patients developed critical disease (PG: 12.2%), two (3.5%) of whom died; 50 had stable disease. Univariate logistic analysis identified elevated lactate dehydrogenase (LDH) (COV: 309 U/l), decreased estimated glomerular filtration rate (eGFR) (COV: 68 ml/min), lymphocytopenia (COV: 980/l), and statin use as significantly associated with disease progression. However, in Cox proportional hazards analysis, lymphocytopenia at symptom onset was not significant.\n\nConclusionsWe identified three candidate risk factors for adult Japanese patients with mild to moderate COVID-19: statin use, elevated LDH level, and decreased eGFR.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Takatoshi Higuchi",
+        "author_inst": "Toyonaka Municipal Hospital"
+      },
+      {
+        "author_name": "Tsutomu Nishida",
+        "author_inst": "Toyonaka Municipal Hospital"
+      },
+      {
+        "author_name": "Hiromi Iwahashi",
+        "author_inst": "Toyonaka Municipal Hospital"
+      },
+      {
+        "author_name": "Osamu Morimura",
+        "author_inst": "Toyonaka Municipal Hospital"
+      },
+      {
+        "author_name": "Yasushi Otani",
+        "author_inst": "Toyonaka Municipal Hospital"
+      },
+      {
+        "author_name": "Yukiyoshi Okauchi",
+        "author_inst": "Toyonaka Municipal Hospital"
+      },
+      {
+        "author_name": "Masaru Yokoe",
+        "author_inst": "Toyonaka Municipal Hospital"
+      },
+      {
+        "author_name": "Norihiro Suzuki",
+        "author_inst": "Toyonaka Municipal Hospital"
+      },
+      {
+        "author_name": "Masami Inada",
+        "author_inst": "Toyonaka Municipal Hospital"
+      },
+      {
+        "author_name": "Kinya Abe",
+        "author_inst": "Toyonaka Municipal Hospital"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.07.24.20148262",
     "rel_title": "Incidence and outcomes of healthcare-associated COVID-19 infections: significance of delayed diagnosis and correlation with staff absence",
@@ -1264353,41 +1263258,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.07.23.20160424",
-    "rel_title": "A Retrospective Study on Efficacy and Safety of Guduchi Ghan Vati for Covid-19 Asymptomatic Patients",
-    "rel_date": "2020-07-29",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.23.20160424",
-    "rel_abs": "BackgroundCoronavirus disease 2019 (Covid-19) has been declared global emergency with immediate safety, preventative and curative measures to control the spread of virus. Confirmed cases are treated with clinical management as they are diagnosed but so far, there is no effective treatment or vaccine yet for Covid-19. Ayurveda has been recommended by preventative and clinical management guidelines in India and several clinical trials are ongoing. But there is no study to assess impact of Ayurveda on Covid-19.\n\nMethodsObjective of present study was to evaluate the clinical outcome in Covid-19 confirmed asymptomatic to mild symptomatic patients who had received Ayurveda and compare with control (who has not received Ayurveda or any support therapy). Patients having Ayurveda intervention (Guduchi Ghan Vati-extract of Tinospora cordifolia) were included from Jodhpur Covid Care Centre and non-recipients were taken from Jaipur Covid Care Centre between May 15 to June 15, 2020. Total 91 patients, who were asymptomatic at the time of hospital admission and between 18 -75 years of age, were included in the study to analyse retrospectively.\n\nResultsIn control group, 11.7% developed mild symptoms after average 1.8 days and none in Ayurveda group reported any symptoms. Significant difference was reported between the group of patients taking Guduchi Ghan Vati (n=40) and patients in standard care (n=51) in terms of virologic clearance at day-7 (97.5% vs 15.6% respectively; p=0.000), at day 14 (100% vs 82.3%) days to stay in hospital (6.4 vs 12.8 respectively; p< 0.0001).\n\nConclusionResults of the study suggest that Guduchi Ghan Vati, a common and widely used Ayurveda preparation, could benefit treating asymptomatic Covid-19 patients. Larger, randomised controlled Trials are required to confirm the findings.\n\nhttps://clinicaltrials.gov/ct2/show/NCT04480398",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Abhimanyu Kumar",
-        "author_inst": "Dr Sarvepalli Radhakrishnan Rajasthan Ayurved University, India"
-      },
-      {
-        "author_name": "Govind Prasad",
-        "author_inst": "Dr Sarvepalli Radhakrishnan Rajasthan Ayurved University, India"
-      },
-      {
-        "author_name": "Sanjay Srivastav",
-        "author_inst": "Dr Sarvepalli Radhakrishnan Rajasthan Ayurved University, India"
-      },
-      {
-        "author_name": "Vinod Kumar Gautam",
-        "author_inst": "Dr Sarvepalli Radhakrishnan Rajasthan Ayurved University, India"
-      },
-      {
-        "author_name": "Neha Sharma",
-        "author_inst": "Aarogyam (UK) CIC"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.07.21.20158337",
     "rel_title": "Endpoint PCR Detection of Sars-CoV-2 RNA",
@@ -1264706,6 +1263576,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "respiratory medicine"
   },
+  {
+    "rel_doi": "10.1101/2020.07.27.20162743",
+    "rel_title": "How much reserve capacity is justifiable for hospital pandemic preparedness? A cost-effectiveness analysis for COVID-19 in Germany",
+    "rel_date": "2020-07-29",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.27.20162743",
+    "rel_abs": "IntroductionIn preparation for a possible second COVID-19 pandemic wave, expanding intensive care unit (ICU) bed capacity is an important consideration. The purpose of this study was to determine the costs and benefits of this strategy in Germany.\n\nMethodsThis study compared the provision of additional capacity to no intervention from a societal perspective. A decision model was developed using, e.g., information on age-specific fatality rates, ICU costs and outcomes, and the herd protection threshold. The net monetary benefit (NMB) was calculated based upon the willingness to pay for new medicines for the treatment of cancer, a condition with a similar disease burden in the near term.\n\nResultsThe marginal cost-effectiveness ratio (MCER) of supplying one additional ICU bed is {euro}24,815 per life year gained and increases with the number of additional beds. The NMB remains positive for utilization rates as low as 1.5% and, assuming full capacity utilization, for multiples of the currently available bed capacity. Expanding the ICU bed capacity by 10,000 beds is projected to result in societal costs of {euro}41 billion and to reduce mortality of ICU candidates by 20% compared with no intervention (assuming full capacity utilization). In a sensitivity analysis, the variables with the highest impact on the MCER were the mortality rates in the ICU and after discharge.\n\nConclusionsIn Germany, the provision of additional ICU bed capacity appears to be cost-effective over a large increase in the number of beds. Nevertheless, bed utilization is constrained by labor supply and possibly other input factors.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Afschin Gandjour",
+        "author_inst": "Frankfurt School of Finance & Management"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health economics"
+  },
   {
     "rel_doi": "10.1101/2020.07.27.20162636",
     "rel_title": "The German Corona Consensus Dataset (GECCO): A standardized dataset for COVID-19 research",
@@ -1265919,25 +1264808,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.07.27.20162362",
-    "rel_title": "Close-range exposure to a COVID-19 carrier: transmission trends in the respiratory tract and estimation of infectious dose",
-    "rel_date": "2020-07-29",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.27.20162362",
-    "rel_abs": "How human respiratory physiology and inhaled airflow therein proceed to impact transmission of SARS-CoV-2, leading to the initial infection, is an open question. An answer can help determine the susceptibility of an individual on exposure to a COVID-2019 carrier and can also quantify the still-unknown infectious dose for the disease. Combining computational fluid mechanics-based tracking of respiratory transport in anatomic domains with sputum assessment data from hospitalized COVID-19 patients and earlier measurements of ejecta size distribution during regular speech - this study shows that the regional deposition of virus-laden inhaled droplets at the initial nasopharyngeal infection sites, located in the upper airway, peaks over the droplet size range of 2.5 - 19 {micro}; and reveals that the number of virions that can potentially establish the infection is, at most, of[O] (102).",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Saikat Basu",
-        "author_inst": "South Dakota State University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "otolaryngology"
-  },
   {
     "rel_doi": "10.1101/2020.07.27.20163147",
     "rel_title": "High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs",
@@ -1266536,6 +1265406,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "allergy and immunology"
   },
+  {
+    "rel_doi": "10.1101/2020.07.28.20163592",
+    "rel_title": "Evaluation of a SARS-CoV-2 surrogate virus neutralization test for detection of antibody in human, canine, cat and hamster sera",
+    "rel_date": "2020-07-29",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.28.20163592",
+    "rel_abs": "Surrogate neutralization assays for SARS-CoV-2 that can be done without biosafety-level-3 containment and across multiple species are desirable. We evaluate a recently developed surrogate virus neutralization test (sVNT) in comparison to 90% plaque reduction neutralization tests (PRNT90) in human, canine, cat and hamster sera and found excellent concordance between the two assays. Using a panel of immune sera to other coronaviruses, we confirm the lack of cross reactivity in sVNT and PRNT90 assays.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Joseph Sriyal Malik Peiris",
+        "author_inst": "University of Hong Kong"
+      },
+      {
+        "author_name": "Ranawaka APM Perera",
+        "author_inst": "The University of Hong Kong"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "allergy and immunology"
+  },
   {
     "rel_doi": "10.1101/2020.07.28.20163543",
     "rel_title": "Prevalence of amyloid blood clots in COVID-19 plasma",
@@ -1267969,69 +1266862,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2020.07.29.226555",
-    "rel_title": "The genetic variants analysis of circulating SARS-CoV-2 in Bangladesh.",
-    "rel_date": "2020-07-29",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.29.226555",
-    "rel_abs": "Genomic mutation of the virus may impact the viral adaptation to the local environment, their transmission, disease manifestation, and the effectiveness of existing treatment and vaccination. The objectives of this study were to characterize genomic variations, non-synonymous amino acid substitutions, especially in target proteins, mutation events per samples, mutation rate, and overall scenario of coronaviruses across the country. To investigate the genetic diversity, a total of 184 genomes of virus strains sampled from different divisions of Bangladesh with sampling dates between the 10th of May 2020 and the 27th of June 2020 were analyzed. To date, a total of 634 mutations located along the entire genome resulting in non-synonymous 274 amino acid substitutions in 22 different proteins were detected with nucleotide mutation rate estimated to be 23.715 substitutions per year. The highest non-synonymous amino acid substitutions were observed at 48 different positions of the papain-like protease (nsp3). Although no mutations were found in nsp7, nsp9, nsp10, and nsp11, yet orf1ab accounts for 56% of total mutations. Among the structural proteins, the highest non-synonymous amino acid substitution (at 36 positions) observed in spike proteins, in which 9 unique locations were detected relative to the global strains, including 516E>Q in the boundary of the ACE2 binding region. The most dominated variant G614 (95%) based in spike protein is circulating across the country with co-evolving other variants including L323 (94%) in RNA dependent RNA polymerase (RdRp), K203 (82%) and R204 (82%) in nucleocapsid, and F120 (78%) in NSP2. These variants are mostly seen as linked mutations and are part of a haplotype observed in Europe. Data suggest effective containment of clade G strains (4.8%) with sub-clusters GR 82.4%, and GH clade 6.4%.\n\nHighlightsO_LIWe have sequenced 137 and analyzed 184 whole-genomes sequences of SARS-CoV-2 strains from different divisions of Bangladesh.\nC_LIO_LIA total of 634 mutation sites across the SARS-CoV-2 genome and 274 non-synonymous amino acid substitutions were detected.\nC_LIO_LIThe mutation rate of SARS-CoV-2 estimated to be 23.715 nucleotide substitutions per year.\nC_LIO_LINine unique variants were detected based on non-anonymous amino acid substitutions in spike protein relative to the global SARS-CoV-2 strains.\nC_LI",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Abu Sayeed Mohammad Mahmud",
-        "author_inst": "Bangladesh Council of Scientific and Industrial Research"
-      },
-      {
-        "author_name": "Tarannum Taznin",
-        "author_inst": "Jashore University of Science and Technology"
-      },
-      {
-        "author_name": "Md. Murshed Hasan Sarkar",
-        "author_inst": "Bangladesh Council of Scientific and Industrial Research"
-      },
-      {
-        "author_name": "Mohammad Samir Uzzaman",
-        "author_inst": "Bangladesh Council of Scientific and Industrial Research"
-      },
-      {
-        "author_name": "Eshrar Osman",
-        "author_inst": "Bangladesh Council of Scientific and Industrial Research"
-      },
-      {
-        "author_name": "Md. Ahasan Habib",
-        "author_inst": "Bangladesh Council of Scientific and Industrial Research"
-      },
-      {
-        "author_name": "Shahina Akter",
-        "author_inst": "Bangladesh Council of Scientific and Industrial Research"
-      },
-      {
-        "author_name": "Tanjina Akhter Banu",
-        "author_inst": "Bangladesh Council of Scientific and Industrial Research"
-      },
-      {
-        "author_name": "Barna Goswami",
-        "author_inst": "Bangladesh Council of Scientific and Industrial Research"
-      },
-      {
-        "author_name": "Iffat Jahan",
-        "author_inst": "Bangladesh Council of Scientific and Industrial Research"
-      },
-      {
-        "author_name": "Md. Saddam Hossain",
-        "author_inst": "Bangladesh Council of Scientific and Industrial Research"
-      },
-      {
-        "author_name": "Md. Salim Khan",
-        "author_inst": "Bangladesh Council of Scientific and Industrial Research"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "genomics"
-  },
   {
     "rel_doi": "10.1101/2020.07.25.20162016",
     "rel_title": "Capping Mobility to Control COVID-19: A Collision-based Infectious Disease Transmission Model",
@@ -1268234,6 +1267064,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.07.25.20162073",
+    "rel_title": "Effectiveness and Safety of Chloroquine or Hydroxychloroquine as a mono-therapy or in combination with Azithromycin in the treatment of COVID-19 patients: Systematic Review and Meta-Analysis",
+    "rel_date": "2020-07-28",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.25.20162073",
+    "rel_abs": "Many recent studies have investigated the role of either Chloroquine (CQ) alone, Hydroxychloroquine (HCQ) alone, or CQ/HCQ in combination with azithromycin (AZM) in management of the emerging coronavirus. This systematic review and meta-analysis of either published or preprint observational or interventional studies were conducted to assess the cure rate, duration of hospital stay, radiological progression, clinical worsening, need for mechanical ventilation, the occurrence of side effects, and mortality. A search of the online database through June 2020 was performed and examined the reference lists of pertinent articles for in-vivo studies only. Pooled relative risks (RRs), standard mean, of 95 % confidence intervals (CIs) were calculated with the random-effects model.\n\nResultsThe duration of hospital stay was shorter in the standard care in comparison with HCQ group, the standard mean of hospital stay was 0.57, 95% CI, and 0.20-0.94. Overall virological cure, or more specifically at day 4, 10, and 14 among patients exposed to HCQ did not differ significantly from the standard care [(RR=0.92, 95% CI 0.78-1.15), (RR=1.11, 95% CI 0.74-1.65), (RR=1.21, 95%CI 0.70-2.01), and (RR=0.98, 95% CI, 0.76-1.27)] respectively. Radiological improvement or clinical worsening was not statistically different between HCQ and standard care [(RR=1.11, 95% CI 0.64-1.65) and (RR=1.28, 95% CI 0.33-4.99)]. The need for mechanical ventilation (MV) was not significant between the HCQ group and the standard care (RR= 1.5, 95%CI 0.78-2.89). Side effects were more reported in the HCQ group than the standard care (RR=3.14, 95% CI 1.58-6.24). Mortality among HCQ was not affected by receiving HCQ (RR=3.14, 95% CI 1.58-6.24), meta-regression analysis revealed that country is a strong predictor of mortality. The duration of hospital stay among the HCQ and AZM didnt differ significantly from the standard care (standard mean= 0.77, 95% CI 0.46-1.08). Despite virological cure and need for MV did not differ significantly [(RR= 3.23, 95% CI 0.70-14.97) and (RR=1.27, 95%CI 0.7-2.13)] respectively. Mortality among the HCQ+AZM was more significantly higher than among the standard care (RR= 1.8, 95% CI 1.19-2.27).\n\nConclusionDespite the scarcity of published data of good quality, the effectiveness and safety of either HCQ alone or in combination with AZM in treating the pandemic of COVID-19 cant be assured. Future randomized control trials need to be carried out to verify this conclusion.\n\nRegistrationPROSPERO registration number: CRD42020192084",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Ramy Mohamed Ghazy",
+        "author_inst": "High Institute of Public Health"
+      },
+      {
+        "author_name": "Abdallah Almaghraby",
+        "author_inst": "Alexandria Faculty of Medicine"
+      },
+      {
+        "author_name": "Ramy Shaaban",
+        "author_inst": "Utah State University"
+      },
+      {
+        "author_name": "Ahmed Kamal",
+        "author_inst": "Alexandria Faculty of Medicine"
+      },
+      {
+        "author_name": "Hatem Beshir",
+        "author_inst": "Mansoura Faculty of Medicine"
+      },
+      {
+        "author_name": "Amr Moursi",
+        "author_inst": "Ninewells University Hospital"
+      },
+      {
+        "author_name": "Sarah Hamed N. Taha",
+        "author_inst": "Cairo University"
+      },
+      {
+        "author_name": "Ahmed Ramadan",
+        "author_inst": "DataClin"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.07.27.20161976",
     "rel_title": "Exploratory analysis of immunization records highlights decreased SARS-CoV-2 rates in individuals with recent non-COVID-19 vaccinations",
@@ -1269559,37 +1268436,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2020.07.22.20160341",
-    "rel_title": "Effects of non-pharmaceutical interventions on COVID-19: A Tale of Two Models",
-    "rel_date": "2020-07-27",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20160341",
-    "rel_abs": "In this paper, we compare the inference regarding the effectiveness of the various non-pharmaceutical interventions (NPIs) for COVID-19 obtained from three SIR models, all developed by the Imperial College COVID-19 Response Team. One model was applied to European countries and published in Nature1 (model 1), concluding that complete lockdown was by far the most effective measure, responsible for 80% of the reduction in Rt, and 3 million deaths were avoided in the examined countries. The Imperial College team applied a different model to the USA states2 (model 2), and in response to our original submission, the Imperial team has proposed in a referee report a third model which is a hybrid of the first two models (model 3). We demonstrate that inference is highly nonrobust to model specification. In particular, inference regarding the relative effectiveness of NPIs changes substantially with the model and decision makers who are unaware of, or ignore, model uncertainty are underestimating the risk attached to any decisions based on that model. Our primary observation is that by applying to European countries the model that the Imperial College team used for the USA states (model 2), complete lockdown has no or little effect, since it was introduced typically at a point when Rt was already very low. Moreover, using several state-of-the-art metrics for Bayesian model comparison, we demonstrate that model 2 (when applied to the European data) is better supported by the data than the model published in Nature1. In particular, serious doubt is cast on the conclusions in Flaxman et al.1, whether we examine the data up to May 5th (as in Flaxman et al.1) or beyond the point when NPIs began to be lifted. Only by objectively considering a wide variety of models in a statistically principled manner, can one begin to address the effectiveness of NPIs such as lockdown. The approach outlined in this paper provides one such path.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Vincent Chin",
-        "author_inst": "The University of Sydney"
-      },
-      {
-        "author_name": "John Ioannidis",
-        "author_inst": "Stanford University"
-      },
-      {
-        "author_name": "Martin Tanner",
-        "author_inst": "Northwestern University"
-      },
-      {
-        "author_name": "Sally Cripps",
-        "author_inst": "The University of Sydney"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health policy"
-  },
   {
     "rel_doi": "10.1101/2020.07.23.20160481",
     "rel_title": "Why (and how) COVID-19 could move us closer to the \"health information for all\" goal",
@@ -1269996,6 +1268842,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.07.21.20153650",
+    "rel_title": "Patient characteristics and predictors of mortality in 470 adults admitted to a district general hospital in England with Covid-19",
+    "rel_date": "2020-07-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20153650",
+    "rel_abs": "BackgroundUnderstanding risk factors for death in Covid-19 is key to providing good quality clinical care. Due to a paucity of robust evidence, we sought to assess the presenting characteristics of patients with Covid-19 and investigate factors associated with death.\n\nMethodsRetrospective analysis of adults admitted with Covid-19 to Royal Oldham Hospital, UK. Logistic regression modelling was utilised to explore factors predicting death.\n\nResults470 patients were admitted, of whom 169 (36%) died. The median age was 71 years (IQR 57-82), and 255 (54.3%) were men. The most common comorbidities were hypertension (n=218, 46.4%), diabetes (n=143, 30.4%) and chronic neurological disease (n=123, 26.1%). The most frequent complications were acute kidney injury (n=157, 33.4%) and myocardial injury (n=21, 4.5%). Forty-three (9.1%) patients required intubation and ventilation, and 39 (8.3%) received non-invasive ventilation Independent risk factors for death were increasing age (OR per 10 year increase above 40 years 1.87, 95% CI 1.57-2.27), hypertension (OR 1.72, 1.10-2.70), cancer (OR 2.20, 1.27-3.81), platelets <150x103/{micro}L (OR 1.93, 1.13-3.30), C-reactive protein [&ge;]100 {micro}g/mL (OR 1.68, 1.05-2.68), >50% chest radiograph infiltrates, (OR 2.09, 1.16-3.77) and acute kidney injury (OR 2.60, 1.64-4.13). There was no independent association between death and gender, ethnicity, deprivation level, fever, SpO2/FiO2 (oxygen saturation index), lymphopenia or other comorbidities.\n\nConclusionsWe characterised the  first wave of patients with Covid-19 in one of Englands highest incidence areas, determining which factors predict death. These findings will inform clinical and shared decision making, including the use of respiratory support and therapeutic agents.\n\nSummaryIncreasing age, hypertension, cancer, platelets <150x103/{micro}L, CRP[&ge;]100 {micro}g/mL, >50% chest radiograph infiltrates, and acute kidney injury predict in-hospital death from Covid-19, whilst gender, ethnicity, deprivation level, fever, SpO2/FiO2 (oxygen saturation index), lymphopenia and other comorbidities do not.",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Joseph V Thompson",
+        "author_inst": "Royal Oldham Hospital"
+      },
+      {
+        "author_name": "Nevan Meghani",
+        "author_inst": "Royal Oldham Hospital"
+      },
+      {
+        "author_name": "Bethan M Powell",
+        "author_inst": "Royal Oldham Hospital"
+      },
+      {
+        "author_name": "Ian Newell",
+        "author_inst": "Royal Oldham Hospital"
+      },
+      {
+        "author_name": "Roanna Craven",
+        "author_inst": "Royal Oldham Hospital"
+      },
+      {
+        "author_name": "Gemma Skilton",
+        "author_inst": "Royal Oldham Hospital"
+      },
+      {
+        "author_name": "Lydia J Bagg",
+        "author_inst": "Royal Oldham Hospital"
+      },
+      {
+        "author_name": "Irha Yaqoob",
+        "author_inst": "Royal Oldham Hospital"
+      },
+      {
+        "author_name": "Michael J Dixon",
+        "author_inst": "Royal Oldham Hospital"
+      },
+      {
+        "author_name": "Eleanor J Evans",
+        "author_inst": "Royal Oldham Hospital"
+      },
+      {
+        "author_name": "Belina Kambele",
+        "author_inst": "Royal Oldham Hospital"
+      },
+      {
+        "author_name": "Asif Rehman",
+        "author_inst": "Royal Oldham Hospital"
+      },
+      {
+        "author_name": "Georges Ng Man Kwong",
+        "author_inst": "Royal Oldham Hospital"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.07.18.20155549",
     "rel_title": "Trends of in-hospital and 30-day mortality after percutaneous coronary intervention in England before and after the COVID-19 era",
@@ -1271377,41 +1270290,6 @@
     "type": "new results",
     "category": "molecular biology"
   },
-  {
-    "rel_doi": "10.1101/2020.07.26.222109",
-    "rel_title": "Development of Remdesivir as a Dry Powder for Inhalation by Thin Film Freezing",
-    "rel_date": "2020-07-27",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.26.222109",
-    "rel_abs": "Remdesivir exhibits in vitro activity against SARS-CoV-2 and was granted approval for Emergency Use. To maximize delivery to the lungs, we formulated remdesivir as a dry powder for inhalation using thin film freezing (TFF). TFF produces brittle matrix nanostructured aggregates that are sheared into respirable low-density microparticles upon aerosolization from a passive dry powder inhaler. In vitro aerodynamic testing demonstrated that drug loading and excipient type affected the aerosol performance of remdesivir. Remdesivir combined with optimal excipients exhibited desirable aerosol performance (up to 93.0% FPF; 0.82m MMAD). Remdesivir was amorphous after the TFF process, which benefitted drug dissolution in simulated lung fluid. TFF remdesivir formulations are stable after one-month storage at 25 {degrees}C/60%RH. In vivo pharmacokinetic evaluation showed that TFF-remdesivir-leucine was poorly absorbed into systemic circulation while TFF-remdesivir-Captisol(R) demonstrated increased systemic uptake compared to leucine. Remdesivir was hydrolyzed to the nucleoside analog GS-441524 in lung, and levels of GS-441524 were greater in lung with the leucine formulation compared to Captisol(R). In conclusion, TFF technology produces high potency remdesivir dry powder formulations for inhalation suitable to treat patients with COVID-19 on an outpatient basis and earlier in the disease course where effective antiviral therapy can reduce related morbidity and mortality.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Sawittree Sahakijpijarn",
-        "author_inst": "The University of Texas at Austin"
-      },
-      {
-        "author_name": "Chaeho Moon",
-        "author_inst": "The University of Austin"
-      },
-      {
-        "author_name": "John J Koleng",
-        "author_inst": "TFF Pharmaceuticals, Inc."
-      },
-      {
-        "author_name": "Dale J Christensen",
-        "author_inst": "TFF Pharmaceuticals, Inc."
-      },
-      {
-        "author_name": "Robert O Williams III",
-        "author_inst": "The University of Texas at Austin"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "pharmacology and toxicology"
-  },
   {
     "rel_doi": "10.1101/2020.07.26.222208",
     "rel_title": "CAR Macrophages for SARS-CoV-2 Immunotherapy",
@@ -1271758,6 +1270636,45 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2020.07.27.222901",
+    "rel_title": "Evolution And Genetic Diversity Of SARSCoV-2 In Africa Using Whole Genome Sequences",
+    "rel_date": "2020-07-27",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.27.222901",
+    "rel_abs": "The ongoing SARSCoV-2 pandemic was introduced into Africa on 14th February 2020 and has rapidly spread across the continent causing severe public health crisis and mortality. We investigated the genetic diversity and evolution of this virus during the early outbreak months using whole genome sequences. We performed; recombination analysis against closely related CoV, Bayesian time scaled phylogeny and investigated spike protein amino acid mutations. Results from our analysis showed recombination signals between the AfrSARSCoV-2 sequences and reference sequences within the N and S genes. The evolutionary rate of the AfrSARSCoV-2 was 4.133 x 10-4 high posterior density HPD (4.132 x 10-4 to 4.134 x 10-4) substitutions/site/year. The time to most recent common ancestor TMRCA of the African strains was December 7th 2019. The AfrSARCoV-2 sequences diversified into two lineages A and B with B being more diverse with multiple sub-lineages confirmed by both maximum clade credibility MCC tree and PANGOLIN software. There was a high prevalence of the D614-G spike protein amino acid mutation (82.61%) among the African strains. Our study has revealed a rapidly diversifying viral population with the G614 spike protein variant dominating, we advocate for up scaling NGS sequencing platforms across Africa to enhance surveillance and aid control effort of SARSCoV-2 in Africa.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Babatunde Olanrewaju Motayo",
+        "author_inst": "Federal Medical Center, Abeokuta"
+      },
+      {
+        "author_name": "Olukunle O Oluwasemowo",
+        "author_inst": "University of Ibadan"
+      },
+      {
+        "author_name": "Paul A Akinduti",
+        "author_inst": "Covenant University, Otta, Nigeria"
+      },
+      {
+        "author_name": "Babatunde A Olusola",
+        "author_inst": "University of Ibadan, Nigeria"
+      },
+      {
+        "author_name": "Olumide T Arege",
+        "author_inst": "University of Ibadan, Nigeria"
+      },
+      {
+        "author_name": "Adedayo O Faneye",
+        "author_inst": "University of Ibadan, Nigeria"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2020.07.26.222117",
     "rel_title": "Predicting the Emergence of SARS-CoV-2 Clades",
@@ -1273315,113 +1272232,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.07.20.20157503",
-    "rel_title": "COVIDOSE: Low-dose tocilizumab in the treatment of Covid-19",
-    "rel_date": "2020-07-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.20.20157503",
-    "rel_abs": "BackgroundInterleukin-6 (IL-6)-mediated hyperinflammation may contribute to the high mortality of coronavirus disease 2019 (Covid-19). Tocilizumab, an IL-6 receptor blocking monoclonal antibody, has been repurposed for Covid-19, but prospective trials and dose-finding studies in Covid-19 are lacking.\n\nMethodsWe conducted a phase 2 trial of low-dose tocilizumab in hospitalized adult patients with Covid-19, radiographic pulmonary infiltrate, fever, and C-reactive protein (CRP) [&ge;] 40 mg/L who did not require mechanical ventilation. Dose cohorts were determined by a trial Operations Committee, stratified by CRP and epidemiologic risk factors. A range of doses from 40 to 200 mg (low-dose tocilizumab) was evaluated, with allowance for one repeat dose at 24-48 hours. The primary objective was to assess the relationship of dose to fever resolution and CRP response. Outcomes were compared with retrospective controls with Covid-19. Correlative studies evaluating host antibody response were performed in parallel.\n\nFindingsA total of 32 patients received low-dose tocilizumab. This cohort had improved fever resolution (75{middle dot}0% vs. 34{middle dot}2%, p = 0{middle dot}001) and CRP decline (86{middle dot}2% vs. 14{middle dot}3%, p < 0{middle dot}001) in the 24-48 hours following drug administration, as compared to the retrospective controls (N=41). The probabilities of fever resolution or CRP decline did not appear to be dose-related (p=0{middle dot}80 and p=0{middle dot}10, respectively). Within the 28-day follow-up, 5 (15{middle dot}6%) patients died. For patients who recovered, median time to clinical recovery was 3 days (IQR, 2-5). Clinically presumed and/or cultured bacterial superinfections were reported in 5 (15{middle dot}6%) patients. Correlative biological studies demonstrated that tocilizumab-treated patients produced anti-SARS-CoV-2 antibodies comparable to controls.\n\nInterpretationLow-dose tocilizumab was associated with rapid improvement in clinical and laboratory measures of hyperinflammation in hospitalized patients with Covid-19. Results of this trial and its correlative biological studies provide rationale for a randomized, controlled trial of low-dose tocilizumab in Covid-19.\n\nFundingClinicalTrials.gov number NCT04331795. Study infrastructure was supported by NIH CTSA UL1 TR000430.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSMany patients with novel coronavirus disease 2019 (Covid-19) develop acute lung injury and hypoxic respiratory failure possibly due to a hyperinflammatory state similar to the cytokine release syndrome that occurs as a complication of chimeric antigen receptor T-cell therapy. Interleukin-6 (IL-6) has been implicated in both processes, leading to the hypothesis that patients with Covid-19 may benefit from IL-6 axis-directed therapies such as the IL-6 receptor-blocking monoclonal antibody tocilizumab. No dose-finding studies have been performed for tocilizumab in the setting of Covid-19.\n\nAdded value of this studyThis prospective phase 2 clinical trial is, to our knowledge, the first to evaluate low-dose tocilizumab in patients with Covid-19 and the first to evaluate the effect of tocilizumab on anti-SARS-CoV-2 antibody response.\n\nImplications of all the available evidenceThe COVIDOSE study, together with retrospective and real-world evidence studies demonstrating the efficacy of tocilizumab, suggests that low-dose tocilizumab is a potential treatment for hyperinflammation among patients with Covid-19 and merits randomized, controlled testing in this patient population.",
-    "rel_num_authors": 23,
-    "rel_authors": [
-      {
-        "author_name": "Garth W Strohbehn",
-        "author_inst": "University of Chicago"
-      },
-      {
-        "author_name": "Brian L Heiss",
-        "author_inst": "University of Chicago"
-      },
-      {
-        "author_name": "Sherin J Rouhani",
-        "author_inst": "University of Chicago"
-      },
-      {
-        "author_name": "Jonathan A Trujillo",
-        "author_inst": "University of Chicago"
-      },
-      {
-        "author_name": "Jovian Yu",
-        "author_inst": "University of Chicago"
-      },
-      {
-        "author_name": "Alec J Kacew",
-        "author_inst": "University of Chicago"
-      },
-      {
-        "author_name": "Emily F Higgs",
-        "author_inst": "University of Chicago"
-      },
-      {
-        "author_name": "Jeffrey C Bloodworth",
-        "author_inst": "University of Chicago"
-      },
-      {
-        "author_name": "Alexandra Cabanov",
-        "author_inst": "University of Chicago"
-      },
-      {
-        "author_name": "Rachel C Wright",
-        "author_inst": "University of Chicago"
-      },
-      {
-        "author_name": "Adriana Koziol",
-        "author_inst": "University of Chicago"
-      },
-      {
-        "author_name": "Alexandra Weiss",
-        "author_inst": "University of Chicago"
-      },
-      {
-        "author_name": "Keith Danahey",
-        "author_inst": "University of Chicago"
-      },
-      {
-        "author_name": "Theodore G Karrison",
-        "author_inst": "University of Chicago"
-      },
-      {
-        "author_name": "Cuoghi C Edens",
-        "author_inst": "University of Chicago"
-      },
-      {
-        "author_name": "Iazsmin Bauer Ventura",
-        "author_inst": "University of Chicago"
-      },
-      {
-        "author_name": "Natasha N Pettit",
-        "author_inst": "University of Chicago"
-      },
-      {
-        "author_name": "Bhakti Patel",
-        "author_inst": "University of Chicago"
-      },
-      {
-        "author_name": "Jennifer Pisano",
-        "author_inst": "University of Chicago"
-      },
-      {
-        "author_name": "Mary E Strek",
-        "author_inst": "University of Chicago"
-      },
-      {
-        "author_name": "Thomas F Gajewski",
-        "author_inst": "University of Chicago"
-      },
-      {
-        "author_name": "Mark J Ratain",
-        "author_inst": "University of Chicago"
-      },
-      {
-        "author_name": "Pankti D Reid",
-        "author_inst": "University of Chicago"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.07.22.20157263",
     "rel_title": "Recent smell loss is the best predictor of COVID-19: a preregistered, cross-sectional study",
@@ -1274232,6 +1273042,161 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.07.21.20125138",
+    "rel_title": "Viral RNA level, serum antibody responses, and transmission risk in discharged COVID-19 patients with recurrent positive SARS-CoV-2 RNA test results: a population-based observational cohort study",
+    "rel_date": "2020-07-26",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20125138",
+    "rel_abs": "SummaryO_ST_ABSBackgroundC_ST_ABSManaging discharged COVID-19 (DC) patients with recurrent positive (RP) SARS-CoV-2 RNA test results is challenging. We aimed to comprehensively characterize the viral RNA level and serum antibody responses in RP-DC patients and evaluate their viral transmission risk.\n\nMethodsA population-based observational cohort study was performed on 479 DC patients discharged from February 1 to May 5, 2020 in Shenzhen, China. We conducted RT-qPCR, antibody assays, neutralisation assays, virus isolation, whole genome sequencing (WGS), and epidemiological investigation of close contacts.\n\nFindingsOf 479 DC patients, the 93 (19%) RP individuals, including 36 with multiple RP results, were characterised by young age (median age: 34 years, 95% confidence interval [CI]: 29-38 years). The median discharge-to-RP length was 8 days (95% CI: 7-14 days; maximum: 90 days). After readmission, RP-DC patients exhibited mild (28%) or absent (72%) symptoms, with no disease progression. The viral RNA level in RP-DC patients ranged from 1{middle dot}9-5{middle dot}7 log10 copies/mL (median: 3{middle dot}2, 95% CI: 3{middle dot}1-3{middle dot}5). At RP detection, the IgM, IgG, IgA, total antibody, and neutralising antibody (NAb) seropositivity rates in RP-DC patients were 38% (18/48), 98% (47/48), 63% (30/48), 100% (48/48), and 91% (39/43), respectively. Regarding antibody levels, there was no significant difference between RP-DC and non-RP-DC patients. The antibody level remained constant in RP-DC patients pre- and post-RP detection. Virus isolation of nine representative specimens returned negative results. WGS of six specimens yielded only genomic fragments. No clinical symptoms were exhibited by 96 close contacts of 23 RP-DC patients; their viral RNA (96/96) and antibody (20/20) test results were negative. After full recovery, 60% of patients (n=162, 78 no longer RP RP-DC and 84 non-RP-DC) had NAb titres of [&ge;]1:32.\n\nInterpretationRP may occur in DC patients following intermittent and non-stable excretion of low viral RNA levels. RP-DC patients pose a low risk of transmitting SARS-CoV-2. An NAb titre of [&ge;] 1:32 may provide a reference indicator for evaluating humoral responses in COVID-19 vaccine clinical trials.\n\nFundingSanming Project of Medicine in Shenzhen, China National Science and Technology Major Projects Foundation, Special Foundation of Science and Technology Innovation Strategy of Guangdong Province of China, and Shenzhen Committee of Scientific and Technical Innovation grants.",
+    "rel_num_authors": 35,
+    "rel_authors": [
+      {
+        "author_name": "Chao Yang",
+        "author_inst": "Shenzhen Centre for Disease Control and Prevention, Shenzhen, China"
+      },
+      {
+        "author_name": "Min Jiang",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen, China"
+      },
+      {
+        "author_name": "Xiaohui Wang",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen, China"
+      },
+      {
+        "author_name": "Xiujuan Tang",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen, China"
+      },
+      {
+        "author_name": "Shisong Fang",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen, China"
+      },
+      {
+        "author_name": "Hao Li",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen, China"
+      },
+      {
+        "author_name": "Le Zuo",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen, China"
+      },
+      {
+        "author_name": "Yixiang Jiang",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen, China"
+      },
+      {
+        "author_name": "Yifan Zhong",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen, China"
+      },
+      {
+        "author_name": "Qiongcheng Chen",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen, China"
+      },
+      {
+        "author_name": "Chenli Zheng",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen, China"
+      },
+      {
+        "author_name": "Lei Wang",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen, China"
+      },
+      {
+        "author_name": "Shuang Wu",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen, China"
+      },
+      {
+        "author_name": "Weihua Wu",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen, China"
+      },
+      {
+        "author_name": "Hui Liu",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen, China"
+      },
+      {
+        "author_name": "Jing Yuan",
+        "author_inst": "State Key Discipline of Infectious Disease, National Clinical Research Center for infectious disease, Shenzhen Third People's Hospital, Second Hospital Affiliat"
+      },
+      {
+        "author_name": "Xuejiao Liao",
+        "author_inst": "State Key Discipline of Infectious Disease, National Clinical Research Center for infectious disease, Shenzhen Third People's Hospital, Second Hospital Affiliat"
+      },
+      {
+        "author_name": "Zhen Zhang",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen, China"
+      },
+      {
+        "author_name": "Yiman Lin",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen, China"
+      },
+      {
+        "author_name": "Yijie Geng",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen, China"
+      },
+      {
+        "author_name": "Huan Zhang",
+        "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangdong, China"
+      },
+      {
+        "author_name": "Huanying Zheng",
+        "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangdong, China"
+      },
+      {
+        "author_name": "Min Wan",
+        "author_inst": "Shenzhen LongHua District Maternity and Child Healthcare Hospital, Shenzhen, China"
+      },
+      {
+        "author_name": "Linying Lu",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen, China"
+      },
+      {
+        "author_name": "Xiaohu Ren",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen, China"
+      },
+      {
+        "author_name": "Yujun Cui",
+        "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China"
+      },
+      {
+        "author_name": "Xuan Zou",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen, China"
+      },
+      {
+        "author_name": "Tiejian Feng",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen, China"
+      },
+      {
+        "author_name": "Junjie Xia",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen, China"
+      },
+      {
+        "author_name": "Ruifu Yang",
+        "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China"
+      },
+      {
+        "author_name": "Yingxia Liu",
+        "author_inst": "State Key Discipline of Infectious Disease, National Clinical Research Center for infectious disease, Shenzhen Third People's Hospital, Second Hospital Affiliat"
+      },
+      {
+        "author_name": "Shujiang Mei",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Baisheng Li",
+        "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangdong, China"
+      },
+      {
+        "author_name": "Zhengrong Yang",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen, China"
+      },
+      {
+        "author_name": "Qinghua Hu",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention, Shenzhen, China"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.07.23.20154369",
     "rel_title": "Potential impact of individual exposure histories to endemic human coronaviruses on age-dependence in severity of COVID-19",
@@ -1275273,237 +1274238,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.07.17.20155218",
-    "rel_title": "ISARIC COVID-19 Clinical Data Report: 8 June 2020",
-    "rel_date": "2020-07-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20155218",
-    "rel_abs": "ISARIC (International Severe Acute Respiratory and emerging Infections Consortium) partnerships and outbreak preparedness initiatives enabled the rapid launch of standardised clinical data collection on COVID-19 in Jan 2020. Extensive global participation has resulted in a large, standardised collection of comprehensive clinical data from hundreds of sites across dozens of countries. Data are analysed regularly and reported publicly to inform patient care and public health response. This report, our 18th and final report, is a part of a series published over 3 years. Data have been entered for 945,317 individuals from 1807 partner institutions and networks across 76 countries.\n\nThe comprehensive analyses detailed in this report includes hospitalised individuals of all ages for whom data collection occurred between 30 January 2020 and up to and including 10 January 2023, AND who have laboratory-confirmed SARS-COV-2 infection or clinically diagnosed COVID-19.\n\nFor the 845,291 cases who meet eligibility criteria for this report, selected findings include:\n\nO_LIMedian age of 57 years, with an approximately equal (50/50) male:female sex distribution\nC_LIO_LI29% of the cohort are at least 70 years of age, whereas 6% are 0-19 years of age\nC_LIO_LIThe most common symptom combination in this hospitalised cohort is shortness of breath, cough, and history of fever, which has remained constant over time\nC_LIO_LIThe five most common symptoms at admission were shortness of breath, cough, history of fever, fatigue/malaise, and altered consciousness/confusion, which is unchanged from the previous reports\nC_LIO_LIAge-associated differences in symptoms are evident, including the frequency of altered consciousness increasing with age, and fever, respiratory and constitutional symptoms being present mostly in those 40 years and above\nC_LIO_LI15% of patients with relevant data available (845,291) were admitted at some point during their illness into an intensive care unit (ICU), which has decreased from 19% during the 3 years of ISARIC reporting\nC_LIO_LIAntibiotic agents were used in 37% of patients for whom relevant data are available (802,241), a significant reduction from our previous reports (80%) which reflects a shifting proportion of data contributed by different institutions; in ICU/HDU admitted patients with data available (64,669), 90% received antibiotics\nC_LIO_LIUse of corticosteroids was reported in 25% of all patients for whom data were available (809,043); in ICU/HDU admitted patients with data available (64,713), 71% received corticosteroids\nC_LIO_LIOutcomes are known for 762,728 patients and the overall estimated case fatality ratio (CFR) is 22% (95%CI 21.9-22), rising to 36% (95%CI 35.6-36.1) for patients who were admitted to ICU/HDU, demonstrating worse outcomes in those with the most severe disease\nC_LI\n\nTo access previous versions of ISARIC COVID-19 Clinical Data Report please use the link below: https://isaric.org/research/covid-19-clinical-research-resources/evidence-reports/",
-    "rel_num_authors": 54,
-    "rel_authors": [
-      {
-        "author_name": "- ISARIC Clinical Characterisation Group",
-        "author_inst": ""
-      },
-      {
-        "author_name": "J. Kenneth Baillie",
-        "author_inst": "ISARIC 4C and Roslin Institute, University of Edinburgh, UK"
-      },
-      {
-        "author_name": "Joaquin Baruch",
-        "author_inst": "International Severe Acute Respiratory and emerging Infections Consortium (ISARIC), University of Oxford, UK"
-      },
-      {
-        "author_name": "Abigail Beane",
-        "author_inst": "Critical Care Asia, Thailand"
-      },
-      {
-        "author_name": "Lucille Blumberg",
-        "author_inst": "National Institute for Communicable Diseases, South Africa"
-      },
-      {
-        "author_name": "Fernando Augusto Bozza",
-        "author_inst": "National Institute of Infectious Disease Evandro Chagas, Oswaldo Cruz Foundation (INI-FIOCRUZ), Ministry of Health, and D?Or Institute of Research and Education"
-      },
-      {
-        "author_name": "Tessa Broadley",
-        "author_inst": "Monash University, Australia"
-      },
-      {
-        "author_name": "Aidan Burrell",
-        "author_inst": "Monash University, Australia"
-      },
-      {
-        "author_name": "Gail Carson",
-        "author_inst": "International Severe Acute Respiratory and emerging Infections Consortium (ISARIC), University of Oxford, UK"
-      },
-      {
-        "author_name": "Barbara Wanjiru Citarella",
-        "author_inst": "International Severe Acute Respiratory and emerging Infections Consortium (ISARIC), University of Oxford, UK"
-      },
-      {
-        "author_name": "Jake Dunning",
-        "author_inst": "International Severe Acute Respiratory and emerging Infections Consortium (ISARIC), University of Oxford, UK"
-      },
-      {
-        "author_name": "Loubna Elotmani",
-        "author_inst": "CHU Caremeau, France"
-      },
-      {
-        "author_name": "Noelia Garcia Barrio",
-        "author_inst": "Hospital 12 de Octubre, Spain"
-      },
-      {
-        "author_name": "Jean-Christophe Goffard",
-        "author_inst": "CUB-Hopital Erasme, Belgium"
-      },
-      {
-        "author_name": "Bronner Goncalves",
-        "author_inst": "University of Oxford, UK"
-      },
-      {
-        "author_name": "Matthew Hall",
-        "author_inst": "International Severe Acute Respiratory and emerging Infections Consortium (ISARIC), University of Oxford, UK"
-      },
-      {
-        "author_name": "Madiha Hashmi",
-        "author_inst": "Critical Care Asia and Ziauddin University, Pakistan"
-      },
-      {
-        "author_name": "Peter Horby",
-        "author_inst": "International Severe Acute Respiratory and emerging Infections Consortium (ISARIC), University of Oxford, UK"
-      },
-      {
-        "author_name": "Waasila Jassat",
-        "author_inst": "National Institute for Communicable Diseases, South Africa"
-      },
-      {
-        "author_name": "Christiana Kartsonaki",
-        "author_inst": "International Severe Acute Respiratory and emerging Infections Consortium (ISARIC), University of Oxford, UK"
-      },
-      {
-        "author_name": "Bharath Kumar Tirupakuzhi Vijayaraghavan",
-        "author_inst": "Critical Care Asia Network, India"
-      },
-      {
-        "author_name": "Pavan Kumar Vecham",
-        "author_inst": "Apollo Hospitals Chennai, India"
-      },
-      {
-        "author_name": "Cedric Laouenan",
-        "author_inst": "INSERM, France"
-      },
-      {
-        "author_name": "Samantha Lissauer",
-        "author_inst": "Malawi-Liverpool Wellcome Trust, Malawi"
-      },
-      {
-        "author_name": "Ignacio Martin-Loeches",
-        "author_inst": "St James?s Hospital, Ireland"
-      },
-      {
-        "author_name": "France Mentre",
-        "author_inst": "INSERM, France"
-      },
-      {
-        "author_name": "Ben Morton",
-        "author_inst": "Liverpool School of Tropical Medicine, UK and Malawi-Liverpool Wellcome Trust, Malawi"
-      },
-      {
-        "author_name": "Daniel Munblit",
-        "author_inst": "Sechenov University, Russia"
-      },
-      {
-        "author_name": "Nikita A. Nekliudov",
-        "author_inst": "Sechenov University, Russia"
-      },
-      {
-        "author_name": "Alistair Nichol",
-        "author_inst": "Irish Critical Care Critical Clinical Trials Network, Ireland"
-      },
-      {
-        "author_name": "David S.Y. Ong",
-        "author_inst": "Franciscus Gasthuis & Vlietland, The Netherlands"
-      },
-      {
-        "author_name": "Prasan Kumar Panda",
-        "author_inst": "All India Institute of Medical Sciences, India"
-      },
-      {
-        "author_name": "Miguel Pedrera Jimenez",
-        "author_inst": "Hospital 12 de Octubre, Spain"
-      },
-      {
-        "author_name": "Michelle Petrovic",
-        "author_inst": "Humber River Hospital, Canada"
-      },
-      {
-        "author_name": "Nagarajan Ramakrishnan",
-        "author_inst": "Apollo Hospitals Chennai, India"
-      },
-      {
-        "author_name": "Grazielle Viana Ramos",
-        "author_inst": "National Institute of Infectious Disease Evandro Chagas, Oswaldo Cruz Foundation (INI-FIOCRUZ), Ministry of Health, and D?Or Institute of Research and Education"
-      },
-      {
-        "author_name": "Claire Roger",
-        "author_inst": "CHU Caremeau, France"
-      },
-      {
-        "author_name": "Amanda Rojek",
-        "author_inst": "International Severe Acute Respiratory and emerging Infections Consortium (ISARIC), University of Oxford, UK"
-      },
-      {
-        "author_name": "Oana Sandulescu",
-        "author_inst": "National Institute for Infectious Diseases Matei Bals, Romania"
-      },
-      {
-        "author_name": "Malcolm G. Semple",
-        "author_inst": "ISARIC 4C and University of Liverpool, UK"
-      },
-      {
-        "author_name": "Pratima Sharma",
-        "author_inst": "University of Michigan Schools of Medicine & Public Health, USA"
-      },
-      {
-        "author_name": "Sally Shrapnel",
-        "author_inst": "University of Queensland - Saint Lucia Campus: The University of Queensland"
-      },
-      {
-        "author_name": "Louise Sigfrid",
-        "author_inst": "International Severe Acute Respiratory and emerging Infections Consortium (ISARIC), University of Oxford, UK"
-      },
-      {
-        "author_name": "Benedict Sim Lim Heng",
-        "author_inst": "National Institutes of Health (NIH), Ministry of Health Malaysia"
-      },
-      {
-        "author_name": "Budha Charan Singh",
-        "author_inst": "All India Institute of Medical Sciences, India"
-      },
-      {
-        "author_name": "Emily Somers",
-        "author_inst": "University of Michigan, USA"
-      },
-      {
-        "author_name": "Anca Streinu-Cercel",
-        "author_inst": "National Institute for Infectious Diseases Matei Bals, Romania"
-      },
-      {
-        "author_name": "Fabio S. Taccone",
-        "author_inst": "CUB-Hopital Erasme, France"
-      },
-      {
-        "author_name": "Jia Wei",
-        "author_inst": "International Severe Acute Respiratory and emerging Infections Consortium (ISARIC), University of Oxford, UK"
-      },
-      {
-        "author_name": "Evert-Jan Wils",
-        "author_inst": "Franciscus Gasthuis & Vlietland, The Netherlands"
-      },
-      {
-        "author_name": "Xin Ci Wong",
-        "author_inst": "National Institutes of Health (NIH), Ministry of Health Malaysia"
-      },
-      {
-        "author_name": "Kyle Young",
-        "author_inst": "University of Queensland - Saint Lucia Campus: The University of Queensland"
-      },
-      {
-        "author_name": "Piero L. Olliaro",
-        "author_inst": "International Severe Acute Respiratory and emerging Infections Consortium (ISARIC), University of Oxford, UK"
-      },
-      {
-        "author_name": "Laura Merson",
-        "author_inst": "International Severe Acute Respiratory and emerging Infections Consortium (ISARIC), University of Oxford, UK"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.07.19.20156869",
     "rel_title": "Paired nasopharyngeal and deep lung testing for SARS-CoV2 reveals a viral gradient in critically ill patients: a multi-centre study",
@@ -1275734,6 +1274468,129 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.07.21.20159053",
+    "rel_title": "Prospective Observational Study of Screening Asymptomatic Healthcare Workers for SARS-CoV-2 at a Canadian Tertiary Care Center",
+    "rel_date": "2020-07-25",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20159053",
+    "rel_abs": "We screened three separate cohorts of healthcare workers for SARS-CoV-2 via nasopharyngeal swab PCR. A seroprevalence analysis using multiple assays was performed in a subgroup. The asymptomatic health care worker cohorts had a combined swap positivity rate of 29/5776 (0.50%, 95%CI 0.32-0.75) compared to the symptomatic cohort rate of 54/1597 (3.4%) (ratio of symptomatic to asymptomatic 6.8:1). Sequencing demonstrated several variants. The seroprevalence (n=996) was 1.4-3.4% depending on assay. Protein microarray analysis showed differing SARS-CoV-2 protein reactivities and helped define likely true positives vs. suspected false positives. Routine screening of asymptomatic health care workers helps identify a significant proportion of infections.",
+    "rel_num_authors": 27,
+    "rel_authors": [
+      {
+        "author_name": "Deepali Kumar",
+        "author_inst": "University Health Network"
+      },
+      {
+        "author_name": "Victor H Ferreira",
+        "author_inst": "University Health Network, Toronto, Canada"
+      },
+      {
+        "author_name": "Andrzej Chruscinski",
+        "author_inst": "University Health Network, Toronto, Canada"
+      },
+      {
+        "author_name": "Vathany Kulasingam",
+        "author_inst": "University Health Network, Toronto, Canada"
+      },
+      {
+        "author_name": "Trevor J Pugh",
+        "author_inst": "University Health Network, Toronto, Canada"
+      },
+      {
+        "author_name": "Tamara Dus",
+        "author_inst": "University Health Network, Toronto, Canada"
+      },
+      {
+        "author_name": "Brad Wouters",
+        "author_inst": "University Health Network, Toronto, Canada"
+      },
+      {
+        "author_name": "Amit Oza",
+        "author_inst": "University Health Network, Toronto, Canada"
+      },
+      {
+        "author_name": "Matthew Ierullo",
+        "author_inst": "University Health Network, Toronto, Canada"
+      },
+      {
+        "author_name": "Terrance J.Y. Ku",
+        "author_inst": "University Health Network, Toronto, Canada"
+      },
+      {
+        "author_name": "Beata Majchrzak-Kita",
+        "author_inst": "University Health Network, Toronto, Canada"
+      },
+      {
+        "author_name": "Sonika Humar",
+        "author_inst": "University Health Network, Toronto, Canada"
+      },
+      {
+        "author_name": "Ilona Bahinskaya",
+        "author_inst": "University Health Network, Toronto, Canada"
+      },
+      {
+        "author_name": "Natalia Pinzon",
+        "author_inst": "University Health Network, Toronto, Canada"
+      },
+      {
+        "author_name": "Jianhua Zhang",
+        "author_inst": "University Health Network, Toronto, Canada"
+      },
+      {
+        "author_name": "Lawrence E Heisler",
+        "author_inst": "Ontario Institute for Cancer Research, Toronto, Canada"
+      },
+      {
+        "author_name": "Paul M Krzyzanowski",
+        "author_inst": "Ontario Institute for Cancer Research, Toronto, Canada"
+      },
+      {
+        "author_name": "Bernard Lam",
+        "author_inst": "Ontario Institute for Cancer Research, Toronto, Canada"
+      },
+      {
+        "author_name": "Ilinca M Lungu",
+        "author_inst": "Ontario Institute for Cancer Research, Toronto, Canada"
+      },
+      {
+        "author_name": "Dorin Manase",
+        "author_inst": "University Health Network Digital Department, Toronto, Canada"
+      },
+      {
+        "author_name": "Krista M Pace",
+        "author_inst": "University Health Network Digital Department, Toronto, Canada"
+      },
+      {
+        "author_name": "Pouria Mashouri",
+        "author_inst": "University Health Network Digital Department,Toronto, Canada"
+      },
+      {
+        "author_name": "Michael Brudno",
+        "author_inst": "University Health Network Digital Department, Toronto, Canada"
+      },
+      {
+        "author_name": "Michael Garrels",
+        "author_inst": "University Health Network, Toronto, Canada"
+      },
+      {
+        "author_name": "Tony Mazzulli",
+        "author_inst": "Sinai Health System, Toronto, Canada"
+      },
+      {
+        "author_name": "Myron Cybulsky",
+        "author_inst": "University Health Network, Toronto, Canada"
+      },
+      {
+        "author_name": "Atul Humar",
+        "author_inst": "University Health Network, Toronto, Canada"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.07.22.20158352",
     "rel_title": "Anatomy of digital contact tracing: role of age, transmission setting, adoption and case detection",
@@ -1276879,37 +1275736,6 @@
     "type": "new results",
     "category": "bioengineering"
   },
-  {
-    "rel_doi": "10.1101/2020.07.21.20159350",
-    "rel_title": "Reducing COVID-19 hospitalization risk through behavior change",
-    "rel_date": "2020-07-24",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20159350",
-    "rel_abs": "Our objective was to determine strategies that could potentially reduce the risk of hospitalizations from COVID-19 due to underlying conditions. We used data (N=444,649) from the 2017 Behavioral Risk Factor Surveillance System to identify potentially modifiable risk factors associated with reporting any of the underlying conditions (cardiovascular disease, asthma, chronic obstructive pulmonary disease, diabetes, hypertension or obesity) found to increase risk of US hospitalizations for COVID-19. Risk factors included lifetime smoking, sedentary lifestyle, and inadequate fruit and vegetable consumption. Multiple logistic regression in Stata produced adjusted odds ratios (AORs) used to estimate population attributable-risk (PAR) in Excel. PARs for the 3 risk factors ranged from 12.4% for inactivity to 15.6% for diet for a combined PAR of 36.3%, implying that total elimination of these 3 risk factors could potentially reduce underlying conditions as much as 36%. This suggests that reducing COVID-19 hospitalizations might be a measurable and feasible US goal for the coronavirus pandemic. The simple lifestyle changes of increasing physical activity and fruit and vegetable consumption could reduce obesity, a key underlying condition and risk factor for 4 others. Reducing obesity and inactivity may also boost immunity. With uncertainly around how long the pandemic might last, other proposed strategies include wearing face masks when social distancing is not feasible, and addressing the special issues for nursing home residents. Such actions have the potential to lessen the impact of COVID-19 in the short term along with providing long term health benefits regarding chronic conditions.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "MARY L ADAMS",
-        "author_inst": "On Target Health Data LLC"
-      },
-      {
-        "author_name": "David L Katz",
-        "author_inst": "True Health Initiative"
-      },
-      {
-        "author_name": "Joseph Grandpre",
-        "author_inst": "Wyoming Department of Health"
-      },
-      {
-        "author_name": "Douglas Shenson",
-        "author_inst": "Yale School of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.07.22.20159707",
     "rel_title": "A reference for mortality in Spain from 2001 to 2019 records with an accurate estimate of excess deaths during the 2020 spring covid-19 outbreak",
@@ -1277208,6 +1276034,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "neurology"
   },
+  {
+    "rel_doi": "10.1101/2020.07.21.20159327",
+    "rel_title": "COVID-19 Vulnerability of Transgender Women With and Without HIV Infection in the Eastern and Southern U.S.",
+    "rel_date": "2020-07-24",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20159327",
+    "rel_abs": "BackgroundCOVID-19 is a new global pandemic and people with HIV may be particularly vulnerable. Gender identity is not reported, therefore data are absent on the impact of COVID-19 on transgender people, including transgender people with HIV. Baseline data from the American Cohort to Study HIV Acquisition Among Transgender Women in High Risk Areas (LITE) Study provide an opportunity to examine pre-COVID vulnerability among transgender women.\n\nSettingAtlanta, Baltimore, Boston, Miami, New York City, Washington, DC\n\nMethodsBaseline data from LITE were analysed for demographic, psychosocial, and material factors that may affect risk for COVID-related harms.\n\nResultsThe 1020 participants had high rates of poverty, unemployment, food insecurity, homelessness, and sex work. Transgender women with HIV (n=273) were older, more likely to be Black, had lower educational attainment, and were more likely to experience material hardship. Mental and behavioural health symptoms were common and did not differ by HIV status. Barriers to healthcare included being mistreated mistreatment, uncomfortable providers, and past negative experiences; as well as material hardships, such as cost and transportation. However, most reported access to material and social support - demonstrating resilience.\n\nConclusionsTransgender women with HIV may be particularly vulnerable to pandemic harms. Mitigating this harm would have positive effects for everyone, given the highly infectious nature of this coronavirus. Collecting gender identity in COVID-19 data is crucial to inform an effective public health response. Transgender-led organizations response to this crisis serve as an important model for effective community-led interventions.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Tonia Poteat",
+        "author_inst": "Department of Social Medicine, University of North Carolina at Chapel Hill"
+      },
+      {
+        "author_name": "Sari Reisner",
+        "author_inst": "Department of Medicine, Harvard Medical School; Department of Epidemiology, Harvard T.H. Chan School of Public Health"
+      },
+      {
+        "author_name": "Marissa Miller",
+        "author_inst": "TransSolutions LLC"
+      },
+      {
+        "author_name": "Andrea Wirtz",
+        "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "hiv aids"
+  },
   {
     "rel_doi": "10.1101/2020.07.21.20159392",
     "rel_title": "Development of a quantum-dot lateral flow immunoassay strip based portable fluorescence smart-phone system for ultrasensitive detection of IgM/IgG to SARS-CoV-2",
@@ -1278417,41 +1277274,6 @@
     "type": "new results",
     "category": "biochemistry"
   },
-  {
-    "rel_doi": "10.1101/2020.07.24.219097",
-    "rel_title": "PACIFIC: A lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses",
-    "rel_date": "2020-07-24",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.24.219097",
-    "rel_abs": "Viral co-infections occur in COVID-19 patients, potentially impacting disease progression and severity. However, there is currently no dedicated method to identify viral co-infections in patient RNA-seq data. We developed PACIFIC, a deep-learning algorithm that accurately detects SARS-CoV-2 and other common RNA respiratory viruses from RNA-seq data. Using in silico data, PACIFIC recovers the presence and relative concentrations of viruses with >99% precision and recall. PACIFIC accurately detects SARS-CoV-2 and other viral infections in 63 independent in vitro cell culture and patient datasets. PACIFIC is an end-to-end tool that enables the systematic monitoring of viral infections in the current global pandemic.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Pablo Acera Mateos",
-        "author_inst": "Australian National University"
-      },
-      {
-        "author_name": "Renzo F. Balboa",
-        "author_inst": "Australian National University"
-      },
-      {
-        "author_name": "Simon Easteal",
-        "author_inst": "Australian National University"
-      },
-      {
-        "author_name": "Eduardo Eyras",
-        "author_inst": "Australian National University"
-      },
-      {
-        "author_name": "Hardip R. Patel",
-        "author_inst": "Australian National University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "bioinformatics"
-  },
   {
     "rel_doi": "10.1101/2020.07.24.20161497",
     "rel_title": "Mathematical modelling of dynamics and containment of COVID-19 in Ukraine",
@@ -1278650,6 +1277472,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "gastroenterology"
   },
+  {
+    "rel_doi": "10.1101/2020.07.23.20160879",
+    "rel_title": "Factors associated with psychological distress in health-care workers during an infectious disease outbreak: A rapid living systematic review",
+    "rel_date": "2020-07-24",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.23.20160879",
+    "rel_abs": "BackgroundHealth-care workers (HCW) are at risk for psychological distress during an infectious disease outbreak due to the demands of dealing with a public health emergency.\n\nAimsTo examine the factors associated with psychological distress among HCW during an outbreak.\n\nMethodWe systematically reviewed literature on the factors associated with psychological distress (demographic characteristics, occupational, social, psychological, and infection-related factors) in HCW during an outbreak (COVID-19, SARS, MERS, H1N1, H7N9, Ebola). Four electronic databases were searched (2000 to 10 July 2020) for relevant peer-reviewed research according to a pre-registered protocol. A narrative synthesis was conducted to identify fixed, modifiable, and infection-related factors.\n\nResultsFrom the 3335 records identified, 52 with data from 54,800 HCW were included. All but two studies were cross-sectional. Consistent evidence indicated that being female, a nurse, experiencing stigma, maladaptive coping, having contact or risk for contact with infected patients, and being quarantined, were risk factors for psychological distress among HCW. Personal and organisational social support, perceiving control, positive work attitudes, sufficient information about the outbreak and proper protection, training and resources, were associated with less psychological distress.\n\nConclusionsHCW who may be most at risk for psychological distress during an outbreak require early intervention and ongoing monitoring as there is some evidence that HCW distress can persist for years after an outbreak. Further research is needed to track the associations of risk factors with distress over time and the extent to which certain factors are inter-related and linked to sustained or transient distress.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Fuschia M Sirois",
+        "author_inst": "University of Sheffield"
+      },
+      {
+        "author_name": "Janine Owens",
+        "author_inst": "University of Sheffield"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "psychiatry and clinical psychology"
+  },
   {
     "rel_doi": "10.1101/2020.07.24.20161422",
     "rel_title": "Adherence to protective measures among health care workers in the UK; a cross-sectional study",
@@ -1279803,45 +1278648,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.07.22.20160432",
-    "rel_title": "Soap versus sanitiser for preventing the transmission of acute respiratory infections: a systematic review with meta-analysis and dose-response analysis",
-    "rel_date": "2020-07-24",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20160432",
-    "rel_abs": "ObjectiveTo compare the effectiveness of hand hygiene using alcohol-based hand sanitiser to soap and water for preventing the transmission of acute respiratory infections (ARIs), and assess the relationship between the dose of hand hygiene and the number of ARI, influenza-like illness (ILI), or influenza events.\n\nMethodsSystematic review of randomised trials that compared a community-based hand hygiene intervention (soap and water, or sanitiser) with a control, or trials that compared sanitiser with soap and water, and measured outcomes of ARI, ILI, or laboratory-confirmed influenza or related consequences. Searches were conducted in CENTRAL, PubMed, Embase, CINAHL and trial registries (April 2020) and data extraction completed by independent pairs of reviewers.\n\nResultsEighteen trials were included. When meta-analysed, three trials of soap and water versus control found a non-significant increase in ARI events (Risk Ratio (RR) 1.23, 95%CI 0.78-1.93); six trials of sanitiser versus control found a significant reduction in ARI events (RR 0.80, 95%CI 0.71-0.89). When hand hygiene dose was plotted against ARI relative risk, no clear dose-response relationship was observable. Four trials were head-to-head comparisons of sanitiser and soap and water but too heterogeneous to pool: two found a significantly greater reduction in the sanitiser group compared to the soap group; two found no significant difference between the intervention arms.\n\nConclusionAdequately performed hand hygiene, with either soap or sanitiser, reduces the risk of ARI virus transmission, however direct and indirect evidence suggest sanitiser might be more effective in practice.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Tammy Hoffmann",
-        "author_inst": "Bond University"
-      },
-      {
-        "author_name": "Mina Bakhit",
-        "author_inst": "Bond University"
-      },
-      {
-        "author_name": "Natalia Krzyzaniak",
-        "author_inst": "Bond University"
-      },
-      {
-        "author_name": "Chris Del Mar",
-        "author_inst": "Bond University"
-      },
-      {
-        "author_name": "Anna Scott",
-        "author_inst": "Bond University"
-      },
-      {
-        "author_name": "Paul Glasziou",
-        "author_inst": "Bond University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.07.23.216770",
     "rel_title": "Co-expression of Mitochondrial Genes and ACE2 in Cornea Involved in COVID-19 Infection",
@@ -1280116,6 +1278922,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.07.22.20160283",
+    "rel_title": "Heat-based Decontamination of N95 Masks Using a Commercial Laundry Dryer",
+    "rel_date": "2020-07-24",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20160283",
+    "rel_abs": "We propose a dry heat method for decontaminating N95 masks of SARS-CoV-2, designed around placing them in resealable plastic bags, packed in large cardboard boxes installed at the rear end of commercial laundry dryers. Our protocol rests on data collected in collaboration with Alliance Laundry Systems (ALS) and the CDC/NIOSH laboratories, under the \"NPPTL Respirator Assessments to Support the COVID-19 Response\" initiative. We test the two most widely available ALS tumbler models, the UTF75N and UT075N, and show that if our procedure is carefully followed, the masks will be subject to suitably high and stable temperatures for decontamination; in particular the masks will be heated to at least 80 {degrees}C for at least 65 min. For the mask models 3M 1860, 3M 8511, and Halyard 62126, we establish that they pass quantitative fit tests and retain sufficient filtration performance after three cycles of our decontamination procedure. All masks used in this study were new and uncontaminated: the evidence for the levels of biological inactivation of SARS-CoV-2 is provided by [1]. While the protocol outlined here is currently specific to certain tested dryer models, this equipment is widely available, with machines estimated to be within 15 minutes of most US hospitals. Models from other manufacturers may also be appropriate for this decontamination method, though we stress the need for explicit testing on alternative models before use.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Yuri D. Lensky",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Edward Mazenc",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Daniel Ranard",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Matthew Vilim",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Manu Prakash",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Bill Brooks",
+        "author_inst": "Alliance Laundry Systems"
+      },
+      {
+        "author_name": "Amanda Bradley",
+        "author_inst": "Alliance Laundry Systems"
+      },
+      {
+        "author_name": "Alain Engelschenschilt",
+        "author_inst": "Alliance Laundry Systems"
+      },
+      {
+        "author_name": "Jason Plutz",
+        "author_inst": "Alliance Laundry Systems"
+      },
+      {
+        "author_name": "Todd Zellmer",
+        "author_inst": "Alliance Laundry Systems"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "occupational and environmental health"
+  },
   {
     "rel_doi": "10.1101/2020.07.23.20159871",
     "rel_title": "Geographic reconstruction of the SARS-CoV-2 outbreak in Lombardy (Italy) during the early phase",
@@ -1281173,29 +1280034,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.07.22.216242",
-    "rel_title": "Phylogeny of the COVID-19 Virus SARS-CoV-2 by Compression",
-    "rel_date": "2020-07-23",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.22.216242",
-    "rel_abs": "We analyze the whole genome phylogeny and taxonomy of the SARS-CoV-2 virus using compression. This is a new fast alignment-free method called the \"normalized compression distance\" (NCD) method. It discovers all effective similarities based on Kolmogorov complexity. The latter being incomputable we approximate it by a good compressor such as the modern zpaq. The results comprise that the SARS-CoV-2 virus is closest to the RaTG13 virus and similar to two bat SARS-like coronaviruses bat-SL-CoVZXC21 and bat-SL-CoVZC4. The similarity is quantified and compared with the same quantified similarities among the mtDNA of certain species. We treat the question whether Pangolins are involved in the SARS-CoV-2 virus. The compression method is simpler and possibly faster than any other whole genome method, which makes it the ideal tool to explore phylogeny.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Paul M B Vitanyi",
-        "author_inst": "CWI"
-      },
-      {
-        "author_name": "Rudi L Cilibrasi",
-        "author_inst": "CWI Research Associate and free-lance"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "bioinformatics"
-  },
   {
     "rel_doi": "10.1101/2020.07.22.202275",
     "rel_title": "Transcriptional response modules characterise IL-1 and IL-6 activity in COVID-19",
@@ -1281630,6 +1280468,61 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2020.07.23.212357",
+    "rel_title": "Single-dose intranasal vaccination elicits systemic and mucosal immunity against SARS-CoV-2",
+    "rel_date": "2020-07-23",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.23.212357",
+    "rel_abs": "A safe and durable vaccine is urgently needed to tackle the COVID19 pandemic that has infected >15 million people and caused >620,000 deaths worldwide. As with other respiratory pathogens, the nasal compartment is the first barrier that needs to be breached by the SARS-CoV-2 virus before dissemination to the lung. Despite progress at remarkable speed, current intramuscular vaccines are designed to elicit systemic immunity without conferring mucosal immunity. We report the development of an intranasal subunit vaccine that contains the trimeric or monomeric spike protein and liposomal STING agonist as adjuvant. This vaccine induces systemic neutralizing antibodies, mucosal IgA responses in the lung and nasal compartments, and T-cell responses in the lung of mice. Single-cell RNA-sequencing confirmed the concomitant activation of T and B cell responses in a germinal center-like manner within the nasal-associated lymphoid tissues (NALT), confirming its role as an inductive site that can lead to long-lasting immunity. The ability to elicit immunity in the respiratory tract has can prevent the initial establishment of infection in individuals and prevent disease transmission across humans.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Xingyue An",
+        "author_inst": "University of Houston"
+      },
+      {
+        "author_name": "Melisa Paniagua Martinez",
+        "author_inst": "University of Houston"
+      },
+      {
+        "author_name": "Ali Rezvan",
+        "author_inst": "University of Houston"
+      },
+      {
+        "author_name": "Mohsen Fathi",
+        "author_inst": "University of Houston"
+      },
+      {
+        "author_name": "Shailbala Singh",
+        "author_inst": "University of Texas M.D. Anderson Cancer Center"
+      },
+      {
+        "author_name": "Sujit Biswas",
+        "author_inst": "University of Houston"
+      },
+      {
+        "author_name": "Melissa Pourpak",
+        "author_inst": "BD Biosciences"
+      },
+      {
+        "author_name": "Cassian Yee",
+        "author_inst": "University of Texas M.D. Anderson Cancer Center"
+      },
+      {
+        "author_name": "Xinli Liu",
+        "author_inst": "University of Houston"
+      },
+      {
+        "author_name": "Navin Varadarajan",
+        "author_inst": "University of Houston"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2020.07.23.217430",
     "rel_title": "SARS-CoV2 genome analysis of Indian isolates and molecular modelling of D614G mutated spike protein with TMPRSS2 depicted its enhanced interaction and virus infectivity",
@@ -1283083,45 +1281976,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.07.21.214577",
-    "rel_title": "FDA approved calcium channel blockers inhibit SARS CoV 2 infectivity in epithelial lung cells",
-    "rel_date": "2020-07-22",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.21.214577",
-    "rel_abs": "COVID-19 is caused by a novel coronavirus, severe acute respiratory syndrome coronavirus (CoV)-2 (SARS-CoV-2). The virus is responsible for an ongoing pandemic and concomitant public health crisis around the world. While vaccine development is proving to be highly successful, parallel drug development approaches are also critical in the response to SARS-CoV-2 and other emerging viruses. Coronaviruses require Ca2+ ions for host cell entry and we have previously shown that Ca2+ modulates the interaction of the viral fusion peptide with host cell membranes. In an attempt to accelerate drug development, we tested a panel of L-type calcium channel blocker (CCB) drugs currently developed for other conditions, to determine whether they would inhibit SARS-CoV-2 infection in cell culture. All the CCBs tested showed varying degrees of inhibition, with felodipine and nifedipine strongly limiting SARS-CoV-2 entry and infection in epithelial lung cells at concentrations where cell toxicity was minimal. Further studies with pseudo-typed particles displaying the SARS-CoV-2 spike protein suggested that inhibition occurs at the level of virus entry. Overall, our data suggest that certain CCBs have potential to treat SARS-CoV-2 infections and are worthy of further examination for possible treatment of COVID-19.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Marco R Straus",
-        "author_inst": "Cornell University"
-      },
-      {
-        "author_name": "Miya Bidon",
-        "author_inst": "Cornell University"
-      },
-      {
-        "author_name": "Tiffany Tang",
-        "author_inst": "Cornell University"
-      },
-      {
-        "author_name": "Javier A. Jaimes",
-        "author_inst": "Cornell University"
-      },
-      {
-        "author_name": "Gary Whittaker",
-        "author_inst": "Cornell University"
-      },
-      {
-        "author_name": "Susan Daniel",
-        "author_inst": "Cornell University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.07.22.215962",
     "rel_title": "Neonatal hyperoxia enhances age-dependent expression of SARS-CoV-2 receptors in mice",
@@ -1283464,6 +1282318,33 @@
     "type": "new results",
     "category": "bioinformatics"
   },
+  {
+    "rel_doi": "10.1101/2020.07.22.215590",
+    "rel_title": "Inadequate level of knowledge, mixed outlook and poor adherence to COVID-19 prevention guideline among Ethiopians",
+    "rel_date": "2020-07-22",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.22.215590",
+    "rel_abs": "COVID-19 has a potential to cause chaos in Ethiopia due to the countrys already daunting economic and social challenges. Living and working conditions are highly conducive for transmission, as people live in crowded inter-generational households that often lack running water and other basic sanitary facilities. Thus, the aim of this study was to investigate the knowledge, attitudes and practices (KAP) of Ethiopians toward COVID-19 following the introduction of state of emergency by the Ethiopian government to curb the spread of the disease. A cross-sectional study design was conducted in nine reginal states and two chartered cities. Data for demographic, Knowledge, attitude and practice toward COVID-19 were collected through telephone interview from 1570 participants. Descriptive and bivariate analyses using chi-square test, t-test or analysis of variance were performed as appropriate. Binary and multiple logistic regression analysis were used to measure the relationship between the categorical dependent variables and one or more socio-demographic independent variables with two-tailed at =0.05 significance level and 95% of confidence interval. The level of good knowledge, favourable attitude and good practice among the respondents were 42%, 53.8% and 24.3% respectively. Being rural resident, older than 50 years, having at least primary education, being resident of Amhara and Oromia regions were independent predictors of knowledge level. While being rural resident, married, employed, having at least basic education, being residents of Afar, Amhara, Gambela, Oromia and Somali regions were found to be the best predictors of the attitude, being rural resident, government employee, having at least basic education, and living outside of the capital were the independent predictors of practice level of the respondents. The finding revealed that Ethiopians have inadequate level of knowledge and are generally have a mixed outlook on overcoming the pandemic with poor adherence to COVID-19 prevention practice. reinforcing preventive measures and intensifying sensitization campaigns to fill the knowledge gap and persuading people to follow the preventive measures set by the government with concurrent evaluation of the impacts of these measures on knowledge and practice is highly recommended to mitigate the disease.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Edessa Negera",
+        "author_inst": "Hawassa University and London School of Hygiene and Tropical Medicine"
+      },
+      {
+        "author_name": "Tesfaye Moti Demissie",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Ketema Tafess",
+        "author_inst": "Arsi University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "new results",
+    "category": "animal behavior and cognition"
+  },
   {
     "rel_doi": "10.1101/2020.07.18.20156794",
     "rel_title": "Statistical analysis of national & municipal corporation level database of COVID-19 cases In India",
@@ -1284521,49 +1283402,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.07.17.20155960",
-    "rel_title": "Observational Study of the Efficiency of Treatments in Patients Hospitalized with Covid-19 in Madrid",
-    "rel_date": "2020-07-21",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20155960",
-    "rel_abs": "BackgroundMany different treatments were heavily administered to patients with COVID-19 during the peak of the pandemic in Madrid without robust evidence supporting them.\n\nMethodsWe examined the association between sixteen treatments in four groups (steroids, antivirals, antibiotics and immunomodulators) and intubation or death. Data were obtained from patients that were admitted to an HM hospital with suspicion of COVID-19 until 24/04/2020, excluding unconfirmed diagnosis, those who were admitted before the epidemic started in Madrid, had an outcome that was not discharge or death or died within 24 hours of presentation. We compared outcomes between treated and untreated patients using propensity-score caliper matching.\n\nResultsOf 2,307 patients in the dataset, 679 were excluded. Of the remaining 1,645 patients, 263 (16%) died and 311 (18.9%) died or were intubated. Except for hydroxychloroquine and prednisone, patients that were treated with any of the medications were more likely to go through an outcome of death or intubation at baseline. After propensity matching we found an association between treatment with hydroxychloroquine and prednisone and better outcomes (hazard ratios with 95% CI of 0.83 {+/-} 0.06 and 0.85 {+/-} 0.03). Results were similar in multiple sensitivity analyses.\n\nConclusionsIn this multicenter study of patients admitted with COVID-19 hydroxychloroquine and prednisone administration was found to be associated with improved outcomes. Other treatments were associated with no effect or worse outcomes. Randomized, controlled trials of these medications in patients with COVID-19 are needed to avoid heavy administration of treatments with no strong evidence to support them.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Nikolas Bernaola",
-        "author_inst": "Universidad Politecnica de Madrid"
-      },
-      {
-        "author_name": "Raquel Mena",
-        "author_inst": "Universidad Complutense de Madrid"
-      },
-      {
-        "author_name": "Ander Bernaola",
-        "author_inst": "Universidad Francisco de Vitoria"
-      },
-      {
-        "author_name": "Antonio Lara",
-        "author_inst": "Hospital Universitario la Zarzuela"
-      },
-      {
-        "author_name": "Cesar Carballo",
-        "author_inst": "Hospital Universitario Ramon y Cajal"
-      },
-      {
-        "author_name": "Pedro Larranaga",
-        "author_inst": "Universidad Politecnica de Madrid"
-      },
-      {
-        "author_name": "Concha Bielza",
-        "author_inst": "Universidad Politecnica de Madrid"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.07.20.211623",
     "rel_title": "Integrative Vectors for Regulated Expression of SARS-CoV-2 Proteins Implicated in RNA Metabolism",
@@ -1284926,6 +1283764,93 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.07.21.213777",
+    "rel_title": "Cellular events of acute, resolving or progressive COVID-19 in SARS-CoV-2 infected non-human primates",
+    "rel_date": "2020-07-21",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.21.213777",
+    "rel_abs": "We investigated the immune events following SARS-CoV-2 infection, from the acute inflammatory state up to four weeks post infection, in non-human primates (NHP) with heterogeneous pulmonary pathology. The acute phase was characterized by a robust and rapid migration of monocytes expressing CD16 from the blood and concomitant increase in CD16+ macrophages in the lungs. We identified two subsets of interstitial macrophages (HLA-DR+ CD206-), a transitional CD11c+ CD16+ cell population that was directly associated with IL-6 levels in plasma, and one long lasting CD11b+ CD16+ cell population. Strikingly, levels of monocytes were a correlate of viral replication in bronchial brushes and we discovered TARC (CCL17) as a new potential mediator of myeloid recruitment to the lungs. Worse disease outcomes were associated with high levels of cell infiltration in lungs including CD11b+ CD16hi macrophages and CD11b+ neutrophils. Accumulation of macrophages was long-lasting and detectable even in animals with mild or no signs of disease. Interestingly, animals with anti-inflammatory responses including high IL-10:IL-6 and kynurenine to tryptophan ratios had less signs of disease. Our results unravel cellular mechanisms of COVID-19 and suggest that NHP may be appropriate models to test immune therapies.",
+    "rel_num_authors": 18,
+    "rel_authors": [
+      {
+        "author_name": "Marissa D Fahlberg",
+        "author_inst": "Tulane National Primate Research Center, Covington, LA"
+      },
+      {
+        "author_name": "Robert V Blair",
+        "author_inst": "Tulane National Primate Research Center, Covington, LA"
+      },
+      {
+        "author_name": "Lara A Doyle-Meyers",
+        "author_inst": "Tulane National Primate Research Center, Covington, LA"
+      },
+      {
+        "author_name": "Cecily C Midkiff",
+        "author_inst": "Tulane National Primate Research Center, Covington, LA"
+      },
+      {
+        "author_name": "Giorgio Zenere",
+        "author_inst": "Tulane National Primate Research Center, Covington, LA"
+      },
+      {
+        "author_name": "Kasi E Russell-Lodrigue",
+        "author_inst": "Tulane National Primate Research Center, Covington, LA"
+      },
+      {
+        "author_name": "Christopher J Monjure",
+        "author_inst": "Tulane National Primate Research Center, Covington, LA"
+      },
+      {
+        "author_name": "Toni P Penney",
+        "author_inst": "Tulane National Primate Research Center, Covington, LA"
+      },
+      {
+        "author_name": "Gabrielle Lehmicke",
+        "author_inst": "Tulane National Primate Research Center, Covington, LA"
+      },
+      {
+        "author_name": "Brienna M Threeton",
+        "author_inst": "Tulane National Primate Research Center, Covington, LA"
+      },
+      {
+        "author_name": "Nadia Golden",
+        "author_inst": "Tulane National Primate Research Center, Covington, LA"
+      },
+      {
+        "author_name": "Presan K Datta",
+        "author_inst": "Tulane National Primate Research Center, Covington, LA"
+      },
+      {
+        "author_name": "Chad J Roy",
+        "author_inst": "Tulane National Primate Research Center, Covington, LA"
+      },
+      {
+        "author_name": "Rudolph P Bohm",
+        "author_inst": "Tulane National Primate Research Center, Covington, LA"
+      },
+      {
+        "author_name": "Nicholas J Maness",
+        "author_inst": "Tulane National Primate Research Center, Covington, LA"
+      },
+      {
+        "author_name": "Tracy Fischer",
+        "author_inst": "Tulane National Primate Research Center, Covington, LA"
+      },
+      {
+        "author_name": "Jay Rappaport",
+        "author_inst": "Tulane National Primate Research Center, Covington, LA"
+      },
+      {
+        "author_name": "Monica Vaccari",
+        "author_inst": "Tulane National Primate Research Center, Covington, LA"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2020.07.20.213082",
     "rel_title": "Discovery of potential imaging and therapeutic targets for severe inflammation in COVID-19 patients",
@@ -1286231,25 +1285156,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.07.14.20151415",
-    "rel_title": "The brief comparison of the operational efficiency of pool-testing strategies for COVID-19 mass testing in PCR laboratories",
-    "rel_date": "2020-07-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.14.20151415",
-    "rel_abs": "This paper addresses the operational efficiency of different pool-testing strategies in typical scenarios of a PCR laboratory working in mass testing for COVID-19 with different values of prevalence, limitations and conditions of testing, and priorities of optimization.\n\nThe research employs a model of the laboratorys testing process, created after interviewing of PCR laboratories and studying their operations. The limitations and operational characteristics of this model were applied in a simulation of the testing process with different pool-testing strategies managed by a computer program developed in the LOMT project.\n\nThe efficiency indicators assessed are the number of assays needed to obtain results of a batch of specimens, the number of specimens identified after the first analysis, and total time to obtain all results.\n\nDepending on prevalence, constraints of testing, and priorities of optimization, different pool-testing strategies provide the best operational efficiency. The binary splitting algorithm provides the maximum reduction of the number of assays: from 1.99x reduction for a high prevalence (10%) to 25x reduction for a low prevalence (0.1%), while other algorithms provide the least amount of time to obtain results or the maximum number of the specimens classified after the first analysis.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Kirill Vechera",
-        "author_inst": "Jetware"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.07.05.20146654",
     "rel_title": "A student made MOOC for medical students during the SARS-CoV-2 pandemic.",
@@ -1286776,6 +1285682,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.07.18.210120",
+    "rel_title": "High expression of angiotensin-converting enzyme-2 (ACE2) on tissue macrophages that may be targeted by virus SARS-CoV-2 in COVID-19 patients",
+    "rel_date": "2020-07-20",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.18.210120",
+    "rel_abs": "Angiotensin-converting enzyme-2 (ACE2) has been recognized as the binding receptor for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that infects host cells, causing the development of the new coronavirus infectious disease (COVID-19). To better understand the pathogenesis of COVID-19 and build up the host anti-viral immunity, we examined the levels of ACE2 expression on different types of immune cells including tissue macrophages. Flow cytometry demonstrated that there was little to no expression of ACE2 on most of the human peripheral blood-derived immune cells including CD4+ T, CD8+ T, activated CD4+ T, activated CD8+ T, CD4+CD25+CD127low/- regulatory T cells (Tregs), Th17 cells, NKT cells, B cells, NK cells, monocytes, dendritic cells (DCs), and granulocytes. Additionally, there was no ACE2 expression (< 1%) found on platelets. Compared with interleukin-4-treated type 2 macrophages (M2), the ACE2 expression was markedly increased on the activated type 1 macrophages (M1) after the stimulation with lipopolysaccharide (LPS). Immunohistochemistry demonstrated that high expressions of ACE2 were colocalized with tissue macrophages, such as alveolar macrophages found within the lungs and Kupffer cells within livers of mice. Flow cytometry confirmed the very low level of ACE2 expression on human primary pulmonary alveolar epithelial cells. These data indicate that alveolar macrophages, as the frontline immune cells, may be directly targeted by the SARS-CoV-2 infection and therefore need to be considered for the prevention and treatment of COVID-19.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Xiang Song",
+        "author_inst": "Center for Discovery and Innovation, Hackensack Meridian Health"
+      },
+      {
+        "author_name": "Wei Hu",
+        "author_inst": "Center for Discovery and Innovation, Hackensack Meridian Health"
+      },
+      {
+        "author_name": "Haibo Yu",
+        "author_inst": "Center for Discovery and Innovation, Hackensack Meridian Health"
+      },
+      {
+        "author_name": "Laura Zhao",
+        "author_inst": "Tianhe Stem Cell Biotechnologies Inc"
+      },
+      {
+        "author_name": "Yeqian Zhao",
+        "author_inst": "Tianhe Stem Cell Biotechnologies Inc"
+      },
+      {
+        "author_name": "Yong Zhao",
+        "author_inst": "Center for Discovery and Innovation, Hackensack Meridian Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2020.07.12.20151878",
     "rel_title": "Inverted covariate effects for mutated 2nd vs 1st waveCovid-19: high temperature spread biased for young",
@@ -1287833,69 +1286778,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
-  {
-    "rel_doi": "10.1101/2020.07.17.20155333",
-    "rel_title": "SARS-CoV-2 viral load in the upper respiratory tract of children and adultswith early acute COVID-19",
-    "rel_date": "2020-07-19",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20155333",
-    "rel_abs": "The role of children in the transmission of SARS-CoV-2 is unclear. We analysed viral load at the time of diagnosis in 53 children vs. 352 adults with COVID-19 in the first 5 days post symptom onset. No significant differences in SARS-CoV-2 RNA loads were seen between children and adults.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "St\u00e9phanie Baggio",
-        "author_inst": "Division of Prison Health, Geneva University Hospitals, Geneva, Switzerland and Office of Corrections, Department of Justice and Home Affairs of the Canton of Z"
-      },
-      {
-        "author_name": "Arnaud G L`Huillier",
-        "author_inst": "Childrens Hospital of Geneva, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland"
-      },
-      {
-        "author_name": "Sabine Yerly",
-        "author_inst": "Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland"
-      },
-      {
-        "author_name": "Mathilde Bellon",
-        "author_inst": "Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland"
-      },
-      {
-        "author_name": "No\u00e9mie Wagner",
-        "author_inst": "Childrens Hospital of Geneva, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland"
-      },
-      {
-        "author_name": "Marie Rohr",
-        "author_inst": "Children Hospital of Geneva, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland"
-      },
-      {
-        "author_name": "Angela Huttner",
-        "author_inst": "Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland"
-      },
-      {
-        "author_name": "G\u00e9raldine Blanchard-Rohner",
-        "author_inst": "Childrens Hospital of Geneva, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland"
-      },
-      {
-        "author_name": "Natasha Loevy",
-        "author_inst": "Childrens Hospital of Geneva, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland"
-      },
-      {
-        "author_name": "Laurent Kaiser",
-        "author_inst": "University of Geneva Hospitals"
-      },
-      {
-        "author_name": "Fr\u00e9d\u00e9rique Jacquerioz",
-        "author_inst": "Division of Infectious Diseases, Department of Medicine, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland"
-      },
-      {
-        "author_name": "Isabella Eckerle",
-        "author_inst": "University Hospitals of Geneva"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.07.17.20155754",
     "rel_title": "Self-Collected Anterior Nasal and Saliva Specimens versus Healthcare Worker-Collected Nasopharyngeal Swabs for the Molecular Detection of SARS-CoV-2",
@@ -1288158,6 +1287040,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.07.17.20155242",
+    "rel_title": "Genetic inhibition of interleukin-6 receptor signaling and Covid-19",
+    "rel_date": "2020-07-19",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20155242",
+    "rel_abs": "There are few effective therapeutic options for the treatment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Early evidence has suggested that IL-6R blockers may confer benefit, particularly in severe coronavirus disease 2019 (Covid-19).\n\nWe leveraged large-scale human genetic data to investigate whether IL6-R blockade may confer therapeutic benefit in Covid-19. A genetic instrument consisting of seven genetic variants in or close to IL6R was recently shown to be linked to altered levels of c-reactive protein (CRP), fibrinogen, circulating IL-6 and soluble IL-6R, concordant to known effects of pharmacological IL- 6R blockade. We investigated the effect of these IL6R variants on risk of hospitalization for Covid- 19 and other SARS-CoV-2-related outcomes using data from The Covid-19 Host Genetics Initiative.\n\nThe IL6R variants were strongly associated with serum CRP levels in UK Biobank. Meta-analysis of scaled estimates revealed a lower risk of rheumatoid arthritis (OR 0.93 per 0.1 SD lower CRP, 95% CI, 0.90-0.96, P = 9.5 x 10-7), recapitulating this established indication for IL-6R blockers (e.g. tocilizumab and sarilumab). The IL-6R instrument was associated with lower risk of hospitalization for Covid-19 (OR 0.88 per 0.1 SD lower CRP, 95% CI, 0.78-0.99, P = 0.03). We found a consistent association when using a population-based control group (i.e. all non-cases; OR 0.91 per 0.1 SD lower CRP, 95% CI, 0.87-0.96, P = 4.9 x 10-4). Evaluation of further SARS- CoV-2-related outcomes suggested association with risk of SARS-CoV-2 infection, with no evidence of association with Covid-19 complicated by death or requiring respiratory support. We performed several sensitivity analyses to evaluate the robustness of our findings.\n\nOur results serve as genetic evidence for the potential efficacy of IL-6R blockade in Covid-19. Ongoing large-scale RCTs of IL-6R blockers will be instrumental in identifying the settings, including stage of disease, in which these agents may be effective.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Jonas Bovijn",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Cecilia M. Lindgren",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Michael V. Holmes",
+        "author_inst": "University of Oxford"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.07.18.210179",
     "rel_title": "Lethality of SARS-CoV-2 infection in K18 human angiotensin converting enzyme 2 transgenic mice",
@@ -1289535,57 +1288444,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.07.17.209304",
-    "rel_title": "Interplay of Monocytes and T Lymphocytes in COVID-19 Severity",
-    "rel_date": "2020-07-18",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.17.209304",
-    "rel_abs": "The COVID-19 pandemic represents an ongoing global crisis that has already impacted over 13 million people. The responses of specific immune cell populations to the disease remain poorly defined, which hinders improvements in treatment and care management. Here, we utilized mass cytometry (CyTOF) to thoroughly phenotype peripheral myeloid cells and T lymphocytes from 30 convalescent patients with mild, moderate, and severe cases of COVID-19. We identified 10 clusters of monocytes and dendritic cells and 17 clusters of T cells. Examination of these clusters revealed that both CD14+CD16+ intermediate and CD14dimCD16+ nonclassical monocytes, as well as CD4+ stem cell memory T (TSCM) cells, correlated with COVID-19 severity, coagulation factor levels, and/or inflammatory indicators. We also identified two nonclassical monocyte subsets distinguished by expression of the sugar residue 6-Sulfo LacNac (Slan). One of these subsets (Slanlo, nMo1) was depleted in moderately and severely ill patients, while the other (Slanhi, nMo2) increased with disease severity and was linked to CD4+ T effector memory (TEM) cell frequencies, coagulation factors, and inflammatory indicators. Intermediate monocytes tightly correlated with loss of naive T cells as well as an increased abundance of effector memory T cells expressing the exhaustion marker PD-1. Our data suggest that both intermediate and non-classical monocyte subsets shape the adaptive immune response to SARS-CoV-2. In summary, our study provides both broad and in-depth characterization of immune cell phenotypes in response to COVID-19 and suggests functional interactions between distinct cell types during the disease.\n\nOne Sentence SummaryUse of mass cytometry on peripheral blood mononuclear cells from convalescent COVID-19 patients allows correlation of distinct monocyte and T lymphocyte subsets with clinical factors.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Lindsey E. Padgett",
-        "author_inst": "La Jolla Institute for Immunology"
-      },
-      {
-        "author_name": "Huy Q. Dinh",
-        "author_inst": "La Jolla Institute for Immunology"
-      },
-      {
-        "author_name": "Serena J. Chee",
-        "author_inst": "University of Southampton"
-      },
-      {
-        "author_name": "Claire E. Olingy",
-        "author_inst": "La Jolla Institute for Immunology"
-      },
-      {
-        "author_name": "Runpei Wu",
-        "author_inst": "La Jolla Institute for Immunology"
-      },
-      {
-        "author_name": "Daniel J. Araujo",
-        "author_inst": "La Jolla Institute for Immunology"
-      },
-      {
-        "author_name": "Pandurangan Vijayanand",
-        "author_inst": "La Jolla Institute for Immunology"
-      },
-      {
-        "author_name": "Christian H. Ottensmeier",
-        "author_inst": "University of Southampton"
-      },
-      {
-        "author_name": "Catherine C. Hedrick",
-        "author_inst": "La Jolla Institute for Immunology"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2020.07.17.207563",
     "rel_title": "Neutralization Assay with SARS-CoV-1 and SARS-CoV-2 Spike Pseudotyped Murine Leukemia Virions",
@@ -1290048,6 +1288906,173 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2020.07.15.204339",
+    "rel_title": "Mutational dynamics and transmission properties of SARS-CoV-2 superspreading events in Austria",
+    "rel_date": "2020-07-17",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.15.204339",
+    "rel_abs": "Superspreading events shape the COVID-19 pandemic. Here we provide a national-scale analysis of SARS-CoV-2 outbreaks in Austria, a country that played a major role for virus transmission across Europe and beyond. Capitalizing on a national epidemiological surveillance system, we performed deep whole-genome sequencing of virus isolates from 576 samples to cover major Austrian SARS-CoV-2 clusters. Our data chart a map of early viral spreading in Europe, including the path from low-frequency mutations to fixation. Detailed epidemiological surveys enabled us to calculate the effective SARS-CoV-2 population bottlenecks during transmission and unveil time-resolved intra-patient viral quasispecies dynamics. This study demonstrates the power of integrating deep viral genome sequencing and epidemiological data to better understand how SARS-CoV-2 spreads through populations.\n\nGraphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY",
+    "rel_num_authors": 38,
+    "rel_authors": [
+      {
+        "author_name": "Alexandra Popa",
+        "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences"
+      },
+      {
+        "author_name": "Jakob-Wendelin Genger",
+        "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences"
+      },
+      {
+        "author_name": "Michael Nicholson",
+        "author_inst": "Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health"
+      },
+      {
+        "author_name": "Thomas Penz",
+        "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences"
+      },
+      {
+        "author_name": "Daniela Schmid",
+        "author_inst": "Austrian Agency for Health and Food Safety"
+      },
+      {
+        "author_name": "Stephan W Aberle",
+        "author_inst": "Center for Virology, Medical University of Vienna"
+      },
+      {
+        "author_name": "Benedikt Agerer",
+        "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences"
+      },
+      {
+        "author_name": "Alexander Lercher",
+        "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences"
+      },
+      {
+        "author_name": "Lukas Endler",
+        "author_inst": "Department of Biomedical Sciences, University of Veterinary Medicine"
+      },
+      {
+        "author_name": "Henrique Colaco",
+        "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences"
+      },
+      {
+        "author_name": "Mark Smyth",
+        "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences"
+      },
+      {
+        "author_name": "Michael Schuster",
+        "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences"
+      },
+      {
+        "author_name": "Miguel Grau",
+        "author_inst": "Institute for Research in Biomedicine"
+      },
+      {
+        "author_name": "Francisco Martinez Jimenez",
+        "author_inst": "IRB"
+      },
+      {
+        "author_name": "Oriol Pich",
+        "author_inst": "Institute for Research in Biomedicine"
+      },
+      {
+        "author_name": "Wegene Tamire Borena",
+        "author_inst": "Institute of Virology, Medical University Innsbruck"
+      },
+      {
+        "author_name": "Erich Pawelka",
+        "author_inst": "Department of Medicine IV, Kaiser Franz Josef Hospital"
+      },
+      {
+        "author_name": "Zsofia Keszei",
+        "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences"
+      },
+      {
+        "author_name": "Martin Senekowitsch",
+        "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences"
+      },
+      {
+        "author_name": "Jan Laine",
+        "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences"
+      },
+      {
+        "author_name": "Judith Aberle",
+        "author_inst": "Center for Virology, Medical University of Vienna"
+      },
+      {
+        "author_name": "Monika Redlberger-Fritz",
+        "author_inst": "Center for Virology, Medical University of Vienna"
+      },
+      {
+        "author_name": "Mario Karolyi",
+        "author_inst": "Department of Medicine IV, Kaiser Franz Josef Hospital"
+      },
+      {
+        "author_name": "Alexander Zoufaly",
+        "author_inst": "Department of Medicine IV, Kaiser Franz Josef Hospital"
+      },
+      {
+        "author_name": "Sabine Maritschnik",
+        "author_inst": "Austrian Agency for Health and Food Safety"
+      },
+      {
+        "author_name": "Martin Borkovec",
+        "author_inst": "Austrian Agency for Health and Food Safety"
+      },
+      {
+        "author_name": "Peter Hufnagl",
+        "author_inst": "Austrian Agency for Health and Food Safety"
+      },
+      {
+        "author_name": "Manfred Nairz",
+        "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck"
+      },
+      {
+        "author_name": "Guenter Weiss",
+        "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck"
+      },
+      {
+        "author_name": "Michael T. Wolfinger",
+        "author_inst": "University of Vienna, Austria"
+      },
+      {
+        "author_name": "Dorothee von Laer",
+        "author_inst": "Institute of Virology, Medical University Innsbruck"
+      },
+      {
+        "author_name": "Giulio Superti-Furga",
+        "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences"
+      },
+      {
+        "author_name": "Nuria Lopez-Bigas",
+        "author_inst": "Barcelona Institute for Research in Biomedicine"
+      },
+      {
+        "author_name": "Elisabeth Puchhammer-Stoeckl",
+        "author_inst": "Medical University of Vienna"
+      },
+      {
+        "author_name": "Franz Allerberger",
+        "author_inst": "Austrian Agency for Health and Food Safety"
+      },
+      {
+        "author_name": "Franziska Michor",
+        "author_inst": "Dana-Farber Cancer Institute"
+      },
+      {
+        "author_name": "Christoph Bock",
+        "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences"
+      },
+      {
+        "author_name": "Andreas Bergthaler",
+        "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2020.07.15.205567",
     "rel_title": "COVID-19 Detection on Chest X-Ray and CT Scan Images Using Multi-image Augmented Deep Learning Model",
@@ -1291773,33 +1290798,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.07.14.20153288",
-    "rel_title": "Use of Powered Air-Purifying Respirator(PAPR) by healthcare workers for preventing highly infectious viral diseases -a systematic review of evidence",
-    "rel_date": "2020-07-17",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.14.20153288",
-    "rel_abs": "BackgroundHealthcare workers (HCWs) are at particular risk during pandemics and epidemics of highly virulent diseases with significant morbidity and case fatality rate. These diseases include Severe Acute Respiratory Syndrome Coronaviruses, SARS-CoV-1 and SARS-CoV-2, Middle Eastern Respiratory Syndrome (MERS) and Ebola. With the current (SARS-CoV-2) global pandemic, it is critical to delineate appropriate contextual respiratory protection for HCWs. The aim of this systematic review was to evaluate the effect of Powered Air Purifying Respirators (PAPRs) as part of respiratory protection versus another device (egN95/FFP2) on HCW infection rates and contamination.\n\nMethodsOur primary outcomes included HCW infection rates with SARS-CoV-2, SARS-CoV-1, Ebola or MERS when utilizing PAPR. We included randomized controlled trials, non-randomized controlled trials, and observational studies. We searched the following databases: MEDLINE, EMBASE, and Cochrane Library (Cochrane Database of Systematic Reviews and CENTRAL). Two reviewers independently screened all citations, full-text articles, and abstracted data. Due to clinical and methodological heterogeneity, we did not conduct a meta-analysis. Where applicable, we constructed Evidence Profile (EP) tables for each individual outcome. Confidence in cumulative evidence for each outcome was classified according to the GRADE system.\n\nResultsWe identified 689 studies during literature searches. We included 10 full text studies. A narrative synthesis was provided. Two on-field studies reported no difference in the rates of healthcare workers performing airway procedures during care of critical patients with SARS-CoV-2. A single simulation trial reported a lower level of cross-contamination of participants using PAPR compared to alternative respiratory protection. There is moderate quality evidence that PAPR use is associated with greater heat tolerance but lower scores for mobility and communication ability. We identified a trend toward greater self-reported wearer comfort with PAPR technology in low quality observational simulation studies.\n\nConclusionField observational studies do not indicate a difference in healthcare worker infection utilizing PAPR devices versus other compliant respiratory equipment. Greater heat tolerance accompanied by lower scores of mobility and audibility in PAPR were identified. Further pragmatic studies are needed in order to delineate actual effectiveness and provider satisfaction with PAPR technology.\n\nPlease note: Protocol for this review was prospectively registered with the International Register of Systematic Reviews identification number CRD42020184724.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Ana Licina",
-        "author_inst": "Austin Health"
-      },
-      {
-        "author_name": "Andrew J Silvers",
-        "author_inst": "Monash Health"
-      },
-      {
-        "author_name": "Rhonda Stuart",
-        "author_inst": "Monash Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.07.16.20155069",
     "rel_title": "Hospital mortality and resource implications of hospitalisation with COVID-19 in London, UK: a prospective cohort study",
@@ -1292170,6 +1291168,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.07.15.20140095",
+    "rel_title": "Preparedness, Perceived Impact and Concerns of health Care Workers in a Teaching Hospital during Coronavirus Disease 2019 (COVID-19)",
+    "rel_date": "2020-07-17",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20140095",
+    "rel_abs": "ObjectiveCoronavirus Disease 2019 is a new threat to human lives worldwide. Preparedness of institutions during epidemic outbreak has a pivotal role in saving lives and preventing further spread. At the same time, these pandemics impact badly on professional and personal life of Health care workers. The objective of this study is to find the opinion of Health care workers regarding their level of preparedness, concerns and perceived impact related to this pandemic outbreak.\n\nMaterials and Methodsin this study, random samples of doctors and nurses was provided with a self-administered questionnaire regarding their preparedness, work and non-work related concerns and impact on their lives during Covid-19 outbreak.\n\nResultsMost of the Health Care Workers believed that their institute preparation to fight Covid-19 pandemic is better than prior to onset of this crisis (p0.001). Work related stress was seen more commonly in nurses whereas higher frequency of non-work related stress was observed among doctors. Nurses (75.55%) faith in their employer was more than doctors faith (46.66%) regarding their medical needs. There was more acceptance of hydroxychloroquine as a prophylactic drug for Covid-19 in doctors compared to nurses (p 0.01).\n\nConclusionsThough this institute was more prepared at the time of pandemic spread, substantial opportunity of improvement remains. The consistency of work and non work related anxiety and stress in health care workers is very high in present study group. Concerns and risks of Health Care Workers should be addressed ethically and adequately by strengthening safety measures and building trust in the system they work.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Kumar Saurabh",
+        "author_inst": "Government Medical College, Bettiah"
+      },
+      {
+        "author_name": "Shilpi Ranjan",
+        "author_inst": "Nalanda Medical College,Patna"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.07.17.20152389",
     "rel_title": "Mapping physical access to healthcare for older adults in sub-Saharan Africa: A cross-sectional analysis with implications for the COVID-19 response",
@@ -1293663,45 +1292684,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.07.17.20156026",
-    "rel_title": "Are we ready when COVID-19 vaccine is available? Study on nurses' vaccine hesitancy in Hong Kong",
-    "rel_date": "2020-07-17",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20156026",
-    "rel_abs": "IntroductionNurses are considered a trustworthy source of vaccine-related information to build public confidence in vaccination. This study estimated nurses influenza vaccine uptake and intention to receive COVID-19 vaccine when available, and examined the corresponding psychological antecedents.\n\nMethodsA cross-sectional online survey among nurses was conducted during the main COVID-19 outbreak in Hong Kong between mid-March and late April 2020. Demographics, influenza vaccination, intention to have COVID-19 vaccine, the 5C vaccine hesitancy components (i.e., confidence, complacency, constraints, calculation, and collective responsibility), work stress and COVID-related work demands (i.e., insufficient supply of personal protective equipment, involvement in isolation rooms, and unfavorable attitudes towards workplace infection control policies) were reported.\n\nResultsThe influenza vaccination coverage and the proportion intending to take COVID-19 vaccine were 49% and 63%, respectively, among 1205 eligible nurses. Influenza vaccine uptake was associated with working in public hospitals and all 5C constructs, whereas stronger COVID-19 vaccination intention was associated with younger age, more confidence, less complacency and more collective responsibility towards the vaccine. COVID-19-related demands were associated with greater work stress, and hence stronger COVID-19 vaccination intention.\n\nConclusionVaccine uptake/intention was well predicted by the 5C constructs. With less work stress among nurses in the post-pandemic period, the intention to take COVID-19 vaccine will likely drop. The 5C constructs should be infused in vaccination campaigns. While a COVID-19 vaccine could be ready soon, communities are not ready to accept it. More research work is needed to boost the uptake.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Kin On Kwok",
-        "author_inst": "The Chinese University of Hong Kong"
-      },
-      {
-        "author_name": "Kin Kit Li",
-        "author_inst": "City University of Hong Kong"
-      },
-      {
-        "author_name": "Wan In Wei",
-        "author_inst": "The Chinese University of Hong Kong"
-      },
-      {
-        "author_name": "Kwok Hung Tang",
-        "author_inst": "Sungkyunkwan University"
-      },
-      {
-        "author_name": "Samuel Yeung Shan Wong",
-        "author_inst": "The Chinese University of Hong Kong"
-      },
-      {
-        "author_name": "Shui Shan Lee",
-        "author_inst": "The Chinese University of Hong Kong"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.07.17.20156091",
     "rel_title": "Cultural values predict national COVID-19 death rates",
@@ -1294100,6 +1293082,129 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "intensive care and critical care medicine"
   },
+  {
+    "rel_doi": "10.1101/2020.07.17.20155937",
+    "rel_title": "Disease-associated antibody phenotypes and probabilistic seroprevalence estimates during the emergence of SARS-CoV-2",
+    "rel_date": "2020-07-17",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20155937",
+    "rel_abs": "Serological studies are critical for understanding pathogen-specific immune responses and informing public health measures1,2. Here, we evaluate tandem IgM, IgG and IgA responses in a cohort of individuals PCR+ for SARS-CoV-2 RNA (n=105) representing different categories of disease severity, including mild and asymptomatic infections. All PCR+ individuals surveyed were IgG-positive against the virus spike (S) glycoprotein. Elevated Ab levels were associated with hospitalization, with IgA titers, increased circulating IL-6 and strong neutralizing responses indicative of intensive care status. Additional studies of healthy blood donors (n=1,000) and pregnant women (n=900), sampled weekly during the initial outbreak in Stockholm, Sweden (weeks 14-25, 2020), demonstrated that anti-viral IgG titers differed over 1,000-fold between seroconverters, highlighting the need for careful evaluation of assay cut-offs for individual measurements and accurate estimates of seroprevalence (SP). To provide a solution to this, we developed probabilistic machine learning approaches to assign likelihood of past infection without setting an assay cut-off, allowing for more quantitative individual and population-level Ab measures. Using these tools, that considered responses against both S and RBD, we report SARS-CoV-2 S-specific IgG in 6.8% of blood donors and pregnant women two months after the peak of spring COVID-19 deaths, with the SP curve and country death rate following similar trajectories.",
+    "rel_num_authors": 27,
+    "rel_authors": [
+      {
+        "author_name": "Xaquin Castro Dopico",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Leo Hanke",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Daniel J Sheward",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Sandra Muschiol",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Soo Aleman",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Nastasiya F Grinberg",
+        "author_inst": "University of Cambridge"
+      },
+      {
+        "author_name": "Murray Christian",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Monika Adori",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Laura Perez Vidakovics",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Kim Chang Il",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Sharesta Khoenkhoen",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Pradeepa Pushparaj",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Ainhoa Moliner Morro",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Marco Mandolesi",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Marcus Ahl",
+        "author_inst": "Karolinska University Hospital"
+      },
+      {
+        "author_name": "Mattias Forsell",
+        "author_inst": "Umea University"
+      },
+      {
+        "author_name": "Jonathan Coquet",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Martin Corcoran",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Joanna Rorbach",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Joakim Dillner",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Gordana Bogdanovic",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Gerald Mcinerney",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Tobias Allander",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Ben Murrell",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Chris Wallace",
+        "author_inst": "University of Cambridge & MRC Biostatistics Unit"
+      },
+      {
+        "author_name": "Jan Albert",
+        "author_inst": "Karolinska Institutet"
+      },
+      {
+        "author_name": "Gunilla B Karlsson Hedestam",
+        "author_inst": "Karolinska Institutet"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "allergy and immunology"
+  },
   {
     "rel_doi": "10.1101/2020.07.16.20138354",
     "rel_title": "Joint CBC-ICT Interpretation for the pre-surgical screening of COVID 19 asymptomatic cases: A cross-sectional study",
@@ -1295393,45 +1294498,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.07.15.20154500",
-    "rel_title": "Short-term analysis and long-term predictions for the COVID-19 epidemic in a seasonality regime: the Italian case",
-    "rel_date": "2020-07-16",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20154500",
-    "rel_abs": "As of July 14th, COVID-19 has caused in Italy 34.984 deaths and 243.344 infection cases. Strict lockdown policies were necessary to contain the first outbreak wave and prevent the Italian healthcare system from being overwhelmed by patients requiring intensive care. After the progressive reopening, predicting how the epidemic situation will evolve is urgent and fundamental to control any future outbreak and prevent a second wave. We defined a time-varying optimization procedure to repeatedly calibrate the SIDARTHE model1 with data up to June 24th. The computed parameter distributions allow us to robustly analyse how the epidemic situation evolved and outline possible future scenarios. Assuming a seasonal regime for COVID-19, we tested different lockdown policies. Our results suggest that an intermittent lockdown where six \"open days\" are allowed every other week may prevent a resurgent exponential outbreak and, at the same time, ease the societal burden of an extensive lockdown.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Giulia Simoni",
-        "author_inst": "Fondazione The Microsoft Research - University of Trento, Centre for Computational and Systems Biology (COSBI)"
-      },
-      {
-        "author_name": "Anna Fochesato",
-        "author_inst": "Fondazione The Microsoft Research - University of Trento, Centre for Computational and Systems Biology (COSBI)"
-      },
-      {
-        "author_name": "Federico Reali",
-        "author_inst": "Fondazione The Microsoft Research - University of Trento, Centre for Computational and Systems Biology (COSBI)"
-      },
-      {
-        "author_name": "Giulia Giordano",
-        "author_inst": "Department of Industrial Engineering, University of Trento"
-      },
-      {
-        "author_name": "Enrico Domenici",
-        "author_inst": "Fondazione The Microsoft Research - University of Trento, Centre for Computational and Systems Biology (COSBI)"
-      },
-      {
-        "author_name": "Luca Marchetti",
-        "author_inst": "Fondazione The Microsoft Research - University of Trento, Centre for Computational and Systems Biology (COSBI)"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.07.15.20154476",
     "rel_title": "Causal analysis of COVID-19 observational data in German districts reveals effects of mobility, awareness, and temperature",
@@ -1295690,6 +1294756,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.07.14.20153775",
+    "rel_title": "Direct-to-Consumer Chat-Based Remote Care Before and During the COVID-19 Outbreak",
+    "rel_date": "2020-07-16",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.14.20153775",
+    "rel_abs": "ObjectiveTo compare the patient population, common complaints, and physician recommendations in direct-to-consumer chat-based consults, before and during the COVID-19 outbreak.\n\nData sourcesData on patient characteristics, patient complaints, and physician recommendations from 36,864 chat-based telemedicine consults with physicians in an online-clinic by patients from across the United States between April 2019 and April 2020.\n\nStudy DesignWe perform a retrospective analysis comparing patient characteristics, visit characteristics, and physician recommendation before and after the COVID-19 outbreak. We examine patient age and gender, visit time, patient chief complains, and physician medical recommendation (including prescription drugs, reassurance, and referrals).\n\nPrincipal FindingsBefore March 2020, most patients were female (75 percent) and 18-44 years old (89 percent). Common complaints such as abdominal pain, dysuria, or sore throat suggested minor acute conditions. Most cases (67 percent) were resolved remotely, mainly via prescriptions; a minority were referred. Since March 2020, the COVID-19 emergency has led to a sharp (fourfold) increase in case volume, including more males (from 25 to 29 percent), patients aged 45 and older (from 11 to 17 percent), and more cases involving mental health complaints and complaints related to COVID-19. Across all symptoms, significantly more cases (78 percent) have been resolved remotely.\n\nConclusionsThe COVID-19 outbreak in the United States has been associated with a sharp increase in the use of chat-based telemedicine services, including by new patient demographics, an increase in both COVID-19 and mental health complains, and an increase in remote case resolutions.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Dan Zeltzer",
+        "author_inst": "Tel Aviv University"
+      },
+      {
+        "author_name": "Alina Vodonos Zilberg",
+        "author_inst": "K Health, Tel Aviv"
+      },
+      {
+        "author_name": "Yehuda Edo Paz",
+        "author_inst": "K Health, New York"
+      },
+      {
+        "author_name": "Roy Malka",
+        "author_inst": "K Health, Tel Aviv"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "primary care research"
+  },
   {
     "rel_doi": "10.1101/2020.07.14.20153908",
     "rel_title": "Application of ARIMA and Holt-Winters forecasting model to predict the spreading of COVID-19 for India and its states",
@@ -1296915,25 +1296012,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "primary care research"
   },
-  {
-    "rel_doi": "10.1101/2020.07.13.20153064",
-    "rel_title": "Differences by country-level income in COVID-19 cases, deaths, case-fatality rates, and rates per million population in the first five months of the pandemic",
-    "rel_date": "2020-07-15",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20153064",
-    "rel_abs": "ObjectiveTo describe differences by country-level income in COVID-19 cases, deaths, case-fatality rates, incidence rates, and death rates per million population.\n\nMethodsPublicly available data on COVID-19 cases and deaths from December 31, 2019 to June 3, 2020 were analyzed. Kruskal-Wallis tests were used to examine associations of country-level income with COVID-19 cases, deaths, case-fatality rates, incidence rates, and death rates.\n\nResultsA total of 380,803 deaths out of 6,348,204 COVID-19 cases were reported from 210 countries and territories globally in the period under study, and the global case-fatality rate was 6.0%. Of the total globally reported cases and deaths, the percentages of cases and deaths were 59.9% and 75.0% for high-income countries, and 30.9% and 20.7% for upper-middle-income countries. Countries in higher income categories had higher incidence rates and death rates. Between April and May, the incidence rates in higher-income groups of countries decreased, but in other groups it increased.\n\nConclusionsIn the first five months of the COVID-19 pandemic, most cases and deaths were reported from high-income and upper-middle-income countries, and those countries had higher incidence rates and death rates per million population than did lower-middle and low-income countries.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Wrishmeen Sabawoon",
-        "author_inst": "The University of Tokyo"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.07.13.20152207",
     "rel_title": "Clinical Electroencephalography Findings and Considerations in Hospitalized Patients with Coronavirus SARS-CoV-2",
@@ -1297212,6 +1296290,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.07.14.20153304",
+    "rel_title": "Post lockdown COVID-19 seroprevalence and circulation at the time of delivery, France",
+    "rel_date": "2020-07-15",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.14.20153304",
+    "rel_abs": "BackgroundTo fight the COVID-19 pandemic, lockdown has been decreed in many countries worldwide. The impact of pregnancy as a severity risk factor is still debated, but strict lockdown measures have been recommended for pregnant women.\n\nObjectivesTo evaluate the impact of the COVID-19 pandemic and lockdown on the seroprevalence and circulation of SARS-CoV-2 in a maternity ward in an area that has been significantly affected by the virus.\n\nStudy designProspective study at the Antoine Beclere Hospital maternity ward (Paris area, France) from May 4 (one week before the end of lockdown) to May 31, 2020 (three weeks after the end of lockdown). All patients admitted to the delivery room during this period were offered a SARS-CoV-2 serology test as well concomitant SARS-CoV-2 RT-PCR on a nasopharyngeal sample.\n\nResultsA total of 249 women were included. Seroprevalence of SARS-CoV-2 was 8%. The RT-PCR positive rate was 0.5%. 47.4% of the SARS-CoV-2-IgG-positive pregnant women never experienced any symptoms. A history of symptoms during the epidemic, such as fever, myalgia and anosmia, was suggestive of previous infection.\n\nConclusionsThree weeks after the end of lockdown, SARS-CoV-2 infections were scarce in our region. A high proportion of SARS-CoV-2-IgG-negative pregnant women must be taken into consideration in the event of a resurgence of the pandemic in order to adapt public health measures to reduce exposure to the virus, such as social distancing and teleworking for this specific population.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Jeremie Mattern",
+        "author_inst": "Division of Obstetrics and Gynecology, Antoine Beclere Hospital, Paris Saclay University, AP-HP, Clamart, France"
+      },
+      {
+        "author_name": "Christelle Vauloup-Fellous",
+        "author_inst": "Division of Virology, Paul Brousse Hospital, Paris Saclay University, AP-HP, INSERM U1193 Villejuif, France"
+      },
+      {
+        "author_name": "Hoda Zakaria",
+        "author_inst": "Division of Obstetrics and Gynecology, Antoine Beclere Hospital, Paris Saclay University, AP-HP, Clamart, France"
+      },
+      {
+        "author_name": "Alexandra Benachi",
+        "author_inst": "Division of Obstetrics and Gynecology, Antoine Beclere Hospital, Paris Saclay University, AP-HP, Clamart, France"
+      },
+      {
+        "author_name": "Julie Carrara",
+        "author_inst": "Division of Obstetrics and Gynecology, Antoine Beclere Hospital, Paris Saclay University, AP-HP, Clamart, France"
+      },
+      {
+        "author_name": "Alexandra Letourneau",
+        "author_inst": "Division of Obstetrics and Gynecology, Antoine Beclere Hospital, Paris Saclay University, AP-HP, Clamart, France"
+      },
+      {
+        "author_name": "Nadege Bourgeois-Nicolaos",
+        "author_inst": "Division of Microbiology, Antoine Beclere Hospital, Paris Saclay University, AP-HP, Clamart, France"
+      },
+      {
+        "author_name": "Daniele De Luca",
+        "author_inst": "Division of Pediatrics and Neonatal Critical Care, Antoine Beclere Hospital, Paris Saclay University, AP-HP, Clamart, France"
+      },
+      {
+        "author_name": "Florence Doucet-Populaire",
+        "author_inst": "Division of Microbiology, Antoine Beclere Hospital, Paris Saclay University, AP-HP, Clamart, France"
+      },
+      {
+        "author_name": "Alexandre J. Vivanti",
+        "author_inst": "Division of Obstetrics and Gynecology, Antoine Beclere Hospital, Paris Saclay University, AP-HP, Clamart, France"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.07.13.20152694",
     "rel_title": "COVID-19 misinformation: mere harmless delusions or much more? A knowledge and attitude cross-sectional study among the general public residing in Jordan",
@@ -1298509,49 +1297642,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.07.15.204610",
-    "rel_title": "Antigenic variation of SARS-CoV-2 in response to immune pressure",
-    "rel_date": "2020-07-15",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.15.204610",
-    "rel_abs": "The ongoing evolution of SARS-CoV-2 is expected to be at least partially driven by the selective pressure imposed by the human immune system. We exploited the availability of a large number of high-quality SARS-CoV-2 genomes, as well as of validated epitope predictions, to show that B cell epitopes in the spike glycoprotein (S) and in the nucleocapsid protein (N) have higher diversity than non-epitope positions. Similar results were obtained for other human coronaviruses. Conversely, in the SARS-CoV-2 population, epitopes for CD4+ and CD8+ T cells were not more variable than non-epitope positions. A significant reduction in epitope variability was instead observed for some of the most immunogenic proteins (S, N, ORF8, and ORF3a). Analysis over longer evolutionary time-frames indicated that this effect is not due to differential constraints. These data indicate that SARS-CoV-2 is evolving to elude the host humoral immune response, whereas recognition by T cells might benefit the virus.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Diego Forni",
-        "author_inst": "Scientific Institute IRCCS E. Medea"
-      },
-      {
-        "author_name": "Rachele Cagliani",
-        "author_inst": "Scientific Institute IRCCS E. MEDEA"
-      },
-      {
-        "author_name": "Chiara Pontremoli",
-        "author_inst": "Scientific Institute IRCCS E. Medea"
-      },
-      {
-        "author_name": "Alessandra Mozzi",
-        "author_inst": "Scientific Institute IRCCS E. Medea"
-      },
-      {
-        "author_name": "Uberto Pozzoli",
-        "author_inst": "Scientific Institute IRCCS E. Medea"
-      },
-      {
-        "author_name": "Mario Clerici",
-        "author_inst": "Chair of Immunology, Department of Biomedical Sciences and Technologies LITA Segrate, University of Milan; IRCCS Don Gnocchi"
-      },
-      {
-        "author_name": "Manuela Sironi",
-        "author_inst": "Scientific Institute IRCCS E. Medea"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.07.15.205211",
     "rel_title": "An Antioxidant Enzyme Therapeutic for COVID-19",
@@ -1298970,6 +1298060,61 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2020.07.15.205229",
+    "rel_title": "The S1 protein of SARS-CoV-2 crosses the blood-brain barrier: Kinetics, distribution, mechanisms, and influence of ApoE genotype, sex, and inflammation",
+    "rel_date": "2020-07-15",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.15.205229",
+    "rel_abs": "Evidence strongly suggests that SARS-CoV-2, the cause of COVID-19, can enter the brain. SARS-CoV-2 enters cells via the S1 subunit of its spike protein, and S1 can be used as a proxy for the uptake patterns and mechanisms used by the whole virus; unlike studies based on productive infection, viral proteins can be used to precisely determine pharmacokinetics and biodistribution. Here, we found that radioiodinated S1 (I-S1) readily crossed the murine blood-brain barrier (BBB). I-S1 from two commercial sources crossed the BBB with unidirectional influx constants of 0.287 {+/-} 0.024 L/g-min and 0.294 {+/-} 0.032 L/g-min and was also taken up by lung, spleen, kidney, and liver. I-S1 was uniformly taken up by all regions of the brain and inflammation induced by lipopolysaccharide reduced uptake in the hippocampus and olfactory bulb. I-S1 crossed the BBB completely to enter the parenchymal brain space, with smaller amounts retained by brain endothelial cells and the luminal surface. Studies on the mechanisms of transport indicated that I-S1 crosses the BBB by the mechanism of adsorptive transcytosis and that the murine ACE2 receptor is involved in brain and lung uptake, but not that by kidney, liver, or spleen. I-S1 entered brain after intranasal administration at about 1/10th the amount found after intravenous administration and about 0.66% of the intranasal dose entered blood. ApoE isoform or sex did not affect whole brain uptake, but had variable effects on olfactory bulb, liver, spleen, and kidney uptakes. In summary, I-S1 readily crosses the murine BBB, entering all brain regions and the peripheral tissues studied, likely by the mechanism of adsorptive transcytosis.\n\nGraphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Elizabeth M Rhea",
+        "author_inst": "VA/UW"
+      },
+      {
+        "author_name": "Aric F Logsdon",
+        "author_inst": "VA/UW"
+      },
+      {
+        "author_name": "Kim M Hansen",
+        "author_inst": "VA"
+      },
+      {
+        "author_name": "Lindsey Williams",
+        "author_inst": "VA"
+      },
+      {
+        "author_name": "May Reed",
+        "author_inst": "VA/UW"
+      },
+      {
+        "author_name": "Kristen Baumann",
+        "author_inst": "VA"
+      },
+      {
+        "author_name": "Sarah Holden",
+        "author_inst": "OHSU"
+      },
+      {
+        "author_name": "Jacob Raber",
+        "author_inst": "OHSU"
+      },
+      {
+        "author_name": "William A Banks",
+        "author_inst": "VA/UW"
+      },
+      {
+        "author_name": "Michelle A Erickson",
+        "author_inst": "VA/UW"
+      }
+    ],
+    "version": "1",
+    "license": "cc0",
+    "type": "new results",
+    "category": "neuroscience"
+  },
   {
     "rel_doi": "10.1101/2020.07.12.20148387",
     "rel_title": "Impact of COVID-19 on 2020 US life expectancy for the Black and Latino populations",
@@ -1300299,33 +1299444,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.07.10.20151258",
-    "rel_title": "Impact of meteorological parameters on the Covid-19 incidence. The case of the city of Oran, Algeria.",
-    "rel_date": "2020-07-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.10.20151258",
-    "rel_abs": "Several studies have confirmed the impact of weather conditions on the evolution of the Covid-19 pandemic. We wanted to verify this phenomenon in the city of Oran in Algeria, which experienced its first case of Covid19 on March 19, 2020.\n\nThe data studied are the new Covid19 cases, the average, minimum and maximum temperatures, as well as the relative humidity rate.\n\nA first analysis of the data with a Spearman rank correlation test did not yield significant results. Taking into account the average incubation period to adjust the data made it possible, during a second analysis, to show that the minimum temperature is significantly correlated with the new cases of Covid19 in Oran. This study can help establish prevention policies against Covid19, especially during fall in temperatures in autumn and winter.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Farid RAHAL",
-        "author_inst": "University of Sciences and Technology of Oran - Mohamed BOUDIAF"
-      },
-      {
-        "author_name": "Salima REZAK",
-        "author_inst": "University of Sciences and Technology of Oran - Mohamed BOUDIAF"
-      },
-      {
-        "author_name": "Fatima Zohra BABA HAMED",
-        "author_inst": "University of Sciences and Technology of Oran - Mohamed BOUDIAF"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.07.10.20150698",
     "rel_title": "Subsequent waves of viral pandemics, a hint for the future course of the SARS-CoV-2 pandemic.",
@@ -1300512,6 +1299630,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.07.10.20150623",
+    "rel_title": "Maternal and perinatal characteristics and outcomes of pregnancies complicated with COVID-19 in Kuwait",
+    "rel_date": "2020-07-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.10.20150623",
+    "rel_abs": "BackgroundIn late December of 2019, a novel coronavirus (SARS-CoV-2) was identified in the Chinese city Wuhan among a cluster of pneumonia patients. While it is known that pregnant women have reduced immunity and they are at risk for COVID-19 infection during the current pandemic, it is not clear if the disease manifestation would be different in pregnant women from non-pregnant women.\n\nObjectivesTo describe the maternal and neonatal clinical features as well as outcome of pregnancies complicated with SARS-CoV-2 infection.\n\nMethodsIn this retrospective national-based study, we analyzed the medical records of all SARS-CoV-2 positive pregnant patients and their neonates who were admitted to New-Jahra Hospital, Kuwait, between March 15th 2020 and May 31st 2020. The outcomes of pregnancies were assessed until the end date of follow-up (June 15th 2020).\n\nResultsA total of 185 pregnant women were enrolled with a median age of 31 years (interquartile range, IQR: 27.5-34), and median gestational age at diagnosis was 29 weeks (IQR: 18-34). The majority (88%) of the patients had mild symptoms, with fever (58%) being the most common presenting symptom followed by cough (50.6%). During the study period, 141 (76.2%) patients continued their pregnancy, 3 (1.6%) had a miscarriage, 1 (0.5%) had intrauterine fetal death and only 2 (1.1%) patients developed severe pneumonia and required intensive care. Most of the neonates were asymptomatic, and only 2 (5%) of them tested positive on day 5 by nasopharyngeal swab testing.\n\nConclusionPregnant women do not appear to be at higher risk to the COVID-19 than the general population. The clinical features of pregnant women with SARS-CoV-2 infection were similar to those of the general population having SARS-CoV-2 infection. Favorable maternal and neonatal outcomes reinforce the existing evidence and may guide healthcare professionals in the management of pregnancies complicated with SARS-CoV-2 infection.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Amal Ayed",
+        "author_inst": "Obstetric and Gynaecology Department, Farwaniya Hospital, Kuwait"
+      },
+      {
+        "author_name": "Alia Embaireeg",
+        "author_inst": "Paediatric Department, Farwaniya Hospital, Kuwait"
+      },
+      {
+        "author_name": "Asmaa Benawadth",
+        "author_inst": "Obstetrics and Gynecology Department, Maternity Hospital, Kuwait"
+      },
+      {
+        "author_name": "Wadha Al-Fouzan",
+        "author_inst": "Department of Microbiology, Faculty of Medicine, Kuwait University"
+      },
+      {
+        "author_name": "Majeda Hammoud",
+        "author_inst": "Paediatrics Department  , Faculty of Medicine, Kuwait University"
+      },
+      {
+        "author_name": "Monif Alhathal",
+        "author_inst": "Neonatal Department, Maternity Hospital, Kuwait"
+      },
+      {
+        "author_name": "Abeer Alzaydai",
+        "author_inst": "Obstetrics and Gynaecology Department, Al-Adan Hospital, Kuwait"
+      },
+      {
+        "author_name": "Mariam Ayed",
+        "author_inst": "Neonatal Department, Farwaniya Hospital, Kuwait"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "obstetrics and gynecology"
+  },
   {
     "rel_doi": "10.1101/2020.07.11.20151688",
     "rel_title": "COVID-19 among people living with HIV: A systematic review",
@@ -1301993,49 +1301158,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "obstetrics and gynecology"
   },
-  {
-    "rel_doi": "10.1101/2020.07.13.20151183",
-    "rel_title": "Stress, burnout and depression in women in health care during COVID-19 Pandemic: Rapid Scoping Review",
-    "rel_date": "2020-07-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20151183",
-    "rel_abs": "ObjectivesThe overall objectives of this rapid scoping review are to (a) synthesize the common triggers of stress, burnout, and depression faced by women in health care during the COVID-19 pandemic, and (b) identify individual-, organizational-, and systems-level interventions that can support the well-being of women HCWs during a pandemic.\n\nDesignThis scoping review is registered on Open Science Framework (OSF) and was guided by the JBI guide to scoping reviews and reported using the Preferred Reporting Items for Systematic reviews and Meta-Analysis (PRISMA) extension to scoping reviews. A systematic search of literature databases (Medline, EMBASE, CINAHL, PsycInfo and ERIC) was conducted from 2003 until June 12, 2020. Two reviewers independently assessed full-text articles according to predefined criteria.\n\nInterventionsWe included review articles and primary studies that reported on stress, burnout, and depression in HCWs; that primarily focused on women; and that included the percentage or number of women included. All English language studies from any geographical setting where COVID-19 has affected the population were reviewed.\n\nPrimary and secondary outcome measuresStudies reporting on mental health outcomes (e.g., stress, burnout, and depression in HCWs), interventions to support mental health well-being were included.\n\nResultsOf the 2,803 papers found, 31 were included. The triggers of stress, burnout and depression are grouped under individual-, organizational-, and systems-level factors. There is a limited amount of evidence on effective interventions that prevents anxiety, stress, burnout and depression during a pandemic.\n\nConclusionsOur preliminary findings show that women HCWs are at increased risk for stress, burnout, and depression during the COVID-19 pandemic. These negative outcomes are triggered by individual level factors such as lack of social support; family status; organizational factors such as access to personal protective equipment or high workload; and systems-level factors such as prevalence of COVID-19, rapidly changing public health guidelines, and a lack of recognition at work.\n\nStrengths and limitations of this studyO_LIA rapid scoping review was conducted to identify stress, burnout and depression faced by women HCWs during COVID-19.\nC_LIO_LITo ensure the relevance of our review, representatives from the women HCWs were engaged in defining the review scope, developing review questions, approving the protocol and literature search strategies, and identifying key messages.\nC_LIO_LIIt provides a descriptive synthesis of current evidence on interventions to prevent mental health for women HCWs.\nC_LIO_LIMost studies used cross-sectional surveys, making it difficult to determine the longitudinal impact.\nC_LIO_LIThere was significant variability in the tools used to measure mental health.\nC_LI",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Abi Sriharan",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Savithiri Ratnapalan",
-        "author_inst": "Hospital for Sick Children"
-      },
-      {
-        "author_name": "Andrea C. Tricco",
-        "author_inst": "Li Ka Shing Research Institute, Knowledge Translation Program, St. Michael's Hospital"
-      },
-      {
-        "author_name": "Doina Lupea",
-        "author_inst": "Ontario Medical Association"
-      },
-      {
-        "author_name": "Ana Patricia Ayala",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Hilary Pang",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Dongjoo Lee",
-        "author_inst": "University of Toronto"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health systems and quality improvement"
-  },
   {
     "rel_doi": "10.1101/2020.07.12.20152124",
     "rel_title": "Assessing required SARS-CoV-2 blanket testing rates for possible control of the outbreak in the epicentre Lusaka province of Zambia with consideration for asymptomatic individuals: a simple mathematical modelling study.",
@@ -1302262,6 +1301384,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.07.13.20152330",
+    "rel_title": "Discrete simulation analysis of COVID-19 and prediction of isolation bed numbers",
+    "rel_date": "2020-07-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20152330",
+    "rel_abs": "The outbreak of COVID-19 has caused tremendous pressure on medical systems. Adequate isolation facilities are essential to control outbreaks, so this study aims to quickly estimate the demand and number of isolation beds. We established a discrete simulation model for epidemiology. By adjusting or fitting necessary epidemic parameters, the effects of the following indicators on the development of the epidemic and the occupation of medical resources were explained: (1) incubation period, (2) response speed and detection capacity of the hospital, (3) disease cure time, and (4) population mobility. Finally, a method for predicting the reasonable number of isolation beds was summarized through multiple linear regression. The prediction equation can be easily and quickly applied to estimate the demanded number of isolation beds in a COVID-19-affected city. A detailed explanation is given for the specific measurement of each parameter in the article.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Xinyu Li",
+        "author_inst": "Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya Hospital,  Central South University,"
+      },
+      {
+        "author_name": "Yufeng Cai",
+        "author_inst": "Department of Biomedical Informatics, School of Life Sciences, Central South University,  Changsha, Hunan"
+      },
+      {
+        "author_name": "Yinghe Ding",
+        "author_inst": "Xiangya School of Medicine, Central South University"
+      },
+      {
+        "author_name": "Jia-da Li",
+        "author_inst": "Department of Biomedical Informatics, School of Life Sciences, Central South University"
+      },
+      {
+        "author_name": "Guoqing Huang",
+        "author_inst": "Department of Emergency, Xiangya Hospital, Central South University"
+      },
+      {
+        "author_name": "Ye Liang",
+        "author_inst": "Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya Hospital,  Central South University,"
+      },
+      {
+        "author_name": "Linyong Xu",
+        "author_inst": "Department of Biomedical Informatics, School of Life Sciences, Central South University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.07.12.20152298",
     "rel_title": "The effect of international travel restrictions on internal spread of COVID-19",
@@ -1303475,33 +1302640,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.07.09.20150235",
-    "rel_title": "The diagnostic accuracy of nucleic acid point-of-care tests for human coronavirus: A systematic review and meta-analysis",
-    "rel_date": "2020-07-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.09.20150235",
-    "rel_abs": "Many recent studies reported coronavirus point of care tests (POCTs) based on isothermal amplification. However, the performances of these tests have not been systematically evaluated. We searched databases for studies that provide data to calculate sensitivity, specificity and diagnostic odds ratio (DOR). We included 43 studies on 5204 specimens. Most studies had high risk of patient selection and index test bias but low risk in other domains. Most studies (n = 21) used reverse transcribed loop mediated isothermal amplification (RT-LAMP) to diagnose Coronavirus disease 2019 (COVID-19). Summary estimated ln(DOR) for RT-LAMP of RNA purified COVID-19 samples is 6.50 (95%CI 5.25-7.76), similar to previously reported value for RT-LAMP of other RNA virus. RT-LAMP from crude samples has significantly lower ln(DOR) at 4.46 (95%CI 3.53-5.38). SAMBA-II has the highest ln(DOR) at 8.00 (95%CI 6.14-9.87). Abbott ID Now performance is similar to RT-LAMP of crude sample. The performances of CRISPR diagnosis and RT-LAMP are not significantly different. Types of coronaviruses and publication status have no significant effect on diagnosis performance. Existing nucleic acid POCTs, particularly RT-LAMP, CRISPR diagnosis and SAMBA-II, have good diagnostic performance. Future work should focus on improving a study design to minimize the risk of biases.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Pakpoom Subsoontorn",
-        "author_inst": "Naresuan University"
-      },
-      {
-        "author_name": "Manupat Lohitnavy",
-        "author_inst": "Naresuan University"
-      },
-      {
-        "author_name": "Chuenjid Kongkaew",
-        "author_inst": "Naresuan University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.07.10.20150375",
     "rel_title": "Poor correlation between antibody titers and neutralizing activity in sera from SARS-CoV-2 infected subjects",
@@ -1303928,6 +1303066,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.07.09.20150219",
+    "rel_title": "Estimating the time-varying reproduction number of COVID-19 with a state-space method",
+    "rel_date": "2020-07-11",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.09.20150219",
+    "rel_abs": "After slowing down the spread of the novel coronavirus COVID-19, many countries have started to relax their confinement measures in the face of critical damage to socioeconomic structures. At this stage, it is desirable to monitor the degree to which political measures or social affairs have exerted influence on the spread of disease. Though it is difficult to trace back individual transmission of infections whose incubation periods are long and highly variable, estimating the average spreading rate is possible if a proper mathematical model can be devised to analyze daily event-occurrences. To render an accurate assessment, we have devised a state-space method for fitting the Hawkes process to a given dataset of daily confirmed cases. The proposed method detects changes occurring in each country and assesses the impact of social events in terms of the temporally varying reproduction number, which corresponds to the average number of cases directly caused by a single infected case. Moreover, the proposed method can be used to predict the possible consequences of alternative political measures. This information can serve as a reference for behavioral guidelines that should be adopted according to the varying risk of infection.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Shinsuke Koyama",
+        "author_inst": "The Institute of Statistical Mathematics, Tokyo 190-8562, Japan"
+      },
+      {
+        "author_name": "Taiki Horie",
+        "author_inst": "Department of Physics, Kyoto University, Kyoto 606-8502, Japan"
+      },
+      {
+        "author_name": "Shigeru Shinomoto",
+        "author_inst": "Kyoto University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.07.09.20150136",
     "rel_title": "An exploratory Integrated Moving Average Time Series Model of the initial outbreak of COVID-19 in six (6) significantly impacted Countries",
@@ -1304989,33 +1304154,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.07.10.20150664",
-    "rel_title": "Using simulation to assess the potential effectiveness of implementing screening at national borders during international outbreaks of influenza, SARS, Ebola virus disease and COVID-19",
-    "rel_date": "2020-07-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.10.20150664",
-    "rel_abs": "The effectiveness of screening travellers during times of international disease outbreak is contentious, especially as the reduction in the risk of disease importation can be very small. Border screening typically consists of travellers being thermally scanned for signs of fever and/or completing a survey declaring any possible symptoms prior to admission to their destination country; while more thorough testing typically exists, these would generally prove more disruptive to deploy. In this paper, we describe a simple Monte Carlo based model that incorporates the epidemiology of COVID-19 to investigate the potential benefit of requiring all travellers to undergo thorough screening upon arrival. This is a purely theoretical study to investigate whether a single test at point of entry might ever prove to be a way of significantly decreasing risk of importation. We therefore assume ideal conditions such as 100% compliance among travellers and the use of a \"perfect\" test. In addition to COVID-19, we also apply the presented model to simulated outbreaks of Influenza, SARS and Ebola for comparison. Our model only considers screening implemented at airports, being the predominant method of international travel. Primary results showed that in the best-case scenario, screening may expect to detect 8.8% of travellers infected with COVID-19, compared to 34.8.%, 9.7% and 3.0% for travellers infected with influenza, SARS and Ebola respectively. While results appear to indicate that screening is more effective at preventing disease ingress when the disease in question has a shorter average incubation period, our results indicate that screening alone does not represent a sufficient method to adequately protect a nation from the importation of COVID-19 cases.\n\nData availabilityAll results described in the work, in addition to technical descriptions of methods used, are made available in the supplementary material. The Python package used to implement these methods and obtain our results has been made accessible online[1].",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Declan Bays",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Emma Bennett",
-        "author_inst": "Public Health England"
-      },
-      {
-        "author_name": "Thomas Finnie",
-        "author_inst": "Public Health England"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.07.10.20150607",
     "rel_title": "Wastewater SARS-CoV-2 Concentration and Loading Variability from Grab and 24-Hour Composite Samples",
@@ -1305310,6 +1304448,89 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.07.09.20149534",
+    "rel_title": "Saliva offers a sensitive, specific and non-invasive alternative to upper respiratory swabs for SARS-CoV-2 diagnosis.",
+    "rel_date": "2020-07-11",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.09.20149534",
+    "rel_abs": "RT-qPCR utilising upper respiratory swabs are the diagnostic gold standard for SARS-CoV-2 despite reported low sensitivity and limited scale up due to global shortages. Saliva is a non-invasive, equipment independent alternative to swabs.\n\nWe collected 145 paired saliva and nasal/throat (NT) swabs at diagnosis (day 0) and repeated on day 2 and day 7 dependent on inpatient care and day 28 for study follow up. Laboratory cultured virus was used to determine the analytical sensitivity of spiked saliva and swabs containing amies preservation media.\n\nSelf-collected saliva samples were found to be consistent, and in some cases superior when compared to healthcare worker collected NT swabs from COVID-19 suspected participants. We report for the first time the analytical limit of detection of 10-2and 100 pfu/ml for saliva and swabs respectively.\n\nSaliva is a easily self-collected, highly sensitive specimen for the detection of SARS-CoV-2.",
+    "rel_num_authors": 17,
+    "rel_authors": [
+      {
+        "author_name": "Rachel Louise Byrne",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Grant A Kay",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Konstantina Kontogianni",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Lottie Brown",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Andrea M Collins",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Luis E Cuevas",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Daniela Ferreira",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Alice J Fraser",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Gala Garrod",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Helen Hill",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Stefanie Menzies",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Elena Mitsi",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Sophie I Owen",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Christopher T Williams",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Angela Hyder-Wright",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Emily R Adams",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Ana I Cubas-Atienzar",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.07.10.20150631",
     "rel_title": "A comprehensive analysis of R0 with different lockdown phase during covid-19 in India",
@@ -1306627,81 +1305848,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
-  {
-    "rel_doi": "10.1101/2020.07.08.20145078",
-    "rel_title": "Validation and comparison of PICTURE analytic and Epic Deterioration Index for COVID-19",
-    "rel_date": "2020-07-10",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.08.20145078",
-    "rel_abs": "IntroductionThe 2019 coronavirus (COVID-19) has led to unprecedented strain on healthcare facilities across the United States. Accurately identifying patients at an increased risk of deterioration may help hospitals manage their resources while improving the quality of patient care. Here we present the results of an analytical model, PICTURE (Predicting Intensive Care Transfers and Other UnfoReseen Events), to identify patients at a high risk for imminent intensive care unit (ICU) transfer, respiratory failure, or death with the intention to improve prediction of deterioration due to COVID-19. We compare PICTURE to the Epic Deterioration Index (EDI), a widespread system which has recently been assessed for use to triage COVID-19 patients.\n\nMethodsThe PICTURE model was trained and validated on a cohort of hospitalized non-COVID-19 patients using electronic health record data from 2014-2018. It was then applied to two hold-out test sets: non-COVID-19 patients from 2019 and patients testing positive for COVID-19 in 2020. PICTURE results were aligned to the EDI for head-to-head comparison via Area Under the Receiver Operator Curve (AUROC) and Area Under the Precision Recall Curve (AUPRC). We compared the models ability to predict an adverse event (defined as ICU transfer, mechanical ventilation use, or death) at two levels of granularity: (1) maximum score across an encounter with a minimum lead time before the first adverse event and (2) predictions at every observation with instances in the last 24 hours before the adverse event labeled as positive. PICTURE and the EDI were also compared on the encounter level using different lead times extending out to 24 hours. Shapley values were used to provide explanations for PICTURE predictions.\n\nResultsPICTURE successfully delineated between high- and low-risk patients and consistently outperformed the EDI in both of our cohorts. In non-COVID-19 patients, PICTURE achieved an AUROC (95% CI) of 0.819 (0.805 - 0.834) and AUPRC of 0.109 (0.089 - 0.125) on the observation level, compared to the EDI AUROC of 0.762 (0.746 - 0.780) and AUPRC of 0.077 (0.062 - 0.090). On COVID-19 positive patients, PICTURE achieved an AUROC of 0.828 (0.794 - 0.869) and AUPRC of 0.160 (0.089 - 0.199), while the EDI scored an AUROC of 0.792 (0.754 - 0.835) and AUPRC of 0.131 (0.092 - 0.159). The most important variables influencing PICTURE predictions in the COVID-19 cohort were a rapid respiratory rate, a high level of oxygen support, low oxygen saturation, and impaired mental status (Glasgow coma score).\n\nConclusionThe PICTURE model is more accurate in predicting adverse patient outcomes for both general ward patients and COVID-19 positive patients in our cohorts compared to the EDI. The ability to consistently anticipate these events may be especially valuable when considering a potential incipient second wave of COVID-19 infections. PICTURE also has the ability to explain individual predictions to clinicians by ranking the most important features for a prediction. The generalizability of the model will require testing in other health care systems for validation.",
-    "rel_num_authors": 15,
-    "rel_authors": [
-      {
-        "author_name": "Brandon C Cummings",
-        "author_inst": "University of Michigan"
-      },
-      {
-        "author_name": "Sardar Ansari",
-        "author_inst": "University of Michigan"
-      },
-      {
-        "author_name": "Jonathan R Motyka",
-        "author_inst": "University of Michigan"
-      },
-      {
-        "author_name": "Guan Wang",
-        "author_inst": "University of Michigan"
-      },
-      {
-        "author_name": "Richard P Medlin Jr.",
-        "author_inst": "University of Michigan"
-      },
-      {
-        "author_name": "Steven L Kronick",
-        "author_inst": "University of Michigan"
-      },
-      {
-        "author_name": "Karandeep Singh",
-        "author_inst": "University of Michigan"
-      },
-      {
-        "author_name": "Pauline K Park",
-        "author_inst": "University of Michigan"
-      },
-      {
-        "author_name": "Lena M Napolitano",
-        "author_inst": "University of Michigan"
-      },
-      {
-        "author_name": "Robert P Dickson",
-        "author_inst": "University of Michigan"
-      },
-      {
-        "author_name": "Michael R Mathis",
-        "author_inst": "University of Michigan"
-      },
-      {
-        "author_name": "Michael W Sjoding",
-        "author_inst": "University of Michigan"
-      },
-      {
-        "author_name": "Andrew J Admon",
-        "author_inst": "University of Michigan"
-      },
-      {
-        "author_name": "Kevin R Ward",
-        "author_inst": "University of Michigan"
-      },
-      {
-        "author_name": "Christopher E Gillies",
-        "author_inst": "University of Michigan"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health informatics"
-  },
   {
     "rel_doi": "10.1101/2020.07.08.20148924",
     "rel_title": "A Holistic Approach to Identification of Covid-19 Patients from Chest X-Ray Images utilizing Transfer Based Learning",
@@ -1307080,6 +1306226,137 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.07.07.20148478",
+    "rel_title": "Natural killer cell activation related to clinical outcome of COVID-19",
+    "rel_date": "2020-07-10",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.07.20148478",
+    "rel_abs": "Understanding innate immune responses in COVID-19 is important for deciphering mechanisms of host responses and interpreting disease pathogenesis. Natural killer (NK) cells are innate effector lymphocytes that respond to acute viral infections, but might also contribute to immune pathology. Here, using 28-color flow cytometry, we describe a state of strong NK cell activation across distinct subsets in peripheral blood of COVID-19 patients, a pattern mirrored in scRNA-seq signatures of lung NK cells. Unsupervised high-dimensional analysis identified distinct immunophenotypes that were linked to disease severity. Hallmarks of these immunophenotypes were high expression of perforin, NKG2C, and Ksp37, reflecting a high presence of adaptive NK cell expansions in circulation of patients with severe disease. Finally, arming of CD56bright NK cells was observed in course of COVID-19 disease states, driven by a defined protein-protein interaction network of inflammatory soluble factors. This provides a detailed map of the NK cell activation-landscape in COVID-19 disease.",
+    "rel_num_authors": 29,
+    "rel_authors": [
+      {
+        "author_name": "Christopher Maucourant",
+        "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden"
+      },
+      {
+        "author_name": "Iva Filipovic",
+        "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden"
+      },
+      {
+        "author_name": "Andrea Ponzetta",
+        "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden"
+      },
+      {
+        "author_name": "Soo Aleman",
+        "author_inst": "Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden"
+      },
+      {
+        "author_name": "Martin Cornillet",
+        "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden"
+      },
+      {
+        "author_name": "Laura Hertwig",
+        "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden"
+      },
+      {
+        "author_name": "Benedikt Strunz",
+        "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden"
+      },
+      {
+        "author_name": "Antonio Lentini",
+        "author_inst": "Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden"
+      },
+      {
+        "author_name": "Bjorn Reinius",
+        "author_inst": "Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden"
+      },
+      {
+        "author_name": "Demi Brownlie",
+        "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden"
+      },
+      {
+        "author_name": "Angelica Cuapio Gomez",
+        "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden"
+      },
+      {
+        "author_name": "Eivind Heggernes Ask",
+        "author_inst": "Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway"
+      },
+      {
+        "author_name": "Ryan M Hull",
+        "author_inst": "SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden"
+      },
+      {
+        "author_name": "Alvaro Haroun-Izquierdo",
+        "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden"
+      },
+      {
+        "author_name": "Marie Schaffer",
+        "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden"
+      },
+      {
+        "author_name": "Jonas Klingstrom",
+        "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden"
+      },
+      {
+        "author_name": "Elin Folkesson",
+        "author_inst": "Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden"
+      },
+      {
+        "author_name": "Marcus Buggert",
+        "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden"
+      },
+      {
+        "author_name": "Johan K Sandberg",
+        "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden"
+      },
+      {
+        "author_name": "Lars I Eriksson",
+        "author_inst": "Function Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden."
+      },
+      {
+        "author_name": "Olav Rooyackers",
+        "author_inst": "Function Perioperative Medicine and Intensive Care, Karolinska University Hospital, Stockholm, Sweden."
+      },
+      {
+        "author_name": "Hans-Gustaf Ljunggren",
+        "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden"
+      },
+      {
+        "author_name": "Karl-Johan Malmberg",
+        "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden"
+      },
+      {
+        "author_name": "Jakob Michaelsson",
+        "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden"
+      },
+      {
+        "author_name": "Nicole Marquardt",
+        "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden"
+      },
+      {
+        "author_name": "Quirin Hammer",
+        "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden"
+      },
+      {
+        "author_name": "Kristoffer Stralin",
+        "author_inst": "Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden"
+      },
+      {
+        "author_name": "Niklas K Bjorkstrom",
+        "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden"
+      },
+      {
+        "author_name": "- Karolinska COVID-19 Study Group",
+        "author_inst": "-"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.07.06.20143719",
     "rel_title": "Performance characteristics of a high throughput automated transcription mediated amplification test for SARS-CoV-2 detection",
@@ -1308461,41 +1307738,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.07.08.20148916",
-    "rel_title": "Adolescents' health literacy, health protective measures, and health-related quality of life during the Covid-19 pandemic",
-    "rel_date": "2020-07-10",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.08.20148916",
-    "rel_abs": "PurposeFirst, to describe adolescents health information sources and knowledge, health literacy (HL), health protective measures, and health-related quality of life (HRQoL) during the initial phase of the Covid-19 pandemic in Norway. Second, to investigate the association between HL and the knowledge and behavior relevant for preventing spread of the virus. Third, to explore variables associated with HRQoL in a pandemic environment.\n\nMethodsThis cross-sectional study includes survey data from 2,205 Norwegian adolescents 16-19 years of age. The participants reported on their health information sources, HL, handwashing knowledge and behavior, number of social interactions, and HRQoL. Associations between study variables and specified outcomes were explored using multiple linear and logistic regression analyses.\n\nResultsTelevision (TV) and family were indicated to be the main sources for pandemic-related health information. Handwashing, physical distancing, and limiting the number of social contacts were the most frequently reported measures. HL and handwashing knowledge and HL and handwashing behavior were significantly associated. For each unit increase on the HL scale, the participants were 5% more likely to socialize less with friends in comparison to normal. The mean HRQoL was very poor compared to European norms. Being quarantined or isolated and having confirmed or suspected Covid-19 were significantly negatively associated with HRQoL, but seeing less friends than normal was not associated. HL was significantly positively associated with HRQoL, albeit of minor clinical importance.\n\nConclusionAdolescents follow the health authorities guidelines and appear highly literate. However, high fidelity requires great sacrifice because the required measures seem to collide with certain aspects that are important for the adolescents HRQoL.\n\nImplications and contributionThis study is among the first to investigate health information sources and knowledge, health literacy, protective measures, and health-related quality of life (HRQoL) among adolescents during the Covid-19 pandemic. It identifies that the participating adolescents have high health literacy and knowledge about preventing the spread of the virus but that, at the same time, their HRQoL is poor.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Kirsti Riiser",
-        "author_inst": "OsloMet -Oslo Metropolitan University"
-      },
-      {
-        "author_name": "Solvi Helseth",
-        "author_inst": "OsloMet -Oslo Metropolitan University"
-      },
-      {
-        "author_name": "Kristin Haraldstad",
-        "author_inst": "University of Agder"
-      },
-      {
-        "author_name": "Astrid Torbjornsen",
-        "author_inst": "OsloMet -Oslo Metropolitan University"
-      },
-      {
-        "author_name": "Kare Ronn Richardsen",
-        "author_inst": "OsloMet -Oslo Metropolitan University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.07.09.196618",
     "rel_title": "A Strategy to Treat COVID-19 Disease with Targeted Delivery of Inhalable Liposomal Hydroxychloroquine: A Non-clinical Pharmacokinetic Study",
@@ -1308834,6 +1308076,65 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2020.07.09.194027",
+    "rel_title": "Severely ill COVID-19 patients display augmented functional properties in SARS-CoV-2-reactive CD8+ T cells",
+    "rel_date": "2020-07-10",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.09.194027",
+    "rel_abs": "The molecular properties of CD8+ T cells that respond to SARS-CoV-2 infection are not fully known. Here, we report on the single-cell transcriptomes of >80,000 virus-reactive CD8+ T cells from 39 COVID-19 patients and 10 healthy subjects. COVID-19 patients segregated into two groups based on whether the dominant CD8+ T cell response to SARS-CoV-2 was  exhausted or not. SARS-CoV-2-reactive cells in the exhausted subset were increased in frequency and displayed lesser cytotoxicity and inflammatory features in COVID-19 patients with mild compared to severe illness. In contrast, SARS-CoV-2-reactive cells in the non-exhausted subsets from patients with severe disease showed enrichment of transcripts linked to co-stimulation, pro-survival NF-{kappa}B signaling, and anti-apoptotic pathways, suggesting the generation of robust CD8+ T cell memory responses in patients with severe COVID-19 illness. CD8+ T cells reactive to influenza and respiratory syncytial virus from healthy subjects displayed polyfunctional features. Cells with such features were mostly absent in SARS-CoV-2 responsive cells from both COVID-19 patients and healthy controls non-exposed to SARS-CoV-2. Overall, our single-cell analysis revealed substantial diversity in the nature of CD8+ T cells responding to SARS-CoV-2.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Anthony Kusnadi",
+        "author_inst": "La Jolla Institute for Immunology"
+      },
+      {
+        "author_name": "Ciro Ram\u00edrez-Su\u00e1stegui",
+        "author_inst": "La Jolla Institute for Immunology"
+      },
+      {
+        "author_name": "Vicente Fajardo",
+        "author_inst": "La Jolla Institute for Immunology"
+      },
+      {
+        "author_name": "Serena J Chee",
+        "author_inst": "University of Southampton"
+      },
+      {
+        "author_name": "Benjamin J Meckiff",
+        "author_inst": "La Jolla Institute for Immunology"
+      },
+      {
+        "author_name": "Hayley Simon",
+        "author_inst": "La Jolla Institute for Immunology"
+      },
+      {
+        "author_name": "Emanuela Pelosi",
+        "author_inst": "University Hospital Southampton"
+      },
+      {
+        "author_name": "Gr\u00e9gory Seumois",
+        "author_inst": "La Jolla Institute for Immunology"
+      },
+      {
+        "author_name": "Ferhat Ay",
+        "author_inst": "La Jolla Institute for Immunology"
+      },
+      {
+        "author_name": "Pandurangan Vijayanand",
+        "author_inst": "La Jolla Institute for Immunology"
+      },
+      {
+        "author_name": "Christian H Ottensmeier",
+        "author_inst": "La Jolla Institute for Immunology"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2020.07.09.196386",
     "rel_title": "Replication-competent vesicular stomatitis virus vaccine vector protects against SARS-CoV-2-mediated pathogenesis",
@@ -1310651,89 +1309952,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2020.07.09.195263",
-    "rel_title": "Structures of potent and convergent neutralizing antibodies bound to the SARS-CoV-2 spike unveil a unique epitope responsible for exceptional potency",
-    "rel_date": "2020-07-09",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.09.195263",
-    "rel_abs": "Understanding the mechanism of neutralizing antibodies (NAbs) against SARS-CoV-2 is critical for effective vaccines and therapeutics development. We recently reported an exceptionally potent NAb, BD-368-2, and revealed the existence of VH3-53/VH3-66 convergent NAbs in COVID-19. Here we report the 3.5-[A] cryo-EM structure of BD-368-2s Fabs in complex with a mutation-induced prefusion-state-stabilized spike trimer. Unlike VH3-53/VH3-66 NAbs, BD-368-2 fully blocks ACE2 binding by occupying all three receptor-binding domains (RBDs) simultaneously, regardless of their \"up\" and \"down\" positions. BD-368-2 also triggers fusogenic-like structural rearrangements of the spike trimer, which could impede viral entry. Moreover, BD-368-2 completely avoids the common epitope of VH3-53/VH3-66 NAbs, evidenced by multiple crystal structures of their Fabs in tripartite complexes with RBD, suggesting a new way of pairing potent NAbs to prevent neutralization escape. Together, these results rationalize a unique epitope that leads to exceptional neutralization potency, and provide guidance for NAb therapeutics and vaccine designs against SARS-CoV-2.",
-    "rel_num_authors": 17,
-    "rel_authors": [
-      {
-        "author_name": "Shuo Du",
-        "author_inst": "Peking University"
-      },
-      {
-        "author_name": "Yunlong Cao",
-        "author_inst": "Peking University"
-      },
-      {
-        "author_name": "Qinyu Zhu",
-        "author_inst": "Peking University"
-      },
-      {
-        "author_name": "Guopeng Wang",
-        "author_inst": "Peking University"
-      },
-      {
-        "author_name": "Xiaoxia Du",
-        "author_inst": "Peking University"
-      },
-      {
-        "author_name": "Runsheng He",
-        "author_inst": "Peking University"
-      },
-      {
-        "author_name": "Hua Xu",
-        "author_inst": "Peking University"
-      },
-      {
-        "author_name": "Yinghui Zheng",
-        "author_inst": "Peking University"
-      },
-      {
-        "author_name": "Bo Wang",
-        "author_inst": "Peking University"
-      },
-      {
-        "author_name": "Yali Bai",
-        "author_inst": "Peking University"
-      },
-      {
-        "author_name": "Chenggong Ji",
-        "author_inst": "Peking University"
-      },
-      {
-        "author_name": "Ayijiang Yisimayi",
-        "author_inst": "Peking University"
-      },
-      {
-        "author_name": "Qisheng Wang",
-        "author_inst": "Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute"
-      },
-      {
-        "author_name": "Ning Gao",
-        "author_inst": "Peking University"
-      },
-      {
-        "author_name": "Sunney Xie",
-        "author_inst": "Peking University"
-      },
-      {
-        "author_name": "Xiao-dong Su",
-        "author_inst": "Peking University"
-      },
-      {
-        "author_name": "Junyu Xiao",
-        "author_inst": "Peking University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2020.07.09.193722",
     "rel_title": "Comprehensive variant and haplotype landscapes of 50,500 global SARS-CoV-2 isolates and accelerating accumulation of country-private variant profiles",
@@ -1311167,6 +1310385,89 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2020.07.09.195230",
+    "rel_title": "Human angiotensin-converting enzyme 2 transgenic mice infected with SARS-CoV-2 develop severe and fatal respiratory disease",
+    "rel_date": "2020-07-09",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.09.195230",
+    "rel_abs": "ABSTRACTThe emergence of SARS-CoV-2 has created an international health crisis. Small animal models mirroring SARS-CoV-2 human disease are essential for medical countermeasure (MCM) development. Mice are refractory to SARS-CoV-2 infection due to low affinity binding to the murine angiotensin-converting enzyme 2 (ACE2) protein. Here we evaluated the pathogenesis of SARS-CoV-2 in male and female mice expressing the human ACE2 gene under the control of the keratin 18 promotor. In contrast to non-transgenic mice, intranasal exposure of K18-hACE2 animals to two different doses of SARS-CoV-2 resulted in acute disease including weight loss, lung injury, brain infection and lethality. Vasculitis was the most prominent finding in the lungs of infected mice. Transcriptomic analysis from lungs of infected animals revealed increases in transcripts involved in lung injury and inflammatory cytokines. In the lower dose challenge groups, there was a survival advantage in the female mice with 60% surviving infection whereas all male mice succumbed to disease. Male mice that succumbed to disease had higher levels of inflammatory transcripts compared to female mice. This is the first highly lethal murine infection model for SARS-CoV-2. The K18-hACE2 murine model will be valuable for the study of SARS-CoV-2 pathogenesis and the assessment of MCMs.Competing Interest StatementThe authors have declared no competing interest.View Full Text",
+    "rel_num_authors": 17,
+    "rel_authors": [
+      {
+        "author_name": "Joseph Golden",
+        "author_inst": "United States Army Medical Research Institute of Infectious Diseases"
+      },
+      {
+        "author_name": "Curtis Cline",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "Xiankun Zeng",
+        "author_inst": "Fort Detrick"
+      },
+      {
+        "author_name": "Aura Garrison",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "Brian Carey",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "Eric Mucker",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "Lauren White",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "Joshua Shamblin",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "Rebecca Brocato",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "Jun Liu",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "April Babka",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "Hypaitia Rauch",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "Jeffrey M Smith",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "Bradley Hollidge",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "Collin Fitzpatrick",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "Catherine Badger",
+        "author_inst": "USAMRIID"
+      },
+      {
+        "author_name": "Jay Hooper",
+        "author_inst": "USAMRIID"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2020.07.07.20148239",
     "rel_title": "Rapid Systematic Review Exploring Historical and Present Day National and International Governance during Pandemics",
@@ -1312536,93 +1311837,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.07.07.20148163",
-    "rel_title": "Epidemiology of SARS-CoV-2 Emergence Amidst Community-Acquired Respiratory Viruses",
-    "rel_date": "2020-07-08",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.07.20148163",
-    "rel_abs": "BackgroundSARS-CoV-2 emerged in China in December 2019 as new cause of severe viral pneumonia (CoVID-19) reaching Europe by late January 2020. We validated the WHO-recommended assay and describe the epidemiology of SARS-CoV-2 and community-acquired respiratory viruses (CARVs).\n\nMethodsNaso-oropharyngeal swabs (NOPS) from 7663 individuals were prospectively tested by the Basel-S-gene and the WHO-based E-gene-assay (Roche) using Basel-N-gene-assay for confirmation. CARVs were tested in 2394 NOPS by multiplex-NAT, including 1816 together with SARS-CoV-2.\n\nResultsBasel-S-gene and Roche-E-gene-assays were concordant in 7475 cases (97.5%) including 825 (11%) positive samples. In 188 (2.5%) discordant cases, SARS-CoV-2 loads were significantly lower than in concordant positive ones and confirmed in 105 NOPS. Adults were more likely to test positive for SARS-CoV-2, while children were more likely to test CARV-positive. CARV co-infections with SARS-CoV-2 occurred in 1.8%. SARS-CoV-2 replaced other CARVs within 3 weeks reaching 48% of all detected respiratory viruses followed by rhino/enterovirus (13%), influenzavirus (12%), coronavirus (9%), respiratory syncytial (6%) and metapneumovirus (6%).\n\nConclusionsThe differential diagnosis for respiratory infections was broad during the early pandemic, affecting infection control and treatment decisions. We discuss the role of pre-existing immunity and competitive CARV replication for the epidemiology of SARS-CoV-2 infection among adults and children.",
-    "rel_num_authors": 18,
-    "rel_authors": [
-      {
-        "author_name": "Karoline Leuzinger",
-        "author_inst": "University of Basel and University Hospital Basel"
-      },
-      {
-        "author_name": "Tim Roloff",
-        "author_inst": "University Hospital Basel"
-      },
-      {
-        "author_name": "Rainer Gosert",
-        "author_inst": "University Hospital Basel"
-      },
-      {
-        "author_name": "Kirstine Soegaard",
-        "author_inst": "University Hospital Basel"
-      },
-      {
-        "author_name": "Klaudia Naegele",
-        "author_inst": "University Hospital Basel"
-      },
-      {
-        "author_name": "Katharina Rentsch",
-        "author_inst": "University Hospital Basel"
-      },
-      {
-        "author_name": "Roland Bingisser",
-        "author_inst": "University Hospital Basel"
-      },
-      {
-        "author_name": "Christian Nickel",
-        "author_inst": "University Hospital Basel"
-      },
-      {
-        "author_name": "Hans Pargger",
-        "author_inst": "University Hospital Basel"
-      },
-      {
-        "author_name": "Stefano Bassetti",
-        "author_inst": "University Hospital Basel"
-      },
-      {
-        "author_name": "Julia Anna Bielicki",
-        "author_inst": "University Children Hospital Basel"
-      },
-      {
-        "author_name": "Nina Khanna",
-        "author_inst": "University Hospital Basel"
-      },
-      {
-        "author_name": "Sarah Tschudin Sutter",
-        "author_inst": "University Hospital Basel"
-      },
-      {
-        "author_name": "Andreas Widmer",
-        "author_inst": "University Hospital Basel"
-      },
-      {
-        "author_name": "Vladimira Hinic",
-        "author_inst": "University Hospital Basel"
-      },
-      {
-        "author_name": "Manuel Battegay",
-        "author_inst": "University Hospital Basel"
-      },
-      {
-        "author_name": "Adrian Egli",
-        "author_inst": "University Hospital Basel"
-      },
-      {
-        "author_name": "Hans H Hirsch",
-        "author_inst": "University of Basel"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.07.07.20146902",
     "rel_title": "Joint Detection of Serum IgM/IgG Antibody is An Important Key to Clinical Diagnosis of SARS-COV-2 Infection",
@@ -1312941,6 +1312155,33 @@
     "type": "new results",
     "category": "genetics"
   },
+  {
+    "rel_doi": "10.1101/2020.07.07.186122",
+    "rel_title": "Towards the design of multiepitope-based peptide vaccine candidate against SARS-CoV-2",
+    "rel_date": "2020-07-08",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.07.186122",
+    "rel_abs": "Coronavirus disease 2019 is a current pandemic health threat especially for elderly patients with comorbidities. This respiratory disease is caused by a beta coronavirus known as severe acute respiratory syndrome coronavirus 2. The disease can progress into acute respiratory distress syndrome that can be fatal. Currently, no specific drug or vaccine are available to combat this pandemic outbreak. Social distancing and lockdown have been enforced in many places worldwide. The spike protein of coronavirus 2 is essential for viral entry into host target cells via interaction with angiotensin converting enzyme 2. This viral protein is considered a potential target for design and development of a drug or vaccine. Previously, we have reported several potential epitopes on coronavirus 2 spike protein with high antigenicity, low allergenicity and good stability against specified proteases. In the current study, we have constructed and evaluated a peptide vaccine from these potential epitopes by using in silico approach. This construct is predicted to have a protective immunogenicity, low allergenicity and good stability with minor structural flaws in model build. The population coverage of the used T-cells epitopes is believed to be high according to the employed restricted alleles. The vaccine construct can elicit efficient and long-lasting immune response as appeared through simulation analysis. This multiepitope-based peptide vaccine may represent a potential candidate against coronavirus 2. However, further in vitro and in vivo verification are required.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Hasanain Abdulhameed Odhar",
+        "author_inst": "Al-Zahrawi University College"
+      },
+      {
+        "author_name": "Salam Waheed Ahjel",
+        "author_inst": "Al-Zahrawi University College"
+      },
+      {
+        "author_name": "Suhad Sami Humadi",
+        "author_inst": "Al-Zahrawi University College"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2020.07.07.191007",
     "rel_title": "SARS-CoV-2 infection induces germinal center responses with robust stimulation of CD4 T follicular helper cells in rhesus macaques",
@@ -1314238,29 +1313479,6 @@
     "type": "new results",
     "category": "evolutionary biology"
   },
-  {
-    "rel_doi": "10.1101/2020.07.07.184374",
-    "rel_title": "Single source of pangolin CoVs with a near identical Spike RBD to SARS-CoV-2",
-    "rel_date": "2020-07-07",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.07.184374",
-    "rel_abs": "Multiple publications have independently described pangolin CoV genomes from the same batch of smuggled pangolins confiscated in Guangdong province in March, 2019. We analyzed the three metagenomic datasets that sampled this batch of pangolins and found that the two complete pangolin CoV genomes, GD_1 by Xiao et al. Nature and MP789 by Liu et al. PLoS Pathogens, were both built primarily using the 2019 dataset first described by Liu et al. Viruses. Other publications, such as Zhang et al. Current Biology and Lam et al. Nature, have also relied on this same dataset by Liu et al. Viruses for their assembly of the Guangdong pangolin CoV sequences and comparisons to SARS-CoV-2. To our knowledge, all of the published pangolin CoV genome sequences that share a highly similar Spike receptor binding domain with SARS-CoV-2 originate from this singular batch of smuggled pangolins. This raises the question of whether pangolins are truly reservoirs or hosts of SARS-CoV-2-related coronaviruses in the wild, or whether the pangolins may have contracted the CoV from another host species during trafficking. Our observations highlight the importance of requiring authors to publish their complete genome assembly pipeline and all contributing raw sequence data, particularly those supporting epidemiological investigations, in order to empower peer review and independent analysis of the sequence data. This is necessary to ensure both the accuracy of the data and the conclusions presented by each publication.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Yujia Alina Chan",
-        "author_inst": "Broad Institute of MIT & Harvard"
-      },
-      {
-        "author_name": "Shing Hei Zhan",
-        "author_inst": "University of British Columbia"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "contradictory results",
-    "category": "genomics"
-  },
   {
     "rel_doi": "10.1101/2020.07.07.192203",
     "rel_title": "A rapidly adaptable biomaterial vaccine for SARS-CoV-2",
@@ -1314455,6 +1313673,93 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pathology"
   },
+  {
+    "rel_doi": "10.1101/2020.07.05.20146878",
+    "rel_title": "Effect of Systemic Inflammatory Response to SARS-CoV-2 on Lopinavir and Hydroxychloroquine Plasma Concentrations",
+    "rel_date": "2020-07-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.05.20146878",
+    "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) leads to inflammatory cytokine release, which can downregulate the expression of metabolizing enzymes. This cascade affects drug concentrations in the plasma. We investigated the association between lopinavir (LPV) and hydroxychloroquine (HCQ) plasma concentrations and the values of acute phase inflammation marker C-reactive protein (CRP).\n\nMethodsLPV plasma concentrations were prospectively collected in 92 patients hospitalized at our institution. Lopinavir/ritonavir was administered 12-hourly, 800/200 mg on day 1, and 400/100 mg on day 2 until day 5 or 7. HCQ was given at 800 mg, followed by 400 mg after 6, 24 and 48 hours. Hematological, liver, kidney, and inflammation laboratory values were analyzed on the day of drug level determination.\n\nResultsThe median age of study participants was 59 (range 24-85) years, and 71% were male. The median duration from symptom onset to hospitalization and treatment initiation was 7 days (IQR 4-10) and 8 days (IQR 5-10), respectively. The median LPV trough concentration on day 3 of treatment was 26.5 g/mL (IQR 18.9-31.5). LPV plasma concentrations positively correlated with CRP values (r=0.37, p<0.001), and were significantly lower when tocilizumab was preadministrated. No correlation was found between HCQ concentrations and CRP values.\n\nConclusionsHigh LPV plasma concentrations were observed in COVID-19 patients. The ratio of calculated unbound drug fraction to published SARS-CoV-2 EC50 values indicated insufficient LPV concentrations in the lung. CRP values significantly correlated with LPV but not HCQ plasma concentrations, implying inhibition of cytochrome P450 3A4 (CYP3A4) metabolism by inflammation.",
+    "rel_num_authors": 18,
+    "rel_authors": [
+      {
+        "author_name": "Catia Marzolini",
+        "author_inst": "University Hospital Basel"
+      },
+      {
+        "author_name": "Felix Stader",
+        "author_inst": "University Hospital Basel"
+      },
+      {
+        "author_name": "Marcel Stoeckle",
+        "author_inst": "University Hospital Basel"
+      },
+      {
+        "author_name": "Fabian Franzeck",
+        "author_inst": "University Hospital Basel"
+      },
+      {
+        "author_name": "Adrian Egli",
+        "author_inst": "University Hospital Basel"
+      },
+      {
+        "author_name": "Stefano Bassetti",
+        "author_inst": "University Hospital Basel"
+      },
+      {
+        "author_name": "Alexa Hollinger",
+        "author_inst": "University Hospital Basel"
+      },
+      {
+        "author_name": "Michael Osthoff",
+        "author_inst": "University Hospital Basel"
+      },
+      {
+        "author_name": "Maja Weisser",
+        "author_inst": "University Hospital Basel"
+      },
+      {
+        "author_name": "Eva Caroline Gebhard",
+        "author_inst": "University Hospital Basel"
+      },
+      {
+        "author_name": "Veronika Baettig",
+        "author_inst": "University Hospital Basel"
+      },
+      {
+        "author_name": "Julia Geenen",
+        "author_inst": "University Hospital Basel"
+      },
+      {
+        "author_name": "Nina Khanna",
+        "author_inst": "University Hospital Basel"
+      },
+      {
+        "author_name": "Sarah Tschudin-Sutter",
+        "author_inst": "University Hospital Basel"
+      },
+      {
+        "author_name": "Daniel Mueller",
+        "author_inst": "University Hospital Basel"
+      },
+      {
+        "author_name": "Hans Hirsch",
+        "author_inst": "University Hospital Basel"
+      },
+      {
+        "author_name": "Manuel Battegay",
+        "author_inst": "University Hospital Basel"
+      },
+      {
+        "author_name": "Parham Sendi",
+        "author_inst": "University Hospital Basel"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "pharmacology and therapeutics"
+  },
   {
     "rel_doi": "10.1101/2020.07.05.20146779",
     "rel_title": "Rats and the COVID-19 pandemic: Early data on the global emergence of rats in response to social distancing",
@@ -1315352,53 +1314657,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.07.06.20147421",
-    "rel_title": "Impact of Congestive Heart Failure and Role of Cardiac Biomarkers in COVID-19 patients: A Systematic Review and Meta-Analysis",
-    "rel_date": "2020-07-07",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.06.20147421",
-    "rel_abs": "ImportanceCoronavirus disease 2019 (COVID-19) has been reported to cause worse outcomes in patients with underlying cardiovascular disease, especially in patients with acute cardiac injury, which is determined by elevated levels of high-sensitivity troponin. There is paucity of data on the impact of congestive heart failure (CHF) on outcomes in COVID-19 patients.\n\nObjectiveTo evaluate the occurrence of acute cardiac injury and arrhythmias and to assess the impact of pre-existing CHF and hypertension (HTN) in COVID-19 patients.\n\nData SourcesWe conducted a literature search of PubMed/Medline, EMBASE, and Google Scholar databases from 11/1/2019 till 06/07/2020. databases using following search terms or keywords: \"(COVID) AND (Clinical); ((heart) OR (myocard*)) AND (COVID); (COVID) AND (Troponin); (Coronavirus) AND (Heart).\"\n\nStudy SelectionWe identified all relevant studies reporting cardiovascular comorbidities, cardiac biomarkers, disease severity, and survival in COVID-19 patients.\n\nData Extraction and SynthesisWe followed preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines for abstracting data. Pooled data was meta-analyzed using random-effects model and between-study heterogeneity was calculated with Higgins I2 statistic.\n\nMain outcome and measuresTo assess the impact of HTN and CHF and to evaluate different cardiac biomarkers in COVID-19 patients based on their disease severity.\n\nResultsWe collected pooled data on 5,967 COVID-19 patients from 20 individual studies. We found that both non-survivors and those with severe disease had an increased risk of acute cardiac injury and cardiac arrhythmias, our pooled relative risk (RR) was -- 8.52 (95% CI 3.63- 19.98) (p<0.001); and 3.61 (95% CI 2.03-6.43) (p=0.001), respectively. Mean difference in the levels of Troponin-I, CK-MB, and NT-proBNP was higher in deceased and severely infected patients. The RR of in-hospital mortality was 2.35 (95% CI 1.18-4.70) (p=0.022) and 1.52 (95% CI 1.12-2.05) (p=0.008) among patients who had pre-existing CHF and hypertension, respectively.\n\nConclusion and RelevanceCardiac involvement in COVID-19 infection appears to significantly adversely impact patient prognosis and survival. Pre-existence of CHF, and high cardiac biomarkers like NT-pro BNP and CK-MB levels in COVID-19 patients correlates with worse outcomes.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Tarun Dalia",
-        "author_inst": "University of Kansas Health System"
-      },
-      {
-        "author_name": "Shubham Lahan",
-        "author_inst": "University College of Medical Sciences"
-      },
-      {
-        "author_name": "Sagar Ranka",
-        "author_inst": "University of Kansas Health System"
-      },
-      {
-        "author_name": "Prakash Acharya",
-        "author_inst": "University of Kansas Health System"
-      },
-      {
-        "author_name": "Archana Gautam",
-        "author_inst": "University of Kansas Health System"
-      },
-      {
-        "author_name": "Ioannis Mastoris",
-        "author_inst": "University of Kansas Health System"
-      },
-      {
-        "author_name": "Andrew Sauer",
-        "author_inst": "University of Kansas Health System"
-      },
-      {
-        "author_name": "Zubair Shah",
-        "author_inst": "University of Kansas Health System"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "cardiovascular medicine"
-  },
   {
     "rel_doi": "10.1101/2020.07.07.20147934",
     "rel_title": "Chest X-Ray Has Poor Diagnostic Accuracy and Prognostic Significance in COVID-19: A Propensity Matched Database Study",
@@ -1315685,6 +1314943,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.07.05.20146837",
+    "rel_title": "Change points in the spread of COVID-19 question the effectiveness of nonpharmaceutical interventions in Germany",
+    "rel_date": "2020-07-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.05.20146837",
+    "rel_abs": "AimsNonpharmaceutical interventions against the spread of SARS-CoV-2 in Germany included the cancellation of mass events (from March 8), closures of schools and child day care facilities (from March 16) as well as a \"lockdown\" (from March 23). This study attempts to assess the effectiveness of these interventions in terms of revealing their impact on infections over time.\n\nMethodsDates of infections were estimated from official German case data by incorporating the incubation period and an empirical reporting delay. Exponential growth models for infections and reproduction numbers were estimated and investigated with respect to change points in the time series.\n\nResultsA significant decline of daily and cumulative infections as well as reproduction numbers is found at March 8 (CI [7, 9]), March 10 (CI [9, 11] and March 3 (CI [2, 4]), respectively. Further declines and stabilizations are found in the end of March. There is also a change point in new infections at April 19 (CI [18, 20]), but daily infections still show a negative growth. From March 19 (CI [18, 20]), the reproduction numbers fluctuate on a level below one.\n\nConclusionsThe decline of infections in early March 2020 can be attributed to relatively small interventions and voluntary behavioural changes. Additional effects of later interventions cannot be detected clearly. Liberalizations of measures did not induce a re-increase of infections. Thus, the effectiveness of most German interventions remains questionable. Moreover, assessing of interventions is impeded by the estimation of true infection dates and the influence of test volume.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Thomas Wieland",
+        "author_inst": "Karlsruhe Institute of Technology"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.07.06.20147660",
     "rel_title": "Predicted effects of summer holidays and seasonality on the SARS-Cov-2 epidemic in France",
@@ -1316794,29 +1316071,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.07.04.20146423",
-    "rel_title": "Explainable death toll motion modeling: COVID-19 narratives and counterfactuals",
-    "rel_date": "2020-07-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.04.20146423",
-    "rel_abs": "Models have gained the spotlight in many discussions surrounding COVID-19. The urgency for timely decisions resulted in a multitude of models as informed policy actions must be made even when so many uncertainties about the pandemic still remain. In this paper, we use machine learning algorithms to build intuitive country-level COVID-19 motion models described by death toll velocity and acceleration. Model explainability techniques provide insightful data-driven narratives about COVID-19 death toll motion models - while velocity is explained by factors that are increasing/reducing death toll pace now, acceleration anticipates the effects of public health measures on slowing the death toll pace. This allows policymakers and epidemiologists to understand factors driving the outbreak and to evaluate the impacts of different public health measures. Finally, our models also predict counterfactuals in order to face the challenge of estimating what is likely to happen as a result of an action.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Adriano Veloso",
-        "author_inst": "Universidade Federal de Minas Gerais"
-      },
-      {
-        "author_name": "Nivio Ziviani",
-        "author_inst": "Kunumi, Universidade Federal de Minas Gerais"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.07.05.20146324",
     "rel_title": "Study of the Dependence of Effective Reproduction Number of COVID-19 on the Temperature and Humidity: A Case Study with the Indian States",
@@ -1317103,6 +1316357,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "intensive care and critical care medicine"
   },
+  {
+    "rel_doi": "10.1101/2020.07.03.20145912",
+    "rel_title": "Ultraviolet A Radiation and COVID-19 Deaths: A Multi Country Study",
+    "rel_date": "2020-07-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.03.20145912",
+    "rel_abs": "ObjectivesTo determine whether UVA exposure might be associated with COVID-19 deaths\n\nDesignEcological regression, with replication in two other countries and pooled estimation\n\nSetting2,474 counties of the contiguous USA, 6,755 municipalities in Italy, 6,274 small areas in England. Only small areas in their  Vitamin D winter (monthly mean UVvitd of under 165 KJ/m2) from Jan to April 2020.\n\nParticipants\n\nThe  at-risk population is the total small area population, with measures to incorporate spatial infection into the model. The model is adjusted for potential confounders including long-term winter temperature and humidity.\n\nMain outcome measuresWe derive UVA measures for each area from remote sensed data and estimate their relationship with COVID-19 mortality with a random effect for States, in a multilevel zero-inflated negative binomial model. In the USA and England death certificates had to record COVID-19. In Italy excess deaths in 2020 over expected from 2015-19.\n\nData sourcesSatellite derived mean daily UVA dataset from Japan Aerospace Exploration Agency. Data on deaths compiled by Center for Disease Control (USA), Office for National Statistics (England) and Italian Institute of Statistics.\n\nResultsDaily mean UVA (January-April 2020) varied between 450 to 1,000 KJ/m2 across the three countries. Our fully adjusted model showed an inverse correlation between UVA and COVID-19 mortality with a Mortality Risk Ratio (MRR) of 0.71 (0.60 to 0.85) per 100KJ/m2 increase UVA in the USA, 0.81 (0.71 to 0.93) in Italy and 0.49 (0.38 to 0.64) in England. Pooled MRR was 0.68 (0.52 to 0.88).\n\nConclusionsOur analysis, replicated in 3 independent national datasets, suggests ambient UVA exposure is associated with lower COVID-19 specific mortality. This effect is independent of vitamin D, as it occurred at irradiances below that likely to induce significant cutaneous vitamin D3 synthesis. Causal interpretations must be made cautiously in observational studies. Nonetheless this study suggests strategies for reduction of COVID-19 mortality.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Mark Cherrie",
+        "author_inst": "University of Edinburgh"
+      },
+      {
+        "author_name": "Tom Clemens",
+        "author_inst": "University of Edinburgh"
+      },
+      {
+        "author_name": "Claudio Colandrea",
+        "author_inst": "University of Edinburgh"
+      },
+      {
+        "author_name": "Zhiqiang Feng",
+        "author_inst": "University of Edinburgh"
+      },
+      {
+        "author_name": "David Webb",
+        "author_inst": "University of Edinburgh"
+      },
+      {
+        "author_name": "Chris Dibben",
+        "author_inst": "University of Edinburgh"
+      },
+      {
+        "author_name": "Richard B Weller",
+        "author_inst": "University of Edinburgh"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.07.05.187344",
     "rel_title": "N and O glycosylation of the SARS-CoV-2 spike protein",
@@ -1318104,61 +1317401,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2020.07.03.20146035",
-    "rel_title": "Age Matters: COVID-19 Prevalence in a Vaping Adolescent Population - An Observational Study",
-    "rel_date": "2020-07-04",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.03.20146035",
-    "rel_abs": "BackgroundCurrently, there is limited or no data demonstrating that vaping is associated with increased transmission or prevalence of coronavirus disease-2019 (COVID-19). Our study aims to investigate the relationship of vaping with the prevalence of COVID-19 infection across the United States and in the District of Columbia.\n\nMethodsCOVID-19 case counts by state and the District of Columbia were obtained via the Worldometers website on 04/30/2020. Prevalence of COVID-19 cases per 100,000 residents were calculated using estimated 2019 population data from the US Census Department. Age ranges analyzed were: high school age children, Ages 18-24, Ages 25-44, and Ages 45-65. Spearman correlation analysis was conducted to determine if the rate of vaping was correlated with a higher prevalence of COVID-19 cases per 100,000 population.\n\nFindingsThe Spearman correlation analysis demonstrated that persons vaping between 18 years and 24 years of age had a correlation coefficient of 0.278 with prevalence of COVID-19 infection (p=0.048). Vaping high school students had a correlation coefficient of 0.153 with prevalence of COVID-19 (p=0.328). Persons vaping in the age group 25-45 years had a correlation coefficient of 0.101 in association to COVID-19 prevalence (p=0.478). And finally, persons vaping between the age 45-65 years old had a correlation coefficient 0.130 with respect to COVID-19 prevalence (p=0.364).\n\nInterpretationIncreased COVID-19 prevalence is associated with vaping in the adolescent population between ages 18 and 24. Further prospective studies need to be performed in order investigate the severity of outcomes of vaping in association with COVID-19 infection.\n\nFundingNothing to disclose.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Nitin Tandan",
-        "author_inst": "Southern Illinois University School of Medicine"
-      },
-      {
-        "author_name": "Manjari Rani Regmi",
-        "author_inst": "Southern Illinois University School of Medicine"
-      },
-      {
-        "author_name": "Ruby Maini",
-        "author_inst": "Southern Illinois University School of Medicine"
-      },
-      {
-        "author_name": "Abdisamad M. Ibrahim",
-        "author_inst": "Southern Illinois University School of Medicine"
-      },
-      {
-        "author_name": "Cameron Koester",
-        "author_inst": "Southern Illinois University School of Medicine"
-      },
-      {
-        "author_name": "Odalys Estefania Lara Garcia",
-        "author_inst": "Southern Illinois University School of Medicine"
-      },
-      {
-        "author_name": "Priyanka Parajuli",
-        "author_inst": "Southern Illinois University School of Medicine"
-      },
-      {
-        "author_name": "Mohammad Al-Akchar",
-        "author_inst": "Southern Illinois University School of Medicine"
-      },
-      {
-        "author_name": "Abhishek Kulkarni",
-        "author_inst": "Southern Illinois University School of Medicine"
-      },
-      {
-        "author_name": "Robert Robinson",
-        "author_inst": "SIU School of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "respiratory medicine"
-  },
   {
     "rel_doi": "10.1101/2020.07.03.20145953",
     "rel_title": "Optimal sample pooling: an efficient tool against SARS-CoV-2",
@@ -1318525,6 +1317767,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "dermatology"
   },
+  {
+    "rel_doi": "10.1101/2020.07.03.20145763",
+    "rel_title": "Oxygen and mortality in COVID-19 pneumonia: a comparative analysis of supplemental oxygen policies and health outcomes across 26 countries.",
+    "rel_date": "2020-07-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.03.20145763",
+    "rel_abs": "IntroductionHypoxia is the main cause of morbidity and mortality in COVID-19. During the COVID-19 pandemic some countries have reduced access to supplemental oxygen (e.g. oxygen rationing), whereas other nations have maintained and even improved access to supplemental oxygen. We examined whether such variation in the access to supplemental oxygen had any bearing on mortality in COVID-19.\n\nMethodsThree independent investigators searched for, identified and extracted the nationally recommended target oxygen levels for the commencement of oxygen in COVID-19 pneumonia from the 29 worst affected countries. Mortality estimates were calculated from three independent sources. We then applied linear regression analysis to examine for potential association between national targets for the commencement of oxygen and case fatality rates.\n\nResultsOf the 26 nations included, 15 had employed conservative oxygen strategies to manage COVID-19 pneumonia. Of them, Belgium, France, USA, Canada, China, Germany, Mexico, Spain, Sweden and the UK guidelines advised commencing oxygen when oxygen saturations (SpO2) fell to 91% or less. Target SpO2 ranged from 92% to 95% in the other 16 nations. Linear regression analysis demonstrated a strong inverse correlation between the national target for the commencement of oxygen and national case fatality rates (Spearmans Rho = -0.622, p < 0.001).\n\nConclusionOur study highlights the disparity in oxygen provision for COVID-19 patients between the nations analysed, and indicates such disparity in access to supplemental oxygen may represent a modifiable factor associated with mortality during the pandemic.\n\nKey MessagesO_ST_ABSWhat is already known?C_ST_ABSO_LIThere were no prospective clinical trials we could identify relating to COVID-19 and supplemental oxygen, nor any published studies examining access to supplemental oxygen and mortality in COVID-19.\nC_LIO_LIThere are a number of studies identifying an association with low oxygen saturations at presentation and mortality in COVID-19 pneumonia.\nC_LIO_LIThere is good quality evidence that a delay in the correction of hypoxia in pneumonia increases mortality.\nC_LI\n\nWhat are the new findings?O_LIThis study highlights the different thresholds for commencing supplemental oxygen in patients with COVID-19 across 26 nations.\nC_LIO_LIThose countries that provide better access to supplemental oxygen have a statistically significant lower mortality rate.\nC_LIO_LIOur results support the consensus view that improving access to supplemental oxygen in COVID-19 pneumonia is likely to reduce mortality.\nC_LI",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "- The Gibraltar COVID-19 Research Group: Health Systems",
+        "author_inst": ""
+      },
+      {
+        "author_name": "Daniel Goyal",
+        "author_inst": "University of Gibraltar, Medicine and Public Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "emergency medicine"
+  },
   {
     "rel_doi": "10.1101/2020.07.03.20146159",
     "rel_title": "Sub-epidemic model forecasts for COVID-19 pandemic spread in the USA and European hotspots, February-May 2020",
@@ -1319554,33 +1318819,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.07.02.20145367",
-    "rel_title": "Early COVID-19 Interventions Failed to Replicate St. Louis vs. Philadelphia Outcomes in the United States",
-    "rel_date": "2020-07-04",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.02.20145367",
-    "rel_abs": "The Coronavirus disease 2019 (COVID-19) pandemic has elicited an abrupt pause in the United States in multiple sectors of commerce and social activity. As the US faces this health crisis, the magnitude, and rigor of their initial public health response was unprecedented. As a response, the entire nation shutdown at the state-level for the duration of approximately one to three months. These public health interventions, however, were not arbitrarily decided, but rather, implemented as a result of evidence-based practices. These practices were a result of lessons learned during the 1918 influenza pandemic and the city-level non-pharmaceutical interventions (NPIs) taken across the US. During the 1918 pandemic, two model cities, St. Louis, MO, and Philadelphia, PA, carried out two different approaches to address the spreading disease, which resulted in two distinctly different outcomes. Our group has evaluated the state-level public health response adopted by states across the US, with a focus on New York, California, Florida, and Texas, and compared the effectiveness of reducing the spread of COVID-19. Our assessments show that while the states mentioned above benefited from the implementations of early preventative measures, they inadequately replicated the desired outcomes observed in St. Louis during the 1918 crisis. Our study indicates that there are other factors, including health disparities that may influence the effectiveness of public health interventions applied. Identifying more specific health determinants may help implement targeted interventions aimed at preventing the spread of COVID-19 and improving health equity.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Aliea M. Jalali",
-        "author_inst": "Grand Canyon University"
-      },
-      {
-        "author_name": "Brent M. Peterson",
-        "author_inst": "Biola University"
-      },
-      {
-        "author_name": "Thushara Galbadage",
-        "author_inst": "Biola University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.07.03.20145607",
     "rel_title": "The mental health impact of the covid-19 pandemic onhealthcare workers, and interventions to help them: a rapid systematic review",
@@ -1319847,6 +1319085,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
+  {
+    "rel_doi": "10.1101/2020.07.02.20144899",
+    "rel_title": "Curve-fitting approach for COVID-19 data and its physical background",
+    "rel_date": "2020-07-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.02.20144899",
+    "rel_abs": "Forecast of the peak-out and settling timing of COVID-19 at an early stage should help the people how to cope with the situation. Curve-fitting method with an asymmetric log-normal function has been applied to daily confirmed cases data in various countries. Most of the curve-fitting could show good forecasts, while the reason has not been clearly shown. The K value has recently been proposed which can provide good reasoning of curve-fitting mechanism by corresponding a long and steep slope on the K curve with fitting stability. Since K can be expressed by a time differential of logarithmic total cases, the physical background of the above correspondence was discussed in terms of the growth rate in epidemic entropy.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Yoshiro Nishimoto",
+        "author_inst": "Science Research Group"
+      },
+      {
+        "author_name": "Kenichi Inoue",
+        "author_inst": "KOBELCO Research Institute, Inc."
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health informatics"
+  },
   {
     "rel_doi": "10.1101/2020.07.02.20144857",
     "rel_title": "Metabolic indicators associated with non-communicable diseases deteriorated in COVID-19 outbreak: evidence from a two-center, retrospective study",
@@ -1321112,65 +1320373,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.07.02.20145102",
-    "rel_title": "Methodological Rigor in COVID-19 Clinical Research: A Systematic Review and Case-Control Analysis",
-    "rel_date": "2020-07-03",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.02.20145102",
-    "rel_abs": "ObjectiveTo systematically evaluate the quality of reporting of currently available COVID-19 studies compared to historical controls.\n\nDesignA systematic review and case-control analysis\n\nData sourcesMEDLINE, Embase, and Cochrane Central Register of Controlled Trials until May 14, 2020\n\nStudy selectionAll original clinical literature evaluating COVID-19 or SARS-CoV2 were identified and 1:1 historical control of the same study type in the same published journal was matched from the previous year\n\nData extractionTwo independent reviewers screened titles, abstracts, and full-texts and independently assessed methodological quality using Cochrane Risk of Bias Tool, Newcastle- Ottawa Scale, QUADAS-2 Score, or case series checklist.\n\nResults9895 titles and abstracts were screened and 686 COVID-19 articles were included in the final analysis in which 380 (55.4%) were case series, 199 (29.0%) were cohort, 63 (9.2%) were diagnostic, 38 (5.5%) were case-control, and 6 (0.9%) were randomized controlled trials. Overall, high quality/low-bias studies represented less than half of COVID-19 articles - 49.0% of case series, 43.9% of cohort, 31.6% of case-control, and 6.4% of diagnostic studies. We matched 539 control articles to COVID-19 articles from the same journal in the previous year for a final analysis of 1078 articles. The median time to acceptance was 13.0 (IQR, 5.0-25.0) days in COVID-19 articles vs. 110.0 (IQR, 71.0-156.0) days in control articles (p<0.0001). Overall, methodological quality was lower in COVID-19 articles with 220 COVID-19 articles of high quality (41.0%) vs. 392 control articles (73.3%, p<0.0001) with similar results when stratified by study design. In both unadjusted and adjusted logistic regression, COVID-19 articles were associated with lower methodological quality (odds ratio, 0.25; 95% CI, 0.20 to 0.33, p<0.0001).\n\nConclusionCurrently published COVID-19 studies were accepted more quickly and were found to be of lower methodological quality than comparative studies published in the same journal. Given the implications of these studies to medical decision making and government policy, greater effort to appropriately weigh the existing evidence in the context of emerging high-quality research is needed.\n\nStudy registrationPROSPERO: CRD42020187318",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Richard G Jung",
-        "author_inst": "University of Ottawa Heart Institute"
-      },
-      {
-        "author_name": "Pietro Di Santo",
-        "author_inst": "University of Ottawa Heart Institute"
-      },
-      {
-        "author_name": "Cole Clifford",
-        "author_inst": "University of Ottawa Heart Institute"
-      },
-      {
-        "author_name": "Graeme Prosperi-Porta",
-        "author_inst": "Cumming School of Medicine"
-      },
-      {
-        "author_name": "Stephanie Skanes",
-        "author_inst": "University of Ottawa Heart Institute"
-      },
-      {
-        "author_name": "Annie Hung",
-        "author_inst": "The Ottawa Hospital"
-      },
-      {
-        "author_name": "Simon Parlow",
-        "author_inst": "University of Ottawa Heart Institute"
-      },
-      {
-        "author_name": "Sarah Visintini",
-        "author_inst": "University of Ottawa Heart Institute"
-      },
-      {
-        "author_name": "F. Daniel Ramirez",
-        "author_inst": "University of Bordeaux"
-      },
-      {
-        "author_name": "Trevor Simard",
-        "author_inst": "University of Ottawa Heart Institute"
-      },
-      {
-        "author_name": "Benjamin Hibbert",
-        "author_inst": "University of Ottawa Heart Institute"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.06.30.20140715",
     "rel_title": "Indication for SARS-CoV-2 serology: first month follow-up",
@@ -1321441,6 +1320643,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.06.30.20143149",
+    "rel_title": "Orthogonal Functions for Evaluating Social Distancing Impact on CoVID-19 Spread",
+    "rel_date": "2020-07-03",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.30.20143149",
+    "rel_abs": "Early CoVID-19 growth often obeys: [Formula], with Ko = [(ln 2)/(tdbl)], where tdbl is the pandemic doubling time, prior to society-wide Social Distancing. Previously, we modeled Social Distancing with tdbl as a linear function of time, where N [t] 1 {approx} exp[+KA t/ (1+,{gamma}ot)] is used here. Additional parameters besides {Ko,{gamma} o} are needed to better model different{rho} [t] = dN [t]/dt shapes. Thus, a new Orthogonal Function Model [OFM] is developed here using these orthogonal function series: O_FD O_INLINEFIG[Formula 1]C_INLINEFIGM_FD(1)C_FD where N (Z) and Z[t] form an implicit N [t] N (Z[t]) function, giving: O_FD O_INLINEFIG[Formula 2]C_INLINEFIGM_FD(2)C_FD with Lm(Z) being the Laguerre Polynomials. At large MF values, nearly arbitrary functions for N [t] and{rho} [t] = dN [t]/dt can be accommodated. How to determine {KA,{gamma} o} and the {gm; m = (0, +MF)} constants from any given N (Z) dataset is derived, with{rho} [t] set by: O_FD O_INLINEFIG[Formula 3]C_INLINEFIGM_FD(3)C_FD\n\nThe bing com USA CoVID-19 data was analyzed using MF = (0, 1, 2) in the OFM. All results agreed to within about 10 percent, showing model robustness. Averaging over all these predictions gives the following overall estimates for the number of USA CoVID-19 cases at the pandemic end: O_FD O_INLINEFIG[Formula 4]C_INLINEFIGM_FD(4)C_FD which compares the pre- and post-early May bing com revisions. The CoVID-19 pandemic in Italy was examined next. The MF = 2 limit was inadequate to model the Italy{rho} [t] pandemic tail. Thus, regions with a quick CoVID-19 pandemic shutoff may have additional Social Distancing factors operating, beyond what can be easily modeled by just progressively lengthening pandemic doubling times (with 13 Figures).",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Genghmun Eng",
+        "author_inst": "Retired Scientist"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.07.01.20144329",
     "rel_title": "Low plasma 25(OH) vitamin D3 level is associated with increased risk of COVID-19 infection: an Israeli population-based study",
@@ -1322842,25 +1322063,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.06.30.20143487",
-    "rel_title": "Social-distancing effectiveness tracking of the COVID-19 hotspot Stockholm",
-    "rel_date": "2020-07-02",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.30.20143487",
-    "rel_abs": "BackgroundThe COVID-19 outbreak in Stockholm, Sweden, is characterized by a near-absence of governmental interventions and high fatalities in the care home population. This study analyses the outbreak and the social-distancing effectiveness timeline in the general population and the care homes.\n\nMethodsA novel distributed-compartmental, time-variant epidemiological model was designed specifically for COVID-19 transmission characteristics, featuring a/pre/symptomatic transmission, a non-linear hospital model, a weakly-coupled sub-model for the care-home population, and parametrized continuous social-distancing functions. The model parameters and the social-distancing timelines are determined by randomization and Monte-Carlo simulations analysing real-world data.\n\nFindingsDespite a high initial reproduction number (3{middle dot}29) and the near-absence of governmental interventions, the model quantitated that the transmission rate in the general population was suppressed by 73%, and in the care homes by 79%. The measures in the care homes took effect 4{middle dot}8 days delayed; and if applied 4 or 8 days earlier, the fatalities could have been reduced by 63{middle dot}2% or 89{middle dot}9%. The infected population is estimated to 16{middle dot}2% (June 10). An expected underestimation of population immunity by antibody studies is confirmed. The infection fatality ratio extrapolates to 0{middle dot}61% (peak: 1{middle dot}34%). The model indicates a seasonal effect which effectively suppressed a new rise. An analysed large-scale public event had no large influence. The asymptomatic ratio was determined to 35%.\n\nInterpretationThe proposed model and methods have proven to analyse a COVID-19 outbreak and to re-construct the social-distancing behaviour with unprecedented accuracy, confirming even minor details indicated by mobility-data analysis, and are applicable to other regions and other emerging infectious diseases of similar transmission characteristics. The self-regulation of the population in Stockholm, influenced by advices by the authorities, was able to suppress a COVID-19 outbreak to a level far beyond that the stringency index of governmental interventions suggests. Proper timing of effective measures in the care homes is important to reduce fatalities.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Joachim Oberhammer",
-        "author_inst": "KTH Royal Institute of Technology"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.07.01.20144279",
     "rel_title": "Using the infection fatality rate to predict the evolution of Covid-19 in Brazil",
@@ -1323051,6 +1322253,77 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.07.01.20144162",
+    "rel_title": "Mass Screening for SARS-CoV-2 Infection among Residents and Staff in Twenty-eight Long-term Care Facilities in Fulton County, Georgia",
+    "rel_date": "2020-07-02",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.01.20144162",
+    "rel_abs": "Mass screening for SARS-CoV-2 infection in long-term care facilities revealed significantly higher prevalence of infection in facilities that screened in response to a known infection compared to those that screened as a prevention measure. \"Response\" facilities had a SARS-CoV-2 prevalence of 28.9% while \"preventive\" facilities prevalence was 1.6% (p <0.001).",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Carson Ted Telford",
+        "author_inst": "Fulton County Board of Health"
+      },
+      {
+        "author_name": "Udodirim Onwubiko",
+        "author_inst": "Fulton County Board of Health"
+      },
+      {
+        "author_name": "David Holland",
+        "author_inst": "Fulton County Board of Health; Emory University Department of Medicine"
+      },
+      {
+        "author_name": "Kim Turner",
+        "author_inst": "Fulton County Board of Health"
+      },
+      {
+        "author_name": "Juliana Prieto",
+        "author_inst": "Fulton County Board of Health"
+      },
+      {
+        "author_name": "Sasha Smith",
+        "author_inst": "Fulton County Board of Health"
+      },
+      {
+        "author_name": "Jane Yoon",
+        "author_inst": "Emory University Department of Medicine"
+      },
+      {
+        "author_name": "Wecheeta Brown",
+        "author_inst": "Fulton County Board of Health"
+      },
+      {
+        "author_name": "Allison Chamberlain",
+        "author_inst": "Fulton County Board of Health; Emory University Rollins School of Public Health"
+      },
+      {
+        "author_name": "Neel Gandhi",
+        "author_inst": "Emory University Department of Medicine; Emory University Rollins School of Public Health"
+      },
+      {
+        "author_name": "Shamimul Khan",
+        "author_inst": "Fulton County Board of Health"
+      },
+      {
+        "author_name": "Steve Williams",
+        "author_inst": "Fulton County Government"
+      },
+      {
+        "author_name": "Fazle Khan",
+        "author_inst": "Fulton County Board of Health"
+      },
+      {
+        "author_name": "Sarita Shah",
+        "author_inst": "Emory University Department of Medicine; Emory University Rollins School of Public Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.06.30.20143909",
     "rel_title": "Exploring Epidemiological Behavior of Novel Coronavirus Outbreak through the Development and Analysis of COVID-19 Daily Dataset in Bangladesh",
@@ -1324224,49 +1323497,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.06.29.20142505",
-    "rel_title": "Inactivated trivalent influenza vaccine is associated with lower mortality among Covid-19 patients in Brazil",
-    "rel_date": "2020-07-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.29.20142505",
-    "rel_abs": "We analyzed data from 92,664 clinically and molecularly confirmed Covid-19 cases in Brazil to understand the potential associations between influenza vaccination and Covid-19 outcomes. Controlling for health facility of treatment, comorbidities as well as an extensive range of sociodemographic factors, we show that patients who received a recent influenza vaccine experienced on average 8% lower odds of needing intensive care treatment (95% CIs [0.86, 0.99]), 18% lower odds of requiring invasive respiratory support (0.74, 0.88) and 17% lower odds of death (0.75, 0.89). Large scale promotion of influenza vaccines seems advisable, especially in populations at high risk of severe SARS-CoV-2 infection.\n\nOne Sentence SummaryCovid-19 patients with recent influenza vaccination experience better health outcomes than non-vaccinated patients in Brazil.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Guenther Fink",
-        "author_inst": "Swiss Tropical and Public Health Institute and University of Basel, Basel, Switzerland"
-      },
-      {
-        "author_name": "Nina Orlova-Fink",
-        "author_inst": "Swiss Tropical and Public Health Institute and University of Basel, Basel, Switzerland"
-      },
-      {
-        "author_name": "Tobias Schindler",
-        "author_inst": "Swiss Tropical and Public Health Institute and University of Basel, Basel, Switzerland"
-      },
-      {
-        "author_name": "Sandra Grisi",
-        "author_inst": "Department of Pediatrics, University of Sao Paulo Medical School, Sao Paulo, Brazil"
-      },
-      {
-        "author_name": "Ana Paula Ferrer",
-        "author_inst": "Department of Pediatrics, University of Sao Paulo Medical School, Sao Paulo, Brazil"
-      },
-      {
-        "author_name": "Claudia Daubenberger",
-        "author_inst": "Swiss Tropical and Public Health Institute and University of Basel, Basel, Switzerland"
-      },
-      {
-        "author_name": "Alexandr Brentani",
-        "author_inst": "Department of Pediatrics, University of Sao Paulo Medical School, Sao Paulo, Brazil"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.06.26.20140699",
     "rel_title": "Superior anticoagulation strategies for renal replacement therapy in critically ill patients with COVID-19: a cohort study",
@@ -1324765,6 +1323995,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.06.30.20143255",
+    "rel_title": "Handyfuge-LAMP: low-cost and electricity-free centrifugation forisothermal SARS-CoV-2 detection in saliva.",
+    "rel_date": "2020-07-01",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.30.20143255",
+    "rel_abs": "Point of care diagnostics for COVID-19 detection are vital to assess infection quickly and at the source so appropriate measures can be taken. The loop-mediated isothermal amplification (LAMP) assay has proven to be a reliable and simple protocol that can detect small amounts of viral RNA in patient samples (<10 genomes per L) (Nagamine, Hase, and Notomi 2002). Recently, Rabe and Cepko at Harvard published a sensitive and simple protocol for COVID-19 RNA detection in saliva using an optimized LAMP assay (Rabe and Cepko, 2020).\n\nThis LAMP protocol has the benefits of being simple, requiring no specialized equipment; rapid, requiring less than an hour from sample collection to readout; and cheap, costing around $1 per reaction using commercial reagents. The pH based colorimetric readout also leaves little ambiguity and is intuitive. However, a shortfall in many nucleic acid-based methods for detection in saliva samples has been the variability in output due to the presence of inhibitory substances in saliva. Centrifugation to separate the reaction inhibitors from inactivated sample was shown to be an effective way to ensure reliable LAMP amplification. However, a centrifuge capable of safely achieving the necessary speeds of 2000 RPM for several minutes often costs hundreds of dollars and requires a power supply.\n\nWe present here an open hardware solution- Handyfuge - that can be assembled with readily available components for the cost of <5 dollars a unit and could be used together with the LAMP assay for point of care detection of COVID-19 RNA from saliva. The device is then validated using the LAMP protocol from Rabe and Cepko. With the use of insulated coolers for reagent supply chain and delivery, the assay presented can be completed without the need for electricity or any laboratory scale infrastructure.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Ethan Li",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Adam Larson",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Anestha Kothari",
+        "author_inst": "Stanford University"
+      },
+      {
+        "author_name": "Manu Prakash",
+        "author_inst": "Stanford University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.06.29.20142562",
     "rel_title": "Male gender and kidney illness associated with an increased risk of severe laboratory-confirmed coronavirus disease",
@@ -1326102,101 +1325363,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2020.06.29.178616",
-    "rel_title": "A Targeted Vaccine against COVID-19: S1-Fc Vaccine Targeting the Antigen-Presenting Cell Compartment Elicits Protection against SARS-CoV-2 Infection",
-    "rel_date": "2020-06-30",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.29.178616",
-    "rel_abs": "Vaccination efficacy is enhanced by targeting the antigen-presenting cell compartment. Here, we show that S1-Fc antigen delivery targeting the Fc{gamma}R+ antigen-presenting cell compartment elicits anti-SARS-CoV-2 S1-antigen specific IgG production in vivo exerting biologically functional and protective activity against live virus infection, assessed in a stringent experimental virus challenge assay in vitro. The S1-domain of the SARS-CoV-2 spike protein was genetically fused to a human immunoglobulin Fc moiety, which contributes to mediate S1-Fc cellular internalization by Fc{gamma}R+ antigen-presenting cells. Immediately upon administration intramuscularly, our novel vaccine candidate recombinant rS1-Fc homes to lymph nodes in vivo where Fc{gamma}R+ antigen-presenting cells reside. Seroconversion is achieved as early as day 7, mounting considerably increased levels of anti-S1 IgGs in vivo. Interestingly, immunization at elevated doses with non-expiring S1-Fc encoding dsDNA favors the education of a desired antigen-specific adaptive T cell response. However, low-dose immunization, safeguarding patient safety, using recombinant rS1-Fc, elicits a considerably elevated protection amplitude against live SARS-CoV-2 infection. Our promising findings on rS1-Fc protein immunization prompted us to further develop an affordable and safe product for delivery to our communities in need for COVID-19 vaccinations.",
-    "rel_num_authors": 20,
-    "rel_authors": [
-      {
-        "author_name": "Andreas Herrmann",
-        "author_inst": "Sorrento Therapeutics"
-      },
-      {
-        "author_name": "Junki Maruyama",
-        "author_inst": "Galveston National Laboratory"
-      },
-      {
-        "author_name": "Chanyu Yue",
-        "author_inst": "Sorrento Therapeutics"
-      },
-      {
-        "author_name": "Christoph Lahtz",
-        "author_inst": "Sorrento Therapeutics"
-      },
-      {
-        "author_name": "Heyue Zhou",
-        "author_inst": "Sorrento Therapeutics"
-      },
-      {
-        "author_name": "Lisa Kerwin",
-        "author_inst": "Sorrento Therapeutics"
-      },
-      {
-        "author_name": "Whenzong Guo",
-        "author_inst": "Sorrento Therapeutics"
-      },
-      {
-        "author_name": "Yanliang Zhang",
-        "author_inst": "Sorrento Therapeutics"
-      },
-      {
-        "author_name": "Wlliam Soo Hoo",
-        "author_inst": "Sorrento Therapeutics"
-      },
-      {
-        "author_name": "Soonpin Yei",
-        "author_inst": "Sorrento Therapeutics"
-      },
-      {
-        "author_name": "Sunkuk Kwon",
-        "author_inst": "Sorrento Therapeutics"
-      },
-      {
-        "author_name": "Yanwen Fu",
-        "author_inst": "Sorrento Therapeutics"
-      },
-      {
-        "author_name": "Sachi Johnson",
-        "author_inst": "Sorrento Therapeutics"
-      },
-      {
-        "author_name": "Arthur Ledesma",
-        "author_inst": "Sorrento Therapeutics"
-      },
-      {
-        "author_name": "Yiran Zhuang",
-        "author_inst": "Sorrento Therapeutics"
-      },
-      {
-        "author_name": "Yingcong Zhuang",
-        "author_inst": "Sorrento Therapeutics"
-      },
-      {
-        "author_name": "Elena Yei",
-        "author_inst": "Sorrento Therapeutics"
-      },
-      {
-        "author_name": "Tomasz Adamus",
-        "author_inst": "Sorrento Therapeutics"
-      },
-      {
-        "author_name": "Slobodan Praessler",
-        "author_inst": "Galveston National Laboratory"
-      },
-      {
-        "author_name": "Henry Ji",
-        "author_inst": "Sorrento Therapeutics"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.06.30.175778",
     "rel_title": "Single-cell transcriptional atlas of the Chinese horseshoe bat (Rhinolophus sinicus) provides insight into the cellular mechanisms which enable bats to be viral reservoirs",
@@ -1326663,6 +1325829,61 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2020.06.30.172833",
+    "rel_title": "Development of RNA-based assay for rapid detection of SARS-CoV-2 in clinical samples",
+    "rel_date": "2020-06-30",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.30.172833",
+    "rel_abs": "The ongoing spread of pandemic coronavirus disease (COVID-19) is caused by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2). In the lack of specific drugs or vaccines for SARS-CoV-2, demands rapid diagnosis and management are crucial for controlling the outbreak in the community. Here we report the development of the first rapid-colorimetric assay capable of detecting SARS-CoV-2 in the human nasopharyngeal RNA sample in less than 30 minutes. We utilized a nanomaterial-based optical sensing platform to detect RNA-dependent RNA polymerase (RdRp) gene of SARS-CoV-2, where the formation of oligo probe-target hybrid led to salt-induced aggregation and changes in gold-colloid color from pink to blue in visible range. Accordingly, we found a change in colloid color from pink to blue in assay containing nasopharyngeal RNA sample from the subject with clinically diagnosed COVID-19. The colloid retained pink color when the test includes samples from COVID-19 negative subjects or human papillomavirus (HPV) infected women. The results were validated using nasopharangeal RNA samples from suspected COVID-19 subjects (n=136). Using RT-PCR as gold standard, the assay was found to have 85.29% sensitivity and 94.12% specificity. The optimized method has detection limit as little as 0.5 ng of SARS-CoV-2 RNA. Overall, the developed assay rapidly detects SARS-CoV-2 RNA in clinical samples in a cost-effective manner and would be useful in pandemic management by facilitating mass screening.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Vinod Kumar",
+        "author_inst": "Sanjay Gandhi Post Graduate Institute of Medical Science (SGPGIMS), Lucknow, India"
+      },
+      {
+        "author_name": "Suman Mishra",
+        "author_inst": "Sanjay Gandhi Post Graduate Institute of Medical Science (SGPGIMS), Lucknow, India"
+      },
+      {
+        "author_name": "Rajni Sharma",
+        "author_inst": "Sanjay Gandhi Post Graduate Institute of Medical Science (SGPGIMS), Lucknow, India"
+      },
+      {
+        "author_name": "Jyotsna Agarwal",
+        "author_inst": "Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, India"
+      },
+      {
+        "author_name": "Ujjala Ghoshal",
+        "author_inst": "Sanjay Gandhi Post Graduate Institute of Medical Science (SGPGIMS), Lucknow, India"
+      },
+      {
+        "author_name": "Tripti Khanna",
+        "author_inst": "Indian Council of Medical Research, Ramalingaswami Bhawan, New Delhi, India"
+      },
+      {
+        "author_name": "Lokendra K Sharma",
+        "author_inst": "Sanjay Gandhi Post Graduate Institute of Medical Science (SGPGIMS), Lucknow, India"
+      },
+      {
+        "author_name": "Santosh K Verma",
+        "author_inst": "Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow, India"
+      },
+      {
+        "author_name": "Swasti Tiwari",
+        "author_inst": "Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India"
+      },
+      {
+        "author_name": "Prabhakar Mishra",
+        "author_inst": "Department of Biostatistics and Health Informatics, Sanjay Gandhi PGIMS, Raibareli Road,  Lucknow -226014, India"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2020.06.30.177097",
     "rel_title": "Conformational dynamics of SARS-CoV-2 trimeric spike glycoprotein in complex with receptor ACE2 revealed by cryo-EM",
@@ -1328132,109 +1327353,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.06.29.20141283",
-    "rel_title": "Inexpensive multi-patient respiratory monitoring system for helmet ventilation during COVID-19 pandemic",
-    "rel_date": "2020-06-30",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.29.20141283",
-    "rel_abs": "BackgroundHelmet continuous positive applied pressure is a form of non-invasive ventilation (NIV) that has been used to provide respiratory support to COVID-19 patients. Helmet NIV is low-cost, readily available, provides viral filters between the patient and clinician, and may reduce the need for invasive ventilation. Its widespread adoption has been limited, however, by the lack of a respiratory monitoring system needed to address known safety vulnerabilities and to monitor patients. To address these safety and clinical needs, we developed an inexpensive respiratory monitoring system based on readily available components suitable for local manufacture. Open-source design and manufacturing documents are provided. The monitoring system comprises flow, pressure and CO2 sensors on the expiratory path of the helmet circuit and a central remote station to monitor up to 20 patients.\n\nMethodsThe system is validated in bench tests, in human-subject tests on healthy volunteers, and in experiments that compare respiratory features obtained at the expiratory path to simultaneous ground-truth measurements from proximal sensors.\n\nFindingsMeasurements of flow and pressure at the expiratory path are shown to deviate at high flow rates, and the tidal volumes reported via the expiratory path are systematically underestimated.\n\nInterpretationHelmet monitoring systems exhibit high-flow rate, non-linear effects from flow and helmet dynamics. These deviations are found to be within a reasonable margin and should, in principle, allow for calibration, correction and deployment of clinically accurate derived quantities.\n\nFundingThis project is supported by Princeton University, and by National Science Foundation grants OAC-1836650, PHY-2031509 and IOS-1845137. The funding sources provided no role in the design or execution of the the work or in the preparation of the manuscript.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSRespiratory monitoring is standard when treating intubated patients undergoing invasive mechanical ventilation. In contrast, respiratory monitoring systems have not been developed for helmet non-invasive ventilation (NIV). Previous measurements of CO2 concentration in the helmet versus flow rate have been published and serve as the primary guide for setting the minimum flow rate for patient treatment of helmet NIV. Similar studies have explored optimal PEEP settings for clinical treatment. However, in practice, respiratory profiles are not measured during helmet treatment and more evidence is needed to evaluate whether clinically useful quantities, such as tidal volume, can be accurately measured during helmet NIV, to provide the same level of clincially relevant monitoring that is standard with invasive ventliation.\n\nAdded value of this studyDue to the widespread need for inexpensive multi-patient respiratory monitoring systems to cope with the COVID-19 pandemic, a helmet NIV monitoring system was developed and validated with bench tests, human-subject tests on healthy volunteers, and in experiments that compare respiratory features obtained at the expiratory path to simultaneous ground-truth measurements from proximal sensors. At high flow rate, the non-linear effects from the flow and helmet dynamics are observed and have a measurable effect on the estimation of tidal volumes and derived quantities.\n\nImplications of all the available evidenceHelmet monitoring systems for NIV are in wide-spread use for the treatment of the coronavirus disease 2019. The introduction of respiratory monitoring systems for helmet NIV addresses important safety concerns and opens up the possibility of providing clinically relevant derived quantities to track disease progression. A systematic study of deviations between expiratory path measurements and ground-truth proximal sensors was conducted in bench tests and human-subject tests of health volunteers. The non-linear flow and helmet dynamics effects the accuracy of derived quantities at high flow rates. These deviations are found to be within a reasonable margin and should, in principle, allow for calibration, correction and deployment of clinically accurate derived quantities. An inexpensive implementation of the respiratory monitoring system was achieved to cope with the immense scale of the COVID-19 pandemic. Further steps to improve the quality of care for COVID-19 helmet NIV treatment can be achieved through the additional of respiratory monitoring systems that adjust for high flow-rate deviations in the estimation of tidal volumes and derived quantities.",
-    "rel_num_authors": 22,
-    "rel_authors": [
-      {
-        "author_name": "- Princeton Open Ventilation Monitor Collaboration",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Philippe Bourrianne",
-        "author_inst": "Princeton University"
-      },
-      {
-        "author_name": "Stanley Chidzik",
-        "author_inst": "Princeton University"
-      },
-      {
-        "author_name": "Daniel J Cohen",
-        "author_inst": "Princeton University"
-      },
-      {
-        "author_name": "Peter Elmer",
-        "author_inst": "Princeton University"
-      },
-      {
-        "author_name": "Thomas Hallowell",
-        "author_inst": "Children's Hospital of Philadelphia"
-      },
-      {
-        "author_name": "Todd J Kilbaugh",
-        "author_inst": "Children's Hospital of Philadelphia"
-      },
-      {
-        "author_name": "David Lange",
-        "author_inst": "Princeton University"
-      },
-      {
-        "author_name": "Andrew M Leifer",
-        "author_inst": "Princeton University"
-      },
-      {
-        "author_name": "Daniel R. Marlow",
-        "author_inst": "Princeton University"
-      },
-      {
-        "author_name": "Peter D. Meyers",
-        "author_inst": "Princeton University"
-      },
-      {
-        "author_name": "Edna Normand",
-        "author_inst": "Princeton University"
-      },
-      {
-        "author_name": "Janine Nunes",
-        "author_inst": "Princeton University"
-      },
-      {
-        "author_name": "Myungchul Oh",
-        "author_inst": "Princeton University"
-      },
-      {
-        "author_name": "Lyman Page",
-        "author_inst": "Princeton University"
-      },
-      {
-        "author_name": "Talmo Pereira",
-        "author_inst": "Princeton University"
-      },
-      {
-        "author_name": "Jim Pivarski",
-        "author_inst": "Princeton University"
-      },
-      {
-        "author_name": "Henry Schreiner",
-        "author_inst": "Princeton University"
-      },
-      {
-        "author_name": "Howard A Stone",
-        "author_inst": "Princeton University"
-      },
-      {
-        "author_name": "David W Tank",
-        "author_inst": "Princeton University"
-      },
-      {
-        "author_name": "Stephan Thiberge",
-        "author_inst": "Princeton University"
-      },
-      {
-        "author_name": "Christopher Tully",
-        "author_inst": "Princeton University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "intensive care and critical care medicine"
-  },
   {
     "rel_doi": "10.1101/2020.06.27.175430",
     "rel_title": "Citizen Scientists Create an Exascale Computer to Combat COVID-19",
@@ -1328693,6 +1327811,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.06.24.20131185",
+    "rel_title": "Sentinel Coronavirus Environmental Monitoring Can Contribute to Detecting Asymptomatic SARS-CoV-2 Virus Spreaders and Can Verify Effectiveness of Workplace COVID-19 Controls",
+    "rel_date": "2020-06-29",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20131185",
+    "rel_abs": "Detecting all workplace asymptomatic COVID-19 virus spreaders would require daily testing of employees, which is not practical. Over a two week period, nine workplace locations were chosen to test employees for SARS-CoV-2 infection (841 tests) and high-frequency-touch point environmental surfaces (5,500 tests) for Coronavirus using Eurofins COVID-19 Sentinel RT-PCR methods. Of the 9 locations, 3 had one or employees infected with SARS-CoV-2, neither of whom had symptoms at the time of testing nor developed symptoms. Locations with Coronavirus contaminated surfaces were 10 times more likely to have clinically positive employees than locations with no or very few positive surfaces. Break room chairs, workbenches, and door handles were the most frequently contaminated surfaces. Coronavirus RNA was detected at very low concentrations (RT-PCR 34 to 38 Cq). Environmental monitoring can be used to validate intervention strategies and be useful to verify the effectiveness of such strategies on a regular basis.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Douglas Marshall",
+        "author_inst": "Eurofins Microbiology Laboratories"
+      },
+      {
+        "author_name": "Frederic Bois",
+        "author_inst": "Eurofins Scientific"
+      },
+      {
+        "author_name": "Soren K.S. Jensen",
+        "author_inst": "Eurofins Steins Laboratorium"
+      },
+      {
+        "author_name": "Svend A. Linde",
+        "author_inst": "Eurofins Steins Laboratorium"
+      },
+      {
+        "author_name": "Richard Higby",
+        "author_inst": "Eurofins Microbiology Laboratories"
+      },
+      {
+        "author_name": "Yvoine Remy-McCort",
+        "author_inst": "Eurofins Scientific"
+      },
+      {
+        "author_name": "Sean Murray",
+        "author_inst": "Eurofins Microbiology Laboratories"
+      },
+      {
+        "author_name": "Bryan Dieckelman",
+        "author_inst": "Eurofins Microbiology Laboratories"
+      },
+      {
+        "author_name": "Fitri Sudradjat",
+        "author_inst": "Eurofins Central Analytical Laboratories"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.06.22.20134957",
     "rel_title": "Effects of Anticoagulants and Corticosteroids therapy in patients affected by severe COVID-19 Pneumonia",
@@ -1330062,69 +1329231,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.06.27.20140582",
-    "rel_title": "THE EXPERIENCE OF UK BLADDER CANCER PATIENTS DURING THE COVID-19 PANDEMIC: A SURVEY-BASED SNAPSHOT",
-    "rel_date": "2020-06-29",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.27.20140582",
-    "rel_abs": "The Covid-19 pandemic has placed unprecedented strain on healthcare systems worldwide. Within this context, UK cancer services have undergone significant disruption to create capacity for the National Health Service. As a charity that endeavours to support bladder cancer (BC) patients and improve outcomes, Action Bladder Cancer UK (ABCUK) designed and administered a SurveyMonkey survey to investigate the prevalence of such disruption for BC patients. From 22nd April to 18th June 2020, 142 BC patients responded. Across all patient groups, 46.8% of patients described disruption to their treatment or follow-up. For non-muscle-invasive BC (NMIBC) patients, disruptions included postponement of: initial transurethral resection of bladder tumour (TURBT) (33.3%), subsequent TURBT (40.0%), and surveillance cystoscopy (58.1%). For NMIBC patients undergoing intravesical therapy, 68.4% experienced treatment postponements or curtailments. For muscle-invasive BC patients, 57.1% had experienced postponement of cystectomy and 14.3% had been changed from cystectomy to radiotherapy. Half of patients undergoing systemic chemotherapy also experienced disruption. Despite the surveys limitations, we have demonstrated considerable disruption to the care of BC patients during the UK Covid-19 pandemic. To avoid a repeat, the UK BC community should define effective contingent ways of working ready for a possible  second wave of Covid-19, or any other such threat.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Sarah Spencer-Bowdage",
-        "author_inst": "Action Bladder Cancer UK"
-      },
-      {
-        "author_name": "Jeannie Rigby",
-        "author_inst": "Action Bladder Cancer UK"
-      },
-      {
-        "author_name": "Jackie O'Kelly",
-        "author_inst": "Action Bladder Cancer UK"
-      },
-      {
-        "author_name": "Phil Kelly",
-        "author_inst": "Action Bladder Cancer UK"
-      },
-      {
-        "author_name": "Mark Page",
-        "author_inst": "Action Bladder Cancer UK"
-      },
-      {
-        "author_name": "Caroline Raw",
-        "author_inst": "Action Bladder Cancer UK"
-      },
-      {
-        "author_name": "Paula Allchorne",
-        "author_inst": "Barts Health NHS Trust, London, UK"
-      },
-      {
-        "author_name": "Peter Harper",
-        "author_inst": "Leaders in Oncology Care, London, UK"
-      },
-      {
-        "author_name": "Jeremy Crew",
-        "author_inst": "Oxford University Hospitals NHS Foundation Trust, UK."
-      },
-      {
-        "author_name": "Roger Kockelbergh",
-        "author_inst": "University Hospitals of Leicester NHS Trust, UK. Leicester Cancer Research Centre, University of Leicester, UK."
-      },
-      {
-        "author_name": "Allen Knight",
-        "author_inst": "Action Bladder Cancer UK"
-      },
-      {
-        "author_name": "Richard T Bryan",
-        "author_inst": "University of Birmingham"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "urology"
-  },
   {
     "rel_doi": "10.1101/2020.06.27.20141499",
     "rel_title": "Cancer inpatient with COVID-19: a report from the Brazilian National Cancer Institute",
@@ -1330483,6 +1329589,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.06.27.20141739",
+    "rel_title": "Aligning SARS-CoV-2 Indicators via an Epidemic Model: Application to Hospital Admissions and RNA Detection in Sewage Sludge",
+    "rel_date": "2020-06-29",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.27.20141739",
+    "rel_abs": "Ascertaining the state of coronavirus outbreaks is crucial for public health decision-making. Absent repeated representative viral test samples in the population, public health officials and researchers alike have relied on lagging indicators of infection to make inferences about the direction of the outbreak and attendant policy decisions. Recently researchers have shown that SARS-CoV-2 RNA can be detected in municipal sewage sludge with measured RNA concentrations rising and falling suggestively in the shape of an epidemic curve while providing an earlier signal of infection than hospital admissions data. The present paper presents a SARS-CoV-2 epidemic model to serve as a basis for estimating the incidence of infection, and shows mathematically how modeled transmission dynamics translate into infection indicators by incorporating probability distributions for indicator-specific time lags from infection. Hospital admissions and SARS-CoV-2 RNA in municipal sewage sludge are simultaneously modeled via maximum likelihood scaling to the underlying transmission model. The results demonstrate that both data series plausibly follow from the transmission model specified, provide a direct estimate of the reproductive number R0 = 2.38, and suggest that the detection of viral RNA in sewage sludge leads hospital admissions by 4.6 days on average.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Edward H Kaplan",
+        "author_inst": "Yale University"
+      },
+      {
+        "author_name": "Dennis Wang",
+        "author_inst": "Yale University"
+      },
+      {
+        "author_name": "Mike Wang",
+        "author_inst": "Yale University"
+      },
+      {
+        "author_name": "Amyn A Malik",
+        "author_inst": "Yale University"
+      },
+      {
+        "author_name": "Alessandro Zulli",
+        "author_inst": "Yale University"
+      },
+      {
+        "author_name": "Jordan H Peccia",
+        "author_inst": "Yale University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.06.28.20141556",
     "rel_title": "Monocyte CD169 expression as a biomarker in the early diagnosis of COVID-19",
@@ -1331532,29 +1330677,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.06.29.20141523",
-    "rel_title": "Data-driven estimation of change points reveal correlation between face mask use and accelerated curtailing of the COVID-19 epidemic in Italy",
-    "rel_date": "2020-06-29",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.29.20141523",
-    "rel_abs": "Italy was the first Western country to be seriously affected by COVID-19, and the first to implement drastic measures, which have successfully curtailed the epidemic. To understand which containment measures altered disease dynamics, we estimate change points in COVID-19 dynamics from official Italian data. We find excellent correlation between nationwide lockdown and the epidemic peak in late March 2020. Surprisingly, we find a change point in mid April, which does not correspond to national measures, but may be explained by regional interventions. Change points in regional COVID-19 dynamics correlate well with local distribution of free face masks and regional orders requiring their mandatory use. Regions with no specific interventions showed no change point during April. We speculate that widespread use of face masks and other protective means has contributed substantially to keeping the number of new Italian COVID-19 cases under control in spite of society turning towards a new normality.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Morten Gram Pedersen",
-        "author_inst": "Universita degli Studi di Padova"
-      },
-      {
-        "author_name": "Matteo Meneghini",
-        "author_inst": "Universita degli studi di Padova"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.06.27.174896",
     "rel_title": "Rational Design of the Remdesivir Binding Site in the RNA-dependent RNA Polymerase of SARS-CoV-2: Implications for Potential Resistance",
@@ -1331865,6 +1330987,33 @@
     "type": "new results",
     "category": "cell biology"
   },
+  {
+    "rel_doi": "10.1101/2020.06.29.177030",
+    "rel_title": "A mobile genetic element in the SARS-CoV-2 genome is shared with multiple insect species",
+    "rel_date": "2020-06-29",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.29.177030",
+    "rel_abs": "Unprecedented quantities of sequence data have been generated from the newly emergent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causative agent of COVID-19. We document here the presence of s2m, a highly conserved, mobile genetic element with unknown function, in both the SARS-CoV-2 genome and a large number of insect genomes. Although s2m is not universally present among coronaviruses and appears to undergo horizontal transfer, the high sequence conservation and universal presence of s2m among isolates of SARS-CoV-2 indicate that, when present, the element is essential for viral function.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Torstein Tengs",
+        "author_inst": "The Norwegian Institute of Public Health"
+      },
+      {
+        "author_name": "Charles F Delwiche",
+        "author_inst": "University of Maryland, College Park"
+      },
+      {
+        "author_name": "Christine M Jonassen",
+        "author_inst": "Ostfold Hospital Trust"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "genetics"
+  },
   {
     "rel_doi": "10.1101/2020.06.29.171173",
     "rel_title": "An in vitro assessment of anti-SARS-CoV-2 activity of oral preparations of iodine complexes (RENESSANS)",
@@ -1332986,69 +1332135,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.06.25.20140269",
-    "rel_title": "Vaporized H2O2 decontamination against surrogate viruses for the reuse of N95 respirators in the COVID-19 emergency",
-    "rel_date": "2020-06-28",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.25.20140269",
-    "rel_abs": "Decontamination of N95 respirators has become critical to alleviate PPE shortages for healthcare workers in the current COVID-19 emergency. The factors that are considered for the effective reuse of these masks are the fit, filter efficiency and decontamination/disinfection level both for SARS-CoV-2, which is the causative virus for COVID-19, and for other organisms of concern in the hospital environment such as Staphylococcus aureus or Clostridium difficile.\n\nIn its guidance entitled  Recommendations for Sponsors Requesting EUAs for Decontamination and Bioburden Reduction Systems for Surgical Masks and Respirators During the Coronavirus Disease 2019 (COVID19) Public Health Emergency (May 2020)[1], the FDA recommends a 6-log10 reduction in either the most resistant bacterial spores for the system or in a mycobacterium species to authorize the use of a decontamination method of N95 respirators for single or multiple users. While the goal is primarily inactivation against SARS-CoV-2, testing of decontamination methods against the virus may not always be available. For decontamination methods considered for only single users, the recommendation is a 6-log10 reduction in the infective virus concentration of 3 non-enveloped viruses or in the concentration of two Gram (+) and two Gram (-) bacteria. Based on these recommendations, we explored the efficacy of vaporized H2O2 (VHP) treatment of N95 respirators against surrogate viruses covering a wide range of disinfection resistance for emergency decontamination and reuse to alleviate PPE shortages for healthcare workers in the COVID-19 emergency.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Ebru Oral",
-        "author_inst": "Massachusetts General Hospital/Harvard Medical School"
-      },
-      {
-        "author_name": "Keith K Wannomae",
-        "author_inst": "Massachusetts General Hospital"
-      },
-      {
-        "author_name": "Rachel L Connolly",
-        "author_inst": "Massachusetts General Hospital/Harvard Medical School"
-      },
-      {
-        "author_name": "Joseph A Gardecki",
-        "author_inst": "Massachusetts General Hospital"
-      },
-      {
-        "author_name": "Hui Min Leung",
-        "author_inst": "Massachusetts General Hospital"
-      },
-      {
-        "author_name": "Orhun K Muratoglu",
-        "author_inst": "Massachusetts General Hospital/Harvard Medical School"
-      },
-      {
-        "author_name": "John Durkin",
-        "author_inst": "B & V Testing"
-      },
-      {
-        "author_name": "Ralph Jones",
-        "author_inst": "B & V Testing"
-      },
-      {
-        "author_name": "Cassidy Collins",
-        "author_inst": "Charles River Laboratories"
-      },
-      {
-        "author_name": "Julian Gjore",
-        "author_inst": "Charles River Laboratories"
-      },
-      {
-        "author_name": "Amanda Budzilowicz",
-        "author_inst": "Charles River Laboratories"
-      },
-      {
-        "author_name": "Tareq Jaber",
-        "author_inst": "Charles River Laboratories"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "occupational and environmental health"
-  },
   {
     "rel_doi": "10.1101/2020.06.26.20140657",
     "rel_title": "The impact of the COVID-19 pandemic on quality of life, physical and psychosocial wellbeing in breast cancer patients and survivors - A prospective, multicenter cohort study",
@@ -1333483,6 +1332569,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "addiction medicine"
   },
+  {
+    "rel_doi": "10.1101/2020.06.26.20138545",
+    "rel_title": "Prevalence of SARS-CoV-2 among workers returning to Bihar gives snapshot of COVID across India",
+    "rel_date": "2020-06-28",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.26.20138545",
+    "rel_abs": "India has reported the fourth highest number of confirmed SARS-CoV-2 cases worldwide. Because there is little community testing for COVID, this case count is likely an underestimate. When India partially exited from lockdown on May 4, 2020, millions of daily laborers left cities for their rural family homes. RNA testing on a near-random sample of laborers returning to the state of Bihar is used to estimate positive testing rate for COVID across India for a 6-week period immediately following the initial lifting of Indias lockdown. Positive testing rates among returning laborers are only moderately correlated with, and 21% higher than, Indian states official reports, which are not based on random sampling. Higher prevalence among returning laborers may also reflect greater COVID spread in crowded poor communities such as slums.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Anup Malani",
+        "author_inst": "University of Chicago"
+      },
+      {
+        "author_name": "Manoj Mohanan",
+        "author_inst": "Duke University"
+      },
+      {
+        "author_name": "Chanchal Kumar",
+        "author_inst": "Government of Bihar"
+      },
+      {
+        "author_name": "Jake Kramer",
+        "author_inst": "University of Chicago"
+      },
+      {
+        "author_name": "Vaidehi Tandel",
+        "author_inst": "IDFC Institute"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.06.26.20140814",
     "rel_title": "Predicting the Trajectory of Any COVID19 Epidemic From the Best Straight Line",
@@ -1334584,61 +1333705,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.06.22.20136036",
-    "rel_title": "Ethnic variation in outcome of people hospitalised with Covid-19 in Wales (UK): A rapid analysis of surveillance data using Onomap, a name-based ethnicity classification tool",
-    "rel_date": "2020-06-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.22.20136036",
-    "rel_abs": "There is growing evidence that ethnic minorities in Europe are disproportionately affected by Covid-19. Using a name-based ethnicity classifier, we found that hospitalised Black, Asian and minority ethnic cases were younger and more likely to be admitted to intensive care (ICU). Pakistani, Bangladeshi and White - other than British or Irish, ethnic groups were most at risk. In this study, older age and male gender, but not ethnicity, were associated with death in hospitalised patients.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Daniel Rhys Thomas",
-        "author_inst": "Public Health Wales"
-      },
-      {
-        "author_name": "Oghogho Orife",
-        "author_inst": "Public Health Wales"
-      },
-      {
-        "author_name": "Amy Plimmer",
-        "author_inst": "Public Health Wales"
-      },
-      {
-        "author_name": "Christopher Williams",
-        "author_inst": "Public Health Wales"
-      },
-      {
-        "author_name": "George Karani",
-        "author_inst": "Cardiff Metropolitan University"
-      },
-      {
-        "author_name": "Meirion Rhys Evans",
-        "author_inst": "Public Health Wales"
-      },
-      {
-        "author_name": "Paul Longley",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Janusz Janiec",
-        "author_inst": "Narodowy Instytut Zdrowia Publicznego"
-      },
-      {
-        "author_name": "Roiyah Saltus",
-        "author_inst": "University of South Wales"
-      },
-      {
-        "author_name": "Giri Shankar",
-        "author_inst": "Public Health Wales"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.06.22.20137653",
     "rel_title": "Timeline from receipt to online publication of COVID-19 original research articles",
@@ -1334961,6 +1334027,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.06.24.20139238",
+    "rel_title": "A Multi-Task Pipeline with Specialized Streams forClassification and Segmentation of InfectionManifestations in COVID-19 Scans",
+    "rel_date": "2020-06-26",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20139238",
+    "rel_abs": "We are concerned with the challenge of coronavirus disease (COVID-19) detection in chest X-ray and Computed Tomography (CT) scans, and the classification and segmentation of related infection manifestations. Even though it is arguably not an established diagnostic tool, using machine learning-based analysis of COVID-19 medical scans has shown the potential to provide a preliminary digital second opinion. This can help in managing the current pandemic, and thus has been attracting significant research attention. In this research, we propose a multi-task pipeline that takes advantage of the growing advances in deep neural network models. In the first stage, we fine-tuned an Inception-v3 deep model for COVID-19 recognition using multi-modal learning, i.e., using X-ray and CT scans. In addition to outperforming other deep models on the same task in the recent literature, with an attained accuracy of 99.4%, we also present comparative analysis for multi-modal learning against learning from X-ray scans alone. The second and the third stages of the proposed pipeline complement one another in dealing with different types of infection manifestations. The former features a convolutional neural network architecture for recognizing three types of manifestations, while the latter transfers learning from another knowledge domain, namely, pulmonary nodule segmentation in CT scans, to produce binary masks for segmenting the regions corresponding to these manifestations. Our proposed pipeline also features specialized streams in which multiple deep models are trained separately to segment specific types of infection manifestations, and we show the significant impact that this framework has on various performance metrics. We evaluate the proposed models on widely adopted datasets, and we demonstrate an increase of approximately 4% and 7% for dice coefficient and mean intersection-over-union (mIoU), respectively, while achieving 60% reduction in computational time, compared to the recent literature.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Shimaa El-bana",
+        "author_inst": "Alexandria Higher Institute of Engineering and Technology"
+      },
+      {
+        "author_name": "Ahmad Al-Kabbany",
+        "author_inst": "Department of Electronics and Communications Engineering, Arab Academy for Science, Technology, and Maritime Transport, Alexandria, Egypt"
+      },
+      {
+        "author_name": "Maha Sharkas",
+        "author_inst": "Department of Electronics and Communications Engineering, Arab Academy for Science, Technology, and Maritime Transport, Alexandria, Egypt"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.06.24.20139410",
     "rel_title": "Determination of Robust Regional CT Radiomics Features for COVID-19",
@@ -1335946,29 +1335039,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.06.25.20138602",
-    "rel_title": "Mathematical modeling of the COVID-19 prevalence in Saudi Arabia",
-    "rel_date": "2020-06-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.25.20138602",
-    "rel_abs": "The swift precautionary and preventive measures and regulations that were adopted by the Saudi authority has ameliorated the exponential escalation of the SARS-CoV-2 virus spread, decreased the fatality rate and critical cases of COVID-19. Understanding the trend of COVID-19 is crucial to establishing the appropriate precautionary measures to mitigate the epidemic spread. The aim of this paper was to modifying and enhancing the mathematical modeling to guide health authority and assist in an early assessment of the epidemic outbreak and can be utilised to monitor non-pharmaceutical interventions (NPIs). Both ARIMA model and Logistic growth model were developed to study the trend and to provide short and long-term forecasting of the prevalence of COVID-19 cases and dynamics. The data analyzed in this study covered the period between 2nd March and 21st June 2020. Two different scenarios were developed to predict the epidemic fluctuating trends and dynamics. The first scenario covered the period between 2nd March and 28th May when the first peak was observed and immediately declined. The analysis projected that the COVID-19 epidemic to reach a peak by 17th May with a total number of 58,534 infected cases and to end on the 4th August, if lockdown were not interrupted and folks followed the recommended personal and social safety guidelines. The second scenario was simulated because of the sudden sharp spike witnessed in the trend of the new confirmed cases on the last week of May and continue to escalate till the time of current writing-21st June. In the 2nd scenario, the analysis estimated the epidemic to peak on 15th June with a total number of 146,004 infected cases and to end on 29th September, 2020 with a final size of 209,607 (185,757 to 244,310) infected cases, assuming that the NPIs will be maintained while new normal life is resumed carefully. ARIMA and Logistic growth models showed excellent performance in projecting the epidemic prevalence, trends and dynamics at different phases. In conclusion, the analysis presented in this paper will assist policy-makers and health care authorities to evaluate the effect of the NPIs applied and to size the resources needed to manage different phases and cope with the final size of the epidemic estimates and to impose extra precautions.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Tusneem Elhassan",
-        "author_inst": "King Faisal Specialist Hospital and Research Centre"
-      },
-      {
-        "author_name": "Ameera Gaafar",
-        "author_inst": "King Faisal Specialist Hospital and Research Center"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.06.25.172312",
     "rel_title": "Using the nucleocapsid protein to investigate the relationship between SARS-CoV-2 and closely related bat and pangolin coronaviruses",
@@ -1336543,6 +1335613,65 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2020.06.26.173872",
+    "rel_title": "Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2",
+    "rel_date": "2020-06-26",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.26.173872",
+    "rel_abs": "ABSTRACTSARS-CoV-2 Nsp15 is a uridylate-specific endoribonuclease with C-terminal catalytic domain belonging to the EndoU family. It degrades the polyuridine extensions in (-) sense strand of viral RNA and some non-translated RNA on (+) sense strand. This activity seems to be responsible for the interference with the innate immune response and evasion of host pattern recognition. Nsp15 is highly conserved in coronaviruses suggesting that its activity is important for virus replication. Here we report first structures with bound nucleotides and show that SARS-CoV-2 Nsp15 specifically recognizes U in a pattern previously predicted for EndoU. In the presence of manganese ions, the enzyme cleaves unpaired RNAs. Inhibitors of Nsp15 have been reported but not actively pursued into therapeutics. The current COVID-19 pandemic brought to attention the repurposing of existing drugs and the rapid identification of new antiviral compounds. Tipiracil is an FDA approved drug that is used with trifluridine in the treatment of colorectal cancer. Here, we combine crystallography, biochemical and whole cell assays, and show that this compound inhibits SARS-CoV-2 Nsp15 and interacts with the uridine binding pocket of the enzyme\u2019s active site, providing basis for the uracil scaffold-based drug development.Competing Interest StatementThe authors have declared no competing interest.View Full Text",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Youngchang Kim",
+        "author_inst": "Argonne National Laboratory/University of Chicago"
+      },
+      {
+        "author_name": "Jacek Wower",
+        "author_inst": "Auburn University"
+      },
+      {
+        "author_name": "Natalia Maltseva",
+        "author_inst": "Argonne National Laboratory/University of Chicago"
+      },
+      {
+        "author_name": "Changsoo Chang",
+        "author_inst": "Argonne National Laboratory/University of Chicago"
+      },
+      {
+        "author_name": "Robert Jedrzejczak",
+        "author_inst": "Argonne National Laboratory/University of Chicago"
+      },
+      {
+        "author_name": "Mateusz Wilamowski",
+        "author_inst": "Argonne National Laboratory/University of Chicago"
+      },
+      {
+        "author_name": "Soowon Kang",
+        "author_inst": "University of Chicago"
+      },
+      {
+        "author_name": "Vlad Nicolaescu",
+        "author_inst": "University of Chicago"
+      },
+      {
+        "author_name": "Glenn Randall",
+        "author_inst": "University of Chicago"
+      },
+      {
+        "author_name": "Karolina Michalska",
+        "author_inst": "Argonne National Laboratory/University of Chicago"
+      },
+      {
+        "author_name": "Andrzej Joachimiak",
+        "author_inst": "Argonne National Laboratory/University of Chicago"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "molecular biology"
+  },
   {
     "rel_doi": "10.1101/2020.06.25.172403",
     "rel_title": "Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor",
@@ -1337516,41 +1336645,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.06.24.20139071",
-    "rel_title": "Modelling COVID-19 using the Fundamentals of Fluid Dynamics",
-    "rel_date": "2020-06-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20139071",
-    "rel_abs": "As of 21st May 2020, there have been 4.89M confirmed cases worldwide and over 323,000 deaths of people who have tested positive for SARS-CoV-2. The outbreak of COVID-19, has not only caused widespread morbidity and mortality, but has also led to a catastrophic breakdown in the global economy and unprecedented social disruption. To lessen the global health consequences of COVID-19, sweeping COVID-19 lockdown and quarantine measures have been imposed within many nations. These measures have significantly impacted the worlds economy and in many cases has led to the loss of livelihood. Mathematical modeling of pandemics is of critical importance to understand the unfolding of transmission events and to formulate control measures. In this research letter, we have introduced a novel approach to forecasting epidemics like COVID-19. The proposed mathematical model stems from the fundamental principles of fluid dynamics, and can be utilized to make projections of the number of infected people. This unique mathematical model can be beneficial for predicting and designing potential strategies to mitigate the spread and impact of pandemics.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Harris Rabbani",
-        "author_inst": "Texas A&M University at Qatar"
-      },
-      {
-        "author_name": "Kofi Osei-Bonsu",
-        "author_inst": "Beekin Inc"
-      },
-      {
-        "author_name": "Jassem Abbasi",
-        "author_inst": "Zodan Solutions"
-      },
-      {
-        "author_name": "Peter Kwame Osei-Bonsu",
-        "author_inst": "Aberdeen Royal Infirmary"
-      },
-      {
-        "author_name": "Thomas Daniel Seers",
-        "author_inst": "Texas A&M University at Qatar"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.06.24.20138990",
     "rel_title": "Liberte, Egalite, Fraternite... Contamine? Estimating the impact of French municipal elections on COVID-19 spread in France",
@@ -1337829,6 +1336923,41 @@
     "type": "new results",
     "category": "biochemistry"
   },
+  {
+    "rel_doi": "10.1101/2020.06.25.170936",
+    "rel_title": "Cellular exocytosis gene (EXOC6/6B): a potential molecular link for the susceptibility and mortality of COVID-19 in diabetic patients",
+    "rel_date": "2020-06-25",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.25.170936",
+    "rel_abs": "Diabetes is one of the most critical comorbidities linked to an increased risk of severe complications in the current coronavirus disease 2019 (COVID-19) pandemic. A better molecular understanding of COVID-19 in people with type diabetes mellitus (T2D) is mandatory, especially in countries with a high rate of T2D, such as the United Arab Emirates (UAE). Identification of the cellular and molecular mechanisms that make T2D patients prone to aggressive course of the disease can help in the discovery of novel biomarkers and therapeutic targets to improve our response to the disease pandemic. Herein, we employed a system genetics approach to explore potential genomic, transcriptomic alterations in genes specific to lung and pancreas tissues, affected by SARS-CoV-2 infection, and study their association with susceptibility to T2D in Emirati patients. Our results identified the Exocyst complex component, 6 (EXOC6/6B) gene (a component for docks insulin granules to the plasma membrane) with documented INDEL in 3 of 4 whole genome sequenced Emirati diabetic patients. Publically available transcriptomic data showed that lung infected with SARS-CoV-2 showed significantly lower expression of EXOC6/6B compared to healthy lungs.\n\nIn conclusion, our data suggest that EXOC6/6B might be an important molecular link between dysfunctional pancreatic islets and ciliated lung epithelium that makes diabetic patients more susceptible to severe SARS-COV-2 complication.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Jalal Taneera",
+        "author_inst": "University of Sharjah"
+      },
+      {
+        "author_name": "Mahmood Yaseen Hachim",
+        "author_inst": "Mohammed bin Rashid University of Medicine and Health Sciences"
+      },
+      {
+        "author_name": "Ibrahim Yaseen Hachim",
+        "author_inst": "University of Sharjah"
+      },
+      {
+        "author_name": "Saba Al Heialy",
+        "author_inst": "Mohammed bin Rashid University of Medicine and Health Sciences"
+      },
+      {
+        "author_name": "Nabil Sulaiman",
+        "author_inst": "University of Sharjah"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "bioinformatics"
+  },
   {
     "rel_doi": "10.1101/2020.06.23.167072",
     "rel_title": "Molecular features similarities between SARS-CoV-2, SARS, MERS and key human genes could favour the viral infections and trigger collateral effects",
@@ -1339185,37 +1338314,6 @@
     "type": "new results",
     "category": "genomics"
   },
-  {
-    "rel_doi": "10.1101/2020.06.23.168252",
-    "rel_title": "The SARS-CoV-2 receptor, Angiotensin converting enzyme 2 (ACE2) is required for human endometrial stromal cell decidualization",
-    "rel_date": "2020-06-24",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.23.168252",
-    "rel_abs": "STUDY QUESTIONIs SARS-CoV-2 receptor, angiotensin-converting enzyme 2 (ACE 2) expressed in the human endometrium during the menstrual cycle, and does it participate in endometrial decidualization?\n\nSUMMARY ANSWERACE2 protein is highly expressed in human endometrial stromal cells during the secretory phase and is essential for human endometrial stromal cell decidualization.\n\nWHAT IS KNOWN ALREADYACE2 is expressed in numerous human tissues including the lungs, heart, intestine, kidneys and placenta. ACE2 is also the receptor by which SARS-CoV-2 enters human cells.\n\nSTUDY DESIGN, SIZE, DURATIONProliferative (n = 9) and secretory (n = 6) phase endometrium biopsies from healthy reproductive-age women and primary human endometrial stromal cells from proliferative phase endometrium were used in the study.\n\nPARTICIPANTS/MATERIALS, SETTING, METHODSACE2 expression and localization were examined by qRT-PCR, Western blot, and immunofluorescence in both human endometrial samples and mouse uterine tissue. The effect of ACE2 knockdown on morphological and molecular changes of human endometrial stromal cell decidualization were assessed. Ovariectomized mice were treated with estrogen or progesterone to determine the effects of these hormones on ACE2 expression.\n\nMAIN RESULTS AND THE ROLE OF CHANCEIn human tissue, ACE2 protein is expressed in both endometrial epithelial and stromal cells in the proliferative phase of the menstrual cycle, and expression increases in stromal cells in the secretory phase. The ACE2 mRNA (P < 0.0001) and protein abundance increased during primary human endometrial stromal cell (HESC) decidualization. HESCs transfected with ACE2-targeting siRNA were less able to decidualize than controls, as evidenced by a lack of morphology change and lower expression of the decidualization markers PRL and IGFBP1 (P < 0.05). In mice during pregnancy, ACE2 protein was expressed in uterine epithelial and stromal cells increased through day six of pregnancy. Finally, progesterone induced expression of Ace2 mRNA in mouse uteri more than vehicle or estrogen (P < 0.05).\n\nLARGE SCALE DATAN/A.\n\nLIMITATIONS, REASONS FOR CAUTIONExperiments assessing the function of ACE2 in human endometrial stromal cell decidualization were in vitro. Whether SARS-CoV-2 can enter human endometrial stromal cells and affect decidualization have not been assessed.\n\nWIDER IMPLICATIONS OF THE FINDINGSExpression of ACE2 in the endometrium allow SARS-CoV-2 to enter endometrial epithelial and stromal cells, which could impair in vivo decidualization, embryo implantation, and placentation. If so, women with COVID-19 may be at increased risk of early pregnancy loss.\n\nSTUDY FUNDINGS/COMPETING INTEREST(S)This study was supported by National Institutes of Health / National Institute of Child Health and Human Development grants R01HD065435 and R00HD080742 to RK and Washington University School of Medicine start-up funds to RK. The authors declare that they have no conflicts of interest.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Sangappa B Chadchan",
-        "author_inst": "Washington University School of Medicine"
-      },
-      {
-        "author_name": "Vineet K Maurya",
-        "author_inst": "Washington University School of Medicine"
-      },
-      {
-        "author_name": "Pooja Popli",
-        "author_inst": "Washington University School of Medicine"
-      },
-      {
-        "author_name": "Ramakrishna Kommagani",
-        "author_inst": "Washington University School of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "cell biology"
-  },
   {
     "rel_doi": "10.1101/2020.06.24.169565",
     "rel_title": "Development of a fluorescence based, high-throughput SARS-CoV-2 3CLpro reporter assay",
@@ -1339546,6 +1338644,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.06.23.20137471",
+    "rel_title": "Initial experience with short-course corticosteroids in a small cohort of adults with severe COVID-19 in a tertiary care hospital in India",
+    "rel_date": "2020-06-24",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.23.20137471",
+    "rel_abs": "Severe COVID 19 disease is associated with high morbidity and mortality with limited therapeutic options. The role of glucocorticoids in treatment of COVID 19 has been riddled with controversy. The study site has been using glucocorticoids in patients with severe COVID 19 since the first few patients of COVID 19 that were admitted. In the initial cohort of 7 patients with severe COVID disease, use of methylprednisolone in a dose of 30 mg twice daily was associated with rapid improvement in oxygenation and decline in CRP levels. While six patients made a complete clinical recovery, one patient died. There were no secondary infections.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Sanjiv Jha",
+        "author_inst": "Kokilaben Dhirubhai Ambani Hospital and Medical Research Institute"
+      },
+      {
+        "author_name": "Kiran Shetty",
+        "author_inst": "Kokilaben Dhirubhai Ambani Hospital and Medical Research Institute"
+      },
+      {
+        "author_name": "Sonali Vadi",
+        "author_inst": "Kokilaben Dhirubhai Ambani Hospital and Medical Research Institute"
+      },
+      {
+        "author_name": "Sourabh Phadtare",
+        "author_inst": "Kokilaben Dhirubhai Ambani Hospital and Medical Research Institute"
+      },
+      {
+        "author_name": "Vatsal Kothari",
+        "author_inst": "Kokilaben Dhirubhai Ambani Hospital and Medical Research Institute"
+      },
+      {
+        "author_name": "Abhijit Raut",
+        "author_inst": "Kokilaben Dhirubhai Ambani Hospital and Medical Research Institute"
+      },
+      {
+        "author_name": "Sweta Shah",
+        "author_inst": "Kokilaben Dhirubhai Ambani Hospital and Medical Research Institute"
+      },
+      {
+        "author_name": "Pallavi Bhargava",
+        "author_inst": "Henry Ford Hospital System"
+      },
+      {
+        "author_name": "Tanu Singhal",
+        "author_inst": "Kokilaben Dhirubhai Ambani Hospital and Medical Research Institute"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.06.23.20138743",
     "rel_title": "Only a combination of social distancing and massive testing can effectively stop COVID-19 progression in densely populated urban areas",
@@ -1340494,41 +1339643,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.06.22.20134270",
-    "rel_title": "A link between inflammatory biomarkers and lung ultrasound observations in patients with SARS-CoV-2 infection",
-    "rel_date": "2020-06-23",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.22.20134270",
-    "rel_abs": "Lung ultrasound (LUS) has shown to correlate well with the findings obtained by chest computed tomography (CT) in acute-phase COVID-19. Although there is a significant correlation between blood biomarkers and CT radiological findings, a potential correlation between biochemical parameters and LUS images is still unknown. Our purpose was to evaluate a potential association between lung lesions visualised by LUS and blood biomarkers as well as the ability to predict mortality from two different lung ultrasound scoring systems (LUSS). We performed a retrospective observational study on 45 patients aged >70 years with SARS-CoV-2 infection who required hospitalisation. LUS was carried out at admission and on day 7, when the clinical course was favourable or earlier in case of worsening. Disease severity was scored by means of LUSS in 8 (LUSS8) and in 12 (LUSS12) quadrants. LUS and blood draw for inflammatory marker analysis were performed at the same time. The correlation between biochemical parameters and either LUSS score was significant for ferritin levels. It was 0.486 (p=0.001) for LUSS8 and 0.458 (p=0.002) for LUSS12. Using a threshold score of 15 with LUSS12 predicted mortality in 86.7% of cases (ORcrude 31, CI 95% 4.79-200.51). Applying a threshold of 10 with LUSS8 predicted mortality in 88.9% (ORcrude 69.75, CI 95% 6.90-705.20). There is a correlation between ferritin levels and LUSS. The prognostic capacity of LUSS12 does not surpass that of LUSS8.\n\n\"Take-home message\"There is a correlation between lung ultrasound scoring results and serum ferritin levels in patients with SARS-CoV-2 infection.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Aurelio Luis Wanguemert Perez",
-        "author_inst": "Pneumology Service, San Juan de Dios Hospital, Santa Cruz de Tenerife, Spain"
-      },
-      {
-        "author_name": "Juan Marco Figueira Goncalvez",
-        "author_inst": "Pneumology and Thoracic Surgery Service, University Hospital Nuestra Senora de Candelaria, Santa Cruz de Tenerife, Spain"
-      },
-      {
-        "author_name": "Jose Maria Hernandez Perez",
-        "author_inst": "Pneumology and Thoracic Surgery Service, University Hospital Nuestra Senora de Candelaria, Santa Cruz de Tenerife, Spain"
-      },
-      {
-        "author_name": "Yolanda Ramallo Farina",
-        "author_inst": "Foundation of the Canary Islands Health Research Institute (FIISC), Santa Cruz de Tenerife, Spain. Health Services Research on Chronic Patients Network (REDISSE"
-      },
-      {
-        "author_name": "Jose Carlos Del Castillo Rodriguez",
-        "author_inst": "Family and Community Medicine, San Juan de Dios Hospital, Santa Cruz de Tenerife, Spain"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "respiratory medicine"
-  },
   {
     "rel_doi": "10.1101/2020.06.20.20136283",
     "rel_title": "On the secondary waves of the pandemic launched in Iran and other countries",
@@ -1340903,6 +1340017,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.06.21.20136341",
+    "rel_title": "Analysis and Prediction of the COVID-19 outbreak in Pakistan",
+    "rel_date": "2020-06-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.21.20136341",
+    "rel_abs": "In this study we estimate the severity of the COVID-19 outbreak in Pakistan prior to and after lock down restrictions were eased. We also project the epidemic curve considering realistic quarantine, social distancing and possible medication scenarios. We use a deterministic epidemic model that includes asymptomatic, quarantined, isolated and medicated population compartments for our analysis. We calculate the basic reproduction number [R]0 for the pre and post lock down periods, noting that during this time no medication was available.1 The pre-lock down value of [R]0 is estimated to be 1.07 and the post lock down value is estimated to be 1.86. We use this analysis to project the epidemic curve for a variety of lock down, social distancing and medication scenarios. We note that if no substantial efforts are made to contain the epidemic, it will peak in mid of September, with the maximum projected active cases being close to 700,000. In a realistic, best case scenario, we project that the epidemic peaks in early to mid July with the maximum active cases being around 120000.We note that social distancing measures and medication if available will help flatten the curve, however without the reintroduction of further lock down it would be very difficult to bring [R]0 below 1. Our study strongly supports the recent WHO recommendation of reintroducing lock downs to control the epidemic.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Mohsin Ali",
+        "author_inst": "Lahore University of Management Sciences Lahore"
+      },
+      {
+        "author_name": "Mudassar Imran",
+        "author_inst": "Gulf University for Science & Technology, Mishref, Kuwait;"
+      },
+      {
+        "author_name": "Adnan Khan",
+        "author_inst": "Lahore University of Management Sciences Lahore;"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.06.21.20136606",
     "rel_title": "Extension and implementation of a system modelling the COVID-19 pandemic in Chile",
@@ -1341928,33 +1341069,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "allergy and immunology"
   },
-  {
-    "rel_doi": "10.1101/2020.06.22.20137711",
-    "rel_title": "A Macroeconomic SIR Model for COVID-19",
-    "rel_date": "2020-06-23",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.22.20137711",
-    "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThe current COVID-19 pandemic and subsequent lockdowns have highlighted the close and delicate relationship between a countrys public health and economic health. Macroeconomic models which use preexisting epidemic models to calculate the impacts of a disease outbreak are therefore extremely useful for policymakers seeking to evaluate the best course of action in such a crisis. We develop an SIR model of the COVID-19 pandemic which explicitly considers herd immunity, behavior-dependent transmission rates, remote workers, and indirect externalities of lockdown. This model is presented as an exit time control problem where the lockdown ends when the population achieves herd immunity, either naturally or via a vaccine. A social planner prescribes separate levels of lockdown for two separate sections of the adult population - those who are low-risk (ages 20-64) and those who are high-risk (ages 65 and over). These levels are determined via optimization of an objective function which assigns a macroeconomic cost to the level of lockdown and the number of deaths. We find that, by ending lockdowns once herd immunity is reached, high-risk individuals are able to leave lockdown significantly before the arrival of a vaccine without causing large increases in mortality. Additionally, if we incorporate a behavior-dependent transmission rate which represents increased personal caution in response to increased infection levels, both output loss and total mortality are lowered. Lockdown efficacy is further increased when there is less interaction between low- and high-risk individuals, and increased remote work decreases output losses. Overall, our model predicts that a lockdown which ends at the arrival of herd immunity, combined with individual actions to slow virus transmission, can reduce total mortality to one-third of the no-lockdown level, while allowing high-risk individuals to leave lockdown well before vaccine arrival.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Erhan Bayraktar",
-        "author_inst": "University of Michigan"
-      },
-      {
-        "author_name": "Asaf Cohen",
-        "author_inst": "University of Michigan"
-      },
-      {
-        "author_name": "April Nellis",
-        "author_inst": "University of Michigan"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.06.22.20137604",
     "rel_title": "Universal scaling law for COVID-19 propagation in urban centers",
@@ -1342165,6 +1341279,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pharmacology and therapeutics"
   },
+  {
+    "rel_doi": "10.1101/2020.06.23.20138032",
+    "rel_title": "Factors Associated with Mental Health Outcomes in Oman during COVID19: Frontline vs Non-frontline Healthcare Workers",
+    "rel_date": "2020-06-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.23.20138032",
+    "rel_abs": "OBJECTIVEThis study aims to assess and compare demographic and psychological factors and sleep status of frontline HCWs in relation to non-frontline HCWs\n\nDESIGN, SETTINGS, AND PARTICIPANTSThis cross-sectional study was conducted using an online survey from the 8th to the 17th of April 2020 across varied health care settings in Oman accruing 1139 HCWS.\n\nMAIN OUTCOMES AND MEASURESMental health status was assessed using Depression, Anxiety, and Stress Scales (DASS-21), and insomnia was evaluated by the Insomnia Severity Index (ISI). Samples were categorized into the frontline and non-frontline groups. Chi-square, odds ratio, and independent t-tests were used to compare groups by demographic and mental health outcomes.\n\nResultsThis study included 1139 HCWs working in Oman. There was a total of 368 (32.3%), 388 (34.1%), 271 (23.8%), and 211 (18.5%) respondents reported to have depression, anxiety, stress, and insomnia, respectively while working during the pandemic period. HCWs in the frontline group were 1.4 times more likely to have anxiety (OR=1.401, p=0.007) and stress (OR=1.404, p=0.015) as compared to those working in the non-frontline group. On indices of sleep-wake cycles, HCWs in the frontline group were 1.37 times more likely to report insomnia (OR=1.377, p=0.037) when compared to those working in the non-frontline group. No significant differences in depression status between workers in the frontline and non-frontline groups were found (p=0.181).\n\nCONCLUSIONS AND RELEVANCETo our knowledge, this is the first study to explore the differential impacts of the COVID-19 pandemic on different grades of HCWs. This study suggests that frontline HCWs are disproportionally affected compared to non-frontline HCWs. The problem with managing sleep-wake cycles and anxiety symptoms were highly endorsed among frontline HCWs. As psychosocial interventions are likely to be constrained owing to the pandemic, mental health care must first be directed to frontline HCWs.\n\nO_TEXTBOXArticle Summary\n\nMethods\n\nO_LIThe study accrued 1139 participants of which 574 were working as frontline HCWs (565 non-frontline workers) serving patients with COVID-19 in different categories of healthcare settings in Oman.\nC_LIO_LIThe following tools used were used alongside the collection of demographic information: The depression, Anxiety and Stress Scale (DASS-21) and Insomnia Severity Index.\nC_LIO_LIStrengths: This nationally representative study is the first of its kind to investigate the differences in magnitude and the covariates of stress and distress between frontline and non-frontline healthcare workers in Oman.\nC_LIO_LILimitations: The use of an online survey and the use of symptom checklists (DASS, ISI) which are typically no match for the  gold-standard interviews.\nC_LIO_LIIt is also not clear whether the observed mental health outcomes constitute adjustment disorders/ acute stress reaction or present a chronic-type and thus irreversible psychological distress.\nC_LI\n\nC_TEXTBOX",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Muna Alshekaili",
+        "author_inst": "Al Masarra Hospital, Ministry of Health, Oman"
+      },
+      {
+        "author_name": "Walid Hassan",
+        "author_inst": "Al Masarra Hospital, Ministry of Health, Oman"
+      },
+      {
+        "author_name": "Nazik Al Said",
+        "author_inst": "Al Masarra Hospital, Ministry of Health, Oman"
+      },
+      {
+        "author_name": "Fatima Alsulaimani",
+        "author_inst": "Al Masarra Hospital, Ministry of Health, Oman"
+      },
+      {
+        "author_name": "Sathish Kumar Jayapal",
+        "author_inst": "Centre of Studies & Research, Directorate General Planning, and studies, Ministry of Health, Oman"
+      },
+      {
+        "author_name": "Adhra Al-Mawali",
+        "author_inst": "Centre of Studies & Research, Directorate General Planning, and studies, Ministry of Health, Oman"
+      },
+      {
+        "author_name": "Moon Fai Chan",
+        "author_inst": "Department of Family Medicine & Public Health, College of Medicine & Health Sciences Sultan Qaboos University"
+      },
+      {
+        "author_name": "Sangeetha Mahadevan",
+        "author_inst": "Department of Behavioral Medicine, College of Medicine & Health Sciences, Sultan Qaboos University"
+      },
+      {
+        "author_name": "Samir Al-Adawi",
+        "author_inst": "Sultan Qaboos University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "psychiatry and clinical psychology"
+  },
   {
     "rel_doi": "10.1101/2020.06.22.20137406",
     "rel_title": "Current infection control behaviour patterns in the UK, and how they can be improved by 'Germ Defence', an online behavioural intervention to reduce the spread of COVID-19 in the home.",
@@ -1343378,29 +1342543,6 @@
     "type": "new results",
     "category": "biophysics"
   },
-  {
-    "rel_doi": "10.1101/2020.06.18.147074",
-    "rel_title": "Climatic-niche evolution of SARS CoV-2",
-    "rel_date": "2020-06-23",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.18.147074",
-    "rel_abs": "COVID-19 pandemic has been extensively studied by many researchers. However, it is still unclear why it was restricted to higher latitudes during the initial days and later cascaded in the tropics. Here, we analyzed 176 SARS-CoV-2 genomes across different latitudes and climate (Koppens climate) that provided insights about within species virus evolution and its relation to abiotic factors. Two genetically variant groups, named as G1 and G2 were identified, well defined by four mutations. The G1 group (ancestor), is mainly restricted to warm and moist, temperate climate (Koppens C climate) while its descendent G2 group surpasses the climatic restrictions of G1, initially cascading into neighboring cold climate (D) of higher latitudes and later into hot climate of the tropics (A). It appears that the gradation of temperate climate (Cfa-Cfb) to cold climate (Dfa-Dfb) drives the evolution of G1 into G2 variant group which later adapted to tropical climate (A) as well. It seems this virus followed inverse latitudinal gradient in the beginning due to its preference towards temperate (C) and cold climate (D). Our work elucidates virus evolutionary studies combined with climatic studies can provide crucial information about the pathogenesis and natural spreading pathways in such outbreaks which is hard to achieve through individual studies. Mutational insights gained may help design an efficacious vaccine.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC=\"FIGDIR/small/147074v3_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (28K):\norg.highwire.dtl.DTLVardef@f39a3org.highwire.dtl.DTLVardef@1910598org.highwire.dtl.DTLVardef@6516corg.highwire.dtl.DTLVardef@cbb48c_HPS_FORMAT_FIGEXP  M_FIG C_FIG In BriefThe authors elucidate adaptation of SARS-CoV-2 to different climates by studying phylogenetics and the distribution of strains on Koppens climate map.\n\nHighlightsO_LIPhylogenetic network divides SARS-CoV-2 strains into two variant groups, G1 and G2.\nC_LIO_LIG1 strains is restricted to Koppens \"temperate\" climate (mainly Cfa-Cfb).\nC_LIO_LIG2 strains has evolved from G1 to sustain in other climates mainly \"humid-continental\" (Dfa-Dfb) and \"tropical-savannah\" (Aw) climate.\nC_LI",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Priyanka Bajaj",
-        "author_inst": "Indian Institute of Science"
-      },
-      {
-        "author_name": "Prakash Chandra Arya",
-        "author_inst": "Indian Institute of Science"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "evolutionary biology"
-  },
   {
     "rel_doi": "10.1101/2020.06.15.150482",
     "rel_title": "SARS-CoV-2 mutations altering regulatory properties: deciphering host's and virus's perspectives",
@@ -1343759,6 +1342901,33 @@
     "type": "new results",
     "category": "cell biology"
   },
+  {
+    "rel_doi": "10.1101/2020.06.22.165787",
+    "rel_title": "Detailed phylogenetic analysis of SARS-CoV-2 reveals latent capacity to bind human ACE2 receptor",
+    "rel_date": "2020-06-23",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.22.165787",
+    "rel_abs": "SARS-CoV-2 is a unique event, having emerged suddenly as a highly infectious viral pathogen for human populations. Previous phylogenetic analyses show its closest known evolutionary relative to be a virus detected in bats (RaTG13), with a common assumption that SARS-CoV-2 evolved from a zoonotic ancestor via recent genetic changes (likely in the Spike protein receptor binding domain - or RBD) that enabled it to infect humans. We used detailed phylogenetic analysis, ancestral sequence reconstruction, and in situ molecular dynamics simulations to examine the Spike-RBDs functional evolution, finding that the common ancestral virus with RaTG13, dating to at least 2013, possessed high binding affinity to the human ACE2 receptor. This suggests that SARS-CoV-2 likely possessed a latent capacity to bind to human cellular targets (though this may not have been sufficient for successful infection) and emphasizes the importance to expand the cataloging and monitoring of viruses circulating in both human and non-human populations.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Erin Brintnell",
+        "author_inst": "University of Calgary"
+      },
+      {
+        "author_name": "Mehul Gupta",
+        "author_inst": "University of Calgary"
+      },
+      {
+        "author_name": "Dave W Anderson",
+        "author_inst": "University of Calgary"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "new results",
+    "category": "evolutionary biology"
+  },
   {
     "rel_doi": "10.1101/2020.06.23.167544",
     "rel_title": "An Enzymatic TMPRSS2 Assay for Assessment of Clinical Candidates and Discovery of Inhibitors as Potential Treatment of COVID-19",
@@ -1344996,93 +1344165,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.06.18.20130377",
-    "rel_title": "Rapid SARS-CoV-2 testing in primary material based on a novel multiplex LAMP assay",
-    "rel_date": "2020-06-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20130377",
-    "rel_abs": "BackgroundRapid and extensive testing of large parts of the population and specific subgroups is crucial for proper management of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and decision-making in times of a pandemic outbreak. However, point-of-care (POC) testing in places such as emergency units, outpatient clinics, airport security points or the entrance of any public building is a major challenge. The need for thermal cycling and nucleic acid isolation hampers the use of standard PCR-based methods for this purpose.\n\nMethodsTo avoid these obstacles, we tested PCR-independent methods for the detection of SARS-CoV-2 RNA from primary material (nasopharyngeal swabs) including loop-mediated isothermal amplification (LAMP) and specific high-sensitivity enzymatic reporter unlocking (SHERLOCK).\n\nResultsWhilst specificity of standard LAMP assays appears to be satisfactory, sensitivity does not reach the current gold-standard quantitative real-time polymerase chain reaction (qPCR) assays yet. We describe a novel multiplexed LAMP approach and validate its sensitivity on primary samples. This approach allows for fast and reliable identification of infected individuals. Primer optimization and multiplexing helps to increase sensitivity significantly. In addition, we directly compare and combine our novel LAMP assays with SHERLOCK.\n\nConclusionIn summary, this approach reveals one-step multiplexed LAMP assays as a prime-option for the development of easy and cheap POC test kits.",
-    "rel_num_authors": 18,
-    "rel_authors": [
-      {
-        "author_name": "Bernhard Schermer",
-        "author_inst": "University Hospital of Cologne"
-      },
-      {
-        "author_name": "Francesca Fabretti",
-        "author_inst": "University Hospital of Cologne"
-      },
-      {
-        "author_name": "Maximilian Damagnez",
-        "author_inst": "University of Cologne"
-      },
-      {
-        "author_name": "Veronica Di Cristanziano",
-        "author_inst": "Institute of Virology"
-      },
-      {
-        "author_name": "Eva Heger",
-        "author_inst": "University of Cologne"
-      },
-      {
-        "author_name": "Sita Arjune",
-        "author_inst": "University Hospital Cologne"
-      },
-      {
-        "author_name": "Nathan A Tanner",
-        "author_inst": "New England Biolabs"
-      },
-      {
-        "author_name": "Thomas Imhof",
-        "author_inst": "University of Cologne"
-      },
-      {
-        "author_name": "Manuel Koch",
-        "author_inst": "University of Cologne"
-      },
-      {
-        "author_name": "Alim Ladha",
-        "author_inst": "MIT, Boston"
-      },
-      {
-        "author_name": "Julia Joung",
-        "author_inst": "MIT, Boston"
-      },
-      {
-        "author_name": "Jonathan S. Gootenberg",
-        "author_inst": "MIT, Boston"
-      },
-      {
-        "author_name": "Omar O. Abudayyeh",
-        "author_inst": "MIT, Boston"
-      },
-      {
-        "author_name": "Volker Burst",
-        "author_inst": "University Hospital Cologne"
-      },
-      {
-        "author_name": "Feng Zhang",
-        "author_inst": "MIT, Boston"
-      },
-      {
-        "author_name": "Florian Klein",
-        "author_inst": "University of Cologne"
-      },
-      {
-        "author_name": "Thomas Benzing",
-        "author_inst": "University Hospital of Cologne"
-      },
-      {
-        "author_name": "Roman-Ulrich Mueller",
-        "author_inst": "University Hospital of Cologne"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.06.18.20135046",
     "rel_title": "Clinical characteristics and outcomes of critically ill patients with COVID-19 in a tertiary community hospital in upstate New York",
@@ -1345269,6 +1344351,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.06.18.20132977",
+    "rel_title": "Covid19 infection spread in Greece: Ensemble forecasting models with statistically calibrated parameters and stochastic noise",
+    "rel_date": "2020-06-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20132977",
+    "rel_abs": "Following the outbreak of the novel coronavirus SARS-Cov2 in Europe and the subsequent failure of national healthcare systems to sufficiently respond to the fast spread of the pandemic, extensive statistical analysis and accurate forecasting of the epidemic in local communities is of primary importance in order to better organize the social and healthcare interventions and determine the epidemiological characteristics of the disease. For this purpose, a novel combination of Monte Carlo simulations, wavelet analysis and least squares optimization is applied to a known basis of SEIR compartmental models, resulting in the development of a novel class of stochastic epidemiological models with promising short and medium-range forecasting performance. The models are calibrated with the epidemiological data of Greece, while data from Switzerland and Germany are used as a supplementary background. The developed models are capable of estimating parameters of primary importance such as the reproduction number and the real magnitude of the infection in Greece. A clear demonstration of how the social distancing interventions managed to promptly restrict the epidemic growth in the country is included. The stochastic models are also able to generate robust 30-day and 60-day forecast scenarios in terms of new cases, deaths, active cases and recoveries.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Georgios Politis Sr.",
+        "author_inst": "National Technical University of Athens"
+      },
+      {
+        "author_name": "Leontios Hadjileontiadis Sr.",
+        "author_inst": "KHALIFA UNIVERSITY"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.06.20.20130476",
     "rel_title": "Characterizing super-spreading events and age-specific infectivity of COVID-19 transmission in Georgia, USA",
@@ -1346485,97 +1345590,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.06.18.20131326",
-    "rel_title": "Transcriptomic Similarities and Differences in Host Response between SARS-CoV-2 and Other Viral Infections",
-    "rel_date": "2020-06-21",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20131326",
-    "rel_abs": "COVID-19 is a pandemic that shares certain clinical characteristics with other acute viral infections. Here, we studied the whole-blood transcriptomic host response to SARS-CoV-2 and compared it with other viral infections to understand similarities and differences in host response. Using RNAseq we profiled peripheral blood from 24 healthy controls and 62 prospectively enrolled patients with community-acquired lower respiratory tract infection by SARS-Cov-2 within the first 24 hours of hospital admission. We also compiled and curated 23 independent studies that profiled 1,855 blood samples from patients with one of six viruses (influenza, RSV, HRV, ebola, Dengue, and SARS-CoV-1). We show gene expression changes in peripheral blood in patients with COVID-19 versus healthy controls are highly correlated with changes in response to other viral infections (r=0.74, p<0.001). However, two genes, ACO1 and ATL3, show significantly opposite changes between conditions. Pathway analysis in patients with COVID-19 or other viral infections versus healthy controls identified similar pathways including neutrophil activation, innate immune response, immune response to viral infection, and cytokine production for over-expressed genes. Conversely, for under-expressed genes, pathways indicated repression of lymphocyte differentiation and T cell activation. When comparing transcriptome profiles of patients with COVID-19 directly with those with other viral infections, we found 114 and 302 genes were over- or under-expressed, respectively, during COVID-19. Pathways analysis did not identify any significant pathways in these genes, suggesting novel responses to further study. Statistical deconvolution using immunoStates found that M1 macrophages, plasmacytoid dendritic cells, CD14+ monocytes, CD4+ T cells, and total B cells showed change consistently in the same direction across all viral infections including COVID-19. Those that increased in COVID-19 but decreased in non-COVID-19 viral infections were CD56bright NK cells, M2 macrophages, and total NK cells. The concordant and discordant responses mapped out here provide a window to explore the pathophysiology of COVID-19 versus other viral infections and show clear differences in signaling pathways and cellularity as part of the host response to SARS-CoV-2.",
-    "rel_num_authors": 19,
-    "rel_authors": [
-      {
-        "author_name": "Simone A Thair",
-        "author_inst": "Inflammatix, Inc. 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA"
-      },
-      {
-        "author_name": "Yudong D He",
-        "author_inst": "Inflammatix, Inc. 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA"
-      },
-      {
-        "author_name": "Yehudit Hasin-Brumshtein",
-        "author_inst": "Inflammatix, Inc. 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA"
-      },
-      {
-        "author_name": "Suraj Sakaram",
-        "author_inst": "Inflammatix, Inc. 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA"
-      },
-      {
-        "author_name": "Rushika Pandya",
-        "author_inst": "Inflammatix, Inc. 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA"
-      },
-      {
-        "author_name": "Jiaying Toh",
-        "author_inst": "Institute for Immunity, Transplantation and Infection, School of Medicine and Center for Biomedical Informatics Research, Department of Medicine, Stanford Unive"
-      },
-      {
-        "author_name": "David Rawling",
-        "author_inst": "Inflammatix, Inc. 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA"
-      },
-      {
-        "author_name": "Melissa Remmel",
-        "author_inst": "Inflammatix, Inc. 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA"
-      },
-      {
-        "author_name": "Sabrina Coyle",
-        "author_inst": "Inflammatix, Inc. 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA"
-      },
-      {
-        "author_name": "George N Dalekos",
-        "author_inst": "Department of Internal Medicine, University of Thessaly, Larissa General Hospital, Greece"
-      },
-      {
-        "author_name": "Ioannis Koutsodimitropoulos",
-        "author_inst": "Intensive Care Unit, Latseion General Hospital of Elefsis, Greece"
-      },
-      {
-        "author_name": "Glykeria Vlachogianni",
-        "author_inst": "Intensive Care Unit, Aghios Dimitrios Thessaloniki General Hospital, Greece"
-      },
-      {
-        "author_name": "Eleni Gkeka",
-        "author_inst": "Intensive Care Unit, AHEPA Thessaloniki General Hospital, Greece"
-      },
-      {
-        "author_name": "Eleni Karakike",
-        "author_inst": "4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece"
-      },
-      {
-        "author_name": "Georgia Damoraki",
-        "author_inst": "8.\t4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece"
-      },
-      {
-        "author_name": "Nikolaos Antonakos",
-        "author_inst": "4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece"
-      },
-      {
-        "author_name": "Purvesh Khatri",
-        "author_inst": "Institute for Immunity, Transplantation and Infection, School of Medicine and Center for Biomedical Informatics Research, Department of Medicine, Stanford Unive"
-      },
-      {
-        "author_name": "Evangelos J Giamarellos-Bourboulis",
-        "author_inst": "4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece"
-      },
-      {
-        "author_name": "Timothy E Sweeney",
-        "author_inst": "Inflammatix, Inc., 863 Mitten Rd, Suite 104, Burlingame, CA, 94010, USA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.06.19.20135517",
     "rel_title": "The Covid-19 epidemic in the UK",
@@ -1347002,6 +1346016,57 @@
     "type": "new results",
     "category": "genomics"
   },
+  {
+    "rel_doi": "10.1101/2020.06.20.162826",
+    "rel_title": "anti-IL-6 versus anti-IL-6R Blocking Antibodies to Treat Acute Ebola Infection in BALB/c Mice with Potential Implications for Treating Patients Presenting with COVID-19",
+    "rel_date": "2020-06-21",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.20.162826",
+    "rel_abs": "Cytokine release syndrome (CRS) is known to be a factor in morbidity and mortality associated with acute viral infections including those caused by filoviruses and coronaviruses. IL-6 has been implicated as a cytokine negatively associated with survival after filovirus and coronavirus infection. However, IL-6 has also been shown to be an important mediator of innate immunity and important for the host response to an acute viral infection. Clinical studies are now being conducted by various researchers to evaluate the possible role of IL-6 blockers to improve outcomes in critically ill patients with CRS. Most of these studies involve the use of anti-IL-6R monoclonal antibodies (-IL-6R mAbs). We present data showing that direct neutralization of IL-6 with an -IL-6 mAb in a BALB/c Ebolavirus (EBOV) challenge model produced a statistically significant improvement in outcome compared with controls when administered within the first 24 hours of challenge and repeated every 72 hours. A similar effect was seen in mice treated with the same dose of -IL-6R mAb when the treatment was delayed 48 hrs post-challenge. These data suggest that direct neutralization of IL-6, early during the course of infection, may provide additional clinical benefits to IL-6 receptor blockade alone during treatment of patients with virus-induced CRS.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Reid Martin Rubsamen",
+        "author_inst": "Flow Pharma, Inc."
+      },
+      {
+        "author_name": "Scott Burkholz",
+        "author_inst": "Flow Pharma, Inc."
+      },
+      {
+        "author_name": "Shane Massey",
+        "author_inst": "University of Texas Medical Branch"
+      },
+      {
+        "author_name": "Trevor Brasel",
+        "author_inst": "University of Texas Medical Branch"
+      },
+      {
+        "author_name": "Tom Hodge",
+        "author_inst": "Flow Pharma, Inc."
+      },
+      {
+        "author_name": "Lu Wang",
+        "author_inst": "Flow Pharma, Inc."
+      },
+      {
+        "author_name": "Charles Herst",
+        "author_inst": "Flow Pharma, Inc."
+      },
+      {
+        "author_name": "Richard Thomas Carback III",
+        "author_inst": "Flow Pharma, Inc"
+      },
+      {
+        "author_name": "Paul Harris",
+        "author_inst": "Columbia University Medical Center"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2020.06.21.163592",
     "rel_title": "RNA-Dependent RNA Polymerase From SARS-CoV-2. Mechanism Of Reaction And Inhibition By Remdesivir.",
@@ -1348295,45 +1347360,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "genetic and genomic medicine"
   },
-  {
-    "rel_doi": "10.1101/2020.06.18.20135103",
-    "rel_title": "Modeling quantitative traits for COVID-19 case reports",
-    "rel_date": "2020-06-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20135103",
-    "rel_abs": "Medical practitioners record the condition status of a patient through qualitative and quantitative observations. The measurement of vital signs and molecular parameters in the clinics gives a complementary description of abnormal phenotypes associated with the progression of a disease. The Clinical Measurement Ontology (CMO) is used to standardize annotations of these measurable traits. However, researchers have no way to describe how these quantitative traits relate to phenotype concepts in a machine-readable manner. Using the WHO clinical case report form standard for the COVID-19 pandemic, we modeled quantitative traits and developed OWL axioms to formally relate clinical measurement terms with anatomical, biomolecular entities and phenotypes annotated with the Uber-anatomy ontology (Uberon), Chemical Entities of Biological Interest (ChEBI) and the Phenotype and Trait Ontology (PATO) biomedical ontologies. The formal description of these relations allows interoperability between clinical and biological descriptions, and facilitates automated reasoning for analysis of patterns over quantitative and qualitative biomedical observations.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Nuria Queralt-Rosinach",
-        "author_inst": "Leids Universitair Medisch Centrum"
-      },
-      {
-        "author_name": "Susan Bello",
-        "author_inst": "The Jackson Laboratory"
-      },
-      {
-        "author_name": "Robert Hoehndorf",
-        "author_inst": "King Abdullah University of Science and Technology"
-      },
-      {
-        "author_name": "Claus Weiland",
-        "author_inst": "Senckenberg Biodiversity and Climate Research Center"
-      },
-      {
-        "author_name": "Philippe Rocca-Serra",
-        "author_inst": "University of Oxford"
-      },
-      {
-        "author_name": "Paul N Schofield",
-        "author_inst": "University of Cambridge"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health informatics"
-  },
   {
     "rel_doi": "10.1101/2020.06.19.20135905",
     "rel_title": "SARS-CoV-2 RT-PCR profile in 298 Indian COVID-19 patients : a retrospective observational study",
@@ -1348608,6 +1347634,77 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.06.19.20135756",
+    "rel_title": "Sensitivity of RT-PCR testing of upper respiratory tract samples for SARS-CoV-2 in hospitalised patients: a retrospective cohort study.",
+    "rel_date": "2020-06-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.19.20135756",
+    "rel_abs": "ObjectivesTo determine the sensitivity and specificity of RT-PCR testing of upper respiratory tract (URT) samples from hospitalised patients with COVID-19, compared to the gold standard of a clinical diagnosis.\n\nMethodsAll URT RT-PCR testing for SARS-CoV-2 in NHS Lothian, Scotland, United Kingdom between the 7th of February and 19th April 2020 (inclusive) was reviewed, and hospitalised patients were identified. All URT RT-PCR tests were analysed for each patient to determine the sequence of negative and positive results. For those who were tested twice or more but never received a positive result, case records were reviewed, and a clinical diagnosis of COVID-19 allocated based on clinical features, discharge diagnosis, and radiology and haematology results. For those who had negative URT RT-PCR tests but a clinical diagnosis of COVID-19, respiratory samples were retested using a multiplex respiratory panel, a second SARS-CoV-2 RT-PCR assay, and a human RNase P control.\n\nResultsCompared to the gold standard of a clinical diagnosis of COVID-19, the sensitivity of an initial URT RT-PCR for COVID-19 was 82.2% (95% confidence interval 79.0-85.1%). Two consecutive URT RT-PCR tests increased sensitivity to 90.6% (CI 88.0-92.7%). A further 2.2% and 0.9% of patients who received a clinical diagnosis of COVID-19 were positive on a third and fourth test.\n\nConclusionsThe sensitivity of a single RT-PCR test of an URT sample in hospitalised patients is 82.2%. Sensitivity increases to 90.6% when patients are tested twice. A proportion of cases with clinically defined COVID-19 never test positive on URT RT-PCR despite repeated testing.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Thomas C Williams",
+        "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, UK"
+      },
+      {
+        "author_name": "Elizabeth Wastnedge",
+        "author_inst": "Clinical Microbiology & Virology, Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK"
+      },
+      {
+        "author_name": "Gina McAllister",
+        "author_inst": "Clinical Microbiology & Virology, Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK"
+      },
+      {
+        "author_name": "Ramya Bhatia",
+        "author_inst": "Clinical Microbiology & Virology, Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK"
+      },
+      {
+        "author_name": "Kate Cuschieri",
+        "author_inst": "Clinical Microbiology & Virology, Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK"
+      },
+      {
+        "author_name": "Kallirroi Kefala",
+        "author_inst": "Edinburgh Critical Care Research Group, University of Edinburgh, Edinburgh, UK"
+      },
+      {
+        "author_name": "Fiona J Hamilton",
+        "author_inst": "Clinical Microbiology & Virology, Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK"
+      },
+      {
+        "author_name": "Ingolfur Johannessen",
+        "author_inst": "Clinical Microbiology & Virology, Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK"
+      },
+      {
+        "author_name": "Ian F Laurenson",
+        "author_inst": "Clinical Microbiology & Virology, Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK"
+      },
+      {
+        "author_name": "Jill Shepherd",
+        "author_inst": "Clinical Microbiology & Virology, Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK"
+      },
+      {
+        "author_name": "Alistair Stewart",
+        "author_inst": "eHealth Directorate, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK"
+      },
+      {
+        "author_name": "Donal Waters",
+        "author_inst": "Clinical Microbiology & Virology, Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK"
+      },
+      {
+        "author_name": "Helen Wise",
+        "author_inst": "Blood Sciences, Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK"
+      },
+      {
+        "author_name": "Kate Templeton",
+        "author_inst": "Clinical Microbiology & Virology, Directorate of Laboratory Medicine, Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, UK"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.06.18.20135137",
     "rel_title": "Epidemiological description and analysis of RdRp, E and N genes dynamic by RT-PCR of SARS-CoV-2 in Moroccan population: Experience of the National Reference Laboratory (LNR)-UM6SS",
@@ -1349649,105 +1348746,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.06.18.20134676",
-    "rel_title": "Cardiometabolic traits, sepsis and severe covid-19 with respiratory failure: a Mendelian randomization investigation",
-    "rel_date": "2020-06-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20134676",
-    "rel_abs": "ObjectivesTo investigate whether there is a causal effect of cardiometabolic traits on risk of sepsis and severe covid-19.\n\nDesignMendelian randomisation analysis.\n\nSettingUK Biobank and HUNT study population-based cohorts for risk of sepsis, and genome-wide association study summary data for risk of severe covid-19 with respiratory failure.\n\nParticipants12,455 sepsis cases (519,885 controls) and 1,610 severe covid-19 with respiratory failure cases (2,205 controls).\n\nExposureGenetic variants that proxy body mass index (BMI), lipid traits, systolic blood pressure, lifetime smoking score, and type 2 diabetes liability - derived from studies considering between 188,577 to 898,130 participants.\n\nMain outcome measuresRisk of sepsis and severe covid-19 with respiratory failure.\n\nResultsHigher genetically proxied BMI and lifetime smoking score were associated with increased risk of sepsis in both UK Biobank (BMI: odds ratio 1.38 per standard deviation increase, 95% confidence interval [CI] 1.27 to 1.51; smoking: odds ratio 2.81 per standard deviation increase, 95% CI 2.09-3.79) and HUNT (BMI: 1.41, 95% CI 1.18 to 1.69; smoking: 1.93, 95% CI 1.02-3.64). Higher genetically proxied BMI and lifetime smoking score were also associated with increased risk of severe covid-19, although with wider confidence intervals (BMI: 1.75, 95% CI 1.20 to 2.57; smoking: 3.94, 95% CI 1.13 to 13.75). There was limited evidence to support associations of genetically proxied lipid traits, systolic blood pressure or type 2 diabetes liability with risk of sepsis or severe covid-19. Similar findings were generally obtained when using Mendelian randomization methods that are more robust to the inclusion of pleiotropic variants, although the precision of estimates was reduced.\n\nConclusionsOur findings support a causal effect of elevated BMI and smoking on risk of sepsis and severe covid-19. Clinical and public health interventions targeting obesity and smoking are likely to reduce sepsis and covid-19 related morbidity, along with the plethora of other health-related outcomes that these traits adversely affect.\n\nSummary boxesO_ST_ABSWhat is already known on this topicC_ST_ABSO_LISepsis and severe covid-19 are major contributors to global morbidity and mortality.\nC_LIO_LICardiometabolic risk factors have been associated with risk of sepsis and severe covid-19, but it is unclear if they are having causal effects.\nC_LI\n\nWhat this study addsO_LIUsing Mendelian randomization analyses, this study provides evidence to support that higher body mass index and lifetime smoking score both increase risk of sepsis and severe covid-19 with respiratory failure.\nC_LIO_LIClinical and public health interventions targeting obesity and smoking are likely to reduce sepsis and covid-19 related morbidity, along with the plethora of other health-related outcomes that these traits adversely affect.\nC_LI",
-    "rel_num_authors": 21,
-    "rel_authors": [
-      {
-        "author_name": "Ponsford J Mark",
-        "author_inst": "University Hospital Wales"
-      },
-      {
-        "author_name": "Apostolos Gkatzionis",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Venexia Walker",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Andrew Grant",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Robyn E Wootton",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Luke S P Moore",
-        "author_inst": "Chelsea & Westminster NHS Foundation Trust"
-      },
-      {
-        "author_name": "Segun Fatumo",
-        "author_inst": "London School of Hygiene & Tropical Medicine"
-      },
-      {
-        "author_name": "Amy Mason",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Verena Zuber",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Cristen Willer",
-        "author_inst": "University of Michigan"
-      },
-      {
-        "author_name": "Humaira Rasheed",
-        "author_inst": "Norwegian University of Science and Technology"
-      },
-      {
-        "author_name": "Ben Brumpton",
-        "author_inst": "Norwegian University of Science and Technology"
-      },
-      {
-        "author_name": "Kristian Hveem",
-        "author_inst": "Norwegian University of Science and Technology"
-      },
-      {
-        "author_name": "Jan Kristian Damas",
-        "author_inst": "Norwegian University of Science and Technology"
-      },
-      {
-        "author_name": "Neil M Davies",
-        "author_inst": "University of Bristol"
-      },
-      {
-        "author_name": "Bjorn Olav Asvold",
-        "author_inst": "Norwegian University of Science and Technology"
-      },
-      {
-        "author_name": "Erik Solligard",
-        "author_inst": "Norwegian University of Science and Technology"
-      },
-      {
-        "author_name": "Simon Jones",
-        "author_inst": "Cardiff University"
-      },
-      {
-        "author_name": "Stephen Burgess",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Tormod Rogne",
-        "author_inst": "Norwegian University of Science and Technology"
-      },
-      {
-        "author_name": "Dipender Gill",
-        "author_inst": "Imperial College London"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.06.18.20134734",
     "rel_title": "Epidemiological characterization of asymptomatic carriers of COVID-19 in Colombia",
@@ -1349994,6 +1348992,141 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
+  {
+    "rel_doi": "10.1101/2020.06.18.20134742",
+    "rel_title": "Racial and ethnic determinants of Covid-19 risk",
+    "rel_date": "2020-06-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20134742",
+    "rel_abs": "BackgroundRacial and ethnic minorities have disproportionately high hospitalization rates and mortality related to the novel coronavirus disease 2019 (Covid-19). There are comparatively scant data on race and ethnicity as determinants of infection risk.\n\nMethodsWe used a smartphone application (beginning March 24, 2020 in the United Kingdom [U.K.] and March 29, 2020 in the United States [U.S.]) to recruit 2,414,601 participants who reported their race/ethnicity through May 25, 2020 and employed logistic regression to determine the adjusted odds ratios (aORs) and 95% confidence intervals (CIs) for a positive Covid-19 test among racial and ethnic groups.\n\nResultsWe documented 8,858 self-reported cases of Covid-19 among 2,259,841 non-Hispanic white; 79 among 9,615 Hispanic; 186 among 18,176 Black; 598 among 63,316 Asian; and 347 among 63,653 other racial minority participants. Compared with non-Hispanic white participants, the risk for a positive Covid-19 test was increased across racial minorities (aORs ranging from 1.24 to 3.51). After adjustment for socioeconomic indices and Covid-19 exposure risk factors, the associations (aOR [95% CI]) were attenuated but remained significant for Hispanic (1.58 [1.24-2.02]) and Black participants (2.56 [1.93-3.39]) in the U.S. and South Asian (1.52 [1.38-1.67]) and Middle Eastern participants (1.56 [1.25-1.95]) in the U.K. A higher risk of Covid-19 and seeking or receiving treatment was also observed for several racial/ethnic minority subgroups.\n\nConclusionsOur results demonstrate an increase in Covid-19 risk among racial and ethnic minorities not completely explained by other risk factors for Covid-19, comorbidities, and sociodemographic characteristics. Further research investigating these disparities are needed to inform public health measures.",
+    "rel_num_authors": 30,
+    "rel_authors": [
+      {
+        "author_name": "Chun-Han Lo",
+        "author_inst": "Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A."
+      },
+      {
+        "author_name": "Long H. Nguyen",
+        "author_inst": "Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A."
+      },
+      {
+        "author_name": "David A. Drew",
+        "author_inst": "Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A."
+      },
+      {
+        "author_name": "Mark S. Graham",
+        "author_inst": "School of Biomedical Engineering & Imaging Sciences, King's College London, London, U.K."
+      },
+      {
+        "author_name": "Erica T. Warner",
+        "author_inst": "Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A."
+      },
+      {
+        "author_name": "Amit D. Joshi",
+        "author_inst": "Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A."
+      },
+      {
+        "author_name": "Christina M. Astley",
+        "author_inst": "Computational Epidemiology Lab and Division of Endocrinology, Boston Children's Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A"
+      },
+      {
+        "author_name": "Chuan-Guo Guo",
+        "author_inst": "Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A."
+      },
+      {
+        "author_name": "Wenjie Ma",
+        "author_inst": "Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A."
+      },
+      {
+        "author_name": "Raaj S. Mehta",
+        "author_inst": "Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A."
+      },
+      {
+        "author_name": "Sohee Kwon",
+        "author_inst": "Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A."
+      },
+      {
+        "author_name": "Mingyang Song",
+        "author_inst": "Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A."
+      },
+      {
+        "author_name": "Richard Davies",
+        "author_inst": "Zoe Global Limited, London, U.K."
+      },
+      {
+        "author_name": "Joan Capdevila",
+        "author_inst": "Zoe Global Limited, London, U.K."
+      },
+      {
+        "author_name": "Karla A. Lee",
+        "author_inst": "Department of Twin Research and Genetic Epidemiology, King's College London, London, U.K."
+      },
+      {
+        "author_name": "Mary Ni Lochlainn",
+        "author_inst": "Department of Twin Research and Genetic Epidemiology, King's College London, London, U.K."
+      },
+      {
+        "author_name": "Thomas Varsavsky",
+        "author_inst": "School of Biomedical Engineering & Imaging Sciences, King's College London, London, U.K."
+      },
+      {
+        "author_name": "Carole H. Sudre",
+        "author_inst": "School of Biomedical Engineering & Imaging Sciences, King's College London, London, U.K."
+      },
+      {
+        "author_name": "Jonathan Wolf",
+        "author_inst": "Zoe Global Limited, London, U.K."
+      },
+      {
+        "author_name": "Yvette C. Cozier",
+        "author_inst": "Slone Epidemiology Center, Boston University, Boston, Massachusetts, U.S.A."
+      },
+      {
+        "author_name": "Lynn Rosenberg",
+        "author_inst": "Slone Epidemiology Center, Boston University, Boston, Massachusetts, U.S.A."
+      },
+      {
+        "author_name": "Lynne R. Wilkens",
+        "author_inst": "Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, U.S.A."
+      },
+      {
+        "author_name": "Christopher A. Haiman",
+        "author_inst": "Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, California, U."
+      },
+      {
+        "author_name": "Loic Le Marchand",
+        "author_inst": "Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, U.S.A."
+      },
+      {
+        "author_name": "Julie R. Palmer",
+        "author_inst": "Slone Epidemiology Center, Boston University, Boston, Massachusetts, U.S.A."
+      },
+      {
+        "author_name": "Tim D. Spector",
+        "author_inst": "Department of Twin Research and Genetic Epidemiology, King's College London, London, U.K."
+      },
+      {
+        "author_name": "Sebastien Ourselin",
+        "author_inst": "School of Biomedical Engineering & Imaging Sciences, King's College London, London, U.K."
+      },
+      {
+        "author_name": "Claire J. Steves",
+        "author_inst": "Department of Twin Research and Genetic Epidemiology, King's College London, London, U.K."
+      },
+      {
+        "author_name": "Andrew T. Chan",
+        "author_inst": "Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School. Boston, Massachusetts, U.S.A."
+      },
+      {
+        "author_name": "- COPE Consortium",
+        "author_inst": ""
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.06.17.20134031",
     "rel_title": "Prolonged low-dose methylprednisolone in patients with severe COVID-19 pneumonia",
@@ -1351887,45 +1351020,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2020.06.19.161620",
-    "rel_title": "Multi-pronged human protein mimicry by SARS-CoV-2 reveals bifurcating potential for MHC detection and immune evasion",
-    "rel_date": "2020-06-19",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.19.161620",
-    "rel_abs": "The hand of molecular mimicry in shaping SARS-CoV-2 evolution and immune evasion remains to be deciphered. We identify 33 distinct 8-mer/9-mer peptides that are identical between SARS-CoV-2 and human proteomes, along similar extents of viral mimicry observed in other viruses. Interestingly, 20 novel peptides have not been observed in any previous human coronavirus (HCoV) strains. Four of the total mimicked 8-mers/9-mers map onto HLA-B*40:01, HLA-B*40:02, and HLA-B*35:01 binding peptides from human PAM, ANXA7, PGD, and ALOX5AP proteins. This mimicry of multiple human proteins by SARS-CoV-2 is made salient by the targeted genes being focally expressed in arteries, lungs, esophagus, pancreas, and macrophages. Further, HLA-A*03 restricted 8-mer peptides are shared broadly by human and coronaviridae helicases with primary expression of the mimicked human proteins in the neurons and immune cells. This study presents the first comprehensive scan of peptide mimicry by SARS-CoV-2 of the human proteome and motivates follow-up research into its immunological consequences.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "AJ Venkatakrishnan",
-        "author_inst": "nference"
-      },
-      {
-        "author_name": "Nikhil Kayal",
-        "author_inst": "nference"
-      },
-      {
-        "author_name": "Praveen Anand",
-        "author_inst": "nference Labs"
-      },
-      {
-        "author_name": "Andrew D Badley",
-        "author_inst": "Mayo Clinic"
-      },
-      {
-        "author_name": "George M Church",
-        "author_inst": "Harvard Medical School"
-      },
-      {
-        "author_name": "Venky Soundararajan",
-        "author_inst": "nference"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "evolutionary biology"
-  },
   {
     "rel_doi": "10.1101/2020.06.19.161141",
     "rel_title": "High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States",
@@ -1352444,6 +1351538,77 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2020.06.17.20133678",
+    "rel_title": "FAR AWAY FROM HERD IMMUNITY TO SARS-CoV-2: results from a survey in healthy blood donors in South Eastern Italy",
+    "rel_date": "2020-06-19",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.17.20133678",
+    "rel_abs": "Here we present results from a survey on anti-SARS-CoV-2 seroprevalence in healthy blood donors from a low incidence COVID-19 area (Apulia region, South Eastern Italy).\n\nAmong 904 subjects tested, only in 9 cases (0.99%) antibodies against SARS-CoV-2 were demonstrated. All the 9 seropositive patients were negative for the research of viral RNA by RT-PCR in nasopharyngeal swab.\n\nThese data, along with those recently reported from other countries, clearly show that we are very far from herd immunity and that the containment measures are at the moment the only realistic instrument we have to slow the spread of the pandemic.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "jose ramon fiore",
+        "author_inst": "University of Foggia"
+      },
+      {
+        "author_name": "michele centra",
+        "author_inst": "Ospedali Riuniti University Hospital Foggia"
+      },
+      {
+        "author_name": "armando de carlo",
+        "author_inst": "Ospedali Riuniti University Hospital, Foggia"
+      },
+      {
+        "author_name": "marco granato",
+        "author_inst": "Ospedali riuniti University Hospital Foggia"
+      },
+      {
+        "author_name": "annamaria rosa",
+        "author_inst": "Ospedali riuniti University Hospital Foggia"
+      },
+      {
+        "author_name": "lucia de feo",
+        "author_inst": "Ospedali riuniti university hospital foggia"
+      },
+      {
+        "author_name": "mariantonietta di stefano",
+        "author_inst": "University of Foggia"
+      },
+      {
+        "author_name": "maria d ' errico",
+        "author_inst": "university of foggia"
+      },
+      {
+        "author_name": "sergio lo caputo",
+        "author_inst": "University of foggia"
+      },
+      {
+        "author_name": "rosella de nittis",
+        "author_inst": "Ospedali riuniti university hospital foggia"
+      },
+      {
+        "author_name": "fabio arena",
+        "author_inst": "university of foggia"
+      },
+      {
+        "author_name": "gaetano corso",
+        "author_inst": "university of foggia"
+      },
+      {
+        "author_name": "maurizio MARGAGLIONE",
+        "author_inst": "UNIVERSITY OF FOGGIA"
+      },
+      {
+        "author_name": "TERESA ANTONIA SANTANTONIO",
+        "author_inst": "UNIVERSITY OF FOGGIA"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.06.16.20126714",
     "rel_title": "Comparative Survival Analysis of Immunomodulatory Therapy for COVID-19 'Cytokine Storm': A Retrospective Observational Cohort Study",
@@ -1353437,25 +1352602,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.06.17.20134254",
-    "rel_title": "Extrapolation of Infection Data for the CoVid-19 Virus in 21 Countries and States and Estimate of the Efficiency of Lock Down.",
-    "rel_date": "2020-06-19",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.17.20134254",
-    "rel_abs": "Predictions about the further development of the Corona pandemic are of great public interest but many approaches demand a large number of country specific parameters and are not easily transferable. A special interest of simulations on the pandemic is to trace the effect of politics for reducing the virus spread, since these measures have had an enormous impact on economy and daily life.\n\nHere a simple yet powerful algorithm is introduced for fitting the infection numbers by simple analytic functions. This way, the increase of the case numbers in periods with different regulations can be distinguished, and by extrapolating the fit functions, a forecast for the maximum numbers and time scales are possible. The effect of the restraints such as lock down are demonstrated by comparing the resulting infection history with the likely unconstrained virus spread, and it is shown that a delay of 1-4 weeks before imposing measures aiming at social distancing could have led to a complete infection of the respective populations.\n\nThe approach is simply transferable to many different states. Here data from six E.U. countries, the UK, Russia, two Asian countries, the USA and ten states inside the USA with significant case numbers are analyzed, and striking qualitative similarities are found.\n\nKeywords: Covid-19, forecast, analytic fit, France, Germany, Italy, Spain South Korea, New York, Washington, Florida, Michigan, Poland, Sweden, USA, Pennsylvania, China, Russia, UK, California, Illinois, Indiana, Maryland, North Carolina.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Walter Langel",
-        "author_inst": "University of Greifswald"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.06.17.20133637",
     "rel_title": "Two distinct immunopathological profiles in lungs of lethal COVID-19",
@@ -1353762,6 +1352908,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.06.16.20133066",
+    "rel_title": "Effect of hydroxychloroquine on SARS-CoV-2 viral load in patients with COVID-19",
+    "rel_date": "2020-06-19",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.16.20133066",
+    "rel_abs": "BackgroundSome studies have shown that hydroxychloroquine (HCQ) is an effective drug in reducing the in vitro replication of SARS-CoV-2. However, the in vivo effect of HCQ still unclear. This study aims to evaluate viral load clearance in patients with COVID-19 who underwent HCQ treatment in comparison with a control group that did not receive the drug.\n\nMethodsThis prospective study comprised consecutive viral load measurements in patients with COVID-19 hospitalized with a moderate illness. Patients received 400 mg of HCQ every 12 hours for 10 days according to the medical decision. Nasal swab samples were collected at the 1st, 7th, and 14th days of the admission.\n\nResults155 samples were collected from 66 patients with COVID-19 (60% female), with a median age of 58 years. The viral load between studied groups, assumed as a semiquantitative measure of cycle threshold (Ct) values, presented no significant difference within the three consecutive measures ({Delta}Ct) (p>0.05). We also analyzed the {Delta}Ct viral load at different intervals of sample collection ({Delta}t <7; 7-12 and >12 days) without significant differences at any {Delta}Ct (p>0.05).\n\nConclusionIn this study, we did not observe any change in viral load in vivo with the use of HCQ.\n\nSummaryWe evaluate viral load clearance in patients with COVID-19 who took hydroxychloroquine (HCQ) for treatment and those who not. Prospective viral load measurements have shown any change in viral load in vivo with the use of HCQ.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Klinger Soares Faico-Filho",
+        "author_inst": "Federal University of Sao Paulo"
+      },
+      {
+        "author_name": "Danielle Dias Conte",
+        "author_inst": "Universidade Federal de Sao Paulo"
+      },
+      {
+        "author_name": "Luciano Kleber Souza Luna",
+        "author_inst": "Universidade Federal de Sao Paulo"
+      },
+      {
+        "author_name": "Joseane Mayara Almeida Carvalho",
+        "author_inst": "Universidade Federal de Sao Paulo"
+      },
+      {
+        "author_name": "Ana Helena Sitta Perosa",
+        "author_inst": "Universidade Federal de Sao Paulo"
+      },
+      {
+        "author_name": "Nancy Bellei",
+        "author_inst": "Universidade Federal de Sao Paulo"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.06.17.20133124",
     "rel_title": "The Endothelial Dysfunction and Pyroptosis Driving the SARS-CoV-2 Immune-Thrombosis",
@@ -1354959,45 +1354144,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
-  {
-    "rel_doi": "10.1101/2020.06.17.20133454",
-    "rel_title": "Associations of Global Country Profiles and Modifiable Risk Factors with COVID-19 Cases and Deaths",
-    "rel_date": "2020-06-18",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.17.20133454",
-    "rel_abs": "Modifiable risk factors affect SARS-CoV-2 infection and mortality raising the possibility that lifestyle modification could play a role. This has not been studied at a global level. We analysed publicly available data from countries reporting COVID-19 cases and deaths. Associations of modifiable risk factors with total cases and excess deaths were determined with and without adjustment for confounders. 4,670,832 cases and 311,384 deaths were reported by 181 countries by 18th May 2020. Wealthier countries had the greatest caseload. Obesity was the primary modifiable risk factor for infection and greater age, male sex, physical inactivity and low salt consumption were associated with excess deaths. Obesity was less influential on mortality than physical inactivity. Globally, obesity confers vulnerability to SARS-CoV-2 infection and physical inactivity likely explains the greater mortality in the obese. High salt consumption may induce reductions in tissue ACE2 expression and subsequently reduce mortality rates.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Samuel Joseph Burden",
-        "author_inst": "Oxford Brookes University"
-      },
-      {
-        "author_name": "Josefien Rademaker",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Benjamin David Weedon",
-        "author_inst": "Oxford Brookes University"
-      },
-      {
-        "author_name": "Luke Whaymand",
-        "author_inst": "Oxford Brookes University"
-      },
-      {
-        "author_name": "Helen Dawes",
-        "author_inst": "Oxford Brookes University"
-      },
-      {
-        "author_name": "Alexander Jones",
-        "author_inst": "University of Oxford"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.06.16.20132787",
     "rel_title": "State-wise estimates of current hospital beds, intensive care unit (ICU) beds and ventilators in India: Are we prepared for a surge in COVID-19 hospitalizations?",
@@ -1355460,6 +1354606,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.06.16.20133140",
+    "rel_title": "COVID-19 outcomes, risk factors and associations by race: a comprehensive analysis using electronic health records data in Michigan Medicine",
+    "rel_date": "2020-06-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.16.20133140",
+    "rel_abs": "Structured AbstractO_ST_ABSImportanceC_ST_ABSBlacks/African-Americans are overrepresented in the number of COVID-19 infections, hospitalizations and deaths. Reasons for this disparity have not been well-characterized but may be due to underlying comorbidities or sociodemographic factors.\n\nObjectiveTo systematically determine patient characteristics associated with racial/ethnic disparities in COVID-19 outcomes.\n\nDesignA retrospective cohort study with comparative control groups.\n\nSettingPatients tested for COVID-19 at University of Michigan Medicine from March 10, 2020 to April 22, 2020.\n\nParticipants5,698 tested patients and two sets of comparison groups who were not tested for COVID-19: randomly selected unmatched controls (n = 7,211) and frequency-matched controls by race, age, and sex (n = 13,351).\n\nMain Outcomes and MeasuresWe identified factors associated with testing and testing positive for COVID-19, being hospitalized, requiring intensive care unit (ICU) admission, and mortality (in/out-patient during the time frame). Factors included race/ethnicity, age, smoking, alcohol consumption, healthcare utilization, and residential-level socioeconomic characteristics (SES; i.e., education, unemployment, population density, and poverty rate). Medical comorbidities were defined from the International Classification of Diseases (ICD) codes, and were aggregated into a comorbidity score.\n\nResultsOf 5,698 patients, (median age, 47 years; 38% male; mean BMI, 30.1), the majority were non-Hispanic Whites (NHW, 59.2%) and non-Hispanic Black/African-Americans (NHAA, 17.2%). Among 1,119 diagnosed, there were 41.2% NHW and 37.4% NHAA; 44.8% hospitalized, 20.6% admitted to ICU, and 3.8% died. Adjusting for age, sex, and SES, NHAA were 1.66 times more likely to be hospitalized (95% CI, 1.09-2.52; P=.02), 1.52 times more likely to enter ICU (95% CI, 0.92-2.52; P=.10). In addition to older age, male sex and obesity, high population density neighborhood (OR, 1.27 associated with one SD change [95% CI, 1.20-1.76]; P=.02) was associated with hospitalization. Pre-existing kidney disease led to 2.55 times higher risk of hospitalization (95% CI, 1.62-4.02; P<.001) in the overall population and 11.9 times higher mortality risk in NHAA (95% CI, 2.2-64.7, P=.004).\n\nConclusions and RelevancePre-existing type II diabetes/kidney diseases and living in high population density areas were associated with high risk for COVID-19 susceptibility and poor prognosis. Association of risk factors with COVID-19 outcomes differed by race. NHAA patients were disproportionately affected by obesity and kidney disease.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhat are the sociodemographic and pre-existing health conditions associated with COVID-19 outcomes and how do they differ by race/ethnicity?\n\nFindingsIn this retrospective cohort of 5,698 patients tested for COVID-19, high population density and comorbidities such as type II diabetes/kidney disease were associated with hospitalization, in addition to older age, male sex and obesity. Adjusting for covariates, non-Hispanic Blacks were 1.66 times more likely to be hospitalized and 1.52 times more likely to be admitted to ICUs than non-Hispanic Whites.\n\nMeaningTargeted interventions to support vulnerable populations are needed. Racial disparities existed in COVID-19 outcomes that cannot be explained after controlling for age, sex, and socioeconomic status.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Tian Gu",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Jasmine A. Mack",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Maxwell Salvatore",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Swaraaj Prabhu Sankar",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Thomas S. Valley",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Karandeep Singh",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Brahmajee K. Nallamothu",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Sachin Kheterpal",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Lynda Lisabeth",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Lars G. Fritsche",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Bhramar G. Mukherjee",
+        "author_inst": "University of Michigan"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.06.16.20133322",
     "rel_title": "KNOWLEDGE AND BEHAVIORS RELATED TO THE COVID-19 PANDEMIC IN MALAWI",
@@ -1356837,29 +1356042,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.06.15.20131433",
-    "rel_title": "A compound Dirichlet-Multinomial model for provincial level Covid-19 predictions in South Africa",
-    "rel_date": "2020-06-17",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20131433",
-    "rel_abs": "Accurate prediction of COVID-19 related indicators such as confirmed cases, deaths and recoveries play an important in understanding the spread and impact of the virus, as well as resource planning and allocation. In this study, we approach the prediction problem from a statistical perspective and predict confirmed cases and deaths on a provincial level. We propose the compound Dirichlet Multinomial distribution to estimate the proportion parameter of each province as mutually exclusive outcomes. Furthermore, we make an assumption of exponential growth of the total cummulative counts in order to predict future total counts. The outcomes of this approach is not only prediction. The variation of the proportion parameter is characterised by the Dirichlet distribution, which provides insight in the movement of the pandemic across provinces over time.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Alta De Waal",
-        "author_inst": "University of Pretoria"
-      },
-      {
-        "author_name": "Daan De Waal",
-        "author_inst": "University of the Free State"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.06.15.20131540",
     "rel_title": "Causes of Death and Comorbidities in Patients with COVID-19",
@@ -1357230,6 +1356412,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.06.12.20127498",
+    "rel_title": "Reducing SARS-CoV-2 infectious spreading patterns by removing S and R compartments from SIR model equation",
+    "rel_date": "2020-06-17",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.12.20127498",
+    "rel_abs": "This research points to the asymptotic instability of SIR model and its variants to predict the behavior of SARS-CoV-2 infection spreading patterns over the population and time aspects. Mainly for the \"S\" and \"R\" terms of the equation, the predictive results fail due to confounding environment of variables that sustain the virus contagion within population complex network basis of analysis. While \"S\" and \"R\" are not homologous data of analysis, thus with improper topological metrics used in many researches, these terms leads to the asymptotic feature of \"I\" term as the most stable point of analysis to achieve proper predictive methods. Having in its basis of formulation the policies adopted by countries, \"I\" therefore presents a stable fixed point orientation in order to be used as a predictive analysis of nearby future patterns of SARS-CoV-2 infection. New metrics using a Weinbull approach for \"I\" are presented and fixed point orientation (sensitivity of the method) are demonstrated empirically by worldwide statistical data.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Charles Roberto Telles",
+        "author_inst": "Secretary of State for Education of Paran"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.06.15.20131680",
     "rel_title": "Artificial Intelligence for COVID-19 Risk Classification in Kidney Disease: Can Technology Unmask an Unseen Disease?",
@@ -1358479,89 +1357680,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.06.15.152835",
-    "rel_title": "A thermostable, closed, SARS-CoV-2 spike protein trimer.",
-    "rel_date": "2020-06-17",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.15.152835",
-    "rel_abs": "The spike (S) protein of SARS-CoV-2 mediates receptor binding and cell entry and is the dominant target of the immune system. S exhibits substantial conformational flexibility. It transitions from closed to open conformations to expose its receptor binding site, and subsequently from prefusion to postfusion conformations to mediate fusion of viral and cellular membranes. S protein derivatives are components of vaccine candidates and diagnostic assays, as well as tools for research into the biology and immunology of SARS-CoV-2. Here we have designed mutations in S which allow production of thermostable, crosslinked, S protein trimers that are trapped in the closed, pre-fusion, state. We have determined the structures of crosslinked and non-crosslinked proteins, identifying two distinct closed conformations of the S trimer. We demonstrate that the designed, thermostable, closed S trimer can be used in serological assays. This protein has potential applications as a reagent for serology, virology and as an immunogen.",
-    "rel_num_authors": 17,
-    "rel_authors": [
-      {
-        "author_name": "Xiaoli Xiong",
-        "author_inst": "Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK"
-      },
-      {
-        "author_name": "Kun Qu",
-        "author_inst": "Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK"
-      },
-      {
-        "author_name": "Katarzyna A Ciazynska",
-        "author_inst": "Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK"
-      },
-      {
-        "author_name": "Myra Hosmillo",
-        "author_inst": "Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK"
-      },
-      {
-        "author_name": "Andrew P Carter",
-        "author_inst": "Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK"
-      },
-      {
-        "author_name": "Zunlong Ke",
-        "author_inst": "Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK"
-      },
-      {
-        "author_name": "Sjors H.W. Scheres",
-        "author_inst": "Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK"
-      },
-      {
-        "author_name": "Laura Bergamaschi",
-        "author_inst": "Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, UK"
-      },
-      {
-        "author_name": "Guinevere L. Grice",
-        "author_inst": "Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, UK"
-      },
-      {
-        "author_name": "Ying Zhang",
-        "author_inst": "Precision Medicine Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China"
-      },
-      {
-        "author_name": "- The CITIID-NIHR COVID-19 BioResource Collaboration",
-        "author_inst": "-"
-      },
-      {
-        "author_name": "James A. Nathan",
-        "author_inst": "Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, UK"
-      },
-      {
-        "author_name": "Stephen Baker",
-        "author_inst": "Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, UK"
-      },
-      {
-        "author_name": "Leo C. James",
-        "author_inst": "Protein and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK"
-      },
-      {
-        "author_name": "Helen E. Baxendale",
-        "author_inst": "Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK"
-      },
-      {
-        "author_name": "Ian Goodfellow",
-        "author_inst": "Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK"
-      },
-      {
-        "author_name": "John A.G. Briggs",
-        "author_inst": "Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "biochemistry"
-  },
   {
     "rel_doi": "10.1101/2020.06.16.155101",
     "rel_title": "Genome-wide CRISPR screen reveals host genes that regulate SARS-CoV-2 infection",
@@ -1359032,6 +1358150,41 @@
     "type": "new results",
     "category": "systems biology"
   },
+  {
+    "rel_doi": "10.1101/2020.06.17.156679",
+    "rel_title": "Rapid assessment of ligand binding to the SARS-CoV-2 main protease by saturation transfer difference NMR spectroscopy",
+    "rel_date": "2020-06-17",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.17.156679",
+    "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological cause of the coronavirus disease 2019, for which no effective therapeutics are available. The SARS-CoV-2 main protease (Mpro) is essential for viral replication and constitutes a promising therapeutic target. Many efforts aimed at deriving effective Mpro inhibitors are currently underway, including an international open-science discovery project, codenamed COVID Moonshot. As part of COVID Moonshot, we used saturation transfer difference nuclear magnetic resonance (STD-NMR) spectroscopy to assess the binding of putative Mpro ligands to the viral protease, including molecules identified by crystallographic fragment screening and novel compounds designed as Mpro inhibitors. In this manner, we aimed to complement enzymatic activity assays of Mpro performed by other groups with information on ligand affinity. We have made the Mpro STD-NMR data publicly available. Here, we provide detailed information on the NMR protocols used and challenges faced, thereby placing these data into context. Our goal is to assist the interpretation of Mpro STD-NMR data, thereby accelerating ongoing drug design efforts.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Anastassia  L. Kantsadi",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Emma Cattermole",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Minos-Timotheos Matsoukas",
+        "author_inst": "University of Patras"
+      },
+      {
+        "author_name": "Georgios A. Spyroulias",
+        "author_inst": "University of Patras"
+      },
+      {
+        "author_name": "Ioannis Vakonakis",
+        "author_inst": "University of Oxford"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "new results",
+    "category": "biochemistry"
+  },
   {
     "rel_doi": "10.1101/2020.06.15.152983",
     "rel_title": "Virus survival in evaporated saliva microdroplets deposited on inanimate surfaces",
@@ -1360193,33 +1359346,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.06.12.20130047",
-    "rel_title": "Spreading Analysis of COVID-19 Epidemic in Bangladesh by Dynamical Mathematical Modelling",
-    "rel_date": "2020-06-16",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.12.20130047",
-    "rel_abs": "The coronavirus disease 2019 (COVID-19), which emerged from Wuhan, China, is now a pandemic, affecting across the globe. Bangladesh also is experiencing the rapid growth of COVID-19 infection and death cases started from 8th March 2020. The purpose of providing a simple yet effective explanatory model for prediction of the future evolution of the contagion and verification of the effectiveness of the containment and lockdown measures in Bangladesh. In this study, using a modified SIR (Susceptible-Infected-Recovered) model a forecast is generated to predict the trends of COVID-19 cases in Bangladesh. The epidemic model was proposed to accommodate the effects of lockdown and individual based precautionary measures. Data has been taken and analyzed for before and after the movement control order (MCO) and during the MCO period. Modified SIR model in this work offers us an idea how the outbreak would progress based on the current data. It also has estimated that, the peak in terms of the number of infected cases will start from last of June 2020. For the total population (100%) the model gets the peaks at 214875 (infected cases) and 7743 (death cases). For the 90% population, the model shows the peaks at 244356 (infected cases) and 9100 (death cases). Analysis revealed that the lockdown and recommended individual hygiene can slow down the outbreak but unable to eradicate the disease from the society. With the current infection and death rate and existing level of personal precautionary the number of infected individuals will be increasing.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "A Arifutzzaman",
-        "author_inst": "Sunway University"
-      },
-      {
-        "author_name": "A Fargana",
-        "author_inst": "International Islamic University, Malaysia."
-      },
-      {
-        "author_name": "A A Rakhimov",
-        "author_inst": "International Islamic University, Malaysia."
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.06.13.20130245",
     "rel_title": "A systematic review protocol of the antiviral activity of chloroquine and hydroxychloroquine against COVID-19.",
@@ -1360382,6 +1359508,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pathology"
   },
+  {
+    "rel_doi": "10.1101/2020.06.13.20130419",
+    "rel_title": "Mental health service activity during COVID-19 lockdown: South London and Maudsley data on working age community and home treatment team services and mortality from February to mid-May 2020",
+    "rel_date": "2020-06-16",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.13.20130419",
+    "rel_abs": "The lockdown and social distancing policy response to the COVID-19 pandemic in the UK has a potentially important impact on provision of mental healthcare; however, there has been relatively little quantification of this. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource with 24-hourly updates of electronic mental health records data, this paper describes daily caseloads and contact numbers (face-to-face and virtual) for home treatment teams (HTTs) and working age adult community mental health teams (CMHTs) from 1st February to 15th May 2020 at the South London and Maudsley NHS Trust (SLaM), a large mental health service provider for 1.2m residents in south London. In addition daily deaths are described for all current and previous SLaM service users over this period and the same dates in 2019. In summary, comparing periods before and after 16th March 2020 the CMHT sector showed relatively stable caseloads and total contact numbers, but a substantial shift from face-to-face to virtual contacts, while HTTs showed the same changeover but reductions in caseloads and total contacts (although potentially an activity rise again during May). Number of deaths for the two months between 16th March and 15th May were 2.4-fold higher in 2020 than 2019, with 958 excess deaths.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Robert Stewart",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Evangelia Martin",
+        "author_inst": "King's College London"
+      },
+      {
+        "author_name": "Matthew Broadbent",
+        "author_inst": "South London and Maudsley NHS Foundation Trust"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "psychiatry and clinical psychology"
+  },
   {
     "rel_doi": "10.1101/2020.06.15.20129080",
     "rel_title": "What Has Been the Impact of Covid-19 on Safety Culture?",
@@ -1361379,45 +1360532,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.06.14.20131201",
-    "rel_title": "First SARS-CoV-2 detection in river water: implications in low sanitation countries",
-    "rel_date": "2020-06-16",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.14.20131201",
-    "rel_abs": "Since the beginning of SARS-CoV-2 pandemic studies on viral shedding have reported that this virus is excreted in feces in most patients. High viral loads are found at the sewage pipeline or at the entrance of wastewater treatment plants from cities where the number of COVID-19 cases are significant. In Quito (Ecuador) as in many other cities worldwide, wastewater is directly discharged into natural waters. The aim of this study was to evaluate SARS-CoV-2 presence in urban streams from a low sanitation context. Three river locations along the urban rivers of Quito were sampled on the 5th of June during a peak of COVID-19 cases. River samples were evaluated for water quality parameters and afterwards, concentrated for viral analysis using skimmed milk flocculation method. The viral concentrates were quantified for SARS-CoV-2 (N1 and N2 genes) and Human Adenovirus as a human viral indicator. The results showed that SARS-CoV-2 was detected for both target genes in all samples analyzed in a range of 2,91E+05 to 3,19E+06 GC/L for N1 and from 2,07E+05 to 2,22E+06 GC/L for N2. The high values detected in natural waters from a low sanitation region have several implications in health and ecology that should be further assessed.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Laura Guerrero-Latorre",
-        "author_inst": "Grupo de Investigacion en Biodiversidad, Medio Ambiente y Salud (BIOMAS), Universidad de Las Americas, Ecuador"
-      },
-      {
-        "author_name": "Isabel Ballesteros",
-        "author_inst": "Grupo de Investigacion en Biodiversidad, Medio Ambiente y Salud (BIOMAS)- Universidad de Las Americas"
-      },
-      {
-        "author_name": "Irina Villacres",
-        "author_inst": "Laboratorios de Investigacion, Universidad de Las Americas, Ecuador"
-      },
-      {
-        "author_name": "Maria Genoveva Granda-Albuja",
-        "author_inst": "Laboratorios de Investigacion, Universidad de Las Americas, Ecuador"
-      },
-      {
-        "author_name": "Byron Freire",
-        "author_inst": "Laboratorios de Investigacion, Universidad de Las Americas, Ecuador"
-      },
-      {
-        "author_name": "Blanca Rios-Touma",
-        "author_inst": "Grupo de Investigacion en Biodiversidad, Medio Ambiente y Salud (BIOMAS), Universidad de Las Americas, Ecuador"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "occupational and environmental health"
-  },
   {
     "rel_doi": "10.1101/2020.06.12.20129056",
     "rel_title": "Symptom clusters in Covid19: A potential clinical prediction tool from the COVID Symptom study app",
@@ -1361784,6 +1360898,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.06.15.20130989",
+    "rel_title": "Predictive accuracy of a hierarchical logistic model of cumulative SARS-CoV-2 case growth",
+    "rel_date": "2020-06-16",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20130989",
+    "rel_abs": "BackgroundInfectious disease predictions models, including virtually all epidemiological models describing the spread of the SARS-CoV-2 pandemic up to June 2020, are rarely evaluated. The aim of the present study was to investigate the predictive accuracy of a prognostic model for forecasting the development of the cumulative number of reported SARS-CoV-2 cases in countries and administrative regions worldwide.\n\nMethodsThe cumulative number of reported SARS-CoV-2 cases was forecasted in 251 regions with a horizon of two weeks, one month, and two months using a previously described hierarchical logistic model at the end of March 2020. Forecasts were compared to actual observations by using a series of evaluation metrics.\n\nResultsOn average, predictive accuracy was very high in nearly all regions at the two weeks forecast, high in most regions at the one month forecast, and notable in the majority of the regions at the two months forecast. Higher accuracy was associated with the availability of more data for estimation and with a more pronounced cumulative case growth from the first case to the date of estimation. In some strongly affected regions, cumulative case counts were considerably underestimated.\n\nConclusionsWith keeping its limitations in mind, the investigated model can be used for the preparation and distribution of resources during the SARS-CoV-2 pandemic. Future research should primarily address the models assumptions and its scope of applicability. In addition, establishing a relationship with known mechanisms and traditional epidemiological models of disease transmission would be desirable.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Levente Kriston",
+        "author_inst": "University Medical Center Hamburg-Eppendorf"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.06.12.20127944",
     "rel_title": "Evaluation of SARS-CoV-2 in Breastmilk from 18 Infected Women",
@@ -1363181,85 +1362314,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2020.06.16.151704",
-    "rel_title": "Massive transient damage of the olfactory epithelium associated with infection of sustentacular cells by SARS-CoV-2 in golden Syrian hamsters",
-    "rel_date": "2020-06-16",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.16.151704",
-    "rel_abs": "Anosmia is one of the most prevalent symptoms of SARS-CoV-2 infection during the COVID-19 pandemic. However, the cellular mechanism behind the sudden loss of smell has not yet been investigated. The initial step of odour detection takes place in the pseudostratified olfactory epithelium (OE) mainly composed of olfactory sensory neurons surrounded by supporting cells known as sustentacular cells. The olfactory neurons project their axons to the olfactory bulb in the central nervous system offering a potential pathway for pathogens to enter the central nervous system by bypassing the blood brain barrier. In the present study, we explored the impact of SARS-COV-2 infection on the olfactory system in golden Syrian hamsters. We observed massive damage of the OE as early as 2 days post nasal instillation of SARS-CoV-2, resulting in a major loss of cilia necessary for odour detection. These damages were associated with infection of a large proportion of sustentacular cells but not of olfactory neurons, and we did not detect any presence of the virus in the olfactory bulbs. We observed massive infiltration of immune cells in the OE and lamina propria of infected animals, which may contribute to the desquamation of the OE. The OE was partially restored 14 days post infection. Anosmia observed in COVID-19 patient is therefore likely to be linked to a massive and fast desquamation of the OE following sustentacular cells infection with SARS-CoV-2 and subsequent recruitment of immune cells in the OE and lamina propria.",
-    "rel_num_authors": 16,
-    "rel_authors": [
-      {
-        "author_name": "Bertrand Bryche",
-        "author_inst": "Universite Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France"
-      },
-      {
-        "author_name": "Audrey Saint-Albin Deliot",
-        "author_inst": "Universite Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France"
-      },
-      {
-        "author_name": "Severine Murri",
-        "author_inst": "Laboratoire de Lyon, ANSES, Unite virologie, Lyon, France"
-      },
-      {
-        "author_name": "Sandra Lacote",
-        "author_inst": "Laboratoire de Lyon, ANSES, Unite virologie, Lyon, France"
-      },
-      {
-        "author_name": "Coralie Pulido",
-        "author_inst": "Laboratoire de Lyon, ANSES, Unite virologie, Lyon, France"
-      },
-      {
-        "author_name": "Meriadeg Ar Gouilh",
-        "author_inst": "Service de Virologie, CHU de Caen, Caen, France"
-      },
-      {
-        "author_name": "Sandrine Lesellier",
-        "author_inst": "Laboratoire rage et faune sauvage, ANSES, Malzeville, France"
-      },
-      {
-        "author_name": "Alexandre Servat",
-        "author_inst": "Laboratoire rage et faune sauvage, ANSES, Malzeville, France"
-      },
-      {
-        "author_name": "Marine Wasniewski",
-        "author_inst": "Laboratoire rage et faune sauvage, ANSES, Malzeville, France"
-      },
-      {
-        "author_name": "Evelyne Picard-Meyer",
-        "author_inst": "Laboratoire rage et faune sauvage, ANSES, Malzeville, France"
-      },
-      {
-        "author_name": "Elodie Montchartre-Leroy",
-        "author_inst": "Laboratoire rage et faune sauvage, ANSES, Malzeville, France"
-      },
-      {
-        "author_name": "Romain Volmer",
-        "author_inst": "Universite de Toulouse, ENVT, INRA, UMR 1225, Toulouse, France"
-      },
-      {
-        "author_name": "Olivier Rampin",
-        "author_inst": "Universite Paris Saclay, INRAE, AgroParisTech, PNCA, 78350, Jouy-en-Josas, France"
-      },
-      {
-        "author_name": "Ronan Le Goffic",
-        "author_inst": "Universite Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France"
-      },
-      {
-        "author_name": "Philippe Marianneau",
-        "author_inst": "Laboratoire de Lyon, ANSES, Unite virologie, Lyon, France"
-      },
-      {
-        "author_name": "Nicolas Meunier",
-        "author_inst": "Universite Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "neuroscience"
-  },
   {
     "rel_doi": "10.1101/2020.06.16.154211",
     "rel_title": "TMPRSS2, a SARS-CoV-2 internalization protease is downregulated in head and neck cancer patients.",
@@ -1363570,6 +1362624,33 @@
     "type": "new results",
     "category": "bioinformatics"
   },
+  {
+    "rel_doi": "10.1101/2020.06.16.155267",
+    "rel_title": "Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection.",
+    "rel_date": "2020-06-16",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.16.155267",
+    "rel_abs": "To understand the difference between benign and severe outcomes after Coronavirus infection, we urgently need ways to clarify and quantify the time course of tissue and immune responses. Here we re-analyze 72-hour time-series microarrays generated in 2013 by Sims and collaborators for SARS-CoV-1 in vitro infection of a human lung epithelial cell line. Transcriptograms, a Bioinformatics tool to analyze genome-wide gene expression data, allow us to define an appropriate context-dependent threshold for mechanistic relevance of gene differential expression. Without knowing in advance which genes are relevant, classical analyses detect every gene with statistically-significant differential expression, leaving us with too many genes and hypotheses to be useful. Using a Transcriptogram-based top-down approach, we identified three major, differentially-expressed gene sets comprising 219 mainly immune-response-related genes. We identified timescales for alterations in mitochondrial activity, signaling and transcription regulation of the innate and adaptive immune systems and their relationship to viral titer. At the individual-gene level, EGR3 was significantly upregulated in infected cells. Similar activation in T-cells and fibroblasts in infected lung could explain the T-cell anergy and eventual fibrosis seen in SARS-CoV-1 infection. The methods can be applied to RNA data sets for SARS-CoV-2 to investigate the origin of differential responses in different tissue types, or due to immune or preexisting conditions or to compare cell culture, organoid culture, animal models, and human-derived samples.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Rita M.C. de Almeida",
+        "author_inst": "Universidade Federal do Rio Grande do Sul"
+      },
+      {
+        "author_name": "Gilberto L Thomas",
+        "author_inst": "Universidade Federal do Rio Grande do Sul"
+      },
+      {
+        "author_name": "James A. Glazier",
+        "author_inst": "Indiana University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "bioinformatics"
+  },
   {
     "rel_doi": "10.1101/2020.06.16.154765",
     "rel_title": "Machine Learning Models Identify Inhibitors of SARS-CoV-2",
@@ -1365043,61 +1364124,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.06.11.20128744",
-    "rel_title": "COVID-19 challenges to dentistry in the new pandemic epicenter: Brazil",
-    "rel_date": "2020-06-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128744",
-    "rel_abs": "A nationwide survey of dentists was carried out in Brazil, a new pandemic epicenter, to analyze how dental coverage has been affected (public versus private networks), changes in routine and burdens, and how the local prevalence of COVID-19 affects dental professionals. Dentists were recruited via email and an Instagram(R) campaign. Responses to an online questionnaire were collected May 15-24, 2020. COVID-19 case/death counts in the state where respondents work was used to test associations between contextual status and decreases in weekly appointments, fear of contracting COVID-19 at work, and current work status (=0.05). Over 10 days, 3,122 responses were received, with region, gender, and age distributions similar to those of dentists in Brazil. Work status was affected for 94% of dentists, with less developed regions being more impacted. The impact on routine was high or very high for 84%, leading to varied changes to clinic infrastructure, personal protective equipment use, patient screening, and increased costs. COVID-19 patients had been seen by 5.3% of respondents, and 90% reported fearing contracting COVID-19 at work. Multilevel statistics showed that greater case and death rates (1000 cases or 100 deaths/million inhabitants) in ones state increased the odds of being fearful of contracting the disease (by 18% and 25%). For each additional 1000 cases or 100 deaths, the odds of currently not working or treating emergencies increased by 36% and 58%. The reduction in patients seen weekly per dentist was greater in public (38.7{+/-}18.6) than in private clinics (22.5{+/-}17.8). This study provides early evidence of three major impacts of the pandemic on dentistry in Brazil: increasing inequalities due to coverage differences between public and private networks; adoption of new clinical routines, which are associated with an economic burden; and associations of regional COVID-19 incidence and mortality with fear of contracting the disease at work.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Rafael R Moraes",
-        "author_inst": "Federal University of Pelotas"
-      },
-      {
-        "author_name": "Marcos B Correa",
-        "author_inst": "Federal University of Pelotas"
-      },
-      {
-        "author_name": "Ana B Queiroz",
-        "author_inst": "Federal University of Pelotas"
-      },
-      {
-        "author_name": "Andrea Daneris",
-        "author_inst": "Federal University of Pelotas"
-      },
-      {
-        "author_name": "Joao P Lopes",
-        "author_inst": "Federal University of Pelotas"
-      },
-      {
-        "author_name": "Tatiana Pereira-Cenci",
-        "author_inst": "Federal University of Pelotas"
-      },
-      {
-        "author_name": "Otavio P D'Avila",
-        "author_inst": "Federal University of Pelotas"
-      },
-      {
-        "author_name": "Maximiliano S Cenci",
-        "author_inst": "Federal University of Pelotas"
-      },
-      {
-        "author_name": "Giana S Lima",
-        "author_inst": "Federal University of Pelotas"
-      },
-      {
-        "author_name": "Flavio F Demarco",
-        "author_inst": "Federal University of Pelotas"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "dentistry and oral medicine"
-  },
   {
     "rel_doi": "10.1101/2020.06.11.20128850",
     "rel_title": "When is SARS-CoV-2 in your shopping list?",
@@ -1365360,6 +1364386,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.06.12.20129114",
+    "rel_title": "How to better communicate exponential growth of infectious diseases",
+    "rel_date": "2020-06-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.12.20129114",
+    "rel_abs": "Exponential growth bias is the phenomenon that humans underestimate exponential growth. In the context of infectious diseases, this bias may lead to failure to understand the effectiveness of non-pharmaceutical interventions (NPIs). Communicating the same scenario in different ways (framing) has been found to have a large impact on peoples evaluations and behavior in the contexts of social behavior, risk taking and health care. We find that framing matters for peoples assessment of the benefits of NPIs. In two commonly used frames, most subjects in our experiment drastically underestimate the number of cases NPIs avoid. Framing growth in terms of doubling times, rather than growth rates, reduces bias. When the scenario is framed in terms of time gained, rather than cases avoided, the median subject assesses the benefit of NPIs correctly. These findings suggest changes that public health authorities can adopt to better communicate the exponential spread of infectious diseases.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Martin Schonger",
+        "author_inst": "ETH Zurich and HSLU"
+      },
+      {
+        "author_name": "Daniela Sele",
+        "author_inst": "ETH-Bereich Hochschulen"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.06.14.149153",
     "rel_title": "X-206 is a potent and selective inhibitor of SARS-CoV-2 infection in vitro",
@@ -1366533,25 +1365582,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.06.12.20105676",
-    "rel_title": "ASSESSING THE ROLE OF ZINC IN COVID-19 INFECTIONS AND MORTALITY: IS ZINC DEFICIENCY A RISK FACTOR FOR COVID-19?",
-    "rel_date": "2020-06-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.12.20105676",
-    "rel_abs": "Variables responsible for the differential COVID-19 pandemic severity among countries remain undefined. Zinc, a micronutrient required for immunocompetence, is found deficient in populations. We hypothesized the differential COVID-19 severity observed among European countries could be associated with the Zn-deficiency prevalence. The COVID-19 data from different stages of pandemic, i.e., 8 April, 12 and 26 May 2020, were analyzed for covariation with the estimated Zn-deficiency. A significant, relatively stable, but negative correlation of Zn-deficiency with cases per million for the time period [r(20): -0.4930 to -0.5335, p-value: 0.02720 to 0.0154] and a steady improvement of covariation with deaths per million [r(20): -0.4056; p-value: 0.0760 on 26 May 2020] was observed. Considering, Zincs key immunomodulatory role, widespread deficiency along with the self- and prescribed intervention in different target groups, e.g. children, women, elderly, carefully planned dedicated exploratory studies to understand the basis of the observed association are advisable.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Samer Singh",
-        "author_inst": "Banaras Hindu University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.06.12.147819",
     "rel_title": "Overhauling a faulty control in the CDC-recommended SARS-CoV-2 RT-PCR test",
@@ -1366982,6 +1366012,53 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2020.06.13.149880",
+    "rel_title": "Multi-epitope Based Peptide Vaccine Design Using Three Structural Proteins (S, E, and M) of SARS-CoV-2: An In Silico Approach",
+    "rel_date": "2020-06-13",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.13.149880",
+    "rel_abs": "Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the novel coronavirus responsible for the ongoing pandemic of coronavirus disease (COVID-19). No sustainable treatment option is available so far to tackle such a public health threat. Therefore, designing a suitable vaccine to overcome this hurdle asks for immediate attention. In this study, we targeted for a design of multi-epitope based vaccine using immunoinformatics tools. We considered the structural proteins S, E and, M of SARS-CoV-2, since they facilitate the infection of the virus into host cell and using different bioinformatics tools and servers, we predicted multiple B-cell and T-cell epitopes having potential for the required vaccine design. Phylogenetic analysis provided insight on ancestral molecular changes and molecular evolutionary relationship of S, E, and M proteins. Based on the antigenicity and surface accessibility of these proteins, eight epitopes were selected by various B cell and T cell epitope prediction tools. Molecular docking was executed to interpret the binding interactions of these epitopes and three potential epitopes WTAGAAAYY, YVYSRVKNL, and GTITVEELK were selected for their noticeable higher binding affinity scores -9.1, -7.4, and -7.0 kcal/mol, respectively. Targeted epitopes had 91.09% population coverage worldwide. In summary, we identified three epitopes having the most significant properties of designing the peptide-based vaccine against SARS-CoV-2.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Arpita Singha Roy",
+        "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University"
+      },
+      {
+        "author_name": "Mahafujul Islam Quadery Tonmoy",
+        "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University"
+      },
+      {
+        "author_name": "Atqiya Fariha",
+        "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University"
+      },
+      {
+        "author_name": "Ithmam Hami",
+        "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University"
+      },
+      {
+        "author_name": "Ibrahim Khalil Afif",
+        "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University"
+      },
+      {
+        "author_name": "Md Adnan Munim",
+        "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University"
+      },
+      {
+        "author_name": "Mohammad Rahanur Alam",
+        "author_inst": "Department of Food Technology and Nutrition Science, Noakhali Science and Technology University"
+      },
+      {
+        "author_name": "Md. Shahadat Hossain",
+        "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "bioinformatics"
+  },
   {
     "rel_doi": "10.1101/2020.06.11.146878",
     "rel_title": "Colon Cancer and SARS-CoV-2: Impact of ACE2 Expression in Susceptibility to COVID-19",
@@ -1367943,33 +1367020,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.06.08.20121541",
-    "rel_title": "A Fully Automated Deep Learning-based Network ForDetecting COVID-19 from a New And Large Lung CT ScanDataset",
-    "rel_date": "2020-06-12",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20121541",
-    "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWCOVID-19 is a severe global problem, and AI can play a significant role in preventing losses by monitoring and detecting infected persons in early-stage. This paper aims to propose a high-speed and accurate fully-automated method to detect COVID-19 from the patients CT scan images. We introduce a new dataset that contains 48260 CT scan images from 282 normal persons and 15589 images from 95 patients with COVID-19 infections. At the first stage, this system runs our proposed image processing algorithm to discard those CT images that inside the lung is not properly visible in them. This action helps to reduce the processing time and false detections. At the next stage, we introduce a novel method for increasing the classification accuracy of convolutional networks. We implemented our method using the ResNet50V2 network and a modified feature pyramid network alongside our designed architecture for classifying the selected CT images into COVlD-19 or normal with higher accuracy than other models. After running these two phases, the system determines the condition of the patient using a selected threshold. We are the first to evaluate our system in two different ways. In the single image classification stage, our model achieved 98.49% accuracy on more than 7996 test images. At the patient identification phase, the system correctly identified almost 234 of 245 patients with high speed. We also investigate the classified images with the Grad-CAM algorithm to indicate the area of infections in images and evaluate our model classification correctness.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Mohammad Rahimzadeh",
-        "author_inst": "Iran University of Science and Technology"
-      },
-      {
-        "author_name": "Abolfazl Attar",
-        "author_inst": "Sharif University of Technology"
-      },
-      {
-        "author_name": "Seyed Mohammad Sakhaei",
-        "author_inst": "Sari Azad University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "radiology and imaging"
-  },
   {
     "rel_doi": "10.1101/2020.06.04.20119206",
     "rel_title": "A Comparative Study of Target Reconstruction of Ultra-High-Resolution CT for Patients with Corona-Virus Disease 2019 (COVID-19)",
@@ -1368276,6 +1367326,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "emergency medicine"
   },
+  {
+    "rel_doi": "10.1101/2020.06.08.20123786",
+    "rel_title": "Oscillations in USA COVID-19 Incidence and Mortality Data reflect societal factors",
+    "rel_date": "2020-06-12",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20123786",
+    "rel_abs": "The COVID-19 pandemic currently in process differs from other infectious disease calamities that have previously plagued humanity in the vast amount of information that is produces each day, which includes daily estimates of the disease incidence and mortality data. Apart from providing actionable information to public health authorities on the trend of the pandemic, the daily incidence reflects the process of disease in a susceptible population and thus reflects the pathogenesis of COVID-19, the public health response and diagnosis and reporting. Both daily new cases and daily mortality data in the US exhibit periodic oscillatory patterns. By analyzing NYC and LA testing data, we demonstrate that this oscillation in the number of cases can be strongly explained by the daily variation in testing. This seems to rule out alternative hypotheses such as increased infections on certain days of the week as driving this oscillation. Similarly, we show that the apparent oscillation in mortality in the US data is mostly an artifact of reporting, which disappears in datasets that record death by episode date, such as the NYC and LA datasets. Periodic oscillations in COVID-19 incidence and mortality data reflect testing and reporting practices and contingencies. Thus, these contingencies should be considered first prior to suggesting social or biological mechanisms.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Aviv Bergman",
+        "author_inst": "Albert Einstein College of Medicine"
+      },
+      {
+        "author_name": "Yehonatan Sella",
+        "author_inst": "Albert Einstein College of Medicine"
+      },
+      {
+        "author_name": "Peter Agre",
+        "author_inst": "Johns Hopkins School of Public Health"
+      },
+      {
+        "author_name": "Arturo Casadevall",
+        "author_inst": "Johns Hopkins School of Public Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.06.09.20124008",
     "rel_title": "An imperfect tool: COVID-19 'test & trace' success relies on minimising the impact of false negatives and continuation of physical distancing.",
@@ -1369301,37 +1368382,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "medical ethics"
   },
-  {
-    "rel_doi": "10.1101/2020.06.10.20127225",
-    "rel_title": "Identifying and Ranking Common COVID-19 Symptoms from Arabic Twitter",
-    "rel_date": "2020-06-12",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20127225",
-    "rel_abs": "BackgroundMassive amount of covid-19 related data is generated everyday by Twitter users. Self-reports of covid-19 symptoms on Twitter can reveal a great deal about the disease and its prevalence in the community. In particular, self-reports can be used as a valuable resource to learn more about the common symptoms and whether their order of appearance differs among different groups in the community. With sufficient available data, this has the potential of developing a covid-19 risk-assessment system that is tailored toward specific group of people.\n\nObjectiveThe aim of this study is to identify the most common symptoms reported by covid-19 patients in the Arabic language and order the symptoms appearance based on the collected data.\n\nMethodsWe search the Arabic content of Twitter for personal reports of covid-19 symptoms from March 1st to May 27th, 2020. We identify 463 Arabic users who tweeted testing positive for covid-19 and extract the symptoms they publicly associate with covid-19. Furthermore, we ask them directly through personal messages to opt in and rank the appearance of the first three symptoms they experienced right before (or after) diagnosed with covid-19. Finally, we track their Twitter timeline to identify additional symptoms that were mentioned within {+/-}5 days from the day of tweeting having covid-19. In summary, a list of 270 covid-19 reports were collected and symptoms were (at least partially) ranked from early to late.\n\nResultsThe collected reports contained roughly 900 symptoms originated from 74% (n=201) male and 26% (n=69) female Twitter users. The majority (82%) of the tracked users were living in Saudi Arabia (46%) and Kuwait (36%). Furthermore, 13% (n=36) of the collected reports were asymptomatic. Out of the users with symptoms (n=234), 66% (n=180) provided a chronological order of appearance for at least three symptoms.\n\nFever 59% (n=139), Headache 43% (n=101), and Anosmia 39% (n=91) were found to be the top three symptoms mentioned by the reports. They count also for the top-3 common first symptoms in a way that 28% (n=65) said their covid journey started with a Fever, 15% (n=34) with a Headache and 12% (n=28) with Anosmia. Out of the Saudi symptomatic reported cases (n=110), the most common three symptoms were Fever 59% (n=65), Anosmia 42% (n=46), and Headache 38% (n=42).\n\nConclusionsThis study demonstrates that Twitter is a valuable resource to analyze and identify COVID-19 early symptoms within the Arabic content of Twitter. It also suggests the possibility of developing a real-time covid-19 risk estimator based on the users tweets.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Eisa Alanazi",
-        "author_inst": "Umm Al-Qura University"
-      },
-      {
-        "author_name": "Abdulaziz Alashaikh",
-        "author_inst": "University of Jeddah"
-      },
-      {
-        "author_name": "Sarah Alqurashi",
-        "author_inst": "Umm Al-Qura University"
-      },
-      {
-        "author_name": "Aued Alanazi",
-        "author_inst": "Umm Al-Qura University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health informatics"
-  },
   {
     "rel_doi": "10.1101/2020.06.10.20126847",
     "rel_title": "Laboratory based surveillance of SARS-CoV-2 in Pakistan",
@@ -1369754,6 +1368804,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "cardiovascular medicine"
   },
+  {
+    "rel_doi": "10.1101/2020.06.10.20127613",
+    "rel_title": "On the interplay between mobility and hospitalization capacity during the COVID-19 pandemic: The SEIRHUD model",
+    "rel_date": "2020-06-12",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20127613",
+    "rel_abs": "Measures to reduce the impact of the COVID-19 pandemic require a mix of logistic, political and social capacity. Depending on the country, different approaches to increase hospitalization capacity or to properly apply lock-downs are observed. In order to better understand the impact of these measures we have developed a compartmental model which, on the one hand allows to calibrate the reduction of movement of people within and among different areas, and on the other hand it incorporates a hospitalization dynamics that differentiates the available kinds of treatment that infected people can receive. By bounding the hospitalization capacity, we are able to study in detail the interplay between mobility and hospitalization capacity.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Tomas Veloz",
+        "author_inst": "Fundacion para el Desarrollo Interdisciplinario de la Ciencia la Tecnologia y la Artes"
+      },
+      {
+        "author_name": "pedro maldonado",
+        "author_inst": "fundacion para el desarrollo interdisciplinario de la ciencia la tecnologia y las artes"
+      },
+      {
+        "author_name": "samuel ropert",
+        "author_inst": "fundacion para el desarrollo interdisciplinario de la ciencia la tecnologia y las artes"
+      },
+      {
+        "author_name": "cesar ravello",
+        "author_inst": "Fundacion Ciencia y vida"
+      },
+      {
+        "author_name": "alejandra barrios",
+        "author_inst": "fundacion ciencia y vida"
+      },
+      {
+        "author_name": "soraya mora",
+        "author_inst": "Fundacion Ciencia y vida"
+      },
+      {
+        "author_name": "Cesar Valdenegro",
+        "author_inst": "Fundacion Ciencia y Vida"
+      },
+      {
+        "author_name": "Tomas Villaseca",
+        "author_inst": "Fundacion Ciencia y Vida"
+      },
+      {
+        "author_name": "Tomas Perez-Acle",
+        "author_inst": "Fundacion Ciencia y Vida"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.06.10.20127563",
     "rel_title": "Multimorbidity, Polypharmacy, and COVID-19 infection within the UK Biobank cohort.",
@@ -1370831,73 +1369932,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.06.10.20127324",
-    "rel_title": "On the sensitivity of non-pharmaceutical intervention models for SARS-CoV-2 spread estimation",
-    "rel_date": "2020-06-12",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20127324",
-    "rel_abs": "IntroductionA series of modelling reports that quantify the effect of non-pharmaceutical interventions (NPIs) on the spread of the SARS-CoV-2 virus have been made available prior to external scientific peer-review. The aim of this study was to investigate the method used by the Imperial College COVID-19 Research Team (ICCRT) for estimation of NPI effects from the system theoretical viewpoint of model identifiability.\n\nMethodsAn input-sensitivity analysis was performed by running the original software code of the systems model that was devised to estimate the impact of NPIs on the reproduction number of the SARS-CoV-2 infection and presented online by ICCRT in Report 13 on March 30 2020. An empirical investigation was complemented by an analysis of practical parameter identifiability, using an estimation theoretical framework.\n\nResultsDespite being simplistic with few free parameters, the system model was found to suffer from severe input sensitivities. Our analysis indicated that the model lacks practical parameter identifiability from data. The analysis also showed that this limitation is fundamental, and not something readily resolved should the model be driven with data of higher reliability.\n\nDiscussionReports based on system models have been instrumental to policymaking during the SARS-CoV-2 pandemic. With much at stake during all phases of a pandemic, we conclude that it is crucial to thoroughly scrutinise any SARS-CoV-2 effect analysis or prediction model prior to considering its use as decision support in policymaking. The enclosed example illustrates what such a review might reveal.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Kristian Soltesz",
-        "author_inst": "Lund University"
-      },
-      {
-        "author_name": "Fredrik Gustafsson",
-        "author_inst": "Linkoping University"
-      },
-      {
-        "author_name": "Toomas Timpka",
-        "author_inst": "Region Ostergotland"
-      },
-      {
-        "author_name": "Joakim Jalden",
-        "author_inst": "KTH Royal Institute of Technology"
-      },
-      {
-        "author_name": "Carl Jidling",
-        "author_inst": "Uppsala University"
-      },
-      {
-        "author_name": "Albin Heimerson",
-        "author_inst": "Lund University"
-      },
-      {
-        "author_name": "Thomas B. Schon",
-        "author_inst": "Uppsala University"
-      },
-      {
-        "author_name": "Armin Spreco",
-        "author_inst": "Region Ostergotland"
-      },
-      {
-        "author_name": "Joakim Ekberg",
-        "author_inst": "Region Ostergotland"
-      },
-      {
-        "author_name": "Orjan Dahlstrom",
-        "author_inst": "Linkoping University"
-      },
-      {
-        "author_name": "Fredrik Bagge Carlson",
-        "author_inst": "National University of Singapore"
-      },
-      {
-        "author_name": "Anna Joud",
-        "author_inst": "Region Skane"
-      },
-      {
-        "author_name": "Bo Bernhardsson",
-        "author_inst": "Lund University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.06.10.20126771",
     "rel_title": "Meso-scale modeling of COVID-19 spatio-temporal outbreak dynamics in Germany",
@@ -1371180,6 +1370214,105 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.06.11.20128900",
+    "rel_title": "Associations between wearing masks, washing hands, and social distancing practices, and risk of COVID-19 infection in public: a cohort-based case-control study in Thailand",
+    "rel_date": "2020-06-12",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128900",
+    "rel_abs": "We evaluated the effectiveness of personal protective measures, including mask-wearing, handwashing, and social distancing, against COVID-19 infection among contacts of cases. We conducted a case-control study with 211 cases and 839 non-matched controls using all contact tracing records of Thailands national Surveillance and Rapid Response Team. Cases were asymptomatic contacts of COVID-19 patients identified between 1 and 31 March 2020 who were diagnosed with COVID-19 by 21 April 2020; controls were asymptomatic contacts who were not diagnosed with COVID-19. Participants were queried about practices during contact periods with a case. Adjusted odds ratios (aOR) and 95% confidence intervals (CI) were estimated for associations between diagnosis of COVID-19 and covariates using multivariable logistic regression models. Wearing masks all the time during contact was independently associated with lower risk of COVID-19 infection compared to not wearing masks (aOR 0.23, 95% CI 0.09- 0.60), while sometimes wearing masks during contact was not (aOR 0.87, 95% CI 0.41-1.84). Maintaining at least 1 meter distance from a COVID patient (aOR 0.15, 95% CI 0.04-0.63), duration of close contact [&le;]15 minutes versus longer (aOR 0.24, 95% CI 0.07-0.90), and handwashing often (aOR 0.34, 95% CI 0.13-0.87) were significantly associated with lower risk of infection. Type of mask was not independently associated with infection. Those who wore masks all the time also were more likely to practice social distancing. Our findings suggest consistent wearing of masks, handwashing, and social distancing in public to protect against COVID-19 infection.",
+    "rel_num_authors": 21,
+    "rel_authors": [
+      {
+        "author_name": "Pawinee Doung-ngern",
+        "author_inst": "Department of Disease Control, Ministry of Public Health, Tiwanon Road, Nonthaburi, 11000, Thailand."
+      },
+      {
+        "author_name": "Rapeepong Suphanchaimat",
+        "author_inst": "Department of Disease Control, Ministry of Public Health, Tiwanon Road, Nonthaburi, 11000, Thailand."
+      },
+      {
+        "author_name": "Apinya Panjagampatthana",
+        "author_inst": "Department of Disease Control, Ministry of Public Health, Tiwanon Road, Nonthaburi, 11000, Thailand."
+      },
+      {
+        "author_name": "Chaiwisar Janekrongtham",
+        "author_inst": "Panjagampatthana"
+      },
+      {
+        "author_name": "Duangrat Ruampoom",
+        "author_inst": "Department of Disease Control, Ministry of Public Health, Tiwanon Road, Nonthaburi, 11000, Thailand."
+      },
+      {
+        "author_name": "Nawaporn Daochaeng",
+        "author_inst": "Department of Disease Control, Ministry of Public Health, Tiwanon Road, Nonthaburi, 11000, Thailand."
+      },
+      {
+        "author_name": "Napatchakorn Eungkanit",
+        "author_inst": "Department of Disease Control, Ministry of Public Health, Tiwanon Road, Nonthaburi, 11000, Thailand."
+      },
+      {
+        "author_name": "Nichakul Pisitpayat",
+        "author_inst": "Department of Disease Control, Ministry of Public Health, Tiwanon Road, Nonthaburi, 11000, Thailand."
+      },
+      {
+        "author_name": "Nuengruethai Srisong",
+        "author_inst": "Department of Disease Control, Ministry of Public Health, Tiwanon Road, Nonthaburi, 11000, Thailand."
+      },
+      {
+        "author_name": "Oiythip Yasopa",
+        "author_inst": "Department of Disease Control, Ministry of Public Health, Tiwanon Road, Nonthaburi, 11000, Thailand."
+      },
+      {
+        "author_name": "Patchanee Plernprom",
+        "author_inst": "Department of Disease Control, Ministry of Public Health, Tiwanon Road, Nonthaburi, 11000, Thailand."
+      },
+      {
+        "author_name": "Pitiphon Promduangsi",
+        "author_inst": "Department of Disease Control, Ministry of Public Health, Tiwanon Road, Nonthaburi, 11000, Thailand."
+      },
+      {
+        "author_name": "Panita Kumphon",
+        "author_inst": "Department of Disease Control, Ministry of Public Health, Tiwanon Road, Nonthaburi, 11000, Thailand."
+      },
+      {
+        "author_name": "Paphanij Suangtho",
+        "author_inst": "Department of Disease Control, Ministry of Public Health, Tiwanon Road, Nonthaburi, 11000, Thailand."
+      },
+      {
+        "author_name": "Peeriya Watakulsin",
+        "author_inst": "Department of Disease Control, Ministry of Public Health, Tiwanon Road, Nonthaburi, 11000, Thailand."
+      },
+      {
+        "author_name": "Sarinya Chaiya",
+        "author_inst": "Department of Disease Control, Ministry of Public Health, Tiwanon Road, Nonthaburi, 11000, Thailand."
+      },
+      {
+        "author_name": "Somkid Kripattanapong",
+        "author_inst": "Department of Disease Control, Ministry of Public Health, Tiwanon Road, Nonthaburi, 11000, Thailand."
+      },
+      {
+        "author_name": "Thanawadee Chantian",
+        "author_inst": "Department of Disease Control, Ministry of Public Health, Tiwanon Road, Nonthaburi, 11000, Thailand."
+      },
+      {
+        "author_name": "Emily Bloss",
+        "author_inst": "Thailand Ministry of Public Health - U.S. Centers for Disease Control and Prevention Collaboration"
+      },
+      {
+        "author_name": "Chawetsan Namwat",
+        "author_inst": "Department of Disease Control, Ministry of Public Health, Tiwanon Road, Nonthaburi, 11000, Thailand."
+      },
+      {
+        "author_name": "Direk Limmathurotsakul",
+        "author_inst": "Mahidol-Oxford Tropical Medicine Research Unit"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.06.11.20128926",
     "rel_title": "Comorbidity and Sociodemographic determinants in COVID-19 Mortality in an US Urban Healthcare System",
@@ -1372133,93 +1371266,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.06.11.20128306",
-    "rel_title": "Performance and health economic evaluation of the Mount Sinai COVID-19 serological assay identifies modification of thresholding as necessary to maximise specificity of the assay",
-    "rel_date": "2020-06-12",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128306",
-    "rel_abs": "We evaluated the FDA approved SARS-CoV-2 immunoassay (developed at Mount Sinai, by Krammer and colleagues) for the identification of COVID-19 seroconversion and potential cross-reactivity of the assay in a United Kingdom (UK) National Health Service (NHS) hospital setting. In our  set up cohort we found that the SARS-CoV-2 IgG was detectable in 100% of patients tested 14 days post positive COVID-19 nucleic acid test. Serum samples taken from pregnant women in 2018 were used as a negative control group with zero false positives. We also analysed samples from patients with non-COVID-19 viral infections, paraproteinaemia or autoantibodies and found false positive results in 6/179. Modification of the sensitivity threshold to five standard deviations from the mean of the control group eliminated all false positive result in the  set up cohort. We confirmed the validity of the test with a revised threshold on an independent prospective  validation cohort of patient samples. Taking data from both cohorts we report a sensitivity of the Mount Sinai assay of 96.6% (28/29) and specificity of 100% (299/299) using a revised threshold cut-off, at a time point at least 14 days since the diagnostic antigen test. Finally, we conducted a health economic probabilistic sensitivity analysis (PSA) on the costs of producing the tests, and the mean cost we estimate to be 13.63 pounds sterling (95%CI 9.63 - 18.40), allowing its cost effectiveness to be tested against other antibody tests. In summary, we report that the Mount Sinai IgG ELISA assay is highly sensitive test for SARS-Cov-2 infection, however modification of thresholding was required to minimise false positive results.",
-    "rel_num_authors": 18,
-    "rel_authors": [
-      {
-        "author_name": "Stuart A Rushworth",
-        "author_inst": "University of East Anglia"
-      },
-      {
-        "author_name": "Benjamin B Johnson",
-        "author_inst": "University of East Anglia"
-      },
-      {
-        "author_name": "Karen Ashurst",
-        "author_inst": "Norfolk and Norwich University Hospital"
-      },
-      {
-        "author_name": "Rose Davidson",
-        "author_inst": "University of East Anglia"
-      },
-      {
-        "author_name": "Paige Paddy",
-        "author_inst": "University of East Anglia"
-      },
-      {
-        "author_name": "Jayna J Mistry",
-        "author_inst": "University of East Anglia"
-      },
-      {
-        "author_name": "Jamie A Moore",
-        "author_inst": "University of East Anglia"
-      },
-      {
-        "author_name": "Charlotte Hellmich",
-        "author_inst": "Norfolk and Norwich University Hospital"
-      },
-      {
-        "author_name": "Dylan R Edwards",
-        "author_inst": "University of East Anglia"
-      },
-      {
-        "author_name": "Daniela D Afonso",
-        "author_inst": "University of East Anglia"
-      },
-      {
-        "author_name": "Georgios Xydopoulos",
-        "author_inst": "University of East Anglia"
-      },
-      {
-        "author_name": "Richard Goodwin",
-        "author_inst": "Norfolk and Norwich University Hospital"
-      },
-      {
-        "author_name": "Javier Gomez",
-        "author_inst": "Norfolk and Norwich University Hospital"
-      },
-      {
-        "author_name": "Reenesh Prakash",
-        "author_inst": "Norfolk and Norwich University Hospital"
-      },
-      {
-        "author_name": "Samir Dervisevic",
-        "author_inst": "Norfolk and Norwich University Hospital"
-      },
-      {
-        "author_name": "Richard Fordham",
-        "author_inst": "University of East Anglia"
-      },
-      {
-        "author_name": "Kristian Bowles",
-        "author_inst": "Norfolk and Norwich University Hospital"
-      },
-      {
-        "author_name": "James Smith",
-        "author_inst": "University of East Anglia"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.06.11.20128884",
     "rel_title": "Stability of SARS-CoV-2 on Critical Personal Protective Equipment",
@@ -1372482,6 +1371528,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.06.11.20128801",
+    "rel_title": "Early epidemic spread, percolation and Covid-19",
+    "rel_date": "2020-06-12",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128801",
+    "rel_abs": "Human to human transmissible infectious diseases spread in a population using human interactions as its transmission vector. The early stages of such an outbreak can be modeled by a graph whose edges encode these interactions between individuals, the vertices. This article attempts to account for the case when each individual entails in different kinds of interactions which have therefore different probabilities of transmitting the disease. The majority of these results can be also stated in the language of percolation theory.\n\nThe main contributions of the article are: (1) Extend to this setting some results which were previously known in the case when each individual has only one kind of interactions. (2) Find an explicit formula for the basic reproduction number R0 which depends only on the probabilities of transmitting the disease along the different edges and the first two moments of the degree distributions of the associated graphs. (3) Motivated by the recent Covid-19 pandemic, we use the framework developed to compute the R0 of a model disease spreading in populations whose trees and degree distributions are adjusted to several different countries. In this setting, we shall also compute the probability that the outbreak will not lead to an epidemic. In all cases we find such probability to be very low if no interventions are put in place.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Goncalo Oliveira",
+        "author_inst": "Universidade Federal Fluminense"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.06.11.20128777",
     "rel_title": "An international assessment of the COVID-19 pandemic using ensemble data assimilation",
@@ -1374159,85 +1373224,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "occupational and environmental health"
   },
-  {
-    "rel_doi": "10.1101/2020.06.09.20126680",
-    "rel_title": "TMPRSS2 variants and their susceptibility to COVID-19: focus in East Asian and European populations.",
-    "rel_date": "2020-06-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20126680",
-    "rel_abs": "The manifestation of the COVID-19 varies from absence of symptoms to Severe Acute Respiratory Syndrome. The epidemiological data indicate that infection and mortality rates are greater in European populations in comparison with eastern Asians. To test if epidemiological patterns may be partly determined by human genetic variation, we investigated, by exomic and databank analyses, the variability found in the TMPRSS2 gene in populations from different continents, since this gene is fundamental to virus access into human cells. The functional variants revealed low diversity. The analyses of the variation in the modifiers of gene expression indicate that the European populations may have much higher levels of pulmonary expression of the TMPRSS2 gene and would be more vulnerable to infection by SARS-CoV-2. By contrast, the pulmonary expression of the TMPRSS2 may be reduced in the populations from East Asia, which implies that they are less susceptible to the virus infection and, these genetic features might also favor their better outcomes. The presented data, if confirmed, indicates a potential genetic contribution of TMPRSS2 to individual susceptibility to viral infection, and might also influence COVID-19 outcome.",
-    "rel_num_authors": 16,
-    "rel_authors": [
-      {
-        "author_name": "Ney Pereira Carneiro Santos",
-        "author_inst": "Federal University of Para"
-      },
-      {
-        "author_name": "Andre Salim Khayat",
-        "author_inst": "Federal University of Para"
-      },
-      {
-        "author_name": "Juliana Carla Gomes Rodrigues",
-        "author_inst": "Federal University of Para"
-      },
-      {
-        "author_name": "Pablo Carmo Pinto",
-        "author_inst": "Federal University of Para"
-      },
-      {
-        "author_name": "Gilderlanio Santana Araujo",
-        "author_inst": "Federal University of Para"
-      },
-      {
-        "author_name": "Lucas Favacho Pastana",
-        "author_inst": "Federal University of Para"
-      },
-      {
-        "author_name": "Jessyca Amanda Gomes Medeiros",
-        "author_inst": "Federal University of Para"
-      },
-      {
-        "author_name": "Marianne Rodrigues Fernandes",
-        "author_inst": "Federal University of Para"
-      },
-      {
-        "author_name": "Arthur Ribeiro dos Santos",
-        "author_inst": "Federal University of Para"
-      },
-      {
-        "author_name": "Bruna Claudia Meireles Khayat",
-        "author_inst": "Federal University of Para"
-      },
-      {
-        "author_name": "Fabiano Cordeiro Moreira",
-        "author_inst": "Federal University of Para"
-      },
-      {
-        "author_name": "Andre Mauricio Ribeiro dos Santos",
-        "author_inst": "Federal University of Para"
-      },
-      {
-        "author_name": "Paula Barauna Assumpcao",
-        "author_inst": "Federal University of Para"
-      },
-      {
-        "author_name": "Andrea Ribeiro dos Santos",
-        "author_inst": "Federal University of Para"
-      },
-      {
-        "author_name": "Paulo Pimentel Assumpcao",
-        "author_inst": "Federal University of Para"
-      },
-      {
-        "author_name": "Sidney Santos",
-        "author_inst": "Federal University of Para"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "genetic and genomic medicine"
-  },
   {
     "rel_doi": "10.1101/2020.06.09.20126326",
     "rel_title": "Mathematical estimation of COVID-19 prevalence in Latin America",
@@ -1374636,6 +1373622,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.06.09.20127050",
+    "rel_title": "Plasma from recovered COVID19 subjects inhibits spike protein binding to ACE2 in a microsphere-based inhibition assay",
+    "rel_date": "2020-06-11",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20127050",
+    "rel_abs": "High throughput serological tests that can establish the presence and functional activity of anti-SARS-COV2 antibodies are urgently needed. Here we present microsphere-based Flow Cytometry assays that quantify both anti-spike IgGs in plasma, and the ability of plasma to inhibit the binding of spike protein to angiotensin converting enzyme 2 (ACE2). First, we detected anti-spike-trimer IgGs in 22/24 and anti-spike-receptor-binding-domain (RBD) IgGs in 21/24 COVID+ subjects at a median of 36 (range 14-73) days following documented SARS-CoV-2 RNA (+) secretions. Next, we find that plasma from all 22/24 subjects with anti-trimer IgGs inhibited ACE2-trimer binding to a greater degree than controls, and that the degree of inhibition correlated with anti-trimer IgG levels. Depletion of trimer-reactive Igs from plasma reduced ACE2-trimer inhibitory capacity to a greater degree than depletion of RBD-reactive Igs, suggesting that inhibitory antibodies act by binding both within and outside of the RBD. Amongst the 24 subjects, presence of fever was associated with higher levels of anti-trimer IgG and inhibition of binding to human ACE2. This inhibition assay may be broadly useful to quantify the functional antibody response of recovered COVID19 patients or vaccine recipients in a cell-free assay system.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Edward P Gniffke",
+        "author_inst": "Seattle Childrens Research Institute"
+      },
+      {
+        "author_name": "Whitney E Harrington",
+        "author_inst": "Seattle Childrens Research Institute"
+      },
+      {
+        "author_name": "Nicolas Dambrauskas",
+        "author_inst": "Seattle Childrens Research Institute"
+      },
+      {
+        "author_name": "Yonghou Jiang",
+        "author_inst": "Seattle Childrens Research Institute"
+      },
+      {
+        "author_name": "Olesya Trakhimets",
+        "author_inst": "Seattle Childrens Reserach Institute"
+      },
+      {
+        "author_name": "Vladimir Vigdorovich",
+        "author_inst": "Seattle Childrens Research Institute"
+      },
+      {
+        "author_name": "Lisa Frenkel",
+        "author_inst": "Seattle Childrens Research Institute"
+      },
+      {
+        "author_name": "D. Noah Sather",
+        "author_inst": "Seattle Childrens Research Institute"
+      },
+      {
+        "author_name": "Stephen E P Smith",
+        "author_inst": "Seattle Childrens Research Institute"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "allergy and immunology"
+  },
   {
     "rel_doi": "10.1101/2020.06.09.20126508",
     "rel_title": "A Novel Approach to Monitoring the COVID-19 Pandemic using Emergency Department Discharge Diagnoses",
@@ -1375745,41 +1374782,6 @@
     "type": "new results",
     "category": "biophysics"
   },
-  {
-    "rel_doi": "10.1101/2020.06.09.143412",
-    "rel_title": "Chimeric synthetic reference standards enable cross-validation of positive and negative controls in SARS-CoV-2 molecular tests.",
-    "rel_date": "2020-06-11",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.09.143412",
-    "rel_abs": "DNA synthesis in vitro has enabled the rapid production of reference standards. These are used as controls, and allow measurement and improvement of the accuracy and quality of diagnostic tests. Current reference standards typically represent target genetic material, and act only as positive controls to assess test sensitivity. However, negative controls are also required to evaluate test specificity. Using a pair of chimeric A/B RNA standards, this allowed incorporation of positive and negative controls into diagnostic testing for the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The chimeric standards constituted target regions for RT-PCR primer/probe sets that are joined in tandem across two separate synthetic molecules. Accordingly, a target region that is present in standard A provides a positive control, whilst being absent in standard B, thereby providing a negative control. This design enables cross-validation of positive and negative controls between the paired standards in the same reaction, with identical conditions. This enables control and test failures to be distinguished, increasing confidence in the accuracy of results. The chimeric A/B standards were assessed using the US Centers for Disease Control real-time RT-PCR protocol, and showed results congruent with other commercial controls in detecting SARS CoV-2 in patient samples. This chimeric reference standard design approach offers extensive flexibility, allowing representation of diverse genetic features and distantly related sequences, even from different organisms.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Bindu Swapna Madala",
-        "author_inst": "Garvan Institute of Medical Research, NSW, Australia"
-      },
-      {
-        "author_name": "Andre L. M. Reis",
-        "author_inst": "Garvan Institute of Medical Research"
-      },
-      {
-        "author_name": "Ira W. Deveson",
-        "author_inst": "Garvan Institute of Medical Research, NSW, Australia"
-      },
-      {
-        "author_name": "William Rawlinson",
-        "author_inst": "University of New South Wales, Sydney, NSW, Australia"
-      },
-      {
-        "author_name": "Tim R Mercer",
-        "author_inst": "Garvan Institute of Medical Research, NSW, Australia"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "molecular biology"
-  },
   {
     "rel_doi": "10.1101/2020.06.10.144964",
     "rel_title": "Hijacking SARS-Cov-2/ACE2 receptor interaction by natural and semi-synthetic steroidal agents acting on functional pockets on receptor binding region",
@@ -1376322,6 +1375324,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.06.10.144196",
+    "rel_title": "Evaluating the efficacy of RT-qPCR SARS-CoV-2 direct approaches in comparison to RNA extraction",
+    "rel_date": "2020-06-10",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.10.144196",
+    "rel_abs": "SARS-CoV-2 genetic identification is based on viral RNA extraction prior to RT-qPCR assay, however recent studies support the elimination of the extraction step. Herein, we assessed the RNA extraction necessity, by comparing RT-qPCR efficacy in several direct approaches vs. the gold standard RNA extraction, in detection of SARS-CoV-2 from laboratory samples as well as clinical Oro-nasopharyngeal SARS-CoV-2 swabs. Our findings show advantage for the extraction procedure, however a direct no-buffer approach might be an alternative, since it identified up to 70% of positive clinical specimens.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Ofir Israeli",
+        "author_inst": "IIBR"
+      },
+      {
+        "author_name": "Adi Beth-Din",
+        "author_inst": "IIBR"
+      },
+      {
+        "author_name": "Nir Paran",
+        "author_inst": "IIBR"
+      },
+      {
+        "author_name": "Dana Stein",
+        "author_inst": "IIBR"
+      },
+      {
+        "author_name": "Shirley Lazar",
+        "author_inst": "IIBR"
+      },
+      {
+        "author_name": "Shay Weiss",
+        "author_inst": "IIBR"
+      },
+      {
+        "author_name": "Elad Milrot",
+        "author_inst": "IIBR"
+      },
+      {
+        "author_name": "Yafit Atiya-Nasagi",
+        "author_inst": "IIBR"
+      },
+      {
+        "author_name": "Shmuel Yitzhaki",
+        "author_inst": "IIBR"
+      },
+      {
+        "author_name": "Orly Laskar",
+        "author_inst": "IIBR"
+      },
+      {
+        "author_name": "Ofir Schuster",
+        "author_inst": "IIBR"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "contradictory results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2020.06.09.142323",
     "rel_title": "The impact of viral transport media on PCR assay results for the detection of nucleic acid from SARS-CoV-2 and other viruses",
@@ -1377511,57 +1376572,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.06.08.20125963",
-    "rel_title": "Benchmarking Deep Learning Models and Automated Model Design for COVID-19 Detection with Chest CT Scans",
-    "rel_date": "2020-06-09",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20125963",
-    "rel_abs": "COVID-19 pandemic has spread all over the world for months. As its transmissibility and high pathogenicity seriously threaten peoples lives, the accurate and fast detection of the COVID-19 infection is crucial. Although many recent studies have shown that deep learning based solutions can help detect COVID-19 based on chest CT scans, there lacks a consistent and systematic comparison and evaluation on these techniques. In this paper, we first build a clean and segmented CT dataset called Clean-CC-CCII by fixing the errors and removing some noises in a large CT scan dataset CC-CCII with three classes: novel coronavirus pneumonia (NCP), common pneumonia (CP), and normal controls (Normal). After cleaning, our dataset consists of a total of 340,190 slices of 3,993 scans from 2,698 patients. Then we benchmark and compare the performance of a series of state-of-the-art (SOTA) 3D and 2D convolutional neural networks (CNNs). The results show that 3D CNNs outperform 2D CNNs in general. With extensive effort of hyperparameter tuning, we find that the 3D CNN model DenseNet3D121 achieves the highest accuracy of 88.63% (F1-score is 88.14% and AUC is 0.940), and another 3D CNN model ResNet3D34 achieves the best AUC of 0.959 (accuracy is 87.83% and F1-score is 86.04%). We further demonstrate that the mixup data augmentation technique can largely improve the model performance. At last, we design an automated deep learning methodology to generate a lightweight deep learning model MNas3DNet41 that achieves an accuracy of 87.14%, F1-score of 87.25%, and AUC of 0.957, which are on par with the best models made by AI experts. The automated deep learning design is a promising methodology that can help health-care professionals develop effective deep learning models using their private data sets. Our Clean-CC-CCII dataset and source code are available at: https://github.com/HKBU-HPML/HKBU_HPML_COVID-19.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Xin He",
-        "author_inst": "Hong Kong Baptist University"
-      },
-      {
-        "author_name": "Shihao Wang",
-        "author_inst": "Hong Kong Baptist University"
-      },
-      {
-        "author_name": "Shaohuai Shi",
-        "author_inst": "Hong Kong Baptist University"
-      },
-      {
-        "author_name": "Xiaowen Chu",
-        "author_inst": "Hong Kong Baptist University"
-      },
-      {
-        "author_name": "Jiangping Tang",
-        "author_inst": "Hangzhou Dianzi University"
-      },
-      {
-        "author_name": "Xin Liu",
-        "author_inst": "Hangzhou Dianzi University"
-      },
-      {
-        "author_name": "Chenggang Yan",
-        "author_inst": "Hangzhou Dianzi University"
-      },
-      {
-        "author_name": "Jiyong Zhang",
-        "author_inst": "Hangzhou Dianzi University"
-      },
-      {
-        "author_name": "Guiguang Ding",
-        "author_inst": "Tsinghua University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.06.08.20125179",
     "rel_title": "Seroprevalence of IgG antibodies against SARS coronavirus 2 in Belgium: a prospective cross-sectional study of residual samples",
@@ -1377752,6 +1376762,77 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "radiology and imaging"
   },
+  {
+    "rel_doi": "10.1101/2020.06.08.20125872",
+    "rel_title": "Cognitive impairment is a common comorbidity in COVID-19 deceased patients. A hospital-based retrospective cohort study.",
+    "rel_date": "2020-06-09",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20125872",
+    "rel_abs": "IntroductionLittle is known about the relation of cognitive impairment (CI) to COVID-19 mortality. Here, we analyse the frequency of CI in deceased COVID-19 patients.\n\nMethodsWe included 477 adult cases that died after admission from March 1 to March 31, 2020: 281 with confirmed COVID-19, 58 probable COVID-19, and 138 who died of other causes.\n\nResultsThe number of comorbidities was high in the confirmed COVID-19, and CI was common (30%: 21.1% dementia; 8.9% mild cognitive impairment). Subjects with CI were older, more lived in nursing homes and had shorter times from symptom onset to death than those without CI. COVID-19 patients with CI were rarely admitted to the ICU and fewer received non-invasive mechanical ventilation, but palliative care was provided more often.\n\nConclusionsDementia is a frequent comorbidity in COVID-19 deceased patients. The burden of COVID-19 in the dementia community will be high.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Paloma Martin-Jimenez",
+        "author_inst": "Department of Neurology. Hospital Universitario 12 de Octubre. Madrid. Spain."
+      },
+      {
+        "author_name": "Mariana I Munoz-Garcia",
+        "author_inst": "Department of Neurology. Hospital Universitario 12 de Octubre. Madrid. Spain"
+      },
+      {
+        "author_name": "David Seoane",
+        "author_inst": "Department of Neurology. Hospital Universitario 12 de Octubre. Madrid. Spain"
+      },
+      {
+        "author_name": "Lucas Roca-Rodriguez",
+        "author_inst": "Department of Neurology. Hospital Universitario 12 de Octubre. Madrid. Spain"
+      },
+      {
+        "author_name": "Ana Garcia-Reyne",
+        "author_inst": "Department of Internal Medicine. Hospital Universitario 12 de Octubre. Madrid. Spain"
+      },
+      {
+        "author_name": "Antonio Lalueza",
+        "author_inst": "Department of Internal Medicine. Hospital Universitario 12 de Octubre. Madrid. Spain."
+      },
+      {
+        "author_name": "Guillermo Maestro",
+        "author_inst": "Department of Internal Medicine. Hospital Universitario 12 de Octubre. Madrid. Spain."
+      },
+      {
+        "author_name": "Dolores Folgueira",
+        "author_inst": "Department of Microbiology. Hospital Universitario 12 de Octubre. Madrid. Spain."
+      },
+      {
+        "author_name": "Victor A Blanco-Palmero",
+        "author_inst": "Department of Neurology. Hospital Universitario 12 de Octubre. Group of Neurodegenerative Diseases, Instituto de Investigacion Hospital 12 de Octubre (I+12). CI"
+      },
+      {
+        "author_name": "Alejandro Herrero-San Martin",
+        "author_inst": "Department of Neurology. Hospital Universitario 12 de Octubre. Group of Neurodegenerative Diseases, Instituto de Investigacion Hospital 12 de Octubre (I+12). CI"
+      },
+      {
+        "author_name": "Sara Llamas-Velasco",
+        "author_inst": "Department of Neurology. Hospital Universitario 12 de Octubre. Group of Neurodegenerative Diseases, Instituto de Investigacion Hospital 12 de Octubre (I+12). CI"
+      },
+      {
+        "author_name": "David A Perez-Martinez",
+        "author_inst": "Department of Neurology. Hospital Universitario 12 de Octubre. Group of Neurodegenerative Diseases, Instituto de Investigacion Hospital 12 de Octubre (I+12). CI"
+      },
+      {
+        "author_name": "Marta Gonzalez-Sanchez",
+        "author_inst": "Department of Neurology. Hospital Universitario 12 de Octubre. Group of Neurodegenerative Diseases, Instituto de Investigacion Hospital 12 de Octubre (I+12). CI"
+      },
+      {
+        "author_name": "Alberto Villarejo-Galende",
+        "author_inst": "Department of Neurology. Hospital Universitario 12 de Octubre. Group of Neurodegenerative Diseases, Instituto de Investigacion Hospital 12 de Octubre (I+12). CI"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "neurology"
+  },
   {
     "rel_doi": "10.1101/2020.06.08.20125898",
     "rel_title": "Sequence analysis of travel-related SARS-CoV-2 cases in the Greater Geelong region, Australia",
@@ -1379504,77 +1378585,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "medical education"
   },
-  {
-    "rel_doi": "10.1101/2020.06.07.20124438",
-    "rel_title": "Predictive usefulness of PCR testing in different patterns of Covid-19 symptomatology - Analysis of a French cohort of 12,810 outpatients",
-    "rel_date": "2020-06-09",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.07.20124438",
-    "rel_abs": "Polymerase Chain reaction (PCR) is a key tool to diagnose Covid-19. Yet access to PCR is often limited. In this paper, we develop a clinical strategy for prescribing PCR to patients based on data from COVIDOM, a French cohort of 54,000 patients with clinically suspected Covid-19 including 12,810 patients tested by PCR. Using a machine learning algorithm (a decision tree), we show that symptoms alone are sufficient to predict PCR outcome with a mean average precision of 86%. We identify combinations of symptoms that are predictive of PCR positivity (90% for anosmia/ageusia) or negativity (only 30% of PCR+ for a subgroup with cardiopulmonary symptoms): in both cases, PCR provides little added diagnostic value. We deduce a prescribing strategy based on clinical presentation that can improve the global efficiency of PCR testing.",
-    "rel_num_authors": 14,
-    "rel_authors": [
-      {
-        "author_name": "- AP-HP / Universities / Inserm COVID-19 research co COVID-19 research collaboration members",
-        "author_inst": "-"
-      },
-      {
-        "author_name": "Caroline Apra",
-        "author_inst": "Sorbonne University"
-      },
-      {
-        "author_name": "Charlotte Caucheteux",
-        "author_inst": "University Paris Saclay"
-      },
-      {
-        "author_name": "Arthur Mensch",
-        "author_inst": "Ecole Normale Superieure, Paris, France"
-      },
-      {
-        "author_name": "Jenny Mansour",
-        "author_inst": "Ecole Polytechnique, Palaiseau, France"
-      },
-      {
-        "author_name": "Melodie Bernaux",
-        "author_inst": "AP-HP, Direction de la strategie et de la transformation, Paris, France"
-      },
-      {
-        "author_name": "Agnes dechartres",
-        "author_inst": "Sorbonne University, INSERM, Institut Pierre Louis d'Epidemiologie et de Sante Publique, UMR-S 1136, Paris, France"
-      },
-      {
-        "author_name": "Erwan Debuc",
-        "author_inst": "Sorbonne University, AP-HP, Saint Antoine Hospital, Service d'Accueil des Urgences, Paris, France"
-      },
-      {
-        "author_name": "Xavier Lescure",
-        "author_inst": "Department of Infectious and Tropical Diseases , APHP, Bichat-Claude Bernard University Hospital, Paris, France"
-      },
-      {
-        "author_name": "Aurelien Dinh",
-        "author_inst": "Infectious disease department, R. Poincare University Hospital, Garches, APHP, Paris Saclay University, Paris, France"
-      },
-      {
-        "author_name": "Nicolas Paris",
-        "author_inst": "Entrepot des Donnees de Sante, Assistance Publique-Hopitaux de Paris, Paris, France"
-      },
-      {
-        "author_name": "Alexandre Gramfort",
-        "author_inst": "University Paris-Saclay, INRIA, CEA, Palaiseau, 91120, France"
-      },
-      {
-        "author_name": "Youri Yordanov",
-        "author_inst": "Sorbonne University, AP-HP, Saint Antoine Hospital, Service d'Accueil des Urgences, Paris, France"
-      },
-      {
-        "author_name": "Patrick Jourdain",
-        "author_inst": "DMU COREVE, GHU Paris Saclay, APHP, Paris, France"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.06.07.20124636",
     "rel_title": "Dynamics of IgG seroconversion and pathophysiology of COVID-19 infections",
@@ -1380053,6 +1379063,97 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.06.08.20122143",
+    "rel_title": "Hydroxychloroquine inhibits trained immunity - implications for COVID-19",
+    "rel_date": "2020-06-09",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20122143",
+    "rel_abs": "SARS-CoV-2 infection can cause severe disease for which currently no specific therapy is available. The use of hydroxychloroquine to prevent or treat SARS-CoV-2 infection is controversial and its mode of action poorly understood. We demonstrate that hydroxychloroquine inhibits trained immunity at the functional and epigenetic level and is accompanied by profound changes in the cellular lipidome as well as reduced expression of interferon-stimulated genes. Trained immunity comprises a functional adaptation induced by epigenetic reprogramming which facilitates the anti-viral innate immune response. Our findings therefore suggest that hydroxychloroquine may not have a beneficial effect on the anti-viral immune response to SARS-CoV-2.",
+    "rel_num_authors": 19,
+    "rel_authors": [
+      {
+        "author_name": "Nils Rother",
+        "author_inst": "Radboudumc"
+      },
+      {
+        "author_name": "Cansu Yanginlar",
+        "author_inst": "Radboudumc"
+      },
+      {
+        "author_name": "Rik G.H. Lindeboom",
+        "author_inst": "Radboud University"
+      },
+      {
+        "author_name": "Siroon Bekkering",
+        "author_inst": "Radboudumc"
+      },
+      {
+        "author_name": "Mandy M.T. van Leent",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Baranca Buijsers",
+        "author_inst": "Radboudumc"
+      },
+      {
+        "author_name": "Inge Jonkman",
+        "author_inst": "Radboudumc"
+      },
+      {
+        "author_name": "Mark de Graaf",
+        "author_inst": "Radboudumc"
+      },
+      {
+        "author_name": "Marijke Baltissen",
+        "author_inst": "Radboud University"
+      },
+      {
+        "author_name": "Lieke A. Lamers",
+        "author_inst": "Radboud University"
+      },
+      {
+        "author_name": "Niels P. Riksen",
+        "author_inst": "Radboudumc"
+      },
+      {
+        "author_name": "Zahi A. Fayad",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Willem J.M. Mulder",
+        "author_inst": "Icahn School of Medicine at Mount Sinai"
+      },
+      {
+        "author_name": "Luuk B. Hilbrands",
+        "author_inst": "Radboudumc"
+      },
+      {
+        "author_name": "Leo A.B. Joosten",
+        "author_inst": "Radboudumc"
+      },
+      {
+        "author_name": "Mihai G. Netea",
+        "author_inst": "Radboudumc"
+      },
+      {
+        "author_name": "Michiel Vermeulen",
+        "author_inst": "Radboud University"
+      },
+      {
+        "author_name": "Johan van der Vlag",
+        "author_inst": "Radboudumc"
+      },
+      {
+        "author_name": "Rapha\u00ebl Duivenvoorden",
+        "author_inst": "Radboudumc"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "allergy and immunology"
+  },
   {
     "rel_doi": "10.1101/2020.06.06.20124388",
     "rel_title": "Protection after Quarantine: Insights from a Q-SEIR Model with Nonlinear Incidence Rates Applied to COVID-19",
@@ -1381322,45 +1380423,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.06.06.20124461",
-    "rel_title": "ICON (Ivermectin in COvid Nineteen) study: Use of Ivermectin is Associated with Lower Mortality in Hospitalized Patients with COVID19",
-    "rel_date": "2020-06-09",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.06.20124461",
-    "rel_abs": "ImportanceNo therapy to date has been shown to improve survival for patients infected with SARS-CoV-2. Ivermectin has been shown to inhibit the replication of SARS-CoV-2 in vitro but clinical response has not been previously evaluated.\n\nObjectiveTo determine whether Ivermectin is associated with lower mortality rate in patients hospitalized with COVID-19.\n\nDesign and SettingRetrospective cohort study of consecutive patients hospitalized at four Broward Health hospitals in South Florida with confirmed SARS-CoV-2. Enrollment dates were March 15, 2020 through May 11, 2020. Follow up data for all outcomes was May 19, 2020.\n\nParticipants280 patients with confirmed SARS-CoV-2 infection (mean age 59.6 years [standard deviation 17.9], 45.4% female), of whom 173 were treated with ivermectin and 107 were usual care were reviewed. 27 identified patients were not reviewed due to multiple admissions, lack of confirmed COVID results during hospitalization, age less than 18, pregnancy, or incarceration.\n\nExposurePatients were categorized into two treatment groups based on whether they received at least one dose of ivermectin at any time during the hospitalization. Treatment decisions were at the discretion of the treating physicians. Severe pulmonary involvement at study entry was characterized as need for either FiO2 [&ge;]50%, or noninvasive or invasive mechanical ventilation.\n\nMain Outcomes and MeasuresThe primary outcome was all-cause in-hospital mortality. Secondary outcomes included subgroup mortality in patients with severe pulmonary involvement and extubation rates for patients requiring invasive ventilation.\n\nResultsUnivariate analysis showed lower mortality in the ivermectin group (15.0% versus 25.2%, OR 0.52, 95% CI 0.29-0.96, P=.03). Mortality was also lower among 75 patients with severe pulmonary disease treated with ivermectin (38.8% vs 80.7%, OR 0.15, CI 0.05-0.47, P=.001), but there was no significant difference in successful extubation rates (36.1% vs 15.4%, OR 3.11 (0.88-11.00), p=.07). After adjustment for between-group differences and mortality risks, the mortality difference remained significant for the entire cohort (OR 0.27, CI 0.09-0.85, p=.03; HR 0.37, CI 0.19-0.71, p=.03).\n\nConclusions and RelevanceIvermectin was associated with lower mortality during treatment of COVID-19, especially in patients who required higher inspired oxygen or ventilatory support. These findings should be further evaluated with randomized controlled trials.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Juliana Cepelowicz Rajter",
-        "author_inst": "Broward Health Medical Center"
-      },
-      {
-        "author_name": "Michael Sherman",
-        "author_inst": "Drexel University"
-      },
-      {
-        "author_name": "Naaz Fatteh",
-        "author_inst": "Broward Health Medical Center"
-      },
-      {
-        "author_name": "Fabio Vogel",
-        "author_inst": "Broward Health Medical Center"
-      },
-      {
-        "author_name": "Jamie Sacks",
-        "author_inst": "Broward Health Medical Center"
-      },
-      {
-        "author_name": "Jean-Jacques Rajter",
-        "author_inst": "Broward Health Medical Center"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.06.07.20115188",
     "rel_title": "Functional and cognitive outcomes after COVID-19 delirium",
@@ -1381627,6 +1380689,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "respiratory medicine"
   },
+  {
+    "rel_doi": "10.1101/2020.06.07.20124933",
+    "rel_title": "Who dies from COVID-19? Post-hoc explanations of mortality prediction models using coalitional game theory, surrogate trees, and partial dependence plots",
+    "rel_date": "2020-06-09",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.07.20124933",
+    "rel_abs": "As of early June, 2020, approximately 7 million COVID-19 cases and 400,000 deaths have been reported. This paper examines four demographic and clinical factors (age, time to hospital, presence of chronic disease, and sex) and utilizes Shapley values from coalitional game theory and machine learning to evaluate their relative importance in predicting COVID-19 mortality. The analyses suggest that out of the 4 factors studied, age is the most important in predicting COVID-19 mortality, followed by time to hospital. Sex and presence of chronic disease were both found to be relatively unimportant, and the two global interpretation techniques differed in ranking them. Additionally, this paper creates partial dependence plots to determine and visualize the marginal effect of each factor on COVID-19 mortality and demonstrates how local interpretation of COVID-19 mortality prediction can be applicable in a clinical setting. Lastly, this paper derives clinically applicable decision rules about mortality probabilities through a parsimonious 3-split surrogate tree, demonstrating that high-accuracy COVID-19 mortality prediction can be achieved with simple, interpretable models.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Russell Yang",
+        "author_inst": "The Harker School"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.06.09.20125237",
     "rel_title": "COVID-19 related mortality and spread of disease in long-term care: first findings from a living systematic review of emerging evidence",
@@ -1382632,25 +1381713,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pharmacology and therapeutics"
   },
-  {
-    "rel_doi": "10.1101/2020.06.06.20124180",
-    "rel_title": "COVID 19 Pandemic: A Real-time Forecasts & Prediction of Confirmed Cases, Active Cases using the ARIMA model &Public Health in West Bengal, India.",
-    "rel_date": "2020-06-08",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.06.20124180",
-    "rel_abs": "BackgroundCOVID-19 is an emerging infectious disease which has been declared a Pandemic by the World Health Organization (WHO) on March 11 2020. This pandemic has spread over the world in more than 200 countries. India is also adversely affected by this pandemic, and there are no signs of slowing down of the virus in coming time. The absence of a vaccine for COVID-19 is making the situation worse for the already overstretched Indian public health care system. As economic burden makes it increasingly difficult for our country to continue imposing control measures, it is vital for states like West Bengal to make predictions using time series forecasting for the upcoming cases, test kits, health care and estimated the requirement of Quarantine centers, isolation beds, ICU beds and ventilators for COVID-19 patients.\n\nObjectiveThis study is forecasting the confirmed and active cases for COVID-19 until August, using time series ARIMA model & Public Health in West Bengal, India.\n\nMethodsWe used ARIMA model, and Auto ARIMA model for forecasting confirmed and active cases till the end of August month using time series data of COVID-19 cases in West Bengal, India from March 1, 2020, to June 4, 2020.\n\nResultsWe are expecting that West Bengal will have around 62279 {+/-} 5000 Cases by the end of August based on our forecasts. Meanwhile Maharashtra, Punjab, Gujarat and Delhi (UT) will be the most affected states, having the highest number of active and confirmed cases at the end of August.\n\nDiscussion and ConclusionThis forecasts show a very crucial situation for West Bengal in coming days and, the actual numbers can go higher than our estimates of confirmed case as Lockdown 5.0 & Unlock 1.0 will be implemented from 1st June 2020 in India, West Bengal will be observing a partial lift of the lockdown and in that case, there will be a surge in the number of daily confirmed and active cases. The requirement of Health care sector needs to be further improved isolation beds, ICUs and ventilators will also be needed to increase in that scenario. Inter State & Intra State Movement restrictions are lifted. Hence, Migrants returning to their homes due to loss of livelihood and income in the lockdown period may lead to a rise in the number of cases, which could not be accounted for in our projections. We suggest more of Public-Private Partnership (PPP) model in the health sector to accommodate COVID-19 patients adequately and reduce the burden of the already overstretched Indian public health care system, which will directly or indirectly affect the States in the time of crisis.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Dibash Sarkar",
-        "author_inst": "Adamas University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.06.06.20124495",
     "rel_title": "Less Wrong COVID-19 Projections With Interactive Assumptions",
@@ -1383017,6 +1382079,77 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.06.06.20124123",
+    "rel_title": "Clinical evaluation of self-collected saliva by RT-qPCR, direct RT-qPCR, RT-LAMP, and a rapid antigen test to diagnose COVID-19",
+    "rel_date": "2020-06-08",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.06.20124123",
+    "rel_abs": "BackgroundThe clinical performance of six molecular diagnostic tests and a rapid antigen test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were clinically evaluated for the diagnosis of coronavirus disease 2019 (COVID-19) in self-collected saliva.\n\nMethodsSaliva samples from 103 patients with laboratory-confirmed COVID-19 (15 asymptomatic and 88 symptomatic) were collected on the day of hospital admission. SARS-CoV-2 RNA in saliva was detected using a quantitative reverse-transcription polymerase chain reaction (RT-qPCR) laboratory-developed tes (LDT), a cobas SARS-CoV-2 high-throughput system, three direct RT-qPCR kits, and reverse-transcription loop mediated isothermal amplification (RT-LAMP). Viral antigen was detected by a rapid antigen immunochromatographic assay.\n\nResultsOf the 103 samples, viral RNA was detected in 50.5-81.6% of the specimens by molecular diagnostic tests and an antigen was detected in 11.7% of the specimens by the rapid antigen test. Viral RNA was detected at a significantly higher percentage (65.6-93.4%) in specimens collected within 9 d of symptom onset compared to that of specimens collected after at least 10 d of symptom onset (22.2-66.7%) and that of asymptomatic patients (40.0-66.7%). Viral RNA was more frequently detected in saliva from males than females.\n\nConclusionsSelf-collected saliva is an alternative specimen diagnosing COVID-19. LDT RT-qPCR, cobas SARS-CoV-2 high-throughput system, direct RT-qPCR except for one commercial kit, and RT-LAMP showed sufficient sensitivity in clinical use to be selectively used according to clinical settings and facilities. The rapid antigen test alone is not recommended for initial COVID-19 diagnosis because of its low sensitivity.\n\nKey pointsSix molecular diagnostic tests showed equivalent and sufficient sensitivity in clinical use in diagnosing COVID-19 in self-collected saliva samples. However, a rapid SARS-CoV-2 antigen test alone is not recommended for use without further study.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Mayu Ikeda",
+        "author_inst": "Self-Defense Forces Central Hospital"
+      },
+      {
+        "author_name": "Kazuo Imai",
+        "author_inst": "Self-Defense Forces Central Hospital"
+      },
+      {
+        "author_name": "Sakiko Tabata",
+        "author_inst": "Self-Defense Forces Central Hospital"
+      },
+      {
+        "author_name": "Kazuyasu Miyoshi",
+        "author_inst": "Self-Defense Forces Central Hospital"
+      },
+      {
+        "author_name": "Tsukasa Mizuno",
+        "author_inst": "Self-Defense Forces Central Hospital"
+      },
+      {
+        "author_name": "Nami Murahara",
+        "author_inst": "Self-Defense Forces Central Hospital"
+      },
+      {
+        "author_name": "Midori Horiuchi",
+        "author_inst": "Self-Defense Forces Central Hospital"
+      },
+      {
+        "author_name": "Kento Kato",
+        "author_inst": "Self-Defense Forces Central Hospital"
+      },
+      {
+        "author_name": "Yoshitaka Imoto",
+        "author_inst": "Self-Defense Forces Central Hospital"
+      },
+      {
+        "author_name": "Maki Iwata",
+        "author_inst": "Self-Defense Forces Central Hospital"
+      },
+      {
+        "author_name": "Satoshi Mimura",
+        "author_inst": "Self-Defense Forces Central Hospital"
+      },
+      {
+        "author_name": "Toshimitsu Ito",
+        "author_inst": "Self-Defense Forces Central Hospital"
+      },
+      {
+        "author_name": "Kaku Tamura",
+        "author_inst": "Self-Defense Forces Central Hospital"
+      },
+      {
+        "author_name": "Yasuyuki Kato",
+        "author_inst": "International University of Health and Welfare Narita Hospital"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.06.05.20123554",
     "rel_title": "The Role of Vitamin D in The Age of COVID-19: A Systematic Review and Meta-Analysis Along with an Ecological Approach",
@@ -1384502,37 +1383635,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.06.05.20123471",
-    "rel_title": "Symptom Course in COVID-19 Outpatients",
-    "rel_date": "2020-06-07",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.05.20123471",
-    "rel_abs": "ObjectiveDescribe the disease course in a cohort of outpatients with covid-19 and evaluate factors predicting duration of symptoms\n\nDesignRetrospective cohort study\n\nSettingTelemedicine clinic at a large medical system in Atlanta, Georgia\n\nParticipants273 patients with COVID-19. Exclusion criteria included: (1) intake more than 10 days after symptom onset, (2) hospitalization for covid-19, (3) symptoms at less than two visits.\n\nMain outcome measuresSymptom duration in days\n\nResultsCommon symptoms at diagnosis are upper respiratory (64% cough, 53% loss of smell or taste, 50% sinus congestion, 22% sore throat), systemic (50% headache, 48% body aches, 36% chills, 22% dizziness, 18% fever). The most frequent remaining symptoms at 30 days were cough (7%), loss of smell or taste (5%), body aches (5%), nasal congestion (5%), shortness of breath with exertion (5%), and joint pain (5%). Day of symptom onset was earliest for upper respiratory symptoms (mean 1.26 days, 95% confidence interval 1.15 to 1.4), followed by systemic symptoms (1.54, 1.39 to 1.7), with later onset of lower respiratory (2.86, 2.54 to 3.22) and gastrointestinal symptoms (3.46, 3.07 to 3.89), when present. Cough had the longest duration when present with 12.2 days (10.9 to 13.6). Loss of smell or taste had the second longest duration with 11.0 days (9.9 to 12.2). Provider-Assessed Symptom Severity (PASS) is the best predictor of symptom duration (P <0.005 for multiple symptoms) and patients with \"Moderate\" PASS compared to \"Mild\" at their intake visit have higher rates of symptoms at 30 days, including cough (12%), nasal congestion (10%), joint pain (10%), body aches (9%), loss of taste or smell (7%), headache (7%), and shortness of breath with exertion (6%).\n\nConclusionsCovid-19 illness in outpatients follows a pattern of progression from systemic symptoms to lower respiratory symptoms and persistent symptoms are common across categories. Provider-assessed symptom severity is the best predictor of disease duration.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "James B O'Keefe",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Elizabeth J Tong",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "Ghazala A Datoo O'Keefe",
-        "author_inst": "Emory University School of Medicine"
-      },
-      {
-        "author_name": "David C Tong",
-        "author_inst": "Emory University School of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.06.05.20123463",
     "rel_title": "UV-C irradiation is highly effective in inactivating and inhibiting SARS-CoV-2 replication",
@@ -1384779,6 +1383881,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "intensive care and critical care medicine"
   },
+  {
+    "rel_doi": "10.1101/2020.06.05.20122903",
+    "rel_title": "Impact of Governmental interventions on epidemic progression and workplace activity during the COVID-19 outbreak",
+    "rel_date": "2020-06-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.05.20122903",
+    "rel_abs": "In the first quarter of 2020, the COVID-19 pandemic brought the world to a state of paralysis. During this period, humanity has seen by far the largest organized travel restrictions and unprecedented efforts and global coordination to contain the spread of the SARS-CoV-2 virus. Using large scale human mobility and fine grained epidemic incidence data, we develop a framework to understand and quantify the effectiveness of the interventions implemented by various countries to control epidemic growth. Our analysis reveals the importance of timing and implementation of strategic policy in controlling the epidemic. Through our analysis, we also unearth significant spatial diffusion of the epidemic before and during the lock-down measures in several countries, casting doubt on the effectiveness or on the implementation quality of the proposed Governmental policies.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Sumit Kumar Ram",
+        "author_inst": "ETH Zurich"
+      },
+      {
+        "author_name": "Didier Sornette",
+        "author_inst": "ETH Zurich"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.06.05.20123695",
     "rel_title": "Non-COVID-19 Deaths After Social Distancing in Norway",
@@ -1385752,85 +1384877,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.06.07.119032",
-    "rel_title": "Molecular mechanism of SARS-Cov-2 components caused ARDS in murine model",
-    "rel_date": "2020-06-07",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.07.119032",
-    "rel_abs": "COVID-19 has become a major challenge to global health, and until now, no efficient antiviral agents have been developed. The SARS-CoV-2 infection is characterized by pulmonary and systemic inflammation in severe patients, and acute respiratory distress syndrome (ARDS) caused respiratory failure contributes to most mortalities. There is an urgent need for developing effective drugs and vaccines against SARS-CoV-2 and COVID-19 caused ARDS. However, most researchers cannot perform SARS-CoV-2 related researches due to lacking P3 or P4 facility. We developed a non-infectious, highly safety, time-saving SARS-CoV-2 components induced murine model to study the SARS-CoV-2 caused ARDS and cytokine storm syndrome (CSS). We also investigated mAbs and inhibitors which potentially neutralize the pro-inflammatory phenotype of COVID-19, and found that anti-IL-1, anti-IL-6, anti-TNF, anti-GM-CSF mAbs, p38 inhibitor, and JAK inhibitor partially relieved CSS. Besides, anti-IL-6, anti-TNF, anti-GM-CSF mAbs and inhibitors of p38, ERK, and MPO somewhat reduced neutrophilic alveolitis in the lung. In all, we established the murine model mimic of COVID-19, opening a biosafety and less time-consuming avenue for clarifying the mechanism of ARDS and CSS in COVID-19 and developing the therapeutic drugs.",
-    "rel_num_authors": 16,
-    "rel_authors": [
-      {
-        "author_name": "Tingxuan Gu",
-        "author_inst": "Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University"
-      },
-      {
-        "author_name": "Simin Zhao",
-        "author_inst": "Affiliated Tumor Hospital of Zhengzhou University"
-      },
-      {
-        "author_name": "Guoguo Jin",
-        "author_inst": "The Henan Luoyang Orthopedic Hospital"
-      },
-      {
-        "author_name": "Mengqiu Song",
-        "author_inst": "Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University"
-      },
-      {
-        "author_name": "Yafei Zhi",
-        "author_inst": "China-US(Henan)Hormel cancer institute"
-      },
-      {
-        "author_name": "Ran Zhao",
-        "author_inst": "Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University"
-      },
-      {
-        "author_name": "Fayang Ma",
-        "author_inst": "Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University"
-      },
-      {
-        "author_name": "Yaqiu Zheng",
-        "author_inst": "China-US(Henan)Hormel cancer institute"
-      },
-      {
-        "author_name": "Keke Wang",
-        "author_inst": "China-US(Henan)Hormel cancer institute"
-      },
-      {
-        "author_name": "Hui Liu",
-        "author_inst": "Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University"
-      },
-      {
-        "author_name": "Mingxia Xin",
-        "author_inst": "China-US(Henan)Hormel cancer institute"
-      },
-      {
-        "author_name": "Wei Han",
-        "author_inst": "China-US(Henan)Hormel cancer institute"
-      },
-      {
-        "author_name": "Xiang Li",
-        "author_inst": "Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University"
-      },
-      {
-        "author_name": "Christopher D Dong",
-        "author_inst": "Wartburg College, Waverly, IA, USA"
-      },
-      {
-        "author_name": "Kangdong Liu",
-        "author_inst": "Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University"
-      },
-      {
-        "author_name": "Zigang Dong",
-        "author_inst": "Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "new results",
-    "category": "pathology"
-  },
   {
     "rel_doi": "10.1101/2020.06.07.138800",
     "rel_title": "Genetic analysis of SARS-CoV-2 isolates collected from Bangladesh: insights into the origin, mutation spectrum, and possible pathomechanism",
@@ -1386145,6 +1385191,29 @@
     "type": "new results",
     "category": "biochemistry"
   },
+  {
+    "rel_doi": "10.1101/2020.06.05.136887",
+    "rel_title": "Protein covariance networks reveal interactions important to the emergence of SARS coronaviruses as human pathogens",
+    "rel_date": "2020-06-06",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.05.136887",
+    "rel_abs": "SARS-CoV-2 is one of three recognized coronaviruses (CoVs) that have caused epidemics or pandemics in the 21st century and that have likely emerged from animal reservoirs based on genomic similarities to bat and other animal viruses. Here we report the analysis of conserved interactions between amino acid residues in proteins encoded by SARS-CoV-related viruses. We identified pairs and networks of residue variants that exhibited statistically high frequencies of covariance with each other. While these interactions are likely key to both protein structure and other protein-protein interactions, we have also found that they can be used to provide a new computational approach (CoVariance-based Phylogeny Analysis) for understanding viral evolution and adaptation. Our data provide evidence that the evolutionary processes that converted a bat virus into human pathogen occurred through recombination with other viruses in combination with new adaptive mutations important for entry into human cells.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "William P Robins",
+        "author_inst": "Harvard Medical School"
+      },
+      {
+        "author_name": "John J Mekalanos",
+        "author_inst": "Harvard Medical School"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "bioinformatics"
+  },
   {
     "rel_doi": "10.1101/2020.06.05.137380",
     "rel_title": "ScRNA-seq discover cell cluster change under OAB: ACE2 expression reveal possible alternation of 2019-nCoV infectious pathway",
@@ -1387654,69 +1386723,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.06.02.20119313",
-    "rel_title": "Early phase of the COVID-19 outbreak in Hungary and post-lockdown scenarios",
-    "rel_date": "2020-06-05",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20119313",
-    "rel_abs": "COVID-19 epidemic has been suppressed in Hungary due to timely non-pharmaceutical interventions, prompting a huge reduction in the number of contacts and transmission of the virus. This strategy was effective in preventing epidemic growth and reducing the incidence of COVID-19 to low levels. In this report, we present the first epidemiological and statistical analysis of the early phase of the COVID-19 outbreak in Hungary. Then, we establish an age-structured compartmental model to explore alternative post-lockdown scenarios. We incorporate various factors, such as age-specific measures, seasonal effects, and spatial heterogeneity to project the possible peak size and disease burden of a COVID-19 epidemic wave after the current measures are relaxed.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Gergely R\u00f6st",
-        "author_inst": "Bolyai Institute, University of Szeged, Hungary"
-      },
-      {
-        "author_name": "Ferenc A. Bartha",
-        "author_inst": "Bolyai Institute, University of Szeged, Hungary"
-      },
-      {
-        "author_name": "Norbert Bogya",
-        "author_inst": "Bolyai Institute, University of Szeged, Hungary"
-      },
-      {
-        "author_name": "P\u00e9ter Boldog",
-        "author_inst": "Bolyai Institute, University of Szeged, Hungary"
-      },
-      {
-        "author_name": "Attila D\u00e9nes",
-        "author_inst": "Bolyai Institute, University of Szeged, Hungary"
-      },
-      {
-        "author_name": "Ferenci Tam\u00e1s",
-        "author_inst": "\u00d3buda University, Hungary"
-      },
-      {
-        "author_name": "Krisztina J. Horv\u00e1th",
-        "author_inst": "National Public Health Center, Hungary"
-      },
-      {
-        "author_name": "Attila Juh\u00e1sz",
-        "author_inst": "Department of Public Health, Government Office of Capital City Budapest, Hungary"
-      },
-      {
-        "author_name": "Csilla Nagy",
-        "author_inst": "Department of Public Health, Government Office of Capital City Budapest, Hungary"
-      },
-      {
-        "author_name": "Tam\u00e1s Tekeli",
-        "author_inst": "Bolyai Institute, University of Szeged, Hungary"
-      },
-      {
-        "author_name": "Zsolt Vizi",
-        "author_inst": "Bolyai Institute, University of Szeged, Hungary"
-      },
-      {
-        "author_name": "Beatrix Oroszi",
-        "author_inst": "National Public Health Center, Hungary"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.06.04.20112011",
     "rel_title": "Reparations for Black American Descendants of Persons Enslaved in the U.S. and Their Estimated Impact on SARS-CoV-2 Transmission",
@@ -1387939,6 +1386945,81 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "medical education"
   },
+  {
+    "rel_doi": "10.1101/2020.06.02.20120642",
+    "rel_title": "Estimating excess visual loss in people with neovascular age-related macular degeneration during the COVID-19 pandemic",
+    "rel_date": "2020-06-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20120642",
+    "rel_abs": "ObjectivesTo report the reduction in new neovascular age-related macular degeneration (nAMD) referrals during the COVID-19 pandemic and estimate the impact of delayed treatment on visual outcomes at one year.\n\nDesignRetrospective clinical audit and simulation model.\n\nSettingMultiple UK NHS ophthalmology centres.\n\nParticipantsData on the reduction in new nAMD referrals was obtained from four NHS Trusts in England comparing April 2020 to April 2019. To estimate the potential impact on one-year visual outcomes, a stratified bootstrap simulation model was developed drawing on an electronic medical records dataset of 20,825 nAMD eyes from 27 NHS Trusts.\n\nMain outcome measuresSimulated mean visual acuity and proportions of eyes with vision [&le;]6/60, [&le;]6/24 and [&ge;]6/12 at one year under four hypothetical scenarios: no treatment delay, 3, 6 and 9-month treatment delays. Estimated additional number of eyes with vision [&le;]6/60 at one year nationally.\n\nResultsThe number of nAMD referrals at four major eye treatment hospital groups based in England dropped on average by 72% (range 65 to 87%) in April 2020 compared to April 2019. Simulated one-year visual outcomes for 1000 nAMD eyes with a 3-month treatment delay suggested an increase in the proportion of eyes with vision [&le;]6/60 from 15.5% (13.2 to 17.9) to 23.3% (20.7 to25.9), and a decrease in the proportion of eyes with vision [&ge;]6/12 (driving vision) from 35.1% (32.1 to 38.1) to 26.4% (23.8 to29.2). Outcomes worsened incrementally with longer modelled delays. Assuming nAMD referrals are reduced to this level at the national level for only one month, these simulated results suggest an additional 186-365 eyes with vision [&le;]6/60 at one-year with even a short treatment delay.\n\nConclusionsWe report a large decrease in nAMD referrals during the first month of COVID-19 lockdown and provide an important public health message regarding the risk of delayed treatment. As a conservative estimate, a treatment delay of 3 months could lead to a >50% relative increase in the number of eyes with vision [&le;]6/60 and 25% relative decrease in the number of eyes with driving vision at one year.",
+    "rel_num_authors": 15,
+    "rel_authors": [
+      {
+        "author_name": "Darren S Thomas",
+        "author_inst": "Institute of Health Informatics, University College London, London, UK"
+      },
+      {
+        "author_name": "Alasdair Warwick",
+        "author_inst": "Institute of Cardiovascular Science, University College London, London, UK & Moorfields Eye Hospital NHS Foundation Trust, London, UK."
+      },
+      {
+        "author_name": "Abraham Olvera-Barrios",
+        "author_inst": "Moorfields Eye Hospital NHS Turst & Institute of Ophthalmology UCL"
+      },
+      {
+        "author_name": "Catherine Egan",
+        "author_inst": "Moorfields Eye Hospital NHS Foundation Trust, London, UK & Institute of Ophthalmology, UCL"
+      },
+      {
+        "author_name": "Roy Schwartz",
+        "author_inst": "Moorfields Eye Hospital NHS Foundation Trust, London, UK & Institute of Health Informatics, University College London, London, UK"
+      },
+      {
+        "author_name": "Sudeshna Patra",
+        "author_inst": "Bart's Health NHS Trust, London, UK"
+      },
+      {
+        "author_name": "Haralabos Eleftheriadis",
+        "author_inst": "King's College Hospital NHS Trust, London, UK"
+      },
+      {
+        "author_name": "Anthony P Khawaja",
+        "author_inst": "Moorfields Eye Hospital NHS Foundation Trust, London, UK & Institute of Ophthalmology, UCL"
+      },
+      {
+        "author_name": "Andrew Lotery",
+        "author_inst": "Faculty of Medicine, University of Southampton, Southampton, UK"
+      },
+      {
+        "author_name": "Philipp L Mueller",
+        "author_inst": "Moorfields Eye Hospital NHS Foundation Trust, London, UK"
+      },
+      {
+        "author_name": "Robin Hamilton",
+        "author_inst": "Moorfields Eye Hospital NHS Foundation Trust, London, UK & Institute of Ophthalmology, UCL"
+      },
+      {
+        "author_name": "Ella Preston",
+        "author_inst": "Moorfields Eye Hospital NHS Foundation Trust, London, UK"
+      },
+      {
+        "author_name": "Paul Taylor",
+        "author_inst": "Institute of Health Informatics, University College London, London, UK"
+      },
+      {
+        "author_name": "Adnan Tufail",
+        "author_inst": "Moorfields Eye Hospital NHS Trust & Institute of Ophthalmology UCL"
+      },
+      {
+        "author_name": "- UK EMR Users Group",
+        "author_inst": ""
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "ophthalmology"
+  },
   {
     "rel_doi": "10.1101/2020.06.03.20121608",
     "rel_title": "COVID-19 DYNAMICS CONSIDERING THE INFLUENCE OF HOSPITAL INFRASTRUCTURE: AN INVESTIGATION OF BRAZILIAN SCENARIOS",
@@ -1389012,65 +1388093,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.06.04.20121434",
-    "rel_title": "The impact of school reopening on the spread of COVID-19 in England",
-    "rel_date": "2020-06-05",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20121434",
-    "rel_abs": "By mid-May, cases of COVID-19 in the UK had been declining for over a month; a multi-phase emergence from lockdown was planned, including a scheduled partial reopening of schools on 1st June. Although evidence suggests that children generally display mild symptoms, the size of the school-age population means the total impact of reopening schools is unclear. Here, we present work from mid-May that focused on the imminent opening of schools and consider what these results imply for future policy.\n\nWe compared eight strategies for reopening primary and secondary schools in England. Modifying a transmission model fitted to UK SARS-CoV-2 data, we assessed how reopening schools affects contact patterns, anticipated secondary infections and the relative change in the reproduction number, R. We determined the associated public health impact and its sensitivity to changes in social-distancing within the wider community.\n\nWe predicted reopening schools with half-sized classes or focused on younger children was unlikely to push R above one. Older children generally have more social contacts, so reopening secondary schools results in more cases than reopening primary schools, while reopening both could have pushed R above one in some regions. Reductions in community social-distancing were found to outweigh and exacerbate any impacts of reopening. In particular, opening schools when the reproduction number R is already above one generates the largest increase in cases.\n\nOur work indicates that while any school reopening will result in increased mixing and infection amongst children and the wider population, reopening schools alone in June was unlikely to push R above one. Ultimately, reopening decisions are a difficult trade-off between epidemiological consequences and the emotional, educational and developmental needs of children. Into the future, there are difficult questions about what controls can be instigated such that schools can remain open if cases increase.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Matt J Keeling",
-        "author_inst": "University of Warwick"
-      },
-      {
-        "author_name": "Michael J Tildesley",
-        "author_inst": "University of Warwick"
-      },
-      {
-        "author_name": "Benjamin D Atkins",
-        "author_inst": "University of Warwick"
-      },
-      {
-        "author_name": "Bridget Penman",
-        "author_inst": "University of Warwick"
-      },
-      {
-        "author_name": "Emma Southall",
-        "author_inst": "University of Warwick"
-      },
-      {
-        "author_name": "Glen Guyver-Fletcher",
-        "author_inst": "University of Warwick"
-      },
-      {
-        "author_name": "Alex Holmes",
-        "author_inst": "University of Warwick"
-      },
-      {
-        "author_name": "Hector McKimm",
-        "author_inst": "University of Warwick"
-      },
-      {
-        "author_name": "Erin E Gorsich",
-        "author_inst": "University of Warwick"
-      },
-      {
-        "author_name": "Edward M Hill",
-        "author_inst": "University of Warwick"
-      },
-      {
-        "author_name": "Louise Dyson",
-        "author_inst": "University of Warwick"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.06.03.20121467",
     "rel_title": "Comparison of epidemiological characteristics of COVID-19 patients in Vietnam",
@@ -1389389,6 +1388411,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.06.03.20121442",
+    "rel_title": "Reduction in preterm births during the COVID-19 lockdown in Ireland: a natural experiment allowing analysis of data from the prior two decades.",
+    "rel_date": "2020-06-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.03.20121442",
+    "rel_abs": "BackgroundAetiology of preterm birth (PTB) is heterogeneous and preventive strategies remain elusive. Socio-environmental measures implemented as Irelands prudent response to the SARS-CoV-2 virus (COVID-19) pandemic represented, in effect, a national lockdown and have possibly influenced the health and wellbeing of pregnant women and unborn infants. Cumulative impact of such socio-environmental factors operating contemporaneously on PTB has never been assessed before.\n\nMethodsRegional PTB trends of very low birth weight (VLBW) infants in one designated health area of Ireland over two decades were analysed. Poisson regression and rate ratio analyses with 95% CI were conducted. Observed regional data from January - April 2020 were compared to historical regional and national data and forecasted national figures for 2020.\n\nResultsPoisson regression analysis found that the regional historical VLBW rate per 1000 live births for January to April, 2001-2019 was 8.18 (95% CI: 7.21, 9.29). During January to April 2020, an unusually low VLBW rate of just 2.17 per 1000 live births was observed. The rate ratio of 3.77 (95% CI: 1.21, 11.75), p = 0.022, estimates that for the last two decades there was, on average, 3.77 times the rate of VLBW, compared to the period January to April 2020 during which there is a 73% reduction. National Irish VLBW rate for 2020 is forecasted to be reduced to 400 per 60,000 births compared to the historical 500-600 range.\n\nConclusionAn unprecedented reduction in PTB of VLBW infants was observed in one health region of Ireland during the COVID-19 lockdown. Potential determinants of this unique temporal trend reside in the summative socio-environmental impact of the COVID-19 dictated lockdown. Our findings, if mirrored in other regions that have adopted similar measures to combat the pandemic, demonstrate the potential to evaluate these implicated interdependent behavioural and socio-environmental modifiers to positively influence PTB rates globally.\n\nKey QuestionsO_ST_ABSWhat is already known?C_ST_ABSO_LIPremature birth is an important contributor for under-five mortality globally.\nC_LIO_LICurrently there is no broadly accepted and effective strategy to prevent the birth of premature very low birth weight infants.\nC_LIO_LIImpact of socio-environmental and maternal behavioural modifications on the incidence of preterm birth has not been assessed.\nC_LI\n\nWhat are the new findings?O_LICOVID-19-triggered national lockdown in Ireland created an opportunity to study the cumulative influence of socio-environmental modifications on pregnant mothers.\nC_LIO_LIAn unprecedented 73% reduction in the rate of very low birth weight deliveries was noted in one designated health region of Ireland during January to April of 2020 in comparison to the preceding 20 year timeframe.\nC_LIO_LIOur observations, if nationally mirrored, indicate that birth rate of very low birth weight premature infants in Ireland is forecasted to decrease considerably in 2020.\nC_LI\n\nWhat do the new findings imply?O_LISocially rooted modifiers such as family support, work related stress and commuting, environmental pollution, infection avoidance, sleep and nutritional support, adequate exercise, reduced exposure to tobacco and illicit drugs, avoidance of financial strain, all cumulatively could contribute to reduce preterm birth rate.\nC_LIO_LIOur observations, if reflected in other countries that adopted COVID-19-prompted lockdown measures, would redefine the antecedents that trigger the yet poorly understood pathways leading to preterm births.\nC_LIO_LIPrematurity rate would be the most important  curve to bend in the context of reducing infant mortality globally and thus promote the achievement of sustainable development goals for children.\nC_LI",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Roy K Philip",
+        "author_inst": "Division of Neonatology, Department of Paediatrics, University Maternity Hospital Limerick, Ireland"
+      },
+      {
+        "author_name": "Helen Purtill",
+        "author_inst": "Department of Mathematics and Statistics, University of Limerick, Limerick, Ireland"
+      },
+      {
+        "author_name": "Elizabeth Reidy",
+        "author_inst": "Department of Midwifery and Neonatal Nursing, University Maternity Hospital, Limerick, Ireland."
+      },
+      {
+        "author_name": "Mandy Daly",
+        "author_inst": "Advocacy and Policymaking, Irish Neonatal Health Alliance (INHA), Bray, Wicklow, Ireland."
+      },
+      {
+        "author_name": "Mendinaro Imcha",
+        "author_inst": "Department of Obstetrics and Gynaecology, University Maternity Hospital, Limerick, Ireland."
+      },
+      {
+        "author_name": "Deirdre McGrath",
+        "author_inst": "Head of School, School of Medicine University ofLimerick, Limerick, Ireland."
+      },
+      {
+        "author_name": "Nuala H O'Connell",
+        "author_inst": "Department of Clinical Microbiology, University Hospital Limerick, Ireland."
+      },
+      {
+        "author_name": "Colum P Dunne",
+        "author_inst": "Head of Research, School of Medicine and Centre for Interventions in Infection, Inflammation and Immunity (4i), University of Limerick, Ireland."
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "pediatrics"
+  },
   {
     "rel_doi": "10.1101/2020.06.04.20121863",
     "rel_title": "COVID-19 and climate: global evidence from 117 countries",
@@ -1391157,29 +1390226,6 @@
     "type": "new results",
     "category": "evolutionary biology"
   },
-  {
-    "rel_doi": "10.1101/2020.06.04.20122119",
-    "rel_title": "The impact of occupational risk from COVID on GP supply in England: A cross-sectional study",
-    "rel_date": "2020-06-05",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20122119",
-    "rel_abs": "ObjectivesTo identify the risk of general practitioner mortality from COVID and the impact of measures to mitigate this risk on the level and socioeconomic distribution of primary care provision in the English NHS\n\nDesignCross sectional study\n\nSettingAll GP practices providing primary care under the NHS in England\n\nParticipants45,858 GPs and 6,771 GP practices in the English NHS\n\nMain outcome measuresNumbers of high-risk GPs, high-risk single-handed GP practices, patients associated with these high-risk single-handed practices and the regional and socioeconomic distribution of each. Mortality rates from COVID by age, sex and ethnicity were used to attribute risk to GPs and the Index of Multiple Deprivation was used to determine socioeconomic distributions of the outcomes.\n\nResultsOf 45,858 GPs in our sample 3,632 (7.9%) were classified as high risk or very high risk. Of 6,771 GP practices in our sample 639 (9.4%) were identified as single-handed practices and of these 209 (32.7%) were run by a GP at high or very high risk. These 209 single-handed practices care for 710,043 patients. GPs at the highest levels of risk from COVID, and single-handed practices run by high-risk GPs were concentrated in the most deprived neighbourhoods in the country. London had the highest proportion of both GPs and single-handed GP practices at very high risk of COVID mortality with 1,160 patients per 100,000 population registered to these practices.\n\nConclusionsA significant proportion of GPs working in England, particularly those serving patients in the most deprived neighbourhoods, are at high risk of dying from COVID. Many of these GPs run single-handed practices. These GPs are particularly concentrated in London. There is an opportunity to provide additional support to mitigate COVID risk for GPs, GP practices and their patients. Failure to do so will likely exacerbate existing health inequalities.\n\nWhat is already knownO_LIKnown risk factors for morbidity and mortality from COVID-19 include age, sex, ethnicity and certain underlying health conditions.\nC_LIO_LINHS England have suggested that NHS staff who may be at higher risk from COVID are risk assessed and have their activities adjusted accordingly, including ceasing face to face patient contact.\nC_LI\n\nWhat this study addsO_LIThis study applies risk scoring to calculate the number of GPs practicing in England who are likely to be at high or very high risk of death from COVID. We examine the potential effect of removing GPs at high or very high risk from COVID from face to face patient contacts, estimating the number of GPs and patients likely to be affected, and relating this to deprivation and geography.\nC_LIO_LIWe estimate that of 45,858 GPs in our sample, 2,253 (4.9%) were classified as high risk, and 1,379 (3%) as very high risk from COVID. These are likely to be conservative estimates.\nC_LIO_LIGPs at high risk of COVID are more likely to work in areas of high socioeconomic deprivation.\nC_LIO_LIAlmost one in three single-handed GP practices (32.7%, or 209 out of 639) is run by a GP we estimate to be at high or very high risk from COVID. If these GPs did not see patients face to face, 710,043 patients would be left without face to face GP appointments. Single-handed GP practices in areas of high socioeconomic deprivation are more likely to be run by GPs at higher risk of COVID.\nC_LI",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Miqdad Asaria",
-        "author_inst": "London School of Economics and Political Science"
-      },
-      {
-        "author_name": "Rebecca Fisher",
-        "author_inst": "The Health Foundation"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health policy"
-  },
   {
     "rel_doi": "10.1101/2020.06.04.20122879",
     "rel_title": "CoVID-19 in Singapore: Impact of Contact Tracing and Self-awareness on Healthcare Demand",
@@ -1391434,6 +1390480,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "cardiovascular medicine"
   },
+  {
+    "rel_doi": "10.1101/2020.06.04.20122176",
+    "rel_title": "What variables can better predict the number of infections and deaths worldwide by SARS-CoV-2? Variation through time",
+    "rel_date": "2020-06-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20122176",
+    "rel_abs": "Using data from 50 very different countries (which represent nearly 70% of worlds population) and by means of a regression analysis, we studied the predictive power of different variables (mobility, air pollution, health & research, economic and social & geographic indicators) over the number of infected and dead by SARS-CoV-2. We also studied if the predictive power of these variables changed during a 4 months period (March, April, May and June). We approached data in two different ways, cumulative data and non-cumulative data.\n\nThe number of deaths by Covid-19 can always be predicted with great accuracy from the number of infected, regardless of the characteristics of the country.\n\nInbound tourism emerged as the variable that best predicts the number of infected (and, consequently, the number of deaths) happening in the different countries. Electricity consumption and air pollution of a country (CO2 emissions, nitrous oxide and methane) are also capable of predicting, with great precision, the number of infections and deaths from Covid-19. Characteristics such as the area and population of a country can also predict, although to a lesser extent, the number of infected and dead. All predictive variables remained significant through time.\n\nIn contrast, a series of variables, which in principle would seem to have a greater influence on the evolution of Covid-19 (hospital bed density, Physicians per 1000 people, Researches in R & D, urban population...), turned out to have very little - or none- predictive power.\n\nOur results explain why countries that opted for travel restrictions and social withdrawal policies at a very early stage of the pandemic outbreak, obtained better results. Preventive policies proved to be the key, rather than having large hospital and medical resources.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Javier Garcia Garcia de Alcaniz",
+        "author_inst": "Veterinary Faculty Complutense University Madrid Genetics Department"
+      },
+      {
+        "author_name": "Julia Romero-Lopez",
+        "author_inst": "Veterinary Faculty Complutense University Madrid Genetics Department"
+      },
+      {
+        "author_name": "Rocio P. Martinez",
+        "author_inst": "Veterinary Faculty Complutense University Madrid Genetics Department"
+      },
+      {
+        "author_name": "Victoria Lopez-Rodas Sr.",
+        "author_inst": "Veterinary Faculty Complutense University Madrid Genetics Department"
+      },
+      {
+        "author_name": "Eduardo Costas Sr.",
+        "author_inst": "Veterinary Faculty Complutense University Madrid, Genetics Department"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.06.04.20122382",
     "rel_title": "Optimal Control Measures to Combat COVID19 Spread in Sri Lanka: A Mathematical ModelConsidering the Heterogeneity of Cases",
@@ -1392735,37 +1391816,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.06.03.20120899",
-    "rel_title": "Estimating the parameters of SIR model of COVID-19 cases in India during lock down periods",
-    "rel_date": "2020-06-04",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.03.20120899",
-    "rel_abs": "From the pandemic scenario of COVID-19 disease cases in all over the world, the outbreak prediction becomes very complex for the emerging scientifically research. Several epidemiological mathematical models of spread are increasing day by day to forecast correctly. Here, the classical SIR modelling approach is carried out to study the different parameters of this model in case of India county. This type of approach analyzed by considering different governmental lock down measures in India. There are some assumptions were taken into account for fitting the model in Python simulation in each lock down scenario. The predicted parameters of SIR model showed some improvement in each case of lock down in India. The outcome results showed the extreme interventions should be taken to tackle this type of pandemic situation in near future.\n\nAuthor approvalThis article does not contain any studies with human participants or animals performed by any of the authors.\n\nCompeting interestsThe authors declare no competing interests.\n\nDeclarationsThe authors declare that there is no conflict of interest regarding the publication of this article.\n\nData availability statementThe working data set used for this study has been submitted to the journal as additional supporting files.\n\nData availability linksO_LIhttps://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data/csse_covid_19_time_series\nC_LIO_LIhttps://www.dropbox.com/sh/akc525jjq3dp485/AADgo6WsT1RBpZqahmj_k-v_a/SIR/italy_fit.py?dl=0.\nC_LI",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "DILIP KUMAR BAGAL",
-        "author_inst": "GOVERNMENT COLLEGE OF ENGINEERING,  KALAHANDI"
-      },
-      {
-        "author_name": "ARATI RATH",
-        "author_inst": "National Institute of Technology Jamshedpur, Jamshedpur"
-      },
-      {
-        "author_name": "Abhishek Barua",
-        "author_inst": "Centre for Advanced Post Graduate Studies, BPUT, Rourkela"
-      },
-      {
-        "author_name": "Dulu Patnaik",
-        "author_inst": "Government College of Engineering, Kalahandi"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.06.03.20121020",
     "rel_title": "Regional Difference in Seroprevalence of SARS-CoV-2 in Tokyo: Results from the community point-of-care antibody testing",
@@ -1393004,6 +1392054,77 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
+  {
+    "rel_doi": "10.1101/2020.06.02.20120014",
+    "rel_title": "Viral load dynamics in transmissible symptomatic patients with COVID-19",
+    "rel_date": "2020-06-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20120014",
+    "rel_abs": "To investigate the relationship between viral load and secondary transmission in novel coronavirus disease 2019 (COVID-19), we reviewed epidemiological and clinical data obtained from immunocompetent laboratory-confirmed patients with COVID-19 at Toyama University Hospital. In total, 28 patients were included in the analysis. Median viral load at the initial sample collection was significantly higher in adults than in children and in symptomatic than in asymptomatic patients. Among symptomatic patients, non-linear regression models showed that the estimated viral load at onset was higher in the index (patients who transmitted the disease to at least one other patient) than in the non-index patients (patients who were not the cause of secondary transmission; median [95% confidence interval]: 6.6 [5.2-8.2] vs. 3.1 [1.5-4.8] log copies/L, respectively). High nasopharyngeal viral loads around onset may contribute to secondary transmission of COVID-19.\n\nArticle Summary LineHigh nasopharyngeal viral load around the onset may contributes to secondary transmission of COVID-19.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Hitoshi Kawasuji",
+        "author_inst": "Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan"
+      },
+      {
+        "author_name": "Yusuke Takegoshi",
+        "author_inst": "Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan"
+      },
+      {
+        "author_name": "Makito Kaneda",
+        "author_inst": "Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan"
+      },
+      {
+        "author_name": "Akitoshi Ueno",
+        "author_inst": "Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan"
+      },
+      {
+        "author_name": "Yuki Miyajima",
+        "author_inst": "Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan"
+      },
+      {
+        "author_name": "Koyomi Kawago",
+        "author_inst": "Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan"
+      },
+      {
+        "author_name": "Yasutaka Fukui",
+        "author_inst": "Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan"
+      },
+      {
+        "author_name": "Yoshihiko Yoshida",
+        "author_inst": "Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan"
+      },
+      {
+        "author_name": "Miyuki Kimura",
+        "author_inst": "Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan"
+      },
+      {
+        "author_name": "Hiroshi Yamada",
+        "author_inst": "Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan"
+      },
+      {
+        "author_name": "Ippei Sakamaki",
+        "author_inst": "Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan"
+      },
+      {
+        "author_name": "Hideki Tani",
+        "author_inst": "Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan"
+      },
+      {
+        "author_name": "Yoshitomo Morinaga",
+        "author_inst": "Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan"
+      },
+      {
+        "author_name": "Yoshihiro Yamamoto",
+        "author_inst": "Toyama University Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.06.02.20120345",
     "rel_title": "Comparative assessment of multiple COVID-19 serological technologies supports continued evaluation of point-of-care lateral flow assays in hospital and community healthcare settings",
@@ -1394109,29 +1393230,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "respiratory medicine"
   },
-  {
-    "rel_doi": "10.1101/2020.05.28.20116400",
-    "rel_title": "Incidence and risk factors of kidney impairment on patients with COVID-19: a systematic review and meta-analysis",
-    "rel_date": "2020-06-03",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20116400",
-    "rel_abs": "BackgroundThe novel coronavirus is pandemic around the world. Several researchers have given the evidence of impacts of COVID-19 on the respiratory, cardiovascular and gastrointestinal system. Studies still have debated on kidney injury of COVID-19 patients. The purpose of the meta-analysis was to evaluate the association of kidney impairment with the development of COVID-19.\n\nMethodsThe PubMed, Embase and MedRxiv databases were searched until April 1, 2020. We extracted data from eligible studies to summarize the clinical manifestations and laboratory indexes of kidney injury on COVID-19 infection patients and further compared the prevalence of acute kidney injury (AKI) and the mean differences of three biomarkers between in ICU/severe and non-ICU/non-severe cases. Heterogeneity was evaluated using the I2 method.\n\nResultsIn the sum of 19 studies with 4375 patients were included in this analysis. The pooled prevalence of AKI, increased serum creatinine (Scr), increased blood urea nitrogen (BUN), increased D-dimer, proteinuria and hematuria in patients with COVID-19 were 7.7%, 6.6%,6.2%, 49.8%, 42% and 30.3% respectively. Moreover, the means of Scr, BUN and D-dimer were shown 6-folds, 1.8-folds and 0.68-folds, respectively, higher in ICU/severe cases than in corresponding non-ICU/non-severe patients. The prevalence of AKI was about 17 folds higher in ICU/severe patients compared with the non-ICU/non-severe cases.\n\nConclusionsOverall, we assessed the incidences of the clinic and laboratory features of kidney injury in COVID-19 patients. And kidney dysfunction may be a risk factor for COVID-19 patients developing into the severe condition. In reverse, COVID-19 can also cause damage to the kidney.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Qixin Yang",
-        "author_inst": "Xiangya Hospital, Central South University"
-      },
-      {
-        "author_name": "Xiyao Yang",
-        "author_inst": "Xiangya Hospital, Central South University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "nephrology"
-  },
   {
     "rel_doi": "10.1101/2020.05.30.20117788",
     "rel_title": "The Role of Host Genetic Factors in Coronavirus Susceptibility: Review of Animal and Systematic Review of Human Literature",
@@ -1394330,6 +1393428,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.05.31.20118455",
+    "rel_title": "Hospital readmissions of discharged patients with COVID-19",
+    "rel_date": "2020-06-03",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.31.20118455",
+    "rel_abs": "BackgroundCOVID-19 infection has led to an overwhelming effort by health institutions to meet the high demand for hospital admissions.\n\nAimTo analyse the clinical variables associated with readmission of patients who had previously been discharged after admission for COVID-19.\n\nDesign and methodsWe studied a retrospective cohort of patients with laboratory-confirmed SARS-CoV-2 infection who were admitted and subsequently discharged alive. We then conducted a nested case-control study paired (1:1 ratio) by age, sex and period of admission.\n\nResultsOut of 1368 patients who were discharged during the study period, 61 patients (4.4%) were readmitted. Immunocompromised patients were at increased risk for readmission. There was also a trend towards a higher probability of readmission in hypertensive patients (p=0.07). Cases had had a shorter hospital stay and a higher prevalence of fever during the 48 hours prior to discharge. There were no significant differences in oxygen levels measured at admission and discharge by pulse oximetry intra-subject or between the groups. Neutrophil/lymphocyte ratio at hospital admission tended to be higher in cases than in controls (p=0.06). The motive for readmission in 10 patients (16.4%), was a thrombotic event in venous or arterial territory (p<0.001). Neither glucocorticoids nor anticoagulants prescribed at hospital discharge were associated with a lower readmission rate.\n\nConclusionsThe rate of readmission after discharge from hospital for COVID-19 was low. Immunocompromised patients and those presenting with fever during the 48 hours prior to discharge are at greater risk of readmission to hospital.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Lina Marcela Parra",
+        "author_inst": "HU Puerta de Hierro-Majadahonda"
+      },
+      {
+        "author_name": "MIreia Cantero",
+        "author_inst": "HU Puerta de Hierro-Majadahonda"
+      },
+      {
+        "author_name": "Ignacio Morras",
+        "author_inst": "HU Puerta de Hierro-Majadahonda"
+      },
+      {
+        "author_name": "Alberto Vallejo",
+        "author_inst": "HU Puerta de Hierro-Majadahonda"
+      },
+      {
+        "author_name": "Itziar Diego",
+        "author_inst": "HU Puerta de Hierro-Majadahonda"
+      },
+      {
+        "author_name": "Elena Jimenez-Tejero",
+        "author_inst": "HU Puerta de Hierro-Majadahonda"
+      },
+      {
+        "author_name": "Elena Munez",
+        "author_inst": "HU Puerta de Hierro-Majadahonda"
+      },
+      {
+        "author_name": "Angel Asensio",
+        "author_inst": "HU Puerta de Hierro-Majadahonda"
+      },
+      {
+        "author_name": "Ana Fernandez-Cruz",
+        "author_inst": "HU Puerta de Hierro-Majadahonda"
+      },
+      {
+        "author_name": "Antonio Ramos-Martinez",
+        "author_inst": "HU Puerta de Hierro-Majadahonda"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.05.29.20117358",
     "rel_title": "Tocilizumab for treatment of mechanically ventilated patients with COVID-19",
@@ -1395355,45 +1394508,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.05.30.20117937",
-    "rel_title": "Repurposed prophylaxis strategies for COVID-19: a systematic review",
-    "rel_date": "2020-06-03",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.30.20117937",
-    "rel_abs": "IntroductionEfficient therapeutic strategies are needed to counter the COVID-19 pandemic, caused by the SARSCoV-2 virus. In a context where specific vaccines are not yet available, the containment of the pandemic would be facilitated with efficient prophylaxis.\n\nMethodsWe screened several clinical trials repositories and platforms in search of the prophylactic strategies that are investigated against COVID-19 in late April 2020.\n\nResultsUp to April 27, 2020, we found 68 clinical trials targeting medical workers (n = 43, 63%), patients relatives (n = 16, 24%) or individuals at risk of severe COVID-19 (n = 5, 7%). (Hydroxy)chloroquine was the most frequently evaluated treatment (n = 46, 68%), before BCG vaccine (n = 5, 7%). Sixty-one (90%) clinical trials were randomized with a median of planned inclusions of 600 (IQR 255-1515).\n\nConclusionThe investigated prophylaxis strategies cover both pre- and post-exposure prophylaxis and study numerous immune enhancers and antivirals, although most research efforts are focused on (hydroxy)chloroquine.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Erwan Sallard",
-        "author_inst": "Ecole Normale Superieure de Paris, 45 Rue D'Ulm, 75005, Paris, France"
-      },
-      {
-        "author_name": "Francois-Xavier Lescure",
-        "author_inst": "Universite de Paris, IAME, INSERM, F-75018, Paris, France; Department of Infectious and Tropical Diseases, Assistance Publique - Hopitaux de Paris, Bichat- Clau"
-      },
-      {
-        "author_name": "Charles Burdet",
-        "author_inst": "Universite de Paris, IAME, INSERM, F-75018, Paris, France; Department of Infectious and Tropical Diseases, Assistance Publique - Hopitaux de Paris, Bichat- Clau"
-      },
-      {
-        "author_name": "Jeremie Guedj",
-        "author_inst": "Universite de Paris, IAME, INSERM, F-75018, Paris, France; Department of Infectious and Tropical Diseases, Assistance Publique - Hopitaux de Paris, Bichat- Clau"
-      },
-      {
-        "author_name": "Yazdan Yazdanpanah",
-        "author_inst": "Universite de Paris, IAME, INSERM, F-75018, Paris, France; Department of Infectious and Tropical Diseases, Assistance Publique - Hopitaux de Paris, Bichat- Clau"
-      },
-      {
-        "author_name": "Nathan Peiffer-Smadja",
-        "author_inst": "Universite de Paris, IAME, INSERM, F-75018, Paris, France; Department of Infectious and Tropical Diseases, Assistance Publique - Hopitaux de Paris, Bichat- Clau"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.06.01.20118018",
     "rel_title": "Continuous positive airway pressure face-mask ventilation to manage massive influx of patients requiring respiratory support during the SARS-CoV-2 outbreak",
@@ -1395648,6 +1394762,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.05.28.122671",
+    "rel_title": "Optimized pseudotyping conditions for the SARS-COV2 Spike glycoprotein",
+    "rel_date": "2020-06-03",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.28.122671",
+    "rel_abs": "The SARS-COV2 Spike glycoprotein is solely responsible for binding to the host cell receptor and facilitating fusion between the viral and host membranes. The ability to generate viral particles pseudotyped with SARS-COV2 Spike is useful for many types of studies, such as characterization of neutralizing antibodies or development of fusion-inhibiting small molecules. Here we characterized the use of a codon-optimized SARS-COV2 Spike glycoprotein for the generation of pseudotyped HIV-1, MLV, and VSV particles. The full-length Spike protein functioned inefficiently with all three systems but was enhanced over 10-fold by deleting the last 19 amino acids of the cytoplasmic tail of Spike. Infection of 293FT target cells was only possible if the cells were engineered to stably express the human ACE-2 receptor, but stably introducing an additional copy of this receptor did not further enhance susceptibility. Stable introduction of the Spike activating protease TMPRSS2 further enhanced susceptibility to infection by 5-10 fold. Substitution of the signal peptide of the Spike protein with an optimal signal peptide did not enhance or reduce infectious particle production. However, modification of a single amino acid in the furin cleavage site of Spike (R682Q) enhanced infectious particle production another 10-fold. With all enhancing elements combined, the titer of pseudotyped particles reached almost 106 infectious particles/ml. Finally, HIV-1 particles pseudotyped with SARS-COV2 Spike was successfully used to detect neutralizing antibodies in plasma from COVID-19 patients, but not plasma from uninfected individuals.\n\nImportanceWhen working with pathogenic viruses, it is useful to have rapid quantitative tests for viral infectivity that can be performed without strict biocontainment restrictions. A common way of accomplishing this is to generate viral pseudoparticles that contain the surface glycoprotein from the pathogenic virus incorporated into a replication-defective viral particle that contains a sensitive reporter system. These pseudoparticles enter cells using the glycoprotein from the pathogenic virus leading to a readout for infection. Conditions that block entry of the pathogenic virus, such as neutralizing antibodies, will also block entry of the viral pseudoparticles. However, viral glycoproteins often are not readily suited for generating pseudoparticles. Here we describe a series of modifications that result in the production of relatively high titer SARS-COV2 pseudoparticles that are suitable for detection of neutralizing antibodies from COVID-19 patients.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Marc C Johnson",
+        "author_inst": "University of Missouri, School of Medicine"
+      },
+      {
+        "author_name": "Terri D Lyddon",
+        "author_inst": "University of Missouri"
+      },
+      {
+        "author_name": "Reinier Suarez",
+        "author_inst": "University of Missouri"
+      },
+      {
+        "author_name": "Braxton Salcedo",
+        "author_inst": "University of Missouri"
+      },
+      {
+        "author_name": "Mary LePique",
+        "author_inst": "University of Missouri"
+      },
+      {
+        "author_name": "Maddie Graham",
+        "author_inst": "University of Missouri"
+      },
+      {
+        "author_name": "Clifton L Ricana",
+        "author_inst": "University of Missouri"
+      },
+      {
+        "author_name": "Carolyn A Robinson",
+        "author_inst": "University of Missouri"
+      },
+      {
+        "author_name": "Detlef G Ritter",
+        "author_inst": "University of Missouri Health System"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2020.05.29.122986",
     "rel_title": "Risk factors associated with mortality in hospitalized patients with SARS-CoV-2 infection. A prospective, longitudinal, unicenter study in Reus, Spain",
@@ -1396553,33 +1395718,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.06.01.20119180",
-    "rel_title": "Willingness to Accept Tradeoffs among Covid-19 Cases, Social-Distancing Restrictions, and Economic Impact: A Nationwide US Study",
-    "rel_date": "2020-06-02",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20119180",
-    "rel_abs": "We designed a discrete-choice experiment to quantify the extent to which US adults would accept greater risk of infection with SARS-CoV-2 in return for lifting social-distancing restrictions and diminishing the economic impact of the COVID-19 pandemic. 5953 adults representing all 50 states had 4 distinctly different preference patterns. About 37% were risk minimizers reluctant to accept any increases in risk of contracting the virus. Another group (26%) was primarily concerned about time required for economic recovery, accepting increases in COVID-19 risk levels up to 16% to shorten recovery from 3 to 2 years. The remaining two groups diverged on the relative importance of reopening nonessential businesses. The larger group (26%) strongly preferred delaying reopening while the smaller group (13%) would accept COVID-19 risks well beyond 20% to avoid a delay in reopening. Political affiliation, race, household income and employment status were predictive of group membership.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Shelby Reed",
-        "author_inst": "Duke Clinical Research Institute"
-      },
-      {
-        "author_name": "Juan Marcos Gonzalez",
-        "author_inst": "Duke Clinical Research Institute"
-      },
-      {
-        "author_name": "Reed Johnson",
-        "author_inst": "Duke Clinical Research Institute"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health economics"
-  },
   {
     "rel_doi": "10.1101/2020.06.01.20119388",
     "rel_title": "A data driven epidemic model to analyse the lockdown effect and predict the course of COVID-19 progress in India",
@@ -1396826,6 +1395964,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.05.25.20112623",
+    "rel_title": "Serological surveys in Reunion Island of the first hospitalized patients revealed that long-lived immunoglobulin G antibodies specific against SARS-CoV2 virus are rapidly vanishing in severe cases",
+    "rel_date": "2020-06-02",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.25.20112623",
+    "rel_abs": "Both cellular and humoral immunities are critically important to control COVID19 infection but little is known about the kinetics of those responses and, in particular, in patients who will go on to develop a severe form of the disease over several weeks. We herein report the first set of data of our prospective cohort study of 90 hospitalized cases. Serological surveys were thoroughly performed over 2 month period by assessing IgG and IgM responses by immunofluorescence, immunoblot, Western blot and conventional ELISA using clinical RUN isolates of SARS-CoV-2 immobilized on 96 well plates. While the IgM and, unexpectedly, the IgG responses were readily detected early during the course of the disease (5-7 days post-first symptoms), our results (n=3-5 and over the full dilution set of the plasma 1/200 to 1/12800) demonstrated a significant decrease (over 2.5-fold) of IgG levels in severe (ICU) hospitalized patients (exemplified in patient 1) by WB and ELISA. In contrast, mild non-ICU patients had a steady and yet robust rise in their specific IgG levels against the virus. Interestingly, both responses (IgM and IgG) were initially against the nucleocapsid (50kDa band on the WB) and spreading to other major viral protein S and domains (S1 and S2. In conclusion, serological testing may be helpful for the diagnosis of patients with negative RT-PCR results and for the identification of asymptomatic cases. Moreover, medical care and protections should be maintained particularly for recovered patients (severe cases) who may remain at risk of relapsing or reinfection. Experiments to ascertain T cell responses but although their kinetics overtime are now highly warranted. All in all, these studies will help to delineate the best routes for vaccination.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Anthony Dobi",
+        "author_inst": "Unite de recherche en Pharmaco-Immunologie (UR-EPI), Universite et CHU de la Reunion, St Denis"
+      },
+      {
+        "author_name": "Etienne Frumence",
+        "author_inst": "Laboratoire immunologie Clinique et experimentale de la ZOI (LICE-OI), Pole de Biologie, CHU de la Reunion, St Denis"
+      },
+      {
+        "author_name": "Mahary LALARIZO RAKOTO",
+        "author_inst": "Laboratoire immunologie Clinique et experimentale de la ZOI (LICE-OI), Pole de Biologie, CHU de la Reunion, St Denis"
+      },
+      {
+        "author_name": "Gregorie Lebeau",
+        "author_inst": "Unite de recherche en Pharmaco-Immunologie (UR-EPI), Universite et CHU de la Reunion, St Denis"
+      },
+      {
+        "author_name": "Damien Vagner",
+        "author_inst": "UMR PIMIT Processus infectieux en milieu Insulaire tropical CNRS 9192, INSERM1187, IRD 249, Universite de la Reunion, St Denis"
+      },
+      {
+        "author_name": "Anne-Laure SANDENON SETEYEN",
+        "author_inst": "Unite de recherche en Pharmaco-Immunologie (UR-EPI), Universite et CHU de la Reunion, St Denis"
+      },
+      {
+        "author_name": "Claude Giry",
+        "author_inst": "CNR associe arbovirus, Laboratoire de Microbiologie, Pole de Biologie, CHU de la Reunion, St Denis"
+      },
+      {
+        "author_name": "Axelle Septembre-Malaterre",
+        "author_inst": "Unite de recherche en Pharmaco-Immunologie (UR-EPI), Universite et CHU de la Reunion, St Denis"
+      },
+      {
+        "author_name": "Marie-Christine Jaffar-Bandjee",
+        "author_inst": "CNR associe arbovirus, Laboratoire de Microbiologie, Pole de Biologie, CHU de la Reunion, St Denis"
+      },
+      {
+        "author_name": "Loic Raffray",
+        "author_inst": "Service de Medecine Interne, CHU de la Reunion, St Denis"
+      },
+      {
+        "author_name": "Philippe Gasque",
+        "author_inst": "Unite de recherche en Pharmaco-Immunologie (UR-EPI), Universite et CHU de la Reunion, St Denis"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.05.22.20110387",
     "rel_title": "Mathematical Modeling and Analysis of COVID-19 pandemic in Nigeria",
@@ -1398171,37 +1397368,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.05.30.20117440",
-    "rel_title": "Is India heading towards a new high? : An optimistic approach to estimate ending life-cycle and cumulative cases by the end of the major COVID-19 pandemic wave in India and some of its states.",
-    "rel_date": "2020-06-02",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.30.20117440",
-    "rel_abs": "Projecting the COVID-19 curve parameters such as ending-lifecycle and cumulative cases are helpful in guiding the policy makers to mitigate the outbreak. However, overestimating these parameters may put the public and policy makers in a muddle. In this paper, an optimistic scenario is simulated, wherein the dynamics of the COVID-19 curve is allowed to spread to such an extent that the projections of the COVID-19 parameters do not take excessively high values. Based on this scenario, the ending life-cycle and cumulative cases for India and some of its states, are predicted. Our study, suggests that the fall of the peak amplitude (95%) of the major COVID-19 wave in India may take place by the 8th of September 2020 with a total count of 655000 cases. Simulation results, also indicate that Maharashtra, Tamil Nadu, Delhi, Gujarat, Uttar Pradesh, Bihar, Madhya Pradesh, and Rajasthan may end up with 263700, 18140, 50600, 21130, 24420, 44170, 27080, and 28200 cumulative cases respectively.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Dr. Praveen Gupta",
-        "author_inst": "Government Polytechnic College, Jaipur, India"
-      },
-      {
-        "author_name": "Prof. K.K. Sharma",
-        "author_inst": "Malviya National Institute of Technology , Jaipur, India"
-      },
-      {
-        "author_name": "Prof. S.D. Joshi",
-        "author_inst": "Indian Institute of Technology, New Delhi, India"
-      },
-      {
-        "author_name": "Dr. Shilpi Goyal",
-        "author_inst": "Department of Medical and Health, Government of Rajasthan, India"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health policy"
-  },
   {
     "rel_doi": "10.1101/2020.05.31.20107276",
     "rel_title": "Risk factors for mortality in pregnant women with SARS-CoV-2 infection",
@@ -1398480,6 +1397646,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
+  {
+    "rel_doi": "10.1101/2020.05.27.20114512",
+    "rel_title": "Diagnostic accuracy of a host response point-of-care test for identifying COVID-19",
+    "rel_date": "2020-06-02",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20114512",
+    "rel_abs": "RationaleManagement of the COVID-19 pandemic is hampered by long delays associated with centralised laboratory PCR testing. In hospitals this leads to poor patient flow and nosocomial transmission and rapid, accurate diagnostic tests are urgently required. The FebriDx is a point-of-care test that detects an antiviral host response protein in finger prick blood within 10 minutes, but its accuracy for the detection of COVID-19 is unknown.\n\nObjectivesTo evaluate the diagnostic accuracy of FebriDx in hospitalised patients during the first wave of the pandemic\n\nMethodsMeasures of diagnostic accuracy were calculated based on FebriDx results compared to the reference standard of PCR, and stratified by duration of symptoms. A multivariable predictive model was developed and underwent internal validation.\n\nResultsFebriDx was performed on 251 patients and gave a valid result in 248. 118 of 248 (48%) were PCR positive for COVID-19. Sensitivity of FebriDx for the identification of COVID-19 was 93% (110/118; 95% CI 87 to 97%) and specificity was 86% (112/130; 95%CI 79 to 92%). Positive and negative likelihood ratios were 6.73 (95%CI 4.37 to 10.37) and 0.08 (95%CI 0.04 to 0.15) respectively. In the multivariate model diagnosis of COVID-19 was not significantly influenced by clinical symptoms and signs, and FebriDx accuracy was not improved by restricting testing to those with duration of symptoms of less than seven days.\n\nConclusionsDuring the first wave of the pandemic, FebriDx had high sensitivity for the identification of COVID-19 in hospitalised adults and could be deployed as a front door triage tool.\n\nTrial registrationISRCTN14966673",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Tristan William Clark",
+        "author_inst": "University of Southampton"
+      },
+      {
+        "author_name": "Nathan James Brendish",
+        "author_inst": "University of Southampton"
+      },
+      {
+        "author_name": "Stephen Poole",
+        "author_inst": "NIHR Southampton Biomedical Research Centre"
+      },
+      {
+        "author_name": "Vasanth V Naidu",
+        "author_inst": "University Hospital Southampton NHS Foundation Trust"
+      },
+      {
+        "author_name": "Christopher Mansbridge",
+        "author_inst": "University Hospital Southampton NHS FoundationTrust"
+      },
+      {
+        "author_name": "Nicholas Norton",
+        "author_inst": "University Hospital Southampton NHS Foundation Trust"
+      },
+      {
+        "author_name": "Helen Wheeler",
+        "author_inst": "University Hospital Southampton NHS Foundation Trust"
+      },
+      {
+        "author_name": "Laura Presland",
+        "author_inst": "University Hospital Southampton NHS Foundation Trust"
+      },
+      {
+        "author_name": "Sean Ewings",
+        "author_inst": "Southampton Clinical Trials Unit, University of Southampton, UK"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.05.27.20115048",
     "rel_title": "Correlation of the global spread of coronavirus disease-19 with atmospheric air temperature",
@@ -1400157,165 +1399374,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.05.27.20115238",
-    "rel_title": "A SYSTEMATIC ANALYSIS OF THE TIME COURSE TO DEVELOP TREATMENTS FOR COVID-19",
-    "rel_date": "2020-06-02",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20115238",
-    "rel_abs": "BACKGROUNDThe spread of COVID-19 from Wuhan China, has been alarmingly rapid. Epidemiologic techniques succeeded in containing the disease in China, but efforts have not been as successful in the rest of the World, with a total of 29,155,581 confirmed cases of COVID-19, including 926,544 deaths worldwide as of September 15, 2020. Projections are for continued new infections and deaths if no effective therapeutic interventions can be initiated over the next several months. We performed a systematic review to determine the potential time course for development of treatments and vaccines, focusing on availability now and continuing in the last half of 2020.\n\nMETHODS\n\nClinical TrialsWe reviewed up-to-date information from several sources to identify potential treatments for COVID-19: The Reagan-Udall Expanded Access Navigator COVID-19 Treatment Hub was used to track the efforts of companies to develop agents. We focused on trials completed as of September 1, 2020 on identified agents We used several different sources: (A) covid-trials.org, then validated results on (B) clinicaltrials.gov and the (C) World Health Organizations International Clinical Trials Registry Platform (WHO ICTRP). We excluded studies which were clearly observational, with no randomization, control, or comparison group. We further set a cutoff of 100 for numbers of subjects, since smaller trial size could lack statistical power to establish superiority of the intervention over the control.\n\nPublicationsWe searched for published trial results on pubmed.gov and on medRxiv, the preprint server, and used a targeted Google search to find announcements of unpublished trial results\n\nRESULTS\n\nClinical Trials in RecruitmentAs of our cutoff date of April 1, 2020, we found 409 trials meeting our minimum requirement of 100 subjects. The WHO Solidarity megatrial for hospitalized patients was launched in over 100 countries, actively comparing hydroxychloroquine (HCQ), lopanovir/ritonavir (LPV/r) alone and in combination with interferon beta-1, and remdesivir. The LPV/r alone and HCQ arms have already been discontinued. Of these, only 9 were conducted on outpatients. A few vaccine trials are hoping to complete Phase 3 enrollment by the end of the third quarter 2020, but a prolonged follow-up of patients will likely be required.\n\nClinical trials CompletedAs of September 1, 2020, there were 231 trials reporting completion, Of these, only 59 studies enrolled 100 or more subjects. There were 34 trials in hospitalized patients, 9 directed at outpatients, and 8 prevention studies,\n\nPublished DataAs of September 1, 2020 we found 70 publications reporting findings in human studies on 13 classes of drugs and on 6 vaccines. There were 33 randomized placebo or active control studies; the rest were retrospective observational. Only seven publications dealt with outpatient care, the rest all in hospitalized patients.\n\nAvailable TreatmentsAt this time, remdesivir and convalescent plasma have been granted emergency use authorization in the U.S.A., solely for hospitalized patients. There is also support for glucocorticoid treatment of the COVID-19 respiratory distress syndrome. No treatments or prophylaxis are offered for outpatients.\n\nCONCLUSIONCOVID-19 is propagated primarily by infected ambulatory individuals. There have been no options brought forward for prevention and non-hospital treatment with only a few randomized, controlled outpatient studies expected to yield results in time to impact on the continuing pandemic by the end of 2020. It will be necessary for public health authorities to make hard decisions, with limited data, to prevent the continued spread of the disease. The choices will be hardest when dealing with possible early release of safe and effective vaccines which would, of course, be of greatest benefit to the Worlds population.",
-    "rel_num_authors": 36,
-    "rel_authors": [
-      {
-        "author_name": "Binh T. Ngo",
-        "author_inst": "Keck USC School of Medicine"
-      },
-      {
-        "author_name": "Paul Marik",
-        "author_inst": "Eastern Virginia School of Medicine"
-      },
-      {
-        "author_name": "Pierre Kory",
-        "author_inst": "aurora st. luke's medical center, milwaukee, wi"
-      },
-      {
-        "author_name": "Leland Shapiro",
-        "author_inst": "Rocky Mountain Regional Veterans Affairs Medical Center in Aurora, CO and University of Colorado Anschutz Medical Campus in Aurora, CO  Supported by The Emily F"
-      },
-      {
-        "author_name": "Denise Brennan-Rieder",
-        "author_inst": "CoronaTracker Community Research Group"
-      },
-      {
-        "author_name": "Raphael Thomadsen",
-        "author_inst": "Washington University in St. Louis"
-      },
-      {
-        "author_name": "Jose Iglesias",
-        "author_inst": "Jersey Shore University Medical Center, Neptune NJ, Hackensack Meridian School of Medicine at Seton Hall"
-      },
-      {
-        "author_name": "Stephen Ditmore",
-        "author_inst": "The Parkchester Times"
-      },
-      {
-        "author_name": "Marc Rendell",
-        "author_inst": "The Rose Salter Medical Research Foundation, Newport Coast, CA 92657"
-      },
-      {
-        "author_name": "Daniel Griffin",
-        "author_inst": "ProHEALTH, an OPTUM Company and   Columbia University College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Joseph Varon",
-        "author_inst": "United Memorial Medical Center University of Texas School of Medicine Houston, Texas, USA"
-      },
-      {
-        "author_name": "Michael Dube",
-        "author_inst": "Keck School of Medicine of USC"
-      },
-      {
-        "author_name": "Neha Nanda",
-        "author_inst": "Keck School of Medicine of USC"
-      },
-      {
-        "author_name": "Gino In",
-        "author_inst": "Keck School of Medicine of USC"
-      },
-      {
-        "author_name": "Daniel Arkfeld",
-        "author_inst": "Keck School of Medicine of USC"
-      },
-      {
-        "author_name": "Preet Chaudhary",
-        "author_inst": "Preet.chaudhary@med.usc.edu"
-      },
-      {
-        "author_name": "Vito M Campese",
-        "author_inst": "Keck School of Medicine of USC"
-      },
-      {
-        "author_name": "Diana Hanna",
-        "author_inst": "Keck School of Medicine of USC"
-      },
-      {
-        "author_name": "David E Sawcer",
-        "author_inst": "Keck School of Medicine of USC"
-      },
-      {
-        "author_name": "Glenn Ehresmann",
-        "author_inst": "Keck School of Medicine of USC"
-      },
-      {
-        "author_name": "David Peng",
-        "author_inst": "Keck School of Medicine of USC"
-      },
-      {
-        "author_name": "Miroslaw Smogorewski",
-        "author_inst": "Keck School of Medicine of USC"
-      },
-      {
-        "author_name": "April W. armstrong",
-        "author_inst": "Keck School of Medicine of USC"
-      },
-      {
-        "author_name": "Fred Sattler",
-        "author_inst": "Keck School of Medicine of USC"
-      },
-      {
-        "author_name": "Rajkumar Dasgupta",
-        "author_inst": "Keck School of Medicine of USC"
-      },
-      {
-        "author_name": "Cristina Mussini",
-        "author_inst": "University of Modena and Reggio Emilia in Italy"
-      },
-      {
-        "author_name": "Oriol Mitja",
-        "author_inst": "Hospital Universitari Germans Trias i Pujol  Badalona, Spain"
-      },
-      {
-        "author_name": "Vicente Soriano",
-        "author_inst": "UNIR Health Sciences School & Medical Center C/ Almansa 101 Madrid 28040, Spain"
-      },
-      {
-        "author_name": "Nicolas Peschanski",
-        "author_inst": "UniversityHospital of Rennes, Rennes, France"
-      },
-      {
-        "author_name": "Gilles Hayem",
-        "author_inst": "Hopital Paris Saint-. Joseph, 75014  Paris, France."
-      },
-      {
-        "author_name": "Marco Confalonieri",
-        "author_inst": "Azienda Ospedaliero-Universitaria di Trieste Trieste, Italia"
-      },
-      {
-        "author_name": "Maria Carmela Piccirillo",
-        "author_inst": "Istituto Nazionale Tumori, IRCCS, Fondazione G. Pascale Napoli, Italia"
-      },
-      {
-        "author_name": "Antonio Lobo Ferreira",
-        "author_inst": "Faculdade de Medicina da Universidade do Porto"
-      },
-      {
-        "author_name": "Bello-Rivero Iraldo",
-        "author_inst": "Center for Genetic Engineering and Biotechnology,  Ave 31 e/ 158 and 190. Cubanacan, Playa, 10600 , Havana, Cuba."
-      },
-      {
-        "author_name": "Eivind H. Vinjevoll",
-        "author_inst": "Volda Hospital HMR, Norway."
-      },
-      {
-        "author_name": "Ivan FN Hung",
-        "author_inst": "Li Ka Shing  Faculty of Medicine University of Hong Kong"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.05.28.20115121",
     "rel_title": "A Simple, SIR-like but Individual-Based l-i AIR Model: Application in Comparison of COVID-19 in New York City and Wuhan",
@@ -1400606,6 +1399664,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.05.28.20116046",
+    "rel_title": "Immunochromatographic assays for COVID-19 epidemiological screening: our experience",
+    "rel_date": "2020-06-02",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20116046",
+    "rel_abs": "In March 2020, the World Health Organization (WHO) declared a pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Due to the absence of effective treatment or biomedical prevention, understanding potential post infection immunity has important implications for epidemiologic assessments. For this reason, increasing number of in vitro diagnostic companies are developing serological assays to detect antibodies against SARS-CoV-2, but most of them lack the validation by third parties in relation to their quality, limiting their usefulness. We submitted to serological screening by two different immunochromatographic (IC) rapid testing for detection of IgG and IgM against SARS-CoV-2, 151 asymptomatic or minimally symptomatic healthcare workers previously tested positive for SARS-CoV-2 RT-PCR in order to evaluate the performance of rapid assays. Results showed discrepancies between molecular and IC results, and an inconsistency of immunoglobulins positivity patterns when compared to ELISA/CLIA results, highlighting the absolute necessity of assays performance validation before their marketing and use, in order to avoid errors in the results evaluation at both clinical and epidemiological level.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Andrea Bartolini",
+        "author_inst": "LUM - Unified Metropolitan Laboratory, AUSL Bologna, Bologna, Italy"
+      },
+      {
+        "author_name": "Margherita Scapaticci",
+        "author_inst": "LUM - Unified Metropolitan Laboratory, AUSL Bologna, Bologna, Italy"
+      },
+      {
+        "author_name": "Marina Bioli",
+        "author_inst": "LUM - Unified Metropolitan Laboratory, AUSL Bologna, Bologna, Italy"
+      },
+      {
+        "author_name": "Tiziana Lazzarotto",
+        "author_inst": "Microbiology Unit - Department of Experimental, Diagnostic and Specialty Medicine, S. Orsola -Malpighi University Hospital, Bologna, Italy"
+      },
+      {
+        "author_name": "Maria Carla Re",
+        "author_inst": "Microbiology Unit - Department of Experimental, Diagnostic and Specialty Medicine, S. Orsola -Malpighi University Hospital, Bologna, Italy"
+      },
+      {
+        "author_name": "Rita Mancini",
+        "author_inst": "LUM - Unified Metropolitan Laboratory, AUSL Bologna, Bologna, Italy"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "pathology"
+  },
   {
     "rel_doi": "10.1101/2020.05.31.20115154",
     "rel_title": "Exhaled breath is a significant source of SARS-CoV-2 emission",
@@ -1401839,41 +1400936,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.06.01.20118877",
-    "rel_title": "Smoking and the risk of COVID-19 in a large observational population study",
-    "rel_date": "2020-06-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20118877",
-    "rel_abs": "BACKGROUNDSmokers are generally more susceptible to infectious respiratory diseases and are at higher risk of developing severe complications from these infections. Conflicting reports exist regarding the impact of smoking on the risk of Coronavirus disease 2019 (COVID-19).\n\nMETHODSWe carried out a population-based study among over 3,000,000 adult members of Clalit Health Services, the largest health provider in Israel. Since the beginning of the disease outbreak, and until May 16, 2020, over 145,000 adults underwent RT-PCR testing for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), and 3.3% had positive results. We performed a case-control study among patients who underwent SARS-CoV-2 testing, to assess the impact of smoking on infection incidence and severity. Individuals with positive tests were matched in a 1:5 ratio to individuals tested negative, of the same sex, age, and ethnicity/religion. Conditional logistic regressions were performed to evaluate odds ratios for current and previous smoking on the risk of testing positive. Multivariable logistic regressions were performed among patients infected with COVID-19 to estimate the association between smoking and fatal or severe disease requiring ventilation. Regressions were performed with and without adjustment for preexisting medical conditions.\n\nRESULTSCurrent smokers (9.8%) were significantly less prevalent among members tested positive compared to the general population (19.4%, P<0.001), and to matched members tested negative (18.2%, P<0.001). Current smoking was associated with significantly reduced odds ratio (OR) for testing positive OR=0.447 (95% confidence interval (CI) 0.400-0.501). Among patients tested positive, there was no evidence of significantly increased risk of developing severe or fatal disease.\n\nCONCLUSIONThe risk of infection by COVID-19 appears to be reduced by half among current smokers. This intriguing finding may reveal unique infection mechanisms present for COVID-19 which may be targeted to combat the disease and reduce its infection rate.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Ariel Israel",
-        "author_inst": "Department of Research and Data, Division of Planning and Strategy, Clalit Health Services, Tel-Aviv, Israel"
-      },
-      {
-        "author_name": "Ilan Feldhamer",
-        "author_inst": "Department of Research and Data, Division of Planning and Strategy, Clalit Health Services, Tel-Aviv, Israel"
-      },
-      {
-        "author_name": "Amnon Lahad",
-        "author_inst": "Departments of Family Medicine, Clalit Health Services and Hebrew University, Jerusalem, Israel"
-      },
-      {
-        "author_name": "Diane Levin-Zamir",
-        "author_inst": "Clalit Health Services; University of Haifa School of Public Health, Israel"
-      },
-      {
-        "author_name": "Gil Lavie",
-        "author_inst": "Division of Planning and Strategy, Clalit Health Services, Tel-Aviv, Israel; Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technolo"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.05.29.20097097",
     "rel_title": "Population mobility reductions during COVID-19 epidemic in France under lockdown",
@@ -1402268,6 +1401330,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "cardiovascular medicine"
   },
+  {
+    "rel_doi": "10.1101/2020.05.31.20118695",
+    "rel_title": "ON THE UNCERTAINTY ABOUT HERD IMMUNITY LEVELS REQUIRED TO STOP COVID-19 EPIDEMICS",
+    "rel_date": "2020-06-01",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.31.20118695",
+    "rel_abs": "COVID-19 evolved into a pandemic in 2020 affecting more than 150 countries. Given the absence of a vaccine, discussion has taken place on the strategy of allowing the virus to spread in a population, to increase population \"herd immunity\". Knowledge of the minimum proportion of a population required to have recovered from COVID-19 infection in order to attain \"herd\" immunity, Pcrit, is important for formulating epidemiological policy. A method for measuring uncertainty about Pcrit based on a widely used package, EpiEstim, is derived. The procedure is illustrated using data from twelve countries at two early times during the COVID-19 epidemic. It is shown that simple plug-in measures of confidence on estimates of Pcrit are misleading, but that a full characterization of statistical uncertainty can be derived from EpiEstim, which reports percentiles only. Because of the important levels of uncertainty, it is risky to design epidemiological policy based on guidance provided by a single point estimate.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "DANIEL GIANOLA",
+        "author_inst": "UNIVERSITY OF WISCONSIN-MADISON"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.05.29.20100735",
     "rel_title": "Psychosocial factors and hospitalisations for COVID-19: Prospective cohort study of the general population",
@@ -1403356,53 +1402437,6 @@
     "type": "new results",
     "category": "neuroscience"
   },
-  {
-    "rel_doi": "10.1101/2020.05.29.20115824",
-    "rel_title": "COVID-19 :Determinants of Hospitalization, ICU and Death among 20,293 reported cases in Portugal",
-    "rel_date": "2020-05-30",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20115824",
-    "rel_abs": "IntroductionDeterminants of hospitalization, intensive care unit (ICU) admission and death are still unclear for Covid-19 and only a few studies have adjusted for confounding for different clinical outcomes including all reported cases in a country. We used routine surveillance data from Portugal to identify risk factors for COVID-19 outcomes, in order to support risk stratification, clinical and public health interventions, and scenarios to plan health care resources.\n\nMethodsWe conducted a retrospective cohort study including 20,293 laboratory confirmed cases of COVID-19 in Portugal extracted in April 28 2020, electronically through the National Epidemic Surveillance System of the Directorate-General of Health(DGS). We calculated absolute risks, relative risks (RR) and adjusted relative risks (aRR) to identify demographic and clinical factors associated with hospitalization, admission to ICU and death using Poisson regressions.\n\nResultsIncreasing age after 60 years was the greatest determinant for all outcomes. Assuming 0-50 years as reference, being aged 80-89 years was the strongest determinant of hospital admission (aRR-5.7), 70-79 years for ICU(aRR-10.4) and > 90 years for death(aRR-226.8) with an aRR of 112.7 in those 70-79. Among comorbidities, Immunodeficiency, cardiac disease, kidney disease, and neurologic disease were independent risk factors for hospitalization (aRR 1.83,1.79,1.56, 1.82), for ICU these were cardiac, Immunodeficiency, kidney and lung disease (aRR 4.33, 2.76, 2.43, 2.04), and for death they were kidney, cardiac and chronic neurological disease (aRR: 2.9, 2.6, 2.0) Male gender was a risk factor for all outcomes. There were small statistically significant differences for the 3 outcomes between regions.\n\nDiscussion and ConclusionsOlder age stands out as the strongest risk factor for all outcomes specially for death as absolute is risk was small for those younger than 50. These findings have implications in terms of risk stratified public health measures that should prioritize protecting older people although preventive behavior is needed in all ages. Epidemiologic scenarios and clinical guidelines may consider these estimated risks, even though under-ascertainment of mild and asymptomatic cases should be considered.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Vasco Ricoca Peixoto",
-        "author_inst": "National School of Public Health"
-      },
-      {
-        "author_name": "Andre Vieira",
-        "author_inst": "NOVA National School of Public Health, Public Health Research Centre, Universidade NOVA de Lisboa, Portugal"
-      },
-      {
-        "author_name": "Pedro Aguiar",
-        "author_inst": "NOVA National School of Public Health, Public Health Research Centre, Universidade NOVA de Lisboa, Portugal"
-      },
-      {
-        "author_name": "Paulo Sousa",
-        "author_inst": "NOVA National School of Public Health, Public Health Research Centre, Universidade NOVA de Lisboa, Portugal"
-      },
-      {
-        "author_name": "Carlos Carvalho",
-        "author_inst": "NOVA National School of Public Health, Public Health Research Centre, Universidade NOVA de Lisboa, Portugal"
-      },
-      {
-        "author_name": "Daniel Rhys Thomas",
-        "author_inst": "Communicable Disease Surveillance Centre, Public Health Wales, Cardiff, UK"
-      },
-      {
-        "author_name": "Alexandre Abrantes",
-        "author_inst": "NOVA National School of Public Health, Public Health Research Centre, Universidade NOVA de Lisboa, Portugal"
-      },
-      {
-        "author_name": "Carla Nunes",
-        "author_inst": "NOVA National School of Public Health, Public Health Research Centre, Universidade NOVA de Lisboa, Portugal"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.05.28.20115899",
     "rel_title": "Disparities in Vulnerability to Severe Complications from COVID-19 in the United States",
@@ -1403637,6 +1402671,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.05.29.124610",
+    "rel_title": "COVID-3D: An online resource to explore the structural distribution of genetic variation in SARS-CoV-2 and its implication on therapeutic development",
+    "rel_date": "2020-05-30",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.29.124610",
+    "rel_abs": "The emergence of the COVID-19 pandemic has spurred a global rush to uncover basic biological mechanisms, to inform effective vaccine and drug development. Despite viral novelty, global sequencing efforts have already identified genomic variation across isolates. To enable easy exploration and spatial visualization of the potential implications of SARS-CoV-2 mutations on infection, host immunity and drug development we have developed COVID-3D (http://biosig.unimelb.edu.au/covid3d/).",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Stephanie Portelli",
+        "author_inst": "University of Melbourne"
+      },
+      {
+        "author_name": "Moshe Olshansky",
+        "author_inst": "Baker Heart and Diabetes Institute"
+      },
+      {
+        "author_name": "Carlos Henrique Miranda Rodrigues",
+        "author_inst": "University of Melbourne"
+      },
+      {
+        "author_name": "YooChan Myung",
+        "author_inst": "University of Melbourne"
+      },
+      {
+        "author_name": "Michael Silk",
+        "author_inst": "University of Melbourne"
+      },
+      {
+        "author_name": "Azadeh Alavi",
+        "author_inst": "Baker Heart and Diabetes Institute"
+      },
+      {
+        "author_name": "Douglas E.V. Pires",
+        "author_inst": "University of Melbourne"
+      },
+      {
+        "author_name": "David B. Ascher",
+        "author_inst": "University of Melbourne"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "bioinformatics"
+  },
   {
     "rel_doi": "10.1101/2020.05.29.20116483",
     "rel_title": "Mortality and use of angiotensin converting enzyme inhibitors in Covid 19 disease - a systematic review.",
@@ -1405074,61 +1404155,6 @@
     "type": "new results",
     "category": "genomics"
   },
-  {
-    "rel_doi": "10.1101/2020.05.28.20115956",
-    "rel_title": "Medical students perceptions and motivations in time of COVID-19 pandemic",
-    "rel_date": "2020-05-30",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20115956",
-    "rel_abs": "BackgroundThere has been a rapid increase in the number of cases of COVID-19 in Latin America, Africa and Asia, in many countries that have an insufficient number of physicians and other health care personnel, and the need for the inclusion of medical students as part of the health teams is a very important issue. It has been recommended that medical students work as volunteers, have appropriate training, do not undertake any activity beyond their level of competence, have continuous supervision and adequate personal protective equipment. However, motivation of medical students must be evaluated in order to make volunteering a more evidence-based initiative. The aim of our study was to evaluate motivation of medical students to be part of the heath team tohelp in the COVID-19 pandemic.\n\nMethods and FindingsWe developed a questionnaire specifically to evaluate medical students perceptions about participating in care of patients with suspected infection due to coronavirus during the COVID-19 pandemic. The questionnaire had two parts: a) individual characteristics, year and geographic location of medical school; b) twenty-eight statements responded on a 5-point Likert scale (totally agree, agree, neither agree nor disagree, disagree and totally disagree). To develop the questionnaire, we performed consensus meetings of a group of faculty and medical students. The questionnaire was sent to student organizations of 257 medical schools in Brazil and answered by 10,433 students. We used multinomial logistic regression models to analyse the data.\n\nStatements with greater odds ratios for participation of medical students in COVID-19 pandemic were related to sense of purpose or duty (\"It is the duty of the medical student to put himself at the service of the population in the pandemic\"), altruism (\"I am willing to take risks by participating in practical in the context of pandemic\"), perception of good performance and professional identity (\"I will be a better health professional for having experienced the pandemic\"). Males had higher odds ratios than females (1.36 [95% CI: 1.24 - 1.49] to 1.68 [95% CI: 1.47 - 1.91]).\n\nConclusionsMedical students are motivated by sense of purpose or duty, altruism, perception of good performance and values of professionalism more than their interest in learning. These results have implications in the developing of programs of volunteering and in the design of health force policies in the present pandemic and in future health emergencies.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Patricia Tempski",
-        "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo"
-      },
-      {
-        "author_name": "Fernanda M Arantes-Costa",
-        "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo"
-      },
-      {
-        "author_name": "Renata Kobayasi",
-        "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo"
-      },
-      {
-        "author_name": "Marina AM Siqueira",
-        "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo"
-      },
-      {
-        "author_name": "Matheus M Torsani",
-        "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo"
-      },
-      {
-        "author_name": "Bianca QRC Amaro",
-        "author_inst": "Universidade Federal de Roraima"
-      },
-      {
-        "author_name": "Maria Eduarda FM Nascimento",
-        "author_inst": "Universidade de Pernambuco"
-      },
-      {
-        "author_name": "Saulo L Siqueira",
-        "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo"
-      },
-      {
-        "author_name": "Itamar S Santos",
-        "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo"
-      },
-      {
-        "author_name": "Milton A Martins",
-        "author_inst": "Faculdade de Medicina da Universidade de Sao Paulo"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "medical education"
-  },
   {
     "rel_doi": "10.1101/2020.05.30.20117572",
     "rel_title": "Assessing visible aerosol generation during vitrectomy in the era of Covid-19",
@@ -1405451,6 +1404477,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.05.28.20115980",
+    "rel_title": "Restarting after COVID-19: A Data-driven Evaluation of Opening Scenarios",
+    "rel_date": "2020-05-30",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20115980",
+    "rel_abs": "To contain the COVID-19 pandemic, several governments introduced strict Non-Pharmaceutical Interventions (NPI) that restricted movement, public gatherings, national and international travel, and shut down large parts of the economy. Yet, the impact of the enforcement and subsequent loosening of these policies on the spread of COVID-19 is not well understood. Accordingly, we measure the impact of NPI on mitigating disease spread by exploiting the spatio-temporal variations in policy measures across the 16 states of Germany. This quasi-experiment identifies each policys effect on reducing disease spread. We adapt the SEIR (Susceptible-Exposed-Infected-Recovered) model for disease propagation to include data on daily confirmed cases, intra- and inter-state movement, and social distancing. By combining the model with measures of policy contributions on mobility reduction, we forecast scenarios for relaxing various types of NPIs. Our model finds that, in Germany, policies that mandated contact restrictions (e.g., movement in public space limited to two persons or people co-living), initial business closures (e.g., restaurant closures), stay-at-home orders (e.g., prohibition of non-essential trips), non-essential services (e.g., florists, museums) and retail outlet closures led to the sharpest drops in movement within and across states. Contact restrictions were the most effective at lowering infection rates, while border closures had only minimal effects at mitigating the spread of the disease, even though cross-border travel might have played a role in seeding the disease in the population. We believe that a deeper understanding of the policy effects on mitigating the spread of COVID-19 allows a more accurate forecast of the disease spread when NPIs are (partially) loosened, and thus also better informs policymakers towards making appropriate decisions.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Ashwin Aravindakshan",
+        "author_inst": "University of California, Davis"
+      },
+      {
+        "author_name": "Jorn Boehnke",
+        "author_inst": "University of California, Davis"
+      },
+      {
+        "author_name": "Ehsan Gholami",
+        "author_inst": "University of California, Davis"
+      },
+      {
+        "author_name": "Ashutosh Nayak",
+        "author_inst": "University of California, Davis"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.05.28.20115949",
     "rel_title": "Socioeconomic disparities in subway use and COVID-19 outcomes in New York City",
@@ -1406456,73 +1405513,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.05.27.120410",
-    "rel_title": "Efficacy of a novel SARS-CoV-2 detection kit without RNA extraction and purification",
-    "rel_date": "2020-05-29",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.27.120410",
-    "rel_abs": "Rapid detection of SARS-CoV-2 is critical for the diagnosis of coronavirus disease 2019 (COVID-19) and preventing the spread of the virus. A novel \"2019 Novel Coronavirus Detection Kit (nCoV-DK)\" halves detection time by eliminating the steps of RNA extraction and purification. We evaluated concordance between the nCoV-DK and direct PCR. The virus was detected in 53/71 fresh samples by the direct method and 55/71 corresponding frozen samples by the nCoV-DK. The overall concordance rate of the virus detection between the two methods was 94.4% (95% CI, 86.2-98.4). Concordance rates were 95.2% (95% CI, 83.8-99.4), 95.5% (95% CI, 77.2-99.9), 85.7% (95% CI, 42.1-99.6) in nasopharyngeal swab, saliva, and sputum samples, respectively. These results indicate that the nCoV-DK effectively detects SARS-CoV-2 in all types of the samples including saliva, while reducing time required for detection, labor, and risk of human error.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Tatsuya Fukumoto",
-        "author_inst": "Hokkaido University Hospital"
-      },
-      {
-        "author_name": "Sumio Iwasaki",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Kasumi Hayasaka",
-        "author_inst": "Hokkaido University Hospital"
-      },
-      {
-        "author_name": "Kaori Sato",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Satoshi Oguri",
-        "author_inst": "Hokkaido University Hospital"
-      },
-      {
-        "author_name": "Keisuke Taki",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Sho Nakakubo",
-        "author_inst": "Hokkaido University Hospital"
-      },
-      {
-        "author_name": "Keisuke Kamada",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Yu Yamashita",
-        "author_inst": "Hokkaido University Hospital"
-      },
-      {
-        "author_name": "Satoshi Konno",
-        "author_inst": "Hokkaido University Hospital"
-      },
-      {
-        "author_name": "Mutsumi Nishida",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Junichi Sugita",
-        "author_inst": "Hokkaido University"
-      },
-      {
-        "author_name": "Takanori Teshima",
-        "author_inst": "Hokkaido University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.05.27.20100297",
     "rel_title": "Automatic Detection of COVID-19 and Pneumonia from Chest X-Ray using Transfer Learning",
@@ -1406741,6 +1405731,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.05.27.20111955",
+    "rel_title": "Age separation dramatically reduces COVID-19 mortality rate in a computational model of a large population",
+    "rel_date": "2020-05-29",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20111955",
+    "rel_abs": "COVID-19 pandemic has caused a global lock down in many countries throughout the world. Faced with a new reality, and until a vaccine or efficient treatment is found, humanity must figure out ways to keep economy going on one hand, yet keep the population safe on the other hand, especially those that are susceptible to this virus. Here we use a network simulation, with parameters that were drawn from what is known about the virus, to explore 5 different scenarios of partial lock down release. We find that separating age groups by reducing interactions between age groups, protects the general population and reduces mortality rates. Furthermore, addition of new connections within the same age group to compensate for the lost connections outside the age group, still has a strong beneficial influence and reduces the total death toll by 66%. While complete isolation from society may be the most protective scenario for the elderly population, it would have an emotional and possibly cognitive impact that might outweigh its benefit. We therefore propose creating age-related social recommendations or even restrictions, thereby allowing social connections but still strong protection for the older population.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Liron Mizrahi",
+        "author_inst": "University of Haifa"
+      },
+      {
+        "author_name": "Shani Stern",
+        "author_inst": "University of Haifa"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.05.27.20115212",
     "rel_title": "Monitoring and forecasting the number of reported and unreported cases of the COVID-19 epidemic in Brazil using Particle Filter",
@@ -1407642,53 +1406655,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
-  {
-    "rel_doi": "10.1101/2020.05.27.20114470",
-    "rel_title": "Lopinavir-Ritonavir in treatment of COVID-19: A dynamic systematic benefit-risk assessment",
-    "rel_date": "2020-05-29",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20114470",
-    "rel_abs": "BackgroundCOVID-19 is an ongoing, global public health crisis for which safe and effective treatments need to be identified. The benefit-risk balance for use of lopinavir-ritonavir in COVID-19 needs to be monitored on an ongoing basis, therefore a systematic benefit-risk assessment was designed and conducted. A key objective of this study was to provide a platform for a dynamic systematic benefit-risk evaluation; although initially this evaluation is likely to contain limited information, it is required due to the urgent unmet public need. Importantly it allows additional data to be incorporated as it becomes available, and re-evaluation of the benefit-risk profile.\n\nMethodsA systematic benefit-risk assessment was conducted using the Benefit-Risk Action team (BRAT) framework. The exposure of interest was lopinavir-ritonavir treatment in COVID-19 compared to standard of care, placebo or other treatments. A literature search was conducted in PubMed and EmBase to identify peer-reviewed papers reporting clinical outcomes. Two clinicians constructed a value tree and ranked key benefits and risks in order of considered clinical importance.\n\nResultsIn comparison to standard of care, data for several key benefits and risks were identified for lopinavir-ritonavir. Time to clinical improvement was not significantly different for lopinavir-ritonavir in comparison to standard of care (HR=1.31, 95% CI:0.95, 1.80). There appeared to be fewer serious adverse events with lopinavir-ritonavir (20%) vs standard of care (32%). In particular, there were fewer cases of acute respiratory distress syndrome with lopinavir-ritonavir compared to standard of care (13% vs 27%). Limited data were available for comparison of lopinavir-ritonavir to other treatments.\n\nConclusionsBased on currently available data, there was no clear benefit for use of lopinavir-ritonavir compared to standard of care in severe COVID-19. Risk data suggested a possible decrease in serious adverse events, including acute respiratory distress syndrome. Overall, the benefit-risk profile for lopinavir-ritonavir in severe COVID-19 cannot be considered positive until further efficacy and effectiveness data become available.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Vicki Osborne",
-        "author_inst": "Drug Safety Research Unit"
-      },
-      {
-        "author_name": "Miranda Davies",
-        "author_inst": "Drug Safety Research Unit"
-      },
-      {
-        "author_name": "Samantha Lane",
-        "author_inst": "Drug Safety Research Unit"
-      },
-      {
-        "author_name": "Alison Evans",
-        "author_inst": "Drug Safety Research Unit"
-      },
-      {
-        "author_name": "Jacqueline Denyer",
-        "author_inst": "Drug Safety Research Unit"
-      },
-      {
-        "author_name": "Sandeep Dhanda",
-        "author_inst": "Drug Safety Research Unit"
-      },
-      {
-        "author_name": "Debabrata Roy",
-        "author_inst": "Drug Safety Research Unit"
-      },
-      {
-        "author_name": "Saad AW Shakir",
-        "author_inst": "Drug Safety Research Unit"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.05.27.20113951",
     "rel_title": "Knowledge, attitude, and perceptions towards the 2019 Coronavirus Pandemic: A bi-national survey in Africa",
@@ -1407975,6 +1406941,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
+  {
+    "rel_doi": "10.1101/2020.05.27.20114652",
+    "rel_title": "A SARS-CoV-2 serological assay to determine the presence of blocking antibodies that compete for human ACE2 binding",
+    "rel_date": "2020-05-29",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20114652",
+    "rel_abs": "As SARS-CoV-2 continues to spread around the world, there is an urgent need for new assay formats to characterize the humoral response to infection. Convalescent serum is being used for treatment and for isolation of patient-derived antibodies. However, currently there is not a simple means to estimate serum bulk neutralizing capability. Here we present an efficient competitive serological assay that can simultaneously determine an individuals seropositivity against the SARS-CoV-2 Spike protein and estimate the neutralizing capacity of anti-Spike antibodies to block interaction with the human angiotensin converting enzyme 2 (ACE2) required for viral entry. In this ELISA-based assay, we present natively-folded viral Spike protein receptor binding domain (RBD)-containing antigens via avidin-biotin interactions. Sera are then supplemented with soluble ACE2-Fc to compete for RBD-binding serum antibodies, and antibody binding quantified. Comparison of signal from untreated serum and ACE2-Fc-treated serum reveals the presence of antibodies that compete with ACE2 for RBD binding, as evidenced by loss of signal with ACE2-Fc treatment. In our test cohort of nine convalescent SARS-CoV-2 patients, we found all patients had developed anti-RBD antibodies targeting the epitope responsible for ACE2 engagement. This assay provides a simple and high-throughput method to screen patient sera for potentially neutralizing anti-Spike antibodies to enable identification of candidate sera for therapeutic use.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "James R. Byrnes",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Xin X. Zhou",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Irene Lui",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Susanna K. Elledge",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Jeff E. Glasgow",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Shion A. Lim",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Rita Loudermilk",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Charles Y. Chiu",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Michael R. Wilson",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Kevin K. Leung",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "James A. Wells",
+        "author_inst": "University of California, San Francisco"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.05.27.20113969",
     "rel_title": "Correlation of population mortality of COVID-19 and testing coverage: a comparison among 36 OECD countries and Taiwan",
@@ -1408952,93 +1407977,6 @@
     "type": "new results",
     "category": "molecular biology"
   },
-  {
-    "rel_doi": "10.1101/2020.05.27.20114363",
-    "rel_title": "Unspecific post-mortem findings despite multiorgan 1 viral spread in COVID-19 patients",
-    "rel_date": "2020-05-28",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20114363",
-    "rel_abs": "BackgroundPost-mortem studies can provide important information for understanding new diseases and small autopsy case series have already reported different findings in COVID-19 patients.\n\nMethodsWe evaluated whether some specific post-mortem features are observed in these patients and if these changes are related to the presence of the virus in different organs. Complete macroscopic and microscopic autopsies were performed on different organs in 17 COVID-19 non-survivors. Presence of SARS-CoV-2 was evaluated with immunohistochemistry (IHC) in lung samples and with real-time reverse-transcription polymerase chain reaction (RT-PCR) test in lung and other organs.\n\nResultsPulmonary findings revealed early-stage diffuse alveolar damage (DAD) in 15 out of 17 patients and microthrombi in small lung arteries in 11 patients. Late-stage DAD, atypical pneumocytes and/or acute pneumonia were also observed. Four lung infarcts, two acute myocardial infarctions and one ischemic enteritis were observed. There was no evidence of myocarditis, hepatitis or encephalitis. Kidney evaluation revealed the presence of hemosiderin in tubules or pigmented casts in most patients. Spongiosis and vascular congestion were the most frequently encountered brain lesions. No specific SARS-CoV-2 lesions were observed in any organ. IHC revealed positive cells with a heterogeneous distribution in the lungs of 11 of the 17 (65%) patients; RT-PCR yielded a wide distribution of SARS-CoV-2 in different tissues, with 8 patients showing viral presence in all tested organs (i.e. lung, heart, spleen, liver, colon, kidney and brain).\n\nConclusionsIn conclusion, autopsies revealed a great heterogeneity of COVID-19-related organ injury and the remarkable absence of any specific viral lesions, even when RT-PCR identified the presence of the virus in many organs.",
-    "rel_num_authors": 18,
-    "rel_authors": [
-      {
-        "author_name": "Myriam Remmelink",
-        "author_inst": "CUB ULB Hopital Erasme"
-      },
-      {
-        "author_name": "Ricardo De Mendoca",
-        "author_inst": "CUB ULB Hopital Erasme"
-      },
-      {
-        "author_name": "Nicky D'Haene",
-        "author_inst": "CUB ULB Hopital Erasme"
-      },
-      {
-        "author_name": "Sarah De Clercq",
-        "author_inst": "CUB ULB Hopital Erasme"
-      },
-      {
-        "author_name": "Camille Verocq",
-        "author_inst": "CUB ULB Hopital Erasme"
-      },
-      {
-        "author_name": "Laetitia Lebrun",
-        "author_inst": "CUB ULB Hopital Erasme"
-      },
-      {
-        "author_name": "Philomene Lavis",
-        "author_inst": "CUB ULB Hopital Erasme"
-      },
-      {
-        "author_name": "Marie Lucie Racu",
-        "author_inst": "CUB ULB Hopital Erasme"
-      },
-      {
-        "author_name": "Anne Laure Trepant",
-        "author_inst": "CUB ULB Hopital Erasme"
-      },
-      {
-        "author_name": "Calliope Maris",
-        "author_inst": "CUB ULB Hopital Erasme"
-      },
-      {
-        "author_name": "Sandrine Rorive",
-        "author_inst": "CUB ULB Hopital Erasme"
-      },
-      {
-        "author_name": "Jean Christophe Goffard",
-        "author_inst": "CUB ULB Hopital Erasme"
-      },
-      {
-        "author_name": "Olivier De Witte",
-        "author_inst": "CUB ULB Hopital Erasme"
-      },
-      {
-        "author_name": "Lorenzo Peluso",
-        "author_inst": "CUB ULB Hopital Erasme"
-      },
-      {
-        "author_name": "Jean Louis Vincent",
-        "author_inst": "CUB ULB Hopital Erasme"
-      },
-      {
-        "author_name": "Christine Decaestecker",
-        "author_inst": "Universite Libre de Bruxelles"
-      },
-      {
-        "author_name": "Fabio Silvio Taccone",
-        "author_inst": "CUB ULB Hopital Erasme"
-      },
-      {
-        "author_name": "Isabelle Salmon",
-        "author_inst": "CUB ULB Hopital Erasme"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "pathology"
-  },
   {
     "rel_doi": "10.1101/2020.05.27.20114447",
     "rel_title": "Automated and partially-automated contact tracing: a rapid systematic review to inform the control of COVID-19",
@@ -1409261,6 +1408199,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "occupational and environmental health"
   },
+  {
+    "rel_doi": "10.1101/2020.05.26.20113886",
+    "rel_title": "COVID-19 (SARS-CoV-2) Ventilator Resource Management Using a Network Optimization Model and Predictive System Demand",
+    "rel_date": "2020-05-28",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20113886",
+    "rel_abs": "The COVID-19 (SARS-CoV-2) pandemic is overwhelming global healthcare delivery systems due to the exponential spike in cases requiring specialty tests, facilities and equipment, including complex, precision devices like ventilators. In particular, the surge in critically ill patients has revealed a significant deficiency in regional availability of respiratory care ventilators. The authors offer a mathematical framework for ventilator distribution under scarcity conditions using an optimized network model and solver. The framework is interoperable with existing COVID-19 healthcare demand models and scales for different user-defined system sizes, including hospital networks, city, state, regional and national-scale prioritization. The authors approach improves current capabilities for medical device resource management within the existing incident command system while accounting for availability of devices, ventilation treatment time periods, disinfection and cleaning between patients, as well as shipping logistics time. The authors present a proof of concept using a high fidelity COVID-19 data set from Colorado, discusses how to scale nationally, and emphasizes the importance of applying ethical human-in-the-loop decision making when using this or similar approaches to managing medical device resources during epidemic emergencies.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Samuel Billingham",
+        "author_inst": "The MITRE Corporation"
+      },
+      {
+        "author_name": "Rebecca Widrick",
+        "author_inst": "The MITRE Corporation"
+      },
+      {
+        "author_name": "Nathan J Edwards",
+        "author_inst": "The MITRE Corporation"
+      },
+      {
+        "author_name": "Sybil Klaus",
+        "author_inst": "The MITRE Corporation"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health systems and quality improvement"
+  },
   {
     "rel_doi": "10.1101/2020.05.27.20113803",
     "rel_title": "A vulnerability index for COVID-19: spatial analysis to inform equitable response in Kenya",
@@ -1410534,33 +1409503,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.05.26.20112946",
-    "rel_title": "Deteriorated Covid19 control due to delayed lockdown resulting from strategic interactions between Governments and oppositions.",
-    "rel_date": "2020-05-27",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20112946",
-    "rel_abs": "BackgroundIn many European countries and the US, the burden of Covid-19 epidemic could be much lower if Governments had been able to learn from the China and Lombardy stories and to declare full lockdown without delays.\n\nMethodsWe use a simple game-theoretic framework for the strategic interaction between the Government, political oppositions and lobbies, combined with a Covid-19 transmission model, to analyse the role of political factors delaying the lockdown declaration, depending on the degrees of \"responsibility\" of political actors.\n\nResultsThe lockdown can always be declared immediately (i.e., without delay) as sustained transmission arises, only if the government feels fully \"responsible\" towards all citizens. If this is not the case, epidemic growth will eventually dominate the agents payoffs, so that sooner or later the lockdown will always be declared i.e., both the government and the opposition will be forced by the epidemic to switch towards a higher degree of responsibility, but with a delay. There is a further nontrivial situation where the lockdown can be declared without delay, occurring when the political opposition is at least as responsible as the Government. This however requires the solution of a coordination issue, which cannot be taken for granted. Eventually, a vicious circle emerges, where the delayed lockdown requires a much longer lockdown period to achieve adequate control results, thereby causing the explosion of economic losses and so calling for unlocking long before it should.\n\nConclusionsLockdown delays have dramatically worsened the impact of the current Covid-19 wave in a number of countries. Citizens should be made cogently aware of this to claim maximal responsibility from political actors and economic lobbies to avoid that such stories repeat in the future when further threats, due to Covid-19 itself or other pathogens, will re-appear.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Alessio Carrozzo Magli",
-        "author_inst": "Alma Mater Studiorum"
-      },
-      {
-        "author_name": "Alberto d'Onofrio",
-        "author_inst": "Stratchclyde University, Glasgow"
-      },
-      {
-        "author_name": "Piero Manfredi",
-        "author_inst": "University of Pisa"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.05.26.20110957",
     "rel_title": "COVID-19: The unreasonable effectiveness of simple models",
@@ -1410743,6 +1409685,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.05.26.20112680",
+    "rel_title": "Fast initial Covid-19 response means greater caution may be needed later",
+    "rel_date": "2020-05-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20112680",
+    "rel_abs": "BackgroundAs the Covid-19 pandemic unfolds it is becoming increasingly clear that the strength of the first wave of the epidemic varies significantly between countries. In this study a simple numerical model is used to illustrate the impact the timing of initial measures against Covid-19 has on the first wave of infection and possible implications this may have for the measures taken as the first wave is ebbing. The results highlight that delaying measures by 10 days is sufficient to largely account for the differences seen between countries such as the UK and Germany for the first wave of infections. A pronounced first wave means that a larger fraction of the total population will have been infected and is therefore likely to display immunity. Even if this fraction is far below the level needed for \"herd immunity\" the effective reproduction factor Re is decreased compared to a population that had no prior exposure to the virus. Even a small reduction in Re can have major influence on the evolution of the epidemic after the first wave of infections. A large first wave means the resulting value for Re will be lower than if the first wave was mild. Without either vaccine or effective treatment countries that experienced a small first wave should therefore relax measures at a slower pace than countries where the first wave was strong.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Joel Joel-Marie Hirschi",
+        "author_inst": "National Oceanography Centre"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.05.26.20113787",
     "rel_title": "COVID-Net: A deep learning based and interpretable predication model for the county-wise trajectories of COVID-19 in the United States",
@@ -1411992,45 +1410953,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.05.26.20098244",
-    "rel_title": "Rapid assessment of the impact of lockdown on the COVID-19 epidemic in Portugal",
-    "rel_date": "2020-05-27",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20098244",
-    "rel_abs": "BackgroundPortugal took early action to control the COVID19 epidemic, imposing a lockdown on March 16 when it recorded only 62 cases of COVID-19 per million inhabitants and no reported deaths. The Portuguese people complied quickly, reducing their overall mobility by 80%. We estimate the impact of the lockdown in Portugal in terms of reducing burden on the health service.\n\nMethodsWe forecasted epidemic curves for: Cases, hospital inpatients (overall and in ICU), and deaths without lockdown, assuming that the impact of containment measures would start 14 days after lockdown was implemented. We used exponential smoothing models for deaths, intensive care (ICU) and hospitalizations and an ARIMA model for number of cases. Models were selected considering fitness to the observed data to the 31st of March 2020. We then compared observed(with intervention) and forecasted curves (without intervention).\n\nResultsBetween April 1 and April 15, there were 146 fewer deaths(-25%), 5568 fewer cases (-23%) and, as of April 15, there were 519 fewer ICU inpatients(-69%) and 508 fewer overall hospital inpatients(-28%) than forecasted without lockdown. On April 15 the number of ICU inpatients could have reached 748, three times higher than the observed value (229) if the intervention had been delayed.\n\nConclusionIf the lockdown had not been implemented in mid-March, Portugal ICU capacity (528 ICU beds) would likely have been breached in the first half of April. The lockdown seems to have been effective in reducing transmission of SARS-Cov-2, serious Covid-19 illness and associated mortality, thereby decreasing demand on health services. Early action allowed time for the National Health Service to acquire protective equipment, to increase capacity to test and cope with the surge in hospital and ICU demand caused by the pandemic.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Vasco Ricoca Peixoto",
-        "author_inst": "NOVA National School of Public Health, Public Health Research Centre, Universidade NOVA de Lisboa, Portugal"
-      },
-      {
-        "author_name": "Andre Vieira",
-        "author_inst": "NOVA National School of Public Health, Public Health Research Centre, Universidade NOVA de Lisboa, Portugal"
-      },
-      {
-        "author_name": "Pedro Aguiar",
-        "author_inst": "NOVA National School of Public Health, Public Health Research Centre, Universidade NOVA de Lisboa, Portugal"
-      },
-      {
-        "author_name": "Carlos Carvalho",
-        "author_inst": "Unit for Multidisciplinary Research in Biomedicine, Abel Salazar Institute of Biomedical Sciences, Universidade do Porto, Portugal"
-      },
-      {
-        "author_name": "Daniel Thomas",
-        "author_inst": "Communicable Disease Surveillance Centre, Public Health Wales, Cardiff, UK"
-      },
-      {
-        "author_name": "Alexandre Abrantes",
-        "author_inst": "NOVA National School of Public Health, Public Health Research Centre, Universidade NOVA de Lisboa, Portugal"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.05.26.20100529",
     "rel_title": "Aerosol blocking assessment by different types of fabrics for homemade respiratory masks: spectroscopy and imaging study",
@@ -1412441,6 +1411363,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.05.26.20113761",
+    "rel_title": "Differentiating COVID-19 from other types of pneumonia with convolutional neural networks",
+    "rel_date": "2020-05-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20113761",
+    "rel_abs": "INTRODUCTIONA widely-used method for diagnosing COVID-19 is the nucleic acid test based on real-time reverse transcriptase-polymerase chain reaction (RT-PCR). However, the sensitivity of real time RT-PCR tests is low and it can take up to 8 hours to receive the test results. Radiologic methods can provide higher sensitivity. The aim of this study is to investigate the use of X-ray and convolutional neural networks for the diagnosis of COVID-19 and to differentiate it from viral and/or bacterial pneumonia, as 2-class (bacterial pneumonia vs COVID-19 and viral pneumonia vs COVID-19) and 3- class (bacterial pneumonia, COVID-19, and healthy group (BCH), and among viral pneumonia, COVID- 19, and healthy group (VCH)) experiments.\n\nMETHODS225 COVID-19, 1,583 healthy control, 2,780 bacterial pneumonia, and 1,493 viral pneumonia chest X-ray images were used. 2-class- and 3-class-experiments were performed with different convolutional neural network (ConvNet) architectures, with different variations of convolutional layers and fully-connected layers.\n\nRESULTSThe results showed that bacterial pneumonia vs COVID-19 and viral pneumonia vs COVID- 19 reached a mean ROC AUC of 97.32% and 96.80%, respectively. In the 3-class-experiments, macro-average F1 scores of 95.79% and 94.59% were obtained in terms of detecting COVID-19 among BCH and VCH, respectively.\n\nCONCLUSIONSThe ConvNet was able to distinguish the COVID-19 images among non-COVID-19 images, namely bacterial and viral pneumonia as well as normal X-ray images.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Ilker Ozsahin",
+        "author_inst": "Near East University"
+      },
+      {
+        "author_name": "Confidence Onyebuchi",
+        "author_inst": "Cyprus International University"
+      },
+      {
+        "author_name": "Boran Sekeroglu",
+        "author_inst": "Near East University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.05.27.20112888",
     "rel_title": "Evaluation of performance of two SARS-CoV-2 Rapid whole-blood finger-stick IgM-IgGCombined Antibody Tests",
@@ -1413646,65 +1412595,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.05.19.20106278",
-    "rel_title": "Benefit-risk analysis of health benefits of routine childhood immunisation against the excess risk of SARS-CoV-2 infections during the Covid-19 pandemic in Africa",
-    "rel_date": "2020-05-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20106278",
-    "rel_abs": "BackgroundNational immunisation programmes globally are at risk of suspension due to the severe health system constraints and physical distancing measures in place to mitigate the ongoing COVID-19 pandemic. Our aim is to compare the health benefits of sustaining routine childhood immunisation in Africa against the risk of acquiring SARS-CoV-2 infections through visiting routine vaccination service delivery points.\n\nMethodsWe used two scenarios to approximate the child deaths that may be caused by immunisation coverage reductions during COVID-19 outbreaks. First, we used previously reported country-specific child mortality impact estimates of childhood immunisation for diphtheria, tetanus, pertussis, hepatitis B, Haemophilus influenzae type b, pneumococcal, rotavirus, measles, meningitis A, rubella, and yellow fever (DTP3, HepB3, Hib3, PCV3, RotaC, MCV1, MCV2, MenA, RCV, YFV) to approximate the future deaths averted before completing five years of age by routine childhood vaccination during a 6-month COVID-19 risk period without catch-up campaigns. Second, we analysed an alternative scenario that approximates the health benefits of sustaining routine childhood immunisation to only the child deaths averted from measles outbreaks during the COVID-19 risk period. The excess number of infections due to additional SARS-CoV-2 exposure during immunisation visits assumes that contact reducing interventions flatten the outbreak curve during the COVID-19 risk period, that 60% of the population will have been infected by the end of that period, that children can be infected by either vaccinators or during transport and that upon child infection the whole household would be infected. Country specific household age structure estimates and age dependent infection fatality rates are then applied to calculate the number of deaths attributable to the vaccination clinic visits. We present benefit-risk ratios for routine childhood immunisation alongside 95% uncertainty range estimates from probabilistic sensitivity analysis.\n\nFindingsFor every one excess COVID-19 death attributable to SARS-CoV-2 infections acquired during routine vaccination clinic visits, there could be 84 (14-267) deaths in children prevented by sustaining routine childhood immunisation in Africa. The benefit-risk ratio for the vaccinated children, siblings, parents or adult care-givers, and older adults in the households of vaccinated children are 85,000 (4,900 - 546,000), 75,000 (4,400 - 483,000), 769 (148 - 2,700), and 96 (14 - 307) respectively. In the alternative scenario that approximates the health benefits to only the child deaths averted from measles outbreaks, the benefit-risk ratio to the households of vaccinated children is 3 (0 - 10) under these highly conservative assumptions and if the risk to only the vaccinated children is considered, the benefit-risk ratio is 3,000 (182 - 21,000).\n\nInterpretationOur analysis suggests that the health benefits of deaths prevented by sustaining routine childhood immunisation in Africa far outweighs the excess risk of COVID-19 deaths associated with vaccination clinic visits, especially for the vaccinated children. However, there are other factors that must be considered for strategic decision making to sustain routine childhood immunisation in African countries during the COVID-19 pandemic. These include logistical constraints of vaccine supply chain problems caused by the COVID-19 pandemic, reallocation of immunisation providers to other prioritised health services, healthcare staff shortages caused by SARS-CoV-2 infections among the staff, decreased demand for vaccination arising from community reluctance to visit vaccination clinics for fear of contracting SARS-CoV-2 infections, and infection risk to healthcare staff providing immunisation services as well as to their households and onward SARS-CoV-2 transmission into the wider community.\n\nFundingGavi, the Vaccine Alliance and Bill & Melinda Gates Foundation (OPP1157270)\n\nResearch in contextO_ST_ABSEvidence before the studyC_ST_ABSNational immunisation programmes globally are at risk of disruption due to the severe health system constraints caused by the ongoing COVID-19 pandemic and the physical distancing measures to mitigate the outbreak. The decrease in vaccination coverage increases the proportion of susceptible children at risk of increased morbidity and mortality from vaccine-preventable disease outbreaks. Outbreaks of vaccine preventable disease have been observed during previous interruptions to routine immunisation services during an ongoing infectious disease epidemic, such as during the 2013-2016 Ebola outbreak in West Africa, when most health resources were shifted towards the Ebola response which led to decreasing vaccination coverage and consequently outbreaks of measles and other vaccine-preventable diseases.\n\nAdded value of this studyWe estimated the benefit-risk ratio by comparing the deaths prevented by sustaining routine childhood immunisation for diphtheria, tetanus, pertussis, hepatitis B, Haemophilus influenzae type b, pneumococcal, rotavirus, measles, meningitis A, rubella, and yellow fever vaccines with the excess COVID-19 deaths associated with vaccination clinic visits. The benefit of routine childhood immunization programmes in all the 54 countries of Africa is higher than the COVID-19 risk associated with these vaccination clinic visits.\n\nImplications of all the available evidenceRoutine childhood immunisation programmes should be safeguarded for continued service delivery and prioritised for the prevention of infectious diseases, as logistically possible, as part of delivering essential health services during the COVID-19 pandemic in Africa. The current immunisation service models will require adaptation, including physical distancing measures, personal protective equipment, and good hygiene practices for infection control at the vaccination clinics, and have to be complemented by new immunisation service models for sustaining routine childhood immunisation in the African countries during the COVID-19 risk period.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Kaja Abbas",
-        "author_inst": "London School of Hygiene & Tropical Medicine"
-      },
-      {
-        "author_name": "Simon R Procter",
-        "author_inst": "London School of Hygiene & Tropical Medicine"
-      },
-      {
-        "author_name": "Kevin van Zandvoort",
-        "author_inst": "London School of Hygiene & Tropical Medicine"
-      },
-      {
-        "author_name": "Andrew Clark",
-        "author_inst": "London School of Hygiene & Tropical Medicine"
-      },
-      {
-        "author_name": "Sebastian Funk",
-        "author_inst": "London School of Hygiene & Tropical Medicine"
-      },
-      {
-        "author_name": "- LSHTM CMMID Covid-19 Working Group",
-        "author_inst": "-"
-      },
-      {
-        "author_name": "Tewodaj Mengistu",
-        "author_inst": "Gavi, the Vaccine Alliance"
-      },
-      {
-        "author_name": "Dan Hogan",
-        "author_inst": "Gavi, the Vaccine Alliance"
-      },
-      {
-        "author_name": "Emily Dansereau",
-        "author_inst": "Bill & Melinda Gates Foundation"
-      },
-      {
-        "author_name": "Mark Jit",
-        "author_inst": "London School of Hygiene & Tropical Medicine"
-      },
-      {
-        "author_name": "Stefan Flasche",
-        "author_inst": "London School of Hygiene & Tropical Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.05.19.20106484",
     "rel_title": "Outdoor Air Pollutant Concentration and COVID-19 Infection in Wuhan, China",
@@ -1413935,6 +1412825,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "otolaryngology"
   },
+  {
+    "rel_doi": "10.1101/2020.05.19.20106575",
+    "rel_title": "Mitigation Policies and Emergency Care Management in Europe's Ground Zero for COVID-19",
+    "rel_date": "2020-05-26",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20106575",
+    "rel_abs": "This paper draws from daily death registry data on 4,000 Italian municipalities to investigate two crucial policies that can dramatically affect the toll of COVID-19: the shutdown of non-essential businesses and the management of the emergency care system. Our results, which are robust to controlling for a host of co-factors, offer strong evidence that the closure of service activities is very effective in reducing COVID-19 mortality - this was about 15% lower in municipalities with a 10 percentage points higher employment share in shut down services. Shutting down factories, instead, is much less effective, plausibly because factory workers engage in more limited physical interactions relative to those in the consumer-facing service sector. Concerning the management of the health care system, we find that mortality strongly increases with distance from the intensive care unit (ICU). Municipalities at 10 km from the closest ICU experienced up to 50% higher mortality. This effect - which is largest within the epicenter and in days of abnormally high volumes of calls to the emergency line - underscores the importance of improving pre-hospital emergency services and building ambulance capacity to ensure timely transportation of critical patients to the ICU.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Gabriele Ciminelli",
+        "author_inst": "MIT Sloan School of Management"
+      },
+      {
+        "author_name": "S\u00edlvia Garcia-Mandic\u00f3",
+        "author_inst": "Organisation for Economic Cooperation and Development"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health economics"
+  },
   {
     "rel_doi": "10.1101/2020.05.19.20106641",
     "rel_title": "Study Data Element Mapping: Feasibility of Defining Common Data Elements Across COVID-19 Studies",
@@ -1415168,41 +1414081,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "neurology"
   },
-  {
-    "rel_doi": "10.1101/2020.05.24.20111732",
-    "rel_title": "Serum responses of children with Kawasaki Disease against SARS-CoV-2 proteins.",
-    "rel_date": "2020-05-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20111732",
-    "rel_abs": "Recently, numerous reports have suggested association of pediatric Coronavirus Disease 2019 (COVID-19) cases and Kawasaki Disease (KD). KD is a major cause of childhood acquired heart disease and vasculitis in the pediatric population. Epidemiological patterns suggest KD is related to an infectious agent; however, the etiology remains unknown1. As past reports have considered other coronaviruses to be related to KD2,3, these reports of pediatric COVID-19 related inflammatory disorder cases leads to the hypothesis of potential cross-coronavirus reactivity that would account for the past controversial proposals of other coronaviruses and these new cases. We sought to address this hypothesis by assessing the antigen targeting of biobanked plasma samples of febrile children, including those with KD, against SARS-CoV-2 proteins.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Arthur Chang",
-        "author_inst": "University at Buffalo"
-      },
-      {
-        "author_name": "Michael Croix",
-        "author_inst": "University at Buffalo"
-      },
-      {
-        "author_name": "Patrick Kenney",
-        "author_inst": "University at Buffalo"
-      },
-      {
-        "author_name": "Sarah Baron",
-        "author_inst": "University at Buffalo"
-      },
-      {
-        "author_name": "Mark Hicar",
-        "author_inst": "University at Buffalo"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "pediatrics"
-  },
   {
     "rel_doi": "10.1101/2020.05.21.20107599",
     "rel_title": "Clinical Utility of SARS-CoV-2 Whole Genome Sequencing in Deciphering Source of Infection",
@@ -1415513,6 +1414391,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "intensive care and critical care medicine"
   },
+  {
+    "rel_doi": "10.1101/2020.05.21.20108522",
+    "rel_title": "Expanding Covid-19 Testing: Mathematical Guidelines for the Optimal Sample Pool Size Given Positive Test Rate",
+    "rel_date": "2020-05-26",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20108522",
+    "rel_abs": "Widespread testing is essential to the mitigation of the spread of any virus, and is particularly central to the discussion on transitioning out of national quarantine. Sample pooling is a method that aims to multiply testing capability by using one testing kit for multiple samples, but will only be successful under certain conditions. This paper gives precise guidelines on those conditions for success: for any proposed sample pool size, explicit bounds on the positive infection rate are given that are informed by both discrete and statistical modeling.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Kayleigh Adams",
+        "author_inst": "UC Davic"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.05.19.20107359",
     "rel_title": "Identification of severity zones for mitigation strategy assessment COVID-19 outbreak in Malaysia",
@@ -1416702,49 +1415599,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "cardiovascular medicine"
   },
-  {
-    "rel_doi": "10.1101/2020.05.21.20109397",
-    "rel_title": "Investigational treatments for COVID-19 may increase ventricular arrhythmia risk through drug interactions",
-    "rel_date": "2020-05-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20109397",
-    "rel_abs": "Many drugs that have been proposed for treatment of COVID-19 are reported to cause cardiac adverse events, including ventricular arrhythmias. In order to properly weigh risks against potential benefits, particularly when decisions must be made quickly, mathematical modeling of both drug disposition and drug action can be useful for predicting patient response and making informed decisions. Here we explored the potential effects on cardiac electrophysiology of 4 drugs proposed to treat COVID-19: lopinavir, ritonavir, chloroquine, and azithromycin, as well as combination therapy involving these drugs. Our study combined simulations of pharmacokinetics (PK) with quantitative systems pharmacology (QSP) modeling of ventricular myocytes to predict potential cardiac adverse events caused by these treatments. Simulation results predicted that drug combinations can lead to greater cellular action potential prolongation, analogous to QT prolongation, compared with drugs given in isolation. The combination effect can result from both pharmacokinetic and pharmacodynamic drug interactions. Importantly, simulations of different patient groups predicted that females with pre-existing heart disease are especially susceptible to drug-induced arrhythmias, compared males with disease or healthy individuals of either sex. Overall, the results illustrate how PK and QSP modeling may be combined to more precisely predict cardiac risks of COVID-19 therapies.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Meera Varshneya",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Itziar Irurzun-Arana",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Chiara Campana",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Rafael Dariolli",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Amy Gutierrez",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Taylor K Pullinger",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Eric A Sobie",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "pharmacology and therapeutics"
-  },
   {
     "rel_doi": "10.1101/2020.05.22.20110064",
     "rel_title": "Estimation of the Final Size of the COVID-19 Epidemic inBalochistan, Pakistan.",
@@ -1417031,6 +1415885,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.05.25.20111047",
+    "rel_title": "Characteristics of Ischemic Stroke in COVID-19: A Need for Early Detection and Management",
+    "rel_date": "2020-05-26",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.25.20111047",
+    "rel_abs": "ObjectiveIn the setting of the Coronavirus Disease 2019 (COVID-19) global pandemic caused by SARS-CoV-2, a potential association of this disease with stroke has been suggested. We aimed to describe the characteristics of patients who were admitted with COVID-19 and had an acute ischemic stroke (AIS).\n\nMethodsThis is a case series of PCR-confirmed COVID-19 patients with ischemic stroke admitted to an academic health system in metropolitan Atlanta (USA) between March 24th,2020, and May 5th, 2020. Demographic, clinical, and radiographic characteristics were described.\n\nResultsOf 124 ischemic stroke patients admitted during this study period, 8 (6.5%) were also diagnosed with COVID-19. The mean age of patients was 64.3 {+/-} 6.5 years, 5 (62.5%) male, mean time from last-normal was 4.8 days [SD 4.8], and none received acute reperfusion therapy. All 8 patients had at least one stroke-associated co-morbidity. The predominant pattern of ischemic stroke was embolic; 3 were explained by atrial fibrillation while 5 (62.5%) were cryptogenic. In contrast, cryptogenic strokes were seen in 20 (16.1%) of 124 total stroke admissions during this time.\n\nConclusionsIn our case series, ischemic stroke affected COVID-19 patients with traditional stroke risk factors with an age of stroke presentation typically seen in non-COVID populations. We observed a predominantly embolic pattern of stroke with a higher than expected rate of cryptogenic strokes and with a prolonged median time to presentation and symptom recognition limiting the use of acute reperfusion treatments. These results highlight the need for increased community awareness, early identification, and management of AIS in COVID-19 patients.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Dinesh V. Jillella",
+        "author_inst": "Emory University School of Medicine"
+      },
+      {
+        "author_name": "Nicholas J. Janocko",
+        "author_inst": "Emory University School of Medicine"
+      },
+      {
+        "author_name": "Fadi Nahab",
+        "author_inst": "Emory University School of Medicine"
+      },
+      {
+        "author_name": "Karima Benameur",
+        "author_inst": "Emory University School of Medicine"
+      },
+      {
+        "author_name": "James G. Greene",
+        "author_inst": "Emory University School of Medicine"
+      },
+      {
+        "author_name": "Wendy L. Wright",
+        "author_inst": "Emory University School of Medicine"
+      },
+      {
+        "author_name": "Mahmoud Obideen",
+        "author_inst": "Emory University School of Medicine"
+      },
+      {
+        "author_name": "Srikant Rangaraju",
+        "author_inst": "Emory University School of Medicine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "neurology"
+  },
   {
     "rel_doi": "10.1101/2020.05.23.20111500",
     "rel_title": "Time delay epidemic model for COVID-19",
@@ -1418344,33 +1417245,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health economics"
   },
-  {
-    "rel_doi": "10.1101/2020.05.25.20112904",
-    "rel_title": "Case fatality risk by age from COVID-19 in a high testing setting in Latin America: Chile, March-May, 2020",
-    "rel_date": "2020-05-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.25.20112904",
-    "rel_abs": "BackgroundEarly severity estimates of COVID-19 are critically needed to better assess the potential impact of the ongoing pandemic in different socio-demographic groups. Using real-time epidemiological data from Chile, the nation in Latin America with the highest testing rate for COVID-19, we derive delay-adjusted severity estimates by age group as of May 18th, 2020.\n\nMethodsWe employed statistical methods and daily series of age-stratified COVID-19 cases and deaths reported in Chile to estimate the delay-adjusted case fatality rate across six age groups.\n\nResultsOur most recent estimates of the time-delay adjusted case fatality rate are 0.08% (95% Credible Interval CrI:0.04-0.13%) among persons aged 0-39, 0.61% (95%CrI:0.41-0.87%) for those aged 40-49, 1.06% (95%CrI:0.76-1.40%) for those aged 50-59, 3.79% (95%CrI:3.04-4.66%) for those aged 60-69, 12.22% (95%CrI:10.40-14.38%) for those aged 70-79, and 26.27% (95%CrI:22.95-2980%) for persons aged 80 and over. The overall time-delay adjusted case fatality rate is1.78% (95%CrI: 1.63-1.95%) across all age groups.\n\nConclusionsSeverity estimates from COVID-19 in Chile indicate a disproportionate impact among seniors, especially among those aged [&ge;] 70 years. COVID-19 is imposing a high death toll in Latin America. Case fatality rates in Chile suggest the health system is not yet overwhelmed, but the epidemic is expanding fast.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Eduardo A Undurraga",
-        "author_inst": "Pontificia Universidad Catolica de Chile"
-      },
-      {
-        "author_name": "Gerardo Chowell",
-        "author_inst": "Georgia State University School of Public Health"
-      },
-      {
-        "author_name": "Kenji Mizumoto",
-        "author_inst": "Kyoto University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.05.23.20111468",
     "rel_title": "Containing the Spread of Coronavirus Disease 2019 (COVID-19): Meteorological Factors and Control Strategies",
@@ -1418557,6 +1417431,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.05.23.20110965",
+    "rel_title": "Association of age, sex, comorbidities, and clinical symptoms with the severity and mortality of COVID-19 cases: a meta-analysis with 85 studies and 67299 cases",
+    "rel_date": "2020-05-26",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.23.20110965",
+    "rel_abs": "BackgroundA new pathogenic disease named COVID-19 became a global threat, first reported in Wuhan, China, in December 2019. The number of affected cases growing exponentially and now, more than 210 countries confirmed the cases.\n\nObjectiveThis meta-analysis aims to evaluate risk factors, the prevalence of comorbidity, and clinical characteristics in COVID-19 death patients compared to survival patients that can be used as a reference for further research and clinical decisions.\n\nMethodsPubMed, Science Direct, SAGE were searched to collect data about demographic, clinical characteristics, and comorbidities of confirmed COVID-19 patients from January 1, 2020, to May 17, 2020. Meta-analysis was performed with the use of Review Manager 5.3\n\nResultsEighty-five studies were included in Meta-analysis, including a total number of 67,299 patients with SARS-CoV-2 infection. Males are severely affected or died than females (OR = 2.26, p < 0.00001; OR = 3.59, p < 0.00001) are severely affected, or died by COVID-19 and cases with age [&ge;]50 are at higher risk of death than age <50 years (OR=334.23). Presence of any comorbidity or comorbidities like hypertension, cardiovascular disease, diabetes, cerebrovascular disease, respiratory disease, kidney disease, liver disease, malignancy significantly increased the risk of death compared to survival (OR = 3.46, 3.16, 4.67, 2.45, 5.84, 2.68, 5.62, 2.81,2.16). Among the clinical characteristics such as fever, cough, myalgia, diarrhea, abdominal pain, dyspnea, fatigue, sputum production, chest tightness headache and nausea or vomiting, only fatigue (OR = 1.31, 95%) and dyspnea increased the death significantly (OR= 1.31, 4.57). The rate of death of COVID-19 cases is 0.03-times lower than the rate of survival (OR = 0.03).\n\nConclusionOur result indicates that male patients are affected severely or died, the rate of death is more in the age [&ge;]50 group, and the rate of death is affected by comorbidities and clinical symptoms.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Mohammad Safiqul Islam",
+        "author_inst": "Noakhali Science and Technology University"
+      },
+      {
+        "author_name": "Md. Abdul Barek",
+        "author_inst": "Noakhali Science and Technology University"
+      },
+      {
+        "author_name": "Md. Abdul Aziz",
+        "author_inst": "Noakhali Science and Technology University"
+      },
+      {
+        "author_name": "Tutun Das Aka",
+        "author_inst": "Noakhali Science and Technology University"
+      },
+      {
+        "author_name": "Md. Jakaria",
+        "author_inst": "The University of Melbourne"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.05.22.20110171",
     "rel_title": "A data first approach to modelling Covid-19",
@@ -1419522,33 +1418431,6 @@
     "type": "new results",
     "category": "genomics"
   },
-  {
-    "rel_doi": "10.1101/2020.05.23.20111278",
-    "rel_title": "The transmission of SARS-CoV-2 is likely comodulated by temperature and by relative humidity",
-    "rel_date": "2020-05-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.23.20111278",
-    "rel_abs": "Inferring the impact of climate upon the transmission of SARS-CoV-2 has been confounded by variability in testing, unknown disease introduction rates, and changing weather. Here we present a data model that accounts for dynamic testing rates and variations in disease introduction rates. We apply this model to data from Colombia, whose varied and seasonless climate, central port of entry, and swift, centralized response to the Covid-19 pandemic present an opportune environment for assessing the impact of climate factors on the spread of Covid-19. We observe strong attenuation of transmission in climates with sustained daily temperatures above 30 degrees Celsius and simultaneous mean relative humidity below 78%, with outbreaks occurring at high humidity even where the temperature is high. We hypothesize that temperature and relative humidity comodulate the infectivity of SARS-CoV-2 within respiratory droplets.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Kevin S Raines",
-        "author_inst": "blank"
-      },
-      {
-        "author_name": "Sebastian Doniach",
-        "author_inst": "Stanford University"
-      },
-      {
-        "author_name": "Gyan Bhanot",
-        "author_inst": "Rutgers University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.05.25.115774",
     "rel_title": "Alveolar early progenitors in the aged human lung have increased expression of ACE2 accompanied with genes involved in beta-amyloid clearance: Indication of SARS-CoV-2 also using soluble ACE2 in aged-lungs to enter ACE2-negative cells",
@@ -1419799,6 +1418681,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
+  {
+    "rel_doi": "10.1101/2020.05.26.116608",
+    "rel_title": "Structure, function and variants analysis of the androgen-regulated TMPRSS2, a drug target candidate for COVID-19 infection",
+    "rel_date": "2020-05-26",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.26.116608",
+    "rel_abs": "SARS-CoV-2 is a novel virus causing mainly respiratory, but also gastrointestinal symptoms. Elucidating the molecular processes underlying SARS-CoV-2 infection, and how the genetic background of an individual is responsible for the variability in clinical presentation and severity of COVID-19 is essential in understanding this disease.\n\nCell infection by the SARS-CoV-2 virus requires binding of its Spike (S) protein to the ACE2 cell surface protein and priming of the S by the serine protease TMPRSS2. One may expect that genetic variants leading to a defective TMPRSS2 protein can affect SARS-CoV-2 ability to infect cells. We used a range of bioinformatics methods to estimate the prevalence and pathogenicity of TMPRSS2 genetic variants in the human population, and assess whether TMPRSS2 and ACE2 are co-expressed in the intestine, similarly to what is observed in lungs.\n\nWe generated a 3D structural model of the TMPRSS2 extracellular domain using the prediction server Phyre and studied 378 naturally-occurring TMPRSS2 variants reported in the GnomAD database. One common variant, p.V160M (rs12329760), is predicted damaging by both SIFT and PolyPhen2 and has a MAF of 0.25. Valine 160 is a highly conserved residue within the SRCS domain. The SRCS is found in proteins involved in host defence, such as CD5 and CD6, but its role in TMPRSS2 remains unknown. 84 rare variants (53 missense and 31 leading to a prematurely truncated protein, cumulative minor allele frequency (MAF) 7.34x10-4) cause structural destabilization and possibly protein misfolding, and are also predicted damaging by SIFT and PolyPhen2 prediction tools. Moreover, we extracted gene expression data from the human protein atlas and showed that both ACE2 and TMPRSS2 are expressed in the small intestine, duodenum and colon, as well as the kidneys and gallbladder.\n\nThe implications of our study are that: i. TMPRSS2 variants, in particular p.V160M with a MAF of 0.25, should be investigated as a possible marker of disease severity and prognosis in COVID-19 and ii. in vitro validation of the co-expression of TMPRSS2 and ACE2 in gastro-intestinal is warranted.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Alessia David",
+        "author_inst": "Imperial College London"
+      },
+      {
+        "author_name": "Tarun Khanna",
+        "author_inst": "Imperial College London"
+      },
+      {
+        "author_name": "Melina Beykou",
+        "author_inst": "Imperial College London"
+      },
+      {
+        "author_name": "Gordon Hanna",
+        "author_inst": "Imperial College London"
+      },
+      {
+        "author_name": "Michael J.E. Sternberg",
+        "author_inst": "Imperial College London"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "new results",
+    "category": "bioinformatics"
+  },
   {
     "rel_doi": "10.1101/2020.05.21.20109512",
     "rel_title": "Treatment of 6 COVID-19 Patients with Convalescent Plasma",
@@ -1420996,45 +1419913,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.05.24.20112169",
-    "rel_title": "Mechanistic rationale of drugs, Primary endpoints, Geographical distribution of clinical trials against Severe acute respiratory syndrome-related coronavirus-2: A Systematic Review",
-    "rel_date": "2020-05-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20112169",
-    "rel_abs": "ObjectiveTo do a systematic review and critical appraisal of the ongoing clinical trials that are assessing various therapeutic interventions against SARS-CoV-2 with an aim to provide insight into the various interventions tested, clinical rationale, geographical distribution of the trials as well as the endpoints assessed in the studies.\n\nDesignRapid systematic review and critical appraisal of the ongoing clinical trials against SARS-CoV-2.\n\nData sourcesClinicalTrials.gov, World health organization (WHO) International Clinical Trials Registry Platform (ICTRP) and Cochrane COVID registry were assessed till May 11th 2020.\n\nStudy selectionStudies on any intervention based randomized controlled trials (RCTs), prospective clinical studies on SARS-CoV-2 in patients [&ge;]18 years of age. Studies on autopsy series, preclinical studies, diagnostic methods, mathematical modelling, epidemiology and health services research, pediatric populations were excluded.\n\nData extractionThe data was extracted by two authors independently into pre-defined forms based on the SPIRIT 2013 checklist. The data was extracted on various domains such as trial number, study title, abstract of the study, interventions assessed, sample size, phase of the study, study sponsor, primary endpoint assessed and country of study.\n\nResultsThe search resulted in 3242 ongoing studies of which 829 studies were included. There are 134 different drug-based interventions being assessed in 463 clinical trials as treatment options. Seventy-two studies assessed preventive options of which 53 are drug-based prophylaxis and 19 assessed vaccines. Herbal medicines are being assessed in 79 studies; convalescent plasma therapy in 56 studies; stem cell-based interventions in 42 studies; anesthesia-based interventions in 31 studies, machine-based interventions in 24 studies, mental health-based interventions in18 studies, rehabilitation-based interventions in 12 studies and miscellaneous interventions in 32 studies. China accounts for 35% of all ongoing clinical studies followed by USA 23%, France 7%, Spain 3.3%,Canada 2%, multi-country studies account only for 1.5% (13) and other countries together account for 28%.Amongst the 463 studies assessing drug-based treatment options, studies that are funded by federal and academic institutions are 79.6%, pharmaceutical company funded studies are 15.11% and no funding information is available in 5.10%. The definitive outcomes like mortality are being assessed as primary outcome in 22.8% of the studies only and need for ventilator in 6.2% of the studies. Rest of the studies has primary outcomes such as clinical recovery (15.9%), viral clearance(17.4%), time to recovery (10.1%), oxygen improvement (5.6%), ICU admission (1.9%), lab and imaging(6.4%), adverse effects (5.3%) and symptom reduction(1.5%),no outcome reported(6.2%) which account for 71% of the studies. Amongst the pharmaceutical company funded drug-based studies, only 20% of the studies had mortality as the primary outcome. Only 5.5% of the ongoing clinical trials are specifically designed to assess the most vulnerable population like elderly, patients with comorbidities and cancer. The most common intervention being tested against COVID-19 are antimalarial medications with 105 clinical studies. Hydroxychloroquine is the most common drug being tested with 83 ongoing studies.\n\nConclusionMultiple intervention based clinical studies against SARS-CoV-2 are being performed throughout the world with a high concentration of clinical trials in the developed world. There is a high concern that most of the studies maybe repetitive; elderly and patients with comorbidities are being underrepresented; definite endpoints like mortality are being assessed in only one-fifth of the studies.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Bhanu Prasad Venkatesulu",
-        "author_inst": "Henry Ford Hospital"
-      },
-      {
-        "author_name": "Viveksandeep Thoguluva Chandrasekar",
-        "author_inst": "University of Kansas Medical Center"
-      },
-      {
-        "author_name": "Prashanth Giridhar",
-        "author_inst": "All India Institute of Medical sciences"
-      },
-      {
-        "author_name": "Pragathee V",
-        "author_inst": "Karpagam faculty medical sciences and research"
-      },
-      {
-        "author_name": "Harsh Patel",
-        "author_inst": "Ochsner Medical Center, New Orleans, Louisiana"
-      },
-      {
-        "author_name": "Jacob Manteuffel",
-        "author_inst": "Henry Ford hospital"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.05.24.20100990",
     "rel_title": "Performance evaluation of the point-of-care SAMBA II SARS-CoV-2 Test for detection of SARS-CoV-2",
@@ -1421281,6 +1420159,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "emergency medicine"
   },
+  {
+    "rel_doi": "10.1101/2020.05.22.20109231",
+    "rel_title": "Association of country-wide coronavirus mortality with demographics, testing, lockdowns, and public wearing of masks.",
+    "rel_date": "2020-05-25",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20109231",
+    "rel_abs": "PurposeTo determine sources of variation between countries in per-capita mortality from COVID-19 (caused by the SARS-CoV-2 virus).\n\nMethodsPotential predictors of per-capita coronavirus-related mortality in 200 countries by May 9, 2020 were examined, including age, sex, obesity prevalence, temperature, urbanization, smoking, duration of infection, lockdowns, viral testing, contact tracing policies, and public mask-wearing norms and policies. Multivariable linear regression analysis was performed.\n\nResultsIn univariate analyses, the prevalence of smoking, per-capita gross domestic product, urbanization, and colder average country temperature were positively associated with coronavirus-related mortality. In a multivariable analysis of 196 countries, the duration of infection in the country, and the proportion of the population 60 years of age or older were positively associated with per-capita mortality, while duration of mask-wearing by the public was negatively associated with mortality (all p<0.001). International travel restrictions and a lower prevalence of obesity were independently associated with mortality in a model which controlled for testing policy. Internal lockdown requirements and viral testing policies and levels were not associated with mortality. The association of contact tracing policy with mortality approached statistical significance (p=0.06). In countries with cultural norms or government policies supporting public mask-wearing, per-capita coronavirus mortality increased on average by just 15.8% each week, as compared with 62.1% each week in remaining countries.\n\nConclusionsSocietal norms and government policies supporting the wearing of masks by the public, as well as international travel controls, are independently associated with lower per-capita mortality from COVID-19.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Christopher T Leffler",
+        "author_inst": "Virginia Commonwealth University"
+      },
+      {
+        "author_name": "Edsel B Ing",
+        "author_inst": "University of Toronto"
+      },
+      {
+        "author_name": "Joseph D. Lykins V",
+        "author_inst": "Virginia Commonwealth University"
+      },
+      {
+        "author_name": "Matthew C. Hogan",
+        "author_inst": "Virginia Commonwealth University"
+      },
+      {
+        "author_name": "Craig A. McKeown",
+        "author_inst": "University of Miami"
+      },
+      {
+        "author_name": "Andrzej Grzybowski",
+        "author_inst": "University of Warmia and Mazury"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.05.21.20109017",
     "rel_title": "SARS-CoV-2 infection in London, England: Impact of lockdown on community point-prevalence, March-May 2020",
@@ -1422226,57 +1421143,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.05.20.20107631",
-    "rel_title": "Immunochromatographic test for the detection of SARS-CoV-2 in saliva",
-    "rel_date": "2020-05-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.20.20107631",
-    "rel_abs": "We evaluated the rapid immunochromatographic test for SARS-CoV-2 antigen detection using 16 saliva specimens collected from 6 COVID-19 hospitalized patients, and detected N-antigen in 4 of 7 RT-PCR positive specimens. The POCT antigen test using saliva is highly considered to be a game-changer for COVID-19 diagnosis.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Katsuhito Kashiwagi",
-        "author_inst": "Toho University Omori Medical Center"
-      },
-      {
-        "author_name": "Yoshikazu Ishii",
-        "author_inst": "Toho University School of Medicine"
-      },
-      {
-        "author_name": "Kotaro Aoki",
-        "author_inst": "Toho University School of Medicine"
-      },
-      {
-        "author_name": "Shintaro Yagi",
-        "author_inst": "Fujirebio Inc."
-      },
-      {
-        "author_name": "Tadashi Maeda",
-        "author_inst": "Toho University Omori Medical Center"
-      },
-      {
-        "author_name": "Tito Miyazaki",
-        "author_inst": "Toho University Omori Medical Center"
-      },
-      {
-        "author_name": "Sadako Yoshizawa",
-        "author_inst": "Toho University School of Medicine"
-      },
-      {
-        "author_name": "Katsumi Aoyagi",
-        "author_inst": "Fujirebio Inc."
-      },
-      {
-        "author_name": "Kazuhiro Tateda",
-        "author_inst": "Toho University School of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.05.20.20107813",
     "rel_title": "SARS-CoV-2 epitopes are recognized by a public and diverse repertoire of human T-cell receptors",
@@ -1422843,6 +1421709,61 @@
     "type": "new results",
     "category": "molecular biology"
   },
+  {
+    "rel_doi": "10.1101/2020.05.24.113043",
+    "rel_title": "Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein",
+    "rel_date": "2020-05-25",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.24.113043",
+    "rel_abs": "Detection of viral RNA by PCR is currently the main diagnostic tool for COVID-19 [1]. The PCR-based test, however, shows limited sensitivity, especially at early and late stages of the disease development [2,3], and is relatively time consuming. Fast and reliable complementary methods for detecting the viral infection would be of help in the current pandemia conditions. Mass-spectrometry is one of such possibilities. We have developed a mass-spectrometry based method for the detection of the SARS CoV-2 virus in nasopharynx epithelial swabs, based on the detection of the viral nucleocapsid N protein. The N protein of the SARS-COV-2 virus, the most abundant protein in the virion, is the best candidate for mass-spectrometric detection of the infection, and MS-based detection of several peptides from the SARS-COoV-2 nucleoprotein has been reported earlier by the Sinz group [4]. Our approach shows confident identification of the N protein in patient samples even with the lowest viral loads and a much simpler preparation procedure. Our main protocol consists of virus inactivation by heating and adding of isopropanol, and tryptic digestion of the proteins sedimented from the swabs followed by MS analysis. A set of unique peptides, produced as a result of proteolysis of the nucleocapsid phosphoprotein of SARS-CoV-2, is detected. The obtained results can further be used to create fast parallel mass-spectrometric approaches for the detection of the virus in the nasopharyngeal mucosa, saliva, sputum and other physiological fluids.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Evgeny (Eugene) N Nikolaev",
+        "author_inst": "Skolkovo Institute of Science and Technology, Moscow, Russia"
+      },
+      {
+        "author_name": "Maria I Indeykina",
+        "author_inst": "Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia"
+      },
+      {
+        "author_name": "Alexander G Brzhozovskiy",
+        "author_inst": "Skolkovo Institute of Science and Technology, Moscow, Russia"
+      },
+      {
+        "author_name": "Anna E Bugrova",
+        "author_inst": "Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia"
+      },
+      {
+        "author_name": "Alexey Kononikhin",
+        "author_inst": "Skolkovo Institute of Science and Technology, Moscow, Russia"
+      },
+      {
+        "author_name": "Natalia L Starodubtseva",
+        "author_inst": "V. I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia"
+      },
+      {
+        "author_name": "Evgeniy V Petrotchenko",
+        "author_inst": "Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, H3T 1E2, Canada"
+      },
+      {
+        "author_name": "Grigoriy I Kovalev",
+        "author_inst": "Skolkovo Institute of Science and Technology, Moscow, Russia"
+      },
+      {
+        "author_name": "Christoph H Borchers",
+        "author_inst": "Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec, H3T 1E2, Canada"
+      },
+      {
+        "author_name": "Gennady T Sukhikh",
+        "author_inst": "V. I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "molecular biology"
+  },
   {
     "rel_doi": "10.1101/2020.05.25.114884",
     "rel_title": "COVID-Align: Accurate online alignment of hCoV-19 genomes using a profile HMM",
@@ -1423900,25 +1422821,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "genetic and genomic medicine"
   },
-  {
-    "rel_doi": "10.1101/2020.05.21.20108894",
-    "rel_title": "Avoiding COVID-19: Aerosol Guidelines",
-    "rel_date": "2020-05-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20108894",
-    "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThe COVID-19 pandemic has brought into sharp focus the need to understand respiratory virus transmission mechanisms. In preparation for an anticipated influenza pandemic, a substantial body of literature has developed over the last few decades showing that the short-range aerosol route is an important, though often neglected transmission path. We develop a simple mathematical model for COVID-19 transmission via aerosols, apply it to known outbreaks, and present quantitative guidelines for ventilation and occupancy in the workplace.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Matthew Evans",
-        "author_inst": "Massachusetts Institute of Technology"
-      }
-    ],
-    "version": "1",
-    "license": "cc0_ng",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.05.21.20109041",
     "rel_title": "Rising evidence of COVID-19 transmission potential to and between animals: do we need to be concerned?",
@@ -1424349,6 +1423251,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.05.23.20110866",
+    "rel_title": "Visualizing the COVID-19 pandemic in Bangladesh using coxcombs: A tribute to Florence Nightingale",
+    "rel_date": "2020-05-24",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.23.20110866",
+    "rel_abs": "Following detection of the first confirmed case of COVID-19 in early December 2019 in Wuhan, China, nearly six months have passed and almost every country in the world is battling against the COVID-19 war. The frontline warriors, namely the doctors, nurses and healthcare staff, have in many countries struggled to care for the sick under conditions of limited resources and protection and the threat of an overwhelmed healthcare system. It is during times such as this, that we draw strength and inspiration from Florence Nightingale - a passionate statistician, social reformer, feminist champion and a pioneer of modern nursing and data visualization. Nightingales famed Florence Night-ingle Diagram also known as \"coxcomb\", which was created 150 years ago and used to display the causes of death in the British Army hospital barracks, demonstrated how data visualization techniques could be a powerful medium of communication and a force for change. This paper pays tribute to Nightingales work by using data from Bangladesh to show that the coxcomb graph is still relevant in the era of COVID-19. The coxcomb graphs that have been produced to display COVID-19 data have provided deeper insights into the trends and relative changes of variables over the course of the pandemic. The paper also describes codes that allow one to easily reproduce the graphs using the statistical programming language R.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Hasinur Rahaman Khan",
+        "author_inst": "University of Dhaka, Bangladesh"
+      },
+      {
+        "author_name": "Tamanna Howlader",
+        "author_inst": "University of Dhaka, Bangladesh"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.05.22.20110429",
     "rel_title": "C-Reactive protein and SOFA score as early predictors of critical care requirement in patients with COVID-19 pneumonia in Spain.",
@@ -1425302,49 +1424227,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.05.22.20110791",
-    "rel_title": "Ethnics and economics in COVID-19: Meta-regression of data from countries in the New York metropolitan area",
-    "rel_date": "2020-05-24",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20110791",
-    "rel_abs": "Ethnics and economics may affect prevalence and case fatality of Coronavirus disease 2019 (COVID-19). To determine whether COVID-19 prevalence and fatality are modulated by ethnics and economics, meta-regression of data from the countries in the New York metropolitan area were herein conducted. We selected 31 countries in the New York metropolitan area. 1) Prevalence and case-fatality rates of confirmed COVID-19 cases on May 20, 2020 and 2) income and poverty estimates were obtained in each country. We performed random-effects meta-regression using OpenMetaAnalys. The covariates included 1) black (%), 2) Hispanic or Latino (%), 3) poverty rates (%), and 4) median household income ($). Statistically significant (P < .05) covariates in the univariable model were together entered into the multivariable model. A slope (coefficient) of the univariable meta-regression line for COVID-19 prevalence was not significant for household income (P = .639), whereas the coefficient was significantly positive for black (coefficient, 0.021; P = .015), Hispanic/Latino (0.033; P < .001), and poverty (0.039; P = .02), which indicated that COVID-19 prevalence increased significantly as black, Hispanic/Latino, and poverty increased. The multivariable model revealed that the slope was significantly positive for only Hispanic/Latino (P < .001). The coefficient in the univariable model for COVID-19 fatality, however, was not significant for all the covariate. In conclusion, black, Hispanic/Latino, and poverty (not household income), especially Hispanic/Latino independently, may be associated with COVID-19 prevalence. There may be no association of black, Hispanic/Latino, poverty, and household income with COVID-19 fatality.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Hisato Takagi",
-        "author_inst": "Shizuoka Medical Center, Kitasato University School of Medicine"
-      },
-      {
-        "author_name": "Toshiki Kuno",
-        "author_inst": "Mount Sinai Beth Israel Medical Center"
-      },
-      {
-        "author_name": "Yujiro Yokoyama",
-        "author_inst": "Easton Hospital"
-      },
-      {
-        "author_name": "Hiroki Ueyama",
-        "author_inst": "Mount Sinai Beth Israel Medical Center"
-      },
-      {
-        "author_name": "Takuya Matsushiro",
-        "author_inst": "Shizuoka Medical Center, Kitasato University School of Medicine"
-      },
-      {
-        "author_name": "Yosuke Hari",
-        "author_inst": "Shizuoka Medical Center, Kitasato University School of Medicine"
-      },
-      {
-        "author_name": "Tomo Ando",
-        "author_inst": "New York Presbyterian Hospital/Columbia University Medical Center"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.05.23.20110882",
     "rel_title": "SARS-CoV-2 lethality decreased over time in two Italian Provinces",
@@ -1425651,6 +1424533,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.05.20.20108340",
+    "rel_title": "The estimations of the COVID-19 incubation period: a systematic review of the literature",
+    "rel_date": "2020-05-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.20.20108340",
+    "rel_abs": "BackgroundA novel coronavirus (COVID-19) has taken the world by storm. The disease has spread very swiftly worldwide. A timely clue which includes the estimation of the incubation period among COVID-19 patients can allow governments and healthcare authorities to act accordingly.\n\nObjectivesto undertake a review and critical appraisal of all published/preprint reports that offer an estimation of incubation periods for COVID-19.\n\nEligibility criteriaThis research looked for all relevant published articles between the dates of December 1, 2019, and April 25, 2020, i.e. those that were related to the COVID-19 incubation period. Papers were included if they were written in English, and involved human participants. Papers were excluded if they were not original (e.g. reviews, editorials, letters, commentaries, or duplications).\n\nSources of evidenceCOVID-19 Open Research Dataset supplied by Georgetowns Centre for Security and Emerging Technology as well as PubMed and Embase via Arxiv, medRxiv, and bioRxiv.\n\nCharting methodsA data-charting form was jointly developed by the two reviewers (NZ and EA), to determine which variables to extract. The two reviewers independently charted the data, discussed the results, and updated the data-charting form.\n\nResults and conclusionsscreening was undertaken 44,000 articles with a final selection of 25 studies referring to 18 different experimental projects related to the estimation of the incubation period of COVID-19. The majority of extant published estimates offer empirical evidence showing that the incubation period for the virus is a mean of 7.8 days, with a median of 5.01 days, which falls into the ranges proposed by the WHO (0 to 14 days) and the ECDC (2 to 12 days). Nevertheless, a number of authors proposed that quarantine time should be a minimum of 14 days and that for estimates of mortality risks a median time delay of 13 days between illness and mortality should be under consideration. It is unclear as to whether any correlation exists between the age of patients and the length of time they incubate the virus.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Nazar Zaki",
+        "author_inst": "UAEU, UAE"
+      },
+      {
+        "author_name": "Elfadil Abdalla Mohamed",
+        "author_inst": "Ajman University, UAE"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.05.21.20108605",
     "rel_title": "Spatial and temporal dynamics of SARS-CoV-2 in COVID-19 patients: A systematic review",
@@ -1426836,173 +1425741,6 @@
     "type": "new results",
     "category": "immunology"
   },
-  {
-    "rel_doi": "10.1101/2020.05.21.109124",
-    "rel_title": "Intestinal inflammation modulates the expression of ACE2 and TMPRSS2 and potentially overlaps with the pathogenesis of SARS-CoV-2 related disease",
-    "rel_date": "2020-05-23",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.21.109124",
-    "rel_abs": "The presence of gastrointestinal symptoms and high levels of viral RNA in the stool suggest active Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) replication within enterocytes. Here, in multiple, large cohorts of patients with inflammatory bowel disease (IBD), we have studied the intersections between Coronavirus Disease 2019 (COVID-19), intestinal inflammation and IBD treatment. A striking expression of ACE2 on the small bowel enterocyte brush border supports intestinal infectivity by SARS-CoV-2. Commonly used IBD medications, both biologic and non-biologic, do not significantly impact ACE2 and TMPRSS2 receptor expression in the uninflamed intestines. Additionally, we have defined molecular responses to COVID-19 infection that are also enriched in IBD, pointing to shared molecular networks between COVID-19 and IBD. These data generate a novel appreciation of the confluence of COVID-19- and IBD-associated inflammation and provide mechanistic insights supporting further investigation of specific IBD drugs in the treatment of COVID-19.",
-    "rel_num_authors": 38,
-    "rel_authors": [
-      {
-        "author_name": "Mayte Su\u00e1rez-Fari\u00f1as",
-        "author_inst": "Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai and Icahn Institute for Data Science and G"
-      },
-      {
-        "author_name": "Minami Tokuyama",
-        "author_inst": "The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai and Precision Institute of Immunology, I"
-      },
-      {
-        "author_name": "Gabrielle Wei",
-        "author_inst": "Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai and Icahn Institute for Data Science and G"
-      },
-      {
-        "author_name": "Ruiqi Huang",
-        "author_inst": "Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai Icahn Institute for Data Science and Genom"
-      },
-      {
-        "author_name": "Alexandra Livanos",
-        "author_inst": "The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai and Precision Institute of Immunology, I"
-      },
-      {
-        "author_name": "Divya Jha",
-        "author_inst": "The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai and Precision Institute of Immunology, I"
-      },
-      {
-        "author_name": "Anais Levescot",
-        "author_inst": "Inserm, UMR1163, Laboratory of Intestinal Immunity and Institute Imagine and Universit\u00e9 de Paris"
-      },
-      {
-        "author_name": "Haritz Irizar",
-        "author_inst": "University College London, Department Mental Health Sciences Unit"
-      },
-      {
-        "author_name": "Roman Kosoy",
-        "author_inst": "Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai and Icahn Institute for Data Science and G"
-      },
-      {
-        "author_name": "Sascha Cording",
-        "author_inst": "Inserm, UMR1163, Laboratory of Intestinal Immunity and Institute Imagine and Universit\u00e9 de Paris"
-      },
-      {
-        "author_name": "Wenhui Wang",
-        "author_inst": "Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai and Icahn Institute for Data Science and G"
-      },
-      {
-        "author_name": "Haritz Irizar",
-        "author_inst": "University College London, Department Mental Health Sciences Unit, London, UK"
-      },
-      {
-        "author_name": "Ryan Ungaro",
-        "author_inst": "The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Antonio Di Narzo",
-        "author_inst": "Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai and Icahn Institute for Data Science and G"
-      },
-      {
-        "author_name": "Gustavo Martinez-Delgado",
-        "author_inst": "The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai and Precision Institute of Immunology, I"
-      },
-      {
-        "author_name": "Maria Suprun",
-        "author_inst": "Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Michael J Corley",
-        "author_inst": "Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine"
-      },
-      {
-        "author_name": "Aleksandar Stojmirovic",
-        "author_inst": "Janssen R&D"
-      },
-      {
-        "author_name": "Sander Houten",
-        "author_inst": "Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai and Icahn Institute for Data Science and G"
-      },
-      {
-        "author_name": "Lauren Peters",
-        "author_inst": "Icahn Institute for Data Science and Genomic Technology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Mark Curran",
-        "author_inst": "Janssen R&D"
-      },
-      {
-        "author_name": "Carrie Brodmerkel",
-        "author_inst": "Janssen R&D"
-      },
-      {
-        "author_name": "Jacqueline Perrigoue",
-        "author_inst": "Janssen R&D"
-      },
-      {
-        "author_name": "Joshua R Friedman",
-        "author_inst": "Janssen R&D"
-      },
-      {
-        "author_name": "Ke Hao",
-        "author_inst": "Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai and Icahn Institute for Data Science and G"
-      },
-      {
-        "author_name": "Eric E Schadt",
-        "author_inst": "Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai and Icahn Institute for Data Science and G"
-      },
-      {
-        "author_name": "Jun Zhu",
-        "author_inst": "Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai and Icahn Institute for Data Science and G"
-      },
-      {
-        "author_name": "Huaibin M Ko",
-        "author_inst": "Department of Pathology, Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Judy Cho",
-        "author_inst": "Icahn Institute for Data Science and Genomic Technology, The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicin"
-      },
-      {
-        "author_name": "Marla C Dubinsky",
-        "author_inst": "The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Bruce E Sands",
-        "author_inst": "The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Lishomwa Ndhlovu",
-        "author_inst": "Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine"
-      },
-      {
-        "author_name": "Nadine Cerf-Bensusan",
-        "author_inst": "Inserm, UMR1163, Laboratory of Intestinal Immunity and Institute Imagine and Universit\u00e9 de Paris"
-      },
-      {
-        "author_name": "Andrew Kasarskis",
-        "author_inst": "Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai and Icahn Institute for Data Science and G"
-      },
-      {
-        "author_name": "Jean-Frederic Colombel",
-        "author_inst": "The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai and Precision Institute of Immunology, I"
-      },
-      {
-        "author_name": "Noam Harpaz",
-        "author_inst": "Department of Pathology, Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Carmen Argmann",
-        "author_inst": "Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai and Icahn Institute for Data Science and G"
-      },
-      {
-        "author_name": "Saurabh Mehandru",
-        "author_inst": "The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai and Precision Institute of Immunology, I"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2020.05.22.111237",
     "rel_title": "Biophysical modeling of the SARS-CoV-2 viral cycle reveals ideal antiviral targets",
@@ -1427345,6 +1426083,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.05.20.20108068",
+    "rel_title": "Demographic and Clinical Characteristics of the Severe Covid-19 Infections: First Report from Mashhad University of Medical Sciences, Iran",
+    "rel_date": "2020-05-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.20.20108068",
+    "rel_abs": "BackgroundCoronavirus Disease 2019 (Covid-19) is expanding worldwide. The characteristics of this infection in patients varies from country to country. To move forward, clinical data on infected patients are needed. Here, we report a comparison between fatalities and recovery of patients with severe Covid-19, based on demographic and clinical characteristics.\n\nMethodsBetween 5 March and 12 May 2020 in Mashhad, Iran, 1,278 of 4,000 suspected Covid-19 patients were confirmed positive by real-time reverse-transcriptase-polymerase-chain-reaction assay of upper respiratory specimens. We compared the demographic, exposure history and clinical symptoms of 925 survivors and 353 fatal cases with confirmed disease.\n\nResultsMean (SD) age for all confirmed patients was 56.9 (18.7) years, 67.1 (15.9) years in fatal cases and 53.0 (18.3) years in survivors. Multivariable logistic regression analysis showed that the outcome of patients was associated with age (OR = 1.049, P = 0.0001, 95% CI = 1.040-1.057). Despite a high burden of Covid-19 infections in the 30-39 and 40-49 year age groups, most of these (89.6% and 87.2%, respectively) recovered. The median (IQR) duration of hospitalization was 9.0 (6.0-14.0) days. The most prevalent co-morbidities were cardiovascular disorders (21%) and diabetes (16.3%). Dyspnoea (72.7%), cough (68.1%) and fever (63.8%) were the most frequent clinical symptoms. Healthcare workers, of whom two (3%) died, comprised 5.2% of infected-cases. Combination antiviral and antibiotic therapy was used in 43.0% of cases.\n\nConclusionsThe characteristics of severe Covid-19 varied substantially between fatal cases and survivors, with diabetes and cardiovascular disorders the most prevalent co-morbidities. In contrast to other studies, there were a higher number of fatalities in younger patients in our settings.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Ladan Goshayeshi",
+        "author_inst": "Mashhad University of Medical Sciences"
+      },
+      {
+        "author_name": "Mina Akbari Rad",
+        "author_inst": "Mashhad University of Medical Sciences"
+      },
+      {
+        "author_name": "Robert Bergquist",
+        "author_inst": "Geospatial Health Journal"
+      },
+      {
+        "author_name": "Abolghasem Allahyari",
+        "author_inst": "Mashhad University of Medical Sciences"
+      },
+      {
+        "author_name": "- MUMS Covid-19 Research Team",
+        "author_inst": ""
+      },
+      {
+        "author_name": "Benyamin Hoseini",
+        "author_inst": "Mashhad University of Medical Sciences"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.05.20.20108365",
     "rel_title": "A Systematic Review and Meta-analysis of Therapeutic options against SARS-CoV-2",
@@ -1428314,57 +1427091,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.05.17.20104695",
-    "rel_title": "A Novel Approach to Data Driven Pandemic Recovery: The Pandemic Recovery Acceleration Model",
-    "rel_date": "2020-05-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.17.20104695",
-    "rel_abs": "A data driven approach to guide the global, regional and local pandemic recovery planning is key to the safety, efficacy and sustainability of all pandemic recovery efforts. The Pandemic Recovery Acceleration Model (PRAM) analytic tool was developed and implemented state wide in Nebraska to allow health officials, public officials, industry leaders and community leaders to capture a real time snapshot of how the COVID-19 pandemic is affecting their local community, a region or the state and use this novel lens to aid in making key mitigation and recovery decisions. This is done by using six commonly available metrics that are monitored daily across the state describing the pandemic impact: number of new cases, percent positive tests, deaths, occupied hospital beds, occupied intensive care beds and utilized ventilators, all directly related to confirmed COVID-19 patients.\n\nNebraska is separated into six Health Care Coalitions based on geography, public health and medical care systems. The PRAM aggregates the data for each of these geographic regions based on disease prevalence acceleration and health care resource utilization acceleration, producing real time analysis of the acceleration of change for each metric individually and also combined into a single weighted index, the PRAM Recovery Index. These indices are then shared daily with the state leadership, coalition leaders and public health directors and also tracked over time, aiding in real time regional and statewide decisions of resource allocation and the extent of use of comprehensive non-pharmacologic interventions.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Jeffrey P Gold",
-        "author_inst": "University of Nebraska Medical Center"
-      },
-      {
-        "author_name": "Christopher Wichman",
-        "author_inst": "University of Nebraska Medical Center"
-      },
-      {
-        "author_name": "Kenneth Bayles",
-        "author_inst": "University of Nebraska Medical Center"
-      },
-      {
-        "author_name": "Ali S Khan",
-        "author_inst": "University of Nebraska Medical Center"
-      },
-      {
-        "author_name": "Christopher Kratochvil",
-        "author_inst": "University of Nebraska Medical Center"
-      },
-      {
-        "author_name": "James V Lawler",
-        "author_inst": "University of Nebraska Medical Center"
-      },
-      {
-        "author_name": "John Martin Lowe",
-        "author_inst": "University of Nebraska Medical Center"
-      },
-      {
-        "author_name": "Shelly Schwedhelm",
-        "author_inst": "Nebraska Medicine"
-      },
-      {
-        "author_name": "Brandon Grimm",
-        "author_inst": "University of Nebraska Medical Center"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.05.18.20097444",
     "rel_title": "Diagnostic power of chest CT for COVID-19: to screen or not to screen",
@@ -1428639,6 +1427365,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.05.18.20105239",
+    "rel_title": "Risks to Children under-five in India from COVID-19",
+    "rel_date": "2020-05-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20105239",
+    "rel_abs": "ObjectiveThe novel coronavirus, COVID-19, has rapidly emerged to become a global pandemic and is known to cause a high risk to patients over the age of 70 and those with co-morbidities, such as hypertension and diabetes. Though children are at comparatively lower risk compared to adults, the Indian population has a large young demographic that is likely to be at higher risk due to exposure to pollution, malnutrition and poor access to medical care. We aimed to quantify the potential impact of COVID-19 on Indias child population.\n\nMethodsWe combined district family household survey data with data from the COVID-19 outbreak in China to analyze the potential impact of COVID-19 on children under the age of 5, under three different scenarios; each of which assumed the prevalence of infection to be 0.5%, 1%, or 5%.\n\nResultsWe find that in the lowest prevalence scenario, across the most populous 18 Indian states, asymptomatic, non-hospitalized symptomatic and hospitalized symptomatic cases could reach 87,200, 412,900 and 31,900, respectively. In a moderate prevalence scenario, these figures reach 174,500, 825,800, and 63,800, and in the worst case, high prevalence scenario these cases could climb as high as 872,200, 4,128,900 and 319,700.\n\nConclusionThese estimates show COVID-19 has the potential to pose a substantial threat to Indias large population of children, particularly those suffering from malnutrition and exposure to indoor air pollution, who may have limited access to health services.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Isabel Frost",
+        "author_inst": "Center for Disease Dynamics Economics & Policy"
+      },
+      {
+        "author_name": "Katie Tseng",
+        "author_inst": "Center for Disease Dynamics Economics & Policy"
+      },
+      {
+        "author_name": "Stephanie Hauck",
+        "author_inst": "Center for Disease Dynamics Economics & Policy"
+      },
+      {
+        "author_name": "Geetanjali Kappor",
+        "author_inst": "Center for Disease Dynamics Economics & Policy"
+      },
+      {
+        "author_name": "Aditi Sriram",
+        "author_inst": "Center for Disease Dynamics Economics & Policy"
+      },
+      {
+        "author_name": "Arindam Nandi",
+        "author_inst": "The Center for Disease Dynamics, Economics & Policy"
+      },
+      {
+        "author_name": "Ramanan Laxminarayan",
+        "author_inst": "Center for Disease Dynamics Economics & Policy"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.05.17.20104638",
     "rel_title": "High Filtration Efficiency Face Masks made from Sterilization Wraps",
@@ -1429932,61 +1428701,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
-  {
-    "rel_doi": "10.1101/2020.05.18.20101618",
-    "rel_title": "Performance of six SARS-CoV-2 immunoassays in comparison with microneutralisation",
-    "rel_date": "2020-05-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20101618",
-    "rel_abs": "There is an urgent need for reliable high-throughput serological assays for the management of the ongoing COVID-19 pandemic. Preferably, the performance of serological tests for a novel virus should be determined with clinical specimens against a gold standard, i.e. virus neutralisation.\n\nWe evaluated specificity and sensitivity of six commercial immunoassays for the detection of SARS-CoV-2 IgG, IgA and IgM antibodies, including four automated assays [Abbott SARS-COV-2 IgG (CE marked), Diasorin Liaison(R) SARS-CoV-2 S1/S2 IgG (research use only), and Euroimmun SARS-CoV-2 IgG and IgA (CE marked)], and two rapid lateral flow (immunocromatographic) tests [Acro Biotech 2019-nCoV IgG/IgM (CE marked) and Xiamen Biotime Biotechnology SARS-CoV-2 IgG/IgM (CE marked)] in comparison with a microneutralisation test (MNT). Two specimen panels from serum samples sent to Helsinki University Hospital Laboratory (HUSLAB) were compiled: the patient panel included sera from PCR confirmed COVID-19 patients, and the negative panel included sera sent for screening of autoimmune diseases and respiratory virus antibodies in 2018 and 2019. The MNT was carried out for all COVID-19 samples (70 serum samples, 62 individuals) and for 53 samples from the negative panel. Forty-one out of 62 COVID-19 patients showed neutralising antibodies with median of 11 days (range 3-51) after onset of symptoms.\n\nThe specificity and sensitivity values of the commercial tests against MNT, respectively, were as follows: 95.1%/80.5% (Abbott Architect SARS-CoV-2 IgG), 94.9%/43.8% (Diasorin Liaison SARS-CoV-2 IgG), 68.3%/87.8% (Euroimmun SARS-CoV-2 IgA), 86.6%/70.7% (Euroimmun SARS-CoV-2 IgG), 74.4%/56.1% (Acro 2019-nCoV IgG), 69.5%/46.3% (Acro 2019-nCoV IgM), 97.5%/71.9% (Xiamen Biotime SARS-CoV-2 IgG), and 88.8%/81.3% (Xiamen Biotime SARSCoV-2 IgM). This study shows variable performance values. Laboratories should carefully consider their testing process, such as a two-tier approach, in order to optimize the overall performance of SARS-CoV-2 serodiagnostics.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Anne J J\u00e4\u00e4skel\u00e4inen",
-        "author_inst": "HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Finland"
-      },
-      {
-        "author_name": "Suvi Kuivanen",
-        "author_inst": "Department of Virology, University of Helsinki, Helsinki, Finland"
-      },
-      {
-        "author_name": "Eliisa Kek\u00e4l\u00e4inen",
-        "author_inst": "Translational Immunology Research Program and Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland"
-      },
-      {
-        "author_name": "Maarit J Ahava",
-        "author_inst": "HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Finland"
-      },
-      {
-        "author_name": "Raisa Loginov",
-        "author_inst": "HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Finland"
-      },
-      {
-        "author_name": "Hannimari Kallio-Kokko",
-        "author_inst": "HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Finland"
-      },
-      {
-        "author_name": "Olli Vapalahti",
-        "author_inst": "University of Helsinki"
-      },
-      {
-        "author_name": "Hanna Jarva",
-        "author_inst": "HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Finland; Translational Immunology Research Progra"
-      },
-      {
-        "author_name": "Satu Kurkela",
-        "author_inst": "HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Finland"
-      },
-      {
-        "author_name": "Maija Lappalainen",
-        "author_inst": "HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Finland"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.05.19.20101832",
     "rel_title": "Serologic responses to SARS-CoV-2 infection among hospital staff with mild disease in eastern France",
@@ -1430325,6 +1429039,149 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.05.18.20086157",
+    "rel_title": "COVID-19 in Great Britain: epidemiological and clinical characteristics of the first few hundred (FF100) cases: a descriptive case series and case control analysis",
+    "rel_date": "2020-05-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20086157",
+    "rel_abs": "ObjectivesFollowing detection of the first virologically-confirmed cases of COVID-19 in Great Britain, an enhanced surveillance study was initiated by Public Health England to describe the clinical presentation, course of disease and underlying health conditions associated with infection of the first few hundred cases.\n\nMethodsInformation was collected on the first COVID-19 cases according to the First Few X WHO protocol. Case-control analyses of the sensitivity, specificity and predictive value of symptoms and underlying health conditions associated with infection were conducted. Point prevalences of underlying health conditions among the UK general population were presented.\n\nFindingsThe majority of FF100 cases were imported (51.4%), of which the majority had recent travel to Italy (71.4%). 24.7% were secondary cases acquired mainly through household contact (40.4%). Children had lower odds of COVID-19 infection compared with the general population.\n\nThe clinical presentation of cases was dominated by cough, fever and fatigue. Non-linear relationships with age were observed for fever, and sensitivity and specificity of symptoms varied by age.\n\nConditions associated with higher odds of COVID-19 infection (after adjusting for age and sex) were chronic heart disease, immunosuppression and multimorbidity.\n\nConclusionThis study presents the first epidemiological and clinical summary of COVID-19 cases in Great Britain. The FFX study design enabled systematic data collection. The study characterized underlying health conditions associated with infection and set relative risks in context with population prevalence estimates. It also provides important evidence for generating case definitions to support public health risk assessment, clinical triage and diagnostic algorithms.",
+    "rel_num_authors": 32,
+    "rel_authors": [
+      {
+        "author_name": "Nicola L Boddington",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Andre Charlett",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Suzanne Elgohari",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Jemma L Walker",
+        "author_inst": "London School of Hygiene and Tropical Medicine"
+      },
+      {
+        "author_name": "Helen Mcdonald",
+        "author_inst": "London School of Hygiene and Tropical Medicine"
+      },
+      {
+        "author_name": "Chloe Byers",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Laura Coughlan",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Tatiana Garcia Vilaplana",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Rosie Whillock",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Mary Sinnathamby",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Nikolaos Panagiotopoulos",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Louise Letley",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Pauline MacDonald",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Roberto Vivancos",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Obaghe Edeghere",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Joseph Shingleton",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Emma Bennett",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Daniel J Grint",
+        "author_inst": "London School of Hygiene and Tropical Medicine"
+      },
+      {
+        "author_name": "Helen Strongman",
+        "author_inst": "London School of Hygiene and Tropical Medicine"
+      },
+      {
+        "author_name": "Kathryn E Mansfield",
+        "author_inst": "London School of Hygiene and Tropical Medicine"
+      },
+      {
+        "author_name": "Christopher Rentsch",
+        "author_inst": "London School of Hygiene and Tropical Medicine"
+      },
+      {
+        "author_name": "Caroline Minassian",
+        "author_inst": "London School of Hygiene and Tropical Medicine"
+      },
+      {
+        "author_name": "Ian J Douglas",
+        "author_inst": "London School of Hygiene and Tropical Medicine"
+      },
+      {
+        "author_name": "Rohini Mathur",
+        "author_inst": "London School of Hygiene and Tropical Medicine"
+      },
+      {
+        "author_name": "Maria Peppa",
+        "author_inst": "London School of Hygiene and Tropical Medicine"
+      },
+      {
+        "author_name": "Simon Cottrell",
+        "author_inst": "Public Health Wales"
+      },
+      {
+        "author_name": "Jim McMenamin",
+        "author_inst": "Public Health Scotland"
+      },
+      {
+        "author_name": "Maria Zambon",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Mary Ramsay",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Gavin Dabrera",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Vanessa Saliba",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Jamie Lopez Bernal",
+        "author_inst": "Public Health England"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.05.18.20102509",
     "rel_title": "Low blood sodium increases risk and severity of COVID-19: a systematic review, meta-analysis and retrospective cohort study",
@@ -1431478,37 +1430335,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.05.17.20104729",
-    "rel_title": "Consensus study of risk factors and symptoms of SARS-CoV-2 (COVID-19) using biomedical literature and social media data",
-    "rel_date": "2020-05-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.17.20104729",
-    "rel_abs": "BackgroundIn December 2019, Coronavirus disease 2019 (COVID-19) outbreak started in China and rapidly spread around the world. Lack of any vaccine or optimized intervention raised the importance of characterizing risk factors and symptoms for the early identification and successful treatment of COVID-19 patients.\n\nMethodsWe systematically integrated and analyzed published biomedical literature and public social media data to expand our landscape of clinical and demographic variables of COVID-19. Through semantic analysis, 45 retrospective cohort studies, which evaluated 303 clinical and demographic variables across 13 different outcomes of COVID-19, and 84,140 tweet posts from 1,036 COVID-19 positive users were collected. In total, 59 symptoms were identified across both datasets.\n\nFindingsApproximately 90% of clinical and demographic variables showed inconsistency across outcomes of COVID-19. From the consensus analysis, we identified clinical and demographic variables that were specific for individual outcomes of COVID-19. Also, 25 novel symptoms that have been not previously well characterized, but were mentioned in social media. Furthermore, we observed that there were certain combinations of symptoms that were frequently mentioned together among COVID-19 patients.\n\nInterpretationIdentified outcome-specific clinical and demographic variables, symptoms, and combinations of symptoms may serve as surrogate indicators to identify COVID-19 patients and predict their clinical outcomes providing appropriate treatments.\n\nFundingThis research was internally funded and received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Jouhyun Jeon",
-        "author_inst": "Klick Inc"
-      },
-      {
-        "author_name": "Gaurav Baruah",
-        "author_inst": "Klick Inc"
-      },
-      {
-        "author_name": "Sarah Sarabadani",
-        "author_inst": "Klick Inc"
-      },
-      {
-        "author_name": "Adam Palanica",
-        "author_inst": "Klick Inc"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.05.20.20104398",
     "rel_title": "Erythrocytes Reveal Complement Activation in Patients with COVID-19",
@@ -1431811,6 +1430637,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.05.17.20104612",
+    "rel_title": "The correspondence between the structure of the terrestrial mobility network and the emergence of COVID-19 in Brazil",
+    "rel_date": "2020-05-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.17.20104612",
+    "rel_abs": "BACKGROUNDthe inter-cities mobility network serves as a proxy for the SARS-CoV-2 spreading network in a country.\n\nOBJECTIVEto investigate the correspondences between the structure of the mobility network and the emergence of COVID-19 cases in Brazilian cities.\n\nMETHODSwe adopt the data from the Brazilian Health Ministry and the terrestrial flow of people between cities from the IBGE database in two scales: Brazilian cities without the North region and cities from the Sao Paulo state. Grounded on the complex networks approach, cities are represented as nodes and the flows as edges. Network centrality measures such as strength and degree are ranked and compared to the list of Brazilian cities, ordered according to the day that they confirmed the first case of COVID-19.\n\nFINDINGSThe strength presents the best correspondences and the interiorization process of SARS-CoV-2 is captured in the Sao Paulo state when different thresholds are applied to the network flows.\n\nMAIN CONCLUSIONSthe strength captures the cities with a higher vulnerability of receiving new cases of COVID-19. Some countryside cities such as Feira de Santana (Bahia state), Ribeirao Preto (Sao Paulo state), and Caruaru (Pernambuco state) have strength comparable to states capitals, making them potential super spreaders.\n\nFinancial supportSao Paulo Research Foundation (FAPESP) Grant Numbers 2015/50122-0, 2018/06205-7 and 2020/06837-3; DFG-IRTG Grant Number 1740/2; CNPq Grant Numbers 420338/2018-7 and 101720/2020-3.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Vander L. S. Freitas",
+        "author_inst": "Federal University of Ouro Preto (UFOP)"
+      },
+      {
+        "author_name": "Thais C. R. O. Konstantyner",
+        "author_inst": "Federal University of Sao Paulo (UNIFESP)"
+      },
+      {
+        "author_name": "Jeferson Feitosa",
+        "author_inst": "Sao Paulo State University (UNESP)"
+      },
+      {
+        "author_name": "Catia S. N. Sepetauskas",
+        "author_inst": "National Center for Monitoring and Early Warning of Natural Disasters (CEMADEN)"
+      },
+      {
+        "author_name": "Leonardo B. L. Santos",
+        "author_inst": "National Center for Monitoring and Early Warning of Natural Disasters (CEMADEN)"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.05.17.20104653",
     "rel_title": "State-by-State estimates of R0 at the start of COVID-19 outbreaks in the USA",
@@ -1432988,37 +1431849,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.05.18.20105551",
-    "rel_title": "Simulating the progression of the COVID-19 disease in Cameroon using SIR models",
-    "rel_date": "2020-05-21",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20105551",
-    "rel_abs": "This paper analyses the evolution of COVID-19 disease in Cameroon over the period March 6--April 2020 using SIR model. Specifically, 1) we evaluate the basic reproduction number of the virus. 2) Determine the peak of the infection and the spread-out period of the disease. 3) Simulate the interventions of public health authorities. Data used in this study is obtained from the Ministry of health of Cameroon. The results suggest that over the period, the reproduction number of the covid-19 in Cameroon is about 1.5 and the peak of the infection could occur at the end of May 2020 with about 7.7% of the population infected. Besides, implementation of efficient public health policies could help flattens the epidemic curve.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Ulrich KAMGUEM NGUEMDJO",
-        "author_inst": "Aix-Marseille University, CNRS, EHESS, Centrale Marseille"
-      },
-      {
-        "author_name": "Freeman MENO",
-        "author_inst": "Lycee Polyvalent Francklin Roosevelt"
-      },
-      {
-        "author_name": "Audric DONGFACK",
-        "author_inst": "Ecole Centrale Marseille"
-      },
-      {
-        "author_name": "Bruno VENTELOU",
-        "author_inst": "Aix-Marseille University, CNRS, EHESS, Centrale Marseille, AMSE"
-      }
-    ],
-    "version": "1",
-    "license": "cc0_ng",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.05.18.20105510",
     "rel_title": "Development and Validation of Two In-house, Low-Cost SARS-CoV-2 Detection Assays",
@@ -1433381,6 +1432211,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.05.16.099242",
+    "rel_title": "Capillary Electrophoresis of PCR fragments with labelled primers for testing the SARS-Cov-2",
+    "rel_date": "2020-05-21",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.16.099242",
+    "rel_abs": "BackgroundDue to the huge demand for SARS-Cov-2 determination, alternatives to the standard qtPCR tests are potentially useful for increasing the number of samples screened. Our aim was to develop a direct fluorescent PCR capillary-electrophoresis detection of the viral genome. We validated this approach on several SARS-Cov-2 positive and negative samples.\n\nStudy designWe isolated the naso-pharingeal RNA from 20 positive and 10 negative samples. The cDNA was synthesised and two fragments of the SARS-Cov-2 were amplified. One of the primers for each pair was 5-end fluorochrome labelled. The amplifications were subjected to capillary electrophoresis in ABI3130 sequencers to visualize the fluorescent peaks.\n\nResultsThe two SARS-Cov-2 fragments were successfully amplified in the positive samples, while the negative samples did not render fluorescent peaks.\n\nConclusionWe describe and alternative method to identify the SARS-Cov-2 genome that could be scaled to the analysis of approximately 100 samples in less than 5 hours. By combining a standard PCR with capillary electrophoresis our approach would overcome the limits imposed to many labs by the qtPCR (lack of reactive and real-time PCR equipment) and increase the testing capacity.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "JUAN GOMEZ",
+        "author_inst": "HUCA"
+      },
+      {
+        "author_name": "SANTIAGO MELON",
+        "author_inst": "HUCA"
+      },
+      {
+        "author_name": "JOSE A BOGA",
+        "author_inst": "HUCA"
+      },
+      {
+        "author_name": "MARTA E Alvarez-Arguelles",
+        "author_inst": "HUCA"
+      },
+      {
+        "author_name": "SUSANA ROJO-ALBA",
+        "author_inst": "HUCA"
+      },
+      {
+        "author_name": "ALVARO LEAL-NEGREDO",
+        "author_inst": "HUCA"
+      },
+      {
+        "author_name": "CRISTIAN Castello-Abietar",
+        "author_inst": "HUCA"
+      },
+      {
+        "author_name": "VICTORIA ALVAREZ",
+        "author_inst": "HUCA"
+      },
+      {
+        "author_name": "ELIAS CUESTA-LLAVONA",
+        "author_inst": "HUCA"
+      },
+      {
+        "author_name": "ELIECER COTO",
+        "author_inst": "HOSPITAL UNIVERSITARIO CENTRAL DE ASTURIAS-HUCA"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2020.05.14.20101444",
     "rel_title": "Detection of SARS-CoV-2 in pets living with COVID-19 owners diagnosed during the COVID-19 lockdown in Spain: A case of an asymptomatic cat with SARS-CoV-2 in Europe",
@@ -1434494,33 +1433379,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "intensive care and critical care medicine"
   },
-  {
-    "rel_doi": "10.1101/2020.05.15.20103333",
-    "rel_title": "THE ROLE OF POINT-OF-CARE ULTRASONOGRAPHY IN THE INITIAL CHARACTERIZATION OF COVID-19 PATIENTS: RESULTS FROM A PROSPECTIVE MULTICENTRIC STUDY.",
-    "rel_date": "2020-05-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.15.20103333",
-    "rel_abs": "INTRODUCTIONCoronavirus Disease 2019 (COVID-19) is a highly contagious illness caused by the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). There is growing evidence regarding the imaging findings of COVID-19, in Chest X-ray and CT scan, however their availability in this pandemic outbreak might be compromised. At this moment, the role of Point-of-care ultrasonography (POCUS) has yet to be explored.\n\nOBJECTIVESThe main purpose of this study is to describe the POCUS findings of the disease in COVID-19 patients admitted to the emergency department (ED). Determining the correlation of these parameters with vital signs, laboratory results and chest X-ray, as well as, therapeutic decisions and prognosis.\n\nMETHODSProspective study carried out in the emergency department (ED) of two academic hospitals. High suspicion or confirmed COVID-19 patients were subjected to the ultrasonographic measurement of the inferior vena cava (IVC), focused cardiac ultrasound (FOCUS), and Lung Ultrasonography (Lung POCUS).\n\nRESULTSBetween March and April 2020, ninety-six patients were enrolled. The mean age was 68.2 years (SD 17.5). The most common finding in Lung POCUS was an irregular pleural line (63.2%) followed by bilateral confluent (55.2%) and isolated B-lines (53.1%), which was associated with a positive RT-PCR (OR 4.729, 95% CI: 1.989-11.246; p<0.001), and correlated with IL-6 levels (rho = 0.622; p = 0.002). The IVC moderately correlated with levels of pO2, expiratory (rho = -0.539; p = 0.014) and inspiratory (rho = -0.527; p = 0.017), with troponin I (rho = 0.509; p=0.03). After POCUS exam, almost 20% of the patients had an associated condition that required a change in the treatment or management.\n\nCONCLUSIONIn this pandemic era, as the shortage of resources constitutes an undeniable public health threat, POCUS presents the potential to impact in diagnosis, management and prognosis of our confirmed or suspected COVID-19 patients.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "yale tung chen",
-        "author_inst": "Hospital Universitario La Paz. Madrid (Spain)."
-      },
-      {
-        "author_name": "Rafael Llamas Fuentes",
-        "author_inst": "hospital reina sofia (cordoba, spain)"
-      },
-      {
-        "author_name": "Pablo Rodriguez Fuertes",
-        "author_inst": "hospital universitario la paz"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "emergency medicine"
-  },
   {
     "rel_doi": "10.1101/2020.05.16.20104240",
     "rel_title": "When Can Elimination of SARS-CoV-2 Infection be Assumed? Simulation Modelling in a Case Study Island Nation",
@@ -1434711,6 +1433569,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.05.16.20104489",
+    "rel_title": "A Computer Simulation Study on novel Corona Virus Transmission among the People in a Queue",
+    "rel_date": "2020-05-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.16.20104489",
+    "rel_abs": "The World Health Organization (WHO) on March 11, 2020, has declared the novel Corona virus (COVID-19) outbreak a global pandemic. It is essential to understand how coronavirus transmits from one person to another and this knowledge will help protect the vulnerable and limit the spread of the Corona virus. The mode of respiratory transmission of Corona virus is not completely understood as of date. Using a computer simulation, this paper analyses the probability of spreading of Corona virus through air among the people who are standing in a queue. The parameters such as the diameter of the virus particle, room temperature, relative humidity, height of the person, distance between the people and the waiting time in the queue are considered in the computer model to determine the distribution of Corona virus and hence identify the risk factor of spreading the Covid-19. This paper describes the possibilities of getting infectious when a Covid-19 infected person present in a queue and the impact on the waiting time, distance between people and the position in the queue on the transmission of Corona virus.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Santhosh Samuel Mathews",
+        "author_inst": "Amzetta"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.05.16.20104315",
     "rel_title": "Modes of transmission of COVID-19 outbreak- a mathematical study",
@@ -1435884,161 +1434761,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.05.20.103549",
-    "rel_title": "Intra-host Variation and Evolutionary Dynamics of SARS-CoV-2 Population in COVID-19 Patients",
-    "rel_date": "2020-05-20",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.20.103549",
-    "rel_abs": "As of middle May 2020, the causative agent of COVID-19, SARS-CoV-2, has infected over 4 million people with more than 300 thousand death as official reports1,2. The key to understanding the biology and virus-host interactions of SARS-CoV-2 requires the knowledge of mutation and evolution of this virus at both inter- and intra-host levels. However, despite quite a few polymorphic sites identified among SARS-CoV-2 populations, intra-host variant spectra and their evolutionary dynamics remain mostly unknown. Here, using deep sequencing data, we achieved and characterized consensus genomes and intra-host genomic variants from 32 serial samples collected from eight patients with COVID-19. The 32 consensus genomes revealed the coexistence of different genotypes within the same patient. We further identified 40 intra-host single nucleotide variants (iSNVs). Most (30/40) iSNVs presented in single patient, while ten iSNVs were found in at least two patients or identical to consensus variants. Comparison of allele frequencies of the iSNVs revealed genetic divergence between intra-host populations of the respiratory tract (RT) and gastrointestinal tract (GIT), mostly driven by bottleneck events among intra-host transmissions. Nonetheless, we observed a maintained viral genetic diversity within GIT, showing an increased population with accumulated mutations developed in the tissue-specific environments. The iSNVs identified here not only show spatial divergence of intra-host viral populations, but also provide new insights into the complex virus-host interactions.",
-    "rel_num_authors": 35,
-    "rel_authors": [
-      {
-        "author_name": "Yanqun Wang",
-        "author_inst": "Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University"
-      },
-      {
-        "author_name": "Daxi Wang",
-        "author_inst": "BGI-Shenzhen"
-      },
-      {
-        "author_name": "Wanying Sun",
-        "author_inst": "BGI-Shenzhen"
-      },
-      {
-        "author_name": "Zhaoyong Zhang",
-        "author_inst": "Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University"
-      },
-      {
-        "author_name": "Weijun Chen",
-        "author_inst": "BGI-Shenzhen"
-      },
-      {
-        "author_name": "Airu Zhu",
-        "author_inst": "Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University"
-      },
-      {
-        "author_name": "Yongbo Huang",
-        "author_inst": "Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University"
-      },
-      {
-        "author_name": "Fei Xiao",
-        "author_inst": "Department of Infectious Diseases, Guangdong Provincial Key Laboratory of Biomedical Imaging, Guangdong Provincial Engineering Research Center of Molecular Imag"
-      },
-      {
-        "author_name": "Jinxiu Yao",
-        "author_inst": "Yangjiang People Hospital"
-      },
-      {
-        "author_name": "Mian Gan",
-        "author_inst": "Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University"
-      },
-      {
-        "author_name": "Fang Li",
-        "author_inst": "Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University"
-      },
-      {
-        "author_name": "Ling luo",
-        "author_inst": "Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University"
-      },
-      {
-        "author_name": "Xiaofang Huang",
-        "author_inst": "Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University"
-      },
-      {
-        "author_name": "Yanjun Zhang",
-        "author_inst": "Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University"
-      },
-      {
-        "author_name": "Sook-san Wong",
-        "author_inst": "Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University"
-      },
-      {
-        "author_name": "Xinyi Cheng",
-        "author_inst": "BGI-Shenzhen"
-      },
-      {
-        "author_name": "Jingkai Ji",
-        "author_inst": "BGI-Shenzhen"
-      },
-      {
-        "author_name": "Zhihua Ou",
-        "author_inst": "BGI-Shenzhen"
-      },
-      {
-        "author_name": "Minfeng Xiao",
-        "author_inst": "BGI-Shenzhen"
-      },
-      {
-        "author_name": "Min Li",
-        "author_inst": "BGI-Shenzhen"
-      },
-      {
-        "author_name": "Jiandong Li",
-        "author_inst": "BGI-Shenzhen"
-      },
-      {
-        "author_name": "Peidi Ren",
-        "author_inst": "BGI-Shenzhen"
-      },
-      {
-        "author_name": "Ziqing Deng",
-        "author_inst": "BGI-Shenzhen"
-      },
-      {
-        "author_name": "Huanzi Zhong",
-        "author_inst": "BGI-Shenzhen"
-      },
-      {
-        "author_name": "Huanming Yang",
-        "author_inst": "BGI-Shenzhen"
-      },
-      {
-        "author_name": "Jian Wang",
-        "author_inst": "BGI-Shenzhen"
-      },
-      {
-        "author_name": "Xun Xu",
-        "author_inst": "BGI-Shenzhen"
-      },
-      {
-        "author_name": "Tie Song",
-        "author_inst": "Guangdong Provincial Center for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Chris Mok",
-        "author_inst": "University of Hong Kong"
-      },
-      {
-        "author_name": "Malik Peiris",
-        "author_inst": "University of Hong Kong"
-      },
-      {
-        "author_name": "Nanshan Zhong",
-        "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff"
-      },
-      {
-        "author_name": "Jingxian Zhao",
-        "author_inst": "Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University"
-      },
-      {
-        "author_name": "Yimin Li",
-        "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease"
-      },
-      {
-        "author_name": "Junhua Li",
-        "author_inst": "BGI-Shenzhen"
-      },
-      {
-        "author_name": "Jincun Zhao",
-        "author_inst": "Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "genomics"
-  },
   {
     "rel_doi": "10.1101/2020.05.20.106294",
     "rel_title": "Deep sequencing of B cell receptor repertoires from COVID-19 patients reveals strong convergent immune signatures",
@@ -1436297,6 +1435019,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.05.14.20102087",
+    "rel_title": "Modeling the Effects of Non-PharmaceuticalInterventions on COVID-19 Spread in Kenya",
+    "rel_date": "2020-05-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20102087",
+    "rel_abs": "May 14, 2020\n\nMathematical modeling of non-pharmaceutical interventions (NPIs) of COVID-19 in Kenya is presented. An SEIR compartment model is considered with additional compartments of hospitalized population whose condition is severe or critical and also the fatalities compartment. The basic reproduction number (R0) is computed by next generation matrix approach and later expressed as a time-dependent function so as to incorporate the NPIs into the model. The resulting system of ordinary differential equations (ODEs) are solved using fourth-order and fifth-order Runge-Kutta methods. Different intervention scenarios are considered and results show that, implementation of closure of education insitutions, curfew and partial lockdown yield predicted delayed peaks of the overall infections, severe cases and fatalities and subsequently containement of the pandemic in the country.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Duncan K. Gathungu",
+        "author_inst": "Jomo Kenyatta University of Agriculture and Technology"
+      },
+      {
+        "author_name": "Viona N. Ojiambo",
+        "author_inst": "Jomo Kenyatta University of Agriculture and Technology"
+      },
+      {
+        "author_name": "Mark E. M. Kimathi",
+        "author_inst": "Machakos University"
+      },
+      {
+        "author_name": "Samuel M. Mwalili",
+        "author_inst": "Jomo Kenyatta University of Agriculture and Technology"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.05.13.20100784",
     "rel_title": "Predicting SARS-CoV-2 infection trend using technical analysis indicators",
@@ -1437170,29 +1435923,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.05.15.20103010",
-    "rel_title": "Social heterogeneity and the COVID-19 lockdown in a multi-group SEIR model",
-    "rel_date": "2020-05-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.15.20103010",
-    "rel_abs": "The goal of the lockdown is to mitigate and if possible prevent the spread of an epidemic. It consists in reducing social interactions. This is taken into account by the introduction of a factor of reduction of social interactions q, and by decreasing the transmission coefficient of the disease accordingly. Evaluating q is a difficult question and one can ask if it makes sense to compute an average coefficient q for a given population, in order to make predictions on the basic reproduction rate [R]0, the dynamics of the epidemic or the fraction of the population that will have been infected by the end of the epidemic. On a very simple example, we show that the computation of [R]0 in a heterogeneous population is not reduced to the computation of an average q but rather to the direct computation of an average coefficient [R]0. Even more interesting is the fact that, in a range of data compatible with the Covid-19 outbreak, the size of the epidemic is deeply modified by social heterogeneity, as is the height of the epidemic peak, while the date at which it is reached mainly depends on the average [R]0 coefficient. This paper illustrates more technical results that can be found in [4], with new numerical computations. It is intended to draw the attention on the role of heterogeneities in a population in a very simple case, which might be difficult to apprehend in more realistic but also more complex models.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Jean Dolbeault",
-        "author_inst": "Universite Paris Dauphine - PSL"
-      },
-      {
-        "author_name": "Gabriel TURINICI",
-        "author_inst": "Universite Paris Dauphine - PSL"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.05.15.20102954",
     "rel_title": "A Human-Pathogen SEIR-P Model for COVID-19 Outbreak under different intervention scenarios in Kenya",
@@ -1437411,6 +1436141,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.05.16.20103903",
+    "rel_title": "Causal Modeling of Twitter Activity During COVID-19",
+    "rel_date": "2020-05-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.16.20103903",
+    "rel_abs": "Understanding the characteristics of public attention and perception is an essential prerequisite for appropriate crisis management during adverse health events. This is even more crucial during a pandemic such as COVID-19, as primary responsibility of risk management is not centralized to a single institution, but distributed across society. While numerous studies utilize Twitter data in descriptive or predictive context during COVID-19 pandemic, causal modeling of public attention has not been investigated. In this study, we propose a causal inference approach to discover and quantify causal relationships between pandemic characteristics (e.g. number of infections and deaths) and Twitter activity as well as public sentiment. Our results show that the proposed method can successfully capture the epidemiological domain knowledge and identify variables that affect public attention and perception. We believe our work contributes to the field of infodemiology by distinguishing events that correlate with public attention from events that cause public attention.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Oguzhan Gencoglu",
+        "author_inst": "Tampere University"
+      },
+      {
+        "author_name": "Mathias Gruber",
+        "author_inst": "-"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health informatics"
+  },
   {
     "rel_doi": "10.1101/2020.05.16.20103838",
     "rel_title": "Preliminary evaluation of COVID-19 disease outcomes, test capacities and management approaches among African countries.",
@@ -1438768,37 +1437521,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.05.12.20099028",
-    "rel_title": "Outcomes of Hydroxychloroquine Treatment Among Hospitalized COVID-19 Patients in the United States- Real-World Evidence From a Federated Electronic Medical Record Network",
-    "rel_date": "2020-05-19",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20099028",
-    "rel_abs": "On March 28, 2020, in response to the rapidly accelerating COVID-19 pandemic, U.S FDA issued emergency use authorization for hydroxychloroquine (HCQ) in hospitalized COVID-19 patients based on limited in-vitro and anecdotal clinical data. Analysis of the accumulated real-world data utilizing electronic medical records (EMR) could indicate HCQ therapy benefits as we await the results of clinical trials. However, any such analysis of retrospective observational data should account for variables such as demographics and comorbidities that could affect treatment strategies or outcomes. Therefore, we report the outcomes of HCQ treatment in a propensity-matched cohort of COVID-19 hospitalized patients. Our analysis of a large retrospective cohort of hospitalized COVID-19 patients treated with HCQ did not show benefits in mortality or the need for mechanical ventilation when compared to a matched cohort of patients who did not receive HCQ.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Shailendra Singh",
-        "author_inst": "Charleston Area Medical Center"
-      },
-      {
-        "author_name": "Ahmad Khan",
-        "author_inst": "Department of Medicine, West Virginia University Health Sciences Center Charleston Division, Charleston, WV"
-      },
-      {
-        "author_name": "Monica Chowdhry",
-        "author_inst": "Department of Medicine, West Virginia University Health Sciences Center Charleston Division, Charleston, WV"
-      },
-      {
-        "author_name": "Arka Chatterjee",
-        "author_inst": "Division of Cardiovascular Disease, University of Alabama at Birmingham"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.05.13.20100743",
     "rel_title": "Detecting the Emergent or Re-Emergent COVID-19 Pandemic in a Country: Modelling Study of Combined Primary Care and Hospital Surveillance",
@@ -1439013,6 +1437735,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "occupational and environmental health"
   },
+  {
+    "rel_doi": "10.1101/2020.05.13.20100602",
+    "rel_title": "Can we use these masks? Rapid Assessment of the Inhalation Resistance Performance of Uncertified Medical Face Masks in the Context of Restricted Resources Imposed during a Public Health Emergency",
+    "rel_date": "2020-05-19",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20100602",
+    "rel_abs": "In the case of a public health emergency such as the COVID-19 pandemic, access to large quantities of appropriate personal protection equipment (PPE) has presented a significant problem. A shortage of face masks and respirators has been widely reported across the world. A concerted effort to manufacture high volumes has not unsurprisingly put pressure on the supply chain and the important certification processes. PPE procured or donated as uncertified stock requires rigorous, expedient and scientifically informed evidence before decisions can be made regarding suitable deployment, expensive certification, return or possible destruction of stock. This paper reports a series of experiments devised in reaction to this situation. In this study, an experimental methodology for the assessment of the filtration performance of samples of real-world, uncertified, fluid resistant surgical masks (FRSM type IIR) was evaluated in the resource limited (lockdown) environment of the COVID-19 pandemic. A steady-state flow rig was adapted to incorporate a bespoke filter flow chamber for mounting face masks in order to evaluate the resistance to air flow as an indicator of mask inhalation performance. Pure air was drawn through a specified control surface area at known flow rate conditions; the resistance to the air flow through the masks was measured as the resulting pressure drop. Over 60 tests were performed from 4 different, randomly sampled batches and compared to a control sample of EN Type IIR certified FRSM masks. Steady-state volumetric airflow rates of 30 and 95 lmin-1 were chosen to represent deep breathing and vigorous exercise conditions respectively. The results showed that the sample masks produced a pressure drop of between 26% to 58% compared to the control batch at the lower flow rate and 22% to 55% at the higher rate. The results for each sample were consistent across both flow rates. Within the group of masks tested, two sets (between 48% and 58% of the reference set) showed the potential to be professionally assessed for appropriate deployment in a suitable setting. Although the absolute values of pressure drop measured by this method are unlikely to correlate with other testing approaches, the observed, indicative trends and relative performance of the masks is key to this approach. Critically, this method does not replace certification but it has enabled a public body to quickly make decisions; certify, re-assign, refund, thus saving time and resources. The total time spent conducting the tests was less than 8 hours and the low cost method proposed can be repurposed for low resource regions.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Steven Begg",
+        "author_inst": "University of Brighton"
+      },
+      {
+        "author_name": "Nwabueze G Emekwuru",
+        "author_inst": "Coventry University"
+      },
+      {
+        "author_name": "Nicolas Miche",
+        "author_inst": "University of Brighton"
+      },
+      {
+        "author_name": "Bill Whitney",
+        "author_inst": "University of Brighton"
+      },
+      {
+        "author_name": "Obuks Ejohwomu",
+        "author_inst": "University of Manchester"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "occupational and environmental health"
+  },
   {
     "rel_doi": "10.1101/2020.05.14.20101576",
     "rel_title": "Characteristics and outcome of SARS-CoV-2 infection in cancer patients.",
@@ -1439870,33 +1438627,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.05.14.20101774",
-    "rel_title": "Hydroxychloroquine in COVID-19: A systematic review and meta-analysis",
-    "rel_date": "2020-05-19",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20101774",
-    "rel_abs": "BackgroundHydroxychloroquine is being administered among patients with COVID-19 infection in many healthcare systems across the world, considering its in vitro effect against the SARS-CoV-2 virus. In spite of several observational studies and a few randomized controlled trials, the effect of hydroxychloroquine on patients with COVID-19 infection remains unclear. We undertook this systematic review with meta-analysis to evaluate the efficacy and safety of hydroxychloroquine among patients with COVID-19 infection.\n\nMethodsWe searched PubMed, Embase, the Cochrane Library, Web of Science, medRxiv, and other relevant resources until August 1, 2020. We included randomized controlled trials and observational studies in which hydroxychloroquine was administered and compared to a control group. Data were extracted, and quality assessment of the studies was carried out. We evaluated symptomatic progression, mortality, viral clearance, evolution of changes on chest CT imaging, and adverse events. A fixed or random-effects model was used depending on outcome heterogeneity.\n\nResultsWe included 23 studies, including seven randomized controlled trials and 16 observational studies. Among these, 11,029 patients received hydroxychloroquine alone or in combination, while 12063 did not. Mortality was reported at different points in time. The overall mortality was not significantly different among patients who received hydroxychloroquine compared to the control group (OR: 0.94, 95% CI: 0.72-1.22; p = 0.63). Clinical worsening did not differ between patients who received hydroxychloroquine compared to those who did not (OR 0.93, 95% CI: 0.57-1.52; p = 0.77). Negative conversion, assessed by RT-PCR, did not differ significantly between the hydroxychloroquine and the control groups (OR: 0.67, CI: 0.21-2.11; p = 0.49). The evolution of changes on chest CT imaging was reported only in two studies; a more pronounced improvement was observed with the use of hydroxychloroquine compared to standard care (OR: 2.68, CI: 1.1-6.55; P = 0.03). The incidence of adverse events was significantly higher with hydroxychloroquine (OR: 5.95, CI: 2.56-13.83; p < 0.00001).\n\nConclusionsOur meta-analysis does not suggest improvement in mortality, clinical progression, or negative conversion by RT-PCR among patients with COVID-19 infection who are treated with hydroxychloroquine. There was a significantly higher incidence of adverse events with hydroxychloroquine use.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Jose Chacko",
-        "author_inst": "Majumdar Shaw Medical Center, Bangalore, India"
-      },
-      {
-        "author_name": "Gagan Brar",
-        "author_inst": "Aster RV Hospital, Bangalore, India"
-      },
-      {
-        "author_name": "Robert Premkumar",
-        "author_inst": "Majumdar Shaw Medical Center, Bangalore, India"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.05.14.20099234",
     "rel_title": "Off-Label Real World Experience Using Tocilizumab for Patients Hospitalized with COVID-19 Disease in a Regional Community Health System: A Case-Control Study",
@@ -1440159,6 +1438889,149 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.05.18.20105197",
+    "rel_title": "SARS-CoV-2 seroconversion in health care workers",
+    "rel_date": "2020-05-19",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20105197",
+    "rel_abs": "BackgroundThe correlates of protection against SARS-CoV-2 and their longevity remain unclear. Studies in severely ill individuals have identified robust cellular and humoral immune responses against the virus. Asymptomatic infection with SARS-CoV-2 has also been described, but it is unknown whether this is sufficient to produce antibody responses.\n\nMethodsWe performed a cross-sectional study recruiting 554 health care workers from University Hospitals Birmingham NHS Foundation Trust who were at work and asymptomatic. Participants were tested for current infection with SARS-CoV-2 by nasopharyngeal swab for real-time polymerase chain reaction and for seroconversion by the measurement of anti-SARS-CoV-2 spike glycoprotein antibodies by enzyme linked immunosorbent assay. Results were interpreted in the context of previous, self-reported symptoms of illness consistent with COVID-19.\n\nResultsThe point prevalence of infection with SARS-CoV-2, determined by the detection of SARS-CoV-2 RNA on nasopharnygeal swab was 2.39% (n=13/544). Serum was available on 516 participants. The overall rate of seroconversion in the cohort was 24.4% (n=126/516). Individuals who had previously experienced a symptomatic illness consistent with COVID-19 had significantly greater seroconversion rates than those who had remained asymptomatic (37.5% vs 17.1%, {chi}2 =21.1034, p<0.0001). In the week preceding peak COVID-19-related mortality at UHBFT, seroconversion rates amongst those who were suffering from symptomatic illnesses peaked at 77.8%. Prior symptomatic illness generated quantitatively higher antibody responses than asymptomatic seroconversion. Seroconversion rates were highest amongst those working in housekeeping (34.5%), acute medicine (33.3%) and general internal medicine (30.3%) with lower rates observed in participants working in intensive care (14.8%) and emergency medicine (13.3%).\n\nConclusionsIn a large cross-sectional seroprevalence study of health-care workers, we demonstrate that asymptomatic seroconversion occurs, however prior symptomatic illness is associated with quantitatively higher antibody responses. The identification that the potential for seroconversion in health-care workers can associate differentially with certain hospital departments may inform future infection control and occupational health practices.\n\nResearch in contextO_ST_ABSEvidence before the studyC_ST_ABSTo date, no study has examined the cross-sectional seroprevalence of anti-SARS-CoV-2 antibodies in health care workers during the COVID-19 pandemic. Existing evidence suggests that the levels of SARS-CoV-2 antibodies developing following infection may vary with disease severity in keeping with previous coronavirus pandemics.\n\nAdded value of this studyWe demonstrate that seroconversion can occur in health care workers who have suffered no previous symptoms of SARS-Cov-2 infection. However, prior symptomatic infection tends to drive quantitatively superior antibody responses against the virus. We observed differential seroconversion rates in individuals working within different hospital departments. Using intensive care as a reference, the relative risk for seroconversion was greatest for those working in housekeeping, acute and general internal medicine.\n\nImplications of all the available evidenceInsight into the current seroprevalence of SARS-CoV-2 antibodies within a high-risk cohort of health-care workers is of direct relevance as a reference point for future community serological surveys. We provide further evidence of asymptomatic infection and seroconversion, strengthening the argument for regular, routine screening of health-care workers. Finally, we provide evidence that individuals working in particular roles within the NHS are at greater risk of seroconversion with significant implications for their occupational health.",
+    "rel_num_authors": 32,
+    "rel_authors": [
+      {
+        "author_name": "Adrian M Shields",
+        "author_inst": "Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, UK"
+      },
+      {
+        "author_name": "Sian E Faustini",
+        "author_inst": "Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, UK"
+      },
+      {
+        "author_name": "Marisol Perez-Toledo",
+        "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK"
+      },
+      {
+        "author_name": "Sian Jossi",
+        "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK"
+      },
+      {
+        "author_name": "Erin L Aldera",
+        "author_inst": "Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK"
+      },
+      {
+        "author_name": "Joel D Allen",
+        "author_inst": "School of Biological Sciences, University of Southampton, Southampton, UK"
+      },
+      {
+        "author_name": "Saly Al-Taei",
+        "author_inst": "Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, UK"
+      },
+      {
+        "author_name": "Claire Backhouse",
+        "author_inst": "Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, UK"
+      },
+      {
+        "author_name": "Andrew Bosworth",
+        "author_inst": "University Hospital Birmingham NHS Foundation Trust, Birmingham, UK"
+      },
+      {
+        "author_name": "Lyndsey Dunbar",
+        "author_inst": "Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, UK"
+      },
+      {
+        "author_name": "Daniel Ebanks",
+        "author_inst": "Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, UK"
+      },
+      {
+        "author_name": "Beena Emmanuel",
+        "author_inst": "Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, UK"
+      },
+      {
+        "author_name": "Joanne Grey",
+        "author_inst": "University Hospital Birmingham NHS Foundation Trust, Birmingham, UK"
+      },
+      {
+        "author_name": "I Michael Kidd",
+        "author_inst": "PHE Public Health Laboratory, Birmingham, UK"
+      },
+      {
+        "author_name": "Golaeh McGinnell",
+        "author_inst": "University Hospital Birmingham NHS Foundation Trust, Birmingham, UK"
+      },
+      {
+        "author_name": "Dee McLoughlin",
+        "author_inst": "Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK"
+      },
+      {
+        "author_name": "Gabriella Morley",
+        "author_inst": "Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK"
+      },
+      {
+        "author_name": "Danai Papakonstantinou",
+        "author_inst": "Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK"
+      },
+      {
+        "author_name": "Oliver Pickles",
+        "author_inst": "Surgical Research Laboratory, Institute of Cancer and Genomics Science, University of Birmingham, UK"
+      },
+      {
+        "author_name": "Charlotte Poxon",
+        "author_inst": "Surgical Research Laboratory, Institute of Cancer and Genomics Science, University of Birmingham, UK"
+      },
+      {
+        "author_name": "Megan Richter",
+        "author_inst": "Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, UK"
+      },
+      {
+        "author_name": "Eloise Walker",
+        "author_inst": "Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK"
+      },
+      {
+        "author_name": "Kasun Wanigasooriya",
+        "author_inst": "Surgical Research Laboratory, Institute of Cancer and Genomics Science, University of Birmingham, UK"
+      },
+      {
+        "author_name": "Yasunori Watanabe",
+        "author_inst": "Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, UK"
+      },
+      {
+        "author_name": "Celina Whalley",
+        "author_inst": "Surgical Research Laboratory, Institute of Cancer and Genomics Science, University of Birmingham, UK"
+      },
+      {
+        "author_name": "Agnieszka E Zielinska",
+        "author_inst": "Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK"
+      },
+      {
+        "author_name": "Max Crispin",
+        "author_inst": "School of Biological Sciences, University of Southampton, Southampton, UK"
+      },
+      {
+        "author_name": "David C Wraith",
+        "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK"
+      },
+      {
+        "author_name": "Andrew D Beggs",
+        "author_inst": "Surgical Research Laboratory, Institute of Cancer and Genomics Science, University of Birmingham, UK"
+      },
+      {
+        "author_name": "Adam F Cunningham",
+        "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK"
+      },
+      {
+        "author_name": "Mark T Drayson",
+        "author_inst": "Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, UK"
+      },
+      {
+        "author_name": "Alex G Richter",
+        "author_inst": "Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, UK"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "allergy and immunology"
+  },
   {
     "rel_doi": "10.1101/2020.05.13.20097675",
     "rel_title": "Assessment of service availability and Infection prevention measures in hospitals of Nepal during the transition phase of COVID-19 case surge",
@@ -1441584,73 +1440457,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.05.11.20086439",
-    "rel_title": "Human coronavirus reinfection dynamics: lessons for SARS-CoV-2",
-    "rel_date": "2020-05-18",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20086439",
-    "rel_abs": "In the current COVID-19 pandemic a key unsolved question is the duration of acquired immunity in recovered individuals. The recent emergence of SARS-CoV-2 precludes a direct study on this virus, but the four seasonal human coronaviruses may reveal common characteristics applicable to all human coronaviruses. We monitored healthy subjects over a time span of 35 years (1985-2020), providing a total of 2473 follow up person-months, and determined a) the time to reinfection by the same seasonal coronavirus and b) the dynamics of coronavirus antibody depletion post-infection. An alarmingly short duration of protective immunity to coronaviruses was found. Reinfections occurred frequently at 12 months post-infection and there was for each virus a substantial reduction in antibody levels as soon as 6 months post-infection.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Arthur WD Edridge",
-        "author_inst": "Amsterdam UMC, Laboratory of Experimental Virology"
-      },
-      {
-        "author_name": "Joanna M Kaczorowska",
-        "author_inst": "Amsterdam UMC, Laboratory of Experimental Virology"
-      },
-      {
-        "author_name": "Alexis CR Hoste",
-        "author_inst": "INGENASA, Inmunologia y Genetica Aplicada"
-      },
-      {
-        "author_name": "Margreet Bakker",
-        "author_inst": "Amsterdam UMC, Laboratory of Experimental Virology"
-      },
-      {
-        "author_name": "Michelle Klein",
-        "author_inst": "Amsterdam UMC, Laboratory of Experimental Virology"
-      },
-      {
-        "author_name": "Maarten F Jebbink",
-        "author_inst": "Amsterdam UMC, Laboratory of Experimental Virology"
-      },
-      {
-        "author_name": "Amy Matser",
-        "author_inst": "Public Health Service of Amsterdam, Department of Infectious Diseases"
-      },
-      {
-        "author_name": "Cormac Kinsella",
-        "author_inst": "Amsterdam UMC, Laboratory of Experimental Virology"
-      },
-      {
-        "author_name": "Paloma Rueda",
-        "author_inst": "INGENASA, Inmunologia y Genetica Aplicada"
-      },
-      {
-        "author_name": "Maria Prins",
-        "author_inst": "Public Health Service of Amsterdam, Department of Infectious Diseases"
-      },
-      {
-        "author_name": "Patricia Sastre",
-        "author_inst": "INGENASA, Inmunologia y Genetica Aplicada"
-      },
-      {
-        "author_name": "Martin Deijs",
-        "author_inst": "Amsterdam UMC, Laboratory of Experimental Virology"
-      },
-      {
-        "author_name": "Lia van der Hoek",
-        "author_inst": "Amsterdam UMC, Laboratory of Experimental Virology"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.05.12.20076794",
     "rel_title": "COVID-19 outbreak in Italy: estimation of reproduction numbers over two months toward the Phase 2",
@@ -1441929,6 +1440735,77 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.05.11.20092692",
+    "rel_title": "Household transmission of COVID-19, Shenzhen, January-February 2020",
+    "rel_date": "2020-05-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20092692",
+    "rel_abs": "Coronavirus disease 2019 has led to more than three million cases globally. Since the first family cluster of COVID-19 cases identified in Shenzhen in early January, most of the local transmission occurred within household contacts. Identifying the factors associated with household transmission is of great importance to guide preventive measures.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Lan Wei",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Qiuying Lv",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Ying Wen",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Shuo Feng",
+        "author_inst": "Oxford Vaccine Group, University of Oxford"
+      },
+      {
+        "author_name": "Wei Gao",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Zhigao Chen",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Bin Cao",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Xiaoliang Wu",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Yan Lu",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Jin Zhao",
+        "author_inst": "zhaoj@szcdc.net"
+      },
+      {
+        "author_name": "Xuan Zou",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Tiejian Feng",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Benjamin J Cowling",
+        "author_inst": "The University of Hong Kong"
+      },
+      {
+        "author_name": "Shujiang Mei",
+        "author_inst": "Shenzhen Center for Disease Control and Prevention"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.05.12.20093799",
     "rel_title": "Video Consultation in Lung Transplant Recipients during the COVID-19 Pandemic",
@@ -1443450,29 +1442327,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.05.10.20097055",
-    "rel_title": "Traces of SARS-CoV-2 RNA in the Blood of COVID-19 Patients",
-    "rel_date": "2020-05-18",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.10.20097055",
-    "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third virus that caused coronavirus-related outbreaks over the past 20 years. The outbreak was first reported in December 2019 in Wuhan, China, but rapidly progressed into a pandemic of an unprecedented scale since the 1918 flu pandemic. Besides respiratory complications in COVID-19 patients, clinical characterizations of severe infection cases showed several other comorbidities, including multiple organ failure (liver, kidney, and heart) and septic shock. To better understand COVID-19 pathogenesis in different human organs, we interrogated the presence of the virus in the blood, or any of its components, which might provide a form of trafficking or hiding to the virus. By computationally analyzing high-throughput sequence data from patients with active COVID-19 infection, we found evidence of only traces of SARS-CoV-2 RNA in peripheral blood mononuclear cells (PBMC), while the virus RNA was abundant in bronchoalveolar lavage specimens from the same patients. We also devised a  viral spike-to-actin RNA normalization, as a metric to compare across various samples and minimize errors caused by intersample variability in human RNA. To the best of our knowledge, the presence of SARS-CoV-2 RNA in the PBMC of COVID-19 patients has not been reported before, and this observation could suggest immune presentation, but discounts the possibility of extensive viral infection of lymphocytes or monocytes.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Ahmed Moustafa",
-        "author_inst": "American University in Cairo"
-      },
-      {
-        "author_name": "Ramy K Aziz",
-        "author_inst": "Cairo University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.05.12.20097105",
     "rel_title": "Distributions and risks of SARS-CoV-2 in hospital outdoor environment",
@@ -1443803,6 +1442657,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.05.12.20094524",
+    "rel_title": "Perceived versus proven SARS-CoV-2 specific immune responses in health care workers",
+    "rel_date": "2020-05-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20094524",
+    "rel_abs": "There have been concerns about high rates of thus far undiagnosed SARS-CoV-2 infections in the health care system. The COVID-19 Contact (CoCo) Study follows 217 frontline healthcare professionals at a university hospital with weekly SARS-CoV-2 specific serology (IgA/IgG). Study participants estimated their personal likelihood of having had a SARS-CoV-2 infection with a mean of 20.9% (range 0 to 90%). In contrast, anti-SARS-CoV-2-IgG prevalence was about 1-2% at baseline. Regular anti-SARS-CoV-2 IgG testing of health-care professionals may aid in directing resources for protective measures and care of COVID-19 patients in the long run.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Georg MN Behrens",
+        "author_inst": "Hannover Medical School"
+      },
+      {
+        "author_name": "Anne Cossmann",
+        "author_inst": "Hannover Medical School"
+      },
+      {
+        "author_name": "Metodi V Stankov",
+        "author_inst": "Hannover Medical School"
+      },
+      {
+        "author_name": "Torsten Witte",
+        "author_inst": "Hannover Medical School"
+      },
+      {
+        "author_name": "Diana Ernst",
+        "author_inst": "Hannover Medical School"
+      },
+      {
+        "author_name": "Christine Happle",
+        "author_inst": "Hannover Medical School"
+      },
+      {
+        "author_name": "Alexandra Jablonka",
+        "author_inst": "Hannover Medical  School"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.05.12.20095885",
     "rel_title": "Cardiac Structural and Functional Characteristics in Patients with Coronavirus Disease 2019: A Serial Echocardiographic Study",
@@ -1444720,49 +1443617,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.05.11.20098673",
-    "rel_title": "Systematic Review and Meta-Analysis of Sex-Specific COVID-19 Clinical Outcomes",
-    "rel_date": "2020-05-18",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20098673",
-    "rel_abs": "To successfully mitigate the extraordinary devastation caused by the Coronavirus disease 2019 (COVID-19) pandemic, it is crucial to identify important risk factors for this disease. One such neglected health determinant is the sex of the patient. This is an essential clinical characteristic, as it can factor into a patients clinical management and preventative measures. Some clinical studies have shown disparities in the proportion between males and females that have more severe clinical outcomes or, subsequently, die from this disease. However, this association has not been unequivocally established. Thus, the purpose of this investigation was to examine the association between male sex and COVID-19 severity. We systematically reviewed the literature, identified non-randomized studies that matched predetermined selection criteria, and performed a meta-analysis to evaluate the proportion of males among four disease severity categories. Appropriate assessment strategies were implemented to assess and minimize potential biases. The results of this meta-analysis indicated that males constituted a significantly higher proportion of those who had adverse clinical outcomes and died from COVID-19. As the coronavirus spread from the East to the West, male sex remained a consistent risk factor. Our results support the establishment of the male sex as an important risk factor for this disease. Early identification and appropriate medical care for males with lab-confirmed COVID-19 may substantially change the course of clinical prognosis, resulting in greater numbers of lives saved.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Thushara Galbadage",
-        "author_inst": "Biola University"
-      },
-      {
-        "author_name": "Brent M. Peterson",
-        "author_inst": "Biola University"
-      },
-      {
-        "author_name": "Joseph Awada",
-        "author_inst": "Biola University"
-      },
-      {
-        "author_name": "Alison S. Buck",
-        "author_inst": "Biola University"
-      },
-      {
-        "author_name": "Danny A. Ramirez",
-        "author_inst": "Biola University"
-      },
-      {
-        "author_name": "Jason Wilson",
-        "author_inst": "Biola University"
-      },
-      {
-        "author_name": "Richard S. Gunasekera",
-        "author_inst": "Biola University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.05.12.20098236",
     "rel_title": "Anti-Spike, anti-Nucleocapsid and neutralizing antibodies in SARS-CoV-2 hospitalized patients and asymptomatic carriers",
@@ -1444981,6 +1443835,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.05.13.20098186",
+    "rel_title": "Excess Out-Of-Hospital Mortality and Declining Oxygen Saturation Documented by EMS During the COVID-19 Crisis in Tijuana, Mexico",
+    "rel_date": "2020-05-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20098186",
+    "rel_abs": "ObjectiveEmergency medical services (EMS) may serve as a key source of real-time data about the evolving health of COVID-19 affected populations, especially in low-and-middle-income countries (LMICs) with less rapid and reliable vital statistic registration systems. Although official COVID-19 statistics in Mexico report almost exclusively in-hospital mortality events, excess out-of-hospital mortality has been identified in other settings, including one EMS study in Italy that showed a 58% increase. EMS and hospital reports from several countries have suggested that silent hypoxemia--low oxygen saturation (SpO2) in the absence of dyspnea--is associated with COVID-19 outbreaks. It is unclear, however, how these phenomena can be generalized to LMICs. We assess how EMS data can be used in a sentinel capacity in Tijuana, a city on the Mexico-United States border with earlier exposure to COVID-19 than many LMIC settings.\n\nMethodsWe calculated numbers of weekly out-of-hospital deaths and respiratory cases seen by EMS in Tijuana, and estimate the difference between peak-epidemic rates (during April 14th-May 11th) and forecasted 2014-2019 trends. Results were compared with official COVID-19 statistics, stratified by neighborhood socioeconomic status (SES), and examined for changing demographic or clinical features, including mean (SpO2).\n\nResultsAn estimated 194.7 (95%CI: 135.5-253.9) excess out-of-hospital deaths events occurred, representing an increase of 145% (70%-338%) compared to forecasted trends. During the same window, only 8 COVID-19-positive, out-of-hospital deaths were reported in official statistics. This corresponded with a rise in respiratory cases of 274% (119%-1142%), and a drop in mean SpO2 to 77.7%, from 90.2% at baseline. The highest out-of-hospital death rates were observed in low-SES areas, although respiratory cases were more concentrated in high-SES areas.\n\nConclusionsEMS systems may play an important sentinel role in monitoring excess out-of-hospital mortality and other trends during the COVID-19 crisis in LMICs. Using EMS data, we observed increases in out-of-hospital deaths in Tijuana that were nearly threefold greater magnitude than increases reported using EMS data in Italy. Increased testing in out-of-hospital settings may be required to determine if excess mortality is being driven by COVID-19 infection, health system saturation, or patient avoidance of healthcare. We also found evidence of worsening rates of hypoxemia among respiratory patients seen by EMS, suggesting a rise in silent hypoxemia, which should be met with increased detection and clinical management efforts. Finally, we observed that social disparities in out-of-hospital death that warrant monitoring and amelioration.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Joseph Friedman",
+        "author_inst": "Center for Social Medicine, University of California, Los Angeles (UCLA), USA"
+      },
+      {
+        "author_name": "Alheli Calderon-Villarreal",
+        "author_inst": "Academia Mexicana de la Salud, Tijuana, Mexico"
+      },
+      {
+        "author_name": "Ietza Bojorquez",
+        "author_inst": "El Colegio de la Frontera Norte, Tijuana, Mexico"
+      },
+      {
+        "author_name": "Carlos Vera Hernandez",
+        "author_inst": "Mexican Red Cross, Tijuana, Mexico"
+      },
+      {
+        "author_name": "David Schriger",
+        "author_inst": "Department of Emergency Medicine, UCLA"
+      },
+      {
+        "author_name": "Eva Tovar Hirashima",
+        "author_inst": "Mexican Red Cross, Tijuana, Mexico"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "emergency medicine"
+  },
   {
     "rel_doi": "10.1101/2020.05.12.20099135",
     "rel_title": "Covid-19 by Race and Ethnicity: A National Cohort Study of 6 Million United States Veterans",
@@ -1445986,61 +1444879,6 @@
     "type": "new results",
     "category": "genomics"
   },
-  {
-    "rel_doi": "10.1101/2020.05.12.091256",
-    "rel_title": "The Host Cell ViroCheckpoint: Identification and Pharmacologic Targeting of Novel Mechanistic Determinants of Coronavirus-Mediated Hijacked Cell States",
-    "rel_date": "2020-05-17",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.12.091256",
-    "rel_abs": "Most antiviral agents are designed to target virus-specific proteins and mechanisms rather than the host cell proteins that are critically dysregulated following virus-mediated reprogramming of the host cell transcriptional state. To overcome these limitations, we propose that elucidation and pharmacologic targeting of host cell Master Regulator proteins--whose aberrant activities govern the reprogramed state of infected-coronavirus cells--presents unique opportunities to develop novel mechanism-based therapeutic approaches to antiviral therapy, either as monotherapy or as a complement to established treatments. Specifically, we propose that a small module of host cell Master Regulator proteins (ViroCheckpoint) is hijacked by the virus to support its efficient replication and release. Conventional methodologies are not well suited to elucidate these potentially targetable proteins. By using the VIPER network-based algorithm, we successfully interrogated 12h, 24h, and 48h signatures from Calu-3 lung adenocarcinoma cells infected with SARS-CoV, to elucidate the time-dependent reprogramming of host cells and associated Master Regulator proteins. We used the NYS CLIA-certified Darwin OncoTreat algorithm, with an existing database of RNASeq profiles following cell perturbation with 133 FDA-approved and 195 late-stage experimental compounds, to identify drugs capable of virtually abrogating the virus-induced Master Regulator signature. This approach to drug prioritization and repurposing can be trivially extended to other viral pathogens, including SARS-CoV-2, as soon as the relevant infection signature becomes available.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Pasquale Laise",
-        "author_inst": "DarwinHealth, Inc"
-      },
-      {
-        "author_name": "Gideon Bosker",
-        "author_inst": "DarwinHealth, Inc"
-      },
-      {
-        "author_name": "Xiaoyun Sun",
-        "author_inst": "DarwinHealth, Inc"
-      },
-      {
-        "author_name": "Yao Shen",
-        "author_inst": "DarwinHealth, Inc"
-      },
-      {
-        "author_name": "Eugene F Douglass",
-        "author_inst": "Columbia University"
-      },
-      {
-        "author_name": "Charles Karan",
-        "author_inst": "Columbia University"
-      },
-      {
-        "author_name": "Ronald B Realubit",
-        "author_inst": "Columbia University"
-      },
-      {
-        "author_name": "Sergey Pampou",
-        "author_inst": "Columbia University"
-      },
-      {
-        "author_name": "Andrea Califano",
-        "author_inst": "Columbia University"
-      },
-      {
-        "author_name": "Mariano J Alvarez",
-        "author_inst": "DarwinHealth Inc"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "new results",
-    "category": "systems biology"
-  },
   {
     "rel_doi": "10.1101/2020.05.16.099499",
     "rel_title": "SARS-CoV-2 amino acid substitutions widely spread in the human population are mainly located in highly conserved segments of the structural proteins",
@@ -1446331,6 +1445169,41 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2020.05.16.099747",
+    "rel_title": "REMBRANDT: A high-throughput barcoded sequencing approach for COVID-19 screening.",
+    "rel_date": "2020-05-17",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.16.099747",
+    "rel_abs": "The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), also known as 2019 novel coronavirus (2019-nCoV), is a highly infectious RNA virus. A still-debated percentage of patients develop coronavirus disease 2019 (COVID-19) after infection, whose symptoms include fever, cough, shortness of breath and fatigue. Acute and life-threatening respiratory symptoms are experienced by 10-20% of symptomatic patients, particularly those with underlying medical conditions that includes diabetes, COPD and pregnancy. One of the main challenges in the containment of COVID-19 is the identification and isolation of asymptomatic/pre-symptomatic individuals. As communities re-open, large numbers of people will need to be tested and contact-tracing of positive patients will be required to prevent additional waves of infections and enable the continuous monitoring of the viral loads COVID-19 positive patients. A number of molecular assays are currently in clinical use to detect SARS-CoV-2. Many of them can accurately test hundreds or even thousands of patients every day. However, there are presently no testing platforms that enable more than 10,000 tests per day. Here, we describe the foundation for the REcombinase Mediated BaRcoding and AmplificatioN Diagnostic Tool (REMBRANDT), a high-throughput Next Generation Sequencing-based approach for the simultaneous screening of over 100,000 samples per day. The REMBRANDT protocol includes direct two-barcoded amplification of SARS-CoV-2 and control amplicons using an isothermal reaction, and the downstream library preparation for Illumina sequencing and bioinformatics analysis. This protocol represents a potentially powerful approach for community screening, a major bottleneck for testing samples from a large patient population for COVID-19.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Dario Palmieri",
+        "author_inst": "The Ohio State University"
+      },
+      {
+        "author_name": "Jalal K Siddiqui",
+        "author_inst": "The Ohio State University"
+      },
+      {
+        "author_name": "Anne Gardner",
+        "author_inst": "The Ohio State University"
+      },
+      {
+        "author_name": "Richard Fishel",
+        "author_inst": "The Ohio State University"
+      },
+      {
+        "author_name": "Wayne Miles",
+        "author_inst": "The Ohio State University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "new results",
+    "category": "molecular biology"
+  },
   {
     "rel_doi": "10.1101/2020.05.16.099317",
     "rel_title": "Distinct conformational states of SARS-CoV-2 spike protein",
@@ -1447256,81 +1446129,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.05.13.20088732",
-    "rel_title": "MRI of the lungs in patients with COVID-19: clinical case",
-    "rel_date": "2020-05-16",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20088732",
-    "rel_abs": "During the pandemic of COVID-19, computed tomography showed its effectiveness in diagnosis of coronavirus infection. However, ionizing radiation during CT studies causes concern for patients who require dynamic observation, as well as for examination of children and young people. For this retrospective study, we included 15 suspected for COVID-19 patients who were hospitalized in April 2020, Russia. There were 4 adults with positive polymerase chain reaction (PCR) test for COVID-19. All patients underwent MRI examinations using MR-LUND PROTOCOL: Single-shot Fast Spin Echo (SSFSE), LAVA 3D and IDEAL 3D, EPI diffusion-weighted imaging (DWI) and Fast Spin Echo (FSE) T2WI without using respiratory or any other trigger. 3 patients also had CT scan performed. In 5 (33,3%) patients, detected lesioins were visualized on T2WI and DWI simultaneously. At the same time, 4 (26.7%) patients revealed lung tissue changes only on T2WI (P(McNemar)= 0,125, OR= 0,00 (95%), kappa=0,500). Pulmonary changes on MRI were also analyzed depending on their localization. In those patients who had CT scan, the changes were comparable to MRI. MRI of the lungs can detect features of viral pneumonia and assess severity of lung damage. The method can be used to diagnose COVID-19. These data may be applicable for interpreting other studies, such as thoracic spine MRI, detecting signs of viral pneumonia of asymptomatic patients. The current study was limited by a small sample size and absence of chest CT scans of all patients.",
-    "rel_num_authors": 15,
-    "rel_authors": [
-      {
-        "author_name": "Yuriy Vasilev",
-        "author_inst": "Research and Practical Clinical Center for Diagnostics and Telemedicine Technologies of the Moscow Health Care Department, Moscow, Russia; Imed Clinic, Grozny, "
-      },
-      {
-        "author_name": "Kristina Sergunova",
-        "author_inst": "Research and Practical Clinical Center for Diagnostics and Telemedicine Technologies of the Moscow Health Care Department, Moscow, Russia"
-      },
-      {
-        "author_name": "Alexander Bazhin",
-        "author_inst": "Research and Practical Clinical Center for Diagnostics and Telemedicine Technologies of the Moscow Health Care Department, Moscow, Russia; Imed Clinic, Grozny, "
-      },
-      {
-        "author_name": "Amir Masri",
-        "author_inst": "Imed Clinic, Grozny, Chechen Republic, Russia"
-      },
-      {
-        "author_name": "Yulia Vasileva",
-        "author_inst": "Imed Clinic, Grozny, Chechen Republic, Russia; A.I. Evdokimov Moscow State University of Medicine and Dentistry, Moscow, Russia"
-      },
-      {
-        "author_name": "Dmitry Semenov",
-        "author_inst": "Research and Practical Clinical Center for Diagnostics and Telemedicine Technologies"
-      },
-      {
-        "author_name": "Nikita Kudryavtsev",
-        "author_inst": "Research and Practical Clinical Center for Diagnostics and Telemedicine Technologies of the Moscow Health Care Department, Moscow, Russia"
-      },
-      {
-        "author_name": "Olga Panina",
-        "author_inst": "Research and Practical Clinical Center for Diagnostics and Telemedicine Technologies of the Moscow Health Care Department, Moscow, Russia"
-      },
-      {
-        "author_name": "Anna Khoruzhaya",
-        "author_inst": "Research and Practical Clinical Center for Diagnostics and Telemedicine Technologies of the Moscow Health Care Department, Moscow, Russia"
-      },
-      {
-        "author_name": "Victoria Znichenko",
-        "author_inst": "Research and Practical Clinical Center for Diagnostics and Telemedicine Technologies of the Moscow Health Care Department, Moscow, Russia"
-      },
-      {
-        "author_name": "Ekaterina Akhmad",
-        "author_inst": "Research and Practical Clinical Center for Diagnostics and Telemedicine Technologies of the Moscow Health Care Department, Moscow, Russia"
-      },
-      {
-        "author_name": "Alexey Petraikin",
-        "author_inst": "Research and Practical Clinical Center for Diagnostics and Telemedicine Technologies of the Moscow Health Care Department, Moscow, Russia"
-      },
-      {
-        "author_name": "Anton Vladzymyrskyy",
-        "author_inst": "Research and Practical Clinical Center for Diagnostics and Telemedicine Technologies of the Moscow Health Care Department, Moscow, Russia"
-      },
-      {
-        "author_name": "Aslanbek Midaev",
-        "author_inst": "Imed Clinic, Grozny, Chechen Republic, Russia"
-      },
-      {
-        "author_name": "Sergey Morozov",
-        "author_inst": "Research and Practical Clinical Center for Diagnostics and Telemedicine Technologies of the Moscow Health Care Department, Moscow, Russia"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "radiology and imaging"
-  },
   {
     "rel_doi": "10.1101/2020.05.16.097238",
     "rel_title": "Mechanistic modeling of the SARS-CoV-2 and immune system interplay unravels design principles for diverse clinicopathological outcomes",
@@ -1447557,6 +1446355,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.05.12.20099481",
+    "rel_title": "The Evaluation of Deep Neural Networks and X-Ray as a Practical Alternative for Diagnosis and Management of COVID-19",
+    "rel_date": "2020-05-16",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20099481",
+    "rel_abs": "High-resolution computed tomography radiology is a critical tool in the diagnosis and management of COVID-19 infection; however, in smaller clinics around the world, there is a shortage of radiologists available to analyze these images. In this paper, we compare the performance of 16 available deep learning algorithms to help identify COVID19. We utilize an already existing diagnostic technology (X-ray) and an already existing neural network (ResNet-50) to diagnose COVID-19. Our approach eliminates the extra time and resources needed to develop new technology and associated algorithm, thus aiding the front-line in the race against the COVID-19 pandemic. Results show that ResNet-50 is the optimal pretrained neural network for the detection of COVID-19, using three different cross-validation ratios, based on training time, accuracy, and network size. We also present a custom visualization of the results that can be used to highlight important visual biomarkers of the disease and disease progression.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Mohamed Elgendi",
+        "author_inst": "University of British Columbia"
+      },
+      {
+        "author_name": "Rich Fletcher",
+        "author_inst": "Massachusetts Institute of Technology"
+      },
+      {
+        "author_name": "Newton Howard",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Carlo Menon",
+        "author_inst": "Simon FraserUniversity"
+      },
+      {
+        "author_name": "Rabab Ward",
+        "author_inst": "University of British Columbia"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.05.13.20099978",
     "rel_title": "A Sparse Gaussian Network Model for Prediction the Growth Trend of COVID-19 Overseas Import Case: When can Hong Kong Lift the International Traffic Blockad?",
@@ -1448738,41 +1447571,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.05.13.20100982",
-    "rel_title": "Correlation between PCR Examination Rate among the Population and the Containment of Pandemic of COVID-19",
-    "rel_date": "2020-05-16",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20100982",
-    "rel_abs": "We investigated the relation between PCR examination rate among population and the success of containment of COVID-19 for each country. Although there was moderate correlation, multiple regression revealed that the success of containment was solely explained by Gross Domestic Product per capita (GDP), which may well be related to the strict compliance to social distancing. Close inspection of individual countries supported this hypothesis. The social distancing must be the largest factor to achieve containment, and the contribution of broad PCR tests is small.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Masahiro Sonoo",
-        "author_inst": "Teikyo University School of Medicine"
-      },
-      {
-        "author_name": "Masashi Idogawa",
-        "author_inst": "Sapporo Medical University School of Medicine"
-      },
-      {
-        "author_name": "Takamichi Kanbayashi",
-        "author_inst": "Teikyo University School of Medicine"
-      },
-      {
-        "author_name": "Takayoshi Shimohata",
-        "author_inst": "Gifu University Graduate School of Medicine"
-      },
-      {
-        "author_name": "Hideyuki Hayashi",
-        "author_inst": "Osaka Medical College"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.05.14.20102491",
     "rel_title": "COVID-19 infection results in alterations of the kynurenine pathway and fatty acid metabolism that correlate with IL-6 levels and renal status",
@@ -1449131,6 +1447929,49 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2020.05.14.095620",
+    "rel_title": "Unveiling diffusion pattern and structural impact of the most invasive SARS-CoV-2 spike mutation",
+    "rel_date": "2020-05-15",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.14.095620",
+    "rel_abs": "Starting in Wuhan, China, SARS-CoV-2 epidemics quickly propagated worldwide in less than three months, geographically sorting genomic variants in newly established propagules of infections. Stochasticity in transmission within and between countries and/or actual advantage in virus transmissibility could explain the high frequency reached by some genomic variants during the course of the outbreak.\n\nUsing a suite of statistical, population genetics, and theoretical approaches, we show that the globally most represented spike protein variant (i.e., the G clade, A [-&gt;] G nucleotide change at genomic position 23,403; D [-&gt;] G amino acid change at spike protein position 614) i) underwent a significant demographic expansion in most countries not explained by stochastic effects or enhanced pathogenicity; ii) affects the spike S1/S2 furin-like site increasing its conformational plasticity (short range effect), and iii) modifies the internal motion of the receptor-binding domain affecting its cross-connection with other functional domains (long-range effect).\n\nOur study unambiguously links the spread of the G614 with a non-random process, and we hypothesize that this process is related to the selective advantage produced by a specific structural modification of the spike protein. We conclude that the different conformation of the S1/S2 proteolytic site is at the basis of the higher transmission rate of this invasive SARS-CoV-2 variant, and provide structural information to guide the design of selective and efficient drugs.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Emiliano Trucchi",
+        "author_inst": "Department of Life and Environmental Science, Marche Polytechnic University, Via Brecce Bianche, 60131, Ancona, Italy"
+      },
+      {
+        "author_name": "Paolo Gratton",
+        "author_inst": "Department of Biology, University of Rome Tor Vergata, Via Cracovia, 1, 00133, Roma, Italy"
+      },
+      {
+        "author_name": "Fabrizio Mafessoni",
+        "author_inst": "Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz, 6, 04103, Leipzig, Germany"
+      },
+      {
+        "author_name": "Stefano Motta",
+        "author_inst": "Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy"
+      },
+      {
+        "author_name": "Francesco Cicconardi",
+        "author_inst": "School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK"
+      },
+      {
+        "author_name": "Giorgio Bertorelle",
+        "author_inst": "Department of Life Sciences and Biotechnology, University of Ferrara, Via Luigi Borsari 46, 44121, Ferrara, Italy"
+      },
+      {
+        "author_name": "Daniele Di Marino",
+        "author_inst": "Department of Life and Environmental Sciences, New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 6013"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "evolutionary biology"
+  },
   {
     "rel_doi": "10.1101/2020.05.14.096131",
     "rel_title": "The Red Queen's Crown: an evolutionary arms race between coronaviruses and mammalian species reflected in positive selection of the ACE2 receptor among many species",
@@ -1450368,33 +1449209,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.05.09.20096370",
-    "rel_title": "Chest Computed Tomography Findings in Asymptomatic Patients with COVID-19",
-    "rel_date": "2020-05-15",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.09.20096370",
-    "rel_abs": "BackgroundLittle is known about the damage to the respiratory system in asymptomatic patients with coronavirus disease (COVID-19).\n\nObjectiveHerein, we evaluated the findings of chest computed tomography (CT) and radiography in patients with COVID-19 who were asymptomatic.\n\nMethodsWe retrospectively investigated patients with a confirmed diagnosis of COVID-19 but who did not show any symptoms. Among the 139 patients with COVID-19 who were hospitalized, 10 (7.2%) were asymptomatic. Their chest CT and radiographic findings were analyzed.\n\nResultsIn the results, all patients (100%) had ground glass opacity (GGO) on chest CT. Further, the GGO lesions were predominantly distributed peripherally and posteriorly in all patients. In 9 (90%) patients, the GGO lesions were combined with reticular opacity. Air-bronchogram due to bronchiolectasis surrounded by GGO was observed in 8 patients (80%). Additionally, the lung lesions were dominant on the right side in all patients.\n\nConclusionsIn conclusion, considering our results that the lung is affected in asymptomatic patients, it will be necessary to extend the indications of COVID-19 testing for effective management of COVID-19 during the pandemic.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Min Cheol Chang",
-        "author_inst": "Yeungnam University Hospital"
-      },
-      {
-        "author_name": "Jian Hur",
-        "author_inst": "Yeungnam University Hospital"
-      },
-      {
-        "author_name": "Donghwi Park",
-        "author_inst": "Ulsan University Hospital"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.05.15.077313",
     "rel_title": "CoV-AbDab: the Coronavirus Antibody Database",
@@ -1450708,6 +1449522,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "cardiovascular medicine"
   },
+  {
+    "rel_doi": "10.1101/2020.05.15.097741",
+    "rel_title": "Analysis of SARS-CoV-2 RNA-Sequences by Interpretable Machine Learning Models",
+    "rel_date": "2020-05-15",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.15.097741",
+    "rel_abs": "We present an approach to investigate SARS-CoV-2 virus sequences based on alignment-free methods for RNA sequence comparison. In particular, we verify a given clustering result for the GISAID data set, which was obtained analyzing the molecular differences in coronavirus populations by phylogenetic trees. For this purpose, we use alignment-free dissimilarity measures for sequences and combine them with learning vector quantization classifiers for virus type discriminant analysis and classification. Those vector quantizers belong to the class of interpretable machine learning methods, which, on the one hand side provide additional knowledge about the classification decisions like discriminant feature correlations, and on the other hand can be equipped with a reject option. This option gives the model the property of self controlled evidence if applied to new data, i.e. the models refuses to make a classification decision, if the model evidence for the presented data is not given. After training such a classifier for the GISAID data set, we apply the obtained classifier model to another but unlabeled SARS-CoV-2 virus data set. On the one hand side, this allows us to assign new sequences to already known virus types and, on the other hand, the rejected sequences allow speculations about new virus types with respect to nucleotide base mutations in the viral sequences.\n\nAuthor summaryThe currently emerging global disease COVID-19 caused by novel SARS-CoV-2 viruses requires all scientific effort to investigate the development of the viral epidemy, the properties of the virus and its types. Investigations of the virus sequence are of special interest. Frequently, those are based on mathematical/statistical analysis. However, machine learning methods represent a promising alternative, if one focuses on interpretable models, i.e. those that do not act as black-boxes. Doing so, we apply variants of Learning Vector Quantizers to analyze the SARS-CoV-2 sequences. We encoded the sequences and compared them in their numerical representations to avoid the computationally costly comparison based on sequence alignments. Our resulting model is interpretable, robust, efficient, and has a self-controlling mechanism regarding the applicability to data. This framework was applied to two data sets concerning SARS-CoV-2. We were able to verify previously published virus type findings for one of the data sets by training our model to accurately identify the virus type of sequences. For sequences without virus type information (second data set), our trained model can predict them. Thereby, we observe a new scattered spreading of the sequences in the data space which probably is caused by mutations in the viral sequences.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Thomas Villmann",
+        "author_inst": "University of Applied Sciences Mittweida"
+      },
+      {
+        "author_name": "Marika Kaden",
+        "author_inst": "Hochschule Mittweida"
+      },
+      {
+        "author_name": "Katrin  Sophie Bohnsack",
+        "author_inst": "Hochschule Mittweida"
+      },
+      {
+        "author_name": "Mirko Weber",
+        "author_inst": "Hochschule Mittweida"
+      },
+      {
+        "author_name": "Mateusz Kudla",
+        "author_inst": "Hochschule Mittweida"
+      },
+      {
+        "author_name": "Kaja Gutowska",
+        "author_inst": "Politechnika Poznanska"
+      },
+      {
+        "author_name": "Jacek Blazewicz",
+        "author_inst": "Politechnika Poznanska"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "new results",
+    "category": "bioinformatics"
+  },
   {
     "rel_doi": "10.1101/2020.05.09.20096834",
     "rel_title": "Triage tool for suspected COVID-19 patients in the emergency room: AIFELL score",
@@ -1451977,37 +1450834,6 @@
     "type": "new results",
     "category": "genomics"
   },
-  {
-    "rel_doi": "10.1101/2020.05.14.095224",
-    "rel_title": "Two mutations P/L and Y/C in SARS-CoV-2 helicase domain exist together and influence helicase RNA binding",
-    "rel_date": "2020-05-15",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.14.095224",
-    "rel_abs": "RNA helicases play pivotal role in RNA replication by catalysing the unwinding of complex RNA duplex structures into single strands in ATP/NTP dependent manner. SARS coronavirus 2 (SARS-CoV-2) is a single stranded positive sense RNA virus belonging to the family Coronaviridae. The viral RNA encodes non structural protein Nsp13 or the viral helicase protein that helps the viral RNA dependent RNA polymerase (RdRp) to execute RNA replication by unwinding the RNA duplexes. In this study we identified a novel mutation at position 541of the helicase where the tyrosine (Y) got substituted with cytosine (C). We found that Y541C is a destabilizing mutation increasing the molecular flexibility and leading to decreased affinity of helicase binding with RNA. Earlier we had reported a mutation P504L in the helicase protein for which had not performed RNA binding study. Here we report that P504L mutation leads to increased affinity of helicase RNA interaction. So, both these mutations have opposite effects on RNA binding. Moreover, we found a significant fraction of isolate population where both P504L and Y541C mutations were co-existing.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Feroza Begum",
-        "author_inst": "CSIR-Indian Institute of Chemical Biology"
-      },
-      {
-        "author_name": "Arup Kumar Banerjee",
-        "author_inst": "North Bengal Medical College and Hospital"
-      },
-      {
-        "author_name": "Prem Prakash Tripathi",
-        "author_inst": "CSIR-Indian Institute of Chemical Biology"
-      },
-      {
-        "author_name": "UPASANA RAY",
-        "author_inst": "CSIR-Indian Institute of Chemical Biology"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.05.15.096719",
     "rel_title": "IgA MAb blocks SARS-CoV-2 Spike-ACE2 interaction providing mucosal immunity",
@@ -1452518,6 +1451344,165 @@
     "type": "new results",
     "category": "neuroscience"
   },
+  {
+    "rel_doi": "10.1101/2020.05.15.096511",
+    "rel_title": "Broad sarbecovirus neutralizing antibodies define a key site of vulnerability on the SARS-CoV-2 spike protein",
+    "rel_date": "2020-05-15",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.15.096511",
+    "rel_abs": "Broadly protective vaccines against known and pre-emergent coronaviruses are urgently needed. Critical to their development is a deeper understanding of cross-neutralizing antibody responses induced by natural human coronavirus (HCoV) infections. Here, we mined the memory B cell repertoire of a convalescent SARS donor and identified 200 SARS-CoV-2 binding antibodies that target multiple conserved sites on the spike (S) protein. A large proportion of the antibodies display high levels of somatic hypermutation and cross-react with circulating HCoVs, suggesting recall of pre-existing memory B cells (MBCs) elicited by prior HCoV infections. Several antibodies potently cross-neutralize SARS-CoV, SARS-CoV-2, and the bat SARS-like virus WIV1 by blocking receptor attachment and inducing S1 shedding. These antibodies represent promising candidates for therapeutic intervention and reveal a new target for the rational design of pan-sarbecovirus vaccines.",
+    "rel_num_authors": 36,
+    "rel_authors": [
+      {
+        "author_name": "Anna Z Wec",
+        "author_inst": "Adimab LLC, Lebanon, NH 03766, USA"
+      },
+      {
+        "author_name": "Daniel Wrapp",
+        "author_inst": "Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA"
+      },
+      {
+        "author_name": "Andrew S Herbert",
+        "author_inst": "U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA"
+      },
+      {
+        "author_name": "Daniel P Maurer",
+        "author_inst": "Adimab LLC, Lebanon, NH 03766, USA"
+      },
+      {
+        "author_name": "Denise Haslwanter",
+        "author_inst": "Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA"
+      },
+      {
+        "author_name": "Mrunal Sakharkar",
+        "author_inst": "Adimab LLC, Lebanon, NH 03766, USA"
+      },
+      {
+        "author_name": "Rohit K Jangra",
+        "author_inst": "Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA"
+      },
+      {
+        "author_name": "M. Eugenia Dieterle",
+        "author_inst": "Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA"
+      },
+      {
+        "author_name": "Asparouh Lilov",
+        "author_inst": "Adimab LLC, Lebanon, NH 03766, USA"
+      },
+      {
+        "author_name": "Deli Huang",
+        "author_inst": "Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA"
+      },
+      {
+        "author_name": "Longping V Tse",
+        "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA."
+      },
+      {
+        "author_name": "Nicole V Johnson",
+        "author_inst": "Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA"
+      },
+      {
+        "author_name": "Ching-Lin Hsieh",
+        "author_inst": "Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA"
+      },
+      {
+        "author_name": "Nianshuang Wang",
+        "author_inst": "Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA"
+      },
+      {
+        "author_name": "Juergen H Nett",
+        "author_inst": "Adimab LLC, Lebanon, NH 03766, USA"
+      },
+      {
+        "author_name": "Elizabeth Champney",
+        "author_inst": "Adimab LLC, Lebanon, NH 03766, USA"
+      },
+      {
+        "author_name": "Irina Burnina",
+        "author_inst": "Adimab LLC, Lebanon, NH 03766, USA"
+      },
+      {
+        "author_name": "Michael Brown",
+        "author_inst": "Adimab LLC, Lebanon, NH 03766, USA"
+      },
+      {
+        "author_name": "Shu Lin",
+        "author_inst": "Adimab LLC, Lebanon, NH 03766, USA"
+      },
+      {
+        "author_name": "Melanie Sinclair",
+        "author_inst": "Adimab LLC, Lebanon, NH 03766, USA"
+      },
+      {
+        "author_name": "Carl Johnson",
+        "author_inst": "Adimab LLC, Lebanon, NH 03766, USA"
+      },
+      {
+        "author_name": "Sarat Pudi",
+        "author_inst": "Adimab LLC, Lebanon, NH 03766, USA"
+      },
+      {
+        "author_name": "Robert Bortz III",
+        "author_inst": "Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA"
+      },
+      {
+        "author_name": "Ariel S Wirchnianski",
+        "author_inst": "Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA"
+      },
+      {
+        "author_name": "Ethan Laudermilch",
+        "author_inst": "Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA"
+      },
+      {
+        "author_name": "Catalina Florez",
+        "author_inst": "Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA"
+      },
+      {
+        "author_name": "J. Maximilian Fels",
+        "author_inst": "Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA"
+      },
+      {
+        "author_name": "Barney S Graham",
+        "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA"
+      },
+      {
+        "author_name": "David Nemazee",
+        "author_inst": "Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA"
+      },
+      {
+        "author_name": "Dennis R Burton",
+        "author_inst": "Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA"
+      },
+      {
+        "author_name": "Ralph S Baric",
+        "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Departments of Microbiology and Immunology, The Univers"
+      },
+      {
+        "author_name": "James E Voss",
+        "author_inst": "Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA"
+      },
+      {
+        "author_name": "Kartik Chandran",
+        "author_inst": "Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, USA"
+      },
+      {
+        "author_name": "John M Dye",
+        "author_inst": "U.S. Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA"
+      },
+      {
+        "author_name": "Jason S McLellan",
+        "author_inst": "Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA"
+      },
+      {
+        "author_name": "Laura M Walker",
+        "author_inst": "Adimab LLC, Lebanon, NH 03766, USA"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "immunology"
+  },
   {
     "rel_doi": "10.1101/2020.05.15.098731",
     "rel_title": "Favipiravir strikes the SARS-CoV-2 at its Achilles heel, the RNA polymerase",
@@ -1453835,41 +1452820,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "primary care research"
   },
-  {
-    "rel_doi": "10.1101/2020.05.11.20097907",
-    "rel_title": "Online COVID-19 diagnosis with chest CT images: Lesion-attention deep neural networks",
-    "rel_date": "2020-05-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20097907",
-    "rel_abs": "Chest computed tomography (CT) scanning is one of the most important technologies for COVID-19 diagnosis and disease monitoring, particularly for early detection of coronavirus. Recent advancements in computer vision motivate more concerted efforts in developing AI-driven diagnostic tools to accommodate the enormous demands for the COVID-19 diagnostic tests globally. To help alleviate burdens on medical systems, we develop a lesion-attention deep neural network (LA-DNN) to predict COVID-19 positive or negative with a richly annotated chest CT image dataset. Based on the textual radiological report accompanied with each CT image, we extract two types of important information for the annotations: One is the indicator of a positive or negative case of COVID-19, and the other is the description of five lesions on the CT images associated with the positive cases. The proposed data-efficient LA-DNN model focuses on the primary task of binary classification for COVID-19 diagnosis, while an auxiliary multi-label learning task is implemented simultaneously to draw the models attention to the five lesions associated with COVID-19. The joint task learning process makes it a highly sample-efficient deep neural network that can learn COVID-19 radiology features more effectively with limited but high-quality, rich-information samples. The experimental results show that the area under the curve (AUC) and sensitivity (recall), precision, and accuracy for COVID-19 diagnosis are 94.0%, 88.8%, 87.9%, and 88.6% respectively, which reach the clinical standards for practical use. A free online system is currently alive for fast diagnosis using CT images at the website https://www.covidct.cn/, and all codes and datasets are freely accessible at our github address.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Bin Liu",
-        "author_inst": "Southwestern University of Finance and Economics"
-      },
-      {
-        "author_name": "Xiaoxue Gao",
-        "author_inst": "Southwestern University of Finance and Economics"
-      },
-      {
-        "author_name": "Mengshuang He",
-        "author_inst": "Southwestern Unviersity of Finance and Economics"
-      },
-      {
-        "author_name": "Fengmao Lv",
-        "author_inst": "Southwestern University of Finance and Economics"
-      },
-      {
-        "author_name": "Guosheng Yin",
-        "author_inst": "The University of Hong Kong"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "radiology and imaging"
-  },
   {
     "rel_doi": "10.1101/2020.05.11.20097808",
     "rel_title": "Prevalence of Hospital PCR Confirmed Covid-19 Cases in Patients with Chronic Inflammatory and Autoimmune Rheumatic Diseases",
@@ -1454116,6 +1453066,41 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2020.05.13.093971",
+    "rel_title": "Insights into molecular evolution recombination of pandemic SARS-CoV-2 using Saudi Arabian sequences",
+    "rel_date": "2020-05-14",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.13.093971",
+    "rel_abs": "The recently emerged SARS-CoV-2 (Coronaviridae; Betacoronavirus) is the underlying cause of COVID-19 disease. Here we assessed SARS-CoV2 from the Kingdom of Saudi Arabia alongside sequences of SARS-CoV, bat SARS-like CoVs and MERS-CoV, the latter currently detected in this region. Phylogenetic analysis, natural selection investigation and genome recombination analysis were performed. Our analysis showed that all Saudi SARS-CoV-2 sequences are of the same origin and closer proximity to bat SARS-like CoVs, followed by SARS-CoVs, however quite distant to MERS-CoV. Moreover, genome recombination analysis revealed two recombination events between SARS-CoV-2 and bat SARS-like CoVs. This was further assessed by S gene recombination analysis. These recombination events may be relevant to the emergence of this novel virus. Moreover, positive selection pressure was detected between SARS-CoV-2, bat SL-CoV isolates and human SARS-CoV isolates. However, the highest positive selection occurred between SARS-CoV-2 isolates and 2 bat-SL-CoV isolates (Bat-SL-RsSHC014 and Bat-SL-CoVZC45). This further indicates that SARS-CoV-2 isolates were adaptively evolved from bat SARS-like isolates, and that a virus with originating from bats triggered this pandemic. This study thuds sheds further light on the origin of this virus.\n\nAUTHOR SUMMARYThe emergence and subsequent pandemic of SARS-CoV-2 is a unique challenge to countries all over the world, including Saudi Arabia where cases of the related MERS are still being reported. Saudi SARS-CoV-2 sequences were found to be likely of the same or similar origin. In our analysis, SARS-CoV-2 were more closely related to bat SARS-like CoVs rather than to MERS-CoV (which originated in Saudi Arabia) or SARS-CoV, confirming other phylogenetic efforts on this pathogen. Recombination and positive selection analysis further suggest that bat coronaviruses may be at the origin of SARS-CoV-2 sequences. The data shown here give hints on the origin of this virus and may inform efforts on transmissibility, host adaptation and other biological aspects of this virus.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Islam Nour",
+        "author_inst": "King Saud University"
+      },
+      {
+        "author_name": "Ibrahim  O. Alanazi",
+        "author_inst": "King Abdulaziz City for Science And Technology"
+      },
+      {
+        "author_name": "Atif Hanif",
+        "author_inst": "King Saud University"
+      },
+      {
+        "author_name": "Alain Kohl",
+        "author_inst": "University of Glasgow"
+      },
+      {
+        "author_name": "Saleh  A Eifan",
+        "author_inst": "King Saud University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2020.05.13.093658",
     "rel_title": "Evolutionary arms race between virus and host drives genetic diversity in bat SARS related coronavirus spike genes",
@@ -1455189,61 +1454174,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2020.05.12.091397",
-    "rel_title": "Origin of Novel Coronavirus (COVID-19): A Computational Biology Study using Artificial Intelligence",
-    "rel_date": "2020-05-13",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.12.091397",
-    "rel_abs": "Origin of the COVID-19 virus (SARS-CoV-2) has been intensely debated in the scientific community since the first infected cases were detected in December 2019. The disease has caused a global pandemic, leading to deaths of thousands of people across the world and thus finding origin of this novel coronavirus is important in responding and controlling the pandemic. Recent research results suggest that bats or pangolins might be the hosts for SARS-CoV-2 based on comparative studies using its genomic sequences. This paper investigates the SARS-CoV-2 origin by using artificial intelligence (AI) and raw genomic sequences of the virus. More than 300 genome sequences of COVID-19 infected cases collected from different countries are explored and analysed using unsupervised clustering methods. The results obtained from various AI-enabled experiments using clustering algorithms demonstrate that all examined SARS-CoV-2 genomes belong to a cluster that also contains bat and pangolin coronavirus genomes. This provides evidence strongly supporting scientific hypotheses that bats and pangolins are probable hosts for SARS-CoV-2. At the whole genome analysis level, our findings also indicate that bats are more likely the hosts for the COVID-19 virus than pangolins.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Thanh Thi Nguyen",
-        "author_inst": "Deakin University"
-      },
-      {
-        "author_name": "Mohamed Abdelrazek",
-        "author_inst": "Deakin University"
-      },
-      {
-        "author_name": "Dung Tien Nguyen",
-        "author_inst": "Deakin University"
-      },
-      {
-        "author_name": "Sunil Aryal",
-        "author_inst": "Deakin University"
-      },
-      {
-        "author_name": "Duc Thanh Nguyen",
-        "author_inst": "Deakin University"
-      },
-      {
-        "author_name": "Sandeep Reddy",
-        "author_inst": "Deakin University"
-      },
-      {
-        "author_name": "Quoc Viet Hung Nguyen",
-        "author_inst": "Griffith University"
-      },
-      {
-        "author_name": "Amin Khatami",
-        "author_inst": "Deakin University"
-      },
-      {
-        "author_name": "Edbert B. Hsu",
-        "author_inst": "Johns Hopkins University"
-      },
-      {
-        "author_name": "Samuel Yang",
-        "author_inst": "Stanford University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "new results",
-    "category": "bioinformatics"
-  },
   {
     "rel_doi": "10.1101/2020.05.08.20094755",
     "rel_title": "Beneficial effect of corticosteroids in severe COVID-19 pneumonia: a propensity score matching analysis.",
@@ -1455698,6 +1454628,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "intensive care and critical care medicine"
   },
+  {
+    "rel_doi": "10.1101/2020.05.08.20095877",
+    "rel_title": "Forecasting Transmission Dynamics of COVID-19 Epidemic in India under Various Containment Measures- A Time-Dependent State-Space SIR Approach",
+    "rel_date": "2020-05-13",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20095877",
+    "rel_abs": "ObjectivesOur primary objective is to predict the dynamics of COVID-19 epidemic in India while adjusting for the effects of various progressively implemented containment measures. Apart from forecasting the major turning points and parameters associated with the epidemic, we intend to provide an epidemiological assessment of the impact of these containment measures in India.\n\nMethodsWe propose a method based on time-series SIR model to estimate time-dependent modifiers for transmission rate of the infection. These modifiers are used in state-space SIR model to estimate reproduction number R0, expected total incidence, and to forecast the daily prevalence till the end of the epidemic. We consider four different scenarios, two based on current developments and two based on hypothetical situations for the purpose of comparison.\n\nResultsAssuming gradual relaxation in lockdown post 17 May 2020, we expect the prevalence of infecteds to cross 9 million, with at least 1 million severe cases, around the end of October 2020. For the same case, estimates of R0 for the phases no-intervention, partial-lockdown and lockdown are 4.46 (7.1), 1.47 (2.33), and 0.817 (1.29) respectively, assuming 14-day (24-day) infectious period.\n\nConclusionsEstimated modifiers give consistent estimates of unadjusted R0 across different scenarios, demonstrating precision. Results corroborate the effectiveness of lockdown measures in substantially reducing R0. Also, predictions are highly sensitive towards estimate of infectious period.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Vishal Deo",
+        "author_inst": "Ramjas College, University of Delhi"
+      },
+      {
+        "author_name": "Anuradha Rajkonwar Chetiya",
+        "author_inst": "Ramjas College, University of delhi"
+      },
+      {
+        "author_name": "Barnali Deka",
+        "author_inst": "Ramjas College, University of Delhi"
+      },
+      {
+        "author_name": "Gurprit Grover",
+        "author_inst": "Department of Statistics, University of Delhi"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.05.08.20095703",
     "rel_title": "The real time effective reproductive number for COVID-19 in the United States",
@@ -1456659,25 +1455620,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.05.09.20096594",
-    "rel_title": "Lower State COVID-19 Deaths and Cases with Earlier School Closure in the U.S.",
-    "rel_date": "2020-05-13",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.09.20096594",
-    "rel_abs": "This study quantifies the relationship between school closure timing and COVID-19 deaths and cases in the general population in all U.S. states. COVID-19 has higher symptomatic infection rates among the elderly, suggesting school closures could be unrelated to transmission. However, predicting daily cumulative COVID-19 deaths by state, earlier school closure is related to fewer deaths per capita and slower growth in deaths per capita. Results are similar for COVID-19 cases per capita.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Emily Rauscher",
-        "author_inst": "Brown University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.05.09.20096255",
     "rel_title": "Effect of preventive actions and health care factors in controlling the outbreaks of COVID-19 pandemic",
@@ -1456968,6 +1455910,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.05.09.20096123",
+    "rel_title": "Breaking the back of COVID-19: Is Bangladesh doing enough testing?",
+    "rel_date": "2020-05-13",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.09.20096123",
+    "rel_abs": "Following detection of the first 100 confirmed cases of COVID-19 in early April, Bangladesh stepped up its efforts to strengthen testing capacity in order to curb the spread of the disease across the country. This paper sheds light on the position of Bangladesh in relation to its South Asian neighbors India and Pakistan with respect to testing capacity and ability to detect cases with increased testing. It also analyzes recent data on case counts and testing numbers in Bangladesh, to provide an idea regarding the number of extra tests needed to detect a substantial number of cases within a short period of time. Findings indicate that compared to India and Pakistan, Bangladesh was able to detect more cases by increasing testing levels and expand its testing capacity by performing more per capita tests. In spite of these achievements, the rate of reported cases per 100 tests was consistently higher for Bangladesh compared to India, which suggests that in addition to increased testing, other factors, such as, effective enforcement of social distancing and efficient contact tracing are just as important in curbing the spread of the disease. The analysis reveals that current testing levels in Bangladesh are not adequate. Based on the findings, we recommend a 30-50% growth of the current test rate in the next few days so that by detecting and isolating more cases, Bangladesh could, in effect, contain the spread of new infections. The challenge, however, is to mobilize resources necessary to expand geographical coverage and improve testing quality while enforcing social distancing and performing efficient contact tracing.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Hasinur Rahaman Khan",
+        "author_inst": "Applied Statistics, ISRT, University of Dhaka, Bangladesh"
+      },
+      {
+        "author_name": "Tamanna Howlader",
+        "author_inst": "Applied Statistics, ISRT, University of Dhaka, Bangladesh"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.05.08.20095968",
     "rel_title": "Effects of pre-existing morbidities on occurrence of death among COVID-19 disease patients: A systematic review and meta-analysis",
@@ -1458257,49 +1457222,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.05.13.093690",
-    "rel_title": "Functional prediction and comparative population analysis of variants in genes for proteases and innate immunity related to SARS-CoV-2 infection",
-    "rel_date": "2020-05-13",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.13.093690",
-    "rel_abs": "New coronavirus SARS-CoV-2 is capable to infect humans and cause a novel disease COVID-19. Aiming to understand a host genetic component of COVID-19, we focused on variants in genes encoding proteases and genes involved in innate immunity that could be important for susceptibility and resistance to SARS-CoV-2 infection.\n\nAnalysis of sequence data of coding regions of FURIN, PLG, PRSS1, TMPRSS11a, MBL2 and OAS1 genes in 143 unrelated individuals from Serbian population identified 22 variants with potential functional effect. In silico analyses (PolyPhen-2, SIFT, MutPred2 and Swiss-Pdb Viewer) predicted that 10 variants could impact the structure and/or function of proteins. These protein-altering variants (p.Gly146Ser in FURIN; p.Arg261His and p.Ala494Val in PLG; p.Asn54Lys in PRSS1; p.Arg52Cys, p.Gly54Asp and p.Gly57Glu in MBL2; p.Arg47Gln, p.Ile99Val and p.Arg130His in OAS1) may have predictive value for inter-individual differences in the response to the SARS-CoV-2 infection.\n\nNext, we performed comparative population analysis for the same variants using extracted data from the 1000 genomes project. Population genetic variability was assessed using delta MAF and Fst statistics. Our study pointed to 7 variants in PLG, TMPRSS11a, MBL2 and OAS1 genes with noticeable divergence in allelic frequencies between populations worldwide. Three of them, all in MBL2 gene, were predicted to be damaging, making them the most promising population-specific markers related to SARS-CoV-2 infection.\n\nComparing allelic frequencies between Serbian and other populations, we found that the highest level of genetic divergence related to selected loci was observed with African, followed by East Asian, Central and South American and South Asian populations. When compared with European populations, the highest divergence was observed with Italian population.\n\nIn conclusion, we identified 4 variants in genes encoding proteases (FURIN, PLG and PRSS1) and 6 in genes involved in the innate immunity (MBL2 and OAS1) that might be relevant for the host response to SARS-CoV-2 infection.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Kristel Klaassen",
-        "author_inst": "Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia"
-      },
-      {
-        "author_name": "Biljana Stankovic",
-        "author_inst": "Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia"
-      },
-      {
-        "author_name": "Branka Zukic",
-        "author_inst": "Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia"
-      },
-      {
-        "author_name": "Nikola Kotur",
-        "author_inst": "Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia"
-      },
-      {
-        "author_name": "Vladimir Gasic",
-        "author_inst": "Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia"
-      },
-      {
-        "author_name": "Sonja Pavlovic",
-        "author_inst": "Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia"
-      },
-      {
-        "author_name": "Maja Stojiljkovic",
-        "author_inst": "Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "genomics"
-  },
   {
     "rel_doi": "10.1101/2020.05.12.092171",
     "rel_title": "Structure of SARS-CoV-2 main protease in the apo state reveals the inactive conformation",
@@ -1458546,6 +1457468,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
+  {
+    "rel_doi": "10.1101/2020.05.08.20095521",
+    "rel_title": "Expected impact of reopening schools after lockdown on COVID-19 epidemic in Ile-de-France",
+    "rel_date": "2020-05-12",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20095521",
+    "rel_abs": "As countries in Europe implement strategies to control COVID-19 pandemic, different options are chosen regarding schools. Through a stochastic age-structured transmission model calibrated to the observed epidemic in Ile-de-France in the first wave, we explored scenarios of partial, progressive, or full school reopening. Given the uncertainty on childrens role, we found that reopening schools after lockdown may increase COVID-19 cases, yet protocols exist that maintain the epidemic controlled. Under a scenario with stable epidemic activity if schools were closed, reopening pre-schools and primary schools would lead up to 76% [67, 84]% occupation of ICU beds if no other school level reopened, or if middle and high schools reopened later. Immediately reopening all school levels may overwhelm the ICU system. Priority should be given to pre- and primary schools allowing younger children to resume learning and development, whereas full attendance in middle and high schools is not recommended for stable or increasing epidemic activity. Large-scale test and trace are required to maintain the epidemic under control. Ex-post assessment shows that progressive reopening of schools, limited attendance, and strong adoption of preventive measures contributed to a decreasing epidemic after lifting the first lockdown.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Laura Di Domenico",
+        "author_inst": "INSERM, Sorbonne Universite"
+      },
+      {
+        "author_name": "Giulia Pullano",
+        "author_inst": "INSERM, Sorbonne Universite"
+      },
+      {
+        "author_name": "Chiara E. Sabbatini",
+        "author_inst": "INSERM, Sorbonne Universite"
+      },
+      {
+        "author_name": "Pierre-Yves Bo\u00eblle",
+        "author_inst": "INSERM"
+      },
+      {
+        "author_name": "Vittoria Colizza",
+        "author_inst": "INSERM"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.05.08.20095448",
     "rel_title": "Genetic drift and environmental spreading dynamics of COVID-19",
@@ -1459639,57 +1458596,6 @@
     "type": "new results",
     "category": "pathology"
   },
-  {
-    "rel_doi": "10.1101/2020.05.11.088013",
-    "rel_title": "Local computational methods to improve the interpretability and analysis of cryo-EM maps",
-    "rel_date": "2020-05-12",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.11.088013",
-    "rel_abs": "Cryo-electron microscopy (cryo-EM) maps usually show heterogeneous distributions of B-factors and electron density occupancies and are typically B-factor sharpened to improve their contrast and interpretability at high-resolutions. However,  over-sharpening due to the application of a single global B-factor can distort processed maps causing connected densities to appear broken and disconnected. This issue limits the interpretability of cryo-EM maps, i.e. ab initio modelling. In this work, we propose 1) approaches to enhance high-resolution features of cryo-EM maps, while preventing map distortions and 2) methods to obtain local B-factors and electron density occupancy maps. These algorithms have as common link the use of the spiral phase transformation and are called LocSpiral, LocBSharpen, LocBFactor and LocOccupancy. Our results, which include improved maps of recent SARS-CoV-2 structures, show that our methods can improve the interpretability and analysis of obtained reconstructions.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Satinder Kaur",
-        "author_inst": "McGill University"
-      },
-      {
-        "author_name": "Josue Gomez-Blanco",
-        "author_inst": "McGill University"
-      },
-      {
-        "author_name": "Swathi Adinarayanan",
-        "author_inst": "McGill University"
-      },
-      {
-        "author_name": "Ahmad Khalifa",
-        "author_inst": "McGill University"
-      },
-      {
-        "author_name": "Ruben Sanchez-Garcia",
-        "author_inst": "Centro Nacional de Biotecnologia-CSIC"
-      },
-      {
-        "author_name": "Daniel Wrapp",
-        "author_inst": "University of Texas at Austin"
-      },
-      {
-        "author_name": "Jason S McLellan",
-        "author_inst": "The University of Texas at Austin"
-      },
-      {
-        "author_name": "Khanh Huy Bui",
-        "author_inst": "McGill University"
-      },
-      {
-        "author_name": "Javier Vargas",
-        "author_inst": "Universidad Complutense de Madrid"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "biophysics"
-  },
   {
     "rel_doi": "10.1101/2020.05.11.089375",
     "rel_title": "The SARS-CoV-2 conserved macrodomain is a highly efficient ADP-ribosylhydrolase enzyme",
@@ -1460148,6 +1459054,37 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2020.05.12.091090",
+    "rel_title": "Static All-Atom Energetic Mappings of the SARS-Cov-2 Spike Protein with Potential Latch Identification of the Down State Protomer",
+    "rel_date": "2020-05-12",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.12.091090",
+    "rel_abs": "The SARS-Cov-2 virion responsible for the current world-wide pandemic Covid-19 has a characteristic Spike protein (S) on its surface that embellishes both a prefusion state and fusion state. The prefusion Spike protein (S) is a large trimeric protein where each protomer may be in a so-called Up state or Down state, depending on the configuration of its receptor binding domain (RBD). The Up state is believed to allow binding of the virion to ACE-2 receptors on human epithelial cells, whereas the Down state is believed to be relatively inactive or reduced in its binding behavior. We have performed detailed all-atom, dominant energy landscape mappings for noncovalent interactions (charge, partial charge, and van der Waals) of the SARS-Cov-2 Spike protein in its static prefusion state based on recent structural information. We included both interchain interactions and intrachain (domain) interactions in our mappings in order to determine any telling differences (different so-called \"glue\" points) between residues in the Up and Down state protomers. In general, the S2 or fusion machinery domain of S is relatively rigid with strong noncovalent interactions facilitated by helical secondary structures, whereas the S1 domain, which contains the RBD and N-terminal domain (NTD), is relatively more flexible and characterized by beta strand structural motifs. The S2 domain demonstrated no appreciable energetic differences between Up and Down protomers, including interchain as well as each protomers intrachain, S1-S2 interactions. However, the S1 domain interactions across neighboring protomers, which include the RBD-NTD cross chain interactions, showed significant energetic differences between Up-Down and Down-Down neighboring protomers. Surprisingly, the Up-Down, RBD-NTD interactions were overall stronger and more numerous than the Down-Down cross chain interactions, including the appearance of the three residue sequence ALA520-PRO521-ALA522 associated with a turn structure in the RBD of the Up state protomer. Additionally, our intrachain dominant energy mappings within each protomer, identified a significant \"glue\" point or possible \"latch\" for the Down state protomer between the S1 subdomain, SD1, and the RBD domain of the same protomer that was completely missing in the Up state protomer analysis. Ironically, this dominant energetic interaction in the Down state protomer involved the backbone atoms of the same three residue sequence ALA520-PRO521-ALA522 of the RBD with the R-group of GLN564 in the SD1 domain. Thus, this same three residue sequence acts as a stabilizer of the RBD in the Up conformation through its interactions with its neighboring NTD chain and a kind of latch in the Down state conformation through its interactions with its own SD1 domain. The dominant interaction energy residues identified here are also conserved across reported variations of SARS-Cov-2, as well as the closely related virions SARS-Cov and the bat corona virus RatG13. To help verify the potential latch for the Down state protomer, we conducted some preliminary molecular dynamic simulations that effectively turn off this specific latch glue point via a single point mutation of GLN564. Interestingly, the single point mutation lead to the latch releasing in less than a few nanoseconds, but the latch remained fixed in the wild state protomer for up to 0.1 microseconds that were simulated. Many more detailed studies are needed to understand the dynamics of the Up and Down states of the Spike protein, including the stabilizing chain-chain interactions and the mechanisms of transition from Down to Up state protomers. Nonetheless, static dominant energy landscape mappings and preliminary molecular dynamic studies given here may represent a useful starting point for more detailed dynamic analyses and hopefully an improved understanding of the structure-function relationship of this highly complex protein associated with COVID-19.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Michael H Peters",
+        "author_inst": "Virginia Commonwealth University"
+      },
+      {
+        "author_name": "Oscar Bastidas",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Daniel S. Kokron",
+        "author_inst": "NASA Ames Research Center"
+      },
+      {
+        "author_name": "Christopher E. Henze",
+        "author_inst": "NASA Ames Research Center"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "biophysics"
+  },
   {
     "rel_doi": "10.1101/2020.05.11.089763",
     "rel_title": "Children's Hospital Los Angeles COVID-19 Analysis Research Database (CARD) - A Resource for Rapid SARS-CoV-2 Genome Identification Using Interactive Online Phylogenetic Tools",
@@ -1461156,33 +1460093,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
-  {
-    "rel_doi": "10.1101/2020.05.06.20090340",
-    "rel_title": "The German COVID-19 Survey on Mental Health: Primary Results",
-    "rel_date": "2020-05-12",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20090340",
-    "rel_abs": "First cases of COVID-19 were reported in Wuhan, China in early December 2019. Preliminary data from China indicated that the pandemic and its associated lockdown measures may have a substantial impact on mental health and well-being, with evidence of increased levels of psychological distress, anxiety, depressive symptoms and insomnia.1,2 In March 2020, the German government agreed upon a substantial catalogue of measures including contact bans that came into effect on 22 March. Such measures are unprecedented for the majority of people and may affect their lives tremendously. Thus, the current survey was immediately developed to systematically assess mental health in response to these measures.\n\nMethodsThe survey was approved by the local ethics committee at Hannover Medical School, Germany and included web-based self-report measures as outlined below. First wave data were taken during the height of lockdown measures in Germany from 1 April to 15 April 2020.\n\nResultsO_ST_ABSDemographicsC_ST_ABSA total of 3,545 volunteers took part in this cross-sectional survey. Mean age was 40.36 years (SD = 11.70; 83.1% female, 15.2% male), mean educational years 15.87 (SD = 4.19), 9.9% were unemployed and 23.9% reported living alone. Acute or chronic disease was reported by 36.7% (physical) and 24.7% (mental) of subjects.\n\nDistress, Anxiety and DepressionPsychosocial distress as measured with the PHQ stress module (items 12a-12j of PHQ-D) was at M = 6.36 (SD = 0.89), implying mild psychosocial distress (range 5-9). Depression and anxiety as assessed by PHQ-4 was at M = 3.80 (SD = 3.03) and significantly higher than in a reference sample (t(6008) = 32.78, p = 0.00).3 The mean well-being score (WHO-5) was 50.7 (SD = 23.8) (range 0-100), with normal individuals having a mean score of 75 and subjects with major depression 37.5.4 The majority of subjects (60%) indicated very good or fair, 26.9% poor or very poor subjective coping with the pandemic and corresponding measures. Calculation of gender differences revealed higher scores for depression and anxiety (t(3459) = 4.93, p = 0.00) and poorer coping in women (U = 678156, p = 0.00).\n\nSleep, irritability & violenceUsing comparative questions on a 5-point Likert scale 45.3% of participants reported worsened sleep compared to pre-pandemic times. Of all participants 50.9% reported being more easily irritated (compared to 12.2% feeling less easily irritated) and 29% reported experiencing more anger and aggression (compared to 12.8% experiencing less). Of these 65.5% directed their anger and aggression at others, while 32.6% directed it at themselves. Most importantly, 5% of all participants reported experiencing interpersonal violence (IPV) on a verbal (98.4%), physical (41.9%) or sexual (30.2%) level. In case of verbal violence, 77.3% reported experiencing more verbal violence lately (compared to 3.4% experiencing less). Regarding physical violence, 19.5% reported experiencing increased levels (compared to 2.8% experiencing less) and in case of sexual violence more people reported experiencing increased sexual violence lately (11.1%) compared to 1.7% that experienced less.\n\nDiscussionThis is one of the first and largest surveys on mental health during COVID pandemic in a European society. Although the cohort reflects a relatively well educated and financially secure sample, there is evidence of substantial mental burden with increased levels of stress, anxiety, depressive symptoms, sleep disturbance and irritability. Most importantly and also most concerning is the finding of a one-month prevalence of 5% IPV, which is already close to one-year prevalence rates5 and for which there were indices that this has currently increased. We think it is of vital importance to continuously monitor the mental health of the general public during this pandemic and its aftermath and to carefully screen for IPV and its risk factors such as stress, sleep problems and anger.6",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Stefanie Jung",
-        "author_inst": "Hannover Medical School"
-      },
-      {
-        "author_name": "Jonas Kneer",
-        "author_inst": "Hannover Medical School"
-      },
-      {
-        "author_name": "Tillmann Krueger",
-        "author_inst": "Hannover Medical School"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "psychiatry and clinical psychology"
-  },
   {
     "rel_doi": "10.1101/2020.05.07.20094466",
     "rel_title": "Text Mining Approach to Analyze Coronavirus Impact: Mexico City as Case of Study",
@@ -1461613,6 +1460523,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.05.06.20073742",
+    "rel_title": "Evaluating transmission heterogeneity and super-spreading event of COVID-19 in a metropolis of China",
+    "rel_date": "2020-05-11",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20073742",
+    "rel_abs": "BackgroundCOVID-19 caused rapid mass infection worldwide. Understanding its transmission characteristics including heterogeneity is of vital importance for prediction and intervention of future epidemics. In addition, transmission heterogeneity usually envokes super spreading events (SSEs) where certain individuals infect large numbers of secondary cases. Till now, studies of transmission heterogeneity of COVID-19 and its underlying reason are far from reaching an agreement.\n\nMethodsWe collected information of all infected cases between January 21 and February 26, 2020 from official public sources in Tianjin, a metropolis of China. . Utilizing a heterogeneous transmission model based on branching process along with a negative binomial offspring distribution, we estimated the reproductive number R and the dispersion parameter k which characterized the transmission potential and heterogeneity, respectively. Furthermore, we studied the SSE in Tianjin outbreak and evaluated the effect of control measures undertaken by local government based on the heterogeneous model.\n\nResultsA total of 135 confirmed cases (including 34 imported cases and 101 local infections) in Tianjin by February 26th 2020 entered the study. We grouped them into 43 transmission chains with the largest chain of 45 cases and the longest chain of 4 generations. The estimated reproduction number R was at 0.67 (95%CI: 0.54~0.84), and the dispersion parameter k was at 0.25 (95% CI: 0.13~0.88). A super spreader causing six infections in Tianjin, was identified. In addition, our simulation results showed that the outbreak in Tianjin would have caused 165 infections and sustained for 7.56 generations on average if no control measures had been taken by local government since January 28th.\n\nConclusionsOur analysis suggested that the transmission of COVID-19 was subcritical but with significant heterogeneity and may incur SSE. More efforts are needed to verify the transmission heterogeneity of COVID-19 in other populations and its contributing factors, which is important for developing targeted measures to curb the pandemic.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Yunjun Zhang",
+        "author_inst": "Peking University"
+      },
+      {
+        "author_name": "Yuying Li",
+        "author_inst": "Peking University"
+      },
+      {
+        "author_name": "Lu Wang",
+        "author_inst": "Peking University"
+      },
+      {
+        "author_name": "Mingyuan Li",
+        "author_inst": "Peking University"
+      },
+      {
+        "author_name": "Xiao-Hua Zhou",
+        "author_inst": "Peking University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.05.07.20083386",
     "rel_title": "A Rapid Decrease in Stroke, Acute Coronary Syndrome, and Corresponding Interventions at 65 United States Hospitals Following Emergence of COVID-19",
@@ -1462794,33 +1461739,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.05.06.20093237",
-    "rel_title": "How robust are the results of one of the first positive trials exploring hydroxychloroquine for treatment of COVID-19?",
-    "rel_date": "2020-05-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20093237",
-    "rel_abs": "An outbreak of a novel human coronavirus infection emerged in Wuhan, China in December 2019. Two months later, the World Health Organization (WHO) announced SARS-CoV-2 as the name for the new virus and COVID-19 for the associated illness. On March 12, 2020, the WHO officially declared COVID-19 as a pandemic. The scientific community has raced to find effective therapeutic agents against the virus. Gautret et al 2020 is among one of the first purportedly positive trials of hydroxychloroquine for the treatment of COVID-19. However, it is imperative that a thorough analysis and understanding of trial data be undertaken prior to making claims about safety and efficacy. Our group assessed the statistical robustness of the trial using the Fragility Index (FI). The FI provides a numerical quantification of a clinical trials conclusions. The index is based on iterative statistical calculations to determine the minimum number of events within a trial that would theoretically need to change from positive to negative in order for the trials endpoint to convert from significant to non-significant; the higher the index, the more statistically robust the study results. For the Gautret et al trial, one endpoint had an FI of 1, two had indices of 2, and another had an index of 4. The primary endpoint of viral clearance on day 6 had an FI of 4. This indicates that if 4 events were to change from positive to negative, the conclusion of the trial would become mathematically non-significant. This index is comparable to many other published trials of established agents; the median FI across the reported literature appears to be 2. In conclusion, the trial results reported by Gautret et al are statistically robust, assuming that data quality is not compromised; however, the study was an open-label trial with non-homogenous groups, with analysis conducted per-protocol. Additionally, SARS-CoV-2 Reverse Transcriptase-PCR (RT-PCR) testing was not conducted in a systematic way amongst the two groups. Further analyses of this trial and future trials of antiviral agents with potential activity against SARS-CoV-2 should be performed with complementary epidemiologic and statistical techniques to determine whether the trials results are clinically important and/or should be explored in depth. Given the statistically robust results reported by Gautret et al, despite the studys inherent methodological and analytical flaws, hydroxychloroquine should be studied as a potential agent against COVID-19 in larger clinical trials.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Ronald Chow",
-        "author_inst": "Schulich School of Medicine & Dentistry, University of Western Ontario"
-      },
-      {
-        "author_name": "Sameer Elsayed",
-        "author_inst": "Schulich School of Medicine & Dentistry, University of Western Ontario"
-      },
-      {
-        "author_name": "Michael Lock",
-        "author_inst": "Schulich School of Medicine & Dentistry, University of Western Ontario"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.05.06.20093138",
     "rel_title": "A study on the relationship between BCG vaccination and Covid-19 prevalence: Do other confounders warrant investigation?",
@@ -1463179,6 +1462097,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health systems and quality improvement"
   },
+  {
+    "rel_doi": "10.1101/2020.05.07.20094094",
+    "rel_title": "Epidemiology of CoVID-19 and predictors of recovery in the Republic of Korea",
+    "rel_date": "2020-05-11",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20094094",
+    "rel_abs": "BackgroundThe recent CoVID-19 pandemic has emerged as a threat to global health. Though current evidence on the epidemiology of the disease is emerging, very little is known about the predictors of recovery.\n\nObjectivesTo describe the epidemiology of confirmed CoVID-19 patients in Republic of Korea and identify predictors of recovery.\n\nMaterials and methodsUsing publicly available data for confirmed CoVID-19 cases from the Korea Centers for Disease Control and Prevention from January 20, 2020 to April 30, 2020, we undertook descriptive analyses of cases stratified by sex, age group, place of exposure, date of confirmation and province. Correlation was tested among all predictors (sex, age group, place of exposure and province) with the Pearsons correlation coefficient. Associations between recovery from CoVID-19 and predictors were estimated using a multivariable logistic regression model.\n\nResultsMajority of the confirmed cases were females (56%), from 20-29 age group (24.3%), and primarily from three provinces -- Gyeongsangbuk-do (36.9%), Gyeonggi-do (20.5%) and Seoul (17.1%). Case fatality ratio was 2.1% and 41.6% cases recovered. Older patients, patients from provinces such as Daegu, Gyeonggi-do, Gyeongsangbuk-do, Jeju-do, Jeollabuk-do and Jeollanam-do, and those contracting the disease from healthcare settings had lower recovery.\n\nConclusionsOur study adds to the very limited evidence base on potential predictors of survival among confirmed CoVID-19 cases. We call additional research to explore the predictors of recovery and support development of policies to protect the vulnerable patient groups.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Ashis Das",
+        "author_inst": "The World Bank"
+      },
+      {
+        "author_name": "Saji Saraswathy Gopalan",
+        "author_inst": "World Bank"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.05.07.20093864",
     "rel_title": "Utility of Cloth Masks in Preventing Respiratory Infections: A Systematic Review",
@@ -1464488,29 +1463429,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.05.07.20094235",
-    "rel_title": "Chaos, Percolation and the Coronavirus Spread: a two-step model.",
-    "rel_date": "2020-05-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20094235",
-    "rel_abs": "We discuss a two-step model for the rise and decay of a new coronavirus (Severe Acute Respiratory Syndrome-CoV-2) first reported in December 2019, COVID-19. The first stage is well described by the same equation for turbulent flows, population growth and chaotic maps: a small number of infected d0 grows exponentially to a saturation value d{infty}. The typical growth {lambda} time (aggressive spreading of the virus) is given by [Formula], where{lambda} is the Lyapunov exponent.!After a time tcrit determined by social distancing and/or other measures, the spread decreases exponentially as for nuclear decays and non-chaotic maps. Some countries, like China, S. Korea and Italy are in this second stage while others including the USA are near the end of the growth stage. The model predicts 15,000 ({+/-}2,250) casualties for the Lombardy region (Italy) at the end of the spreading around May 10,2020. Without the quarantine, the casualties would have been more than 50,000, hundred days after the start of the pandemic. The data from the 50 US states are of very poor quality because of an extremely late and confused response to the pandemic, resulting unfortunately in a large number of casualties, more than 70,000 on May 6, 2020. S. Korea, notwithstanding the high population density (511/km2) and the closeness to China, responded best to the pandemic with 255 deceased as of May 6,2020.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Aldo Bonasera",
-        "author_inst": "texas A&M university"
-      },
-      {
-        "author_name": "hua zheng",
-        "author_inst": "School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710119, China."
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.05.07.20093963",
     "rel_title": "Serological signatures of SARS-CoV-2 infection: Implications for antibody-based diagnostics",
@@ -1464825,6 +1463743,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.05.07.20094714",
+    "rel_title": "DOUBLE POWER LAW FOR COVID-19: PREDICTION OF NEW CASES AND DEATH RATES IN ITALY AND SPAIN",
+    "rel_date": "2020-05-11",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20094714",
+    "rel_abs": "1.The novel corona virus SARS-CoV-2 appeared at the end of 2019, spreading rapidly and causing a severe respiratory syndrome (COVID-19) with high mortality (2-5%). Until a vaccine or therapy is found, the most effective method of prophylaxis has been to minimize transmission via rigorous social distancing and seclusion of all but essential workers. Such measures, implemented at different times and to varying degrees world-wide, have reduced the rate of transmission compared with early phases of the pandemic, resulting in \"flattening of the curve\" followed by a gradual reduction in mortality after >6 weeks of rigorous social distancing measures. The cost of rigorous social distancing has been seen in radically reduced economic activity, job losses, disruption of schooling and social institutions. A key question facing policy makers and individuals is when to resume normal economic and social activity in the face of persistent community transmission of SARS-CoV-2. To help address this question, we have developed a model that accurately describes the entire transmission and mortality curves in Italy and Spain, two hard-hit countries that have maintained severe social distancing measures for over 2 months. Our model quantitatively describes the rapid rise and slow decay of new cases and deaths observed under stringent social distancing (the \"long tail\" effect). We predict that even when social distancing is rigorously maintained, the number of COVID-19 deaths after peak mortality may be 2 - 3 times larger than the total number of deaths up to the peak. Our model has important policy implications for countries currently debating how to ease social distancing measures.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Vladimir A. Osherovich",
+        "author_inst": "NASA/GSFC/CUA"
+      },
+      {
+        "author_name": "Joseph Fainberg",
+        "author_inst": "NASA/GSFC"
+      },
+      {
+        "author_name": "Lev Z. Osherovich",
+        "author_inst": "Versant Ventures"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.05.07.20094250",
     "rel_title": "Racial and Ethnic Disparities in Population Level Covid-19 Mortality",
@@ -1465878,41 +1464823,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.05.06.20093401",
-    "rel_title": "Immunity Passports for SARS-CoV-2: an online experimental study of the impact of antibody test terminology on perceived risk and behaviour",
-    "rel_date": "2020-05-10",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20093401",
-    "rel_abs": "WHAT IS ALREADY KNOWN ON THIS TOPICO_LITest results indicating the presence of antibodies to SARS-CoV-2 are often referred to as Immunity Passports or Certificates.\nC_LIO_LIDue to the limitations of such tests, including uncertainty about the duration of immunity conferred by detected antibodies, those receiving results indicating the presence of antibodies retain a risk of becoming infected by SARS-CoV-2.\nC_LIO_LIIt is unknown whether the use of the terms Immunity Passports or Certificates reduces awareness of the residual risk inherent in an antibody-positive test result and adherence to protective behaviours, thereby increasing risk of transmission.\nC_LI\n\nWHAT THIS STUDY ADDSO_LIUsing the term Immunity - as opposed to Antibody - to describe antibody tests for SARS-CoV-2 more than doubled the proportion who erroneously perceived they would have no risk of catching coronavirus in the future given an antibody-positive test result, from 9.8% for Antibody to 19.1% for Immunity.\nC_LIO_LIPerceiving no risk of infection with coronavirus given an antibody-positive test result was associated with an intention to wash hands less frequently.\nC_LIO_LIUsing the terms Passport, Certificate or Test had no significant effect.\nC_LI\n\nObjectiveTo assess the impact of describing an antibody-positive test result using the terms Immunity and Passport or Certificate, alone or in combination, on perceived risk of becoming infected with SARS-CoV-2 and intention to continue protective behaviours.\n\nDesign2 x 3 experimental design.\n\nSettingOnline with data collected between 28th April and 1st May 2020.\n\nParticipants1,204 adults registered with a UK research panel.\n\nInterventionParticipants were randomised to receive one of six descriptions of an antibody test and results showing SARS-CoV-2 antibodies, differing in the terms used to describe the type of test (Immunity vs Antibody) and the test result (Passport vs Certificate vs Test).\n\nMain outcome measuresThe primary outcome was the proportion of participants perceiving no risk of becoming infected with SARS-CoV-2 given an antibody positive test result. Other outcomes include intended changes to frequency of handwashing and physical distancing.\n\nResultsWhen using the term Immunity (vs Antibody), 19.1% of participants [95% CI: 16.1 to 22.5] (vs 9.8% [95% CI: 7.5 to 12.4]) perceived no risk of catching coronavirus at some point in the future given an antibody-positive test result (AOR: 2.91 [95% CI: 1.52 to 5.55]). Using the terms Passport or Certificate - as opposed to Test - had no significant effect (AOR: 1.24 [95% CI: 0.62 to 2.48] and AOR: 0.96 [95% CI: 0.47 to 1.99] respectively). There was no significant interaction between the effects of the test and result terminology. Across groups, perceiving no risk of infection was associated with an intention to wash hands less frequently (AOR: 2.32 [95% CI: 1.25 to 4.28]) but there was no significant association with intended avoidance of physical contact with others outside of the home (AOR: 1.37 [95% CI: 0.93-2.03]).\n\nConclusionsUsing the term Immunity (vs Antibody) to describe antibody tests for SARS-CoV-2 increases the proportion of people believing that an antibody-positive result means they have no risk of catching coronavirus in the future, a perception that may be associated with less frequent handwashing. The way antibody testing is described may have implications for the likely impact of testing on transmission rates.\n\nStudy registrationOpen Science Framework: https://osf.io/tjw78/files/",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Jo Waller",
-        "author_inst": "Kings College London"
-      },
-      {
-        "author_name": "G James Rubin",
-        "author_inst": "Kings College London"
-      },
-      {
-        "author_name": "Henry W W Potts",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Abigail Mottershaw",
-        "author_inst": "Behavioural Insights Team, London"
-      },
-      {
-        "author_name": "Theresa M Marteau",
-        "author_inst": "University of Cambridge"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.05.06.20093344",
     "rel_title": "Who can go back to work when the COVID-19 pandemic remits?",
@@ -1466135,6 +1465045,57 @@
     "type": "new results",
     "category": "genomics"
   },
+  {
+    "rel_doi": "10.1101/2020.05.09.086249",
+    "rel_title": "Cholesterol and COVID19 lethality in elderly.",
+    "rel_date": "2020-05-10",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.09.086249",
+    "rel_abs": "Coronavirus disease 2019 (COVID19) is a respiratory infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originating in Wuhan, China in 2019. The disease is notably severe in elderly and those with underlying chronic conditions. A molecular mechanism that explains why the elderly are vulnerable and why children are resistant is largely unknown. Here we show loading cells with cholesterol from blood serum using the cholesterol transport protein apolipoprotein E (apoE) enhances the entry of pseudotyped SARS-CoV-2 and the infectivity of the virion. Super resolution imaging of the SARS-CoV-2 entry point with high cholesterol shows almost twice the total number of endocytic entry points. Cholesterol concomitantly traffics angiotensinogen converting enzyme (ACE2) to the endocytic entry site where SARS-CoV-2 presumably docks to efficiently exploit entry into the cell. Furthermore, in cells producing virus, cholesterol optimally positions furin for priming SARS-CoV-2, producing a more infectious virion with improved binding to the ACE2 receptor. In vivo, age and high fat diet induces cholesterol loading by up to 40% and trafficking of ACE2 to endocytic entry sites in lung tissue from mice. We propose a component of COVID19 severity based on tissue cholesterol level and the sensitivity of ACE2 and furin to cholesterol. Molecules that reduce cholesterol or disrupt ACE2 localization with viral entry points or furin localization in the producer cells, may reduce the severity of COVID19 in obese patients.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Hao Wang",
+        "author_inst": "The Scripps Research Institute"
+      },
+      {
+        "author_name": "Zixuan Yuan",
+        "author_inst": "The Scripps Research Institute"
+      },
+      {
+        "author_name": "Mahmud Arif Pavel",
+        "author_inst": "The Scripps Research Institute"
+      },
+      {
+        "author_name": "Sonia Mediouni Jablonski",
+        "author_inst": "Scripps Research"
+      },
+      {
+        "author_name": "Joseph Jablonski",
+        "author_inst": "Scripps Research"
+      },
+      {
+        "author_name": "Robert Hobson",
+        "author_inst": "Bruker"
+      },
+      {
+        "author_name": "Susana Valente",
+        "author_inst": "Scripps Research"
+      },
+      {
+        "author_name": "Chakravarthy B. Reddy",
+        "author_inst": "University of Utah Health Sciences Center"
+      },
+      {
+        "author_name": "Scott Hansen",
+        "author_inst": "The Scripps Research Institute"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2020.05.09.086223",
     "rel_title": "Multiple introductions, regional spread and local differentiation during the first week of COVID-19 epidemic in Montevideo, Uruguay",
@@ -1467648,37 +1466609,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.05.05.20092379",
-    "rel_title": "Are Vapers More Susceptible to COVID-19 Infection?",
-    "rel_date": "2020-05-09",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20092379",
-    "rel_abs": "BackgroundCOVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was declared a global pandemic in March 2020. Electronic cigarette use (vaping) rapidly gained popularity in the US in recent years. Whether electronic cigarette users (vapers) are more susceptible to COVID-19 infection is unknown.\n\nMethodsUsing integrated data in each US state from the 2018 Behavioral Risk Factor Surveillance System (BRFSS), United States Census Bureau and the 1Point3Acres.com website, generalized estimating equation (GEE) models with negative binomial distribution assumption and log link functions were used to examine the association of weighted proportions of vapers with number of COVID-19 infections and deaths in the US.\n\nResultsThe weighted proportion of vapers who used e-cigarettes every day or some days ranged from 2.86% to 6.42% for US states. Statistically significant associations were observed between the weighted proportion of vapers and number of COVID-19 infected cases as well as COVID-19 deaths in the US after adjusting for the weighted proportion of smokers and other significant covariates in the GEE models. With every one percent increase in weighted proportion of vapers in each state, the number of COVID-19 infected cases increase by 0.3139 (95% CI: 0.0554 -0.5723) and the number of COVID-19 deaths increase by 0.3705 (95% CI: 0.0623 - 0.6786) in log scale in each US state.\n\nConclusionsThe positive associations between the proportion of vapers and the number of COVID-19 infected cases and deaths in each US state suggest an increased susceptibility of vapers to COVID-19 infections and deaths.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Dongmei Li",
-        "author_inst": "Department of Clinical & Translational Research, University of Rochester Medical Center, Rochester, NY, USA"
-      },
-      {
-        "author_name": "Daniel P. Croft",
-        "author_inst": "Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA"
-      },
-      {
-        "author_name": "Deborah J. Ossip",
-        "author_inst": "Department of Public Health Sciences, University of Rochester Medical Center, 265 Crittenden Blvd, Rochester, NY, USA"
-      },
-      {
-        "author_name": "Zidian Xie",
-        "author_inst": "Department of Clinical & Translational Research, University of Rochester Medical Center, Rochester, NY, USA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.05.05.20091520",
     "rel_title": "Epidemic Situation and Forecasting of COVID-19 in Saudi Arabia using the SIR model",
@@ -1467949,6 +1466879,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.05.05.20091918",
+    "rel_title": "Identification and Analysis of Shared Risk Factors in Sepsis and High Mortality Risk COVID-19 Patients",
+    "rel_date": "2020-05-09",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20091918",
+    "rel_abs": "BACKGROUNDCoronavirus disease 2019 (COVID-19) is a novel coronavirus strain disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The disease is highly transmissible and severe disease including viral sepsis has been reported in up to 16% of hospitalized cases. The admission characteristics associated with increased odds of hospital mortality among confirmed cases of COVID-19 include severe hypoxia, low platelet count, elevated bilirubin, hypoalbuminemia and reduced glomerular filtration rate. These symptoms correlate highly with severe sepsis cases. The diseases also share similar comorbidity risks including dementia, type 2 diabetes mellitus, coronary heart disease, hypertension and chronic renal failure. Sepsis has been observed in up to 59% of hospitalized COVID-19 patients.\n\nIt is highly desirable to identify risk factors and novel therapy/drug repurposing avenues for late-stage severe COVID-19 patients. This would enable better protection of at-risk populations and clinical stratification of COVID-19 patients according to their risk for developing life threatening disease.\n\nMETHODSAs there is currently insufficient data available for confirmed COVID-19 patients correlating their genomic profile, disease severity and outcome, co-morbidities and treatments as well as epidemiological risk factors (such as ethnicity, blood group, smoking, BMI etc.), a direct study of the impact of host genomics on disease severity and outcomes is not yet possible. We therefore ran a study on the UK Biobank sepsis cohort as a surrogate to identify sepsis associated signatures and genes, and correlated these with COVID-19 patients.\n\nSepsis is itself a life-threatening inflammatory health condition with a mortality rate of approximately 20%. Like the initial studies for COVID-19 patients, standard genome wide association studies (GWAS) have previously failed to identify more than a handful of genetic variants that predispose individuals to developing sepsis.\n\nRESULTSWe used a combinatorial association approach to analyze a sepsis population derived from UK Biobank. We identified 70 sepsis risk-associated genes, which provide insights into the disease mechanisms underlying sepsis pathogenesis. Many of these targets can be grouped by common mechanisms of action such as endothelial cell dysfunction, PI3K/mTOR pathway signaling, immune response regulation, aberrant GABA and neurogenic signaling.\n\nCONCLUSIONThis study has identified 70 sepsis related genes, many of them for the first time, that can reasonably be considered to be potentially relevant to severe COVID-19 patients. We have further identified 59 drug repurposing candidates for 13 of these targets that can be used for the development of novel therapeutic strategies to increase the survival rate of patients who develop sepsis and potentially severe COVID-19.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Sayoni Das",
+        "author_inst": "PrecisionLife Ltd"
+      },
+      {
+        "author_name": "Krystyna Taylor",
+        "author_inst": "PrecisionLife Ltd"
+      },
+      {
+        "author_name": "Matthew Pearson",
+        "author_inst": "PrecisionLife Ltd"
+      },
+      {
+        "author_name": "James Kozubek",
+        "author_inst": "PrecisionLife Ltd"
+      },
+      {
+        "author_name": "Marcin Pawlowski",
+        "author_inst": "PrecisionLife Ltd"
+      },
+      {
+        "author_name": "Claus Erik Jensen",
+        "author_inst": "PrecisionLife Ltd"
+      },
+      {
+        "author_name": "Zbigniew Skowron",
+        "author_inst": "PrecisionLife Ltd"
+      },
+      {
+        "author_name": "Gert Lykke M\u00f8ller",
+        "author_inst": "PrecisionLife Ltd"
+      },
+      {
+        "author_name": "Mark Strivens",
+        "author_inst": "PrecisionLife Ltd"
+      },
+      {
+        "author_name": "Steve Gardner",
+        "author_inst": "PrecisionLife Ltd"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.05.05.20091975",
     "rel_title": "BCG vaccine-induced protection from COVID-19 infection, wishful thinking or a game changer?",
@@ -1469094,45 +1468079,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2020.05.09.086165",
-    "rel_title": "ACE2 and TMPRSS2 are expressed on the human ocular surface, suggesting susceptibility to SARS-CoV-2 infection",
-    "rel_date": "2020-05-09",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.09.086165",
-    "rel_abs": "Purpose Conjunctival signs and symptoms are observed in a subset of patients with COVID-19, and SARS-CoV-2 has been detected in tears, raising concerns regarding the eye both as a portal of entry and carrier of the virus. The purpose of this study was to determine whether ocular surface cells possess the key factors required for cellular susceptibility to SARS-CoV-2 entry/infection.Methods We analyzed human post-mortem eyes as well as surgical specimens for the expression of ACE2 (the receptor for SARS-CoV-2) and TMPRSS2, a cell surface-associated protease that facilitates viral entry following binding of the viral spike protein to ACE2.Results Across all eye specimens, immunohistochemical analysis revealed expression of ACE2 in the conjunctiva, limbus, and cornea, with especially prominent staining in the superficial conjunctival and corneal epithelial surface. Surgical conjunctival specimens also showed expression of ACE2 in the conjunctival epithelium, especially prominent in the superficial epithelium, as well as the substantia propria. All eye and conjunctival specimens also expressed TMPRSS2. Finally, western blot analysis of protein lysates from human corneal epithelium obtained during refractive surgery confirmed expression of ACE2 and TMPRSS2.Conclusions Together, these results indicate that ocular surface cells including conjunctiva are susceptible to infection by SARS-CoV-2, and could therefore serve as a portal of entry as well as a reservoir for person-to-person transmission of this virus. This highlights the importance of safety practices including face masks and ocular contact precautions in preventing the spread of COVID-19 disease.Competing Interest StatementThe authors have declared no competing interest.View Full Text",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Lingli Zhou",
-        "author_inst": "Johns Hopkins University School of Medicine"
-      },
-      {
-        "author_name": "Zhenhua Xu",
-        "author_inst": "Johns Hopkins University School of Medicine"
-      },
-      {
-        "author_name": "Gianni M Castiglione",
-        "author_inst": "Johns Hopkins University School of Medicine"
-      },
-      {
-        "author_name": "Uri S Soiberman",
-        "author_inst": "Johns Hopkins University School of Medicine"
-      },
-      {
-        "author_name": "Charles G Eberhart",
-        "author_inst": "Johns Hopkins University School of Medicine"
-      },
-      {
-        "author_name": "Elia J Duh",
-        "author_inst": "Johns Hopkins University School of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "pathology"
-  },
   {
     "rel_doi": "10.1101/2020.05.08.084996",
     "rel_title": "Elevated ACE2 expression in the olfactory neuroepithelium: implications for anosmia and upper respiratory SARS-CoV-2 entry and replication",
@@ -1469315,6 +1468261,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.05.02.20086314",
+    "rel_title": "Testing lags and emerging COVID-19 outbreaks in federal penitentiaries in Canada",
+    "rel_date": "2020-05-08",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.02.20086314",
+    "rel_abs": "ObjectivesTo provide the first known comprehensive analysis of COVID-19 outcomes in a federal penitentiary system. We examined the following COVID-19 outcomes within federal penitentiaries in Canada and contrasted them with estimates for the overall population in the penitentiaries respective provincial jurisdictions: testing, prevalence, the proportion recovered, and fatality.\n\nMethodsData for prisons were obtained from the Correctional Service of Canada and, for the general population, from the Esri COVID-19 Canadian Outbreak Tracking Hub. Data were retrieved between March 30 and April 21, 2020, and are accurate to this date. Penitentiary-, province- and sex-specific frequency statistics for each outcome were calculated.\n\nResultsData on 50 of 51 penitentiaries (98%) were available. Of these, 72% of penitentiaries reported fewer tests per 1000 population than the Canadian general population average (16 tests/1000 population), and 24% of penitentiaries reported zero tests. Penitentiaries with high levels of testing were those that already had elevated COVID-19 prevalence. Five penitentiaries reported an outbreak (at least one case). Hardest hit penitentiaries were those in Quebec, Ontario, and British Columbia, with some prisons reporting COVID-19 prevalence of 30% to 40%. Of these, two were womens prisons. Female prisoners were over-represented among cases (31% of cases overall, despite representing 5% of the total prison population).\n\nConclusionIncreased sentinel or universal testing may be appropriate given the confined nature of prison populations. This, along with rigorous infection prevention control practices and the potential release of prisoners, will be needed to curb current outbreaks and those likely to come.\n\nGRAPHICAL SUMMARY\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC=\"FIGDIR/small/20086314v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (21K):\norg.highwire.dtl.DTLVardef@1502c7eorg.highwire.dtl.DTLVardef@991027org.highwire.dtl.DTLVardef@f378f4org.highwire.dtl.DTLVardef@89f447_HPS_FORMAT_FIGEXP  M_FIG C_FIG O_LIBetween 20% and 57% fewer tests per 1000 population have been conducted in federal prisons in Saskatchewan, New Brunswick, Nova Scotia and Alberta than in the general population of those provinces.\nC_LIO_LIThough Alberta, Manitoba, Saskatchewan, New Brunswick and Nova Scotia are reporting lower counts of COVID-19 cases, these are also the regions reporting the lowest levels of testing.\nC_LIO_LICase incidence has been highest in federal prisons in Quebec, Ontario, and British Columbia, where a total of five prisons are experiencing outbreaks (1 or more cases). These regions are those reporting the highest levels of testing - higher than the testing levels in the general population.\nC_LI",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Alexandra Blair",
+        "author_inst": "University of Toronto Dalla Lana School of Public Health, Toronto, Canada"
+      },
+      {
+        "author_name": "Abtin Parnia",
+        "author_inst": "University of Toronto Dalla Lana School of Public Health, Toronto, Canada"
+      },
+      {
+        "author_name": "Arjumand Siddiqi",
+        "author_inst": "University of Toronto Dalla Lana School of Public Health, Toronto, Canada;  Gillings School of Global Public Health, University of North Carolina-Chapel Hill, C"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.05.05.20085902",
     "rel_title": "CoVID-19 prediction for India from the existing data and SIR(D) model study",
@@ -1470836,69 +1469809,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
-  {
-    "rel_doi": "10.1101/2020.05.06.20093575",
-    "rel_title": "Clinical Performance of SARS-CoV-2 Molecular Testing",
-    "rel_date": "2020-05-08",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20093575",
-    "rel_abs": "Molecular testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the gold standard for diagnosis of coronavirus disease 2019 (COVID-19), but the test clinical performance is poorly understood. From 3/10/2020-5/1/2020 NewYork-Presbyterian laboratories performed 27,377 SARS-CoV-2 molecular assays from 22,338 patients. Repeat testing was performed in 3,432 patients, of which 2,413 had negative and 1,019 had positive first day results. Repeat-tested patients were more likely to be older, male, African-American or Hispanic, and to have severe disease. Among the patients with initially negative results, 18.6% became positive upon repeat-testing. Only 58.1% of any-time positive patients had a result of \"detected\" on the first test. The clinical sensitivity of COVID-19 molecular assays is estimated between 66.2 % and 95.6%, depending on the unknown number of false negative results in single-tested patients. Conversion to a negative result is unlikely to occur before 15 to 20 days after initial testing or 20-30 days after the onset of symptoms, with 50% conversion occurring at 28 days after initial testing. Forty-nine initially-positive patients converted to negative and then back to positive in subsequent days. Conversion from first day negative to positive results increased linearly with each day of testing, reaching 25% probability in 20 days. In summary, our study provides estimates of the clinical performance of SARS-CoV-2 molecular assays and suggests time frames for appropriate repeat testing, namely 15 to 20 days after a positive test and the same or next 2 days after a negative test in a patient with high suspicion for COVID-19.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Daniel A. Green",
-        "author_inst": "Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Jason E. Zucker",
-        "author_inst": "Columbia University Medical Center"
-      },
-      {
-        "author_name": "Lars F Westblade",
-        "author_inst": "Weill Cornell Medicine"
-      },
-      {
-        "author_name": "Susan Whittier",
-        "author_inst": "Columbia University Medical Center"
-      },
-      {
-        "author_name": "Hanna Rennert",
-        "author_inst": "Weill Cornell Medicine"
-      },
-      {
-        "author_name": "Priya Velu",
-        "author_inst": "Weill Cornell Medicine"
-      },
-      {
-        "author_name": "Arryn Craney",
-        "author_inst": "Weill Cornell Medicine"
-      },
-      {
-        "author_name": "Melissa Cushing",
-        "author_inst": "Weill Cornell Medicine"
-      },
-      {
-        "author_name": "Dakai Liu",
-        "author_inst": "NewYork-Presbyterian Queens Hospital"
-      },
-      {
-        "author_name": "Magdalena E Sobieszczyk",
-        "author_inst": "Columbia University Medical Center"
-      },
-      {
-        "author_name": "Amelia K Boehme",
-        "author_inst": "Columbia University Medical Center"
-      },
-      {
-        "author_name": "Jorge Sepulveda",
-        "author_inst": "Columbia University Irving Medical Center"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.05.05.20091728",
     "rel_title": "Suboptimal biological sampling as a probable cause of false-negative COVID-19 diagnostic test results",
@@ -1471241,6 +1470151,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.05.04.20091132",
+    "rel_title": "Phenomenological Modelling of COVID-19 epidemics in Sri Lanka, Italy and Hebei Province of China",
+    "rel_date": "2020-05-08",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20091132",
+    "rel_abs": "The COVID-19 pandemic has resulted in increasing number of infections and deaths on a daily basis. There is no specific treatment or vaccine identified and the focus has been preventive measures based on statistical and mathematical models. These have relied on analyzing the behavior of populations and characteristics of the infection and applying modelling techniques. The analysis of epidemiological curve fitting on number of daily infections across affected countries could give useful insights on the characteristics of the epidemic. A variety of phenomenological models are available to capture dynamics of disease spread and growth. Data for this study used the number of daily new infections and cumulative number of infections in COVID-19 in three selected countries, Sri Lanka, Italy and Hebei province of China, from the first day of appearance of cases to 20th April 2020. In this study Gompertz, Logistic and Exponential growth curves were fitted on cumulative number of infections across countries. Akaikes information criteria (AIC) was used in determining the best fitting curve for each country. Results revealed that the most appropriate growth curves for Sri Lanka, Italy and China-Hebei are Exponential, Gompertz and Logistic curves respectively. The overall growth rate and final epidemic size evaluated from best models for the three countries and short-term forecasts were also generated. Log incidences over time in each country were regressed before and after the identified peak time of the respective outbreaks of countries. Hence, doubling time/halving time together with daily growth rates and predictions were estimated. Findings altogether demonstrate that outbreak seems extinct in Hebei-China whereas further transmissions are possible in Sri Lanka. In Italy, current outbreak transmits in a decreasing rate.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "A M C H Attanayake",
+        "author_inst": "University of Kelaniya"
+      },
+      {
+        "author_name": "sanjeewa Perera",
+        "author_inst": "University of Colombo"
+      },
+      {
+        "author_name": "Saroj Jayasinghe",
+        "author_inst": "University of Colombo Faculty of Medicine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.05.04.20090902",
     "rel_title": "More than just smell - COVID-19 is associated with severe impairment of smell, taste, and chemesthesis",
@@ -1472802,113 +1471739,6 @@
     "type": "new results",
     "category": "evolutionary biology"
   },
-  {
-    "rel_doi": "10.1101/2020.05.05.078154",
-    "rel_title": "Identification of neutralizing human monoclonal antibodies from Italian Covid-19 convalescent patients",
-    "rel_date": "2020-05-08",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.05.078154",
-    "rel_abs": "In the absence of approved drugs or vaccines, there is a pressing need to develop tools for therapy and prevention of Covid-19. Human monoclonal antibodies have very good probability of being safe and effective tools for therapy and prevention of SARS-CoV-2 infection and disease. Here we describe the screening of PBMCs from seven people who survived Covid-19 infection to isolate human monoclonal antibodies against SARS-CoV-2. Over 1,100 memory B cells were single-cell sorted using the stabilized prefusion form of the spike protein and incubated for two weeks to allow natural production of antibodies. Supernatants from each cell were tested by ELISA for spike protein binding, and positive antibodies were further tested for neutralization of spike binding to receptor(s) on Vero E6 cells and for virus neutralization in vitro. From the 1,167 memory B specific for SARS-CoV-2, we recovered 318 B lymphocytes expressing human monoclonals recognizing the spike protein and 74 of these were able to inhibit the binding of the spike protein to the receptor. Finally, 17 mAbs were able to neutralize the virus when assessed for neutralization in vitro. Lead candidates to progress into the drug development pipeline will be selected from the panel of neutralizing antibodies identified with the procedure described in this study.\n\nOne Sentence SummaryNeutralizing human monoclonal antibodies isolated from Covid-19 convalescent patients for therapeutic and prophylactic interventions.",
-    "rel_num_authors": 23,
-    "rel_authors": [
-      {
-        "author_name": "Emanuele Andreano",
-        "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy"
-      },
-      {
-        "author_name": "Emanuele Nicastri",
-        "author_inst": "National Institute for Infectious Diseases Lazzaro Spallanzani, IRCCS, Rome, Italy"
-      },
-      {
-        "author_name": "Ida Paciello",
-        "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy"
-      },
-      {
-        "author_name": "Piero Pileri",
-        "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy"
-      },
-      {
-        "author_name": "Noemi Manganaro",
-        "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy"
-      },
-      {
-        "author_name": "Giulia Piccini",
-        "author_inst": "VisMederi S.r.l, Siena, Italy"
-      },
-      {
-        "author_name": "Alessandro Manenti",
-        "author_inst": "VisMederi S.r.l, Siena, Italy; VisMederi Research S.r.l., Siena, Italy"
-      },
-      {
-        "author_name": "Marco Troisi",
-        "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy"
-      },
-      {
-        "author_name": "Fabiola Vacca",
-        "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy"
-      },
-      {
-        "author_name": "Elisa Pantano",
-        "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy"
-      },
-      {
-        "author_name": "Concetta De Santi",
-        "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy"
-      },
-      {
-        "author_name": "Dario Cardamone",
-        "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy"
-      },
-      {
-        "author_name": "Anna Kabanova",
-        "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy; Tumour Immunology Unit, Fondazione Toscana Life Sciences, Siena, Italy"
-      },
-      {
-        "author_name": "Chiara Agrati",
-        "author_inst": "National Institute for Infectious Diseases Lazzaro Spallanzani, IRCCS, Rome, Italy"
-      },
-      {
-        "author_name": "Concetta Castilletti",
-        "author_inst": "National Institute for Infectious Diseases Lazzaro Spallanzani, IRCCS, Rome, Italy"
-      },
-      {
-        "author_name": "Maria Rosaria Capobianchi",
-        "author_inst": "National Institute for Infectious Diseases Lazzaro Spallanzani, IRCCS, Rome, Italy"
-      },
-      {
-        "author_name": "Arianna Emiliozzi",
-        "author_inst": "Department of Medical Biotechnologies, University of Siena, Siena, Italy; Department of Specialized and Internal Medicine, Tropical and Infectious Diseases Unit"
-      },
-      {
-        "author_name": "Massimiliano Fabbiani",
-        "author_inst": "Department of Specialized and Internal Medicine, Tropical and Infectious Diseases Unit, University Hospital of Siena, Siena, Italy"
-      },
-      {
-        "author_name": "Francesca Montagnani",
-        "author_inst": "Department of Medical Biotechnologies, University of Siena, Siena, Italy; Department of Specialized and Internal Medicine, Tropical and Infectious Diseases Unit"
-      },
-      {
-        "author_name": "Emanuele Montomoli",
-        "author_inst": "VisMederi S.r.l, Siena, Italy; VisMederi Research S.r.l., Siena, Italy; Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy"
-      },
-      {
-        "author_name": "Claudia Sala",
-        "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy"
-      },
-      {
-        "author_name": "Giuseppe Ippolito",
-        "author_inst": "National Institute for Infectious Diseases Lazzaro Spallanzani, IRCCS, Rome, Italy"
-      },
-      {
-        "author_name": "Rino Rappuoli",
-        "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy; Faculty of Medicine, Imperial College, London, United Kingdom"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2020.05.06.081026",
     "rel_title": "Epigenetic regulator miRNA pattern differences among SARS-CoV, SARS-CoV-2 and SARS-CoV-2 world-wide isolates delineated the mystery behind the epic pathogenicity and distinct clinical characteristics of pandemic COVID-19",
@@ -1473071,6 +1471901,37 @@
     "type": "new results",
     "category": "genomics"
   },
+  {
+    "rel_doi": "10.1101/2020.05.03.20089755",
+    "rel_title": "Who maintains a good mental health in a locked-down country? A French nationwide online survey of 11,391 participants",
+    "rel_date": "2020-05-08",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.03.20089755",
+    "rel_abs": "BackgroundLockdown measures induce massive societal perturbations and can differentially affect mental wellbeing in populations depending on individual determinants. We aim at investigating the sociodemographic and environmental determinants of wellbeing during global lockdown due to the SARS-CoV-2 pandemic.\n\nMethodsA nationwide survey was sent online to the French population during the second week of global lockdown during the SARS-CoV-2 pandemic, between March 25, 2020 and March 30, 2020. Volunteers were recruited on social networks, online newspapers, and mailing lists. We analyzed sociodemographic and environmental variables obtained from a co-built and evidence-based questionnaire. Mental wellbeing was measured by the Warwick-Edinburgh Mental Wellbeing Scale (WEMWBS).\n\nResultsWe analyzed data from 11,391 (56.6%) out of 20,235 participants who answered the questionnaire. After weighting data on age and gender distributions, 5415 of the respondents were male (47.5%), 5932 were female (52.1%), and 52 (0.5%) registered as \"other.\" Multivariate analyses indicated that various factors impacted mental wellbeing. Being female (p < .001), a student (p < .001), disabled (p = .001), or having no access to outdoor space (p = 0.02) was associated with lower WEMWBS scores. Conversely, being employed (p < .001) and having more social contacts (p < .01) were both associated with greater mental wellbeing.\n\nInterpretationWe revealed differences in mental wellbeing among the French population at the early stages of global lockdown. Authorities should consider the particular vulnerability of students, persons with disabilities, and those living in constrained housing conditions that could increase the negative impact of lockdown on mental health.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Frederic HAESEBAERT",
+        "author_inst": "CH le Vinatier"
+      },
+      {
+        "author_name": "Julie Haesebaert",
+        "author_inst": "Lyon University"
+      },
+      {
+        "author_name": "Elodie Zante",
+        "author_inst": "Ch Le Vinatier"
+      },
+      {
+        "author_name": "Nicolas Franck",
+        "author_inst": "Lyon University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "psychiatry and clinical psychology"
+  },
   {
     "rel_doi": "10.1101/2020.05.06.080960",
     "rel_title": "The transcriptomic profiling of COVID-19 compared to SARS, MERS, Ebola, and H1N1",
@@ -1474296,69 +1473157,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.05.04.20090118",
-    "rel_title": "Multivariable prediction model of intensive care unit transfer and death: a French prospective cohort study of COVID-19 patients.",
-    "rel_date": "2020-05-08",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20090118",
-    "rel_abs": "BackgroundPrognostic factors of coronavirus disease 2019 (COVID-19) patients among European population are lacking. Our objective was to identify early prognostic factors upon admission to optimize the management of COVID-19 patients hospitalized in a medical ward.\n\nMethodsFrench single-center prospective cohort study of 152 patients with positive Severe acute respiratory syndrome coronavirus 2 (SARS-Cov2) real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay, hospitalized in a medical ward. Multivariable models and a simplified scoring system assessed predictive factors of intensive care unit (ICU) transfer or death at day 14 (D14), of being discharge alive and severe status at D14 (remaining with ventilation, or death). A validation was performed on an external sample of 132 patients.\n\nFindingsAt D14, the probability of ICU transfer or death was 32% (95% CI 25-40). Older age (OR 2{middle dot}61, 95% CI 0{middle dot}96-7{middle dot}10), poorer respiratory presentation (OR 4{middle dot}04 per 1-point increment on World Health Organization (WHO) clinical scale, 95% CI 1{middle dot}76-9{middle dot}25), higher CRP-level (OR 1{middle dot}63 per 100mg/L increment, 95% CI 0{middle dot}98-2{middle dot}71) and lower lymphocytes count (OR 0{middle dot}36 per 1000/mm3 increment, 95% CI 0{middle dot}13-0{middle dot}99) were associated with an increased risk of ICU requirement or death. A 8-point ordinal scale scoring system defined low (score 0-2), moderate (score 3-5), and high (score 6-8) risk patients, with predicted respectively 2%, 25% and 81% risk of ICU transfer or death at D14.\n\nInterpretationIn this prospective cohort study of laboratory-confirmed COVID-19 patients hospitalized in a medical ward in France, 32% were transferred to ICU or died. A simplified scoring system at admission predicted the outcome at D14.\n\nFundingNo funding.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Yves Allenbach",
-        "author_inst": "Sorbonne Universites, AP-HP, Groupe Hospitalier Pitie-Salpetriere, Department of Internal Medicine and Clinical Immunology, F-75013, Paris, France, Centre Natio"
-      },
-      {
-        "author_name": "David Saadoun",
-        "author_inst": "Sorbonne Universites, AP-HP, Groupe Hospitalier Pitie-Salpetriere, Department of Internal Medicine and Clinical Immunology, F-75013, Paris, France, Centre Natio"
-      },
-      {
-        "author_name": "Georgina Maalouf",
-        "author_inst": "Sorbonne Universites, AP-HP, Groupe Hospitalier Pitie-Salpetriere, Department of Internal Medicine and Clinical Immunology, F-75013, Paris, France, Centre Natio"
-      },
-      {
-        "author_name": "Matheus Vieira",
-        "author_inst": "Sorbonne Universites, AP-HP, Groupe Hospitalier Pitie-Salpetriere, Department of Internal Medicine and Clinical Immunology, F-75013, Paris, France, Centre Natio"
-      },
-      {
-        "author_name": "Alexandra Hellio",
-        "author_inst": "Sorbonne Universites, AP-HP, Groupe Hospitalier Pitie-Salpetriere, Department of Internal Medicine and Clinical Immunology, F-75013, Paris, France, Centre Natio"
-      },
-      {
-        "author_name": "Jacques Boddaert",
-        "author_inst": "Sorbonne Universite, AP-HP, Groupe Hospitalier Pitie-Salpetriere, Department of Geriatrics, F-75013, Paris, France"
-      },
-      {
-        "author_name": "Helene Gros",
-        "author_inst": "Robert-Ballanger Hospital, Aulnay-sous-Bois cedex, France"
-      },
-      {
-        "author_name": "Joe Elie Salem",
-        "author_inst": "Sorbonne Universite, AP-HP, Groupe Hospitalier Pitie-Salpetriere, CIC Pitie-Salpetriere (CIC-1901), Department of Pharmacology and Clinical Investigation Center"
-      },
-      {
-        "author_name": "Matthieu Resche-Rigon",
-        "author_inst": "Department of Biostatistics and Medical Information, AP-HP Saint-Louis University Hospital; ECSTRRA Team, CRESS UMR 1153, INSERM, University of Paris"
-      },
-      {
-        "author_name": "Lucie Biard",
-        "author_inst": "Department of Biostatistics and Medical Information, AP-HP Saint-Louis University Hospital; ECSTRRA Team, CRESS UMR 1153, INSERM, University of Paris"
-      },
-      {
-        "author_name": "Olivier Benveniste",
-        "author_inst": "Sorbonne Universites, AP-HP, Groupe Hospitalier Pitie-Salpetriere, Department of Internal Medicine and Clinical Immunology, F-75013, Paris, France, Centre Natio"
-      },
-      {
-        "author_name": "Patrice Cacoub",
-        "author_inst": "Sorbonne Universites, AP-HP, Groupe Hospitalier Pitie-Salpetriere, Department of Internal Medicine and Clinical Immunology, F-75013, Paris, France, Centre Natio"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.05.04.20090027",
     "rel_title": "Detection of SARS-CoV-2 antibodies using commercial assays and seroconversion patterns in hospitalized patients",
@@ -1474649,6 +1473447,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.05.05.20092635",
+    "rel_title": "Studies of Novel Coronavirus Disease 19 (COVID-19) Pandemic: A Global Analysis of Literature",
+    "rel_date": "2020-05-08",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20092635",
+    "rel_abs": "An exponential growth of literature about novel coronavirus disease 19 (COVID-19) has been observed in the last few months. This textual analysis of 5,780 publications extracted from the Web of Science, Medline, and Scopus databases was performed to explore the current research focuses and propose further research agenda. The Latent Dirichlet allocation was used for topic modeling. Regression analysis was conducted to examine country variations in the research focuses. Results indicated that publications were mainly contributed by the United States, China, and European countries. Guidelines for emergency care and surgical, viral pathogenesis, and global responses in the COVID-19 pandemic were the most common topics. There was variation in the research approaches to mitigate COVID-19 problems in countries with different income and transmission levels. Findings highlighted the need for global research collaboration among high- and low/middle-income countries in the different stages of prevention and control the pandemic.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Bach Xuan Tran",
+        "author_inst": "Hanoi Medical University"
+      },
+      {
+        "author_name": "Giang Hai Ha",
+        "author_inst": "Duy Tan University, Da Nang 550000, Vietnam"
+      },
+      {
+        "author_name": "Long Hoang Nguyen",
+        "author_inst": "VNU School of Medicine and Pharmacy, Vietnam National University, Hanoi 100000, Vietnam"
+      },
+      {
+        "author_name": "Giang Thu Vu",
+        "author_inst": "Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam"
+      },
+      {
+        "author_name": "Hai Thanh Phan",
+        "author_inst": "Duy Tan University, Da Nang 550000, Vietnam"
+      },
+      {
+        "author_name": "Huong Thi Le",
+        "author_inst": "Hanoi Medical University, Hanoi 100000, Vietnam"
+      },
+      {
+        "author_name": "Carl A. Latkin",
+        "author_inst": "Johns Hopkins University, Baltimore, MD 21205, United States"
+      },
+      {
+        "author_name": "Cyrus S.H. Ho",
+        "author_inst": "Department of Psychological Medicine, National University Hospital, Singapore 119074, Singapore"
+      },
+      {
+        "author_name": "Roger C.M. Ho",
+        "author_inst": "Department of Psychological Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.05.02.20088724",
     "rel_title": "The Infection Rate of the Coronavirus Disease 2019 (COVID-19) in Wuhan, China",
@@ -1476014,41 +1474863,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "cardiovascular medicine"
   },
-  {
-    "rel_doi": "10.1101/2020.05.05.20090795",
-    "rel_title": "Characteristics of patients presenting, and not presenting, to the emergency department during the early days of COVID-19",
-    "rel_date": "2020-05-08",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20090795",
-    "rel_abs": "ObjectiveSocietal responses to the COVID-19 pandemic have had a substantial effect upon the number of patients seeking healthcare. An initial step in estimating the impact of these changes is characterizing the patients, visits, and diagnoses for whom care is being delayed or deferred.\n\nMethodsWe conducted an observational study, examining demographics and diagnoses for all patient visits to the ED of an urban Level-1 trauma center before and after the state declaration and compared them to visits from a similar period in 2019. We estimated the ratios of the before and after periods using Poisson regression, calculated the percent change with respect to 2019 for total ED visits, patient characteristics, and diagnoses, and then evaluated the interactions between each factor and the overall change in ED visits.\n\nResultsThere was a significant 35.2% drop in overall ED visits after the state declaration. Disproportionate declines were seen in visits by pediatric and older patients, women, and Medicare recipients as well as for presentations of syncope, cerebrovascular accidents, urolithiasis, abdominal and back pain. Significantly disproportionate increases were seen in ED visits for potential symptoms of COVID-19, including URIs, shortness of breath, and chest pain.\n\nConclusionsPatient concerns about health care settings and public health have significantly altered care-seeking during the COVID-19 pandemic. Overall and differential declines in ED visits for certain demographic groups and disease processes should prompt efforts to encourage care-seeking and research to monitor for the morbidity and mortality that is likely to result from delayed or deferred care.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Bjorn C Westgard",
-        "author_inst": "Regions Hospital"
-      },
-      {
-        "author_name": "Matthew W Morgan",
-        "author_inst": "Regions Hospital"
-      },
-      {
-        "author_name": "Gabriela Vazquez-Benitez",
-        "author_inst": "HealthPartners Institute"
-      },
-      {
-        "author_name": "Lauren O Erickson",
-        "author_inst": "HealthPartners Institute"
-      },
-      {
-        "author_name": "Michael D. Zwank",
-        "author_inst": "Regions Hospital"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "emergency medicine"
-  },
   {
     "rel_doi": "10.1101/2020.05.04.20091009",
     "rel_title": "A mathematical assessment of the efficiency of quarantining and contact tracing in curbing the COVID-19 epidemic",
@@ -1476331,6 +1475145,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.05.04.20090324",
+    "rel_title": "Estimating Excess Deaths in the United States Early in the COVID-19 Pandemic",
+    "rel_date": "2020-05-08",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20090324",
+    "rel_abs": "1Deaths are frequently under-estimated during emergencies, times when accurate mortality estimates are crucial for pandemic response and public adherence to non-pharmaceutical interventions. This study estimates excess all-cause, pneumonia, and influenza mortality during the COVID-19 health emergency using the June 12, 2020 release of weekly mortality data from the United States (U.S.) Mortality Surveillance Survey (MSS) from September 27, 2015 to May 9, 2020, using semiparametric and conventional time-series models in 9 states with high reported COVID-19 deaths and apparently complete mortality data: California, Colorado, Florida, Illinois, Massachusetts, Michigan, New Jersey, New York, and Washington. The May 9 endpoint was chosen due to apparently increased reporting lags in provisional mortality counts. We estimated greater excess mortality than official COVID-19 mortality in the U.S. (excess mortality 95% confidence interval (CI) (80862, 107284) vs. 78834 COVID-19 deaths) and 6 states: California (excess mortality 95% CI (2891, 5873) vs. 2849 COVID-19 deaths); Illinois (95% CI (4412, 5871) vs. 3525 COVID-19 deaths); Massachusetts (95% CI (5061, 6317) vs. 5050 COVID-19 deaths); New Jersey (95% CI (12497, 15307) vs. 10465 COVID-19 deaths); and New York (95% CI (30469, 37722) vs. 26584 COVID-19 deaths). Conventional model results were consistent with semiparametric results but less precise.\n\nOfficial COVID-19 mortality substantially understates actual mortality, suggesting greater case-fatality rates. Mortality reporting lags appeared to worsen during the pandemic, when timeliness in surveillance systems was most crucial for improving pandemic response.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Roberto Rivera",
+        "author_inst": "University of Puerto Rico - Mayaguez"
+      },
+      {
+        "author_name": "Janet Rosenbaum",
+        "author_inst": "SUNY downstate"
+      },
+      {
+        "author_name": "Walter Quispe",
+        "author_inst": "University of Puerto Rico - Mayaguez"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.05.04.20090233",
     "rel_title": "Search for the trend of COVID-19 infection following Farr's law, IDEA model and power law.",
@@ -1477575,85 +1476416,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.05.07.083048",
-    "rel_title": "A simple RNA preparation method for SARS-CoV-2 detection by RT-qPCR",
-    "rel_date": "2020-05-07",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.07.083048",
-    "rel_abs": "The technique RT-qPCR for viral RNA detection is the current worldwide strategy used for early detection of the novel coronavirus SARS-CoV-2. RNA extraction is a key pre-analytical step in RT-qPCR, often achieved using commercial kits. However, the magnitude of the COVID-19 pandemic is causing disruptions to the global supply chains used by many diagnostic laboratories to procure the commercial kits required for RNA extraction. Shortage in these essential reagents is even more acute in developing countries with no means to produce kits locally. We sought to find an alternative procedure to replace commercial kits using common reagents found in molecular biology laboratories. Here we report a method for RNA extraction that takes about 40 min to complete ten samples, and is not more laborious than current commercial RNA extraction kits. We demonstrate that this method can be used to process nasopharyngeal swab samples and yields RT-qPCR results comparable to those obtained with commercial kits. Most importantly, this procedure can be easily implemented in any molecular diagnostic laboratory. Frequent testing is crucial for individual patient management as well as for public health decision making in this pandemic. Implementation of this method could maintain crucial testing going despite commercial kit shortages.",
-    "rel_num_authors": 16,
-    "rel_authors": [
-      {
-        "author_name": "Aniela Wozniak",
-        "author_inst": "Pontificia Universidad Catolica de Chile"
-      },
-      {
-        "author_name": "Ariel Cerda",
-        "author_inst": "Pontificia Universidad Catolica de Chile"
-      },
-      {
-        "author_name": "Catalina Ibarra-Henriquez",
-        "author_inst": "Pontificia Universidad Catolica de Chile"
-      },
-      {
-        "author_name": "Valentina Sebastian",
-        "author_inst": "Pontificia Universidad Catolica de Chile"
-      },
-      {
-        "author_name": "Grace Armijo",
-        "author_inst": "Pontificia Universidad Catolica de Chile"
-      },
-      {
-        "author_name": "Liliana Lamig",
-        "author_inst": "Pontificia Universidad Catolica de Chile"
-      },
-      {
-        "author_name": "Carolina Miranda",
-        "author_inst": "Pontificia Universidad Catolica de Chile"
-      },
-      {
-        "author_name": "Marcela Lagos",
-        "author_inst": "Pontificia Universidad Catolica de Chile"
-      },
-      {
-        "author_name": "Sandra Solari",
-        "author_inst": "Pontificia Universidad Catolica de Chile"
-      },
-      {
-        "author_name": "Ana Maria Guzman",
-        "author_inst": "Pontificia Universidad Catolica de Chile"
-      },
-      {
-        "author_name": "Teresa Quiroga",
-        "author_inst": "Pontificia Universidad Catolica de Chile"
-      },
-      {
-        "author_name": "Susan Hitschfeld",
-        "author_inst": "Pontificia Universidad Catolica de Chile"
-      },
-      {
-        "author_name": "Eleodoro Riveras",
-        "author_inst": "Pontificia Universidad Catolica de Chile"
-      },
-      {
-        "author_name": "Marcela Ferres",
-        "author_inst": "Pontificia Universidad Catolica de Chile"
-      },
-      {
-        "author_name": "Rodrigo A Gutierrez",
-        "author_inst": "Pontificia Universidad Catolica de Chile"
-      },
-      {
-        "author_name": "Patricia Garcia",
-        "author_inst": "Pontificia Universidad Catolica de Chile"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "new results",
-    "category": "molecular biology"
-  },
   {
     "rel_doi": "10.1101/2020.05.06.080630",
     "rel_title": "In Silico Trial to test COVID-19 candidate vaccines: a case study with UISS platform",
@@ -1478004,6 +1476766,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "occupational and environmental health"
   },
+  {
+    "rel_doi": "10.1101/2020.05.04.20090670",
+    "rel_title": "Projection of COVID-19 Cases and Deaths in the US as Individual States Re-open May 4,2020",
+    "rel_date": "2020-05-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20090670",
+    "rel_abs": "In March and April 2020, control measures enforcing social distancing and restricting individual movement and contact were adopted across the United States in an effort to slow the spread and growth of COVID-19. However, a number of states have now begun to ease these restrictions. Here, we evaluate the effects of loosening stay-at-home orders on COVID-19 incidence and related outcomes. We use a metapopulation model applied at county resolution to simulate the spread and growth of COVID-19 incidence in the United States. We calibrate the model against county-level daily case and death data collected from February 21, 2020 to May 2, 2020, and project the outbreak in 3,142 US counties for 6 weeks into the future. Projections for daily reported cases, daily new infections (both reported and unreported), new and cumulative hospital bed demand, ICU bed and ventilator demand, as well as daily mortality, are generated. We observe a rebound in COVID-19 incidence and deaths beginning in late May, approximately 2 to 4 weeks after states begin to reopen. Importantly, the lag between infection acquisition and case confirmation, coupled with insufficient broader testing and contact tracing, will mask any rebound and exponential growth of the COVID-19 until it is well underway.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Teresa Yamana",
+        "author_inst": "Columbia University"
+      },
+      {
+        "author_name": "Sen Pei",
+        "author_inst": "Columbia University"
+      },
+      {
+        "author_name": "Sasikiran Kandula",
+        "author_inst": "Columbia University"
+      },
+      {
+        "author_name": "Jeffrey Shaman",
+        "author_inst": "Columbia University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.05.05.20092361",
     "rel_title": "Cooperative virus propagation underlies COVID-19 transmission dynamics",
@@ -1479005,49 +1477798,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2020.05.05.079558",
-    "rel_title": "Development and simulation of fully glycosylated molecular models of ACE2-Fc fusion proteins and their interaction with the SARS-CoV-2 spike protein binding domain",
-    "rel_date": "2020-05-06",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.05.079558",
-    "rel_abs": "We develop fully glycosylated computational models of ACE2-Fc fusion proteins which are promising targets for a COVID-19 therapeutic. These models are tested in their interaction with a fragment of the receptor-binding domain (RBD) of the Spike Protein S of the SARS-CoV-2 virus, via atomistic molecular dynamics simulations. We see that some ACE2 glycans interact with the S fragments, and glycans are influencing the conformation of the ACE2 receptor. Additionally, we optimize algorithms for protein glycosylation modelling in order to expedite future model development. All models and algorithms are openly available.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Austen Bernardi",
-        "author_inst": "UC Davis"
-      },
-      {
-        "author_name": "Yihan Huang",
-        "author_inst": "UC Davis"
-      },
-      {
-        "author_name": "Bradley S Harris",
-        "author_inst": "UC Davis"
-      },
-      {
-        "author_name": "Yongao Xiong",
-        "author_inst": "UC Davis"
-      },
-      {
-        "author_name": "Somen Nandi",
-        "author_inst": "UC Davis"
-      },
-      {
-        "author_name": "Karen A McDonald",
-        "author_inst": "UC Davis"
-      },
-      {
-        "author_name": "Roland Faller",
-        "author_inst": "UC Davis"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "biophysics"
-  },
   {
     "rel_doi": "10.1101/2020.05.06.077883",
     "rel_title": "Coronavirus activates a stem cell-mediated defense mechanism that accelerates the activation of dormant tuberculosis: implications for the COVID-19 pandemic",
@@ -1479266,6 +1478016,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
+  {
+    "rel_doi": "10.1101/2020.05.01.20081034",
+    "rel_title": "Evaluation of nCoV-QS (MiCo BioMed) for RT-qPCR detection of SARS-CoV-2 from nasopharyngeal samples using CDC FDA EUA qPCR kit as a gold standard: an example of the need of validation studies.",
+    "rel_date": "2020-05-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20081034",
+    "rel_abs": "BackgroundSeveral qPCR kits are available for SARS-CoV-2 diagnosis, mostly lacking of evaluation due to covid19 emergency.\n\nObjectiveWe evaluated nCoV-QS (MiCo BioMed) kit using CDC kit as gold standard.\n\nResultsWe found limitations for nCoV-QS: 1) lower sensitivity 2) lack of RNA quality control probe 3) no capacity to quantify viral load.\n\nConclussionsValidation studies should be implemented for any SARS-CoV-2 RT-qPCR commercial kit to prevent unreliable diagnosis.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Byron Freire-Paspuel",
+        "author_inst": "Universidad de las Americas"
+      },
+      {
+        "author_name": "Patricio Vega",
+        "author_inst": "ABG- Galapagos"
+      },
+      {
+        "author_name": "Alberto Velez",
+        "author_inst": "ABG-Galapagos"
+      },
+      {
+        "author_name": "Paulina Castello",
+        "author_inst": "ABG-Galapagos"
+      },
+      {
+        "author_name": "Marilyn Cruz",
+        "author_inst": "ABG-Galapagos"
+      },
+      {
+        "author_name": "Miguel Angel Garcia Bereguiain",
+        "author_inst": "Universidad de Las Americas"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.05.02.20088898",
     "rel_title": "Repeated seroprevalence of anti-SARS-CoV-2 IgG antibodies in a population-based sample from Geneva, Switzerland",
@@ -1480527,45 +1479316,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.30.20086975",
-    "rel_title": "Sex-specific differences in COVID-19 testing, cases and outcomes: a population-wide study in Ontario, Canada",
-    "rel_date": "2020-05-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20086975",
-    "rel_abs": "In this population-wide study in Ontario, Canada we report on all 194,372 unique residents who received testing for SARS-CoV-2 between January 23, 2020 and April 28, 2020. We found that while more women than men were tested for SARS-CoV-2, men had a higher rate of laboratory-confirmed COVID-19 infection, hospitalization, ICU admission and death. These findings were consistent even with age adjustment, suggesting that the observed differences in outcomes between women and men were not explained by age or systematic differences in testing by sex. Instead, they may be due to sex-based immunological or other gendered differences, such as higher rates of smoking leading to cardiovascular disease.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Nathan M. Stall",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Wei Wu",
-        "author_inst": "Women's College Hospital, Toronto, Canada"
-      },
-      {
-        "author_name": "Lauren Lapointe-Shaw",
-        "author_inst": "University Health Network, Toronto, Canada"
-      },
-      {
-        "author_name": "David Fisman",
-        "author_inst": "University of Toronto"
-      },
-      {
-        "author_name": "Michael Hillmer",
-        "author_inst": "Ontario Ministry of Health, Toronto, Canada"
-      },
-      {
-        "author_name": "Paula A. Rochon",
-        "author_inst": "Women's College Hospital, Toronto, Canada"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.05.01.20087155",
     "rel_title": "Asymptomatic infection and herd immunity of COVID-19 in Wuhan and Japan",
@@ -1480828,6 +1479578,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.05.01.20087114",
+    "rel_title": "Lung disease severity, Coronary Artery Calcium, Coronary inflammation and Mortality in Coronavirus Disease 2019.",
+    "rel_date": "2020-05-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20087114",
+    "rel_abs": "The authors have withdrawn this manuscript at the request of their local IRB, because the objectives outlined in this study were not specifically approved by the IRB. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Nicola Gaibazzi",
+        "author_inst": "University Hospital of Parma"
+      },
+      {
+        "author_name": "Chiara Martini",
+        "author_inst": "University Hospital of Parma"
+      },
+      {
+        "author_name": "Maria Mattioli",
+        "author_inst": "University Hospital of Parma"
+      },
+      {
+        "author_name": "Domenico Tuttolomondo",
+        "author_inst": "University Hospital of Parma"
+      },
+      {
+        "author_name": "Angela Guidorossi",
+        "author_inst": "University Hospital of Parma"
+      },
+      {
+        "author_name": "Sergio Suma",
+        "author_inst": "University Hospital of Parma"
+      },
+      {
+        "author_name": "Damini Dey",
+        "author_inst": "Cedars-Sinai Medical Center, Los Angeles"
+      },
+      {
+        "author_name": "Anselmo Palumbo",
+        "author_inst": "University Hospital of Parma"
+      },
+      {
+        "author_name": "Massimo De Filippo",
+        "author_inst": "University Hospital of Parma"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.05.01.20087130",
     "rel_title": "Dose prediction for repurposing nitazoxanide in SARS-CoV-2 treatment or chemoprophylaxis",
@@ -1481693,53 +1480494,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.05.02.20087270",
-    "rel_title": "Accounting for underreporting in mathematical modelling of transmission and control of COVID-19 in Iran",
-    "rel_date": "2020-05-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.02.20087270",
-    "rel_abs": "BackgroundIran has been the hardest hit country by the outbreak of SARS-CoV-2 in the Middle East with 74,877 confirmed cases and 4,683 deaths as of 15 April 2020. With a relatively high case fatality ratio and limited testing capacity, the number of confirmed cases reported is suspected to suffer from significant under-reporting. Therefore, understanding the transmission dynamics of COVID-19 and assessing the effectiveness of the interventions that have taken place in Iran while accounting for the uncertain level of underreporting is of critical importance. We use a mathematical epidemic model utilizing official confirmed data and estimates of underreporting to understand how transmission in Iran has been changing between February and April 2020.\n\nMethodsWe developed a compartmental transmission model to estimate the effective reproduction number and its fluctuations since the beginning of the outbreak in Iran. We associate the variations in the effective reproduction number with a timeline of interventions and national events. The estimation method also accounts for the underreporting due to low case ascertainment by estimating the percentage of symptomatic cases using delay-adjusted case fatality ratio based on the distribution of the delay from hospitalization-to-death.\n\nFindingsOur estimates of the effective reproduction number ranged from 0.66 to 1.73 between February and April 2020, with a median of 1.16. We estimate a reduction in the effective reproduction number during this period, from 1.73 (95% CI 1.60 - 1.87) on 1 March 2020 to 0.69 (95% CI 0.68-0.70) on 15 April 2020, due to various non-pharmaceutical interventions including school closures, a ban on public gatherings including sports and religious events, and full or partial closure of non-essential businesses. Based on these estimates and given that a near complete containment is no longer feasible, it is likely that the outbreak may continue until the end of the 2020 if the current level of physical distancing and interventions continue and no effective vaccination or therapeutic are developed and made widely available.\n\nInterpretationThe series of non-pharmaceutical interventions and the public compliance that took place in Iran are found to be effective in slowing down the speed of the spread of COVID-19 within the studied time period. However, we argue that if the impact of underreporting is overlooked, the estimated transmission and control dynamics could mislead the public health decisions, policy makers, and general public especially in the earlier stages of the outbreak.\n\nFundingNil.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Meead Saberi",
-        "author_inst": "University of New South Wales"
-      },
-      {
-        "author_name": "Homayoun Hamedmoghadam",
-        "author_inst": "Monash University"
-      },
-      {
-        "author_name": "Kaveh Madani",
-        "author_inst": "Yale University"
-      },
-      {
-        "author_name": "Helen D. Dolk",
-        "author_inst": "Ulster University"
-      },
-      {
-        "author_name": "Andrei Morgan",
-        "author_inst": "INSERM; University College of London"
-      },
-      {
-        "author_name": "Joan K. Morris",
-        "author_inst": "St George's, University of London"
-      },
-      {
-        "author_name": "Kaveh Khoshnood",
-        "author_inst": "Yale University"
-      },
-      {
-        "author_name": "Babak Khoshnood",
-        "author_inst": "INSERM"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.05.02.20087221",
     "rel_title": "Evaluating efficiency of pooling specimens for PCR-based detection of COVID-19",
@@ -1482098,6 +1480852,69 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
+  {
+    "rel_doi": "10.1101/2020.05.01.20088179",
+    "rel_title": "Impact of policy interventions and social distancing on SARS-CoV-2 transmission in the United States",
+    "rel_date": "2020-05-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20088179",
+    "rel_abs": "BackgroundPolicymakers have employed various non-pharmaceutical interventions (NPIs) such as stay-at-home orders and school closures to limit the spread of Coronavirus disease (COVID-19). However, these measures are not without cost, and careful analysis is critical to quantify their impact on disease spread and guide future initiatives. This study aims to measure the impact of NPIs on the effective reproductive number (Rt) and other COVID-19 outcomes in U.S. states.\n\nMethodsIn order to standardize the stage of disease spread in each state, this study analyzes the weeks immediately after each state reached 500 cases. The primary outcomes were average Rt in the week following 500 cases and doubling time from 500 to 1000 cases. Linear and logistic regressions were performed in R to assess the impact of various NPIs while controlling for population density, GDP, and certain health metrics. This analysis was repeated for deaths with doubling time from 50 to 100 deaths and included several healthcare infrastructure control variables.\n\nResultsStates that had a stay-at-home order in place at the time of their 500th case are associated with lower average Rt the following week compared to states without a stay-at-home order (p < 0.001) and are significantly less likely to have an Rt>1 (OR 0.07, 95% CI 0.01 to 0.37, p = 0.004). These states also experienced a significantly longer doubling time from 500 to 1000 cases (HR 0.35, 95% CI 0.17 to 0.72, p = 0.004). States in the highest quartile of average time spent at home were also slower to reach 1000 cases than those in the lowest quartile (HR 0.18, 95% CI 0.06 to 0.53, p = 0.002).\n\nDiscussionFew studies have analyzed the effect of statewide stay-at-home orders, school closures, and other social distancing measures in the U.S., which has faced the largest COVID-19 case burden. States with stay-at-home orders have a 93% decrease in the odds of having a positive Rt at a standardized point in disease burden. States that plan to scale back such measures should carefully monitor transmission metrics.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Nickolas Dreher",
+        "author_inst": "Mount Sinai"
+      },
+      {
+        "author_name": "Zachary Spiera",
+        "author_inst": "Mount Sinai"
+      },
+      {
+        "author_name": "Fiona M McAuley",
+        "author_inst": "Mount Sinai"
+      },
+      {
+        "author_name": "Lindsey Kuohn",
+        "author_inst": "Mount Sinai"
+      },
+      {
+        "author_name": "John R Durbin",
+        "author_inst": "Mount Sinai"
+      },
+      {
+        "author_name": "Naoum Fares Marayati",
+        "author_inst": "Mount Sinai"
+      },
+      {
+        "author_name": "Muhammad Ali",
+        "author_inst": "Mount Sinai"
+      },
+      {
+        "author_name": "Adam Y Li",
+        "author_inst": "Mount Sinai"
+      },
+      {
+        "author_name": "Theodore C Hannah",
+        "author_inst": "Mount Sinai"
+      },
+      {
+        "author_name": "Alex Gometz",
+        "author_inst": "Concussion Management of New York"
+      },
+      {
+        "author_name": "JT Kostman",
+        "author_inst": "ProtectedBy.AI"
+      },
+      {
+        "author_name": "Tanvir F Choudhri",
+        "author_inst": "Mount Sinai"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health policy"
+  },
   {
     "rel_doi": "10.1101/2020.05.01.20087932",
     "rel_title": "Correlation of coagulation parameters with clinical outcomes in Coronavirus-19 affected minorities in United States: Observational cohort",
@@ -1483239,37 +1482056,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.04.29.20084400",
-    "rel_title": "How many lives can be saved? A global view on the impact of testing, herd immunity and demographics on COVID-19 fatality rates",
-    "rel_date": "2020-05-05",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20084400",
-    "rel_abs": "In this work, we assess the global impact of COVID-19 showing how demographic factors, testing policies and herd immunity are key for saving lives. We extend a standard epidemiological SEIR model in order to: (a) identify the role of demographics (population size and population age distribution) on COVID-19 fatality rates; (b) quantify the maximum number of lives that can be saved according to different testing strategies, different levels of herd immunity, and specific population characteristics; and (d) infer from the observed case fatality rates (CFR) what the true fatality rate might be. Different from previous SEIR model extensions, we implement a Bayesian Melding method in our calibration strategy which enables us to account for data limitation on the total number of deaths. We derive a distribution of the set of parameters that best replicate the observed evolution of deaths by using information from both the model and the data.\n\nOne Sentence SummaryDemographics factors, testing policies and herd immunity are key for quantifying the maximum number of lives that can be saved from COVID-19.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Miguel Sanchez-Romero",
-        "author_inst": "Wittgenstein Centre for Demography and Global Human Capital (Univ. Vienna, IIASA, VID/OAW), Vienna Institute of Demography/Austrian Academy of Sciences and Inst"
-      },
-      {
-        "author_name": "Vanessa di Lego",
-        "author_inst": "Wittgenstein Centre (Univ. Vienna, IIASA, VID/OAW), Vienna Institute of Demography"
-      },
-      {
-        "author_name": "Alexia Prskawetz",
-        "author_inst": "Wittgenstein Centre for Demography and Global Human Capital (Univ. Vienna, IIASA, VID/OAW), Vienna Institute of Demography/Austrian Academy of Sciences and Inst"
-      },
-      {
-        "author_name": "Bernardo L Queiroz",
-        "author_inst": "Centro de Desenvolvimento e Planejamento Regional (CEDEPLAR)"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.04.29.20085068",
     "rel_title": "Antibody Profiling and Prevalence in the US population during the SARS-CoV2 Pandemic",
@@ -1483668,6 +1482454,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pharmacology and therapeutics"
   },
+  {
+    "rel_doi": "10.1101/2020.04.29.20085563",
+    "rel_title": "Public knowledge, attitudes and practices towards COVID-19: A cross-sectional study in Malaysia",
+    "rel_date": "2020-05-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20085563",
+    "rel_abs": "In an effort to mitigate the outbreak of COVID-19, many countries have imposed drastic lockdown, movement control or shelter in place orders on their residents. The effectiveness of these mitigation measures is highly dependent on cooperation and compliance of all members of society. The knowledge, attitudes and practices people hold toward the disease play an integral role in determining a societys readiness to accept behavioural change measures from health authorities. The aim of this study was to determine the knowledge levels, attitudes and practices toward COVID-19 among the Malaysian public. A cross-sectional online survey of 4,850 Malaysian residents was conducted between 27th March and 3rd April 2020. The survey instrument consisted of demographic characteristics, 13 items on knowledge, 3 items on attitudes and 3 items on practices, modified from a previously published questionnaire on COVID-19. Descriptive statistics, chi-square tests, t-tests and one-way analysis of variance (ANOVA) were conducted. The overall correct rate of the knowledge questionnaire was 80.5%. Most participants held positive attitudes toward the successful control of COVID-19 (83.1%), the ability of Malaysia to conquer the disease (95.9%) and the way the Malaysian government was handling the crisis (89.9%). Most participants were also taking precautions such as avoiding crowds (83.4%) and practising proper hand hygiene (87.8%) in the week before the movement control order started. However, the wearing of face masks was less common (51.2%). This survey is among the first to assess knowledge, attitudes and practice in response to the COVID-19 pandemic in Malaysia. The results highlight the importance of consistent messaging from health authorities and the government as well as the need for tailored health education programs to improve levels of knowledge, attitudes and practices.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Emma MW Mohamad",
+        "author_inst": "UNIVERSITI KEBANGSAAN MALAYSIA"
+      },
+      {
+        "author_name": "Arina Anis Azlan",
+        "author_inst": "Universiti Kebangsaan Malaysia"
+      },
+      {
+        "author_name": "Mohammad Rezal Hamzah",
+        "author_inst": "Universiti Malaysia Perlis"
+      },
+      {
+        "author_name": "Jen Sern Tham",
+        "author_inst": "Universiti Putra Malaysia"
+      },
+      {
+        "author_name": "Suffian Hadi Ayub",
+        "author_inst": "Sunway University Malaysia"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.04.30.20085928",
     "rel_title": "COVID-19 in breast cancer patients: a cohort at the Institut Curie hospitals in the Paris area",
@@ -1484825,57 +1483646,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health systems and quality improvement"
   },
-  {
-    "rel_doi": "10.1101/2020.04.29.20085878",
-    "rel_title": "Viable circulating endothelial cells and their progenitors are increased in Covid-19 patients",
-    "rel_date": "2020-05-05",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20085878",
-    "rel_abs": "During the course of Covid-19, the disease caused by the new Coronavirus SARS-CoV-2, thrombotic phenomena and/or diffuse vascular damage are frequent, and viral elements have been observed within endothelial cells. Circulating endothelial cells (CECs) and their progenitors (CEPs) are increased in cardiovascular, thrombotic, infectious and cancer diseases. Using a validated flow cytometry procedure, we found that viable CEPs/mL were significantly increased in Covid-19 patients compared to healthy controls. This increase was observed in patients with mild symptoms and not further augmented in patients with severe symptoms. In patients who recovered, CEPs decreased, but were in a range still significantly higher than normal controls. Regarding mature CECs, in Covid-19 patients their absolute number was similar to those observed in healthy controls, but the viable/apoptotic CEC ratio was significantly different. Both mild and severe Covid-19 patients had significantly more viable CECs compared to healthy controls. Patients who recovered had significantly less CECs/mL when compared to controls as well as to mild and severe Covid-19 patients. A positive correlation was found between the copies of SARS-CoV-2 RNA in the cellular fraction and apoptotic CEPs/mL in severe Covid-19 patients. These findings suggest that CECs and CEPs might be investigated as candidate biomarkers of endothelial damage in Covid-19 patients.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Patrizia Mancuso",
-        "author_inst": "European Institute of Oncology"
-      },
-      {
-        "author_name": "Antonio Gidaro",
-        "author_inst": "Sacco Hospital"
-      },
-      {
-        "author_name": "Giuliana Gregato",
-        "author_inst": "European Institute of Oncology"
-      },
-      {
-        "author_name": "Alessandro Raveane",
-        "author_inst": "European Institute of Oncology"
-      },
-      {
-        "author_name": "Paola Cremonesi",
-        "author_inst": "European Institute of Oncology"
-      },
-      {
-        "author_name": "Jessica Quarna",
-        "author_inst": "European Institute of Oncology"
-      },
-      {
-        "author_name": "Sonia Caccia",
-        "author_inst": "Sacco Hospital"
-      },
-      {
-        "author_name": "Chiara Cogliati",
-        "author_inst": "Sacco Hospital"
-      },
-      {
-        "author_name": "Francesco Bertolini",
-        "author_inst": "European Institute of Oncology"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.04.30.20086538",
     "rel_title": "Novel Spatiotemporal Feature Extraction Parallel Deep Neural Network for Forecasting Confirmed Cases of Coronavirus Disease 2019",
@@ -1485070,6 +1483840,69 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.30.20086652",
+    "rel_title": "Perspectives of Cancer Patients and Their Health during the COVID-19 Pandemic",
+    "rel_date": "2020-05-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20086652",
+    "rel_abs": "IntroductionThe immunosuppressive nature of some cancers and many cancer-directed treatments may increase the risk of infection with and severe sequelae from Coronavirus Disease 2019 (COVID-19). The objective of this study was to compare concerns about COVID-19 among individuals undergoing cancer treatment to those with a history of cancer not currently receiving therapy and to those without a cancer history.\n\nMethodsWe conducted a cross-sectional anonymous online survey study of adults currently residing in the United States. Participants were recruited over a one-week period (April 3-11, 2020) using promoted advertisements on Facebook and Twitter. Groups were compared using chi-squared tests, Fishers exact tests, and t-tests.\n\nResults543 respondents from 47 states provided information on their cancer history and were included in analyses. Participants receiving active treatment reported greater concern about coronavirus infection (p<0.0001), higher levels of family distress caused by the COVID-19 pandemic (p=0.004), and greater concern that the general public does not adequately understand the seriousness of COVID-19 (p=0.04). Those with metastatic disease were more likely to indicate that COVID-19 had negatively affected their cancer care compared to patients with non-metastatic cancer (50.8% vs. 31.0%; p=0.02). The most commonly reported treatment modifications included chemotherapy delays.\n\nConclusionsPatients undergoing active treatment for cancer were most concerned about the short-term effects of the COVID-19 pandemic on the logistics as well as potential efficacy of ongoing cancer treatment, longer term effects, and overarching societal concerns that the population at large is not as concerned about the public health implications of the coronavirus.",
+    "rel_num_authors": 12,
+    "rel_authors": [
+      {
+        "author_name": "Emil Lou",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Deanna Teoh",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Katherine Brown",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Anne Blaes",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Shernan G. Holtan",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Patricia Jewett",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Helen Parsons",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "E. Waruiru Mburu",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Lauren Thomaier",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Jane Yuet Ching Hui",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Heather H. Nelson",
+        "author_inst": "University of Minnesota"
+      },
+      {
+        "author_name": "Rachel I. Vogel",
+        "author_inst": "University of Minnesota"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.04.30.20085316",
     "rel_title": "Worldwide Effectiveness of Various Non-Pharmaceutical Intervention Control Strategies on the Global COVID-19 Pandemic: A Linearised Control Model",
@@ -1485991,41 +1484824,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pathology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.27.20081877",
-    "rel_title": "Distinguishing between COVID-19 and the common cold in a primary care setting - comparison of patients with positive and negative SARS-CoV-2 PCR results.",
-    "rel_date": "2020-05-05",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20081877",
-    "rel_abs": "BackgroundCombating the COVID-19 pandemic is a major challenge for health systems, citizens and policy makers worldwide. Early detection of affected patients within the large and heterogeneous group of patients with common cold symptoms is an important element of this effort, but often hindered by limited testing resources and the lack of pathognomonic symptoms in COVID-19. Therefore, we aimed to identify predictive risk factors for a positive SARS-CoV-2 PCR (CovPCR) result in a primary care setting.\n\nMethodWe performed a multi-center cross-sectional cohort study on predictive clinical characteristics for a positive CovPCR over a period of 4 weeks in primary care patients in Germany.\n\nFindingsIn total, 374 patients in 14 primary care centers received CovPCR and were included in this analysis. The median age was 44.0 (IQR: 31.0-59.0) and a fraction of 10.7% (n=40) tested positive for COVID-19. Patients who reported anosmia had a higher odds ratio (OR: 4.54; 95%-CI: 1.51-13.67) for a positive test result while patients with a sore throat had a lower OR (OR: 0.33; 95%-CI: 0.11-0.97). Patients who had a first grade contact with an infected persons and showed symptoms themselves also had an increased OR for positive testing (OR: 5.16; 95% CI: 1.72-15.51). This correlation was also present when they themselves were still asymptomatic (OR: 12.55; 95% CI: 3.97-39.67).\n\nConclusionsSeveral anamnestic criteria may be helpful to assess pre-test probability of COVID-19 in patients with common cold symptoms",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Johannes Just",
-        "author_inst": "Witten/Herdecke University, Institute of General Practice and Interprofessional Care"
-      },
-      {
-        "author_name": "Marie-Therese Puth",
-        "author_inst": "Department of Medical Biometry, Informatics and Epidemiology (IMBIE), University Hospital Bonn"
-      },
-      {
-        "author_name": "Felix Regenold",
-        "author_inst": "Witten/Herdecke University, Institute of General Practice and Interprofessional Care"
-      },
-      {
-        "author_name": "Klaus Weckbecker",
-        "author_inst": "Witten/Herdecke University, Institute of General Practice and Interprofessional Care"
-      },
-      {
-        "author_name": "Markus Bleckwenn",
-        "author_inst": "Leipzig University, Department of General Practice"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "primary care research"
-  },
   {
     "rel_doi": "10.1101/2020.04.28.20082990",
     "rel_title": "A simple model to show the relative risk of viral aerosol infection and the benefit of  wearing masks in different settings with implications for Covid-19 .",
@@ -1486328,6 +1485126,93 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.04.30.20082172",
+    "rel_title": "Monitoring social distancing and SARS-CoV-2 transmission in Brazil using cell phone mobility data",
+    "rel_date": "2020-05-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20082172",
+    "rel_abs": "Social distancing measures have emerged as the predominant intervention for containing the spread of COVID-19, but evaluating adherence and effectiveness remains a challenge. We assessed the relationship between aggregated mobility data collected from mobile phone users and the time-dependent reproduction number R(t), using severe acute respiratory illness (SARI) cases reported by Sao Paulo and Rio de Janeiro. We found that the proportion of individuals staying home all day (isolation index) had a strong inverse correlation with R(t) (rho<-0.7) and was predictive of COVID-19 transmissibility (p<0.0001). Furthermore, indexs of 46.7% had the highest accuracy (93.9%) to predict R(t) below one. This metric can be monitored in real time to assess adherence to social distancing measures and predict their effectiveness for controlling SARS-CoV-2 transmission.\n\nOne Sentence SummaryMobility data to monitoring social distancing in the COVID-19 outbreak",
+    "rel_num_authors": 18,
+    "rel_authors": [
+      {
+        "author_name": "Silvano B de Oliveira",
+        "author_inst": "National Immunization Program, Department of Immunization and Communicable Diseases, Secretariat of Health Surveillance, Ministry of Health, Brazil"
+      },
+      {
+        "author_name": "Victor Bertollo Gomes Porto",
+        "author_inst": "National Immunization Program, Department of Immunization and Communicable Diseases, Secretariat of Health Surveillance, Ministry of Health, Brazil."
+      },
+      {
+        "author_name": "Fabiana Ganem",
+        "author_inst": "National Immunization Program, Department of Immunization and Communicable Diseases, Secretariat of Health Surveillance, Ministry of Health, Brazil."
+      },
+      {
+        "author_name": "Fabio Macedo Mendes",
+        "author_inst": "University of Brasilia, Brazil"
+      },
+      {
+        "author_name": "Maria Almiron",
+        "author_inst": "Panamerican Health Organization, Brazil"
+      },
+      {
+        "author_name": "Wanderson Kleber de Oliveira",
+        "author_inst": "Secretariat of Health Surveillance, Ministry of Health, Brazil."
+      },
+      {
+        "author_name": "Francieli Fontana Sutile Tardetti Fantinato",
+        "author_inst": "National Immunization Program, Department of Immunization and Communicable Diseases, Secretariat of Health Surveillance, Ministry of Health, Brazil."
+      },
+      {
+        "author_name": "Walquiria Aparecida Ferreira de Almeida",
+        "author_inst": "National Immunization Program, Department of Immunization and Communicable Diseases, Secretariat of Health Surveillance, Ministry of Health, Brazil."
+      },
+      {
+        "author_name": "Abel Pereira de Macedo Borges",
+        "author_inst": "InLoco company"
+      },
+      {
+        "author_name": "Hector Natan Batista Pinheiro",
+        "author_inst": "Inloco company"
+      },
+      {
+        "author_name": "Raiza dos Santos Oliveira",
+        "author_inst": "Inloco company"
+      },
+      {
+        "author_name": "Jason R Andrews",
+        "author_inst": "Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, USA."
+      },
+      {
+        "author_name": "Nuno R. Faria",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Marcelo Barreto Lopes",
+        "author_inst": "Arbor Research Collaborative for Health, USA."
+      },
+      {
+        "author_name": "Wildo Araujo",
+        "author_inst": "Universidade de Brasilia"
+      },
+      {
+        "author_name": "Fredi A Diaz-Quijano",
+        "author_inst": "Universidade de Sao Paulo"
+      },
+      {
+        "author_name": "Helder I Nakaya",
+        "author_inst": "University of Sao Paulo"
+      },
+      {
+        "author_name": "Julio Croda",
+        "author_inst": "Oswaldo Cruz Foundation"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.04.29.20082099",
     "rel_title": "Rapid development of COVID-19 rapid diagnostics for low resource settings: accelerating delivery through transparency, responsiveness, and open collaboration",
@@ -1487653,61 +1486538,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
-  {
-    "rel_doi": "10.1101/2020.04.29.20085142",
-    "rel_title": "A model to estimate demand for personal protective equipment for Ontario acute care hospitals during the COVID-19 pandemic",
-    "rel_date": "2020-05-05",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20085142",
-    "rel_abs": "In addition to instituting public health measures for COVID-19, managing healthcare resources is important for outcomes. The experiences in Italy and New York have shown that personal protective equipment (PPE) shortages can cause increased morbidity and mortality. We demonstrate a method to predict PPE demand across a health care system.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Kali A Barrett",
-        "author_inst": "Institute of Health Policy, Management and Evaluation, University of Toronto. University Health Network. IDDCCM, Toronto. THETA Collaborative. Department of Med"
-      },
-      {
-        "author_name": "Yoshiko Nakamachi",
-        "author_inst": "University Health Network, Sinai Health System."
-      },
-      {
-        "author_name": "Terra Ierasts",
-        "author_inst": "University Health Network"
-      },
-      {
-        "author_name": "Yasin Khan",
-        "author_inst": "Institute of Health Policy, Management and Evaluation, University of Toronto. University Health Network. IDDCCM, University of Toronto. Department of Medicine, "
-      },
-      {
-        "author_name": "Stephen Mac",
-        "author_inst": "Institute of Health Policy, Management and Evaluation, University of Toronto. THETA Collaborative."
-      },
-      {
-        "author_name": "David Naimark",
-        "author_inst": "Institute of Health Policy, Management and Evaluation, University of Toronto. THETA Collaborative. Sunnybrook Hospital"
-      },
-      {
-        "author_name": "Nathan Stall",
-        "author_inst": "Institute of Health Policy, Management and Evaluation, University of Toronto. Department of Medicine, University of Toronto. Sinai Health System. Women's Colleg"
-      },
-      {
-        "author_name": "Raphael Ximenes",
-        "author_inst": "THETA Collaborative"
-      },
-      {
-        "author_name": "Andrew Morris",
-        "author_inst": "University Health Network. Department of Medicine, University of Toronto. Sinai Health System"
-      },
-      {
-        "author_name": "Beate Sander",
-        "author_inst": "Institute of Health Policy, Management and Evaluation, University of Toronto. THETA Collaborative. Public Health Ontario. ICES."
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health systems and quality improvement"
-  },
   {
     "rel_doi": "10.1101/2020.04.29.20084236",
     "rel_title": "Battling the COVID-19 Pandemic: Is Bangladesh Prepared?",
@@ -1488018,6 +1486848,137 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.04.29.20084533",
+    "rel_title": "Pre-Existing Characteristics Associated with Covid-19 Illness Severity",
+    "rel_date": "2020-05-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20084533",
+    "rel_abs": "BackgroundCertain individuals, when infected by SARS-CoV-2, tend to develop the more severe forms of Covid-19 illness for reasons that remain unclear.\n\nMethodsWe studied N=442 patients who presented with laboratory confirmed Covid-19 illness to our U.S. metropolitan healthcare system. We curated data from the electronic health record, and used multivariable logistic regression to examine the association of pre-existing traits with a Covid-19 illness severity defined by level of required care: need for hospital admission, need for intensive care, and need for intubation.\n\nResultsOf all patients studied, 48% required hospitalization, 17% required intensive care, and 12% required intubation. In multivariable-adjusted analyses, patients requiring a higher levels of care were more likely to be older (OR 1.5 per 10 years, P<0.001), male (OR 2.0, P=0.001), African American (OR 2.1, P=0.011), obese (OR 2.0, P=0.021), with diabetes mellitus (OR 1.8, P=0.037), and with a higher comorbidity index (OR 1.8 per SD, P<0.001). Several clinical associations were more pronounced in younger compared to older patients (Pinteraction<0.05). Of all hospitalized patients, males required higher levels of care (OR 2.5, P=0.003) irrespective of age, race, or morbidity profile.\n\nConclusionsIn our healthcare system, greater Covid-19 illness severity is seen in patients who are older, male, African American, obese, with diabetes, and with greater overall comorbidity burden. Certain comorbidities paradoxically augment risk to a greater extent in younger patients. In hospitalized patients, male sex is the main determinant of needing more intensive care. Further investigation is needed to understand the mechanisms underlying these findings.",
+    "rel_num_authors": 29,
+    "rel_authors": [
+      {
+        "author_name": "Joseph E. Ebinger",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "Natalie Achamallah",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "Hongwei Ji",
+        "author_inst": "Tongji University"
+      },
+      {
+        "author_name": "Brian L. Claggett",
+        "author_inst": "Brigham and Womens Hospital"
+      },
+      {
+        "author_name": "Nancy Sun",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "Patrick Botting",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "Trevor-Trung Nguyen",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "Eric Luong",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "Elizabeth H. Kim",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "Eunice Park",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "Yunxian Liu",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "Ryan Rosenberry",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "Yuri Matusov",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "Steven Zhao",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "Isabel Pedraza",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "Tanzira Zaman",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "Michael Thompson",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "Koen Raedschelders",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "Anders H. Berg",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "Jonathan D. Grein",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "Paul W. Noble",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "Sumeet S. Chugh",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "C. Noel Bairey Merz",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "Eduardo Marb\u00e1n",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "Jennifer E. Van Eyk",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "Scott D. Solomon",
+        "author_inst": "Brigham and Womens Hospital"
+      },
+      {
+        "author_name": "Christine M. Albert",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "Peter Chen",
+        "author_inst": "Cedars-Sinai Medical Center"
+      },
+      {
+        "author_name": "Susan Cheng",
+        "author_inst": "Cedars-Sinai Medical Center"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.04.28.20084053",
     "rel_title": "Periodic COVID-19 Testing in Emergency Department Staff",
@@ -1489639,93 +1488600,6 @@
     "type": "new results",
     "category": "genetics"
   },
-  {
-    "rel_doi": "10.1101/2020.05.04.075945",
-    "rel_title": "The UCSC SARS-CoV-2 Genome Browser",
-    "rel_date": "2020-05-04",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.04.075945",
-    "rel_abs": "BackgroundResearchers are generating molecular data pertaining to the SARS-CoV-2 RNA genome and its proteins at an unprecedented rate during the COVID-19 pandemic. As a result, there is a critical need for rapid and continuously updated access to the latest molecular data in a format in which all data can be quickly cross-referenced and compared. We adapted our genome browser visualization tool to the viral genome for this purpose. Molecular data, curated from published studies or from database submissions, are mapped to the viral genome and grouped together into \"annotation tracks\" where they can be visualized along the linear map of the viral genome sequence and programmatically downloaded in standard format for analysis.\n\nResultsThe UCSC Genome Browser for SARS-CoV-2 (https://genome.ucsc.edu/covid19.html) provides continuously updated access to the mutations in the many thousands of SARS-CoV-2 genomes deposited in GISAID and the international nucleotide sequencing databases, displayed alongside phylogenetic trees. These data are augmented with alignments of bat, pangolin, and other animal and human coronavirus genomes, including per-base evolutionary rate analysis. All available annotations are cross-referenced on the virus genome, including those from major databases (PDB, RFAM, IEDB, UniProt) as well as up-to-date individual results from preprints. Annotated data include predicted and validated immune epitopes, promising antibodies, RT-PCR and sequencing primers, CRISPR guides (from research, diagnostics, vaccines, and therapies), and points of interaction between human and viral genes. As a community resource, any user can add manual annotations which are quality checked and shared publicly on the browser the next day.\n\nConclusionsWe invite all investigators to contribute additional data and annotations to this resource to accelerate research and development activities globally. Contact us at genome-www@soe.ucsc.edu with data suggestions or requests for support for adding data. Rapid sharing of data will accelerate SARS-CoV-2 research, especially when researchers take time to integrate their data with those from other labs on a widely-used community browser platform with standardized machine-readable data formats, such as the SARS-CoV-2 Genome Browser.",
-    "rel_num_authors": 18,
-    "rel_authors": [
-      {
-        "author_name": "Jason D Fernandes",
-        "author_inst": "Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA"
-      },
-      {
-        "author_name": "Angie S Hinrichs",
-        "author_inst": "Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA"
-      },
-      {
-        "author_name": "Hiram Clawson",
-        "author_inst": "Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA"
-      },
-      {
-        "author_name": "Jairo Navarro Gonzales",
-        "author_inst": "Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA"
-      },
-      {
-        "author_name": "Brian T Lee",
-        "author_inst": "Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA"
-      },
-      {
-        "author_name": "Luis R Nassar",
-        "author_inst": "Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA"
-      },
-      {
-        "author_name": "Brian J Raney",
-        "author_inst": "Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA"
-      },
-      {
-        "author_name": "Kate R Rosenbloom",
-        "author_inst": "Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA"
-      },
-      {
-        "author_name": "Santrupti Nerli",
-        "author_inst": "Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA"
-      },
-      {
-        "author_name": "Arjun A Rao",
-        "author_inst": "ImmunoX Initiative, University of California San Francisco, San Francisco, CA 94143, USA"
-      },
-      {
-        "author_name": "Daniel Schmelter",
-        "author_inst": "Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA"
-      },
-      {
-        "author_name": "Ann S Zweig",
-        "author_inst": "Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA"
-      },
-      {
-        "author_name": "Todd M Lowe",
-        "author_inst": "Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA, 95064, USA"
-      },
-      {
-        "author_name": "Manuel Ares Jr.",
-        "author_inst": "Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA"
-      },
-      {
-        "author_name": "Russell Corbett-Detig Jr.",
-        "author_inst": "Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA"
-      },
-      {
-        "author_name": "W. James Kent",
-        "author_inst": "Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA"
-      },
-      {
-        "author_name": "David Haussler",
-        "author_inst": "Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA"
-      },
-      {
-        "author_name": "Maximilian Haeussler",
-        "author_inst": "Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "confirmatory results",
-    "category": "genomics"
-  },
   {
     "rel_doi": "10.1101/2020.05.03.074971",
     "rel_title": "Pathogen Reduction Of SARS-CoV-2 Virus In Plasma And Whole Blood Using Riboflavin And UV Light",
@@ -1489932,6 +1488806,61 @@
     "type": "new results",
     "category": "biophysics"
   },
+  {
+    "rel_doi": "10.1101/2020.04.29.20084061",
+    "rel_title": "Psychological Stress and Gender Differences during COVID-19 Pandemic in Chinese Population",
+    "rel_date": "2020-05-03",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20084061",
+    "rel_abs": "About 83000 COVID-19 patients were confirmed in China up to May 2020. The effects of this public health crisis - and the varied efforts to contains its spread - have altered individuals \"normal\" daily functioning. This impact on social, psychological, and emotional well-being remain relatively unexplored, especially the ways in which Chinese men and women experience and respond to potential behavioral-related stressors. A cross-sectional study was conducted in late February 2020. Demographic characteristics and residential living conditions were measured along with psychological stress and behavior responses to the COVID-19 epidemic. 3088 questionnaires were received: 1749 females (56.6%) and 1339 males (43.4%). The mean level of stress, as measured by a visual analog scale, was 3.4 (SD=2.4) - but differed significantly by sex. Besides sex, factors positively associated with stress included: age ([&le;]45 years), employment (unsteady income, unemployed), risk infection population (exposed to COVID-19, completed medical observation), difficulties encountered (diseases, work/study, financial, mental), behaviors(higher desire for COVID-19 knowledge, more time spent on the COVID-19). \"Protective\" factors included frequently contact with colleagues, calmness, and psychological resilience. Males and females also differed significantly in adapting to current living/working status, coping with heating, and psychological support service needs. Among Chinese, self-reported stress related to the COVID-19 epidemic were significantly related to sex, age, employment, resilience and coping styles. Future responses to such public health threats may wish to provide sex- and/or age-appropriate supports for psychological health and emotional well-being to those at greatest risk of experiencing stress.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Kangxing Song",
+        "author_inst": "Department of Cardiology, the First Medical Center, Chinese PLA General Hospital"
+      },
+      {
+        "author_name": "Rui Xu",
+        "author_inst": "Institute of Clinical Basic Medicine, China Academy of Chinese Medical Sciences"
+      },
+      {
+        "author_name": "Terry D. Stratton",
+        "author_inst": "Department of Behavioral Science, College of Medicine, University of Kentucky"
+      },
+      {
+        "author_name": "Voyko Kavcic",
+        "author_inst": "Institute of Gerontology, Wayne State University"
+      },
+      {
+        "author_name": "Dan Luo",
+        "author_inst": "School of Public Health, Central South University"
+      },
+      {
+        "author_name": "Fengsu Hou",
+        "author_inst": "Shenzhen Kangning Hospital"
+      },
+      {
+        "author_name": "Fengying Bi",
+        "author_inst": "School of Public Health, Central South University"
+      },
+      {
+        "author_name": "Rong Jiao",
+        "author_inst": "The First Clinical College, Hainan Meidical University"
+      },
+      {
+        "author_name": "Shiyan Yan",
+        "author_inst": "Institute of Clinical Basic Medicine, China Academy of Chinese Medical Sciences"
+      },
+      {
+        "author_name": "Yang Jiang",
+        "author_inst": "Department of Behavioral Science, College of Medicine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.04.28.20083329",
     "rel_title": "Releasing the lockdown in the UK Covid-19 epidemic: a stochastic model",
@@ -1491053,149 +1489982,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.04.27.20081810",
-    "rel_title": "Clinical classifiers of COVID-19 infection from novel ultra-high-throughput proteomics",
-    "rel_date": "2020-05-03",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20081810",
-    "rel_abs": "The COVID-19 pandemic is an unprecedented global challenge. Highly variable in its presentation, spread and clinical outcome, novel point-of-care diagnostic classifiers are urgently required. Here, we describe a set of COVID-19 clinical classifiers discovered using a newly designed low-cost high-throughput mass spectrometry-based platform. Introducing a new sample preparation pipeline coupled with short-gradient high-flow liquid chromatography and mass spectrometry, our methodology facilitates clinical implementation and increases sample throughput and quantification precision. Providing a rapid assessment of serum or plasma samples at scale, we report 27 biomarkers that distinguish mild and severe forms of COVID-19, of which some may have potential as therapeutic targets. These proteins highlight the role of complement factors, the coagulation system, inflammation modulators as well as pro-inflammatory signalling upstream and downstream of Interleukin 6. Application of novel methodologies hence transforms proteomics from a research tool into a rapid-response, clinically actionable technology adaptable to infectious outbreaks.\n\nHighlights- A completely redesigned clinical proteomics platform increases throughput and precision while reducing costs.\n- 27 biomarkers are differentially expressed between WHO severity grades for COVID-19.\n- The study highlights potential therapeutic targets that include complement factors, the coagulation system, inflammation modulators as well as pro-inflammatory signalling both upstream and downstream of interleukin 6.",
-    "rel_num_authors": 32,
-    "rel_authors": [
-      {
-        "author_name": "Christoph B. Messner",
-        "author_inst": "The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, United Kingdom"
-      },
-      {
-        "author_name": "Vadim Demichev",
-        "author_inst": "The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, United Kingdom"
-      },
-      {
-        "author_name": "Daniel Wendisch",
-        "author_inst": "Charite Universitaetsmedizin, Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany"
-      },
-      {
-        "author_name": "Laura Michalick",
-        "author_inst": "Charite Universitaetsmedizin, Institute of Physiology, 10117 Berlin, Germany"
-      },
-      {
-        "author_name": "Matthew White",
-        "author_inst": "The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, United Kingdom"
-      },
-      {
-        "author_name": "Anja Freiwald",
-        "author_inst": "Charite Universitaetsmedizin, Core Facility - High Throughput Mass Spectrometry, 10117 Berlin, German"
-      },
-      {
-        "author_name": "Kathrin Textoris-Taube",
-        "author_inst": "Charite Universitaetsmedizin, Core Facility - High Throughput Mass Spectrometry, 10117 Berlin, Germany"
-      },
-      {
-        "author_name": "Spyros I. Vernardis",
-        "author_inst": "The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, United Kingdom"
-      },
-      {
-        "author_name": "Anna-Sophia Egger",
-        "author_inst": "The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, United Kingdom"
-      },
-      {
-        "author_name": "Marco Kreidl",
-        "author_inst": "The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW11AT, United Kingdom"
-      },
-      {
-        "author_name": "Daniela Ludwig",
-        "author_inst": "Charite Universitaetsmedizin, Department of Biochemistry, 10117 Berlin, Germany"
-      },
-      {
-        "author_name": "Christiane Kilian",
-        "author_inst": "Charite Universitaetsmedizin, Department of Biochemistry, 10117 Berlin, Germany"
-      },
-      {
-        "author_name": "Federica Agostini",
-        "author_inst": "Charite Universitaetsmedizin, Department of Biochemistry, 10117 Berlin, Germany"
-      },
-      {
-        "author_name": "Aleksej Zelezniak",
-        "author_inst": "Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden"
-      },
-      {
-        "author_name": "Charlotte Thibeault",
-        "author_inst": "Charite Universitaetsmedizin, Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany"
-      },
-      {
-        "author_name": "Moritz Pfeiffer",
-        "author_inst": "Charite Universitaetsmedizin, Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany"
-      },
-      {
-        "author_name": "Stefan Hippenstiel",
-        "author_inst": "Charite Universitaetsmedizin, Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany"
-      },
-      {
-        "author_name": "Andreas Hocke",
-        "author_inst": "Charite Universitaetsmedizin, Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany"
-      },
-      {
-        "author_name": "Christof von Kalle",
-        "author_inst": "Berlin Institute of Health (BIH), and  Charite Universitaetsmedizin, Clinical Study Center (CSC), 10117 Berlin, Germany"
-      },
-      {
-        "author_name": "Archie Campbell",
-        "author_inst": "Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh United Kingdom and Usher Institute, Universi"
-      },
-      {
-        "author_name": "Caroline Hayward",
-        "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom"
-      },
-      {
-        "author_name": "David J. Porteous",
-        "author_inst": "Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh EH4 2XU, United Kingdom"
-      },
-      {
-        "author_name": "Riccardo E. Marioni",
-        "author_inst": "Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh EH4 2XU, United Kingdom"
-      },
-      {
-        "author_name": "Claudia Langenberg",
-        "author_inst": "MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, United Kingdom"
-      },
-      {
-        "author_name": "Kathryn S. Lilley",
-        "author_inst": "Department of Biochemistry, The University of Cambridge, Cambridge, CB21GA, United Kingdom"
-      },
-      {
-        "author_name": "Wolfgang M. Kuebler",
-        "author_inst": "Charite Universitaetsmedizin, Berlin, Institute of Physiology, 10117 Berlin, Germany"
-      },
-      {
-        "author_name": "Michael Muelleder",
-        "author_inst": "Charite Universitaetsmedizin, Core Facility - High Throughput Mass Spectrometry, 10117 Berlin, Germany"
-      },
-      {
-        "author_name": "Christian Drosten",
-        "author_inst": "Charite Universitaetsmedizin, Berlin, Department of Virology, 10117 Berlin, Germany"
-      },
-      {
-        "author_name": "Martin Witzenrath",
-        "author_inst": "Charite Universitaetsmedizin, Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany"
-      },
-      {
-        "author_name": "Florian Kurth",
-        "author_inst": "Charite Universitaetsmedizin, Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany and Department of Tropical Medicine, Bernhard"
-      },
-      {
-        "author_name": "Leif Erik Sander",
-        "author_inst": "Charite Universitaetsmedizin, Berlin, Dept. of Infectious Diseases and Respiratory Medicine, 10117 Berlin, Germany"
-      },
-      {
-        "author_name": "Markus Ralser",
-        "author_inst": "Charite Universitaetsmedizin, Berlin, Department of Biochemistry, 10117 Berlin, and The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, Lon"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.04.28.20083311",
     "rel_title": "Anosmia in COVID-19 patients",
@@ -1491562,6 +1490348,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.28.20083378",
+    "rel_title": "Ocular toxicity and Hydroxychloroquine: A Rapid Meta-Analysis",
+    "rel_date": "2020-05-03",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20083378",
+    "rel_abs": "Rapid access to evidence is crucial in times of evolving clinical crisis. To that end, we propose a novel mechanism to answer clinical queries: Rapid Meta-Analysis (RMA). Unlike traditional meta-analysis, RMA balances quick time-to-production with reasonable data quality assurances, leveraging Artificial Intelligence to strike this balance. This article presents an example RMA to a currently relevant clinical question: Is ocular toxicity and vision compromise a side effect with hydroxychloroquine therapy?\n\nAs of this writing, hydroxychloroquine is a leading candidate in the treatment of COVID-19. By combining AI with human analysis, our RMA identified 11 studies looking at ocular toxicity as a side effect and estimated the incidence to be 3.4% (95% CI: 1.11-9.96%). The heterogeneity across the individual study findings was high, and interpretation of the result should take this into account. Importantly, this RMA, from search to screen to analysis, took less than 30 minutes to produce.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Matthew Michelson",
+        "author_inst": "Evid Science, InferLink"
+      },
+      {
+        "author_name": "Steven Minton",
+        "author_inst": "InferLink"
+      },
+      {
+        "author_name": "Tiffany Chow",
+        "author_inst": "Evid Science"
+      },
+      {
+        "author_name": "Neil Martin",
+        "author_inst": "Pacific Neuroscience Institute, Providence St John's Health Center"
+      },
+      {
+        "author_name": "Mike Ross",
+        "author_inst": "Evid Science"
+      },
+      {
+        "author_name": "Amelia Tee",
+        "author_inst": "Evid Science"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health informatics"
+  },
   {
     "rel_doi": "10.1101/2020.04.27.20081901",
     "rel_title": "Enhanced Contact Investigations for Nine Early Travel-Related Cases of SARS-CoV-2 in the United States",
@@ -1492915,97 +1491740,6 @@
     "type": "new results",
     "category": "biochemistry"
   },
-  {
-    "rel_doi": "10.1101/2020.05.02.073320",
-    "rel_title": "Identification of Drugs Blocking SARS-CoV-2 Infection using Human Pluripotent Stem Cell-derived Colonic Organoids",
-    "rel_date": "2020-05-02",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.02.073320",
-    "rel_abs": "Summary ParagraphThe current COVID-19 pandemic is caused by SARS-coronavirus 2 (SARS-CoV-2). There are currently no therapeutic options for mitigating this disease due to lack of a vaccine and limited knowledge of SARS-CoV-2 biology. As a result, there is an urgent need to create new disease models to study SARS-CoV-2 biology and to screen for therapeutics using human disease-relevant tissues. COVID-19 patients typically present with respiratory symptoms including cough, dyspnea, and respiratory distress, but nearly 25% of patients have gastrointestinal indications including anorexia, diarrhea, vomiting, and abdominal pain. Moreover, these symptoms are associated with worse COVID-19 outcomes1. Here, we report using human pluripotent stem cell-derived colonic organoids (hPSC-COs) to explore the permissiveness of colonic cell types to SARS-CoV-2 infection. Single cell RNA-seq and immunostaining showed that the putative viral entry receptor ACE2 is expressed in multiple hESC-derived colonic cell types, but highly enriched in enterocytes. Multiple cell types in the COs can be infected by a SARS-CoV-2 pseudo-entry virus, which was further validated in vivo using a humanized mouse model. We used hPSC-derived COs in a high throughput platform to screen 1280 FDA-approved drugs against viral infection. Mycophenolic acid and quinacrine dihydrochloride were found to block the infection of SARS-CoV-2 pseudo-entry virus in COs both in vitro and in vivo, and confirmed to block infection of SARS-CoV-2 virus. This study established both in vitro and in vivo organoid models to investigate infection of SARS-CoV-2 disease-relevant human colonic cell types and identified drugs that blocks SARS-CoV-2 infection, suitable for rapid clinical testing.",
-    "rel_num_authors": 19,
-    "rel_authors": [
-      {
-        "author_name": "Xiaohua Duan",
-        "author_inst": "Weill Cornell Medical College"
-      },
-      {
-        "author_name": "Yuling Han",
-        "author_inst": "Weill Cornell Medical College"
-      },
-      {
-        "author_name": "Liuliu Yang",
-        "author_inst": "Weill Cornell Medical College"
-      },
-      {
-        "author_name": "Benjamin Nilsson",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Pengfei Wang",
-        "author_inst": "Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Tuo Zhang",
-        "author_inst": "Weill Cornell Medical College"
-      },
-      {
-        "author_name": "Xing Wang",
-        "author_inst": "Weill Cornell Medical College"
-      },
-      {
-        "author_name": "Dong Xu",
-        "author_inst": "Weill Cornell Medical College"
-      },
-      {
-        "author_name": "Jenny Zhaoying Xiang",
-        "author_inst": "Weill Cornell Medical College"
-      },
-      {
-        "author_name": "skyler uhl",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Yaoxing Huang",
-        "author_inst": "Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Huanhuan Chen",
-        "author_inst": "the University of Chicago"
-      },
-      {
-        "author_name": "Hui Wang",
-        "author_inst": "School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China"
-      },
-      {
-        "author_name": "Benjamin R. tenOever",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Robert  E. Schwartz",
-        "author_inst": "Weill Cornell Graduate School of Medical Sciences"
-      },
-      {
-        "author_name": "David D Ho",
-        "author_inst": "Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Fong Cheng Pan",
-        "author_inst": "Weill Cornell Medical College"
-      },
-      {
-        "author_name": "Shuibing Chen",
-        "author_inst": "Weill Cornell Medical College"
-      },
-      {
-        "author_name": "Todd R. Evans",
-        "author_inst": "Weill Cornell Medical College"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.05.02.073411",
     "rel_title": "Rapid adaptation of SARS-CoV-2 in BALB/c mice: Novel mouse model for vaccine efficacy",
@@ -1493368,6 +1492102,45 @@
     "type": "new results",
     "category": "evolutionary biology"
   },
+  {
+    "rel_doi": "10.1101/2020.05.01.071050",
+    "rel_title": "CoV-Seq: SARS-CoV-2 Genome Analysis and Visualization",
+    "rel_date": "2020-05-02",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.01.071050",
+    "rel_abs": "SummaryCOVID-19 has become a global pandemic not long after its inception in late 2019. SARS-CoV-2 genomes are being sequenced and shared on public repositories at a fast pace. To keep up with these updates, scientists need to frequently refresh and reclean datasets, which is ad hoc and labor-intensive. Further, scientists with limited bioinformatics or programming knowledge may find it difficult to analyze SARS-CoV-2 genomes. In order to address these challenges, we developed CoV-Seq, a webserver to enable simple and rapid analysis of SARS-CoV-2 genomes. Given a new sequence, CoV-Seq automatically predicts gene boundaries and identifies genetic variants, which are presented in an interactive genome visualizer and are downloadable for further analysis. A command-line interface is also available for high-throughput processing.\n\nAvailability and ImplementationCoV-Seq is implemented in Python and Javascript. The webserver is available at http://covseq.baidu.com/ and the source code is available from https://github.com/boxiangliu/covseq.\n\nContactjollier.liu@gmail.com\n\nSupplementary informationSupplementary information are available at bioRxiv online.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Boxiang Liu",
+        "author_inst": "Baidu Research USA, Sunnyvale, California, 94089, USA"
+      },
+      {
+        "author_name": "Kaibo Liu",
+        "author_inst": "Baidu Research USA, Sunnyvale, California, 94089, USA"
+      },
+      {
+        "author_name": "He Zhang",
+        "author_inst": "Baidu Research USA, Sunnyvale, California, 94089, USA"
+      },
+      {
+        "author_name": "Liang Zhang",
+        "author_inst": "School of Electrical Engineering & Computer Science, Oregon State University, Corvallis, OR 97330, USA"
+      },
+      {
+        "author_name": "Yuchen Bian",
+        "author_inst": "Baidu Research USA, Sunnyvale, California, 94089, USA"
+      },
+      {
+        "author_name": "Liang Huang",
+        "author_inst": "School of Electrical Engineering & Computer Science, Oregon State University, Corvallis, OR 97330, USA"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "bioinformatics"
+  },
   {
     "rel_doi": "10.1101/2020.05.01.073262",
     "rel_title": "SARS-CoV-2 is well adapted for humans. What does this mean for re-emergence?",
@@ -1494569,133 +1493342,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
-  {
-    "rel_doi": "10.1101/2020.04.26.20079418",
-    "rel_title": "COVID-19 in healthcare workers in three hospitals in the South of the Netherlands, March 2020",
-    "rel_date": "2020-05-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20079418",
-    "rel_abs": "Ten days after the first reported case of SARS-CoV-2 infection in the Netherlands, 3.9% of healthcare workers (HCWs) in nine hospitals located in the South of the Netherlands tested positive for SARS-CoV-2 RNA. The extent of nosocomial transmission that contributed to the HCW infections was unknown.\n\nWe combined epidemiological data, collected by means of structured interviews of HCWs, with whole genome sequencing (WGS) of SARS-CoV-2 in clinical samples from HCWs and patients in three of nine hospitals that participated in the HCW screening, to perform an in-depth analysis of sources and modes of transmission of SARS -CoV-2 in HCWs and patients.\n\nA total of 1,796 out of 12,022 HCWs (15%) of the three participating hospitals were screened, based on clinical symptoms, of whom 96 (5%) tested positive for SARS-CoV-2. We obtained complete genome sequences of 50 HCWs and 18 patients. Most sequences grouped in 3 clusters, with 2 clusters displaying local circulation within the region. The observed patterns are most consistent with multiple introductions into the hospitals through community acquired infections, and local amplification in the community.\n\nAlthough direct transmission in the hospitals cannot be ruled out, the data does not support widespread nosocomial transmission as source of infection in patients or healthcare workers.",
-    "rel_num_authors": 28,
-    "rel_authors": [
-      {
-        "author_name": "Reina S Sikkema",
-        "author_inst": "Viroscience, ErasmusMC, Rotterdam"
-      },
-      {
-        "author_name": "Suzan Pas",
-        "author_inst": "Microvida Laboratory for Microbiology, Bravis Hospital, Roosendaal/ Microvida Laboratory for Microbiology, Amphia Hospital, Breda"
-      },
-      {
-        "author_name": "David F. Nieuwenhuijse",
-        "author_inst": "Viroscience, ErasmusMC, Rotterdam"
-      },
-      {
-        "author_name": "Aine O'Toole",
-        "author_inst": "University of Edinburgh, Edinburgh"
-      },
-      {
-        "author_name": "Jaco Verweij",
-        "author_inst": "Laboratory for Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg"
-      },
-      {
-        "author_name": "Anne van der Linden",
-        "author_inst": "Viroscience, ErasmusMC, Rotterdam"
-      },
-      {
-        "author_name": "Irina Chestakova",
-        "author_inst": "Viroscience, ErasmusMC, Rotterdam"
-      },
-      {
-        "author_name": "Claudia Schapendonk",
-        "author_inst": "Viroscience, ErasmusMC, Rotterdam"
-      },
-      {
-        "author_name": "Mark R Pronk",
-        "author_inst": "Viroscience, ErasmusMC, Rotterdam"
-      },
-      {
-        "author_name": "Pascal Lexmond",
-        "author_inst": "Viroscience, ErasmusMC, Rotterdam"
-      },
-      {
-        "author_name": "Theo Bestebroer",
-        "author_inst": "Viroscience, ErasmusMC, Rotterdam"
-      },
-      {
-        "author_name": "Ronald J Overmars",
-        "author_inst": "Viroscience, ErasmusMC, Rotterdam"
-      },
-      {
-        "author_name": "Stefan van Nieuwkoop",
-        "author_inst": "Viroscience, ErasmusMC, Rotterdam"
-      },
-      {
-        "author_name": "Wouter van den Bijllaardt",
-        "author_inst": "Microvida Laboratory for Microbiology, Amphia Hospital, Breda"
-      },
-      {
-        "author_name": "Robbert G. Bentvelsen",
-        "author_inst": "Microvida Laboratory for Microbiology, Amphia Hospital, Breda/ Department of Medical Microbiology, Leiden University Medical Center, Leiden"
-      },
-      {
-        "author_name": "Miranda M.L. van Rijen",
-        "author_inst": "Microvida Laboratory for Microbiology, Amphia Hospital, Breda"
-      },
-      {
-        "author_name": "Anton G.M. Buiting",
-        "author_inst": "Laboratory for Medical Microbiology and Immunology, Elisabeth-TweeSteden Hospital, Tilburg/ Department of Infection Control, Elisabeth-TweeSteden Hospital, Tilb"
-      },
-      {
-        "author_name": "Anne J.G. van Oudheusden",
-        "author_inst": "Department of Infection Control, Elisabeth-TweeSteden Hospital, Tilburg"
-      },
-      {
-        "author_name": "Bram M. Diederen",
-        "author_inst": "Microvida Laboratory for Microbiology, Bravis Hospital, Roosendaal"
-      },
-      {
-        "author_name": "Anneke M.C. Bergmans",
-        "author_inst": "Microvida Laboratory for Microbiology, Bravis Hospital, Roosendaal"
-      },
-      {
-        "author_name": "Annemiek van der Eijk",
-        "author_inst": "Viroscience, ErasmusMC, Rotterdam"
-      },
-      {
-        "author_name": "Richard Molenkamp",
-        "author_inst": "Viroscience, ErasmusMC, Rotterdam"
-      },
-      {
-        "author_name": "Andrew Rambaut",
-        "author_inst": "University of Edinburgh, Edinburgh"
-      },
-      {
-        "author_name": "Aura Timen",
-        "author_inst": "LCI, RIVM, Bilthoven/ VU University Amsterdam"
-      },
-      {
-        "author_name": "Jan A.J.W. Kluytmans",
-        "author_inst": "Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht/ Department of Infection Control, Amphia Hospital, Breda/ Microvi"
-      },
-      {
-        "author_name": "Bas B. Oude Munnink",
-        "author_inst": "Viroscience, ErasmusMC, Rotterdam"
-      },
-      {
-        "author_name": "Marjolein Kluytmans",
-        "author_inst": "Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht/ Department of Infection Control, Amphia Hospital, Breda/Microvid"
-      },
-      {
-        "author_name": "Marion P.G. Koopmans",
-        "author_inst": "Viroscience, ErasmusMC, Rotterdam"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.04.26.20079822",
     "rel_title": "Estimation of seroprevalence of novel coronavirus disease (COVID-19) using preserved serum at an outpatient setting in Kobe, Japan: A cross-sectional study.",
@@ -1494934,6 +1493580,193 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.04.27.20080309",
+    "rel_title": "Serial measurements in COVID-19-induced acute respiratory disease to unravel heterogeneity of the disease course: design of the Maastricht Intensive Care COVID cohort; MaastrICCht",
+    "rel_date": "2020-05-01",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20080309",
+    "rel_abs": "BackgroundThe course of the disease in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in mechanically ventilated patients is unknown. To unravel the clinical heterogeneity of the SARS-CoV-2 infection in these patients, we designed the prospective observational Maastricht Intensive Care COVID cohort; MaastrICCht. We incorporated serial measurements that harbour aetiological, diagnostic and predictive information. The study aims to investigate the heterogeneity of the natural course of critically ill patients with SARS-CoV-2 infection.\n\nStudy populationMechanically ventilated patients admitted to the Intensive Care with SARS- CoV-2 infection.\n\nMain messageWe will collect clinical variables, vital parameters, laboratory variables, mechanical ventilator settings, chest electrical impedance tomography, electrocardiograms, echocardiography as well as other imaging modalities to assess heterogeneity of the natural course of SARS-CoV-2 infection in critically ill patients. The MaastrICCht cohort is, also designed to foster various other studies and registries and intends to create an open-source database for investigators. Therefore, a major part of the data collection is aligned with an existing national Intensive Care data registry and two international COVID-19 data collection initiatives. Additionally, we create a flexible design, so that additional measures can be added during the ongoing study based on new knowledge obtained from the rapidly growing body of evidence.\n\nConclusionThe spread of the COVID-19 pandemic requires the swift implementation of observational research to unravel heterogeneity of the natural course of the disease of SARS- CoV-2 infection in mechanically ventilated patients. Our design is expected to enhance aetiological, diagnostic and prognostic understanding of the disease. This paper describes the design of the MaastrICCht cohort.\n\nStrengths and limitations of this studyO_LISerial measurements that characterize the disease course of SARS-CoV-2 infection in mechanically ventilated patients\nC_LIO_LIData collection and analysis according to a predefined protocol\nC_LIO_LIFlexible, evolving design enabling the study of multiple aspects of SARS-CoV-2 infection in mechanically ventilated patients\nC_LIO_LISingle centre, including only ICU patients\nC_LI",
+    "rel_num_authors": 43,
+    "rel_authors": [
+      {
+        "author_name": "Jeanette Tas",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Rob J.J. van Gassel",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Serge J.H. heines",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Mark M.G. Mulder",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Nanon F.L. heijnen",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Melanie J Acampo -  de Jong",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Julia L.M. Bels",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Frank C Bennis",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Marcel Koelmann",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Rald V.M. Groven",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Moniek A Donkers",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Frank van Rosmalen",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Ben J.M. Hermans",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "- Maastricht Intensive Care COVID Study Group",
+        "author_inst": ""
+      },
+      {
+        "author_name": "Steven J.R. Meex",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Alma M.A. Mingels",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Otto Bekers",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Paul H.M. Savelkoul",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Astrid M.L Oude Lashof",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Joachim E Wildberger",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Fabian H Tijssen",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Wolfgang F.F.A. Buhre",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Jan-Willem E.M. Sels",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Chahinda Ghossein-Doha",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Rob G.H. Driessen",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Pieter L Kubben",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Marcus L.F. Janssen",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Gerry A.F. Nicolaes",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Uli Strauch",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Zafer Geyik",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Thijs S.R. Delnoij",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Kim H.M. Walraven",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Coen D.A. Stehouwer",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Jeanine A.M.C.F. Verbunt",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Walther N.K.A. van Mook",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Susanne van Santen",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Ronny M. Schnabel",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Marcel J.H. Aries",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Marcel C.G. van de Poll",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Dennis C.J.J. Bergmans",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Iwan C.C. van der Horst",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Sander M.J. van Kuijk",
+        "author_inst": "MUMC"
+      },
+      {
+        "author_name": "Bas C.T. van Bussel",
+        "author_inst": "MUMC"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "intensive care and critical care medicine"
+  },
   {
     "rel_doi": "10.1101/2020.04.26.20080317",
     "rel_title": "Fast and easy disinfection of coronavirus-contaminated face masks using ozone gas produced by a dielectric barrier discharge plasma generator",
@@ -1496039,45 +1494872,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.27.20078048",
-    "rel_title": "Communicating with patients and families about difficult matters: A rapid review in the context of the COVID-19 pandemic",
-    "rel_date": "2020-05-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20078048",
-    "rel_abs": "BackgroundPandemics pose significant challenges for healthcare systems, including an increase in difficult discussions about future illness progression and end of life.\n\nObjectivesTo synthesise existing evidence about communication practices used to discuss difficult matters, including prognosis and end of life, and to use this evidence to make recommendations for clinical practice. The aim of this study was to use rapid review methods to update findings from a previous systematic review published in 2014.\n\nData sourcesMEDLINE, EMBASE, CINAHL, PsycINFO, Sociological Abstracts, Web of Science, Scopus, ASSIA and Amed.\n\nStudy eligibility criteriaStudies using conversation analysis or discourse analysis to examine recordings of actual conversations about difficult matters relating to future illness progression and end of life.\n\nStudy appraisal and synthesis methodsData appraisal and extraction procedures used in the 2014 review were modified for this rapid review.\n\nResultsFollowing screening, 18 sources were deemed to meet eligibility criteria, which were added to the 19 sources included in the 2014 systematic review. Synthesis of study findings identified 11 communication practices: providing opportunities for patient or family members to propose matters to discuss (7 out of 37 included sources); seeking a patient or family members perspective (6/37); discussing the future indirectly (11/37); discussing the future explicitly (7/37) linking to something previously said or done (11/37); using hypothetical scenarios (13/37); framing a difficult matter as universal (5/37); acknowledging uncertainty (3/37); exploring options (2/37); displaying sensitivity (7/37); emphasising the positive (7/37).\n\nLimitationsDividing work amongst the study authors to enable rapid review may have created inconsistencies.\n\nConclusions and implications of key findingsThis synthesis of high-quality evidence from actual clinical practice supports a series of recommendations for communicating about difficult matters during and beyond the COVID-19 pandemic.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Stuart Ekberg",
-        "author_inst": "Queensland University of Technology"
-      },
-      {
-        "author_name": "Ruth Parry",
-        "author_inst": "Loughborough University"
-      },
-      {
-        "author_name": "Victoria Land",
-        "author_inst": "Loughborough University"
-      },
-      {
-        "author_name": "Katie Ekberg",
-        "author_inst": "Queensland University of Technology"
-      },
-      {
-        "author_name": "Marco Pino",
-        "author_inst": "Loughborough University"
-      },
-      {
-        "author_name": "Charles Antaki",
-        "author_inst": "Loughborough University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "intensive care and critical care medicine"
-  },
   {
     "rel_doi": "10.1101/2020.04.26.20081042",
     "rel_title": "Fitting SIR model to COVID-19 pandemic data and comparative forecasting with machine learning",
@@ -1496308,6 +1495102,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.26.20080655",
+    "rel_title": "Preparedness and Mitigation by projecting the risk against COVID-19 transmission using Machine Learning Techniques",
+    "rel_date": "2020-05-01",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20080655",
+    "rel_abs": "The outbreak of COVID-19 is first identified in China, which later spread to various parts of the globe and was pronounced pandemic by the World Health Organization (WHO). The disease of transmissible person-to-person pneumonia caused by the extreme acute respiratory coronavirus 2 syndrome (SARS-COV-2, also known as COVID-19), has sparked a global warning. Thermal screening, quarantining, and later lockdown were methods employed by various nations to contain the spread of the virus. Though exercising various possible plans to contain the spread help in mitigating the effect of COVID-19, projecting the rise and preparing to face the crisis would help in minimizing the effect. In the scenario, this study attempts to use Machine Learning tools to forecast the possible rise in the number of cases by considering the data of daily new cases. To capture the uncertainty, three different techniques: (i) Decision Tree algorithm, (ii) Support Vector Machine algorithm, and (iii) Gaussian process regression are used to project the data and capture the possible deviation. Based on the projection of new cases, recovered cases, deceased cases, medical facilities, population density, number of tests conducted, and facilities of services, are considered to define the criticality index (CI). CI is used to classify all the districts of the country in the regions of high risk, low risk, and moderate risk. An online dashpot is created, which updates the data on daily bases for the next four weeks. The prospective suggestions of this study would aid in planning the strategies to apply the lockdown/ any other plan for any country, which can take other parameters to define the CI.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Akshay Kumar",
+        "author_inst": "Birla Institute of Technology and Science, Pilani Campus, Rajasthan, 333031, India"
+      },
+      {
+        "author_name": "Farhan Mohammad Khan",
+        "author_inst": "Birla Institute of Technology and Science, Pilani Campus, Rajasthan, 333031, India"
+      },
+      {
+        "author_name": "Rajiv Gupta",
+        "author_inst": "Birla Institute of Technology and Science, Pilani Campus, Rajasthan, 333031, India"
+      },
+      {
+        "author_name": "Harish Puppala",
+        "author_inst": "BML Munjal University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health informatics"
+  },
   {
     "rel_doi": "10.1101/2020.04.27.20079962",
     "rel_title": "Epidemic analysis of COVID-19 Outbreak and Counter-Measures in France",
@@ -1497273,69 +1496098,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.30.071274",
-    "rel_title": "Comparative transcriptome analysis reveals the intensive early-stage responses of host cells to SARS-CoV-2 infection",
-    "rel_date": "2020-05-01",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.30.071274",
-    "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a widespread outbreak of highly pathogenic COVID-19. It is therefore important and timely to characterize interactions between the virus and host cell at the molecular level to understand its disease pathogenesis. To gain insights, we performed high-throughput sequencing that generated time-series data simultaneously for bioinformatics analysis of virus genomes and host transcriptomes implicated in SARS-CoV-2 infection. Our analysis results showed that the rapid growth of the virus was accompanied by an early intensive response of host genes. We also systematically compared the molecular footprints of the host cells in response to SARS-CoV-2, SARS-CoV and MERS-CoV. Upon infection, SARS-CoV-2 induced hundreds of up-regulated host genes hallmarked by a significant cytokine production followed by virus-specific host antiviral responses. While the cytokine and antiviral responses triggered by SARS-CoV and MERS-CoV were only observed during the late stage of infection, the host antiviral responses during the SARS-CoV-2 infection were gradually enhanced lagging behind the production of cytokine. The early rapid host responses were potentially attributed to the high efficiency of SARS-CoV-2 entry into host cells, underscored by evidence of a remarkably up-regulated gene expression of TPRMSS2 soon after infection. Taken together, our findings provide novel molecular insights into the mechanisms underlying the infectivity and pathogenicity of SARS-CoV-2.",
-    "rel_num_authors": 12,
-    "rel_authors": [
-      {
-        "author_name": "Jiya Sun",
-        "author_inst": "Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College; Suzhou Institute of System"
-      },
-      {
-        "author_name": "Fei Ye",
-        "author_inst": "Key Laboratory of Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, China CDC"
-      },
-      {
-        "author_name": "Aiping Wu",
-        "author_inst": "Suzhou Institute of Systems Medicine"
-      },
-      {
-        "author_name": "Ren Yang",
-        "author_inst": "Key Laboratory of Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, China CDC"
-      },
-      {
-        "author_name": "Mei Pan",
-        "author_inst": "Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College; Suzhou Institute of System"
-      },
-      {
-        "author_name": "Jie Sheng",
-        "author_inst": "Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College; Suzhou Institute of System"
-      },
-      {
-        "author_name": "Wenjie Zhu",
-        "author_inst": "Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College; Suzhou Institute of System"
-      },
-      {
-        "author_name": "Longfei Mao",
-        "author_inst": "Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College; Suzhou Institute of System"
-      },
-      {
-        "author_name": "Ming Wang",
-        "author_inst": "Department of Otolaryngology, Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University"
-      },
-      {
-        "author_name": "Baoying Huang",
-        "author_inst": "Key Laboratory of Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, China CDC"
-      },
-      {
-        "author_name": "Wenjie Tan",
-        "author_inst": "Key Laboratory of Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, China CDC"
-      },
-      {
-        "author_name": "Taijiao Jiang",
-        "author_inst": "Suzhou Institute of Systems Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.04.30.071290",
     "rel_title": "Potent antiviral effect of protoporphyrin IX and verteporfin on SARS-CoV-2 infection",
@@ -1497718,6 +1496480,41 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2020.05.01.071654",
+    "rel_title": "Mutational spectra of SARS-CoV-2 orf1ab polyprotein and Signature mutations in the United States of America",
+    "rel_date": "2020-05-01",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.01.071654",
+    "rel_abs": "Pandemic COVID-19 outbreak has been caused due to SARS-COV2 pathogen, resulting millions of infection and death worldwide, USA being on top at the present moment. The long, complex orf1ab polyproteins of SARS-COV2 play an important role in viral RNA synthesis. To assess the impact of mutations in this important domain, we analyzed 1134 complete protein sequences of orf1ab polyprotein from NCBI Virus database from affected patients across various states of USA from December 2019 to 25th April, 2020. Multiple sequence alignment using Clustal Omega followed by statistical significance was calculated. Four significant mutations T265I (nsp 2), P4715L (nsp 12) and P5828L and Y5865C (both at nsp 13) were identified in important non-structural proteins, which function either as replicase or helicase. A comparative analysis shows 265T>I, 5828P>L and 5865Y>C are unique to USA and not reported from Europe or Asia; while one, 4715P>L is predominant in both Europe and USA. Mutational changes in amino acids are predicted to alter structure and function of corresponding proteins, thereby it is imperative to consider the mutational spectra while designing new antiviral therapeutics targeting viral orf1ab.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Shuvam Banerjee",
+        "author_inst": "University of Calcutta"
+      },
+      {
+        "author_name": "Sohan Seal",
+        "author_inst": "Ramakrishna Mission Vidyamandira, Belur Math, Howrah"
+      },
+      {
+        "author_name": "Riju Dey",
+        "author_inst": "Ramakrishna Mission Vidyamandira, Belur Math, Howrah"
+      },
+      {
+        "author_name": "Kousik kr. Mondal",
+        "author_inst": "University of Calcutta"
+      },
+      {
+        "author_name": "Pritha Bhattacharjee",
+        "author_inst": "University of Calcutta"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "new results",
+    "category": "bioinformatics"
+  },
   {
     "rel_doi": "10.1101/2020.05.01.071985",
     "rel_title": "On spatial molecular arrangements of SARS-CoV2 genomes of Indian patients",
@@ -1498707,29 +1497504,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.26.20078618",
-    "rel_title": "Nonpharmaceutical interventions for pandemic COVID-19: A cross-sectional investigation of US general public beliefs, attitudes, and actions",
-    "rel_date": "2020-05-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20078618",
-    "rel_abs": "Nonpharmaceutical interventions (NPIs) represent the primary mitigation strategy for pandemic COVID-19. Despite this, many government agencies and members of the general public may be resistant to NPI adoption. We sought to understand public attitudes and beliefs regarding various NPIs and self-reported adoption of NPIs, and explore associations between NPI performance and the baseline characteristics of respondents. We performed a cross-sectional age-, sex-, and race- stratified survey of the general US population. Of the 1,005 respondents, 37% (95% CI 34.0, 39.9) felt that NPIs were inconvenient, while only 0.9% (95% CI 0.3, 1.5) of respondents believed that NPIs would not reduce their personal risk of illness. Respondents were most uncertain regarding the efficacy of mask and eye protection use, with 30.6% and 22.1%, respectively, unsure whether their use would slow disease spread. On univariate logistic regression analyses, NPI adherence was associated with a belief that NPIs would reduce personal risk of developing COVID-19 (OR 3.06, 95% CI [1.25, 7.48], p=0.014) and with a belief that the NPIs were not difficult to perform (OR 1.79, 95% CI [1.38, 2.31], p<0.0001). Respondents were compliant with straightforward, familiar, and heavily-encouraged NPI recommendations such as hand-washing; more onerous approaches, such as avoiding face touching, disinfecting surfaces, and wearing masks or goggles, were performed less frequently. NPI non-adherence is associated with both outcome expectations (belief that NPIs are effective) and process expectations (belief that NPIs are not overly inconvenient); these findings have important implications for designing public health outreach efforts, where the feasibility, as well as the effectiveness, of NPIs should be stressed.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Bella Nichole Kantor",
-        "author_inst": "Harvard University"
-      },
-      {
-        "author_name": "Jonathan Kantor",
-        "author_inst": "University of Pennsylvania Perelman School of Medicine"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.04.26.20079756",
     "rel_title": "Racial, Economic and Health Inequality and COVID-19 Infection in the United States",
@@ -1499048,6 +1497822,77 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.04.24.20077487",
+    "rel_title": "SUCCESSFUL MANUFACTURING OF CLINICAL-GRADE SARS-CoV-2 SPECIFIC T CELLS FOR ADOPTIVE CELL THERAPY",
+    "rel_date": "2020-04-30",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20077487",
+    "rel_abs": "BackgroundAdoptive therapy with SARS-CoV-2 specific T cells for COVID-19 has not been reported. The feasibility of rapid clinical-grade manufacturing of virus-specific T cells from convalescent donors has not been demonstrated for this or prior pandemics.\n\nMethodsOne unit of whole blood was collected from each convalescent donor following standard blood bank practices. After the plasma was separated and stored separately, the leukocytes were stimulated using overlapping peptides of SARS-CoV-2, covering the immunodominant sequence domains of the S protein and the complete sequence of the N and M proteins. Thereaftesr, functionally reactive cells were enriched overnight using an automated device capturing IFN{gamma}-secreting cells.\n\nFindingsFrom 1x109 leukocytes, 0.56 to 1.16x106 IFN{gamma}+ T cells were produced from each of the first two donors. Most of the T cells (64% to 71%) were IFN{gamma}+, with preferential enrichment of CD56+ T cells, effector memory T cells, and effector memory RA+ T cells. TCRV{beta} spectratyping revealed oligoclonal distribution, with over-representation of subfamilies including V{beta}3, V{beta}16 and V{beta}17. With just two donors, the probability that a recipient in the same ethnic group would share at least one donor HLA allele or one haplotype could be as high as >90% and >30%, respectively.\n\nInterpretationsThis study is limited by small number of donors and absence of recipient data; however, crucial first proof-of-principle data are provided demonstrating the feasibility of clinical-grade production of SARS-CoV-2 specific T cells for urgent clinical use, conceivably with plasma therapy concurrently. Our data showing that virus-specific T cells can be detected easily after brief stimulation with SARS-CoV-2 specific peptides suggest that a parallel diagnostic assay can be developed alongside serology testing.\n\nFundingThe study was funded by a SingHealth Duke-NUS Academic Medicine COVID-19 Rapid Response Research Grant.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Wing Leung",
+        "author_inst": "KKH, SingHealth Duke-NUS"
+      },
+      {
+        "author_name": "Teck Guan Soh",
+        "author_inst": "National University Hospital"
+      },
+      {
+        "author_name": "Yeh Ching Linn",
+        "author_inst": "Singapore General Hospital"
+      },
+      {
+        "author_name": "Jenny Guek-Hong Low",
+        "author_inst": "Singapore General Hospital"
+      },
+      {
+        "author_name": "Jiashen Loh",
+        "author_inst": "Sengkang General Hospital"
+      },
+      {
+        "author_name": "Marieta Chan",
+        "author_inst": "Health Sciences Authority"
+      },
+      {
+        "author_name": "Wee Joo Chng",
+        "author_inst": "National University Hospital"
+      },
+      {
+        "author_name": "Liang Piu Koh",
+        "author_inst": "National University Hospital"
+      },
+      {
+        "author_name": "Michelle Li-Mei Poon",
+        "author_inst": "National University Hospital"
+      },
+      {
+        "author_name": "King Pan Ng",
+        "author_inst": "KKH"
+      },
+      {
+        "author_name": "Chik Hong Kuick",
+        "author_inst": "KKH"
+      },
+      {
+        "author_name": "Thuan Tong Tan",
+        "author_inst": "Singapore General Hospital"
+      },
+      {
+        "author_name": "Lip Kun Tan",
+        "author_inst": "National University Hospital"
+      },
+      {
+        "author_name": "Michaela Su-fern Seng",
+        "author_inst": "KKH"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.04.24.20078741",
     "rel_title": "Modelling of Systemic versus Pulmonary Chloroquine Exposure in Man for COVID-19 Dose Selection",
@@ -1500017,89 +1498862,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2020.04.30.070771",
-    "rel_title": "Origin of imported SARS-CoV-2 strains in The Gambia identified from Whole Genome Sequences.",
-    "rel_date": "2020-04-30",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.30.070771",
-    "rel_abs": "Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a positive-sense single stranded RNA virus with high human transmissibility. This study generated Whole Genome data to determine the origin and pattern of transmission of SARS-CoV-2 from the first six cases tested in The Gambia. Total RNA from SARS-CoV-2 was extracted from inactivated nasopharyngeal-oropharyngeal swabs of six cases and converted to cDNA following the ARTIC COVID-19 sequencing protocol. Libraries were constructed with the NEBNext ultra II DNA library prep kit for Illumina and Oxford Nanopore Ligation sequencing kit and sequenced on Illumina MiSeq and Nanopore GridION, respectively. Sequencing reads were mapped to the Wuhan reference genome and compared to eleven other SARS-CoV-2 strains of Asian, European and American origins. A phylogenetic tree was constructed with the consensus genomes for local and non-African strains. Three of the Gambian strains had a European origin (UK and Spain), two strains were of Asian origin (Japan). In The Gambia, Nanopore and Illumina sequencers were successfully used to identify the sources of SARS-CoV-2 infection in COVID-19 cases.",
-    "rel_num_authors": 17,
-    "rel_authors": [
-      {
-        "author_name": "Abdoulie Kanteh",
-        "author_inst": "Genomics Core Facility, Lab service, MRCG at LSHTM, Fajara, The Gambia"
-      },
-      {
-        "author_name": "Jarra Manneh",
-        "author_inst": "Genomics Core Facility, Lab service, MRCG at LSHTM, Fajara, The Gambia"
-      },
-      {
-        "author_name": "Sona Jabang",
-        "author_inst": "Genomics Core Facility, Lab service, MRCG at LSHTM, Fajara, The Gambia"
-      },
-      {
-        "author_name": "Mariama A Kujabo",
-        "author_inst": "Genomics Core Facility, Lab service, MRCG at LSHTM, Fajara, The Gambia"
-      },
-      {
-        "author_name": "Bakary Sanyang",
-        "author_inst": "Genomics Core Facility, Lab service, MRCG at LSHTM, Fajara, The Gambia"
-      },
-      {
-        "author_name": "Mary Aigbiremo Oboh",
-        "author_inst": "Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine"
-      },
-      {
-        "author_name": "Abdoulie Bojang",
-        "author_inst": "Disease Control and Elimination, MRCG at LSHTM, Fajara, The Gambia"
-      },
-      {
-        "author_name": "Haruna S Jallow",
-        "author_inst": "National Public Health, Laboratories, Kotu, The Gambia"
-      },
-      {
-        "author_name": "Davis Nwakama",
-        "author_inst": "Laboratory Services, MRCG at LSHTM, Fajara, The Gambia"
-      },
-      {
-        "author_name": "Ousman Secka",
-        "author_inst": "Laboratory Services, MRCG at LSHTM, Fajara, The Gambia"
-      },
-      {
-        "author_name": "Anna Roca",
-        "author_inst": "Disease Control and Elimination, MRCG at LSHTM, Fajara, The Gambia"
-      },
-      {
-        "author_name": "Alfred Amambua-Ngwa",
-        "author_inst": "Disease Control and Elimination, MRCG at LSHTM, Fajara, The Gambia"
-      },
-      {
-        "author_name": "Martin Antonio",
-        "author_inst": "West Africa Platform, MRCG at LSHTM, Fajara, The Gambia"
-      },
-      {
-        "author_name": "Ignatius Baldeh",
-        "author_inst": "National Public Health, Laboratories, Kotu, The Gambia"
-      },
-      {
-        "author_name": "Karen Forest",
-        "author_inst": "Clinical Service Department, MRCG at LSHTM, Fajara, The Gambia"
-      },
-      {
-        "author_name": "Ahmadou Lamin Samateh",
-        "author_inst": "Ministry of Health, Banjul, The Gambia"
-      },
-      {
-        "author_name": "Abdul Karim Sesay",
-        "author_inst": "Genomics Core Facility, Lab service, MRCG at LSHTM, Fajara, The Gambia"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "confirmatory results",
-    "category": "genomics"
-  },
   {
     "rel_doi": "10.1101/2020.04.30.071027",
     "rel_title": "Identification of variable sites in Sars-CoV-2 and their abundance profiles in time",
@@ -1500462,6 +1499224,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.04.28.20083873",
+    "rel_title": "Bayesian Inference of COVID-19 Spreading Rates in South Africa",
+    "rel_date": "2020-04-30",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20083873",
+    "rel_abs": "The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has highlighted the need for the development of prompt mitigating responses under conditions of high uncertainty. Fundamental to the design of rapid state reactions is the ability to perform epidemiological model parameter inference for localised trajectory predictions. In this work, we perform Bayesian parameter inference using Markov Chain Monte Carlo (MCMC) methods on the Susceptible-Infected-Recovered (SIR) and Susceptible-Exposed-Infected-Recovered (SEIR) epidemiological models with time-varying spreading rates for South Africa. The results find two change points in the spreading rate of COVID-19 in South Africa as inferred from the confirmed cases. The first change point coincides with state enactment of a travel ban and the resultant containment of imported infections. The second change point coincides with the start of a state-led mass screening and testing programme which has highlighted community-level disease spread that was not well represented in the initial largely traveller based and private laboratory dominated testing data. The results further suggest that due to the likely effect of the national lockdown, community level transmissions are slower than the original imported case driven spread of the disease.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Rendani Mbuvha",
+        "author_inst": "University of Witwatersrand"
+      },
+      {
+        "author_name": "Tshilidzi Marwala",
+        "author_inst": "University of Johannesburg"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.04.28.20083865",
     "rel_title": "Fractional SIR Epidemiological Models",
@@ -1501279,37 +1500064,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.24.20078485",
-    "rel_title": "On the reliability of model-based predictions in the context of the current COVID epidemic event: impact of outbreak peak phase and data paucity",
-    "rel_date": "2020-04-29",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20078485",
-    "rel_abs": "The pandemic spread of the COVID-19 virus has, as of 20th of April 2020, reached most countries of the world. In an effort to design informed public health policies, many modelling studies have been performed to predict crucial outcomes of interest, including ICU solicitation, cumulated death counts, etc... The corresponding data analyses however, mostly rely on restricted (openly available) data sources, which typically include daily death rates and confirmed COVID cases time series. In addition, many of these predictions are derived before the peak of the outbreak has been observed yet (as is still currently the case for many countries). In this work, we show that peak phase and data paucity have a substantial impact on the reliability of model predictions. Although we focus on a recent model of the COVID pandemics, our conclusions most likely apply to most existing models, which are variants of the so-called \"Susceptible-Infected-Removed\" or SIR framework. Our results highlight the need for performing systematic reliability evaluations for all models that currently inform public health policies. They also motivate a plea for gathering and opening richer and more reliable data time series (e.g., ICU occupancy, negative test rates, social distancing commitment reports, etc).",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Jean Daunizeau",
-        "author_inst": "INSERM, France"
-      },
-      {
-        "author_name": "Rosalyn J Moran",
-        "author_inst": "King's College London, UK"
-      },
-      {
-        "author_name": "Jeremie Mattout",
-        "author_inst": "INSERM, France"
-      },
-      {
-        "author_name": "Karl Friston",
-        "author_inst": "University College London, UK"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.04.24.20078550",
     "rel_title": "The impact of the COVID19 pandemic and initial period of lockdown on the mental health and wellbeing of UK adults",
@@ -1501540,6 +1500294,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
+  {
+    "rel_doi": "10.1101/2020.04.25.20079830",
+    "rel_title": "FIRST DETECTION OF SARS-COV-2 IN UNTREATED WASTEWATERS IN ITALY",
+    "rel_date": "2020-04-29",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.25.20079830",
+    "rel_abs": "Several studies have demonstrated the advantages of environmental surveillance through the monitoring of sewer systems for the assessment of viruses circulating in a given community (wastewater-based epidemiology, WBE).\n\nDuring the COVID-19 public health emergency, many reports have described the presence of SARS-CoV-2 RNA in stools from COVID-19 patients, and a few studies reported the occurrence of SARS-CoV-2 in wastewaters worldwide. Italy is among the worlds worst-affected countries in the COVID-19 pandemic, but so far there are no studies assessing the presence of SARS-CoV-2 in Italian wastewaters. To this aim, twelve influent sewage samples, collected between February and April 2020 from Wastewater Treatment Plants in Milan and Rome, were tested adapting, for concentration, the standard WHO procedure for Poliovirus surveillance. Molecular analysis was undertaken with three nested protocols, including a newly designed SARS-CoV-2 specific primer set.\n\nSARS-CoV-2 RNA detection occurred in volumes of 250 mL of wastewaters collected in both areas at high (Milan) and low (Rome) epidemic circulation, according to clinical data. Overall, 6 out of 12 samples were positive. One of the positive results was obtained in a Milan wastewater sample collected a few days after the first notified Italian case of autochthonous SARS-CoV-2.\n\nThe study shows that WBE has the potential to be applied to SARS-CoV-2 as a sensitive tool to study spatial and temporal trends of virus circulation in the population.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Giuseppina La Rosa",
+        "author_inst": "National Institute of Health"
+      },
+      {
+        "author_name": "Marcello Iaconelli",
+        "author_inst": "National Institute of Health"
+      },
+      {
+        "author_name": "Pamela Mancini",
+        "author_inst": "National Institute of Health"
+      },
+      {
+        "author_name": "Giusy Bonanno Ferraro",
+        "author_inst": "National Institute of Health"
+      },
+      {
+        "author_name": "Carolina Veneri",
+        "author_inst": "National Institute of Health"
+      },
+      {
+        "author_name": "Lucia Bonadonna",
+        "author_inst": "National Institute of Health"
+      },
+      {
+        "author_name": "Luca Lucentini",
+        "author_inst": "National Institute of Health"
+      },
+      {
+        "author_name": "Elisabetta Suffredini",
+        "author_inst": "National Institute of Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.04.25.20079848",
     "rel_title": "Effects of latency and age structure on the dynamics and containment of COVID-19",
@@ -1502749,33 +1501550,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.28.066951",
-    "rel_title": "Noncanonical junctions in subgenomic RNAs of SARS-CoV-2 lead to variant open reading frames.",
-    "rel_date": "2020-04-29",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.28.066951",
-    "rel_abs": "BackgroundSARS-CoV-2, a positive-sense RNA virus in the family Coronaviridae, has caused a worldwide pandemic of coronavirus disease 2019 or COVID-19 Coronaviruses generate a tiered series of subgenomic RNAs (sgRNAs) through a process involving homology between transcriptional regulatory sequences (TRS) located after the leader sequence in the 5 UTR (the TRS-L) and TRS located near the start of structural and accessory proteins (TRS-B) near the 3 end of the genome. In addition to the canonical sgRNAs generated by SARS-CoV-2, non-canonical sgRNAs (nc-sgRNAs) have been reported. However, the consistency of these nc-sgRNAs across viral isolates and infection conditions is unknown. The comprehensive definition of SARS-CoV-2 RNA products is a key step in understanding SARS-CoV-2 pathogenesis.\n\nMethodsHere, we report an integrative analysis of eight independent SARS-CoV-2 transcriptomes generated using three sequencing strategies, five host systems, and seven viral isolates. Read-mapping to the SARS-CoV-2 genome was used to determine the 5 and 3 coordinates of all identified junctions in viral RNAs identified in these samples.\n\nResultsUsing junctional abundances, we show nc-sgRNAs make up as much as 33% of total sgRNAs in vitro, are largely consistent in abundance across independent transcriptomes, and increase in abundance over time during in vitro infection. By assessing the homology between sequences flanking the 5 and 3 junction points, we show that nc-sgRNAs are not associated with TRS-like homology. By incorporating read coverage information, we find strong evidence for subgenomic RNAs that contain only 5 regions of ORF1a. Finally, we show that non-canonical junctions change the landscape of viral open reading frames.\n\nConclusionsWe identify canonical and non-canonical junctions in SARS-CoV-2 sgRNAs and show that these RNA products are consistently generated across many independent viral isolates and sequencing approaches. These analyses highlight the diverse transcriptional activity of SARS-CoV-2 and offer important insights into SARS-CoV-2 biology.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Jason Nomburg",
-        "author_inst": "Dana-Farber Cancer Institute"
-      },
-      {
-        "author_name": "Matthew Meyerson",
-        "author_inst": "Dana-Farber Cancer Institute"
-      },
-      {
-        "author_name": "James A. DeCaprio",
-        "author_inst": "Dana-Farber Cancer Institute"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.04.28.066985",
     "rel_title": "Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India",
@@ -1503102,6 +1501876,57 @@
     "type": "new results",
     "category": "biophysics"
   },
+  {
+    "rel_doi": "10.1101/2020.04.29.068098",
+    "rel_title": "Mass spectrometry analysis of newly emerging coronavirus HCoV-19 spike S protein and human ACE2 reveals camouflaging glycans and unique post-translational modifications",
+    "rel_date": "2020-04-29",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.29.068098",
+    "rel_abs": "The pneumonia-causing COVID-19 pandemia has prompt worldwide efforts to understand its biological and clinical traits of newly identified HCoV-19 virus. In this study, post-translational modification (PTM) of recombinant HCoV-19 S and hACE2 were characterized by LC-MSMS. We revealed that both proteins were highly decorated with specific proportions of N-glycan subtypes. Out of 21 possible glycosites in HCoV-19 S protein, 20 were confirmed completely occupied by N-glycans, with oligomannose glycans being the most abundant type. All 7 possible glycosylation sites in hACE2 were completely occupied mainly by complex type N-glycans. However, we showed that glycosylation did not directly contribute to the binding affinity between SARS-CoV spike protein and hACE2. Additionally, we also identified multiple sites methylated in both proteins, and multiple prolines in hACE2 were converted to hydroxylproline. Refined structural models were built by adding N-glycan and PTMs to recently published cryo-EM structure of the HCoV-19 S and hACE2 generated with glycosylation sites in the vicinity of binding surface. The PTM and glycan maps of both HCoV-19 S and hACE2 provide additional structural details to study mechanisms underlying host attachment, immune response mediated by S protein and hACE2, as well as knowledge to develop remedies and vaccines desperately needed nowadays.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Zeyu Sun",
+        "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Disease,The First Affiliated Hospital, Zhejiang University"
+      },
+      {
+        "author_name": "Keyi Ren",
+        "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Disease,The First Affiliated Hospital, Zhejiang University"
+      },
+      {
+        "author_name": "Xing Zhang",
+        "author_inst": "Department of Biophysics & Center of Cryo-Electron Microscopy, Zhejiang University School of Medicine, Zhejiang University"
+      },
+      {
+        "author_name": "Jinghua Chen",
+        "author_inst": "Department of Biophysics & Center of Cryo-Electron Microscopy, Zhejiang University School of Medicine, Zhejiang University"
+      },
+      {
+        "author_name": "Zhengyi Jiang",
+        "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Disease,The First Affiliated Hospital, Zhejiang University"
+      },
+      {
+        "author_name": "Jing Jiang",
+        "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Disease,The First Affiliated Hospital, Zhejiang University"
+      },
+      {
+        "author_name": "Feiyang Ji",
+        "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Disease,The First Affiliated Hospital, Zhejiang University"
+      },
+      {
+        "author_name": "Xiaoxi Ouyang",
+        "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Disease,The First Affiliated Hospital, Zhejiang University"
+      },
+      {
+        "author_name": "Lanjuan Li",
+        "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Disease,The First Affiliated Hospital, Zhejiang University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "confirmatory results",
+    "category": "molecular biology"
+  },
   {
     "rel_doi": "10.1101/2020.04.26.20080242",
     "rel_title": "Systematic review of international guidelines for tracheostomy in COVID-19 patients.",
@@ -1504479,29 +1503304,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.04.23.20076992",
-    "rel_title": "COVID-19 Disease Dynamics in Germany: First Models and Parameter Identification",
-    "rel_date": "2020-04-29",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20076992",
-    "rel_abs": "Since the end of 2019 an outbreak of a new strain of coronavirus, called SARS- CoV-2, is reported from China and later other parts of the world. Since January 21, WHO reports daily data on confirmed cases and deaths from both China and other countries [1]. The Johns Hopkins University [5] collects those data from various sources worldwide on a daily basis. For Germany, the Robert-Koch-Institute (RKI) also issues daily reports on the current number of infections and infection related fatal cases [2]. However, due to delays in the data collection, the data from RKI always lags behind those reported by Johns Hopkins. In this work we present an extended SEIR-model to describe the disease dynamics in Germany. The parameter values are identified by matching the model output to the officially reported cases. An additional parameter to capture the influence of unidentified cases is also included in the model.\n\nO_QDTheres an evil virus thats\n\nthreatening mankind [...]\n\nA menace to society\n\nIron Maiden, Virus, 1996.\n\nC_QD",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Thomas Goetz",
-        "author_inst": "University Koblenz"
-      },
-      {
-        "author_name": "Peter Heidrich",
-        "author_inst": "University Koblenz and Magister Laukhard IGS Herrstein-Rhaunen"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.04.23.20077651",
     "rel_title": "Characterizing COVID-19 case detection utilizing influenza surveillance data in the United States, January-March, 2020",
@@ -1504708,6 +1503510,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.23.20077446",
+    "rel_title": "On the estimation of the total number of SARS-CoV-2 infections",
+    "rel_date": "2020-04-29",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20077446",
+    "rel_abs": "We introduce a simple methodology to estimate the infection fatality rate (IFR) and from here the total number of infected with SARS-CoV-2. The virus has shown to be highly infectious and thus we based our method under the assumption that all members of a household with at least one confirmed case of COVID-19 should be infected, therefore we estimate the IFR using the number of secondary fatalities in households. The simplicity of the methodology allows for large sample sizes, since it requires minimal laboratory testing capabilities. We applied this methodology to a database of 3,232 confirmed cases in Mexico and arrived to an IFR estimate within the range reported in other studies.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "CARLOS M HERNANDEZ-SUAREZ",
+        "author_inst": "UNIVERSIDAD DE COLIMA"
+      },
+      {
+        "author_name": "Paolo Verme",
+        "author_inst": "World Bank"
+      },
+      {
+        "author_name": "Efren Murillo-Zamora",
+        "author_inst": "Departamento de Epidemiologia, Unidad de Medicina Familiar No. 19,  IMSS"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.04.24.20077289",
     "rel_title": "The role of spatial structure in the infection spread models: population density map of England example",
@@ -1506017,61 +1504846,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.04.23.20074310",
-    "rel_title": "Resident physician exposure to novel coronavirus (2019-nCoV, SARS-CoV-2) within New York City during exponential phase of COVID-19 pandemic: Report of the New York City Residency Program Directors COVID-19 Research Group",
-    "rel_date": "2020-04-28",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20074310",
-    "rel_abs": "BackgroundFrom March 2-April 12, 2020, New York City (NYC) experienced exponential growth of the COVID-19 pandemic due to novel coronavirus (SARS-CoV-2). Little is known regarding how physicians have been affected. We aimed to characterize COVID-19 impact on NYC resident physicians.\n\nMethodsIRB-exempt and expedited cross-sectional analysis through survey to NYC residency program directors (PDs) April 3-12, 2020, encompassing events from March 2-April 12, 2020.\n\nFindingsFrom an estimated 340 residency programs around NYC, recruitment yielded 91 responses, representing 24 specialties and 2,306 residents. 45.1% of programs reported at least one resident with confirmed COVID-19: 101 resident physicians were confirmed COVID-19-positive, with additional 163 residents presumed positive for COVID-19 based on symptoms but awaiting or unable to obtain testing. 56.5% of programs had a resident waiting for, or unable to obtain, COVID-19 testing. Two COVID-19-positive residents were hospitalized, with one in intensive care. Among specialties with >100 residents represented, negative binomial regression indicated that infection risk differed by specialty (p=0.039). Although most programs (80%) reported quarantining a resident, with 16.8% of residents experiencing quarantine, 14.9% of COVID-19-positive residents were not quarantined. 90 programs, encompassing 99.2% of the resident physicians, reported reuse or extended mask use, and 43 programs, encompassing 60.4% of residents, felt that personal protective equipment (PPE) was suboptimal. 65 programs (74.7%) have redeployed residents elsewhere to support COVID-19 efforts.\n\nInterpretationMany resident physicians around NYC have been affected by COVID-19 through direct infection, quarantine, or redeployment. Lack of access to testing and concern regarding suboptimal PPE are common among residency programs. Infection risk may differ by specialty.\n\nFundingAHA, MPB, RWSC, CGM, LRDG, JDH are supported by NEI Core Grant P30EY019007 and an unrestricted grant from RPB. ACP and JS are supported by the Parker Family Chair. SXX is supported by the University of Pennsylvania.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Mark Philip Breazzano",
-        "author_inst": "Columbia University Medical Center"
-      },
-      {
-        "author_name": "Junchao Shen",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Aliaa H Abdelhakim",
-        "author_inst": "Columbia University Medical Center"
-      },
-      {
-        "author_name": "Lora R Dagi Glass",
-        "author_inst": "Columbia University Medical Center"
-      },
-      {
-        "author_name": "Jason D Horowitz",
-        "author_inst": "Columbia University Medical Center"
-      },
-      {
-        "author_name": "Sharon X Xie",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "C Gustavo de Moraes",
-        "author_inst": "Columbia University Medical Center"
-      },
-      {
-        "author_name": "Alice Chen-Plotkin",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Royce W S Chen",
-        "author_inst": "Columbia University Medical Center"
-      },
-      {
-        "author_name": "- New York City Residency Program Directors COVID-19 Research Group",
-        "author_inst": "-"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.04.24.20073957",
     "rel_title": "The incubation period of COVID-19: A rapid systematic review and meta-analysis of observational research",
@@ -1506362,6 +1505136,89 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.04.24.20069633",
+    "rel_title": "Lung injury in patients with or suspected COVID-19 : a comparison between lung ultrasound and chest CT-scanner severity assessments, an observational study",
+    "rel_date": "2020-04-28",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20069633",
+    "rel_abs": "BackgroundChest CT (CT) is the reference for assessing pulmonary injury in suspected or diagnosed COVID-19 with signs of clinical severity. We explored the role of lung ultrasonography (LU) in quickly assessing lung status in these patients.\n\nMethodseChoVid is a multicentric study based on routinely collected data, conducted in 3 emergency units of Assistance Publique des Hopitaux de Paris (APHP); 107 patients were included between March 19, 2020 and April 01, 2020 and underwent LU, a short clinical assessment by 2 emergency physicians blinded to each others and a CT. LU consisted of scoring lesions in 8 chest zones from 0 to 3, defining a severity global score (GS) ranging from 0 to 24. CT severity score ranged from 0 to 3 according to the extent of interstitial pneumonia signs. 48 patients underwent LU by both an expert and a newly trained physician.\n\nFindingsThe GS showed good performance to predict CT severity assessment of COVID-19 as normal versus pathologic: AUC=0.93, maximal Youden index 1 with 95% sensitivity, and 83% specificity. Similar performance was found for CT assessment as normal or minimal versus moderate or severe (n=90): AUC 0.89, maximal Youden index 7 with 86% sensitivity, and 78% specificity. Good agreement was found for zone scoring assessed by new trainee (30mn theory + 30mn practice) and expert (n=14,14*8 checkpoints), weighted kappa 0.85-1; moderate agreement was found for new trainee (n=48, 30mn theory) and expert, kappa 0.62-0.81.\n\nInterpretationGS score is a simple tool to assess lung damage severity in patients with suspected or diagnosed COVID-19. Comparing the performance of new trainees and expert physicians opens a path for adoption beyond the scope of experts. LU is a good candidate for patients triage, especially in case of CT availability issues.",
+    "rel_num_authors": 17,
+    "rel_authors": [
+      {
+        "author_name": "Mehdi Benchoufi",
+        "author_inst": "Center for Clinical Epidemiology, Hotel-Dieu Hospital, Assistance Publique-Hopitaux de Paris (AP-HP), Paris, France - METHODS Team, Center for Research in Epide"
+      },
+      {
+        "author_name": "Jerome Bokobza",
+        "author_inst": "Adult Emergency Department, Cochin Hospital, Assistance Publique Hopitaux de Paris, Paris, France"
+      },
+      {
+        "author_name": "Anthony Anthony Chauvin",
+        "author_inst": "Adult Emergency Department, Hopital Lariboisiere, Assistance Publique Hopitaux de Paris, University Diderot, Paris, France"
+      },
+      {
+        "author_name": "Elisabeth Dion",
+        "author_inst": "Imaging department Hotel Dieu, Assistance Publique-Hopitaux de Paris, Universite de Paris,Paris, France."
+      },
+      {
+        "author_name": "Marie-Laure Baranne",
+        "author_inst": "Center for Clinical Epidemiology, Hotel-Dieu Hospital, Assistance Publique-Hopitaux de Paris (AP-HP), Paris, France"
+      },
+      {
+        "author_name": "Fabien Levan",
+        "author_inst": "Adult Emergency Department, Hopital Cochin, Assistance Publique Hopitaux de Paris, Paris, France"
+      },
+      {
+        "author_name": "Maxime Gautier",
+        "author_inst": "Adult Emergency Department, Hopital Lariboisiere, Assistance Publique Hopitaux de Paris, Paris, France"
+      },
+      {
+        "author_name": "Delphine Cantin",
+        "author_inst": "Adult Emergency Department, Hotel Dieu Hospital, Assistance Publique Hopitaux de Paris, Paris, France"
+      },
+      {
+        "author_name": "Thomas d Humieres",
+        "author_inst": "Physiology department, Henri Mondor University Hospital, APHP, Creteil, France"
+      },
+      {
+        "author_name": "Cedric Gil-Jardine",
+        "author_inst": "Adult Emergency Department SAMU-SMUR, Pellegrin Hospital, University Hospital Center, Bordeaux, France - Bordeaux Population Health,  INSERM U1219, IETO Team, B"
+      },
+      {
+        "author_name": "Sylvain Benenati",
+        "author_inst": "Adult Emergency Department, Hospital Group South Ile-de-France, Melun, France"
+      },
+      {
+        "author_name": "Mathieu Oberlin",
+        "author_inst": "Adult Emergency Department, New Civil Hospital, Strasbourg, France"
+      },
+      {
+        "author_name": "Mikael Martinez",
+        "author_inst": "Adult Emergency Department, Forez Hospital Center, Montbrison, France - Nord Emergency Network Ligerien Ardeche (REULIAN), Hospital Center Le Corbusier, Firminy"
+      },
+      {
+        "author_name": "Nathalie Kahn",
+        "author_inst": "Imaging department Hotel Dieu, Assistance Publique Hopitaux de Paris, Paris University, France"
+      },
+      {
+        "author_name": "Abdourahmane Diallo",
+        "author_inst": "Clinical Trial Unit Hospital, Lariboisiere St-Louis Fernand-Widal Hospital Group, Assistance Publique Hopitaux de Paris, Paris University, Paris, France"
+      },
+      {
+        "author_name": "Eric Vicaut",
+        "author_inst": "Clinical Trial Unit Hospital, Lariboisiere St-Louis Fernand-Widal Hospital Group, Assistance Publique-Hopitaux de Paris, Paris University, Paris, France"
+      },
+      {
+        "author_name": "Pierre Bourrier",
+        "author_inst": "Imaging Department Saint-Louis Hospital, Assistance Publique des Hopitaux de Paris, Paris, France"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "radiology and imaging"
+  },
   {
     "rel_doi": "10.1101/2020.04.24.20075333",
     "rel_title": "Regional differences in reported Covid-19 cases show genetic correlations with higher socio-economic status and better health, potentially confounding studies on the genetics of disease susceptibility",
@@ -1507419,53 +1506276,6 @@
     "type": "new results",
     "category": "bioinformatics"
   },
-  {
-    "rel_doi": "10.1101/2020.04.23.20076653",
-    "rel_title": "Clinical and historical features associated with severe COVID-19 infection: a systematic review",
-    "rel_date": "2020-04-27",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20076653",
-    "rel_abs": "BackgroundThere is an urgent need for rapid assessment methods to guide pathways of care for COVID-19 patients, as frontline providers need to make challenging decisions surrounding rationing of resources. This study aimed to evaluate existing literature for factors associated with COVID-19 illness severity.\n\nMethodsA systematic review identified all studies published between 1/12/19 and 19/4/20 that used primary data and inferential statistics to assess associations between the outcome of interest - disease severity - and historical or clinical variables. PubMed, Scopus, Web of Science, and the WHO Database of Publications on Coronavirus Disease were searched. Data were independently extracted and cross-checked independently by two reviewers using PRISMA guidelines, after which they were descriptively analysed. Quality and risk of bias in available evidence were assessed using the Grading of Recommendations, Assessment, Development and Evaluations (GRADE) framework. This review was registered with PROSPERO, registration number CRD42020178098.\n\nResultsOf the 6202 relevant articles found, 63 were eligible for inclusion; these studies analysed data from 17648 COVID-19 patients. The majority (n=57, 90{middle dot}5%) were from China and nearly all (n=51, 90{middle dot}5%) focussed on admitted adult patients. Patients had a median age of 52{middle dot}5 years and 52{middle dot}8% were male. The predictors most frequently associated with COVID-19 disease severity were age, absolute lymphocyte count, hypertension, lactate dehydrogenase (LDH), C-reactive protein (CRP), and history of any pre-existing medical condition.\n\nConclusionThis study identified multiple variables likely to be predictive of severe COVID-19 illness. Due to the novelty of SARS-CoV-2 infection, there is currently no severity prediction tool designed to, or validated for, COVID-19 illness severity. Findings may inform such a tool that can offer guidance on clinical treatment and disposition, and ultimately reduce morbidity and mortality due to the pandemic.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Jennifer L Pigoga",
-        "author_inst": "Division of Emergency Medicine, University of Cape Town"
-      },
-      {
-        "author_name": "Alexandra Friedman",
-        "author_inst": "University of California, San Francisco"
-      },
-      {
-        "author_name": "Morgan Broccoli",
-        "author_inst": "Department of Emergency Medicine, Boston Medical Center"
-      },
-      {
-        "author_name": "Sarah Hirner",
-        "author_inst": "University of Colorado School of Medicine"
-      },
-      {
-        "author_name": "Antoinette Vanessa Naidoo",
-        "author_inst": "Division of Emergency Medicine, University of Cape Town"
-      },
-      {
-        "author_name": "Swasthi Singh",
-        "author_inst": "Division of Emergency Medicine, University of Cape Town"
-      },
-      {
-        "author_name": "Kalin Werner",
-        "author_inst": "Division of Emergency Medicine, University of Cape Town"
-      },
-      {
-        "author_name": "Lee A Wallis",
-        "author_inst": "Division of Emergency Medicine, University of Cape Town"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.04.23.20076513",
     "rel_title": "Intention to participate in a COVID-19 vaccine clinical trial and to get vaccinated against COVID-19 in France during the pandemic",
@@ -1507680,6 +1506490,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.21.20044594",
+    "rel_title": "Smart Pooled sample Testing for COVID-19: A Possible Solution for Sparsity of Test Kits",
+    "rel_date": "2020-04-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20044594",
+    "rel_abs": "There is an exponential growth of COVID-19. The adaptation of preventive measures to limit the spread of infection among the people is the best solution to this health issue. The identification of infected cases and their isolation from healthy people is one of the most important preventive measures. In this regard, screening of the samples from a large number of people is needed which requires a lot of reagent kits for the detection of SARS-CoV-2. The use of smart pooled sample testing with the help of algorithms may be a quite useful strategy in the current prevailing scenario of the COVID-19 pandemic. With the help of this strategy, the optimum number of samples to be pooled for a single test may be determined based on the total positivity rate of the particular community.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Syed Usama Khalid Bukhari",
+        "author_inst": "The University of Lahore"
+      },
+      {
+        "author_name": "Syed Safwan Khalid",
+        "author_inst": "COMSATS University, Islamabad, Pakistan"
+      },
+      {
+        "author_name": "Asmara Syed",
+        "author_inst": "Faculty of Medicine, Northern Border University, Arar- Kingdom of Saudi Arabia"
+      },
+      {
+        "author_name": "Syed Sajid Hussain Shah",
+        "author_inst": "Faculty of Medicine, Northern Border University, Arar- Kingdom of Saudi Arabia"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "pathology"
+  },
   {
     "rel_doi": "10.1101/2020.04.24.20078477",
     "rel_title": "COVID-19 in Iran: A Deeper Look Into The Future",
@@ -1508861,89 +1507702,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.04.22.20076190",
-    "rel_title": "Characterization of clinical progression of COVID-19 patients in Shenzhen, China",
-    "rel_date": "2020-04-27",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20076190",
-    "rel_abs": "BackgroundUnderstanding clinical progression of COVID-19 is a key public health priority that informs resource allocation during an emergency. We characterized clinical progression of COVID-19 and determined important predictors for faster clinical progression to key clinical events and longer use of medical resources.\n\nMethods and FindingsThe study is a single-center, observational study with prospectively collected data from all 420 patients diagnosed with COVID-19 and hospitalized in Shenzhen between January 11th and March 10th, 2020 regardless of clinical severity. Using competing risk regressions according to the methods of Fine and Gray, we found that males had faster clinical progression than females in the older age group and the difference could not be explained by difference in baseline conditions or smoking history. We estimated the proportion of cases in each severity stage over 80 days following symptom onset using a nonparametric method built upon estimated cumulative incidence of key clinical events. Based on random survival forest models, we stratified cases into risk sets with very different clinical trajectories. Those who progressed to the severe stage (22%,93/420), developed acute respiratory distress syndrome (9%,39/420), and were admitted to the intensive care unit (5%,19/420) progressed on average 9.5 days (95%CI 8.7,10.3), 11.0 days (95%CI 9.7,12.3), and 10.5 days (95%CI 8.2,13.3), respectively, after symptom onset. We estimated that patients who were admitted to ICUs remained there for an average of 34.4 days (95%CI 24.1,43.2). The median length of hospital stay was 21.3 days (95%CI, 20.5,22.2) for cases who did not progress to the severe stage, but increased to 52.1 days (95%CI, 43.3,59.5) for those who required critical care.\n\nConclusionsOur analyses provide insights into clinical progression of cases starting early in the course of infection. Patient characteristics near symptom onset both with and without lab parameters have tremendous potential for predicting clinical progression and informing strategic response.",
-    "rel_num_authors": 17,
-    "rel_authors": [
-      {
-        "author_name": "Qifang Bi",
-        "author_inst": "Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA"
-      },
-      {
-        "author_name": "Chengcheng Hong",
-        "author_inst": "Harbin Institute of Technology at Shenzhen, Shenzhen, Guangdong, China; Peng Cheng Laboratory, Shenzhen, Guangdong, China"
-      },
-      {
-        "author_name": "Juan Meng",
-        "author_inst": "National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong,"
-      },
-      {
-        "author_name": "Zhenke Wu",
-        "author_inst": "University of Michigan School of Public Health, Ann Arbor, MI, USA; Michigan Institute for Data Science, University of Michigan, Ann Arbor, MI, USA"
-      },
-      {
-        "author_name": "Pengzheng Zhou",
-        "author_inst": "Peng Cheng Laboratory, Shenzhen, Guangdong, China"
-      },
-      {
-        "author_name": "Chenfei Ye",
-        "author_inst": "Peng Cheng Laboratory, Shenzhen, Guangdong, China"
-      },
-      {
-        "author_name": "Binbin Sun",
-        "author_inst": "Harbin Institute of Technology at Shenzhen, Shenzhen, Guangdong, China; Peng Cheng Laboratory, Shenzhen, Guangdong, China"
-      },
-      {
-        "author_name": "Lauren M Kucirka",
-        "author_inst": "Johns Hopkins School of Medicine"
-      },
-      {
-        "author_name": "Andrew S Azman",
-        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
-      },
-      {
-        "author_name": "Tong Wang",
-        "author_inst": "Harbin Institute of Technology at Shenzhen, Shenzhen, Guangdong, China"
-      },
-      {
-        "author_name": "Jiancong Chen",
-        "author_inst": "Peng Cheng Laboratory, Shenzhen, Guangdong, China"
-      },
-      {
-        "author_name": "Zhaoqin Wang",
-        "author_inst": "National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong,"
-      },
-      {
-        "author_name": "Lei Liu",
-        "author_inst": "National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong,"
-      },
-      {
-        "author_name": "Justin Lessler",
-        "author_inst": "Johns Hopkins Bloomberg School of Public Health"
-      },
-      {
-        "author_name": "Jessie K Edwards",
-        "author_inst": "University of North Carolina at Chapel Hill"
-      },
-      {
-        "author_name": "Ting Ma",
-        "author_inst": "Harbin Institute of Technology at Shenzhen, Shenzhen, Guangdong, China; Peng Cheng Laboratory, Shenzhen, Guangdong, China"
-      },
-      {
-        "author_name": "Guoliang Zhang",
-        "author_inst": "National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, Guangdong,"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.04.22.20075804",
     "rel_title": "Assessing suppression strategies against epidemic outbreaks like COVID-19: the SPQEIR model",
@@ -1509122,6 +1507880,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.22.20075861",
+    "rel_title": "The Potential Impact of Interruptions to HIV Services: A Modelling Case Study for South Africa",
+    "rel_date": "2020-04-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20075861",
+    "rel_abs": "The numbers of deaths caused by HIV could increase substantially if the COVID-19 epidemic leads to interruptions in the availability of HIV services. We compare publicly available scenarios for COVID-19 mortality with predicted additional HIV-related mortality based on assumptions about possible interruptions in HIV programs. An interruption in the supply of ART for 40% of those on ART for 3 months could cause a number of deaths on the same order of magnitude as the number that are anticipated to be saved from COVID-19 through social distancing measures. In contrast, if the disruption can be managed such that the supply and usage of ART is maintained, the increase in AIDS deaths would be limited to 1% over five years, although this could still be accompanied by substantial increases in new HIV infections if there are reductions in VMMC, oral PrEP use, and condom availability.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Britta L Jewell",
+        "author_inst": "Imperial College London"
+      },
+      {
+        "author_name": "Jennifer A Smith",
+        "author_inst": "Imperial College London"
+      },
+      {
+        "author_name": "Timothy B Hallett",
+        "author_inst": "Imperial College London"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.04.22.20075770",
     "rel_title": "Influenza-Negative Influenza-Like Illness (fnILI) Z-Score as a Proxy for Incidence and Mortality of COVID-19",
@@ -1509891,25 +1508676,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "intensive care and critical care medicine"
   },
-  {
-    "rel_doi": "10.1101/2020.04.23.20076786",
-    "rel_title": "Estimating population immunity without serological testing",
-    "rel_date": "2020-04-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20076786",
-    "rel_abs": "We propose an approximate methodology for estimating the overall level of immunity against COVID-19 in a population that has been affected by the recent epidemic. The methodology relies on the currently available mortality data and utilizes the properties of the SIR model. We illustrate the application of the method by estimating the recent levels of immunity in 10 US states with highest case numbers of COVID-19.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Andrew Lesniewski",
-        "author_inst": "Baruch College"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.04.24.059527",
     "rel_title": "A transcriptional regulatory atlas of coronavirus infection of human cells",
@@ -1510140,6 +1508906,77 @@
     "type": "new results",
     "category": "bioinformatics"
   },
+  {
+    "rel_doi": "10.1101/2020.04.25.060947",
+    "rel_title": "MINERVA: A facile strategy for SARS-CoV-2 whole genome deep sequencing of clinical samples",
+    "rel_date": "2020-04-25",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.25.060947",
+    "rel_abs": "The novel coronavirus disease 2019 (COVID-19) pandemic poses a serious public health risk. Analyzing the genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from clinical samples is crucial for the understanding of viral spread and viral evolution, as well as for vaccine development. Existing sample preparation methods for viral genome sequencing are demanding on user technique and time, and thus not ideal for time-sensitive clinical samples; these methods are also not optimized for high performance on viral genomes. We have developed MetagenomIc RNA EnRichment VirAl sequencing (MINERVA), a facile, practical, and robust approach for metagenomic and deep viral sequencing from clinical samples. This approach uses direct tagmentation of RNA/DNA hybrids using Tn5 transposase to greatly simplify the sequencing library construction process, while subsequent targeted enrichment can generate viral genomes with high sensitivity, coverage, and depth. We demonstrate the utility of MINERVA on pharyngeal, sputum and stool samples collected from COVID-19 patients, successfully obtaining both whole metatranscriptomes and complete high-depth high-coverage SARS-CoV-2 genomes from these clinical samples, with high yield and robustness. MINERVA is compatible with clinical nucleic extracts containing carrier RNA. With a shortened hands-on time from sample to virus-enriched sequencing-ready library, this rapid, versatile, and clinic-friendly approach will facilitate monitoring of viral genetic variations during outbreaks, both current and future.",
+    "rel_num_authors": 14,
+    "rel_authors": [
+      {
+        "author_name": "Chen Chen",
+        "author_inst": "Beijing Ditan Hospital"
+      },
+      {
+        "author_name": "Jizhou Li",
+        "author_inst": "Tsinghua University"
+      },
+      {
+        "author_name": "Lin Di",
+        "author_inst": "Peking University"
+      },
+      {
+        "author_name": "Qiuyu Jing",
+        "author_inst": "The Hong Kong University of Science and Technology"
+      },
+      {
+        "author_name": "Pengcheng Du",
+        "author_inst": "Beijing Ditan Hospital"
+      },
+      {
+        "author_name": "Chuan Song",
+        "author_inst": "Beijing Ditan Hospital"
+      },
+      {
+        "author_name": "Jiarui Li",
+        "author_inst": "Beijing Ditan Hospital"
+      },
+      {
+        "author_name": "Qiong Li",
+        "author_inst": "Tsinghua University"
+      },
+      {
+        "author_name": "Yunlong Cao",
+        "author_inst": "Peking University"
+      },
+      {
+        "author_name": "Sunney Xie",
+        "author_inst": "Peking University"
+      },
+      {
+        "author_name": "Angela Ruohao Wu",
+        "author_inst": "The Hong Kong University of Science and Technology"
+      },
+      {
+        "author_name": "Hui Zeng",
+        "author_inst": "Beijing Ditan Hospital"
+      },
+      {
+        "author_name": "Yanyi Huang",
+        "author_inst": "Peking University"
+      },
+      {
+        "author_name": "Jianbin Wang",
+        "author_inst": "Tsinghua University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "new results",
+    "category": "molecular biology"
+  },
   {
     "rel_doi": "10.1101/2020.04.21.050633",
     "rel_title": "Rapid SARS-CoV-2 whole genome sequencing for informed public health decision making in the Netherlands",
@@ -1511501,29 +1510338,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.04.22.20075192",
-    "rel_title": "Modelling the transmission dynamics of COVID-19 in six high burden countries",
-    "rel_date": "2020-04-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20075192",
-    "rel_abs": "The new coronavirus disease, officially known as COVID-19, originated in China in 2019 and has since spread around the globe. We presented a modified Susceptible-Latent-Infected-Removed (SLIR) compartmental model of COVID-19 disease transmission with nonlinear incidence during the epidemic period. We provided the model calibration to estimate parameters with day wise corona virus (COVID-19) data i.e. reported cases by worldometer from the period of 15th February to 30th March, 2020 in six high burden countries including Australia, Italy, Spain, USA, UK and Canada. We estimate transmission rates for each countries and found that the highest transmission rate country in Spain, which may be increase the new cases and deaths in Spain than the other countries. Sensitivity analysis was used to identify the most important parameters through the partial rank correlation coefficient method. We found that the transmission rate of COVID-19 had the largest influence on the prevalence. We also provides the prediction of new cases in COVID-19 until May 18, 2020 using the developed model and recommends, control strategies of COVID-19. The information that we generated from this study would be useful to the decision makers of various organizations across the world including the Ministry of Health in Australia, Italy, Spain, USA, UK and Canada to control COVID-19.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Azizur Rahman",
-        "author_inst": "Charles Sturt University"
-      },
-      {
-        "author_name": "Md Abdul Kuddus",
-        "author_inst": "James Cook University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.04.22.20075267",
     "rel_title": "Knowledge and Beliefs of General Public of India on COVID-19: A Web-based Cross-sectional Survey",
@@ -1511734,6 +1510548,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.22.20074914",
+    "rel_title": "Antibody tests in detecting SARS-CoV-2 infection: a meta-analysis",
+    "rel_date": "2020-04-25",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20074914",
+    "rel_abs": "BackgroundWith the emergence of SARS-CoV-2 and the associated Coronavirus disease 2019 (COVID-19), there is an imperative need for diagnostic tests that can identify the infection. Although Nucleic Acid Test (NAT) is considered to be the gold standard, serological tests based on antibodies could be very helpful. However, individual studies measuring the accuracy of the various tests are usually underpowered and inconsistent, thus, a comparison of different tests is needed.\n\nMethodsWe performed a systematic review and meta-analysis following the PRISMA guidelines. We conducted the literature search in PubMed, medRxiv and bioRxiv. For the statistical analysis we used the bivariate method for meta-analysis of diagnostic tests pooling sensitivities and specificities. We evaluated IgM and IgG tests based on Enzyme-linked immunosorbent assay (ELISA), Chemiluminescence Enzyme Immunoassays (CLIA), Fluorescence Immunoassays (FIA) and the point-of-care (POC) Lateral Flow Immunoassays (LFIA) that are based on immunochromatography.\n\nFindingsIn total, we identified 38 eligible studies that include data from 7,848 individuals. The analyses showed that tests using the S antigen are more sensitive than N antigen-based tests. IgG tests perform better compared to IgM ones, and show better sensitivity when the samples were taken longer after the onset of symptoms. Moreover, irrespective of the method, a combined IgG/IgM test seems to be a better choice in terms of sensitivity than measuring either antibody type alone. All methods yielded high specificity with some of them (ELISA and LFIA) reaching levels around 99%. ELISA- and CLIA-based methods performed better in terms of sensitivity (90-94%) followed by LFIA and FIA with sensitivities ranging from 80% to 86%.\n\nInterpretationELISA tests could be a safer choice at this stage of the pandemic. POC tests (LFIA), that are more attractive for large seroprevalence studies show high specificity but lower sensitivity and this should be taken into account when designing and performing seroprevalence studies.\n\nFundingNone",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Panagiota I Kontou",
+        "author_inst": "University of Thessaly"
+      },
+      {
+        "author_name": "Georgia G Braliou",
+        "author_inst": "University of Thessaly"
+      },
+      {
+        "author_name": "Niki L Dimou",
+        "author_inst": "International Agency for Research on Cancer"
+      },
+      {
+        "author_name": "Georgios Nikolopoulos",
+        "author_inst": "University of Cyprus"
+      },
+      {
+        "author_name": "Pantelis G Bagos",
+        "author_inst": "University of Thessaly"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.04.22.20074898",
     "rel_title": "Non-Linear fitting of Sigmoidal Growth Curves to predict a maximum limit to the total number of COVID-19 cases in the United States.",
@@ -1512987,49 +1511836,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.19.20062174",
-    "rel_title": "Higher mortality in men from COVID19 infection-understanding the factors that drive the differences between the biological sexes.",
-    "rel_date": "2020-04-24",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20062174",
-    "rel_abs": "The emergent global pandemic caused by the rapid spread of Severe Acute Respiratory syndrome-Coronavirus-2 (SARS-CoV-2) has led to increased mortality and negatively impacted day to day activities of humankind within a short period of time. As the data is rapidly emerging from earlier outbreak locations around the world, there are efforts to assimilate this with the knowledge from prior epidemics and find rapid solutions for this. One of the observations and a recurring theme is the disproportionate differences in the incidence of infection and the consequent mortality between males and females. We, therefore, analyzed retrospective datasets from the previous epidemics and the ongoing pandemic in order to address these differences in clinical outcomes. The data shows that even though the infection rates are similar, the odds ratio of male mortality remains high, indicating a divergence in the crosstalk between the three pathogenic human Coronavirus (hCoVs)-the SARS-CoV, MERS-CoV and the SARS-CoV-2 and immune effectors in the two sexes. One proximate cause is the sex-specific modulation of the X-linked genes that can influence susceptibility to infection. Future studies are needed to confirm these findings, which can form the basis for developing rational strategies for ending the current and preventing future pandemics.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Swaminathan P Iyer",
-        "author_inst": "University of Texas MD Anderson Cancer Center"
-      },
-      {
-        "author_name": "Joe Ensor",
-        "author_inst": "Houston Methodist Research Institute"
-      },
-      {
-        "author_name": "Kartik Anand",
-        "author_inst": "Great Plains Health"
-      },
-      {
-        "author_name": "Patrick Hwu",
-        "author_inst": "University of Texas MD Anderson Cancer Center"
-      },
-      {
-        "author_name": "Vivek Subbiah",
-        "author_inst": "University of Texas MD Anderson Cancer Center"
-      },
-      {
-        "author_name": "Christopher Flowers",
-        "author_inst": "University of Texas MD Anderson Cancer Center"
-      },
-      {
-        "author_name": "Rudragouda Channappanavar",
-        "author_inst": "University of Tennessee Health Science Center"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.04.22.055863",
     "rel_title": "Genomic, geographic and temporal distributions of SARS-CoV-2 mutations",
@@ -1513372,6 +1512178,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "allergy and immunology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.21.20066761",
+    "rel_title": "Risk of drug-induced Long QT Syndrome associated with the use of repurposed COVID-19 drugs: a systematic review",
+    "rel_date": "2020-04-24",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20066761",
+    "rel_abs": "The risk-benefit ratio associated with the use of repurposed drugs to treat 2019 SARS-CoV-2 related infectious disease (COVID-19) is complicated since benefits are awaited, not proven. A thorough literature search was conducted to source information on the pharmacological properties of 5 drugs and 1 combination (azithromycin, chloroquine, favipiravir, hydroxychloroquine, remdesivir, and lopinavir/ritonavir) repurposed to treat COVID-19. A risk assessment of drug-induced Long QT Syndrome (LQTS) associated with COVID-19 repurposed drugs was performed and compared to 23 well-known torsadogenic and 10 low torsadogenic risk compounds. Computer calculations were performed using pharmacokinetic and pharmacodynamic data, including affinity to block the rapid component of the delayed rectifier cardiac potassium current (IKr) encoded by the human ether-a-go-go gene (hERG), propensity to prolong cardiac repolarization (QT interval) and cause torsade de pointes (TdP). Seven different LQTS indices were calculated and compared. The U.S. Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) database was queried with specific key words relating to arrhythmogenic events. Estimators of LQTS risk levels indicated a very high or moderate risk for all COVID-19 repurposed drugs with the exception for azithromycin, although cases of TdP have been reported with this drug. There was excellent agreement among the various indices used to assess risk of drug-induced LQTS for the 6 repurposed medications and 23 torsadogenic compounds. Based on our results, monitoring of the QT interval shall be performed when some COVID-19 repurposed drugs are used, as such monitoring is possible for hospitalized patients or with the use of biodevices for outpatients.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Veronique Michaud",
+        "author_inst": "Tabula Rasa HealthCare"
+      },
+      {
+        "author_name": "Pamela Dow",
+        "author_inst": "Tabula Rasa HealthCare"
+      },
+      {
+        "author_name": "Sweilem B Al Rihani",
+        "author_inst": "Tabula Rasa HealthCare"
+      },
+      {
+        "author_name": "Malavika Deodhar",
+        "author_inst": "Tabula Rasa HealthCare"
+      },
+      {
+        "author_name": "Meghan Arwood",
+        "author_inst": "Tabula Rasa HealthCare"
+      },
+      {
+        "author_name": "Brian Cicali",
+        "author_inst": "University of Florida"
+      },
+      {
+        "author_name": "Jacques Turgeon",
+        "author_inst": "Tabula Rasa HealthCare"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "pharmacology and therapeutics"
+  },
   {
     "rel_doi": "10.1101/2020.04.20.20068676",
     "rel_title": "Understanding the Collective Responses of Populations to the COVID-19 Pandemic in Mainland China",
@@ -1514861,41 +1513710,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.21.20064915",
-    "rel_title": "High prevalence of putative invasive pulmonary aspergillosis in critically ill COVID-19 patients",
-    "rel_date": "2020-04-24",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20064915",
-    "rel_abs": "We are currently facing a frightening increase in COVID-19 patients admitted to the ICU. Aiming at screening for fungal secondary pneumonia, we collected the data of our first 27 ICU patients, who underwent bronchoalveolar lavage or bronchial aspirates. We classified the patients based on the recently published study on invasive aspergillosis in influenza patients (Schauwvlinghe et al., 2018.) and found 33% of our COVID-19 patients with putative invasive pulmonary aspergillosis. Observing such a high prevalence in COVID-infected patients was somehow unexpected since the 30% prevalence of invasive aspergillosis in influenza patients has been attributed to the action of oseltamivir on anti-Aspergillus immunity. Almost all critically ill COVID-19 patients develop ARDS and are likely to receive high-dose steroids or immunomodulatory therapies to prevent worsening as suggested by reports from China. In the COVID-19 patients with putative invasive aspergillosis, antifungal prophylactic therapy may be questioned to avoid increased lung inflammation that may compromise the outcome. This issue remains to be addressed in future clinical trials. We are strongly convinced that testing deep lung specimens for Aspergillus in severe COVID-19 patients should be recommended.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Alexandre Alanio",
-        "author_inst": "Assistance Publique Hopitaux de Paris"
-      },
-      {
-        "author_name": "Sarah Delliere",
-        "author_inst": "Assistance Publique Hopitaux de Paris"
-      },
-      {
-        "author_name": "Sofiane Fodil",
-        "author_inst": "Assistance Publique Hopitaux de Paris"
-      },
-      {
-        "author_name": "Stephane Bretagne",
-        "author_inst": "Assistance Publique Hopitaux de Paris"
-      },
-      {
-        "author_name": "Bruno Megarbane",
-        "author_inst": "Assistance Publique Hopitaux de Paris"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "intensive care and critical care medicine"
-  },
   {
     "rel_doi": "10.1101/2020.04.18.20069955",
     "rel_title": "The impact of current and future control measures on the spread of COVID-19 in Germany",
@@ -1515086,6 +1513900,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.20.20072470",
+    "rel_title": "Prevalence of SARS-CoV-2 infection in previously undiagnosed health care workers at the onset of the U.S. COVID-19 epidemic",
+    "rel_date": "2020-04-24",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20072470",
+    "rel_abs": "ImportanceHealthcare workers are presumed to be at increased risk of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection due to occupational exposure to infected patients. However, no epidemiological study has examined the prevalence of SARS-CoV-2 infection in a cohort of healthcare workers during the early phase of community transmission.\n\nObjectiveTo determine the baseline prevalence of SARS-CoV-2 infection in a cohort of previously undiagnosed healthcare workers and a comparison group of non-healthcare workers.\n\nDesignProspective cohort study\n\nSettingA large U.S. university and two affiliated university hospitals\n\nParticipants546 health care workers and 283 non-health care workers with no known prior SARS-CoV-2 infection\n\nExposureHealthcare worker status and role\n\nMain outcome(s) and measure(s)SARS-CoV-2 infection status as determined by presence of SARS-CoV-2 RNA in oropharyngeal swabs.\n\nResultsAt baseline, 41 (5.0%) of participants tested positive for SARS-CoV-2 infection, of whom 14 (34.2%) reported symptoms. The prevalence of SARS-CoV-2 infection was higher among healthcare workers (7.3%) than in non-healthcare workers (0.4%), representing a 7.0% greater absolute risk (95% confidence interval for risk difference 4.7%, 9.3%). The majority of infected healthcare workers (62.5%) worked as nurses. Positive tests increased across the two weeks of cohort recruitment in line with rising confirmed cases in the hospitals and surrounding counties.\n\nConclusions and relevanceIn a prospective cohort conducted in the early phases of community transmission, healthcare workers had a higher prevalence of SARS-CoV-2 infection than non-healthcare workers, attesting to the occupational hazards of caring for patients in this crisis. Baseline data reported here will enable us to monitor the spread of infection and examine risk factors for transmission among healthcare workers. These results will inform optimal strategies for protecting the healthcare workforce, their families, and their patients.\n\nClinicaltrials.gov registration number:NCT04336215\n\nKey pointsO_ST_ABSQuestionC_ST_ABSAmong previously undiagnosed individuals, is the prevalence of SARS-CoV-2 infection higher in U.S. healthcare workers compared to non-healthcare workers in the early phase of the U.S. COVID-19 epidemic?\n\nFindingsThe prevalence of SARS-CoV-2 infection was 7.3% in healthcare workers and 0.4% in non-healthcare workers, representing 7.0% greater absolute risk in the former (95% confidence interval for risk difference 4.7%, 9.3%). Infections were most common among nursing staff.\n\nMeaningHealth care workers, particularly those with high levels of close patient contact, may be particularly vulnerable to SARS-CoV-2 infection. Additional strategies are needed to protect these critical frontline workers.",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Emily S Barrett",
+        "author_inst": "Rutgers School of Public Health"
+      },
+      {
+        "author_name": "Daniel B. Horton",
+        "author_inst": "Rutgers Robert Wood Johnson Medical School"
+      },
+      {
+        "author_name": "Jason Roy",
+        "author_inst": "Rutgers School of Public Health"
+      },
+      {
+        "author_name": "Maria Laura Gennaro",
+        "author_inst": "New Jersey Medical School"
+      },
+      {
+        "author_name": "Andrew Brooks",
+        "author_inst": "RUCDR Infinite Biologics, Rutgers University"
+      },
+      {
+        "author_name": "Jay Tischfield",
+        "author_inst": "RUCDR Infinite Biologics, Rutgers University"
+      },
+      {
+        "author_name": "Patricia Greenberg",
+        "author_inst": "Rutgers School of Public Health"
+      },
+      {
+        "author_name": "Tracy Andrews",
+        "author_inst": "Rutgers School of Public Health"
+      },
+      {
+        "author_name": "Sugeet Jagpal",
+        "author_inst": "Rutgers Robert Wood Johnson Medical School"
+      },
+      {
+        "author_name": "Nancy Reilly",
+        "author_inst": "Rutgers Institute for Translational Medicine & Science"
+      },
+      {
+        "author_name": "Martin J. Blaser",
+        "author_inst": "Center for Advanced Biotechnology and Medicine; Rutgers University"
+      },
+      {
+        "author_name": "Jeffrey Carson",
+        "author_inst": "Rutgers Robert Wood Johnson Medical School"
+      },
+      {
+        "author_name": "Reynold A. Panettieri Jr.",
+        "author_inst": "Rutgers Institute for Translational Medicine & Science"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.04.21.20074138",
     "rel_title": "Prediction of the COVID-19 Epidemic Trends Based on SEIR and AI Models",
@@ -1516123,25 +1515004,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.20.20072272",
-    "rel_title": "A simulation of a COVID-19 epidemic based on a deterministic SEIR model",
-    "rel_date": "2020-04-24",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20072272",
-    "rel_abs": "An epidemic disease caused by a new coronavirus has spread in Northern Italy with a strong contagion rate. We implement an SEIR model to compute the infected population and number of casualties of this epidemic. The example may ideally regard the situation in the Italian Region of Lombardy, where the epidemic started on February 24, but by no means attempts to perform a rigorous case study in view of the lack of suitable data and uncertainty of the different parameters, namely, the variation of the degree of home isolation and social distancing as a function of time, the number of initially exposed individuals and infected people, the incubation and infectious periods and the fatality rate.\n\nFirst, we perform an analysis of the results of the model, by varying the parameters and initial conditions (in order the epidemic to start, there should be at least one exposed or one infectious human). Then, we consider the Lombardy case and calibrate the model with the number of dead individuals to date (April 28, 2020) and constraint the parameters on the basis of values reported in the literature. The peak occurs at day 37 (March 31) approximately, when there is a rapid decrease, with a reproduction ratio R0 = 3 initially, 1.36 at day 22 and 0.78 after day 35, indicating different degrees of lockdown. The predicted death toll is almost 15325 casualties, with 2.64 million infected individuals at the end of the epidemic. The incubation period providing a better fit of the dead individuals is 4.25 days and the infectious period is 4 days, with a fatality rate of 0.00144/day [values based on the reported (official) number of casualties]. The infection fatality rate (IFR) is 0.57 %, and 2.36 % if twice the reported number of casualties is assumed. However, these rates depend on the initially exposed individuals. If approximately nine times more individuals are exposed, there are three times more infected people at the end of the epidemic and IFR = 0.47 %. If we relax these constraints and use a wider range of lower and upper bounds for the incubation and infectious periods, we observe that a higher incubation period (13 versus 4.25 days) gives the same IFR (0.6 % versus 0.57 %), but nine times more exposed individuals in the first case. Other choices of the set of parameters also provide a good fit of the data, but some of the results may not be realistic. Therefore, an accurate determination of the fatality rate and characteristics of the epidemic is subject to the knowledge of precise bounds of the parameters.\n\nBesides the specific example, the analysis proposed in this work shows how isolation measures, social distancing and knowledge of the diffusion conditions help us to understand the dynamics of the epidemic. Hence, the importance to quantify the process to verify the effectiveness of the lockdown.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Jose' M Carcione",
-        "author_inst": "OGS - https://www.inogs.it/it/users/jos%C3%A9-maria-carcione"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.04.19.20071548",
     "rel_title": "Current Understanding of COVID-19 Clinical Course and Investigational Treatments",
@@ -1516644,6 +1515506,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.17.20070219",
+    "rel_title": "From Community Acquired Pneumonia to COVID-19: A Deep Learning Based Method for Quantitative Analysis of COVID-19 on thick-section CT Scans",
+    "rel_date": "2020-04-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20070219",
+    "rel_abs": "BackgroundThick-section CT scanners are more affordable for the developing countries. Considering the widely spread COVID-19, it is of great benefit to develop an automated and accurate system for quantification of COVID-19 associated lung abnormalities using thick-section chest CT images.\n\nPurposeTo develop a fully automated AI system to quantitatively assess the disease severity and disease progression using thick-section chest CT images.\n\nMaterials and MethodsIn this retrospective study, a deep learning based system was developed to automatically segment and quantify the COVID-19 infected lung regions on thick-section chest CT images. 531 thick-section CT scans from 204 patients diagnosed with COVID-19 were collected from one appointed COVID-19 hospital from 23 January 2020 to 12 February 2020. The lung abnormalities were first segmented by a deep learning model. To assess the disease severity (non-severe or severe) and the progression, two imaging bio-markers were automatically computed, i.e., the portion of infection (POI) and the average infection HU (iHU). The performance of lung abnormality segmentation was examined using Dice coefficient, while the assessment of disease severity and the disease progression were evaluated using the area under the receiver operating characteristic curve (AUC) and the Cohens kappa statistic, respectively.\n\nResultsDice coefficient between the segmentation of the AI system and the manual delineations of two experienced radiologists for the COVID-19 infected lung abnormalities were 0.74{+/-}0.28 and 0.76{+/-}0.29, respectively, which were close to the inter-observer agreement, i.e., 0.79{+/-}0.25. The computed two imaging bio-markers can distinguish between the severe and non-severe stages with an AUC of 0.9680 (p-value< 0.001). Very good agreement ({kappa} = 0.8220) between the AI system and the radiologists were achieved on evaluating the changes of infection volumes.\n\nConclusionsA deep learning based AI system built on the thick-section CT imaging can accurately quantify the COVID-19 associated lung abnormalities, assess the disease severity and its progressions.\n\nKey ResultsA deep learning based AI system was able to accurately segment the infected lung regions by COVID-19 using the thick-section CT scans (Dice coefficient [&ge;] 0.74).\n\nThe computed imaging bio-markers were able to distinguish between the non-severe and severe COVID-19 stages (area under the receiver operating characteristic curve 0.968).\n\nThe infection volume changes computed by the AI system was able to assess the COVID-19 progression (Cohens kappa 0.8220).\n\nSummary StatementA deep learning based AI system built on the thick-section CT imaging can accurately quantify the COVID-19 infected lung regions, assess patients disease severity and their disease progressions.",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Zhang Li",
+        "author_inst": "College of Aerospace Science and Engineering, National University of Defense Technology, Changsha, China"
+      },
+      {
+        "author_name": "Zheng Zhong",
+        "author_inst": "Department of Radiology, The First Hospital of Changsha City, Changsha, China"
+      },
+      {
+        "author_name": "Yang Li",
+        "author_inst": "College of Aerospace Science and Engineering, National University of Defense Technology, Changsha, China"
+      },
+      {
+        "author_name": "Tianyu Zhang",
+        "author_inst": "Department of Radiology, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands"
+      },
+      {
+        "author_name": "Liangxin Gao",
+        "author_inst": "PingAn Technology, Shenzhen, China"
+      },
+      {
+        "author_name": "Dakai Jin",
+        "author_inst": "PAII Inc., Bethesda, MD, USA"
+      },
+      {
+        "author_name": "Yue Sun",
+        "author_inst": "Department of Electrical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands"
+      },
+      {
+        "author_name": "Xianghua Ye",
+        "author_inst": "Department of Radiotherapy, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China"
+      },
+      {
+        "author_name": "Li Yu",
+        "author_inst": "Hunan LanXi Biotechnology Ltd., Changsha, China"
+      },
+      {
+        "author_name": "Zheyu Hu",
+        "author_inst": "Hunan Cancer Hospital, the Affiliated Cancer Hospital of Xiangya Medical School, Central South University, Changsha, China"
+      },
+      {
+        "author_name": "Jing Xiao",
+        "author_inst": "PingAn Technology, Shenzhen, China"
+      },
+      {
+        "author_name": "Lingyun Huang",
+        "author_inst": "PingAn Technology, Shenzhen, China"
+      },
+      {
+        "author_name": "Yuling Tang",
+        "author_inst": "Department of Respiratory Medicine, The First Hospital of Changsha City, Changsha, China"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "radiology and imaging"
+  },
   {
     "rel_doi": "10.1101/2020.04.20.20072991",
     "rel_title": "Monitoring COVID-19 progression: Look at Us Today, See Yourself Tomorrow",
@@ -1517733,153 +1516662,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.22.056283",
-    "rel_title": "Preliminary support for a 'dry swab, extraction free' protocol for SARS-CoV-2 testing via RT-qPCR",
-    "rel_date": "2020-04-23",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.22.056283",
-    "rel_abs": "Structured AbstractO_ST_ABSBackgroundC_ST_ABSThe urgent need for massively scaled clinical testing for SARS-CoV-2, along with global shortages of critical reagents and supplies, has necessitated development of streamlined laboratory testing protocols. Conventional nucleic acid testing for SARS-CoV-2 involves collection of a clinical specimen with a nasopharyngeal swab in transport medium, nucleic acid extraction, and quantitative reverse transcription PCR (RT-qPCR) (1). As testing has scaled across the world, the global supply chain has buckled, rendering testing reagents and materials scarce (2). To address shortages, we developed SwabExpress, an end-to-end protocol developed to employ mass produced anterior nares swabs and bypass the requirement for transport media and nucleic acid extraction.\n\nMethodsWe evaluated anterior nares swabs, transported dry and eluted in low-TE buffer as a direct-to-RT-qPCR alternative to extraction-dependent viral transport media. We validated our protocol of using heat treatment for viral activation and added a proteinase K digestion step to reduce amplification interference. We tested this protocol across archived and prospectively collected swab specimens to fine-tune test performance.\n\nResultsAfter optimization, SwabExpress has a low limit of detection at 2-4 molecules/uL, 100% sensitivity, and 99.4% specificity when compared side-by-side with a traditional RT-qPCR protocol employing extraction. On real-world specimens, SwabExpress outperforms an automated extraction system while simultaneously reducing cost and hands-on time.\n\nConclusionSwabExpress is a simplified workflow that facilitates scaled testing for COVID-19 without sacrificing test performance. It may serve as a template for the simplification of PCR-based clinical laboratory tests, particularly in times of critical shortages during pandemics.",
-    "rel_num_authors": 33,
-    "rel_authors": [
-      {
-        "author_name": "Sanjay Srivatsan",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Sarah Heidl",
-        "author_inst": "Brotman Baty Institute"
-      },
-      {
-        "author_name": "Brian Pfau",
-        "author_inst": "Brotman Baty Institute"
-      },
-      {
-        "author_name": "Beth Martin",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Peter D Han",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Weizhi Zhong",
-        "author_inst": "Brotman Baty Institute"
-      },
-      {
-        "author_name": "Katrina van Raay",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Evan McDermot",
-        "author_inst": "Brotman Baty Institute"
-      },
-      {
-        "author_name": "Jordan Opsahl",
-        "author_inst": "Brotman Baty Institute"
-      },
-      {
-        "author_name": "Luis Gamboa",
-        "author_inst": "Brotman Baty Institute"
-      },
-      {
-        "author_name": "Nahum Smith",
-        "author_inst": "Brotman Baty Institute"
-      },
-      {
-        "author_name": "Melissa Truong",
-        "author_inst": "Brotman Baty Institute"
-      },
-      {
-        "author_name": "Shari Cho",
-        "author_inst": "Brotman Baty Institute"
-      },
-      {
-        "author_name": "Jeremy Stone",
-        "author_inst": "Brotman Baty Institute"
-      },
-      {
-        "author_name": "Caitlin R Wolf",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Denise J McCulloch",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Ashley E Kim",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Elisabeth Brandstetter",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Sarah L Sohlberg",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Misja Ilcisin",
-        "author_inst": "Fred Hutch Cancer Research Institute"
-      },
-      {
-        "author_name": "Rachel E. Geyer",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Wei Chen",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Jase M Gehring",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "- Seattle Flu Study Investigators",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Sriram Kosuri",
-        "author_inst": "Octant, Inc, University of California, Los Angeles"
-      },
-      {
-        "author_name": "Trevor Bedford",
-        "author_inst": "Fred Hutchinson Cancer Research Center"
-      },
-      {
-        "author_name": "Mark J Reider",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Helen Y Chu",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Eric Q Konnick",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Deborah A Nickerson",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Jay Shendure",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Christina M Lockwood",
-        "author_inst": "University of Washington"
-      },
-      {
-        "author_name": "Lea M Starita",
-        "author_inst": "University of Washington"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "molecular biology"
-  },
   {
     "rel_doi": "10.1101/2020.04.21.054387",
     "rel_title": "Identification of potential treatments for COVID-19 through artificial intelligence-enabled phenomic analysis of human cells infected with SARS-CoV-2",
@@ -1518218,6 +1517000,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.04.18.20070565",
+    "rel_title": "Clinical Characteristics of 20,662 Patients with COVID-19 in mainland China: A Systemic Review and Meta-analysis",
+    "rel_date": "2020-04-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.18.20070565",
+    "rel_abs": "Coronavirus disease 2019 (COVID-19) is a global pandemic and has been widely reported; however, a comprehensive systemic review and meta-analysis has not been conducted. We systematically investigated the clinical characteristics of COVID-19 in mainland China to guide diagnosis and treatment. We searched the PubMed, Embase, Scopus, Web of Science, Cochrane Library, bioRxiv, medRxiv, and SSRN databases for studies related to COVID-19 published or preprinted in English or Chinese from January 1 to March 15, 2020. Clinical studies on COVID-19 performed in mainland China were included. We collected primary outcomes including signs and symptoms, chest CT imaging, laboratory tests, and treatments. Study selection, data extraction, and risk of bias assessment were performed by two independent reviewers. Qualitative and quantitative synthesis was conducted, and random-effects models were applied to pooled estimates. This study is registered with PROSPERO (number CRD42020171606). Of the 3624 records identified, 147 studies (20,662 patients) were analyzed. The mean age of patients with COVID-19 was 49.40 years, 53.45% were male, and 38.52% had at least one comorbidity. Fever and cough were the most common symptoms, followed by fatigue, expectoration, and shortness of breath. Most patients with COVID-19 had abnormal chest CT findings with ground glass opacity (70.70%) or consolidation (29.91%). Laboratory findings shown lymphopenia, increased lactate dehydrogenase, increased infection-related indicators, and fibrinolytic hyperactivity. Antiviral therapy, antibiotic therapy, and corticosteroids were administered to 89.75%, 79.13%, and 35.64% of patients, respectively. Most clinical characteristics of COVID-19 are non-specific. Patients with suspected should be evaluated by virological assays and clinically treated.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Chong Tang",
+        "author_inst": "Peking university shougang hospital"
+      },
+      {
+        "author_name": "Keshi Zhang",
+        "author_inst": "Peking university shougang hospital"
+      },
+      {
+        "author_name": "Wenlong Wang",
+        "author_inst": "Peking university shougang hospital"
+      },
+      {
+        "author_name": "Zheng Pei",
+        "author_inst": "Peking university shougang hospital"
+      },
+      {
+        "author_name": "Zheng Liu",
+        "author_inst": "Peking university shougang hospital"
+      },
+      {
+        "author_name": "Ping Yuan",
+        "author_inst": "Peking university shougang hospital"
+      },
+      {
+        "author_name": "Zhenpeng Guan",
+        "author_inst": "Peking university shougang hospital"
+      },
+      {
+        "author_name": "Jin Gu",
+        "author_inst": "Peking university shougang hospital"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.04.18.20070920",
     "rel_title": "Trends of SARS-Cov-2 infection in 67 countries: Role of climate zone, temperature, humidity and curve behavior of cumulative frequency on duplication time",
@@ -1519615,41 +1518444,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "gastroenterology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.19.20065219",
-    "rel_title": "The association between age, COVID-19 symptoms, and social distancing behavior in the United States",
-    "rel_date": "2020-04-23",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20065219",
-    "rel_abs": "BackgroundPublic health authorities recommend that people practice social distancing, especially if they have symptoms of coronavirus disease (COVID-19), or are older and more at risk of serious illness if they become infected. We test the hypothesis that these groups are following these recommendations and are more likely to undertake social distancing.\n\nMethodsWe conducted an open online survey of 4,676 U.S. adults aged 18 and older between April 4 and April 7, 2020. We model the effects of age and common COVID-19 symptoms in the last two weeks on going out of the home for non-healthcare reasons the day before taking the survey, using a logistic model and the number of close contacts (within 6 feet) that respondents had with non-household members, using a Poisson count model. Our models control for several covariates, including other flu-like symptoms, sex, education, income, whether the respondent worked in February, household size, population density in the respondents ZIP code, state fixed effects, and the day of completion of the survey. We also weight our analyses to make the sample representative of the U.S. adult population.\n\nFindingsAbout 52 percent of the adult United States population went out of their home the previous day. On average, adults had close contact with 1.9 non-household members. We find that having at least one COVID-19 symptom (fever, dry cough, or shortness of breath) increased the likelihood of going out the previous day and having additional close contacts with non-household members; however, the estimates were not statistically significant. When disaggregating our analysis by COVID-19 symptoms, we find no strong evidence of greater social distancing by people with a fever or cough in the last two weeks, but we do find that those who experienced shortness of breath have fewer close contacts, with an incidence rate ratio (IRR) of 0.49 (95% CI: 0.30-0.78). Having other flu-like symptoms reduces the odds of going out by 0.32 (95% CI: 0.18-0.60) and the incidence rate of having close contacts by 42 percent (IRR = 0.58; 95% CI: 0.38-0.88). We find that older people are just as likely to leave their homes as younger people, but people over the age of 50 had less than half the predicted number of close contacts than those who were younger than 30. Our approach has the limitation that the survey sample is self-selected. Our findings may therefore be subject to selection bias that is not adequately controlled for by weighting. In addition, the possibility exists of confounding of the results due to omitted variable bias.\n\nConclusionsWe provide evidence that older people are having significantly fewer close contacts than younger people, which is in line with the public health authorities recommendations. We also find that people experiencing shortness of breath are practicing more intense social distancing. However, we find that those with two other common COVID-19 symptoms, fever and dry cough, are not engaging in greater social distancing, suggesting that increased targeting on relevant symptoms, and messaging, may be required.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "David Canning",
-        "author_inst": "Harvard T.H. Chan School of Public Health"
-      },
-      {
-        "author_name": "Mahesh Karra",
-        "author_inst": "Frederick S. Pardee School of Global Studies at Boston University"
-      },
-      {
-        "author_name": "Rashmi Dayalu",
-        "author_inst": "Harvard T.H. Chan School of Public Health"
-      },
-      {
-        "author_name": "Muqi Guo",
-        "author_inst": "Harvard T.H. Chan School of Public Health"
-      },
-      {
-        "author_name": "David E Bloom",
-        "author_inst": "Harvard T.H. Chan School of Public Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.04.19.20068015",
     "rel_title": "Impaired type I interferon activity and exacerbated inflammatory responses in severe Covid-19 patients",
@@ -1520060,6 +1518854,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "respiratory medicine"
   },
+  {
+    "rel_doi": "10.1101/2020.04.13.20064287",
+    "rel_title": "Does TB Vaccination Reduce COVID-19 Infection?: No Evidence from a Regression Discontinuity Analysis",
+    "rel_date": "2020-04-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20064287",
+    "rel_abs": "In the middle of the global COVID-19 pandemic, the BCG hypothesis, the prevalence and severity of the COVID-19 outbreak seems to be correlated with whether a country has a universal coverage of Bacillus-Calmette-Guerin (BCG), a vaccine for tuberculosis disease (TB), has emerged and attracted the attention of scientific community and media outlets. However, all existing claims are based on cross-country correlations that do not exclude the possibility of spurious correlation. We merged country-age-level case statistics with the start/termination years of BCG vaccination policy and conducted a regression discontinuity and difference-indifference analysis. The results do not support the BCG hypothesis.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Masao Fukui",
+        "author_inst": "Massachusetts Institute of Technology"
+      },
+      {
+        "author_name": "Kohei Kawaguchi",
+        "author_inst": "Hong Kong University of Science and Technology"
+      },
+      {
+        "author_name": "Hiroaki Matsuura",
+        "author_inst": "Shoin University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health economics"
+  },
   {
     "rel_doi": "10.1101/2020.04.16.20067421",
     "rel_title": "Self-reported COVID-19 symptoms on Twitter: An analysis and a research resource",
@@ -1521273,45 +1520094,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.04.19.20069948",
-    "rel_title": "A Chronological and Geographical Analysis of Personal Reports of COVID-19 on Twitter",
-    "rel_date": "2020-04-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20069948",
-    "rel_abs": "The rapidly evolving outbreak of COVID-19 presents challenges for actively monitoring its spread. In this study, we assessed a social media mining approach for automatically analyzing the chronological and geographical distribution of users in the United States reporting personal information related to COVID-19 on Twitter. The results suggest that our natural language processing and machine learning framework could help provide an early indication of the spread of COVID-19.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Ari Klein",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Arjun Magge",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Karen O'Connor",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Haitao Cai",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Davy Weissenbacher",
-        "author_inst": "University of Pennsylvania"
-      },
-      {
-        "author_name": "Graciela Gonzalez-Hernandez",
-        "author_inst": "University of Pennsylvania"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health informatics"
-  },
   {
     "rel_doi": "10.1101/2020.04.17.20068916",
     "rel_title": "Statistical and network-based analysis of Italian COVID-19 data: communities detection and temporal evolution",
@@ -1521526,6 +1520308,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.04.17.20069823",
+    "rel_title": "An ecological study of socioeconomic predictors in detection of COVID-19 cases across neighborhoods in New York City",
+    "rel_date": "2020-04-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20069823",
+    "rel_abs": "BackgroundNew York City was the first major urban center of the COVID-19 pandemic in the USA. Cases are clustered in the city, with certain neighborhoods experiencing more cases than others. We investigate whether potential socioeconomic factors can explain between-neighborhood variation in the number of detected COVID-19 cases.\n\nMethodsData were collected from 177 Zip Code Tabulation Areas (ZCTA) in New York City (99.9% of the population). We fit multiple Bayesian Besag-York-Mollie (BYM) mixed models using positive COVID-19 tests as the outcome and a set of 10 representative economic, demographic, and health-care associated ZCTA-level parameters as potential predictors. The BYM model includes both spatial and nonspatial random effects to account for clustering and overdispersion.\n\nResultsMultiple different regression approaches indicated a consistent, statistically significant association between detected COVID-19 cases and dependent (under 18 or 65+ years old) population, male to female ratio, and median household income. In the final model, we found that an increase of only 1% in dependent population is associated with a 2.5% increase in detected COVID-19 cases (95% confidence interval (CI): 1.6% to 3.4%, p < 0.0005). An increase of 1 male per 100 females is associated with a 1.0% (95% CI: 0.6% to 1.5%, p < 0.0005) increases in detected cases. A decrease of $10,000 median household income is associated with a 2.5% (95% CI: 1.0% to 4.1% p = 0.002) increase in detected COVID-19 cases.\n\nConclusionsOur findings indicate associations between neighborhoods with a large dependent population, those with a high proportion of males, and low-income neighborhoods and detected COVID-19 cases. Given the elevated mortality in aging populations, the study highlights the importance of public health management during and after the current COVID-19 pandemic. Further work is warranted to fully understand the mechanisms by which these factors may have affected the number of detected cases, either in terms of the true number of cases or access to testing.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Richard Stuart Whittle",
+        "author_inst": "Texas A&M University"
+      },
+      {
+        "author_name": "Ana Diaz-Artiles",
+        "author_inst": "Texas A&M University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.04.17.20070102",
     "rel_title": "Social Distancing and Personal Protective Measures Decrease Influenza Morbidity and Mortality",
@@ -1522671,37 +1521476,6 @@
     "type": "new results",
     "category": "bioengineering"
   },
-  {
-    "rel_doi": "10.1101/2020.04.17.20068585",
-    "rel_title": "Mathematical modeling of COVID-19 containment strategies with considerations for limited medical resources",
-    "rel_date": "2020-04-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20068585",
-    "rel_abs": "The outbreak of SARS-CoV-2 in China has spread around the world, infecting millions and causing governments to implement strict policies to counteract the spread of the disease. One of the most effective strategies in reducing the severity of the pandemic is social distancing, where members of the population systematically reduce their interactions with others to limit the transmission rate of the virus. However, the implementation of social distancing can be difficult and costly, making it imperative that both policy makers and the citizenry understand the potential benefits if done correctly and the risks if not. In this work, a mathematical model is developed to study the effects of social distancing on the spread of the SARS-CoV-2 virus in Canada. The model is based upon a standard epidemiological SEIRD model that has been stratified to directly incorporate the proportion of individuals who are following social distancing protocols. The model parameters characterizing the disease are estimated from current epidemiological data on COVID-19 using machine learning techniques. The results of the model show that social distancing policies in Canada have already saved thousands of lives and that the prolonged adherence to social distancing guidelines could save thousands more. Importantly, our model indicates that social distancing can significantly delay the onset of infection peaks, allowing more time for the production of a vaccine or additional medical resources. Furthermore, our results stress the importance of easing social distancing restrictions gradually, rather than all at once, in order to prevent a second wave of infections. Model results are compared to the current capacity of the Canadian healthcare system by examining the current and future number of ventilators available for use, emphasizing the need for the increased production of additional medical resources.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Brydon Eastman",
-        "author_inst": "University of Waterloo"
-      },
-      {
-        "author_name": "Cameron Meaney",
-        "author_inst": "University of Waterloo"
-      },
-      {
-        "author_name": "Michelle Przedborski",
-        "author_inst": "University of Waterloo"
-      },
-      {
-        "author_name": "Mohammad Kohandel",
-        "author_inst": "University of Waterloo"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.04.21.052639",
     "rel_title": "Structural Basis of SARS-CoV-2 Spike Protein Priming by TMPRSS2",
@@ -1523216,6 +1521990,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.04.17.20068577",
+    "rel_title": "Aerosolized Hydrogen Peroxide Decontamination of N95 Respirators, with Fit-Testing and Virologic Confirmation of Suitability for Re-Use During the COVID-19 Pandemic",
+    "rel_date": "2020-04-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20068577",
+    "rel_abs": "In response to the demand for N95 respirators by healthcare workers during the COVID-19 pandemic, we evaluated decontamination of N95 respirators using an aerosolized hydrogen peroxide (aHP) system. This system is designed to dispense a consistent atomized spray of aerosolized, 7% hydrogen peroxide (H2O2) solution over a treatment cycle. Multiple N95 respirator models were subjected to ten or more cycles of respirator decontamination, with a select number periodically assessed for qualitative and quantitative fit testing. In parallel, we assessed the ability of aHP treatment to inactivate multiple viruses absorbed onto respirators, including phi6 bacteriophage, HSV-1, CVB3, and SARS-CoV-2. For pathogens transmitted via respiratory droplets and aerosols, it is critical to address respirator safety for reuse. This study provided experimental validation of an aHP treatment process that decontaminates the respirators while maintaining N95 function. External NIOSH certification verified respirator structural integrity and filtration efficiency after ten rounds of aHP treatment. Virus inactivation by aHP was comparable to the decontamination of commercial spore-based biological indicators. These data demonstrate that the aHP process is effective, with successful fit-testing of respirators after multiple aHP cycles, effective decontamination of multiple virus species including SARS-CoV- 2, successful decontamination of bacterial spores, and filtration efficiency maintained at or greater than 95%. While this study did not include extended or clinical use of N95 respirators between aHP cycles, these data provide proof of concept for aHP decontamination of N95 respirators before reuse in a crisis-capacity scenario.\n\nImportanceThe COVID-19 pandemic led to unprecedented pressure on healthcare and research facilities to provide personal protective equipment. The respiratory nature of the SARS-CoV2 pathogen makes respirator facepieces a critical protection measure to limit inhalation of this virus. While respirator facepieces were designed for single-use and disposal, the pandemic increased overall demand for N95 respirators, and corresponding manufacturing and supply chain limitations necessitated the safe reuse of respirators when necessary. In this study, we repurposed an aerosolized hydrogen peroxide (aHP) system that is regularly utilized to decontaminate materials in a biosafety level 3 (BSL3) facility, to develop methods for decontamination of N95 respirators. Results from virus inactivation, biological indicators, respirator fit testing, and filtration efficiency testing all indicated that the process was effective at rendering N95 respirators safe for reuse. This proof-of-concept study establishes baseline data for future testing of aHP in crisis capacity respirator-reuse scenarios.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "T. Hans Derr",
+        "author_inst": "Pennsylvania State University"
+      },
+      {
+        "author_name": "Melissa A. James",
+        "author_inst": "Pennsylvania State University"
+      },
+      {
+        "author_name": "Chad V. Kuny",
+        "author_inst": "Pennsylvania State University"
+      },
+      {
+        "author_name": "Devanshi Patel",
+        "author_inst": "Pennsylvania State University"
+      },
+      {
+        "author_name": "Prem P. Kandel",
+        "author_inst": "Pennsylvania State University"
+      },
+      {
+        "author_name": "Cassandra Field",
+        "author_inst": "Pennsylvania State University"
+      },
+      {
+        "author_name": "Matthew D. Beckman",
+        "author_inst": "Pennsylvania State University"
+      },
+      {
+        "author_name": "Kevin L. Hockett",
+        "author_inst": "Pennsylvania State University"
+      },
+      {
+        "author_name": "Mark A. Bates",
+        "author_inst": "Pennsylvania State University"
+      },
+      {
+        "author_name": "Troy C Sutton",
+        "author_inst": "Pennsylvania State University"
+      },
+      {
+        "author_name": "Moriah L Szpara",
+        "author_inst": "Pennsylvania State University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.04.16.20068031",
     "rel_title": "Psychological impact of infectious disease outbreaks on pregnant women: Rapid evidence review",
@@ -1524073,213 +1522906,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.04.20.20072116",
-    "rel_title": "Characterization and Clinical Course of 1000 Patients with COVID-19 in New York: retrospective case series",
-    "rel_date": "2020-04-22",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20072116",
-    "rel_abs": "ObjectiveTo characterize patients with coronavirus disease 2019 (COVID-19) in a large New York City (NYC) medical center and describe their clinical course across the emergency department (ED), inpatient wards, and intensive care units (ICUs).\n\nDesignRetrospective manual medical record review.\n\nSettingNewYork-Presbyterian/Columbia University Irving Medical Center (NYP/CUIMC), a quaternary care academic medical center in NYC.\n\nParticipantsThe first 1000 consecutive patients with laboratory-confirmed COVID-19.\n\nMethodsWe identified the first 1000 consecutive patients with a positive RT-SARS-CoV-2 PCR test who first presented to the ED or were hospitalized at NYP/CUIMC between March 1 and April 5, 2020. Patient data was manually abstracted from the electronic medical record.\n\nMain outcome measuresWe describe patient characteristics including demographics, presenting symptoms, comorbidities on presentation, hospital course, time to intubation, complications, mortality, and disposition.\n\nResultsAmong the first 1000 patients, 150 were ED patients, 614 were admitted without requiring ICU-level care, and 236 were admitted or transferred to the ICU. The most common presenting symptoms were cough (73.2%), fever (72.8%), and dyspnea (63.1%). Hospitalized patients, and ICU patients in particular, most commonly had baseline comorbidities including of hypertension, diabetes, and obesity. ICU patients were older, predominantly male (66.9%), and long lengths of stay (median 23 days; IQR 12 to 32 days); 78.0% developed AKI and 35.2% required dialysis. Notably, for patients who required mechanical ventilation, only 4.4% were first intubated more than 14 days after symptom onset. Time to intubation from symptom onset had a bimodal distribution, with modes at 3-4 and 9 days. As of April 30, 90 patients remained hospitalized and 211 had died in the hospital.\n\nConclusionsHospitalized patients with COVID-19 illness at this medical center faced significant morbidity and mortality, with high rates of AKI, dialysis, and a bimodal distribution in time to intubation from symptom onset.",
-    "rel_num_authors": 48,
-    "rel_authors": [
-      {
-        "author_name": "Michael G Argenziano",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Samuel L Bruce",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Cody L Slater",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Jonathan R Tiao",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Matthew R Baldwin",
-        "author_inst": "NewYork-Presbyterian/Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "R Graham Barr",
-        "author_inst": "NewYork-Presbyterian/Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Bernard P Chang",
-        "author_inst": "NewYork-Presbyterian/Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Katherine H Chau",
-        "author_inst": "NewYork-Presbyterian/Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Justin J Choi",
-        "author_inst": "Weill Cornell Medicine"
-      },
-      {
-        "author_name": "Nicholas Gavin",
-        "author_inst": "NewYork-Presbyterian/Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Parag Goyal",
-        "author_inst": "Weill Cornell Medicine"
-      },
-      {
-        "author_name": "Angela M Mills",
-        "author_inst": "NewYork-Presbyterian/Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Ashmi A Patel",
-        "author_inst": "NewYork-Presbyterian/Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Marie-Laure S Romney",
-        "author_inst": "NewYork-Presbyterian/Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Monika M Safford",
-        "author_inst": "Weill Cornell Medicine"
-      },
-      {
-        "author_name": "Neil W Schluger",
-        "author_inst": "NewYork-Presbyterian/Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Soumitra Sengupta",
-        "author_inst": "Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Magdalena E Sobieszczyk",
-        "author_inst": "NewYork-Presbyterian/Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Jason E Zucker",
-        "author_inst": "NewYork-Presbyterian/Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Paul A Asadourian",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Fletcher M Bell",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Rebekah Boyd",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Matthew F Cohen",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "MacAlistair I Colquhoun",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Lucy A Colville",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Joseph H de Jonge",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Lyle B Dershowitz",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Shirin A Dey",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Katherine A Eiseman",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Zachary P Girvin",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Daniella T Goni",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Amro A Harb",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Nicholas Herzik",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Sarah Householder",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Lara E Karaaslan",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Heather Lee",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Evan Lieberman",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Andrew Ling",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Ree Lu",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Arthur Y Shou",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Alexander C Sisti",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Zachary E Snow",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Colin P Sperring",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Yuqing Xiong",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Henry W Zhou",
-        "author_inst": "Columbia University Vagelos College of Physicians and Surgeons"
-      },
-      {
-        "author_name": "Karthik Natarajan",
-        "author_inst": "Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "George Hripcsak",
-        "author_inst": "Columbia University Irving Medical Center"
-      },
-      {
-        "author_name": "Ruijun Chen",
-        "author_inst": "Columbia University Irving Medical Center"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "intensive care and critical care medicine"
-  },
   {
     "rel_doi": "10.1101/2020.04.19.20071639",
     "rel_title": "How best to use limited tests? Improving COVID-19 surveillance in long-term care",
@@ -1524506,6 +1523132,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.19.20071951",
+    "rel_title": "Seasonality and uncertainty in COVID-19 growth rates",
+    "rel_date": "2020-04-22",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20071951",
+    "rel_abs": "The virus causing COVID-19 has spread rapidly worldwide and threatens millions of lives. It remains unknown if summer weather will reduce its continued spread, thereby alleviating strains on hospitals and providing time for vaccine development. Early insights from laboratory studies of related coronaviruses predicted that COVID-19 would decline at higher temperatures, humidity, and ultraviolet light. Using current, fine-scaled weather data and global reports of infection we developed a model that explained 36% of variation in early growth rates before intervention, with 17% based on weather or demography and 19% based on country-specific effects. We found that ultraviolet light was most strongly associated with lower COVID-19 growth rates. Projections suggest that, in the absence of intervention, COVID-19 will decrease temporarily during summer, rebound by autumn, and peak next winter. However, uncertainty remains high and the probability of a weekly doubling rate remained >20% throughout the summer in the absence of control. Consequently, aggressive policy interventions will likely be needed in spite of seasonal trends.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Cory Merow",
+        "author_inst": "University of Connecticut"
+      },
+      {
+        "author_name": "Mark C Urban",
+        "author_inst": "University of Connecticut"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.04.17.20057125",
     "rel_title": "COVID-19 Critical Illness Pathophysiology Driven by Diffuse Pulmonary Thrombi and Pulmonary Endothelial Dysfunction Responsive to Thrombolysis",
@@ -1525679,61 +1524328,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.04.16.20062141",
-    "rel_title": "Estimating the impact of non-pharmaceutical interventions on documented infections with COVID-19: A cross-country analysis",
-    "rel_date": "2020-04-21",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20062141",
-    "rel_abs": "BackgroundThe novel coronavirus (SARS-CoV-2) has rapidly evolved into a global epidemic. To control its spread, countries have implemented non-pharmaceutical interventions (NPIs), such as school or border closures, while others have even enforced complete lockdowns. Here we study the impact of NPIs in reducing documented cases of COVID-19. Documented case numbers are selected because they are essential for decision-makers in the area of health-policy when monitoring and evaluating current control mechanisms.\n\nMethodsWe empirically estimate the relative reduction in the number of new cases attributed to each NPI. A cross-country analysis is performed using documented cases through April 15, 2020 from n = 20 countries (i.e., the United States, Canada, Australia, the EU-15 countries, Norway, and Switzerland).\n\nResultsAs of April 15, venue closures were associated with a reduction in the number of new cases by 36 % (95% credible interval [CrI] 20-48 %), closely followed by gathering bans (34 %; 95% CrI 21-45 %), border closures (31 %; 95% CrI 19-42 %), and work bans on non-essential business activities (31 %; 95% CrI 16-44 %). Event bans lead to a slightly less pronounced reduction (23 %; 95% CrI 8-35 %). School closures (8 %; 95% CrI 0-23 %) and lockdowns (5 %; 95% CrI 0-14 %) appeared to be the least effective among the NPIs considered in this analysis.\n\nConclusionsWith this cross-country analysis, we provide early estimates regarding the impact of different NPIs for controlling the COVID-19 epidemic. These findings are relevant for evaluating current health-policies.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Nicolas Banholzer",
-        "author_inst": "ETH Zurich"
-      },
-      {
-        "author_name": "Eva van Weenen",
-        "author_inst": "ETH Zurich"
-      },
-      {
-        "author_name": "Bernhard Kratzwald",
-        "author_inst": "ETH Zurich"
-      },
-      {
-        "author_name": "Arne Seeliger",
-        "author_inst": "ETH Zurich"
-      },
-      {
-        "author_name": "Daniel Tschernutter",
-        "author_inst": "ETH Zurich"
-      },
-      {
-        "author_name": "Pierluigi Bottrighi",
-        "author_inst": "ETH Zurich"
-      },
-      {
-        "author_name": "Alberto Cenedese",
-        "author_inst": "ETH Zurich"
-      },
-      {
-        "author_name": "Joan Puig Salles",
-        "author_inst": "ETH Zurich"
-      },
-      {
-        "author_name": "Werner Vach",
-        "author_inst": "Basel Academy, University of Basel"
-      },
-      {
-        "author_name": "Stefan Feuerriegel",
-        "author_inst": "ETH Zurich"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.04.16.20064709",
     "rel_title": "Multi-task Deep Learning Based CT Imaging Analysis For COVID-19: Classification and Segmentation",
@@ -1526024,6 +1524618,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.04.16.20067553",
+    "rel_title": "Early forecasts of the evolution of the COVID-19 outbreaks and quantitative assessment of the effectiveness of countering measures.",
+    "rel_date": "2020-04-21",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20067553",
+    "rel_abs": "We discovered that the time evolution of the inverse fractional daily growth of new infections, N/{Delta} N, in the current outbreak of COVID-19 is accurately described by a universal function, namely the two-parameter Gumbel cumulative function, in all countries that we have investigated. While the two Gumbel parameters, as determined bit fits to the data, vary from country to country (and even within different regions of the same country), reflecting the diversity and efficacy of the adopted containment measures, the functional form of the evolution of {Delta} N/N appears to be universal. The result of the fit in a given region or country appears to be stable against variations of the selected time interval. This makes it possible to robustly estimate the two parameters from the data data even over relatively small time periods. In turn, this allows one to predict with large advance and well-controlled confidence levels, the time of the peak in the daily new infections, its magnitude and duration (hence the total infections), as well as the time when the daily new infections decrease to a pre-set value (e.g. less than about 2 new infections per day per million people), which can be very useful for planning the reopening of economic and social activities. We use this formalism to predict and compare these key features of the evolution of the COVID-19 disease in a number of countries and provide a quantitative assessment of the degree of success in in their efforts to countain the outbreak.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Emanuele Daddi",
+        "author_inst": "CEA Saclay"
+      },
+      {
+        "author_name": "Mauro Giavalisco",
+        "author_inst": "University of Massachusetts Amherst"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.04.16.20067504",
     "rel_title": "The effect of inter-city travel restrictions on geographical spread of COVID-19: Evidence from Wuhan, China",
@@ -1527737,45 +1526354,6 @@
     "type": "new results",
     "category": "systems biology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.15.20064485",
-    "rel_title": "Trends and prediction in daily incidence and deaths of COVID-19 in the United States: a search-interest based model",
-    "rel_date": "2020-04-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20064485",
-    "rel_abs": "Background and ObjectivesThe coronavirus disease 2019 (COVID-19) infected more than 586,000 patients in the U.S. However, its daily incidence and deaths in the U.S. are poorly understood. Internet search interest was found correlated with COVID-19 daily incidence in China, but not yet applied to the U.S. Therefore, we examined the association of internet search-interest with COVID-19 daily incidence and deaths in the U.S.\n\nMethodsWe extracted the COVDI-19 daily incidence and death data in the U.S. from two population-based datasets. The search interest of COVID-19 related terms was obtained using Google Trends. Pearson correlation test and general linear model were used to examine correlations and predict future trends, respectively.\n\nResultsThere were 555,245 new cases and 22,019 deaths of COVID-19 reported in the U.S. from March 1 to April 12, 2020. The search interest of COVID, \"COVID pneumonia,\" and \"COVID heart\" were correlated with COVDI-19 daily incidence with [~]12-day of delay (Pearsons r=0.978, 0.978 and 0.979, respectively) and deaths with 19-day of delay (Pearsons r=0.963, 0.958 and 0.970, respectively). The COVID-19 daily incidence and deaths appeared to both peak on April 10. The 4-day follow-up with prospectively collected data showed moderate to good accuracies for predicting new cases (Pearsons r=-0.641 to -0.833) and poor to good accuracies for daily new deaths (Pearsons r=0.365 to 0.935).\n\nConclusionsSearch terms related to COVID-19 are highly correlated with the trends in COVID-19 daily incidence and deaths in the U.S. The prediction-models based on the search interest trend reached moderate to good accuracies.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Xiaoling Yuan",
-        "author_inst": "Department of Infectious Disease, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, Chin"
-      },
-      {
-        "author_name": "Jie Xu",
-        "author_inst": "Department of Infectious Disease, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China"
-      },
-      {
-        "author_name": "Sabiha Hussain",
-        "author_inst": "Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA"
-      },
-      {
-        "author_name": "He Wang",
-        "author_inst": "Department of Pathology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA"
-      },
-      {
-        "author_name": "Nan Gao",
-        "author_inst": "Department of Biological Sciences, Rutgers University Newark, NJ, USA"
-      },
-      {
-        "author_name": "Lanjing Zhang",
-        "author_inst": "Princeton Medical Center/Rutgers University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.04.14.20064618",
     "rel_title": "Efficient high throughput SARS-CoV-2 testing to detect asymptomatic carriers",
@@ -1528098,6 +1526676,305 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.04.15.20066407",
+    "rel_title": "Evaluation of antibody testing for SARS-Cov-2 using ELISA and lateral flow immunoassays",
+    "rel_date": "2020-04-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20066407",
+    "rel_abs": "BackgroundThe COVID-19 pandemic caused >1 million infections during January-March 2020. There is an urgent need for reliable antibody detection approaches to support diagnosis, vaccine development, safe release of individuals from quarantine, and population lock-down exit strategies. We set out to evaluate the performance of ELISA and lateral flow immunoassay (LFIA) devices.\n\nMethodsWe tested plasma for COVID (SARS-CoV-2) IgM and IgG antibodies by ELISA and using nine different LFIA devices. We used a panel of plasma samples from individuals who have had confirmed COVID infection based on a PCR result (n=40), and pre-pandemic negative control samples banked in the UK prior to December-2019 (n=142).\n\nResultsELISA detected IgM or IgG in 34/40 individuals with a confirmed history of COVID infection (sensitivity 85%, 95%CI 70-94%), vs. 0/50 pre-pandemic controls (specificity 100% [95%CI 93-100%]). IgG levels were detected in 31/31 COVID-positive individuals tested [&ge;]10 days after symptom onset (sensitivity 100%, 95%CI 89-100%). IgG titres rose during the 3 weeks post symptom onset and began to fall by 8 weeks, but remained above the detection threshold. Point estimates for the sensitivity of LFIA devices ranged from 55-70% versus RT-PCR and 65-85% versus ELISA, with specificity 95-100% and 93-100% respectively. Within the limits of the study size, the performance of most LFIA devices was similar.\n\nConclusionsCurrently available commercial LFIA devices do not perform sufficiently well for individual patient applications. However, ELISA can be calibrated to be specific for detecting and quantifying SARS-CoV-2 IgM and IgG and is highly sensitive for IgG from 10 days following first symptoms.",
+    "rel_num_authors": 71,
+    "rel_authors": [
+      {
+        "author_name": "Emily R Adams",
+        "author_inst": "Liverpool School of Tropical Medicine"
+      },
+      {
+        "author_name": "Mark Ainsworth",
+        "author_inst": "Oxford University Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "Rekha Anand",
+        "author_inst": "NHSBT Birmingham,"
+      },
+      {
+        "author_name": "Monique I Andersson",
+        "author_inst": "Department of Microbiology, Oxford University Hospital NHS Foundation Trust"
+      },
+      {
+        "author_name": "Kathryn Auckland",
+        "author_inst": "The Wellcome Centre for Human Genetics, University of Oxford"
+      },
+      {
+        "author_name": "J Kenneth Baillie",
+        "author_inst": "Roslin Institute, University of Edinburgh"
+      },
+      {
+        "author_name": "Eleanor Barnes",
+        "author_inst": "Nuffield Department of Medicine, University of Oxford"
+      },
+      {
+        "author_name": "Sally Beer",
+        "author_inst": "Oxford University Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "John Bell",
+        "author_inst": "Department of Medicine, University of Oxford"
+      },
+      {
+        "author_name": "Tamsin Berry",
+        "author_inst": "Department of Health and Social Care, University of Oxford"
+      },
+      {
+        "author_name": "Sagida Bibi",
+        "author_inst": "Oxford Vaccine group, Department of Pediatrics, University of Oxford"
+      },
+      {
+        "author_name": "Miles Carroll",
+        "author_inst": "Nuffield Department of Medicine, Centre of Tropical Medicine and Global Health and Public Health England"
+      },
+      {
+        "author_name": "Senthil Chinnakannan",
+        "author_inst": "Nuffield Department of Medicine, University of Oxford"
+      },
+      {
+        "author_name": "Elizabeth Clutterbuck",
+        "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford"
+      },
+      {
+        "author_name": "Richard J Cornall",
+        "author_inst": "Nuffield Department of Medicine, University of Oxford"
+      },
+      {
+        "author_name": "Derrick W Crook",
+        "author_inst": "NIHR Oxford Biomedical Research Centre"
+      },
+      {
+        "author_name": "Thushan De Silva",
+        "author_inst": "Department of Infection, Immunity and Cardiovascular, Disease, The Medical School, University of Sheffield"
+      },
+      {
+        "author_name": "Wanwisa Dejnirattisai",
+        "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford"
+      },
+      {
+        "author_name": "Kate E Dingle",
+        "author_inst": "NIHR Oxford Biomedical Research Centre, University of Oxford"
+      },
+      {
+        "author_name": "Christina Dold",
+        "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford"
+      },
+      {
+        "author_name": "Alexis Espinosa",
+        "author_inst": "Oxford University Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "David W Eyre",
+        "author_inst": "Big Data Institute, University of Oxford"
+      },
+      {
+        "author_name": "Helen Farmer",
+        "author_inst": "Department of Health and Social Care, University of Oxford"
+      },
+      {
+        "author_name": "Maria Fernandez Mendoza",
+        "author_inst": "Oxford University Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "Dominique Georgiou",
+        "author_inst": "Oxford University Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "Sarah J Hoosdally",
+        "author_inst": "Nuffield Department of Medicine, University of Oxford"
+      },
+      {
+        "author_name": "Alistair Hunter",
+        "author_inst": "NHSBT Basildon"
+      },
+      {
+        "author_name": "Katie Jeffrey",
+        "author_inst": "Department of Clinical Medicine, Oxford University Hospitals NHS Foundation Trusts"
+      },
+      {
+        "author_name": "Paul Klenerman",
+        "author_inst": "Nuffield Department so Medicine, University of Oxford"
+      },
+      {
+        "author_name": "Julian Knight",
+        "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford"
+      },
+      {
+        "author_name": "Clarice Knowles",
+        "author_inst": "Department of Health and Social Care, University of Oxford"
+      },
+      {
+        "author_name": "Andrew J Kwok",
+        "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford"
+      },
+      {
+        "author_name": "Ullrich Leuschner",
+        "author_inst": "NHSBT Oxford"
+      },
+      {
+        "author_name": "Robert Levin",
+        "author_inst": "Worthing Hospital, Worthing, West Sussex"
+      },
+      {
+        "author_name": "Chang Liu",
+        "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford"
+      },
+      {
+        "author_name": "Cesar Lopez-Camacho",
+        "author_inst": "Wellcome Centre of Genetics, Nuffield Department of Medicine, University of Oxford"
+      },
+      {
+        "author_name": "Jose Carlos Martinez Garrido",
+        "author_inst": "Oxford University Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "Philippa C Matthews",
+        "author_inst": "Nuffield Department of Medicine, University of Medicine"
+      },
+      {
+        "author_name": "Hannah McGivern",
+        "author_inst": "Nuffield Department of Surgical Sciences, University of Oxford and UK QUOD Consortium"
+      },
+      {
+        "author_name": "Alexander J Mentzer",
+        "author_inst": "Wellcome Centre for Human Genetics, University of Oxford"
+      },
+      {
+        "author_name": "Jonathan Milton",
+        "author_inst": "Nuffield Department of Surgical Sciences, University of Oxford and UK QUOD Consortium"
+      },
+      {
+        "author_name": "Juthathip Mongkolsapaya",
+        "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford"
+      },
+      {
+        "author_name": "Shona C Moore",
+        "author_inst": "NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, University of Liverpool"
+      },
+      {
+        "author_name": "Marta S Oliveira",
+        "author_inst": "Nuffield Department of Surgical Sciences,  University of Oxford and UK QUOD Consortium"
+      },
+      {
+        "author_name": "Fiona Pereira",
+        "author_inst": "Imperial College London"
+      },
+      {
+        "author_name": "Elena Perez Lopez",
+        "author_inst": "Oxford University Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "Timothy Peto",
+        "author_inst": "NIHR Oxford Biomedical Research centre, University of Oxford"
+      },
+      {
+        "author_name": "Rutger J Ploeg",
+        "author_inst": "Nuffield Department of Surgical Sciences, University of Oxford and UK QUOD Consortium"
+      },
+      {
+        "author_name": "Andrew Pollard",
+        "author_inst": "Department of Paediatrics, University of Oxford"
+      },
+      {
+        "author_name": "Tessa Prince",
+        "author_inst": "NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, University of Liverpool"
+      },
+      {
+        "author_name": "David J Roberts",
+        "author_inst": "NHSBT Oxford"
+      },
+      {
+        "author_name": "Justine K Rudkin",
+        "author_inst": "Nuffield Department of Population Health & Big Data Institute, University of Oxford"
+      },
+      {
+        "author_name": "Veronica Sanchez",
+        "author_inst": "Oxford University Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "Gavin R Screaton",
+        "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford"
+      },
+      {
+        "author_name": "Malcolm G Semple",
+        "author_inst": "Health Protection Unit In Emerging and Zoonotic Infection, University of Liverpool"
+      },
+      {
+        "author_name": "Donal T Skelly",
+        "author_inst": "Nuffield Department of Clinical Neurosciences, University of Oxford"
+      },
+      {
+        "author_name": "Jose Slon-Campos",
+        "author_inst": "University of Oxford"
+      },
+      {
+        "author_name": "Elliot Nathan Smith",
+        "author_inst": "Department of Health and Social Care, University of Oxford"
+      },
+      {
+        "author_name": "Alberto Jose Sobrino Diaz",
+        "author_inst": "Oxford University Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "Julie Staves",
+        "author_inst": "Oxford University Hospitals,"
+      },
+      {
+        "author_name": "David Stuart",
+        "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine"
+      },
+      {
+        "author_name": "Piyada Supasa",
+        "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford"
+      },
+      {
+        "author_name": "Tomas Surik",
+        "author_inst": "Nuffield Department of Surgical Sciences, University of Oxford and UK QUOD Consortium"
+      },
+      {
+        "author_name": "Hannah Thraves",
+        "author_inst": "Oxford University Hospitals NHS Foundation Trust"
+      },
+      {
+        "author_name": "Pat Tsang",
+        "author_inst": "NHSBT Oxford"
+      },
+      {
+        "author_name": "Lance Turtle",
+        "author_inst": "NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, University of Liverpool"
+      },
+      {
+        "author_name": "A Sarah Walker",
+        "author_inst": "Nuffield Department of Medicine, University of Oxford"
+      },
+      {
+        "author_name": "Beibei Wang",
+        "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford"
+      },
+      {
+        "author_name": "Charlotte Washington",
+        "author_inst": "NHSBT, Birmingham"
+      },
+      {
+        "author_name": "Nicholas Watkins",
+        "author_inst": "NHSBT, Cambridge"
+      },
+      {
+        "author_name": "James Whitehouse",
+        "author_inst": "Department of Health and Social Care, University of Oxford"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.04.15.20067074",
     "rel_title": "Total COVID-19 Mortality in Italy: Excess Mortality and Age Dependence through Time-Series Analysis",
@@ -1529187,25 +1528064,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.16.20067652",
-    "rel_title": "Prevent the resurgence of infectious disease with asymptomatic carriers",
-    "rel_date": "2020-04-19",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20067652",
-    "rel_abs": "After reaching the peak of the COVID-19 outbreak, many regions are in search of a reopening plan that would minimize resurgence. Here we show to prevent resurgence local governments need to estimate how early and how many COVID-19 cases can be detected. It is safe to end social distancing if the majority of cases are detected early in the infection window. If cases are detected later, a 2-layer quarantine may be necessary to prevent resurgence. If fewer cases are detected, community events, schools, and large businesses may need to remain in virtual mode. Our results demonstrate that detecting more cases earlier is essential for preventing COVID-19 resurgence.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Zhechun Zhang",
-        "author_inst": "Harvard University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.04.14.20064741",
     "rel_title": "Health Education for Parents During the COVID-19 OutbreakPublic Health Education for Parents During the Outbreak of COVID-19: A Rapid Review",
@@ -1529604,6 +1528462,33 @@
     "type": "new results",
     "category": "biochemistry"
   },
+  {
+    "rel_doi": "10.1101/2020.04.13.20064295",
+    "rel_title": "Benefits and Risks of Chloroquine and Hydroxychloroquine in The Treatment of Viral Diseases: A Meta-Analysis of Placebo Randomized Controlled Trials",
+    "rel_date": "2020-04-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20064295",
+    "rel_abs": "Background and ObjectiveRecently, in the scramble to find drugs to treat COVID-19, chloroquine (CQ) and its derivative hydroxychloroquine (HCQ) have rapidly gained the publics attention. In this study, we conducted a meta-analysis of randomized clinical trials (RCTs) to evaluate the efficacy and safety of CQ and HCQ in the treatment of viral diseases.\n\nMethodsWe searched PubMed, EMBASE, Cochrane Central, Web of Science, Clinical Trials Registries, CNKI, Wanfang Data, CQVIP, and Preprint Servers through April 4, 2020, for randomized controlled trials (RCTs) that examined the efficacy and safety of CQ and HCQ against viral infection. We analyzed pooled data on the overall efficacy, the relative risks over the placebo, and the prevalence of adverse events. Trial sequential analysis (TSA) was also performed to evaluate the random errors in the meta-analysis. Potential moderators of drug-placebo efficacy differences were analyzed by meta-regression.\n\nResultsThe analysis included 11 RCTs with 2613 adult patients. Both the plasma viral load (standard mean difference: 0.29, 95% CI: -1.19 - 1.76, P = 0.70) and the improvement of clinical symptoms (odds ratio: 2.36, 95% CI: 0.81 - 6.92, P = 0.11) were not different between the intervention and placebo arm. There was significant heterogeneity for the efficacy assessment, which was primarily explained by the mean patients age and the sample size. Compared to the placebo, CQ and HCQ had increased risk of mild adverse events (risk ratio: 1.51, 95% CI: 1.35 - 1.70, P < 0.05, TSA adjusted 95% CI: 1.31 - 2.19), which were statistically significant in nervous, integumentary, and gastrointestinal systems. The most common adverse events were observed in the nervous system, with the pooled prevalence of 31.4 % (95% CI: 10.5% - 56.7%).\n\nConclusionsInsufficient data were available to support the antiviral efficacy of CQ and HCQ due to the high heterogeneity caused by patients age. Mild side effects are expected for the current antiviral dose regimens of CQ and HCQ. Treatment outcomes may be enhanced by better-selected patients based on age and well-controlled adverse events.\n\nThis meta-analysis was registered on OSF (ID: https://osf.io/386aw)",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Jing Wang",
+        "author_inst": "Yantai Yuhuangding Hospital, China"
+      },
+      {
+        "author_name": "Li Yu",
+        "author_inst": "Shengjing Hospital of China Medical University"
+      },
+      {
+        "author_name": "Kefeng Li",
+        "author_inst": "University of California, San Diego"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "pharmacology and therapeutics"
+  },
   {
     "rel_doi": "10.1101/2020.04.15.037564",
     "rel_title": "Supramolecular Organization Predicts Protein Nanoparticle Delivery to Neutrophils for Acute Lung Inflammation Diagnosis and Treatment",
@@ -1531117,37 +1530002,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.04.15.20065102",
-    "rel_title": "A Validation Study for the Successful Isolation Policy in China: a Meta-Analysis in COVID-19",
-    "rel_date": "2020-04-18",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20065102",
-    "rel_abs": "COVID-19 is quickly spreading around the world and carries along with it a significant threat to public health. This study sought to apply meta-analysis to more precisely and accurately estimate the basic reproduction number (R0) of COVID-19 in order to evaluate the effectiveness of the isolation policy across countries, and the corresponding public health capability to care for patients. Prior estimates of R0 have varied widely and range from 1.95 to 6.49. Utilizing meta-analysis techniques we determined a more robust estimation of 3.05 for R0, which is substantially larger than that provided by the WHO. We also present the infectious rate standardized to per million population, which has proved to be a good index to determine whether the isolation measures in specific countries are effective. Also, this standardized infection rate can be used to determine whether the current infectious severity status is out of range of the national health capacity. Finally, we utilize our robust estimate of R0 and the standardized infectious rate to illustrate that the early and aggressive isolation measures enforced by the Chinese government were substantially more effective in controlling the negative impact COVID-19 than the more permissive measures enacted early in Italy and the United States.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Jianghu Dong",
-        "author_inst": "College of Public Health"
-      },
-      {
-        "author_name": "Yongdao Zhou",
-        "author_inst": "Nankai University"
-      },
-      {
-        "author_name": "Ying Zhang",
-        "author_inst": "University of Nebraska Medical Center"
-      },
-      {
-        "author_name": "Douglas Franz",
-        "author_inst": "University of Nebraska Medical Center"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "respiratory medicine"
-  },
   {
     "rel_doi": "10.1101/2020.04.15.20066472",
     "rel_title": "Objective olfactory testing in patients presenting with sudden onset olfactory dysfunction as the first manifestation of confirmed COVID-19 infection",
@@ -1531394,6 +1530248,73 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.04.15.20065995",
+    "rel_title": "SARS-Cov-2 RNA Found on Particulate Matter of Bergamo in Northern Italy: First Preliminary Evidence",
+    "rel_date": "2020-04-18",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20065995",
+    "rel_abs": "In previous communications, we have hypothesized the possibility that SARS-CoV-2 virus could be present on particulate matter (PM) during the spreading of the infection, consistently with evidence already available for other viruses. Here, we present the first results of the analyses that we have performed on 34 PM10 samples of outdoor/airborne PM10 from an industrial site of Bergamo Province, collected with two different air samplers over a continuous 3-weeks period, from February 21st to March 13th. We can confirm to have reasonably demonstrated the presence of SARS-CoV-2 viral RNA by detecting highly specific RtDR gene on 8 filters in two parallel PCR analyses. This is the first preliminary evidence that SARS-CoV-2 RNA can be present on outdoor particulate matter, thus suggesting that, in conditions of atmospheric stability and high concentrations of PM, SARS-CoV-2 could create clusters with outdoor PM and, by reducing their diffusion coefficient, enhance the persistence of the virus in the atmosphere. Further confirmations of this preliminary evidence are ongoing, and should include real-time assessment about the vitality of the SARS-CoV-2 as well as its virulence when adsorbed on particulate matter. At the present, no assumptions can be made concerning the correlation between the presence of the virus on PM and COVID-19 outbreak progression. Other issues to be specifically addressed are the average concentrations of PM eventually required for a potential boost effect of the contagion (in case it is confirmed that PM might act as a carrier for the viral droplet nuclei), or even the theoretic possibility of immunization consequent to minimal dose exposures at lower thresholds of PM.",
+    "rel_num_authors": 13,
+    "rel_authors": [
+      {
+        "author_name": "Leonardo Setti",
+        "author_inst": "University of Bologna"
+      },
+      {
+        "author_name": "Fabrizio Passarini",
+        "author_inst": "University of Bologna"
+      },
+      {
+        "author_name": "Gianluigi De Gennaro",
+        "author_inst": "University of Bari, Italy"
+      },
+      {
+        "author_name": "Pierluigi Baribieri",
+        "author_inst": "University of Trieste"
+      },
+      {
+        "author_name": "Maria Grazia Perrone",
+        "author_inst": "Environmental Research Division, TCR TECORA, Milan, Italy"
+      },
+      {
+        "author_name": "Massimo Borelli",
+        "author_inst": "University of Trieste, Italy"
+      },
+      {
+        "author_name": "Jolanda Palmisani",
+        "author_inst": "University of Bari"
+      },
+      {
+        "author_name": "Alessia Di Gilio",
+        "author_inst": "University of Bari"
+      },
+      {
+        "author_name": "Valentina Torboli",
+        "author_inst": "University of Trieste"
+      },
+      {
+        "author_name": "Alberto Pallavicini",
+        "author_inst": "University of Trieste"
+      },
+      {
+        "author_name": "Maurizio Ruscio",
+        "author_inst": "Division of Laboratory Medicine, University Hospital Giuliano Isontina (ASU GI), Trieste, Italy"
+      },
+      {
+        "author_name": "PRISCO PISCITELLI",
+        "author_inst": "ISBEM"
+      },
+      {
+        "author_name": "Alessandro Miani",
+        "author_inst": "Italian Society of Environmental Medicine, SIMA, Milan, Italy"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.04.15.20066308",
     "rel_title": "Analysis of the mitigation strategies for COVID-19: from mathematical modelling perspective",
@@ -1532643,45 +1531564,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.16.20067405",
-    "rel_title": "Links between air pollution and COVID-19 in England",
-    "rel_date": "2020-04-17",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20067405",
-    "rel_abs": "In December 2019 a novel disease coronavirus disease 19 (COVID-19) emerged in the Wuhan province of the Peoples Republic of China. COVID-19 is caused by a novel coronavirus (SARS-CoV-2) thought to have jumped species, from another mammal to humans. A pandemic caused by this virus is running rampant throughout the world. Thousands of cases of COVID-19 are reported in England and over 10,000 patients have died. Whilst there has been progress in managing this disease, it is not clear which factors, besides age, affect the severity and mortality of COVID-19. A recent analysis of COVID-19 in Italy identified links between air pollution and death rates. Here, we explored the correlation between three major air pollutants linked to fossil fuels and SARS-CoV-2 lethality in England. We compare up-to-date, real-time SARS-CoV-2 cases and death measurements from public databases to air pollution data monitored across over 120 sites in different regions. We found that the levels of some markers of poor air quality, nitrogen oxides and ozone, are associated with COVID-19 lethality in different English regions. We conclude that the levels of some air pollutants are linked to COVID-19 cases and morbidity. We suggest that our study provides a useful framework to guide health policy in countries affected by this pandemic.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Marco Travaglio",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Yizhou Yu",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Rebeka Popovic",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Liza Selley",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Nuno Santos Leal",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "L. Miguel Martins",
-        "author_inst": "University of Cambridge"
-      }
-    ],
-    "version": "1",
-    "license": "",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "toxicology"
-  },
   {
     "rel_doi": "10.1101/2020.04.17.046193",
     "rel_title": "Shotgun proteomics of SARS-CoV-2 infected cells and its application to the optimisation of whole viral particle antigen production for vaccines",
@@ -1532972,6 +1531854,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.14.20065375",
+    "rel_title": "Informing Homemade Emergency Facemask Design: The Ability of Common Fabrics to Filter Ultrafine Particles",
+    "rel_date": "2020-04-17",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20065375",
+    "rel_abs": "ObjectivesWe examined the ability of fabrics which might be used to create homemade face masks to filter out ultrafine (0.1m and smaller in diameter) particles at the velocity of adult human coughing.\n\nMethodTwenty commonly available fabrics and materials were evaluated for their ability to reduce air concentrations of ultrafine particles at a face velocity of 16.5 m/s. Further assessment was made on the filtration ability of select fabrics while damp and of fabric combinations which might be used to construct homemade masks.\n\nResultsSingle fabric layers blocked a range of ultrafine particles. When fabrics were layered, significantly more ultrafine particles were filtered. Nonwoven fusible interfacing significantly increased filtration.\n\nConclusionsThe current coronavirus pandemic has left many communities without access N95 facemasks. Our findings suggest that face masks made from layered common fabric can help filter ultrafine particles and provide some protection for the wearer when commercial facemasks are unavailable.\n\nSTRENGHTS AND LIMITATIONS OF THIS STUDYO_LITested a large number of potential facemask materials, including materials currently in common use such as Lycra which have not been previously tested\nC_LIO_LIEvaluated filtration efficiency at coughing velocities, more closely mimicking use-case of masks worn for community protection than previous studies\nC_LIO_LIAssess the data from prior published work and current study, creating a picture of Filtration Efficiency and the impact of velocity\nC_LIO_LIDid not discriminate between pathogenic and non-pathogenic particles\nC_LIO_LIBreathing resistance was estimated based on qualitative feedback\nC_LI",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Eugenia O'Kelly",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "Sophia Pirog",
+        "author_inst": "Northwestern University"
+      },
+      {
+        "author_name": "James Ward",
+        "author_inst": "Cambridge University"
+      },
+      {
+        "author_name": "P John Clarkson",
+        "author_inst": "Cambridge University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.04.14.20065607",
     "rel_title": "Applying the SEIR Model in Forecasting The COVID-19 Trend in Malaysia: A Preliminary Study",
@@ -1534137,33 +1533050,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.14.20064824",
-    "rel_title": "Estimating the last day for COVID-19 outbreak in mainland China",
-    "rel_date": "2020-04-17",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20064824",
-    "rel_abs": "Our main aim is to estimate the end of the first wave epidemic of COVID-19 outbreak in mainland China. We developed mathematical models to predict reasonable bounds on the date of end of the COVID-19 epidemics in mainland China with strong quarantine and testing measures for a sufficiently long time. We used reported data in China from January 20, 2020 to April 9, 2020. We firstly used a deterministic approach to obtain a formula to compute the probability distribution of the extinction date by combining the models and continuous-time Markov processes. Then we present the individual based model (IMB) simulations to compare the result by deterministic approach and show the absolute difference between the estimated cumulative probability distribution computed by simulations and formula. We provide the predictions of the end of the first wave epidemic for different fractions f of asymptomatic infectious that become reported symptomatic infectious.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Quentin Griette",
-        "author_inst": "University of Bordeaux"
-      },
-      {
-        "author_name": "Zhihua Liu",
-        "author_inst": "Beijing Normal University"
-      },
-      {
-        "author_name": "pierre magal",
-        "author_inst": "University of Bordeaux"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.04.14.20064949",
     "rel_title": "Novel Coronavirus in Nigeria: Epidemiological analysis of the first 45 days of the pandemic",
@@ -1534314,6 +1533200,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.14.20065318",
+    "rel_title": "State-level variation of initial COVID-19 dynamics in the United States: The role of local government interventions",
+    "rel_date": "2020-04-17",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20065318",
+    "rel_abs": "During an epidemic, metrics such as R0, doubling time, and case fatality rates are important in understanding and predicting the course of an epidemic. However, if collected over country or regional scales, these metrics hide important smaller-scale, local dynamics. We examine how commonly used epidemiological metrics differ for each individual state within the United States during the initial COVID-19 outbreak. We found that the case number, and trajectory of cases, differs considerably between states. We show that early non-pharmaceutical, government actions, were the most important determinant of epidemic dynamics. In particular, restricting restaurant operations was correlated with increased doubling times. Although individual states are clearly not independent, they can serve as small, natural experiments in how different demographic patterns and government responses can impact the course of an epidemic.\n\nDaily updates to figures in this manuscript are available at: https://github.com/eastonwhite/COVID19_US_States",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Easton R White",
+        "author_inst": "University of Vermont"
+      },
+      {
+        "author_name": "Laurent R H\u00e9bert-Dufresne",
+        "author_inst": "University of Vermont"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.04.14.20065342",
     "rel_title": "Estimate of COVID-19 case prevalence in India based on surveillance data of patients with severe acute respiratory illness",
@@ -1535259,33 +1534168,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.04.13.20062802",
-    "rel_title": "Public policy and economic dynamics of COVID-19 spread: a mathematical modeling study",
-    "rel_date": "2020-04-17",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20062802",
-    "rel_abs": "With the COVID-19 pandemic infecting millions of people, large-scale isolation policies have been enacted across the globe. To assess the impact of isolation measures on deaths, hospitalizations, and economic output, we create a mathematical model to simulate the spread of COVID-19, incorporating effects of restrictive measures and segmenting the population based on health risk and economic vulnerability. Policymakers make isolation policy decisions based on current levels of disease spread and economic damage. For 76 weeks in a population of 330 million, we simulate a baseline scenario leaving strong isolation restrictions in place, rapidly reducing isolation restrictions for non-seniors shortly after outbreak containment, and gradually relaxing isolation restrictions for non-seniors. We used 76 weeks as an approximation of the time at which a vaccine will be available. In the baseline scenario, there are 235,724 deaths and the economy shrinks by 34.0%. With a rapid relaxation, a second outbreak takes place, with 525,558 deaths, and the economy shrinks by 32.3%. With a gradual relaxation, there are 262,917 deaths, and the economy shrinks by 29.8%. We also show that hospitalizations, deaths, and economic output are quite sensitive to disease spread by asymptomatic people. Strict restrictions on seniors with very gradual lifting of isolation for non-seniors results in a limited number of deaths and lesser economic damage. Therefore, we recommend this strategy and measures that reduce non-isolated disease spread to control the pandemic while making isolation economically viable.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Uri Goldsztejn",
-        "author_inst": "Washington University in St. Louis"
-      },
-      {
-        "author_name": "David Schwartzman",
-        "author_inst": "Washington University in St. Louis."
-      },
-      {
-        "author_name": "Arye Nehorai",
-        "author_inst": "Washington University in St. Louis"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.04.11.20061804",
     "rel_title": "Ivermectin as a potential COVID-19 treatment from the pharmacokinetic point of view",
@@ -1535544,6 +1534426,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.04.12.20061929",
+    "rel_title": "Ad-hoc Assembly of Lean Extracorporeal Membrane Oxygenation Systems for COVID-19",
+    "rel_date": "2020-04-17",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.12.20061929",
+    "rel_abs": "BackgroundThe COVID-19 epidemic is overwhelming intensive care units with bilateral pneumonia patients requiring respiratory assistance. Bottlenecks in availability of ventilators and extracorporeal membrane oxygenation may contribute to mortality, implying ethically difficult rationing decisions. It is unclear if accelerated equipment production will meet demand, calling for fallback solutions for life support in worst-case scenarios.\n\nMethodsVeno-venous extracorporeal gas exchange (VV-ECMO) can provide vital support in bilateral lung failure. VV-ECMO essentially comprises large flow venous accesses, membrane gas exchange, and a blood pump. As thousands of FDA and CE certified Impella blood pumps and consoles are distributed globally for cardiac support, we explored ad-hoc assembly of lean ECMO systems by embedding Impella pumps coaxially in tubes in combination with standard gas exchangers.\n\nResultsAd-hoc integration of Impella blood pumps with gas exchange modules, standard cannulas for large bore venous access, regular ECMO tubing, Y-pieces and connectors led to lean ECMO systems with stable performance over several days. Oxygenation of 2.5-5 L of blood/minute is realistic. Benefit/risk analysis appears favorable if a patient requires respiratory support but cannot be supported because of lack of ventilators or unavailability of a required ECMO system.\n\nConclusionAd-hoc assembly of veno-venous ECMOs using Impella pumps is feasible and results in stable blood flow across gas exchange modules. However, such off-label use of the devices calls for specific ethical and regulatory considerations prior to their use as last resort in patients for whom no other treatment modalities are available.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Patrick Hunziker",
+        "author_inst": "University Hospital Basel"
+      },
+      {
+        "author_name": "Urs Zenklusen",
+        "author_inst": "University Hospital Basel"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "intensive care and critical care medicine"
+  },
   {
     "rel_doi": "10.1101/2020.04.12.20062166",
     "rel_title": "Immediate and Near Future Prediction of COVID-19 Patients in the U.S. Population Aged 65+ With the Prior Medical Conditions of Hypertension, Cardiovascular and Lung Diseases: Methods, Models and Acute Care Estimates",
@@ -1536493,29 +1535398,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.13.20063388",
-    "rel_title": "Using ICU data to improve the real-time estimation of the effective reproductive number of the COVID-19 epidemic in 9 European countries",
-    "rel_date": "2020-04-17",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20063388",
-    "rel_abs": "1.We replicate a recent study by the Imperial College COVID-19 Response Team (Flaxman et al, 2020) that estimates both the effective reproductive number, Rt, of the current COVID-19 epidemic in 11 European countries, and the impact of different nonpharmaceutical interventions that have been implemented to try to contain the epidemic, including case isolation, the closure of schools and universities, banning of mass gatherings and/or public events, and most recently, widescale social distancing including local and national lockdowns. The main indicator they use for measuring the evolution of the epidemic is the daily number of deaths by COVID-19 in each country, which is a better statistic than the number of identified cases because it doesnt depend so much on the testing strategy that is in place in each country at each moment in time.\n\nWe improve on their estimation by using data from the number of patients in intensive care, which provides two advantages over the number of deaths: first, it can be used to construct a signal with less bias: as the healthcare system of a country reaches saturation, the mortality rate would be expected to increase, which would bias the estimates of Rt and of the impact of measures implemented to contain the epidemic; and second, it is a signal with less lag, as the time from onset of symptoms to ICU admission is shorter than the time from onset to death (on average, 7.5 days shorter). The intensive care signal we use is not just the number of people in ICU, as this would also be biased if the healthcare system has reached saturation (in this case, biased downwards, as admissions are no longer possible when all units are in use). Instead, we estimate the daily demand of intensive care, as the sum of two components: the part that is satisfied (new ICU admissions) and the part that is not (which results in excess mortality).\n\nThanks to the advantages of this ICU signal in terms of timeliness and bias, we find that most of the countries in the study have already reached Rt<1 with 95% confidence (Italy, Spain, Austria, Denmark, France, Norway and Switzerland, but not Belgium or Sweden), whereas the original methodology of Flaxman et al (2020), even with updated data, would only find Rt<1 with 95% confidence for Italy and Switzerland.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Samuel Hurtado",
-        "author_inst": "NA"
-      },
-      {
-        "author_name": "David Tinajero",
-        "author_inst": "NA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.04.13.20063511",
     "rel_title": "Estimating the Fraction of Unreported Infections in Epidemics with a Known Epicenter: an Application to COVID-19",
@@ -1536658,6 +1535540,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.13.20062760",
+    "rel_title": "Estimates of regional infectivity of COVID-19in the United Kingdom following imposition of social distancingmeasures",
+    "rel_date": "2020-04-17",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20062760",
+    "rel_abs": "We describe regional variation in the reproduction number of SARS-CoV-2 infections observed using publicly reported data in the UK, with a view to understanding both if there are clear hot spots in viral spread in the country, or other spatial patterns. Based on case data up to the 9th April, we estimate that the viral replication number remains above 1 overall in the UK but that its trend is to decrease. This suggests the peak of the first wave of COVID-19 patients is imminent. We find that there is significant regional variation in the UK and that this is changing over time. Within England currently the reproductive ratio is lowest in the Midlands (1.11 95% CI 1.07; 1.14), and highest in the North East of England (1.38 95% CI 1.33-1.42). There are long and variable time delays between infection and detection of cases, and thus it remains unclear whether the reduction in the reproductive number is a result of social distancing measures. If we are to prevent further outbreaks, it is critical that we both reduce the time taken for detection and improve our ability to predict the regional spread of outbreaks.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Robert J Challen",
+        "author_inst": "EPSRC Centre for Predictive Modelling in Healthcare, University of Exeter, Exeter, Devon, UK."
+      },
+      {
+        "author_name": "Krasimira Tsaneva-Atanasova",
+        "author_inst": "EPSRC Centre for Predictive Modelling in Healthcare, University of Exeter, Exeter, Devon, UK."
+      },
+      {
+        "author_name": "Martin Pitt",
+        "author_inst": "NIHR CLAHRC for the South West Peninsula, St Lukes Campus, University of Exeter Medical School, Exeter, UK."
+      },
+      {
+        "author_name": "Tom Edwards",
+        "author_inst": "Taunton and Somerset NHS Foundation Trust, Taunton, Somerset, UK"
+      },
+      {
+        "author_name": "Luke Gompels",
+        "author_inst": "Taunton and Somerset NHS Foundation Trust, Taunton, Somerset, UK"
+      },
+      {
+        "author_name": "Lucas Lacasa",
+        "author_inst": "School of Mathematical Sciences, Queen Mary University of London, London E1 4NS, UK"
+      },
+      {
+        "author_name": "Ellen Brooks-Pollock",
+        "author_inst": "Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK"
+      },
+      {
+        "author_name": "Leon Danon",
+        "author_inst": "Data Science Institute, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, UK."
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.04.14.20062463",
     "rel_title": "COVID-19 Antibody Seroprevalence in Santa Clara County, California",
@@ -1537543,49 +1536472,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.04.13.20063545",
-    "rel_title": "Characteristics and outcomes of a cohort of SARS-CoV-2 patients in the Province of Reggio Emilia, Italy",
-    "rel_date": "2020-04-16",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20063545",
-    "rel_abs": "ObjectivesTo describe the age- and sex-specific prevalence of SARS-CoV-2 disease (COVID-19) and its prognostic factors.\n\nDesignPopulation-based prospective cohort study on archive data.\n\nSettingPreventive services and hospital care in the province of Reggio Emilia, Northern Italy.\n\nParticipantsAll 2653 symptomatic patients who tested positive for SARS-CoV-2 from February 27 to April 2, 2020 in the province of Reggio Emilia.\n\nMain outcome measuresHospitalization and death up to April 2, 2020.\n\nResultsFemales had higher prevalence of infection than males below age 50 (2.61 vs. 1.84 {per thousand}), but lower in older ages (16.49 vs. 20.86 {per thousand} over age 80). Case fatality rate reached 20.7% (22/106) in cases with more than 4 weeks follow up. After adjusting for age and comorbidities, men had a higher risk of hospitalization (hazard ratio (HR) 1.4 95% confidence interval (95% CI) 1.2 to 1.6) and of death (HR 1.6, 95% CI 1.2 to 2.1). Patients over age 80 compared to < age 50 had HR 7.1 (95% CI 5.4 to 9.3) and HR 27.8 (95% CI 12.5 to 61.7) for hospitalization and death, respectively. Immigrants had a higher risk of hospitalization (HR 1.3, 95% CI 0.99 to 1.81) than Italians and a similar risk of death. Risk of hospitalization and of death were higher in patients with heart failure (HR 1.6, 95% CI 1.2 to 2.1and HR 2.3, 95% CI 1.6 to 3.2, respectively), arrhythmia (HR 1.5, 95% CI 1.2 to 1.9 and HR 1.8, 95% CI 1.3 to 2.5, respectively), dementia (HR 1.2, 95% CI 0.9 to 1.8 and HR 1.8, 95% CI 1.1 to 2.8, respectively), ischemic heart disease (HR 1.3, 95% CI 1.0 to 1.7 and HR 1.7, 95% CI 1.2 to 2.5, respectively), diabetes (HR 1.5, 95% CI 1.3 to 1.9 and HR 1.6, 95% CI 1.1 to 2.2, respectively), and hypertensions(HR 1.4, 95% CI 1.2 to 2.6 and HR 1.6, 95% CI 1.2 to 2.1, respectively), while COPD increased the risk of hospitalization (HR 1.9, 95% CI 1.4 to 2.5) but not of death (HR 1.1, 95% CI 0.7 to 1.7). Previous use of ACE inhibitors has no effect on risk of death (HR 0.97, 95% CI 0.69 to 1.34)\n\nConclusionsThe mechanisms underlying these associations are mostly unknown. A deeper understanding of the causal chain from infection, disease onset, and immune response to outcomes may explain how these prognostic factors act.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Paolo Giorgi Rossi",
-        "author_inst": "Epidemiology unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy"
-      },
-      {
-        "author_name": "Massimiliano Marino",
-        "author_inst": "Department of Clinical Governance, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy"
-      },
-      {
-        "author_name": "Debora Formisano",
-        "author_inst": "Department of Clinical Governance, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy"
-      },
-      {
-        "author_name": "Francesco Venturelli",
-        "author_inst": "Epidemiology unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy"
-      },
-      {
-        "author_name": "Massimo Vicentini",
-        "author_inst": "Epidemiology unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy"
-      },
-      {
-        "author_name": "Roberto Grilli",
-        "author_inst": "Department of Clinical Governance, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy"
-      },
-      {
-        "author_name": "- The Reggio Emilia COVID-19 Working Group",
-        "author_inst": ""
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.04.13.20063529",
     "rel_title": "Impact of population mask wearing on Covid-19 post lockdown",
@@ -1537764,6 +1536650,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.13.20063669",
+    "rel_title": "Smoking is Associated with COVID-19 Progression: A Meta-Analysis",
+    "rel_date": "2020-04-16",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20063669",
+    "rel_abs": "ObjectiveTo determine the association between smoking and progression of COVID-19.\n\nDesignA meta-analysis of 12 published papers.\n\nData SourcePubMed database was searched on April 6, 2020.\n\nEligibility criteria and data analysisWe included studies reporting smoking behavior of COVID-19 patients and progression of disease. Search terms included \"smoking\", \"smoker*\", \"characteristics\", \"risk factors\", \"outcomes\", and \"COVID-19\", \"COVID\", \"coronavirus\", \"sar cov-2\", \"sar cov 2\". There were no language limitations. One author extracted information for each study, screened the abstract or the full text, with questions resolved through discussion among both authors. A random effects meta-analysis was applied.\n\nMain Outcome MeasuresThe study outcome was progression of COVID-19 among people who already had the disease.\n\nResultsWe identified 12 papers with a total of 9,025 COVID-19 patients, 878 (9.7%) with severe disease and 495 with a history of smoking (5.5%). The meta-analysis showed a significant association between smoking and progression of COVID-19 (OR 2.25, 95% CI 1.49-3.39, p=0.001). Limitations in the 12 papers suggest that the actual risk of smoking may be higher.\n\nConclusionsSmoking is a risk factor for progression of COVID-19, with smokers having higher odds of COVID-19 progression than never smokers. Physicians and public health professionals should collect data on smoking as part of clinical management and add smoking cessation to the list of practices to blunt the COVID-19 pandemic.\n\nWhat is already known on this topicO_LISmoking increases risk and severity of pulmonary infections because of damage to upper airways and a decrease in pulmonary immune function.\nC_LI\n\nWhat this study addsO_LISmoking is associated with COVID-19 severity.\nC_LIO_LISmoking history should be part of clinical management of COVID-19 patients and cessation should be added to the list of practices to blunt the COVID-19 pandemic.\nC_LI",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Roengrudee Patanavanich",
+        "author_inst": "University of California San Francisco"
+      },
+      {
+        "author_name": "Stanton A Glantz",
+        "author_inst": "University of California San Francisco"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.04.11.20062026",
     "rel_title": "Vapor H2O2 sterilization as a decontamination method for the reuse of N95 respirators in the COVID-19 emergency",
@@ -1538836,29 +1537745,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.04.11.20061507",
-    "rel_title": "A High-Coverage SARS-CoV-2 Genome Sequence Acquired by Target Capture Sequencing",
-    "rel_date": "2020-04-15",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.11.20061507",
-    "rel_abs": "This manuscript is based on the method we developed urgently to deal with the research requirement in the conflict between achieving a complete genome sequence for the evolutionary history of SARS-CoV-2 study and the low viral RNA concentration. Here, in this manuscript, we developed a set of SARS-CoV-2 enrichment probes to increase the sensitivity of sequence-based virus detection and characterization via obtaining the comprehensive genome sequence. Following the CDC health and safety guidelines, we test the concept using the culturing supernatant contain SARS-CoV-2 particles, and its full-length sequence was used for further analysis. The fraction of SARS-CoV-2 endogenous DNA was 93.47% with Cluster Factor about 1.1, which demonstrate that the numbers of mapped reads to SARS-CoV-2 reference sequence significantly increased, compared to metagenomic sequencing technology, following SARS-CoV-2 probe enrichment. Moreover, based on the high-quality sequence, we discussed the heterozygosity and viral expression during replication of coronavirus, and its phylogenetic relationship with other selected high-quality samples from The Genome Variation Map (GVM) (on 2020/03/22). We believe this manuscript is valuable for all the researchers who are interested in using clinical warp samples to obtain the high coverage of SARS-CoV-2 genome sequence with a relatively low concentration of viral particles. This would allow the clinician to correlate the diagnostic data with molecular monitoring in viral evolutional, the most importantly, to track the functional mutation of SARS-CoV-2.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "shaoqing wen",
-        "author_inst": "Fudan University"
-      },
-      {
-        "author_name": "Xiao Zhang",
-        "author_inst": "Guangzhou Regeneration Medicine and Health Guangdong Laboratory"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.04.10.20061374",
     "rel_title": "Covid-19 clinical data analysis using Ball Mapper",
@@ -1539113,6 +1537999,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.11.20061408",
+    "rel_title": "A Preliminary Assessment of Novel Coronavirus (COVID-19) Knowledge and Perceptions in Nigeria",
+    "rel_date": "2020-04-15",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.11.20061408",
+    "rel_abs": "This study assessed knowledge and perceptions about COVID-19 among the general public in Nigeria during the initial week of the pandemic lockdown in the country. From March 28 to April 4, 2020, this cross-sectional survey used an anonymous online questionnaire to collect data from respondents within Nigeria. Purposive and snowball sampling techniques were used to recruit 1357 respondents, aged 15-70 years, from 180 cities and towns within Nigeria. Study data were analysed using descriptive statistics. Approximately more than half (57.02%) of the respondents were male with high level of education (48.86% bachelors degree or higher). Approximately half of the respondents (46.94%) opined that COVID-19 was \"a biological weapon designed by the Chinese government.\" About 94% of the respondents identified \"contact with airborne droplets via breathing, sneezing, or coughing\" as the most common mode of transmission; most respondents associated COVID-19 with coughing (81.13%), shortness of breath (73.47%) and fever (62.79%). \"Regular hand washing and social distancing\" was selected by most respondents (94.25%) as a way of preventing infection whereas 11.86% reported \"consuming gins, garlic, ginger, herbal mixtures and African foods/soups\" as preventive measures against COVID-19. Majority of the respondents (91.73%) thought COVID-19 is deadly; and most respondents (84.3%) got 4 or more answers correctly. It was also observed that the traditional media (TV/Radio) are the most common source of health information about COVID-19 (93.5%). Findings revealed that Nigerians have relatively high knowledge, mostly derived from traditional media, about COVID-19. Their perceptions of COVID-19 bear implications across public health initiatives, compliance with precautionary behavior as well as bilateral relations with foreign nations. Evidence-based campaign should be intensified to remove misconceptions and promote precautionary measures.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Peter O OLAPEGBA",
+        "author_inst": "University of Ibadan"
+      },
+      {
+        "author_name": "Olusola AYANDELE",
+        "author_inst": "The Polytechnic Ibadan"
+      },
+      {
+        "author_name": "Samson Olowo KOLAWOLE",
+        "author_inst": "Nigeria Police Academy, Wudil, Kano"
+      },
+      {
+        "author_name": "Rotimi OGUNTAYO",
+        "author_inst": "University of Ilorin"
+      },
+      {
+        "author_name": "Joshua Chiroma GANDI",
+        "author_inst": "University of Jos"
+      },
+      {
+        "author_name": "Abdullahi Lawal DANGIWA",
+        "author_inst": "Federal University, Dutse"
+      },
+      {
+        "author_name": "Iboro Friday Akpan OTTU",
+        "author_inst": "University of Uyo"
+      },
+      {
+        "author_name": "Steven Kator IORFA",
+        "author_inst": "University of Nigeria, Nsukka"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.04.11.20062091",
     "rel_title": "Cardiac or Infectious? Transfer Learning with Chest X-Rays for ER Patient Classification",
@@ -1540378,33 +1539311,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
-  {
-    "rel_doi": "10.1101/2020.04.09.20059196",
-    "rel_title": "Efficacy of remdesivir versus placebo for the treatment of COVID-19: A protocol for systematic review and meta-analysis of randomized controlled trials",
-    "rel_date": "2020-04-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20059196",
-    "rel_abs": "BackgroundIn spite of the global containment on prevention efforts, the spread of coronavirus disease 2019 (COVID-19) is continuing to rise, with 1.1 million confirmed cases and 60,124 deaths recorded worldwide since 04 April 2020. The outbreak has a significant threat to international health and economy. At present, there is no approved vaccine or treatment for the disease, while efforts are underway. Remdesivir, a nucleotide-analogue antiviral drug developed for Ebola, is determined to prevent and stop infections with COVID-19, while results are yet controversial. Here, we aim to conduct a systematic review and meta-analysis of randomized controlled trials to compare the effectiveness of remdesivir and placebo in patients with COVID-19.\n\nMethod and analysisWe will search MEDLINE-PubMed, Embase, Cochrane Library, ClinicalTrials.gov, and Google scholar databases without restriction in year of publication. We will include randomized controlled trials that assessed the effectiveness of remdesivir versus placebo for patients confirmed with COVID-19. We will follow the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA 2015) guidelines for the design and reporting of the results. The primary endpoint will be time to clinical recovery. The secondary endpoints will be all cause mortality, discharged date, frequency of respiratory progression, and treatment-emergent adverse events. Two independent authors will perform study selection, data extraction, and methodology quality assessment. RevMan 5.3 software will be used for statistical analysis. Random/fixed effect model will be carried out to calculate mean differences for continuous outcomes and risk ratio for dichotomous outcomes between remdesivir and placebo.\n\nEthics and disseminationThis study does not require ethical approval, because no participants data will be involved in this systematic review and meta-analysis. The findings of this study will be published in reputable and peer-reviewed journal.\n\nRegistrationThis review protocol is submitted in PROSPERO database for registration and we will include the registration number in the revised version of the manuscript.\n\nStrengths and limitations of this study This systematic review and meta-analysis will be derived from only randomized controlled trials which will increase the quality of evidences.\n This systematic review and meta-analysis will be derived from only randomized controlled trials which will reduce between study heterogeneity.\n Subgroup and sensitivity analysis will be carried out to identify possible reasons that may cause significant heterogeneity between studies.\n The use of Cochrane risk of bias tool to assess risk of bias for each included studies to extract and synthesize evidence based conclusions.\n One of the limitation of this study might be the restriction of trials published in English language.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Desye Gebrie",
-        "author_inst": "1Center for Innovative Drug Development and Therapeutic Trials for Africa, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia 2School of "
-      },
-      {
-        "author_name": "Desalegn Getnet",
-        "author_inst": "Pharmacology and Toxicology Course and Research Team, Department of Pharmacy, College of Health Sciences, Adigrat University, Adigrat, Ethiopia"
-      },
-      {
-        "author_name": "Tsegahun Manyazewal",
-        "author_inst": "Center for Innovative Drug Development and Therapeutic Trials for Africa, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "respiratory medicine"
-  },
   {
     "rel_doi": "10.1101/2020.04.09.20059352",
     "rel_title": "Analysis of factors associated early diagnosis in coronavirus disease 2019 (COVID-19)",
@@ -1540647,6 +1539553,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.04.09.20059311",
+    "rel_title": "Real-time forecasts and risk assessment of novel coronavirus (COVID-19) cases: A data-driven analysis",
+    "rel_date": "2020-04-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20059311",
+    "rel_abs": "The coronavirus disease 2019 (COVID-19) has become a public health emergency of international concern affecting 201 countries and territories around the globe. As of April 4, 2020, it has caused a pandemic outbreak with more than 11,16,643 confirmed infections and more than 59,170 reported deaths worldwide. The main focus of this paper is two-fold: (a) generating short term (real-time) forecasts of the future COVID-19 cases for multiple countries; (b) risk assessment (in terms of case fatality rate) of the novel COVID-19 for some profoundly affected countries by finding various important demographic characteristics of the countries along with some disease characteristics. To solve the first problem, we presented a hybrid approach based on autoregressive integrated moving average model and Wavelet-based forecasting model that can generate short-term (ten days ahead) forecasts of the number of daily confirmed cases for Canada, France, India, South Korea, and the UK. The predictions of the future outbreak for different countries will be useful for the effective allocation of health care resources and will act as an early-warning system for government policymakers. In the second problem, we applied an optimal regression tree algorithm to find essential causal variables that significantly affect the case fatality rates for different countries. This data-driven analysis will necessarily provide deep insights into the study of early risk assessments for 50 immensely affected countries.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Tanujit Chakraborty",
+        "author_inst": "Indian Statistical Institute, Kolkata"
+      },
+      {
+        "author_name": "Indrajit Ghosh",
+        "author_inst": "Indian Statistical Institute, Kolkata"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.04.09.20059865",
     "rel_title": "Forecasting the scale of the COVID-19 epidemic in Kenya",
@@ -1541492,33 +1540421,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.10.20060764",
-    "rel_title": "COVID-19: Recovering estimates of the infected fatality rate during an ongoing pandemic through partial data",
-    "rel_date": "2020-04-14",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20060764",
-    "rel_abs": "In an ongoing epidemic, the case fatality rate is not a reliable estimate of a diseases severity. This is particularly so when a large share of asymptomatic or pauci-symptomatic patients escape testing, or when overwhelmed healthcare systems are forced to limit testing further to severe cases only. By leveraging data on COVID-19, we propose a novel way to estimate a diseases infected fatality rate, the true lethality of the disease, in the presence of sparse and partial information. We show that this is feasible when the disease has turned into a pandemic and data comes from a large number of countries, or regions within countries, as long as testing strategies vary sufficiently. For Italy, our method estimates an IFR of 1.1% (95% CI: 0.2% - 2.1%), which is strongly in line with other methods. At the global level, our method estimates an IFR of 1.6% (95% CI: 1.1% - 2.1%). This method also allows us to show that the IFR varies according to each countrys age structure and healthcare capacity.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Matteo Villa",
-        "author_inst": "Italian Institute for International Political Studies (ISPI)"
-      },
-      {
-        "author_name": "James F. Myers",
-        "author_inst": "King's College London"
-      },
-      {
-        "author_name": "Federico Turkheimer",
-        "author_inst": "King's College London"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.04.08.20047134",
     "rel_title": "Calcium channel blocker amlodipine besylate is associated with reduced case fatality rate of COVID-19 patients with hypertension",
@@ -1541949,6 +1540851,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "genetic and genomic medicine"
   },
+  {
+    "rel_doi": "10.1101/2020.04.10.20061192",
+    "rel_title": "COVID-19 most vulnerable Mexican cities lack the public health infrastructure to face the pandemic: a new temporally-explicit model",
+    "rel_date": "2020-04-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20061192",
+    "rel_abs": "Recently, a wide array of epidemiological models have been developed to guide public health actors in containing the rapid dissemination of the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), cause of COVID-19. Despite their usefulness, many epidemiological models recently developed to understand the spread of SARS-CoV-2 and infection rates of COVID-19 fall short as they ignore human mobility, limiting our understanding of the spread of the disease, together with the vulnerability of population centers in a broad scale. We developed a new temporally-explicit model and simulated several social distancing scenarios to predict the vulnerability to COVID-19 of 50 Mexican cities that are interconnected by their air transportation network. Additionally, we assessed the sufficiency of the public health infrastructure in the focal cities to face the pandemic over time. Based on our model, we show that the most important cities within the Mexican air transportation network are the most vulnerable to COVID-19, with all assessed public health infrastructure being insufficient to face the modeled scenario for the pandemic after 100 days. Despite these alarming findings, our results show that social distancing could dramatically decrease the total number of infected people (77% drop-off for the 45% distancing scenario when contrasted with no distancing), flattening the growth of infection rate. Thus, we consider that this study provides useful information that may help decision-makers to timely implement health policies to anticipate and lessen the impact of the current pandemic in Mexico.\n\nSignificance StatementWe used a new temporally-explicit model focused on air transportation networks to predict the vulnerability of 50 focal Mexican cities to COVID-19. We found that most vulnerable cities lack of the required public health infrastructure (i.e., number of inpatient and intensive care unit beds) to face this new pandemic, overloading in all cases after 100 days. However, our results show that a 45% social distancing scenario can reduce the number of infected people by up to 78.7%, flattening the growth rate of people with COVID-19 before infection rates soar exponentially countrywide.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Wesley Dattilo Sr.",
+        "author_inst": "Instituto de Ecologia AC"
+      },
+      {
+        "author_name": "Alcides Castro e Silva",
+        "author_inst": "Universidade Federal de Ouro Preto"
+      },
+      {
+        "author_name": "Roger Guevara Sr.",
+        "author_inst": "Instituto de Ecologia AC"
+      },
+      {
+        "author_name": "Ian MacGregor-Fors",
+        "author_inst": "Instituto de Ecologia AC"
+      },
+      {
+        "author_name": "Servio Pontes Ribeiro",
+        "author_inst": "Universidade Federal de Ouro Preto"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.04.09.20060103",
     "rel_title": "Acceptance and preference for COVID-19 vaccination in health-care workers (HCWs)",
@@ -1542966,149 +1541903,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.13.039917",
-    "rel_title": "Human organs-on-chips as tools for repurposing approved drugs as potential influenza and COVID19 therapeutics in viral pandemics",
-    "rel_date": "2020-04-14",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.13.039917",
-    "rel_abs": "The rising threat of pandemic viruses, such as SARS-CoV-2, requires development of new preclinical discovery platforms that can more rapidly identify therapeutics that are active in vitro and also translate in vivo. Here we show that human organ-on-a-chip (Organ Chip) microfluidic culture devices lined by highly differentiated human primary lung airway epithelium and endothelium can be used to model virus entry, replication, strain-dependent virulence, host cytokine production, and recruitment of circulating immune cells in response to infection by respiratory viruses with great pandemic potential. We provide a first demonstration of drug repurposing by using oseltamivir in influenza A virus-infected organ chip cultures and show that co-administration of the approved anticoagulant drug, nafamostat, can double oseltamivirs therapeutic time window. With the emergence of the COVID-19 pandemic, the Airway Chips were used to assess the inhibitory activities of approved drugs that showed inhibition in traditional cell culture assays only to find that most failed when tested in the Organ Chip platform. When administered in human Airway Chips under flow at a clinically relevant dose, one drug - amodiaquine - significantly inhibited infection by a pseudotyped SARS-CoV-2 virus. Proof of concept was provided by showing that amodiaquine and its active metabolite (desethylamodiaquine) also significantly reduce viral load in both direct infection and animal-to-animal transmission models of native SARS-CoV-2 infection in hamsters. These data highlight the value of Organ Chip technology as a more stringent and physiologically relevant platform for drug repurposing, and suggest that amodiaquine should be considered for future clinical testing.",
-    "rel_num_authors": 32,
-    "rel_authors": [
-      {
-        "author_name": "Longlong Si",
-        "author_inst": "Wyss institute at Harvard university"
-      },
-      {
-        "author_name": "Haiqing Bai",
-        "author_inst": "Wyss Institute for Biologically Inspired Engineering"
-      },
-      {
-        "author_name": "Melissa Rodas",
-        "author_inst": "Wyss Institute for Biologically Inspired Engineering"
-      },
-      {
-        "author_name": "Wuji Cao",
-        "author_inst": "Wyss Institute for Biologically Inspired Engineering"
-      },
-      {
-        "author_name": "Crystal Yur Oh",
-        "author_inst": "Wyss Institute for Biologically Inspired Engineering"
-      },
-      {
-        "author_name": "Amanda Jiang",
-        "author_inst": "Wyss institute at Harvard university"
-      },
-      {
-        "author_name": "Rasmus Moller",
-        "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Daisy Hoagland",
-        "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Kohei Oishi",
-        "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Shu Horiuchi",
-        "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Skyler Uhl",
-        "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Daniel Blanco-Melo",
-        "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Randy A. Albrecht",
-        "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Wen-Chun Liu",
-        "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Tristan Jordan",
-        "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai,"
-      },
-      {
-        "author_name": "Benjamin E. Nilsson-Payant",
-        "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "James Logue",
-        "author_inst": "Department of Microbiology and Immunology, University of Maryland School of Medicine"
-      },
-      {
-        "author_name": "Robert Haupt",
-        "author_inst": "Department of Microbiology and Immunology, University of Maryland School of Medicine"
-      },
-      {
-        "author_name": "Marisa McGrath",
-        "author_inst": "Department of Microbiology and Immunology, University of Maryland School of Medicine"
-      },
-      {
-        "author_name": "Stuart Weston",
-        "author_inst": "Department of Microbiology and Immunology, University of Maryland School of Medicine"
-      },
-      {
-        "author_name": "Atiq Nurani",
-        "author_inst": "Wyss Institute for Biologically Inspired Engineering"
-      },
-      {
-        "author_name": "Seong Min Kim",
-        "author_inst": "Wyss institute at Harvard University"
-      },
-      {
-        "author_name": "Danni Y Zhu",
-        "author_inst": "Wyss Institute for Biologically Inspired Engineering"
-      },
-      {
-        "author_name": "Kambez H. Benam",
-        "author_inst": "Wyss institute at Harvard University"
-      },
-      {
-        "author_name": "Girija Goyal",
-        "author_inst": "Wyss Institute for Biologically Inspired Engineering"
-      },
-      {
-        "author_name": "Sarah Gilpin",
-        "author_inst": "Wyss Institute for Biologically Inspired Engineering"
-      },
-      {
-        "author_name": "Rachelle Prantil-Baun",
-        "author_inst": "Wyss institute at Harvard university"
-      },
-      {
-        "author_name": "Rani K. Powers",
-        "author_inst": "Wyss institute at Harvard University"
-      },
-      {
-        "author_name": "Kenneth Carlson",
-        "author_inst": "Wyss institute at Harvard University"
-      },
-      {
-        "author_name": "Matthew Frieman",
-        "author_inst": "University of Maryland School of Medicine"
-      },
-      {
-        "author_name": "Benjamin R. tenOever",
-        "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Donald E. Ingber",
-        "author_inst": "Wyss Institute"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.04.09.20060053",
     "rel_title": "COVID-19 pandemics modeling with SEIR(+CAQH), social distancing, and age stratification. The effect of vertical confinement and release in Brazil.",
@@ -1543335,6 +1542129,29 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.09.20059345",
+    "rel_title": "Chasing the ghost of infection past: identifying thresholds of change during the COVID-19 infection in Spain",
+    "rel_date": "2020-04-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20059345",
+    "rel_abs": "COVID-19 pandemic has spread worldwide rapidly from its first outbreak in China, with different impacts depending on the age and social structure of the populations, and the measures taken by each government. Within Europe, the first countries to be strongly affected have been Italy and Spain. In Spain, infection has expanded in highly populated areas, resulting in one of the largest nationwide bursts so far by early April. We analyze the evolution of the growth curve of the epidemic in both the whole of Spain, Madrid Autonomous Region (the second largest conurbation in Europe), and Catalonia (which includes Spains second largest city), based on the cumulative numbers of reported cases and deaths. We conducted segmented, poisson regressions on log-transformed data to identify changes in the slope of these curves and/or sudden shifts in the number of cases (i.e. changes in the intercept) at fitted breaking points, and compared their results with a timeline including both key events of the epidemic and containment measures taken by the national and regional governments. Results were largely consistent in the six curves analyzed (reported infections and deaths for Spain, Madrid and Catalonia, respectively), showing three major clusters of shifts in slopes (growth rates) on March 13-19, March 23-29 and April 1-5 that resulted in 33-71% reductions of slope, and originated in infections on March 3-9, 13-19 and 22-26; as well as a decrease in the infection rate following the strengthened lockdown of 29-30 April, only for Madrid and Catalonia. Small upward shifts in the progress of the disease in Madrid were not associated with significant increases in the intercept of the curve, and seem related with unevenness in case reporting; but they did so in Spain and Catalonia, where they were probably associated to specific events of group infection in Vitoria and to the onset of the outbreak in Catalonia. These results evidence an early deceleration in the spread of COVID-19 coinciding with personal hygiene and social distancing recommendations, as well as the general awareness of the population; and a second, stronger decrease when harder isolation measures were enforced. The combination of these two inflection points seemingly led to the start of the contention of the disease outbreak by early April, the limit of our time series. This highlights the importance of adopting public health strategies that include disseminating basic knowledge on personal hygiene and reduced social contact at the onset of the epidemic, and the importance of early enforcement of hard confinement measures for its subsequent contention.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Luis Santamaria",
+        "author_inst": "Donana Biological Station (EBD-CSIC)"
+      },
+      {
+        "author_name": "Joaquin Hortal",
+        "author_inst": "Museo Nacional de Ciencias Naturales (MNCN-CSIC)"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.04.09.20060129",
     "rel_title": "COVID-19 Global Pandemic Planning: Decontamination and Reuse Processes for N95 Respirators",
@@ -1544388,153 +1543205,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.08.031807",
-    "rel_title": "Comparison of SARS-CoV-2 infections among 3 species of non-human primates",
-    "rel_date": "2020-04-12",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.08.031807",
-    "rel_abs": "COVID-19, caused by SARS-CoV-2 infection, has recently been announced as a pandemic all over the world. Plenty of diagnostic, preventive and therapeutic knowledges have been enriched from clinical studies since December 2019. However, animal models, particularly non-human primate models, are urgently needed for critical questions that could not be answered in clinical patients, evaluations of anti-viral drugs and vaccines. In this study, two families of non-human primates, Old world monkeys (12 Macaca mulatta, 6 Macaca fascicularis) and New world monkeys (6 Callithrix jacchus), were experimentally inoculated with SARS-CoV-2. Clinical signs were recorded. Samples were collected for analysis of viral shedding, viremia and histopathological examination. Increased body temperature was observed in 100% (12/12) M. mulatta, 33.3% (2/6) M. fascicularis and none (0/6) of C. jacchus post inoculation of SARS-CoV-2. All of M. mulatta and M. fascicularis showed chest radiographic abnormality. Viral genomes were detected in nasal swabs, throat swabs, anal swabs and blood from all 3 species of monkeys. Viral shedding from upper respiratory samples reached the peak between day 6 and day 8 post inoculation. From necropsied M. mulatta and M. fascicularis, the tissues showing virus positive were mainly lung, weasand, bronchus and spleen. No viral genome was seen in any of tissues from 2 necropsied C. jacchus. Severe gross lesions and histopathological changes were observed in lung, heart and stomach of SARS-CoV-2 infected animals. In summary, we have established a NHP model for COVID-19, which could be used to evaluate drugs and vaccines, and investigate viral pathogenesis. M. mulatta is the most susceptible to SARS-CoV-2 infection, followed by M. fascicularis and C. jacchus.\n\nOne Sentence SummaryM. mulatta is the most susceptible to SARS-CoV-2 infection as compared to M. fascicularis and C. jacchus.",
-    "rel_num_authors": 33,
-    "rel_authors": [
-      {
-        "author_name": "Shuaiyao Lu",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Yuan Zhao",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Wenhai Yu",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Yun Yang",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Jiahong Gao",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Junbin Wang",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Dexuan Kuang",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Mengli Yang",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Jing Yang",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Chunxia Ma",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Jingwen Xu",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Haiyan Li",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Siwen Zhao",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Jingmei Li",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Haixuan Wang",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Haiting Long",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Jingxian Zhou",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Fangyu Luo",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Kaiyun Ding",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Daoju Wu",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Yong Zhang",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Yingliang Dong",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Yuqin Liu",
-        "author_inst": "Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences"
-      },
-      {
-        "author_name": "Yingqiu Zheng",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Xiaochen Lin",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Li Jiao",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Huanying Zheng",
-        "author_inst": "Guangdong Provincial Center for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Qing Dai",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Qiangmin Sun",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Yunzhang Hu",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Changwen Ke",
-        "author_inst": "Guangdong Provincial Center for Disease Control and Prevention"
-      },
-      {
-        "author_name": "Hongqi Liu",
-        "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College"
-      },
-      {
-        "author_name": "Xiaozhong Peng",
-        "author_inst": "Institute of Medical Biology & Institute of Basic Medical Sciences, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical C"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.04.10.035824",
     "rel_title": "Scutellaria baicalensis extract and baicalein inhibit replication of SARS-CoV-2 and its 3C-like protease in vitro",
@@ -1544833,6 +1543503,33 @@
     "type": "new results",
     "category": "bioinformatics"
   },
+  {
+    "rel_doi": "10.1101/2020.04.05.026005",
+    "rel_title": "Immuno-informatics Characterization SARS-CoV-2 Spike Glycoprotein for Prioritization of Epitope based Multivalent Peptide Vaccine",
+    "rel_date": "2020-04-12",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.05.026005",
+    "rel_abs": "The COVID-19 pandemic caused by SARS-CoV-2 is a public-health emergency of international concern and thus calling for the development of safe and effective therapeutics and prophylactics particularly a vaccine to protect against the infection. SARS-CoV-2 spike glycoprotein is an attractive candidate for vaccine, antibodies and inhibitor development because of many roles it plays in attachment, fusion and entry into the host cell. In this study, we characterized the SARS-CoV-2 spike glycoprotein by immune-informatics techniques to put forward potential B and T cell epitopes, followed by the use of epitopes in construction of a multi-epitope peptide vaccine construct (MEPVC). The MEPVC revealed robust host immune system simulation with high production of immunoglobulins, cytokines and interleukins. Stable conformation of the MEPVC with a representative innate immune TLR3 receptor was observed involving strong hydrophobic and hydrophilic chemical interactions, along with enhanced contribution from salt-bridges towards inter-molecular stability. Molecular dynamics simulation in solution aided further in interpreting strong affinity of the MEPVC for TLR3. This stability is the attribute of several vital residues from both TLR3 and MEPVC as shown by radial distribution function (RDF) and a novel analytical tool axial frequency distribution (AFD). Comprehensive binding free energies estimation was provided at the end that concluded major domination by electrostatic and minor from van der Waals. Summing all, the designed MEPVC has tremendous potential of providing protective immunity against COVID-19 and thus has the potential to be considered in experimental studies.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Saba Ismail",
+        "author_inst": "Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University Islamabad, Pakistan"
+      },
+      {
+        "author_name": "Sajjad Ahmad",
+        "author_inst": "Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University Islamabad, Pakistan"
+      },
+      {
+        "author_name": "Syed Sikander Azam",
+        "author_inst": "Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University Islamabad, Pakistan"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "bioinformatics"
+  },
   {
     "rel_doi": "10.1101/2020.04.06.20054841",
     "rel_title": "The need of health policy perspective to protect Healthcare Workers during COVID-19 pandemic. A GRADE rapid review on the N95 respirators effectiveness.",
@@ -1545746,49 +1544443,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.04.07.20056606",
-    "rel_title": "Efficient network immunization under limited knowledge",
-    "rel_date": "2020-04-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20056606",
-    "rel_abs": "Targeted immunization or attacks of large-scale networks has attracted significant attention by the scientific community. However, in real-world scenarios, knowledge and observations of the network may be limited thereby precluding a full assessment of the optimal nodes to immunize (or remove) in order to avoid epidemic spreading such as that of current COVID-19 epidemic. Here, we study a novel immunization strategy where only n nodes are observed at a time and the most central between these n nodes is immunized (or attacked). This process is continued repeatedly until 1 - p fraction of nodes are immunized (or attacked). We develop an analytical framework for this approach and determine the critical percolation threshold pc and the size of the giant component P{infty}; for networks with arbitrary degree distributions P(k). In the limit of n [-&gt;] {infty} we recover prior work on targeted attack, whereas for n = 1 we recover the known case of random failure. Between these two extremes, we observe that as n increases, pc increases quickly towards its optimal value under targeted immunization (attack) with complete information. In particular, we find a new scaling relationship between |pc({infty}) - pc(n) | and n as |pc({infty}) - pc(n)| ~ n-1 exp(-n). For Scale-free (SF) networks, where P(k) ~ k-{gamma}, 2 <{gamma} < 3, we find that pc has a transition from zero to non-zero when n increases from n = 1 to order of logN (N is the size of network). Thus, for SF networks, knowledge of order of logN nodes and immunizing them can reduce dramatically an epidemics.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Yangyang Liu",
-        "author_inst": "Department of Systems Science,  College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, Hunan 410073, China"
-      },
-      {
-        "author_name": "Hillel Sanhedrai",
-        "author_inst": "Department of Physics, Bar-Ilan University, Ramat Gan 5290002, Israel"
-      },
-      {
-        "author_name": "Gaogao Dong",
-        "author_inst": "Jiangsu University"
-      },
-      {
-        "author_name": "Louis M. Shekhtman",
-        "author_inst": "Networks Science Institute, Northeastern University, Boston, MA 02115"
-      },
-      {
-        "author_name": "Fan Wang",
-        "author_inst": "Department of Physics, Bar-Ilan University, Ramat Gan 5290002, Israel"
-      },
-      {
-        "author_name": "Sergey V. Buldyrev",
-        "author_inst": "Department of Physics, Yeshiva University, New York, New York 10033, USA"
-      },
-      {
-        "author_name": "Shlomo Havlin",
-        "author_inst": "Department of Physics, Bar-Ilan University, Ramat Gan 5290002, Israel"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.04.10.20056697",
     "rel_title": "Predication of Pandemic COVID-19 situation in Maharashtra, India",
@@ -1546047,6 +1544701,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "respiratory medicine"
   },
+  {
+    "rel_doi": "10.1101/2020.04.06.20055640",
+    "rel_title": "Gaussian Statistics and Data-Assimilated Model of Mortality due to COVID-19: China, USA, Italy, Spain, UK, Iran, and the World Total",
+    "rel_date": "2020-04-11",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.06.20055640",
+    "rel_abs": "Covid-19 is characterized by rapid transmission and severe symptoms, leading to deaths in some cases (ranging from 1.5 to 12% of the affected, depending on the country). We identify the Gaussian nature of mortality due to covid-19, as shown in China where it appears to have run its course (during the first sweep of the pandemic at least) and other coutnries, and also in Imperial College modeling. Gaussian distribution involves three parameters, the height, peak location and the width, and the streaming data can be used to infer function value, slope and inflection location as a minimum set of constraints to estimate the subsequent trajectories. Thus, we apply the Gaussian function template as the basis for a data-assimilated model of covid-19 trajectories, first to USA, United Kingdom (UK), Iran and the world total in this study. As more data become available, the Gaussian trajectories are updated, for other nations and also for state-by-state projections in USA.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "T.-W. Lee",
+        "author_inst": "Arizona State University"
+      },
+      {
+        "author_name": "J.E. Park",
+        "author_inst": "Arizona State University"
+      },
+      {
+        "author_name": "David Hung",
+        "author_inst": "Shanghai Jiatong University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health informatics"
+  },
   {
     "rel_doi": "10.1101/2020.04.06.20055632",
     "rel_title": "Association of County-Level Socioeconomic and Political Characteristics with Engagement in Social Distancing for COVID-19",
@@ -1547060,57 +1545741,6 @@
     "type": "new results",
     "category": "genetics"
   },
-  {
-    "rel_doi": "10.1101/2020.04.08.20058495",
-    "rel_title": "Fast SARS-CoV-2 detection by RT-qPCR in preheated nasopharyngeal swab samples",
-    "rel_date": "2020-04-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20058495",
-    "rel_abs": "The current reference for COVID-19 diagnosis is based on the detection of SARS-CoV-2 on RNA extracts using one-step retrotranscription and quantitative PCR (RT-qPCR). Based on the urgent need for high-throughput COVID-19 screening, we tested the performance of three alternative, simple and affordable protocols to rapidly detect SARS-CoV-2, overcoming the long and tedious RNA extraction step. Although with an average increase of 6.1 ({+/-} 1.6) cycles compared to standard tests with RNA extracts, we show that RT-qPCR yielded consistent results in nasopharyngeal swab samples that were subject to a direct 70{degrees}C incubation for 10 min. Our findings provide viable options to overcome any supply chain issue and help to increase the throughput of diagnostic tests by using any qPCR device, thereby complementing standard COVID-19 testing.",
-    "rel_num_authors": 9,
-    "rel_authors": [
-      {
-        "author_name": "Julia Alcoba-Florez",
-        "author_inst": "Servicio de Microbiologia, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain"
-      },
-      {
-        "author_name": "Rafaela Gonzalez-Montelongo",
-        "author_inst": "Genomics Division, Instituto Tecnologico y de Energias Renovables, Santa Cruz de Tenerife, Spain"
-      },
-      {
-        "author_name": "Antonio Inigo-Campos",
-        "author_inst": "Genomics Division, Instituto Tecnologico y de Energias Renovables, Santa Cruz de Tenerife, Spain"
-      },
-      {
-        "author_name": "Diego Garcia-Martinez de Artola",
-        "author_inst": "Servicio de Microbiologia, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain"
-      },
-      {
-        "author_name": "Helena Gil-Campesino",
-        "author_inst": "Servicio de Microbiologia, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain"
-      },
-      {
-        "author_name": "The Microbiology Technical Support Team",
-        "author_inst": ""
-      },
-      {
-        "author_name": "Laura Ciuffreda",
-        "author_inst": "Research Unit, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain"
-      },
-      {
-        "author_name": "Agustin Valenzuela-Fernandez",
-        "author_inst": "Laboratorio de Inmunologia Celular y Viral, Unidad de Farmacologia, Facultad de Medicina, Universidad de La Laguna, San Cristobal de La Laguna, Spain"
-      },
-      {
-        "author_name": "Carlos Flores",
-        "author_inst": "Research Unit, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.04.09.034942",
     "rel_title": "Analysis of the mutation dynamics of SARS-CoV-2 reveals the spread history and emergence of RBD mutant with lower ACE2 binding affinity",
@@ -1547373,6 +1546003,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.09.033910",
+    "rel_title": "Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis",
+    "rel_date": "2020-04-11",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.09.033910",
+    "rel_abs": "COVID-19 (Coronavirus disease 2019) is a respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). While the pathophysiology of this deadly virus is complex and largely unknown, we employ a network biology-fueled approach and integrated multiomics data pertaining to lung epithelial cells-specific coexpression network and human interactome to generate Calu-3-specific human-SARS-CoV-2 Interactome (CSI). Topological clustering and pathway enrichment analysis show that SARS-CoV-2 target central nodes of host-viral network that participate in core functional pathways. Network centrality analyses discover 28 high-value SARS-CoV-2 targets, which are possibly involved in viral entry, proliferation and survival to establish infection and facilitate disease progression. Our probabilistic modeling framework elucidates critical regulatory circuitry and molecular events pertinent to COVID-19, particularly the host modifying responses and cytokine storm. Overall, our network centric analyses reveal novel molecular components, uncover structural and functional modules, and provide molecular insights into SARS-CoV-2 pathogenicity.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Nilesh Kumar",
+        "author_inst": "University of Alabama at Birmingham"
+      },
+      {
+        "author_name": "Bharat Mishra",
+        "author_inst": "University of Alabama at Birmingham"
+      },
+      {
+        "author_name": "Adeel Mehmood",
+        "author_inst": "University of Alabama at Birmingham"
+      },
+      {
+        "author_name": "Mohammad Athar",
+        "author_inst": "University of Alabama at Birmingham"
+      },
+      {
+        "author_name": "M Shahid Mukhtar",
+        "author_inst": "University of Alabama at Birmingham"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "systems biology"
+  },
   {
     "rel_doi": "10.1101/2020.04.08.20057661",
     "rel_title": "Towards reduction in bias in epidemic curves due to outcome misclassification through Bayesian analysis of time-series of laboratory test results: Case study of COVID-19 in Alberta, Canada and Philadelphia, USA",
@@ -1548245,45 +1546910,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health systems and quality improvement"
   },
-  {
-    "rel_doi": "10.1101/2020.04.07.20053439",
-    "rel_title": "Modeling the impact of human mobility and travel restrictions on the potential spread of SARS-CoV-2 in Taiwan",
-    "rel_date": "2020-04-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20053439",
-    "rel_abs": "BackgroundAs COVID-19 continues to spread around the world, understanding how patterns of human mobility and connectivity affect outbreak dynamics, especially before outbreaks establish locally, is critical for informing response efforts. In Taiwan, most cases to date were imported or linked to imported cases.\n\nMethodsIn collaboration with Facebook Data for Good, we characterized changes in movement patterns in Taiwan since February 2020, and built metapopulation models that incorporate human movement data to identify the high risk areas of disease spread and assess the potential effects of local travel restrictions in Taiwan.\n\nResultsWe found that mobility changed with the number of local cases in Taiwan in the past few months. For each city, we identified the most highly connected areas that may serve as sources of importation during an outbreak. We showed that the risk of an outbreak in Taiwan is enhanced if initial infections occur around holidays. Intracity travel reductions have a higher impact on the risk of an outbreak than intercity travel reductions, while intercity travel reductions can narrow the scope of the outbreak and help target resources. The timing, duration, and level of travel reduction together determine the impact of travel reductions on the number of infections, and multiple combinations of these can result in similar impact.\n\nConclusionsTo prepare for the potential spread within Taiwan, we utilized Facebooks aggregated and anonymized movement and colocation data to identify cities with higher risk of infection and regional importation. We developed an interactive application that allows users to vary inputs and assumptions and shows the spatial spread of the disease and the impact of intercity and intracity travel reduction under different initial conditions. Our results can be used readily if local transmission occurs in Taiwan after relaxation of border control, providing important insights into future disease surveillance and policies for travel restrictions.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Meng-Chun Chang",
-        "author_inst": "National Tsing Hua University"
-      },
-      {
-        "author_name": "Rebecca Kahn",
-        "author_inst": "Harvard T.H. Chan School of Public Health"
-      },
-      {
-        "author_name": "Yu-An Li",
-        "author_inst": "National Tsing Hua University"
-      },
-      {
-        "author_name": "Cheng-Sheng Lee",
-        "author_inst": "National Tsing Hua University"
-      },
-      {
-        "author_name": "Caroline O Buckee",
-        "author_inst": "Harvard T.H. Chan School of Public Health"
-      },
-      {
-        "author_name": "Hsiao-Han Chang",
-        "author_inst": "National Tsing Hua University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.04.08.20056929",
     "rel_title": "Introductions and early spread of SARS-CoV-2 in the New York City area",
@@ -1548662,6 +1547288,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "intensive care and critical care medicine"
   },
+  {
+    "rel_doi": "10.1101/2020.04.08.20057588",
+    "rel_title": "On the corona infection model with contact restriction",
+    "rel_date": "2020-04-11",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20057588",
+    "rel_abs": "This article presents a mathematical infection model that is designed to estimate the course of coronavirus infection in Germany for several days in advance: How many people become ill or die, what is the temporal development? If the contact restriction is perfect, then the model predicts the development of the virus infection after the initial subsidence of the infection. However, since this restriction cannot always be strictly adhered to, the model is dynamically adapted to the development. This makes it possible to estimate the number of infected people, the number of new infections and deaths in Germany about a week in advance.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Juergen Mimkes",
+        "author_inst": "Paderborn University"
+      },
+      {
+        "author_name": "Rainer Janssen",
+        "author_inst": "Engineering Bureau Paderborn"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.04.08.20055095",
     "rel_title": "Prediction on Covid-19 epidemic for different countries: Focusing on South Asia under various precautionary measures",
@@ -1549427,53 +1548076,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.04.07.20056234",
-    "rel_title": "Clinical evaluation of a SARS-CoV-2 RT-PCR assay on a fully automated system for rapid on-demand testing in the hospital setting",
-    "rel_date": "2020-04-11",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20056234",
-    "rel_abs": "1BackgroundThe ongoing SARS-CoV-2 pandemic presents a unique challenge for diagnostic laboratories around the world. Automation of workflows in molecular diagnostics are instrumental for coping with the large number of tests ordered by clinicians, as well as providing fast-tracked rapid testing for highly urgent cases. In this study we evaluated a SARS-CoV-2 LDT for the NeuMoDx 96 system, a fully automated device performing extraction and real-time PCR.\n\nMethodsA publicly available SARS-CoV-2 RT-PCR assay was adapted for the automated system. Analytical performance was evaluated using in-vitro transcribed RNA and clinical performance was compared to the cobas 6800-based reference assay within the lab.\n\nResultsThe NeuMoDx-sarbeco-LDT displayed good analytical performance with an LoD of 95.55 cp/ml and no false positives during evaluation of cross-reactivity. A total of 176 patient samples were tested with both the Sarbeco-LDT and the reference assay. Positive and negative agreement were 100% and 99.2% respectively. Invalid-rate was 6.3%.\n\nConclusionThe NeuMoDx-sarbeco-LDT showed analytical and clinical performance comparable to the cobas6800-based reference assay. Due to its random-access workflow concept and rapid time-to-result of about 80 minutes, the device is very well suited for providing fast-tracked SARS-CoV-2 diagnostics for urgent clinical samples in the hospital setting.\n\nHighlightsO_LIA publicly available SARS-CoV-2 RT-PCR assay was adapted and evaluated on the open mode of the NeuMoDx 96 system (Qiagen)\nC_LIO_LIThe assay showed comparable analytical and clinical performance to the reference assay\nC_LIO_LIFast turn-around times (80 minutes) and random-access workflow of the system makes the assay well suited for urgent clinical samples.\nC_LI",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Dominik Noerz",
-        "author_inst": "University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene"
-      },
-      {
-        "author_name": "Nicole Fischer",
-        "author_inst": "University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene"
-      },
-      {
-        "author_name": "Alexander Schultze",
-        "author_inst": "University Medical Center Hamburg-Eppendorf, Department of Emergency Medicine"
-      },
-      {
-        "author_name": "Stefan Kluge",
-        "author_inst": "University Medical Center Hamburg-Eppendorf, Department of Intensive Care"
-      },
-      {
-        "author_name": "Ulrich Mayer-Runge",
-        "author_inst": "University Medical Center Hamburg-Eppendorf, Department of Emergency Medicine"
-      },
-      {
-        "author_name": "Martin Aepfelbacher",
-        "author_inst": "University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene"
-      },
-      {
-        "author_name": "Susanne Pfefferle",
-        "author_inst": "University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene"
-      },
-      {
-        "author_name": "Marc Luetgehetmann",
-        "author_inst": "University Medical Center Hamburg-Eppendorf, Institute of Medical Microbiology, Virology and Hygiene"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.04.08.20056861",
     "rel_title": "Epidemiological characteristics of COVID-19 cases in Italy and estimates of the reproductive numbers one month into the epidemic",
@@ -1549744,6 +1548346,61 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.06.20042580",
+    "rel_title": "Interferon-a2b treatment for COVID-19",
+    "rel_date": "2020-04-10",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.06.20042580",
+    "rel_abs": "BackgroundThe global pandemic of COVID-19 cases caused by infection with SARS-CoV-2 is ongoing, with no approved antiviral intervention. We describe here the effects of treatment with interferon-2b in a cohort of confirmed COVID-19 cases in Wuhan, China.\n\nMethodsIn this retrospective study, 77 adults hospitalized with confirmed COVID-19 were treated with either nebulized IFN-2b (5mU b.i.d.), arbidol (200mg t.i.d.) or a combination of IFN-2b plus arbidol. Serial SARS-CoV-2 testing along with hematological measurements, including cell counts and blood biochemistry, serum cytokine levels, temperature and blood oxygen saturation levels were recorded for each patient during their hospital stay.\n\nResultsTreatment with IFN-2b with or without arbidol significantly reduced the duration of detectable virus in the upper respiratory tract and in parallel reduced duration of elevated blood levels for the inflammatory markers IL-6 and CRP.\n\nConclusionThese findings suggest that IFN-2b should be further investigated as a therapy in COVID-19 cases.",
+    "rel_num_authors": 10,
+    "rel_authors": [
+      {
+        "author_name": "Qiong Zhou",
+        "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Xiao-Shan Wei",
+        "author_inst": "Union Hospital, Tongii Medical College,Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Xuan Xiang",
+        "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Xu Wang",
+        "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Zi-Hao Wang",
+        "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Virginia Chen",
+        "author_inst": "Prevention of Organ Failure (PROOF) Centre of Excellence  & University of British Columbia"
+      },
+      {
+        "author_name": "Casey P Shannon",
+        "author_inst": "Prevention of Organ Failure (PROOF) Centre of Excellence & University of British Columbia"
+      },
+      {
+        "author_name": "Scott J Tebbutt",
+        "author_inst": "Prevention of Organ Failure (PROOF) Centre of Excellence & University of British Columbia"
+      },
+      {
+        "author_name": "Tobias R Kollmann",
+        "author_inst": "Telethon Kids Institute Western Australia"
+      },
+      {
+        "author_name": "Eleanor N Fish",
+        "author_inst": "University Health Network & University of Toronto"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.04.07.20052142",
     "rel_title": "Spatial Correlation of Particulate Matter Pollution and Death Rate of COVID-19",
@@ -1550709,29 +1549366,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.07.20057075",
-    "rel_title": "A simple method to quantify country-specific effects of COVID-19 containment measures",
-    "rel_date": "2020-04-10",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20057075",
-    "rel_abs": "Most of the world is currently fighting to limit the impact of the COVID-19 pandemic. Italy, the Western country with most COVID-19 related deaths, was the first to implement drastic containment measures in early March, 2020. Since then most other European countries, the USA, Canada and Australia, have implemented similar restrictions, ranging from school closures, banning of recreational activities and large events, to complete lockdown. Such limitations, and softer promotion of social distancing, may be more effective in one society than in another due to cultural or political differences. It is therefore important to evaluate the effectiveness of these initiatives by analyzing country-specific COVID-19 data. We propose to model COVID-19 dynamics with a SIQR (susceptible - infectious - quarantined - recovered) model, since confirmed positive cases are isolated and do not transmit the disease. We provide an explicit formula that is easily implemented and permits us to fit official COVID-19 data in a series of Western countries. We found excellent agreement with data-driven estimation of the day-of-change in disease dynamics and the dates when official interventions were introduced. Our analysis predicts that for most countries only the more drastic restrictions have reduced virus spreading. Further, we predict that the number of unidentified COVID-19-positive individuals at the beginning of the epidemic is [~]10 times the number of confirmed cases. Our results provide important insight for future planning of non-pharmacological interventions aiming to contain spreading of COVID-19 and similar diseases.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Morten Gram Pedersen",
-        "author_inst": "Universita degli Studi di Padova"
-      },
-      {
-        "author_name": "Matteo Meneghini",
-        "author_inst": "University of Padova"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.04.08.031963",
     "rel_title": "BioLaboro: A bioinformatics system for detecting molecular assay signature erosion and designing new assays in response to emerging and reemerging pathogens",
@@ -1550942,6 +1549576,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
+  {
+    "rel_doi": "10.1101/2020.04.05.026377",
+    "rel_title": "On the interactions of the receptor-binding domain of SARS-CoV-1 and SARS-CoV-2 spike proteins with monoclonal antibodies and the receptor ACE2",
+    "rel_date": "2020-04-10",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.05.026377",
+    "rel_abs": "A new betacoronavirus named SARS-CoV-2 has emerged as a new threat to global health and economy. A promising target for both diagnosis and therapeutics treatments of the new disease named COVID-19 is the coronavirus (CoV) spike (S) glycoprotein. By constant-pH Monte Carlo simulations and the PROCEEDpKa method, we have mapped the electrostatic epitopes for four monoclonal antibodies and the angiotensin-converting enzyme 2 (ACE2) on both SARS-CoV-1 and the new SARS-CoV-2 S receptor binding domain (RBD) proteins. We also calculated free energy of interactions and shown that the S RBD proteins from both SARS viruses binds to ACE2 with similar affinities. However, the affinity between the S RBD protein from the new SARS-CoV-2 and ACE2 is higher than for any studied antibody previously found complexed with SARS-CoV-1. Based on physical chemical analysis and free energies estimates, we can shed some light on the involved molecular recognition processes, their clinical aspects, the implications for drug developments, and suggest structural modifications on the CR3022 antibody that would improve its binding affinities for SARS-CoV-2 and contribute to address the ongoing international health crisis.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Carolina Correa Giron",
+        "author_inst": "Universidade Federal do Triangulo Mineiro, Departamento de Saude Coletiva, Rua Vigario Carlos, 38025-350 - Uberaba - MG, Brazil"
+      },
+      {
+        "author_name": "Aatto Laaksonen",
+        "author_inst": "Department of Materials and Environmental Chemistry, Arrhenius Laboratory,  Stockholm University, SE-106 91 Stockholm, Sweden"
+      },
+      {
+        "author_name": "Fernando Luis Barroso da Silva",
+        "author_inst": "University of Sao Paulo"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "biophysics"
+  },
   {
     "rel_doi": "10.1101/2020.04.07.20056960",
     "rel_title": "Effects of latency on estimates of the COVID-19 replication number",
@@ -1552475,73 +1551136,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.07.024455",
-    "rel_title": "JAK1 inhibition blocks lethal sterile immune responses:implications for COVID-19 therapy",
-    "rel_date": "2020-04-09",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.07.024455",
-    "rel_abs": "Cytokine storms are drivers of pathology and mortality in myriad viral infections affecting the human population. In SARS-CoV-2-infected patients, the strength of the cytokine storm has been associated with increased risk of acute respiratory distress syndrome, myocardial damage, and death. However, the therapeutic value of attenuating the cytokine storm in COVID-19 remains to be defined. Here, we report results obtained using a novel mouse model of lethal sterile anti-viral immune responses. Using a mouse model of Down syndrome (DS) with a segmental duplication of a genomic region encoding four of the six interferon receptor genes (Ifnrs), we demonstrate that these animals overexpress Ifnrs and are hypersensitive to IFN stimulation. When challenged with viral mimetics that activate Toll-like receptor signaling and IFN anti-viral responses, these animals overproduce key cytokines, show exacerbated liver pathology, rapidly lose weight, and die. Importantly, the lethal immune hypersensitivity, accompanying cytokine storm, and liver hyperinflammation are blocked by treatment with a JAK1-specific inhibitor. Therefore, these results point to JAK1 inhibition as a potential strategy for attenuating the cytokine storm and consequent organ failure during overdrive immune responses. Additionally, these results indicate that people with DS, who carry an extra copy of the IFNR gene cluster encoded on chromosome 21, should be considered at high risk during the COVID-19 pandemic.\n\nOne Sentence SummaryInhibition of the JAK1 kinase prevents pathology and mortality caused by a rampant innate immune response in mice.",
-    "rel_num_authors": 13,
-    "rel_authors": [
-      {
-        "author_name": "Kathryn Tuttle",
-        "author_inst": "University of Colorado Anschutz Medical Campus"
-      },
-      {
-        "author_name": "Ross Minter",
-        "author_inst": "University of Colorado Anschutz Medical Campus"
-      },
-      {
-        "author_name": "Katherine Waugh",
-        "author_inst": "University of Colorado Anschutz Medical Campus"
-      },
-      {
-        "author_name": "Paula Araya",
-        "author_inst": "University of Colorado Anschutz Medical Campus"
-      },
-      {
-        "author_name": "Michael Ludwig",
-        "author_inst": "University of Colorado Anschutz Medical Campus"
-      },
-      {
-        "author_name": "Colin Sempeck",
-        "author_inst": "University of Colorado Anschutz Medical Campus"
-      },
-      {
-        "author_name": "Keith Smith",
-        "author_inst": "University of Colorado Anschutz Medical Campus"
-      },
-      {
-        "author_name": "Zdenek Andrysik",
-        "author_inst": "University of Colorado Anschutz Medical Campus"
-      },
-      {
-        "author_name": "Matthew Burchill",
-        "author_inst": "University of Colorado Anschutz Medical Campus"
-      },
-      {
-        "author_name": "Beth Tamburini",
-        "author_inst": "University of Colorado Anschutz Medical Campus"
-      },
-      {
-        "author_name": "David Orlicky",
-        "author_inst": "University of Colorado Anschutz Medical Campus"
-      },
-      {
-        "author_name": "Kelly D Sullivan",
-        "author_inst": "University of Colorado Anschutz Medical Campus"
-      },
-      {
-        "author_name": "Joaquin Espinosa",
-        "author_inst": "University of Colorado Anschutz Medical Campus"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2020.04.07.029884",
     "rel_title": "Immunoglobulin fragment F(ab')2 against RBD potently neutralizes SARS-CoV-2 in vitro",
@@ -1552940,6 +1551534,53 @@
     "type": "new results",
     "category": "immunology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.07.030650",
+    "rel_title": "The spatial and cell-type distribution of SARS-CoV-2 receptor ACE2 in human and mouse brain",
+    "rel_date": "2020-04-09",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.07.030650",
+    "rel_abs": "By engaging angiotensin-converting enzyme 2 (ACE2 or Ace2), the novel pathogenic SARS-coronavirus 2 (SARS-CoV-2) may invade host cells in many organs, including the brain. However, the distribution of ACE2 in the brain is still obscure. Here we investigated the ACE2 expression in the brain by analyzing data from publicly available brain transcriptome databases. According to our spatial distribution analysis, ACE2 was relatively highly expressed in some brain locations, such as the choroid plexus and paraventricular nuclei of the thalamus. According to cell-type distribution analysis, nuclear expression of ACE2 was found in many neurons (both excitatory and inhibitory neurons) and some non-neuron cells (mainly astrocytes, oligodendrocytes, and endothelial cells) in human middle temporal gyrus and posterior cingulate cortex. A few ACE2-expressing nuclei were found in a hippocampal dataset, and none were detected in the prefrontal cortex. Except for the additional high expression of Ace2 in the olfactory bulb areas for spatial distribution as well as in the pericytes and endothelial cells for cell-type distribution, the distribution of Ace2 in mouse brain was similar to that in the human brain. Thus, our results reveal an outline of ACE2/Ace2 distribution in the human and mouse brain, which indicates the brain infection of SARS-CoV-2 may be capable of inducing central nervous system symptoms in coronavirus disease 2019 (COVID-19) patients. Potential species differences should be considered when using mouse models to study the neurological effects of SARS-CoV-2 infection.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Rongrong Chen",
+        "author_inst": "Zhejiang Chinese Medical University"
+      },
+      {
+        "author_name": "Jie Yu",
+        "author_inst": "Zhejiang Chinese Medical University"
+      },
+      {
+        "author_name": "Keer Wang",
+        "author_inst": "Zhejiang Chinese Medical University"
+      },
+      {
+        "author_name": "Derek Howard",
+        "author_inst": "Centre for Addiction and Mental Health"
+      },
+      {
+        "author_name": "Leon French",
+        "author_inst": "Centre for Addiction and Mental Health"
+      },
+      {
+        "author_name": "Zhong Chen",
+        "author_inst": "Zhejiang Chinese Medical University"
+      },
+      {
+        "author_name": "Chengping Wen",
+        "author_inst": "Zhejiang Chinese Medical University"
+      },
+      {
+        "author_name": "Zhenghao Xu",
+        "author_inst": "Zhejiang Chinese Medical University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "neuroscience"
+  },
   {
     "rel_doi": "10.1101/2020.04.07.030445",
     "rel_title": "3D Models of glycosylated SARS-CoV-2 spike protein suggest challenges and opportunities for vaccine development",
@@ -1553996,37 +1552637,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.06.026476",
-    "rel_title": "Nelfinavir inhibits replication of severe acute respiratory syndrome coronavirus 2 in vitro.",
-    "rel_date": "2020-04-08",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.06.026476",
-    "rel_abs": "In December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, Hubei Province, China. No specific treatment has been established against coronavirus disease-2019 (COVID-19) so far. Therefore, it is urgently needed to identify effective antiviral agents for the treatment of this disease, and several approved drugs such as lopinavir have been evaluated. Here, we report that nelfinavir, an HIV-1 protease inhibitor, potently inhibits replication of SARS-CoV-2. The effective concentrations for 50% and 90% inhibition (EC50 and EC90) of nelfinavir were 1.13 {micro}M and 1.76 {micro}M respectively, the lowest of the nine HIV-1 protease inhibitors including lopinavir. The trough and peak serum concentrations of nelfinavir were three to six times higher than EC50 of this drug. These results suggest that nelfinavir is a potential candidate drug for the treatment of COVID-19 and should be assessed in patients with COVID-19.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Norio Yamamoto",
-        "author_inst": "Tokai University"
-      },
-      {
-        "author_name": "Shutoku Matsuyama",
-        "author_inst": "National Institute of Infectious Diseases"
-      },
-      {
-        "author_name": "Tyuji Hoshino",
-        "author_inst": "Chiba University"
-      },
-      {
-        "author_name": "Naoki Yamamoto",
-        "author_inst": "Tokyo Medical and Dental University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.04.06.20054320",
     "rel_title": "Derivation of the effective reproduction number R for COVID-19 in relation to mobility restrictions and confinement",
@@ -1554313,6 +1552923,53 @@
     "type": "new results",
     "category": "molecular biology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.03.20052548",
+    "rel_title": "Lack of Antiviral Activity of Darunavir against SARS-CoV-2",
+    "rel_date": "2020-04-08",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.03.20052548",
+    "rel_abs": "Given the high need and the absence of specific antivirals for treatment of COVID-19 (the disease caused by severe acute respiratory syndrome-associated coronavirus-2 [SARS-CoV-2]), human immunodeficiency virus (HIV) protease inhibitors are being considered as therapeutic alternatives. Prezcobix/Rezolsta is a fixed-dose combination of 800 mg of the HIV protease inhibitor darunavir (DRV) and 150 mg cobicistat, a CYP3A4 inhibitor, which is indicated in combination with other antiretroviral agents for the treatment of HIV infection. There are currently no definitive data on the safety and efficacy of DRV/cobicistat for treatment of COVID-19. The in vitro antiviral activity of darunavir against a clinical isolate from a patient infected with SARS-CoV-2 was assessed. DRV showed no activity against SARS-CoV-2 at clinically relevant concentrations (EC50 >100 M). Remdesivir, used as a positive control, showed potent antiviral activity (EC50 = 0.38 M). Overall, the data do not support the use of DRV for treatment of COVID-19.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Sandra De Meyer",
+        "author_inst": "Janssen Pharmaceutica"
+      },
+      {
+        "author_name": "Denisa Bojkova",
+        "author_inst": "Institute of Medical Virology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany"
+      },
+      {
+        "author_name": "Jindrich Cinati",
+        "author_inst": "Institute of Medical Virology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany"
+      },
+      {
+        "author_name": "Ellen Van Damme",
+        "author_inst": "Janssen Pharmaceutica NV, Beerse, Belgium"
+      },
+      {
+        "author_name": "Christophe Buyck",
+        "author_inst": "Janssen Pharmaceutica NV, Beerse, Belgium"
+      },
+      {
+        "author_name": "Marnix Van Loock",
+        "author_inst": "Janssen Pharmaceutica NV, Beerse, Belgium"
+      },
+      {
+        "author_name": "Brian Woodfall",
+        "author_inst": "Janssen Biopharma Inc, South San Francisco, CA, USA"
+      },
+      {
+        "author_name": "Sandra Ciesek",
+        "author_inst": "Institute of Medical Virology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany; German Center for Infection Research (DZIF), Frankf"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.04.06.028811",
     "rel_title": "The Potential Use of Unprocessed Sample for RT-qPCR Detection of COVID-19 without an RNA Extraction Step",
@@ -1555346,41 +1554003,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "rheumatology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.06.20045393",
-    "rel_title": "Sudden hyposmia as a prevalent symptom of COVID-19 infection.",
-    "rel_date": "2020-04-07",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.06.20045393",
-    "rel_abs": "Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has recently caused a pandemic that has involved Italy as the second worldwide nation in terms of infected patients and deaths. The clinical manifestation of Covid-19 ranges from asymptomatic carrier status to severe pneumonia. Asymptomatic individuals in Covid-19 are those who are carriers of the virus but do not show clinical symptoms and are able to transmit the disease in the same degree as symptomatic carriers. In order to contain contagions is of supreme importance to identify asymptomatic patients because this subpopulation is one of the main factors contributing to the spread of this disease. We report on six Italian patients with COVID-19 who presented sudden hyposmia as the only or most prominent disease manifestation, without upper or lower respiratory tract involvement or other major features of the disease. A supra-threshold olfaction test confirmed the hyposmia in all patients. The onset of hyposmia during a Covid-19 outbreak should be considered as a warning sign of an infection that requires a diagnostic test for Covid-19",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Rosario Marchese-Ragona",
-        "author_inst": "University of Padova, Department of Neurosciences, Otolaryingology section"
-      },
-      {
-        "author_name": "Giancarlo Ottaviano",
-        "author_inst": "University of Padova, Department of Neurosciences, Otolaryingology section"
-      },
-      {
-        "author_name": "Piero Nicolai",
-        "author_inst": "Department of Neurosciences, Otolaryngology section"
-      },
-      {
-        "author_name": "Andrea Vianello",
-        "author_inst": "Department of Cardiological, Thoracic and Vascular Sciences, Respiratory Pathophysiology Unit, University of Padua, Padua, Italy"
-      },
-      {
-        "author_name": "Miryam Carecchio",
-        "author_inst": "University of Padova, Department of Neurosciences, section ofNeurology"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "otolaryngology"
-  },
   {
     "rel_doi": "10.1101/2020.04.03.20047175",
     "rel_title": "Corona Epidemic in Indian context: Predictive Mathematical Modelling",
@@ -1555627,6 +1554249,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.02.20050914",
+    "rel_title": "A statistical method of batch screening entrying population from abroad by stages and groups in COVID-19 nucleic acid testing",
+    "rel_date": "2020-04-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20050914",
+    "rel_abs": "PurposeTo screen for COVID-19 patients in immigration using minimal nucleic acid testing (NAT).\n\nMethodsIn the first phase, nasopharyngeal swab samples from the inbound population were numbered and grouped. The samples in the group were mixed together, and a NAT test was performed. When the test result is negative, it means that everyone in the group is not infected and the screening of the group is complete. When the test results were positive, the group moved on to the second stage. In the second stage, all samples in the positive group will be tested individually for NAT.\n\nResultsThe advantages and considerations of the method are discussed. Prevalence in the incoming population was a determinant of the sample size within the group. The lower the incidence, the larger the sample size within the group, the higher the savings in NAT and testing costs.\n\nConclusionThis method has significant efficiency and cost advantages in COVID-19 screening. It can also be used to screen other populations, such as community populations and people at high risk of infection, etc.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Cheng Yuan yuan",
+        "author_inst": "Henan University Huaihe hospital"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.04.02.20050153",
     "rel_title": "CoViD19 Meta heuristicoptimization based forecast methodon time dependent bootstrappeddata",
@@ -1556560,29 +1555201,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
-  {
-    "rel_doi": "10.1101/2020.04.05.20054627",
-    "rel_title": "Investigating the likely association between genetic ancestry and COVID-19 manifestation",
-    "rel_date": "2020-04-07",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.05.20054627",
-    "rel_abs": "BackgroundThe novel coronavirus: severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread rapidly throughout the world leading to catastrophic consequences. However, SARS-CoV-2 infection has shown discernible variability across the globe. While in some countries people are recovering relatively quickly, in others, recovery times have been comparatively longer and number of individuals succumbing to it are high. This variability in coronavirus disease 2019 (COVID-19) susceptibility is suggestive of a likely association between the genetic-make up of affected individuals modulated by their ancestry and the severity of COVID-19 manifestations.\n\nObjectiveIn this study, we aimed to evaluate the potential association between an individuals genetic ancestry and the extent of COVID-19 disease presentation employing Europeans as the case study. In addition, using a genome wide association (GWAS) approach we sought to discern the putative single nucleotide polymorphism (SNP) markers and genes that may be likely associated with differential COVID-19 manifestations by comparative analyses of the European and East Asian genomes.\n\nMethodTo this end, we employed 10,215 ancient and modern genomes across the globe assessing 597,573 SNPs obtained from the databank of Dr. David Reich, Harvard Medical School, USA to evaluate the likely correlation between European ancestry and COVID-19 manifestations. Ancestry proportions were determined using qpAdm program implemented in AdmixTools v5.1. Pearsons correlation coefficient (r) between various ancestry proportions of European genomes and COVID-19 death/recovery ratio was calculated and its significance was statistically evaluated. Genome wide association study (GWAS) was performed in PLINK v1.9 to investigate SNPs with significant allele frequency variations among European and East Asian genomes that likely correlated with differential COVID-19 infectivity.\n\nResultsWe found significant positive correlation (r=0.58, P=0.03) between West European hunter gatherers (WHG) ancestral fractions and COVID-19 death/recovery ratio for data as of 5th April 2020. This association discernibly amplified (r=0.77, P=0.009) upon reanalyses based on data as of 30th June 2020, removing countries with small sample sizes and adding those that are a bridge between Europe and Asia. Using GWAS we further identified 404 immune response related SNPs by comparing publicly available 753 genomes from various European countries against 838 genomes from various Eastern Asian countries. Prominently, we identified that SNPs associated with immune-system related pathways such as interferon stimulated antiviral response, adaptive and innate immune system and IL-6 dependent immune responses show significant differences in allele frequencies [Chi square values ([&ge;]1500; P{approx}0)] between Europeans and East Asians.\n\nConclusionSo far, to the best of our knowledge, this is the first study investigating the likely association between host genetic ancestry and COVID-19 severity. These findings improve our overall understanding of the putative genetic modifiers of COVID-19 clinical presentation. We note that the development of effective therapeutics will benefit immensely from more detailed analyses of individual genomic sequence data from COVID-19 patients of varied ancestries.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Ranajit Das",
-        "author_inst": "Yenepoya (Deemed to be University)"
-      },
-      {
-        "author_name": "Sudeep D Ghate",
-        "author_inst": "Yenepoya Research Centre, Yenepoya (Deemed to be University)"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health informatics"
-  },
   {
     "rel_doi": "10.1101/2020.04.04.20053058",
     "rel_title": "Indoor transmission of SARS-CoV-2",
@@ -1556845,6 +1555463,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.04.20053629",
+    "rel_title": "Association of COVID-19 Infections in San Francisco in Early March 2020 with Travel to New York and Europe",
+    "rel_date": "2020-04-07",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.04.20053629",
+    "rel_abs": "Real-time dissemination of epidemiological survey data from positive COVID-19 cases is critical to support efforts to contain or reduce spread of viral infection in the community. Here we detected a significant association between domestic travel or travel to Europe and the identification of new cases in San Francisco, California, USA. These findings suggest that domestic and European travelers may need to be prioritized for evaluation of acute infection from COVID-19 in the setting of limited testing capacity.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Wei Gu",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Kevin Reyes",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Elaine Hsu",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Steve Miller",
+        "author_inst": "University of California, San Francisco"
+      },
+      {
+        "author_name": "Charles Y Chiu",
+        "author_inst": "University of California, San Francisco"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.04.04.20053637",
     "rel_title": "Estimate of the development of the epidemic reproduction number Rt from Coronavirus SARS-CoV-2 case data and implications for political measures based on prognostics",
@@ -1557878,25 +1556531,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.03.30.20048082",
-    "rel_title": "Partial unlock model for COVID-19 or similar pandemic averts medical and economic disaster",
-    "rel_date": "2020-04-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.30.20048082",
-    "rel_abs": "Data as of March 29, 2020 show that the \"flattening\" strategy for COVID-19 in the U.S. is working so well that a clean removal of social distancing (aka \"unlock\") at any time in 2020 will produce a renewed catastrophe, overloading the healthcare system. Leaving the economy locked down for a long time is its own catastrophe. An SIR-type model with clear parameters suitable for public information, and both tracking and predictive capabilities which \"learns\" disease spread characteristics rapidly as policy changes, suggests that a solution to the problem is a partial unlock. Case load can be managed so as not to exceed critical resources such as ventilators, yet allow enough people to get sick that herd immunity develops and a full unlock can be achieved in as little as five weeks from beginning of implementation. The partial unlock could be for example 3 full working days per week. Given that not all areas or individuals will respond, and travel and public gatherings are still unlikely, the partial unlock might be 5 full working days per week. The model can be regionalized easily, and by expediting the resolution of the pandemic in the U.S. medical equipment and volunteers, many of them with already acquired immunity, can be made available to other countries.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Robert L Shuler",
-        "author_inst": "Shuler Research (former NASA JSC)"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.04.02.20051334",
     "rel_title": "Rapid implementation of mobile technology for real-time epidemiology of COVID-19",
@@ -1558279,6 +1556913,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.02.20051680",
+    "rel_title": "COVID-19 epidemic: Power law spread and flattening of the curve",
+    "rel_date": "2020-04-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20051680",
+    "rel_abs": "In this paper, we analyze the real-time infection data of COVID-19 epidemic for nine nations. Our analysis is up to 7 April 2020. For China and South Korea, who have already flattened their infection curves, the number of infected individuals (I(t)) exhibits power-law behavior before flattening of the curve. Italy has transitioned to the power-law regime for some time. For the other six nations--USA, Spain, Germany, France, Japan, and India--a power-law regime is beginning to appear after exponential growth. We argue that the transition from an exponential regime to a power-law regime may act as an indicator for flattening of the epidemic curve. We also argue that long-term community transmission and/or the transmission by asymptomatic carriers traveling long distances may be inducing the power-law growth of the epidemic.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Mahendra K. Verma",
+        "author_inst": "I. I. T.  Kanpur"
+      },
+      {
+        "author_name": "Ali Asad",
+        "author_inst": "I. I. T. Kanpur"
+      },
+      {
+        "author_name": "Soumyadeep Chatterjee",
+        "author_inst": "I. I. T. Kanpur"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.04.03.20051821",
     "rel_title": "Predicting clinical needs derived from the COVID-19 pandemic: the case of Spain",
@@ -1559252,65 +1557913,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.04.02.20049676",
-    "rel_title": "Public perspectives on social distancing and other protective measures in Europe: a cross-sectional survey study during the COVID-19 pandemic",
-    "rel_date": "2020-04-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20049676",
-    "rel_abs": "ObjectivesThe extent to which people implement government-issued protective measures is critical in preventing further spread of coronavirus disease 2019 (COVID-19) caused by coronavirus SARS-CoV-2. Our study aimed to evaluate the public belief in the effectiveness of protective measures, the reported implementation of these measures in daily life, and to identify communication channels used to acquire relevant information on COVID-19 in European countries.\n\nDesignA cross-sectional online survey available in multiple languages was disseminated on social media starting March 19th, 2020. After five days, we computed descriptive statistics for countries with more than 500 respondents. Each day, we compiled and categorized community containment measures enacted in each country by stringency (stage I-IV). Response collection continued for one week to explore possible dynamics as containment strategies intensified.\n\nParticipantsIn total, 9,796 adults responded, of whom 8,611 resided in the Netherlands (stage III), 604 in Germany (stage III), and 581 in Italy (stage IV). An additional 1,365 respondents completed the survey in the following week.\n\nResultsParticipants indicated support for governmental measures related to avoiding social gatherings, selective closure of public places, and hand hygiene and respiratory measures (range for all measures: 95.0%-99.7%). Respondents from the Netherlands were less likely to consider a complete social lockdown effective (59.2%), compared to respondents in Germany (76.6%) or Italy (87.2%). Italian residents did not only apply enforced social distancing measures more frequently (range: 90.2%-99.3%, German and Dutch residents: 67.5%-97.0%), but also self-initiated hygienic and social distancing behaviors (range: 36.3%-96.6%, German and Dutch residents: 28.3%-95.7%). Respondents largely reported being sufficiently informed about the COVID-19 outbreak and about behaviors to avoid infection (range across countries: 90.2%-91.1%). Information channels most commonly reported included television (range: 53.0%-82.0%), newspapers (range: 31.0%-63.0%), official health websites (range: 39.0%-54.1%), and social media (range: 40.0%-55.8%). We observed no major changes in answers over time.\n\nConclusionsIn European countries, the degree of public belief in the effectiveness of protective measures was high and residents reported to be sufficiently informed by various communication channels. In March 2020, implementation of enacted and self-initiated measures differed between countries and were highest among Italian respondents, who were subjected to the most elaborate measures of social lockdown and greatest COVID-19 burden in Europe.",
-    "rel_num_authors": 11,
-    "rel_authors": [
-      {
-        "author_name": "Karien Meier",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Toivo Glatz",
-        "author_inst": "Charite - Universitatsmedizin Berlin"
-      },
-      {
-        "author_name": "Mathijs C Guijt",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Marco Piccininni",
-        "author_inst": "Charite - Universitatsmedizin Berlin"
-      },
-      {
-        "author_name": "Merel van der Meulen",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Khaled Atmar",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Anne-Tess C Jolink",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "Tobias Kurth",
-        "author_inst": "Charite - Universitatsmedizin Berlin"
-      },
-      {
-        "author_name": "Jessica L Rohmann",
-        "author_inst": "Charite - Universitatsmedizin Berlin"
-      },
-      {
-        "author_name": "Amir H Zamanipoor Najafabadi",
-        "author_inst": "Leiden University Medical Center"
-      },
-      {
-        "author_name": "on behalf of the COVID-19 Survey Study group",
-        "author_inst": ""
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.04.02.20050351",
     "rel_title": "Capacities and predicted demands of Brazil's health system in view of the novel coronavirus disease outbreak",
@@ -1559521,6 +1558123,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.04.02.20050955",
+    "rel_title": "Reduction of lymphocyte at early stage elevates severity and death risk of COVID-19 patients: a hospital-based case-cohort study",
+    "rel_date": "2020-04-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20050955",
+    "rel_abs": "Background and objectiveSevere acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-induced coronavirus disease 2019 (COVID-19) has been pandemic worldwide. Several reports observed a reduction of lymphocytes among COVID-19 patients. However, clinical significance of lymphocyte reduction in COVID-19 patients remains unclear. The objective of this study was to analyze the association between lymphocyte reduction at early stage and the prognosis of COVID-19 patients.\n\nMethodsAll 192 hospitalized patients with COVID-19 were enrolled. Electronic medical records, including demographic data, clinical characteristics, comorbidities and exposure history, were collected. Biochemical indexes on admission and chest computed tomography (CT) were detected. Patients prognosis was followed up.\n\nResultsOn admission, 84 (43.8%) patients suffered from lymphocyte reduction among COVID-19 patients. The count and percentage of lymphocytes on admission were lower among more than seventy-year-old patients than those of younger patients. Multivariate logistic regression revealed that older age was a risk factor of lymphocyte reduction. Of interest, chest CT score, a key marker of lung injury, was increased among COVID-19 patients with lymphocyte reduction. By contrast, PaCO2, SpO2 and oxygenation index, several respiratory function markers, were decreased in COVID-19 patients with lymphocyte reduction. Moreover, TBIL and DBIL, two markers of hepatic injury, creatinine and urea nitrogen, two indices of renal function, and creatine kinase, AST and LDH, three myocardial enzymes, were elevated in COVID-19 patients with lymphocyte reduction. Among 84 COVID-19 patients with lymphocyte reduction, 32.1% died. Fatality rate was obviously higher in COVID-19 patients with lymphocyte reduction than those with normal lymphocyte (RR=5.789, P<0.001).\n\nConclusionOlder COVID-19 patients are more susceptible to lymphocyte reduction. Lymphocyte reduction at early stage aggravates the severity of multiple organ injuries and elevates death risk of COVID-19 patients.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Jun Fei",
+        "author_inst": "Anhui Medical University"
+      },
+      {
+        "author_name": "Lin Fu",
+        "author_inst": "Anhui Medical University"
+      },
+      {
+        "author_name": "Ying Li",
+        "author_inst": "Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Hui-Xian Xiang",
+        "author_inst": "Anhui Medical University"
+      },
+      {
+        "author_name": "Ying Xiang",
+        "author_inst": "Anhui Medical University"
+      },
+      {
+        "author_name": "Meng-Die Li",
+        "author_inst": "Anhui Medical University"
+      },
+      {
+        "author_name": "Fang-Fang Liu",
+        "author_inst": "Anhui Medical University"
+      },
+      {
+        "author_name": "De-xiang Xu",
+        "author_inst": "Anhui Medical University"
+      },
+      {
+        "author_name": "Hui Zhao",
+        "author_inst": "Anhui Medical University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.04.02.20050674",
     "rel_title": "Dynamics of COVID-19 epidemics: SEIR models underestimate peak infection rates and overestimateepidemic duration",
@@ -1560346,41 +1558999,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.03.30.20047787",
-    "rel_title": "Automatic X-ray COVID-19 Lung Image Classification System based on Multi-Level Thresholding and Support Vector Machine",
-    "rel_date": "2020-04-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.30.20047787",
-    "rel_abs": "The early detection of SARS-CoV-2, the causative agent of (COVID-19) is now a critical task for the clinical practitioners. The COVID-19 spread is announced as pandemic outbreak between people worldwide by WHO since 11/ March/ 2020. In this consequence, it is top critical priority to become aware of the infected people so that prevention procedures can be processed to minimize the COVID-19 spread and to begin early medical health care of those infected persons. In this paper, the deep studying based totally methodology is usually recommended for the detection of COVID-19 infected patients using X-ray images. The help vector gadget classifies the corona affected X-ray images from others through usage of the deep features. The technique is useful for the clinical practitioners for early detection of COVID-19 infected patients. The suggested system of multi-level thresholding plus SVM presented high accuracy in classification of the infected lung with Covid-19. All images were of the same size and stored in JPEG format with 512 * 512 pixels. The average sensitivity, specificity, and accuracy of the lung classification using the proposed model results were 95.76%, 99.7%, and 97.48%, respectively.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Aboul Ella Hassanien Sr.",
-        "author_inst": "Cairo University"
-      },
-      {
-        "author_name": "Lamia Nabil Mahdy Jr.",
-        "author_inst": "Higher Technological Institute, Biomedical Engineering Department"
-      },
-      {
-        "author_name": "Kadry Ali Ezzat Jr.",
-        "author_inst": "Higher Technological Institute, Biomedical Engineering Department"
-      },
-      {
-        "author_name": "Haytham H. Elmousalami Jr.",
-        "author_inst": "Scientific Research Group in Egypt (SRGE), Egypt"
-      },
-      {
-        "author_name": "Hassan Aboul Ella Jr.",
-        "author_inst": "Faculty of Veterinary medicine, Cairo University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health informatics"
-  },
   {
     "rel_doi": "10.1101/2020.04.02.20050468",
     "rel_title": "Using network science to propose strategies for effectively dealing with pandemics: The COVID-19 example",
@@ -1560607,6 +1559225,85 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
+  {
+    "rel_doi": "10.1101/2020.04.03.20051722",
+    "rel_title": "Urinalysis, but not blood biochemistry, detects the early renal-impairment in patients with COVID-19",
+    "rel_date": "2020-04-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.03.20051722",
+    "rel_abs": "BackgroundIn December 2019, a novel coronavirus (SARS-CoV-2) caused infectious disease, termed COVID-19, outbroke in Wuhan, China. COVID-19 patients manifested as lung injury with complications in other organs, such as liver, heart, gastrointestinal tract, especially for severe cases. However, whether COVID-19 causes significant acute kidney injury (AKI) remained controversial.\n\nMethodsWe retrospectively analyzed the clinical characteristics, urine and blood routine tests and other laboratory parameters of hospitalized COVID-19 patients in Wuhan Union Hospital.\n\nFindings178 patients, admitted to Wuhan Union hospital from February 02 to February 29, 2020, were included in this study. No patient (0 [0%]) presented increased serum creatinine (Scr), and 5 (2.8%) patients showed increased blood urea nitrogen (BUN), indicating few cases with \"kidney dysfunction\". However,for patients (83) with no history of kidney disease who received routine urine test upon hospitalization, 45 (54.2%) patients displayed abnormality in urinalysis, such as proteinuria, hematuria and leukocyturia, while none of the patients was recorded to have acute kidney injury (AKI) throughout the study. Meanwhile, the patients with abnormal urinalysis usually had worse disease progression reflecting by laboratory parameters presentations, including markers of liver injury, inflammation, and coagulation.\n\nConclusionMany patients manifested by abnormal urinalysis on admission, including proteinuria or hematuria. Our results revealed that urinalysis is better in unveiling potential kidney impairment of COVID-19 patients than blood chemistry test and urinalysis could be used to reflect and predict the disease severity. We therefore recommend pay more attention in urinalysis and kidney impairment in COVID-19 patients.",
+    "rel_num_authors": 16,
+    "rel_authors": [
+      {
+        "author_name": "Haifeng zhou Jr.",
+        "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Zili Zhang Jr.",
+        "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Heng Fan Sr.",
+        "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Junyi Li Jr.",
+        "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Mingyue Li Jr.",
+        "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Yalan Dong Jr.",
+        "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Weina Guo Jr.",
+        "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Lan Lin Jr.",
+        "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Zhenyu Kang Jr.",
+        "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Ting Yu Jr.",
+        "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Chunxia Tian Jr.",
+        "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Yang Gui Jr.",
+        "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Renjie Qin Jr.",
+        "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Haijun Wang Sr.",
+        "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "ShanShan Luo Sr.",
+        "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Desheng Hu",
+        "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "urology"
+  },
   {
     "rel_doi": "10.1101/2020.04.03.20047977",
     "rel_title": "ACE2 variants underlie interindividual variability and susceptibility to COVID-19 in Italian population",
@@ -1561676,93 +1560373,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.04.04.020925",
-    "rel_title": "Atazanavir inhibits SARS-CoV-2 replication and pro-inflammatory cytokine production",
-    "rel_date": "2020-04-05",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.04.020925",
-    "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is already responsible for far more deaths than previous pathogenic coronaviruses (CoVs) from 2002 and 2012. The identification of clinically approved drugs to be repurposed to combat 2019 CoV disease (COVID-19) would allow the rapid implementation of potentially life-saving procedures. The major protease (Mpro) of SARS-CoV-2 is considered a promising target, based on previous results from related CoVs with lopinavir (LPV), an HIV protease inhibitor. However, limited evidence exists for other clinically approved antiretroviral protease inhibitors, such as atazanavir (ATV). ATV is of high interest because of its bioavailability within the respiratory tract. Our results show that ATV could dock in the active site of SARS-CoV-2 Mpro, with greater strength than LPV. ATV blocked Mpro activity. We confirmed that ATV inhibits SARS-CoV-2 replication, alone or in combination with ritonavir (RTV) in Vero cells, human pulmonary epithelial cell line and primary monocytes, impairing virus-induced enhancement of IL-6 and TNF- levels. Together, our data strongly suggest that ATV and ATV/RTV should be considered among the candidate repurposed drugs undergoing clinical trials in the fight against COVID-19.",
-    "rel_num_authors": 18,
-    "rel_authors": [
-      {
-        "author_name": "Natalia Fintelman-Rodrigues",
-        "author_inst": "Fiocruz"
-      },
-      {
-        "author_name": "Carolina Q Sacramento",
-        "author_inst": "Fiocruz"
-      },
-      {
-        "author_name": "Carlyle Ribeiro Lima",
-        "author_inst": "Fiocruz"
-      },
-      {
-        "author_name": "Franklin Souza da Silva",
-        "author_inst": "Fiocruz"
-      },
-      {
-        "author_name": "Andre Ferreira",
-        "author_inst": "Fiocruz"
-      },
-      {
-        "author_name": "Mayara Mattos",
-        "author_inst": "Fiocruz"
-      },
-      {
-        "author_name": "Caroline S. de Freitas",
-        "author_inst": "Fiocruz"
-      },
-      {
-        "author_name": "Vinicius Cardoso Soares",
-        "author_inst": "Fiocruz"
-      },
-      {
-        "author_name": "Suelen da Silva Gomes Dias",
-        "author_inst": "Fiocruz"
-      },
-      {
-        "author_name": "Jairo R. Temerozo",
-        "author_inst": "Fiocruz"
-      },
-      {
-        "author_name": "Milene Miranda",
-        "author_inst": "Fiocruz"
-      },
-      {
-        "author_name": "Aline R. Matos",
-        "author_inst": "Fiocruz"
-      },
-      {
-        "author_name": "Fernando A Bozza",
-        "author_inst": "Fiocruz"
-      },
-      {
-        "author_name": "Nicolas Carels",
-        "author_inst": "Fiocruz"
-      },
-      {
-        "author_name": "Carlos Roberto Alves",
-        "author_inst": "Fiocruz"
-      },
-      {
-        "author_name": "Marilda M Siqueira",
-        "author_inst": "Fiocruz"
-      },
-      {
-        "author_name": "Patricia T. Bozza",
-        "author_inst": "Fiocruz"
-      },
-      {
-        "author_name": "Thiago Moreno L. Souza",
-        "author_inst": "Fiocruz"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.04.02.021469",
     "rel_title": "LY6E Restricts the Entry of Human Coronaviruses, including the currently pandemic SARS-CoV-2",
@@ -1562009,6 +1560619,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.04.01.20041186",
+    "rel_title": "Countrywide quarantine only mildly increased anxiety level during COVID-19 outbreak in China",
+    "rel_date": "2020-04-04",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.01.20041186",
+    "rel_abs": "In the recent outbreak of COVID-19, many countries have taken various kinds of quarantine measures to slow down the explosive spreading of COVID-19. Although these measures were proven to be successful in stopping the outbreak in China, the potential adverse effects of countrywide quarantine have not been thoroughly investigated. In this study, we performed an online survey to evaluate the psychological effects of quarantine in China using Zung Self-rating Anxiety Scale in February 2020 when the outbreak was nearly peaked in China. Along with the anxiety scores, limited personal information such as age, gender, region, education, occupation and specifically, the type and duration of quarantine were collected for analysis. For a total number of 992 valid questionnaires, clinical significance of anxiety symptoms was observed in 9.58% respondents according to clinical diagnostic standards in China. Statistical results showed population with different age, education level, health status and personnel category responded differently. Other characteristics such as gender, marital status, region, and acquaintance with suspected or confirmed cases of COVID-19 did not affect anxiety levels significantly. Respondents experienced different forms of quarantine showed different anxiety levels. Unexpectedly, longer durations of quarantine did not lead to significant increase of anxiety level. Our results suggest a rather mild psychological influence caused by the countrywide quarantine during COVID-19 outbreak in China and provided reference for other countries and regions to battle COVID-19.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Wei Hu",
+        "author_inst": "Xuzhou Oriental People's Hospital"
+      },
+      {
+        "author_name": "Li Su",
+        "author_inst": "Institute of Psychology, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Juan Qiao",
+        "author_inst": "Xuzhou Oriental People's Hospital"
+      },
+      {
+        "author_name": "Jing Zhu",
+        "author_inst": "Xuzhou Oriental People's Hospital"
+      },
+      {
+        "author_name": "Yi Zhou",
+        "author_inst": "Army Medical University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.03.30.20044545",
     "rel_title": "A Mini Review on Current Clinical and Research Findings for Children Suffering from COVID-19",
@@ -1563058,33 +1561703,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.03.31.20049122",
-    "rel_title": "Globalized low-income countries may experience higher COVID-19 mortality rates",
-    "rel_date": "2020-04-03",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.31.20049122",
-    "rel_abs": "Understanding the factors underpinning COVID-19 infection and mortality rates is essential in order to implement actions that help mitigate the current pandemic. Here we evaluate how a suit of 15 climatic and socio-economic variables influence COVID-19 exponential growth-phase infection and mortality rates across 36 countries. We found that imports of goods and services, international tourism and the number of published scientific papers are good predictors of COVID-19 infection rates, indicating that more globalized countries may have experienced multiple and recurrent introductions of the virus. However, high-income countries showed lower mortality rates, suggesting that the consequences of the current pandemic will be worse for globalized low-income countries. International aid agencies could use this information to help mitigate the consequences of the current pandemic in the most vulnerable countries.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Rodolfo Jaffe",
-        "author_inst": "Instituto Tecnologico Vale"
-      },
-      {
-        "author_name": "Mabel Patricia Ortiz Vera",
-        "author_inst": "Instituto Tecnologico Vale"
-      },
-      {
-        "author_name": "Klaus Jaffe",
-        "author_inst": "Universidad Simon Bolivar"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.03.31.20049304",
     "rel_title": "COVID-19 infection during pregnancy: a systematic review to summarize possible symptoms, treatments, and pregnancy outcomes",
@@ -1563339,6 +1561957,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.04.01.20050526",
+    "rel_title": "Meteorological factors correlate with transmission of 2019-nCoV: Proof of incidence of novel coronavirus pneumonia in Hubei Province, China",
+    "rel_date": "2020-04-03",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.01.20050526",
+    "rel_abs": "Objectivemany potential factors contribute to the outbreak of COVID-19.It aims to explore the effects of various meteorological factors on the incidence of COVID-19.\n\nMethodsTaking Hubei province of China as an example, where COVID-19 was first reported and there were the most cases, we collected 53 days of confirmed cases (total 67773 cases) and ten meteorological parameters up to March 10. Correlation analysis and linear regression were used to judge the relationship of meteorological factors and increment of COVID-19 confirmed cases.\n\nResultsUnder 95% CI, the increment of confirmed cases in Hubei were correlated with four meteorological parameters of average pressure, average temperature, minimum temperature and average water vapor pressure (equivalent to absolute humidity).The average pressure was positively correlated with the increment (r=+0.358).The negative correlations included average temperature (r=-0.306), minimum temperature (r=-0.347), and average water vapor pressure (r=-0.326). The linear regression results show if minimum temperature increases by 1{square}, the incremental confirmed cases in Hubei decreases by 72.470 units on average.\n\nConclusionStatistically, the incidence of COVID-19 was correlated with average pressure, average temperature, minimum temperature and average water vapor pressure. It is positively correlated with the average pressure and negatively correlated with the other three parameters. Compared with relative humidity, 2019-nCov is more sensitive to water vapor pressure. The reason why the epidemic situation in Hubei expanded rapidly is significantly related to the climate characteristics of low temperature and dryness of Hubei in winter.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Jianfeng Li",
+        "author_inst": "Beijing Municipal Institute of Labour Protections, Beijing Academy of Science and Technology"
+      },
+      {
+        "author_name": "Linyuan Zhang",
+        "author_inst": "National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Zhihua Ren",
+        "author_inst": "National Meteorological Information Center, China Meteorological Administration Meteorological Data Center"
+      },
+      {
+        "author_name": "Caihong Xing",
+        "author_inst": "National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Peihuan Qiao",
+        "author_inst": "National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention"
+      },
+      {
+        "author_name": "Bing Chang",
+        "author_inst": "National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.04.01.20050542",
     "rel_title": "Using ILI surveillance to estimate state-specific case detection rates and forecast SARS-CoV-2 spread in the United States",
@@ -1564164,33 +1562821,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.03.30.20043919",
-    "rel_title": "Population based estimates of comorbidities affecting risk for complications from COVID-19 in the US",
-    "rel_date": "2020-04-02",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.30.20043919",
-    "rel_abs": "We used 2017 Behavioral Risk Factor Surveillance System (BRFSS) data (N=444,649) to estimate the proportion of US adults who report comorbidities that suggest heightened risk of complications from COVID-19. Co-morbidities included cardiovascular disease, chronic obstructive pulmonary disease (COPD), diabetes, asthma, hypertension, and/or cancer other than skin, based on data from China. Overall 45.4% (95% CI 45.1-45.7) of adults reported any of the 6 comorbidities, increasing from 19.8% (19.1-20.4) for ages 18-29 years to 80.7% (79.5-81.8) for ages 80+ years. State rates ranged from 37.3% (36.2-38.5) in Utah to 58.7% (57.0-60.4) in West Virginia. Rates also varied by race/ethnicity, health insurance status, and employment. Excluded were residents of nursing homes or assisted living facilities. Although almost certainly an underestimate of all adults at risk due to these exclusions, these results should help in estimating healthcare needs for adults with COVID-19 complications living in the community.\n\nArticle Summary LineOverall, 45.4% of US adults were estimated to be at heightened risk of COVID-19 complications due to co-morbidities, increasing from 19.8% for ages 18-29 years to 80.7% for ages 80+ years, with state-to-state variation.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Mary L Adams",
-        "author_inst": "On Target Health Data LLC"
-      },
-      {
-        "author_name": "David L Katz",
-        "author_inst": "Yale-Griffin Prevention Research Center"
-      },
-      {
-        "author_name": "Joseph Grandpre",
-        "author_inst": "Wyoming Department of Health"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.03.30.20047688",
     "rel_title": "Growth rate and acceleration analysis of the COVID-19 pandemic reveals the effect of public health measures in real time",
@@ -1564485,6 +1563115,85 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2020.03.31.019216",
+    "rel_title": "Virus-host interactome and proteomic survey of PMBCs from COVID-19 patients reveal potential virulence factors influencing SARS-CoV-2 pathogenesis",
+    "rel_date": "2020-04-02",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.31.019216",
+    "rel_abs": "The ongoing coronavirus disease (COVID-19) pandemic caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a global public health concern due to relatively easy person-to-person transmission and the current lack of effective antiviral therapy. However, the exact molecular mechanisms of SARS-CoV-2 pathogenesis remain largely unknown. We exploited an integrated proteomics approach to systematically investigate intra-viral and virus-host interactomes for the identification of unrealized SARS-CoV-2 host targets and participation of cellular proteins in the response to viral infection using peripheral blood mononuclear cells (PBMCs) isolated from COVID-19 patients. Using this approach, we elucidated 251 host proteins targeted by SARS-CoV-2 and more than 200 host proteins that are significantly perturbed in COVID-19 derived PBMCs. From the interactome, we further identified that non-structural protein nsp9 and nsp10 interact with NKRF, a NF-[Kcy]B repressor, and may precipitate the strong IL-8/IL-6 mediated chemotaxis of neutrophils and overexuberant host inflammatory response observed in COVID-19 patients. Our integrative study not only presents a systematic examination of SARS-CoV-2-induced perturbation of host targets and cellular networks to reflect disease etiology, but also reveals insights into the mechanisms by which SARS-CoV-2 triggers cytokine storms and represents a powerful resource in the quest for therapeutic intervention.",
+    "rel_num_authors": 16,
+    "rel_authors": [
+      {
+        "author_name": "Qiming Liang",
+        "author_inst": "Shanghai Jiao Tong University School of Medicine"
+      },
+      {
+        "author_name": "Jingjiao Li",
+        "author_inst": "Shanghai Jiao Tong University School of Medicine"
+      },
+      {
+        "author_name": "Mingquan Guo",
+        "author_inst": "Shanghai Public Health Clinical Center, Fudan University,"
+      },
+      {
+        "author_name": "Xiaoxu Tian",
+        "author_inst": "Shanghai Advanced Research Institute, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Chengrong Liu",
+        "author_inst": "Shanghai Jiao Tong University School of Medicine"
+      },
+      {
+        "author_name": "Xin Wang",
+        "author_inst": "Shanghai Jiao Tong University School of Medicine"
+      },
+      {
+        "author_name": "Xing Yang",
+        "author_inst": "Shanghai Jiao Tong University School of Medicine"
+      },
+      {
+        "author_name": "Ping Wu",
+        "author_inst": "Shanghai Advanced Research Institute, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Zixuan Xiao",
+        "author_inst": "University of Alberta, Canada"
+      },
+      {
+        "author_name": "Yafei Qu",
+        "author_inst": "Shanghai Jiao Tong University School of Medicine"
+      },
+      {
+        "author_name": "Yue Yin",
+        "author_inst": "Shanghai Advanced Research Institute, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Joyce Fu",
+        "author_inst": "University of California, Riverside"
+      },
+      {
+        "author_name": "Zhaoqin Zhu",
+        "author_inst": "Shanghai Public Health Clinical Center, Fudan University"
+      },
+      {
+        "author_name": "Zhenshan Liu",
+        "author_inst": "Shanghai Jiao Tong University School of Medicine"
+      },
+      {
+        "author_name": "Chao Peng",
+        "author_inst": "Shanghai Advanced Research Institute, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Tongyu Zhu",
+        "author_inst": "Shanghai Public Health Clinical Center, Fudan University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2020.03.31.013268",
     "rel_title": "SARS-CoV-2 receptor and entry genes are expressed by sustentacular cells in the human olfactory neuroepithelium",
@@ -1565398,29 +1564107,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "pharmacology and therapeutics"
   },
-  {
-    "rel_doi": "10.1101/2020.03.30.20048207",
-    "rel_title": "Impact of COVID-19 on psychiatric assessment in emergency and outpatient settings measured using electronic health records",
-    "rel_date": "2020-04-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.30.20048207",
-    "rel_abs": "Key PointsO_ST_ABSQuestionC_ST_ABSHow did documentation of psychiatric symptoms in outpatient and emergency room settings change with onset of COVID-19 infection in Eastern Massachusetts?\n\nFindingsIn this cohort study spanning 2 academic medical centers and 3 community hospitals, prevalence of narrative notes referencing depression or anxiety decreased 75-81% in outpatient settings following onset of coronavirus in March 2019, and by 44-45% in emergency departments.\n\nMeaningThe observation that documentation of psychiatric symptoms declined sharply with increasing coronavirus infection in Massachusetts, even as prevalence of such symptoms is anticipated to increase, suggests additional efforts may be required to address these symptoms in the context of COVID-19.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Victor M. Castro",
-        "author_inst": "Massachusetts General Hospital"
-      },
-      {
-        "author_name": "Roy H Perlis",
-        "author_inst": "Massachusetts General Hospital"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "psychiatry and clinical psychology"
-  },
   {
     "rel_doi": "10.1101/2020.03.29.20046490",
     "rel_title": "Early surveillance and public health emergency disposal measures between novel coronavirus disease 2019 and avian influenza in China: a case-comparison study",
@@ -1565611,6 +1564297,25 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
+  {
+    "rel_doi": "10.1101/2020.03.27.20045062",
+    "rel_title": "How lethal is the novel coronavirus, and how many undetected cases there are? The importance of being tested.",
+    "rel_date": "2020-04-01",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.27.20045062",
+    "rel_abs": "There is big concern for estimating the lethality and the extent of undetected infections associated with the novel coronavirus SARS-CoV2 outbreak. While detailed epidemiological models are certainly needed, I suggest here an orthogonal approach based on a minimum number of parameters robustly fitted from the cumulative data easily accessible for all countries at the John Hopkins University database that became the worldwide reference for the pandemics. I show that, after few days from the beginning of the outbreak, the apparent death rate can be extrapolated to infinite time through regularized regression such as rescaled ridge regression. The variation from country to country of these extrapolated death rates appears to depend almost only (r2 = 0.91) on the ratio between performed tests and detected cases even when the apparent instantaneous lethality rates are as different as 9% in Italy and 0.4% in Germany. Extrapolating to the limit of infinite number of tests, I obtain a death rate of 0.012 {+/-} 0.012, in agreement with other estimates. The inverse relationship between the extrapolated death rate and the intensity tests allows estimating that more than 50% of cases were undetected in most countries, with more than 90% undetected cases in countries severely hit by the epidemics such as Italy. Finally, I propose to adopt the ratio between the cumulative number of recovered and deceased persons as an indicator that can anticipate the halting of the epidemics.",
+    "rel_num_authors": 1,
+    "rel_authors": [
+      {
+        "author_name": "Ugo Bastolla",
+        "author_inst": "CSIC"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.03.29.20046862",
     "rel_title": "Stochastic Compartmental Modelling of SARS-CoV-2 with Approximate Bayesian Computation",
@@ -1566500,29 +1565205,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.03.28.20046094",
-    "rel_title": "Determination of daily reproduction numbers of SARS-CoV2 based on death cases suggests more rapid initial spread in Italy and the United States",
-    "rel_date": "2020-03-31",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.28.20046094",
-    "rel_abs": "Population density, behaviour and cultural habits strongly influence the spread of pathogens. Consequently, key epidemiological parameters may vary from country to country. Confirmed COVID-19 cases in in China have been used to estimate those parameters, that vary largely (reviewed in 1). The estimates also depend on testing frequency and case definitions that are prone to change during ongoing epidemics, providing additional uncertainties. The rise in fatal cases due to SARS-CoV2 could be a more reliable parameter, since missing of deaths is less likely. In the absence of changes in the management of severe COVID-19 cases, the rise in death cases should be proportional to the rise in virus infections. Although the fluctuating low numbers of fatal cases very early in the epidemic may lead to some uncertainty, more than 100 deaths per day are reported since 10.03.2020 in Italy and since 21.03.2020 in the US. Therefore, the dynamics of deaths were analysed to estimate the daily reproduction numbers (Rt) and the effectiveness of control measures.\n\nThus, our analysis provides evidence that basic epidemiological parameters differ between countries to an extent compromising epidemiological predictions of the pandemic. It also suggests that suppression of spread in Italy and the US may be more difficult to achieve. Although we assume that variations in social behaviour are responsible for the different estimates of R0, selection of more rapidly spreading variants of SARS-CoV-2 cannot be excluded. Despite uncertainty in the reliability of the data used and lack of information on possible changes in the effectiveness of registration of COVID-19 deaths during the observation period, our findings should be considered as a working hypothesis demanding further investigations. As the number of deaths rapidly increases worldwide, we encourage more sophisticated modelling of the epidemic based on the dynamics of death cases by experts in the field.",
-    "rel_num_authors": 2,
-    "rel_authors": [
-      {
-        "author_name": "Armin Ensser",
-        "author_inst": "Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg FAU"
-      },
-      {
-        "author_name": "Klaus Ueberla",
-        "author_inst": "Institute of Clinical and Molecular Virology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg FAU"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.03.26.20044610",
     "rel_title": "The diagnostic evaluation of Convolutional NeuralNetwork (CNN) for the assessment of chest X-ray ofpatients infected with COVID-19",
@@ -1566844,6 +1565526,33 @@
     "type": "new results",
     "category": "cell biology"
   },
+  {
+    "rel_doi": "10.1101/2020.03.28.013607",
+    "rel_title": "Computational Design of Peptides to Block Binding of the SARS-CoV-2 Spike Protein to Human ACE2",
+    "rel_date": "2020-03-31",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.28.013607",
+    "rel_abs": "The outbreak of COVID-19 has now become a global pandemic and it continues to spread rapidly worldwide, severely threatening lives and economic stability. Making the problem worse, there is no specific antiviral drug that can be used to treat COVID-19 to date. SARS-CoV-2 initiates its entry into human cells by binding to angiotensin-converting enzyme 2 (hACE2) via the receptor binding domain (RBD) of its spike protein. Therefore, molecules that can block SARS-CoV-2 from binding to hACE2 may potentially prevent the virus from entering human cells and serve as an effective antiviral drug. Based on this idea, we designed a series of peptides that can strongly bind to SARS-CoV-2 RBD in computational experiments. Specifically, we first constructed a 31-mer peptidic scaffold by linking two fragments grafted from hACE2 (a.a. 22-44 and 351-357) with a linker glycine, and then redesigned the peptide sequence to enhance its binding affinity to SARS-CoV-2 RBD. Compared with several computational studies that failed to identify that SARS-CoV-2 shows higher binding affinity for hACE2 than SARS-CoV, our protein design scoring function, EvoEF2, makes a correct identification, which is consistent with the recently reported experimental data, implying its high accuracy. The top designed peptide binders exhibited much stronger binding potency to hACE2 than the wild-type (-53.35 vs. -46.46 EvoEF2 energy unit for design and wild-type, respectively). The extensive and detailed computational analyses support the high reasonability of the designed binders, which not only recapitulated the critical native binding interactions but also introduced new favorable interactions to enhance binding. Due to the urgent situation created by COVID-19, we share these computational data to the community, which should be helpful to develop potential antiviral peptide drugs to combat this pandemic.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Xiaoqiang Huang",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Robin Pearce",
+        "author_inst": "University of Michigan"
+      },
+      {
+        "author_name": "Yang Zhang",
+        "author_inst": "University of Michigan"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "bioinformatics"
+  },
   {
     "rel_doi": "10.1101/2020.03.29.013342",
     "rel_title": "A one-enzyme RT-qPCR assay for SARS-CoV-2, and procedures for reagent production",
@@ -1568009,49 +1566718,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.03.27.20043836",
-    "rel_title": "A considerable proportion of individuals with asymptomatic SARS-CoV-2 infection in Tibetan population",
-    "rel_date": "2020-03-30",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.27.20043836",
-    "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) quickly became a major epidemic threat in the whole China. We analysed SARS-Cov-2 infected cases from Tibetan Autonomous Prefecture, and noted divergent characteristics of these Tibetans infected cases compared to Han Chinese, characterizing by a considerable proportion of asymptomatic carriers (21.7%), and few symptomatic patients with initial symptom of fever (7.7%). Here, we did a descriptive study on clinical characteristics of 18 asymptomatic individuals with SARS-CoV-2 infection. The median age of these asymptomatic carriers was 31 years and one third of them were students, aged under 20 years. Notably, some of asymptomatic carriers had recognizable changes in radiological and laboratory indexes. Our finding indicates a potentially big number of SARS-CoV-2 asymptomatic carriers in prevalent area, highlighting a necessity of screening individuals with close contact of infected patients, for a better control on the spread of SARS-CoV-2 infection.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Huan Song",
-        "author_inst": "West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China"
-      },
-      {
-        "author_name": "Jun Xiao",
-        "author_inst": "Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University"
-      },
-      {
-        "author_name": "Jiajun Qiu",
-        "author_inst": "West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China"
-      },
-      {
-        "author_name": "Jin Yin",
-        "author_inst": "West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China"
-      },
-      {
-        "author_name": "Huazhen Yang",
-        "author_inst": "West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China"
-      },
-      {
-        "author_name": "Rui Shi",
-        "author_inst": "Department of orthopedics, West China Hospital, Sichuan University"
-      },
-      {
-        "author_name": "Wei Zhang",
-        "author_inst": "West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.03.26.20043943",
     "rel_title": "A Multi-hospital Study in Wuhan, China\uff1aProtective Effects of Non-menopause and Female Hormones on SARS-CoV-2 infection",
@@ -1568474,6 +1567140,85 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
+  {
+    "rel_doi": "10.1101/2020.03.27.20045757",
+    "rel_title": "Changing transmission dynamics of COVID-19 in China: a nationwide population-based piecewise mathematical modelling study",
+    "rel_date": "2020-03-30",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.27.20045757",
+    "rel_abs": "BackgroundThe first case of COVID-19 atypical pneumonia was reported in Wuhan, China on December 1, 2019. Since then, at least 33 other countries have been affected and there is a possibility of a global outbreak. A tremendous amount of effort has been made to understand its transmission dynamics; however, the temporal and spatial transmission heterogeneity and changing epidemiology have been mostly ignored. The epidemic mechanism of COVID-19 remains largely unclear.\n\nMethodsEpidemiological data on COVID-19 in China and daily population movement data from Wuhan to other cities were obtained and analyzed. To describe the transmission dynamics of COVID-19 at different spatio-temporal scales, we used a three-stage continuous-time Susceptible-Exposed-Infectious-Recovered (SEIR) meta-population model based on the characteristics and transmission dynamics of each stage: 1) local epidemic from December 1, 2019 to January 9, 2020; 2) long-distance spread due to the Spring Festival travel rush from January 10 to 22, 2020; and 3) intra-provincial transmission from January 23, 2020 when travel restrictions were imposed. Together with the basic reproduction number (R0) for mathematical modelling, we also considered the variation in infectivity and introduced the controlled reproduction number (Rc) by assuming that exposed individuals to be infectious; we then simulated the future spread of COVID across Wuhan and all the provinces in mainland China. In addition, we built a novel source tracing algorithm to infer the initial exposed number of individuals in Wuhan on January 10, 2020, to estimate the number of infections early during this epidemic.\n\nFindingsThe spatial patterns of disease spread were heterogeneous. The estimated controlled reproduction number (Rc) in the neighboring provinces of Hubei province were relatively large, and the nationwide reproduction number - except for Hubei - ranged from 0.98 to 2.74 with an average of 1.79 (95% CI 1.77-1.80). Infectivity was significantly greater for exposed than infectious individuals, and exposed individuals were predicted to have become the major source of infection after January 23. For the epidemic process, most provinces reached their epidemic peak before February 10, 2020. It is expected that the maximum number of infections will be approached by the end of March. The final infectious size is estimated to be about 58,000 for Wuhan, 20,800 for the rest of Hubei province, and 17,000 for the other provinces in mainland China. Moreover, the estimated number of the exposed individuals is much greater than the officially reported number of infectious individuals in Wuhan on January 10, 2020.\n\nInterpretationThe transmission dynamics of COVID-19 have been changing over time and were heterogeneous across regions. There was a substantial underestimation of the number of exposed individuals in Wuhan early in the epidemic, and the Spring Festival travel rush played an important role in enhancing and accelerating the spread of COVID-19. However, Chinas unprecedented large-scale travel restrictions quickly reduced Rc. The next challenge for the control of COVID-19 will be the second great population movement brought by removing these travel restrictions.",
+    "rel_num_authors": 16,
+    "rel_authors": [
+      {
+        "author_name": "Jiawen Hou",
+        "author_inst": "Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China; Centre for Computational Systems Biology and Rese"
+      },
+      {
+        "author_name": "Jie Hong",
+        "author_inst": "Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai 200032, China; Key Laboratory of Public Health Safety, Min"
+      },
+      {
+        "author_name": "Boyun Ji",
+        "author_inst": "School of Mathematical Sciences and Shanghai Center for Mathematical Sciences, Fudan University, Shanghai 200433, China"
+      },
+      {
+        "author_name": "Bowen Dong",
+        "author_inst": "School of Mathematical Sciences and Shanghai Center for Mathematical Sciences, Fudan University, Shanghai 200433, China"
+      },
+      {
+        "author_name": "Yue Chen",
+        "author_inst": "Department of Epidemiology and Community Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Rd, Ottawa, Ontario, Canada"
+      },
+      {
+        "author_name": "Michael P Ward",
+        "author_inst": "Faculty of Veterinary Science, The University of Sydney NSW, Sydney, Australia"
+      },
+      {
+        "author_name": "Wei Tu",
+        "author_inst": "Department of Geology and Geography, Georgia Southern University, Statesboro, GA 30460, USA"
+      },
+      {
+        "author_name": "Zhen Jin",
+        "author_inst": "Complex Systems Research Center, Shanxi University, Taiyuan, Shan'xi 030006"
+      },
+      {
+        "author_name": "Jian Hu",
+        "author_inst": "Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai 200032, China; Key Laboratory of Public Health Safety, Min"
+      },
+      {
+        "author_name": "Qing Su",
+        "author_inst": "Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai 200032, China; Key Laboratory of Public Health Safety, Min"
+      },
+      {
+        "author_name": "Wenge Wang",
+        "author_inst": "Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai 200032, China; Key Laboratory of Public Health Safety, Min"
+      },
+      {
+        "author_name": "Zheng Zhao",
+        "author_inst": "Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai 200032, China; Key Laboratory of Public Health Safety, Min"
+      },
+      {
+        "author_name": "Shuang Xiao",
+        "author_inst": "Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai 200032, China; Key Laboratory of Public Health Safety, Min"
+      },
+      {
+        "author_name": "Jiaqi Huang",
+        "author_inst": "Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai 200032, China; Key Laboratory of Public Health Safety, Min"
+      },
+      {
+        "author_name": "Wei Lin",
+        "author_inst": "School of Mathematical Sciences and Shanghai Center for Mathematical Sciences, Fudan University, Shanghai 200433, China"
+      },
+      {
+        "author_name": "Zhijie Zhang",
+        "author_inst": "Department of Epidemiology and Health Statistics, School of Public Health, Fudan University, Shanghai 200032, China; Key Laboratory of Public Health Safety, Min"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.03.23.20041350",
     "rel_title": "Genetic Profiles in Pharmacogenes Indicate Personalized Drug Therapy for COVID-19",
@@ -1569327,49 +1568072,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
-  {
-    "rel_doi": "10.1101/2020.03.26.20044883",
-    "rel_title": "Diagnostic Indexes of a Rapid IgG/IgM Combined Antibody Test for SARS-CoV-2",
-    "rel_date": "2020-03-30",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044883",
-    "rel_abs": "[Abstract]O_ST_ABSObjectiveC_ST_ABSCoronavirus disease 2019 (COVID-19) has become pandemic in the world. The need for IgG-IgM combined antibody test is booming, but data on diagnostic indexes evaluation was inadequate. The aim of this study was to evaluate diagnostic indexes of a rapid IgG-IgM combined antibody test for SARS-CoV-2.\n\nMethodsA total of 179 patients were enrolled. Serum were collected for IgG-IgM combined antibody test and corresponding nasal and pharyngeal swab specimens were collected for SARS-CoV-2 RT-PCR. According to SARS-CoV-2 RT-PCR results, patients under study were categorized as PCR positive group in 90 patients and PCR negative group in 89 patients.\n\nResults1. Of the 90 PCR positive samples, 77 were tested positive by SARS-CoV-2 IgG-IgM test kit, yielding a sensitivity of 85.6%. Meanwhile, of the 89 PCR negative sample, 8 samples were detected positive, resulting in a specificity of 91%. Positive predictive value, negative predictive value and accuracy of this test kit was 95.1%, 82.7%, and 88.3%, respectively. Kappa efficiency between IgG/IgM test kit and RT-PCR were 0.75. 2. Accuracy in mild/common and severe/critical subgroup were 73.9% and 97.7%, respectively. Accuracy in clinical confirmed, suspected cases and other disease subgroups were 70%, 60%, and 100%, respectively. 3. Patients were further divided into  0 - 7,  8 - 15 and  >= 16 groups according to the time from illness onset to sample collection. Sensitivity, specificity and accuracy in these three groups were 18.8%, 77.8% and 40%; 100%, 50% and 87.5%; 100%, 64.3%, and 93.9, respectively.\n\nConclusionThe sensitivity and specificity of this ease-of-use IgG/IgM combined test kit were adequate, plus short turnaround time, no specific requirements for additional equipment or skilled technicians, all of these collectively contributed to its competence for mass testing. At the current stage, it cannot take the place of SARA-CoV-2 nucleic acid RT-PCR, but can be served as a complementary option for RT-PCR. The combination of RT-PCR and IgG-IgM combined test kit could provide further insight into SARS-CoV-2 infection diagnosis.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Ying Liu",
-        "author_inst": "General Hospital of Central Theater Command"
-      },
-      {
-        "author_name": "Yueping Liu",
-        "author_inst": "General Hospital of Central Theater Command"
-      },
-      {
-        "author_name": "Bo Diao",
-        "author_inst": "General Hospital of Central Theater Command"
-      },
-      {
-        "author_name": "Feifei Ren",
-        "author_inst": "General Hospital of Central Theater Command"
-      },
-      {
-        "author_name": "Yue Wang",
-        "author_inst": "General Hospital of Central Theater Command"
-      },
-      {
-        "author_name": "Jinya Ding",
-        "author_inst": "General Hospital of Central Theater Command"
-      },
-      {
-        "author_name": "Qianchuan Huang",
-        "author_inst": "General Hospital of Central Theater Command"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.03.24.20042374",
     "rel_title": "What is required to prevent a second major outbreak of the novel coronavirus SARS-CoV-2 upon lifting the metropolitan-wide quarantine of Wuhan city, China",
@@ -1569612,6 +1568314,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.03.27.20045005",
+    "rel_title": "A modified SEIR model to predict the COVID-19 outbreak in Spain: simulating control scenarios and multi-scale epidemics",
+    "rel_date": "2020-03-30",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.27.20045005",
+    "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWAfter the spread of SARS-CoV-2 epidemic out of China, evolution in the pandemic worldwide shows dramatic differences among countries. In Europe, the situation of Italy first and later Spain has generated great concern, and despite other countries show better prospects, large uncertainties yet remain on the future evolution and the efficacy of containment, mitigation or attack strategies. Here we applied a modified SEIR compartmental model accounting for the spread of infection during the latent period, in which we also incorporate effects of varying proportions of containment. We fit data to quarantined populations in order to account for the uncertainties in case reporting and study the scenario projections for the 17 individual regions (CCAA). Results indicate that with data for March 23, the epidemics follows an evolution similar to the isolation of 1, 5 percent of the population and if there were no effects of intervention actions it might reach a maximum over 1.4M infected around April27. The effect on the epidemics of the ongoing partial confinement measures is yet unknown (an update of results with data until March 31st is included), but increasing the isolation around ten times more could drastically reduce the peak to over 100k cases by early April, while each day of delay in taking this hard containment scenario represents an 90 percent increase of the infected population at the peak. Dynamics at the sub aggregated levels of CCAA show epidemics at the different levels of progression with the most worrying situation in Madrid an Catalonia. Increasing alpha values up to 10 times, in addition to a drastic reduction in clinical cases, would also more than halve the number of deaths. Updates for March 31st simulations indicate a substantial reduction in burden is underway. A similar approach conducted for Italy pre- and post-interventions also begins to suggest substantial reduction in both infected and deaths has been achieved, showing the efficacy of drastic social distancing interventions.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Leonardo R Lopez",
+        "author_inst": "Barcelona Institute for Global Health"
+      },
+      {
+        "author_name": "Xavier Rodo",
+        "author_inst": "Barcelona Institute for Global Health"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.03.27.20045237",
     "rel_title": "Dynamic Modeling to Identify Mitigation Strategies for Covid-19 Pandemic",
@@ -1570701,37 +1569426,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
-  {
-    "rel_doi": "10.1101/2020.03.26.20044263",
-    "rel_title": "An Evaluation of the Vulnerable Physician Workforce in the United States During the Coronavirus Disease-19 Pandemic",
-    "rel_date": "2020-03-30",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044263",
-    "rel_abs": "BackgroundThe coronavirus disease-19 (COVID-19) pandemic threatens to overwhelm the healthcare resources of the country, but also poses a personal hazard to healthcare workers, including physicians. To address the potential impact of excluding physicians with a high risk of adverse outcomes based on age, we evaluated the current patterns of age of licensed physicians across the United States.\n\nMethodsWe compiled information from the 2018 database of actively licensed physicians in the Federation of State Medical Boards (FSMB) across the US. Both at a national- and the state-level, we assessed the number and proportion of physicians who would be at an elevated risk due to age over 60 years.\n\nResultsOf the 985,026 licensed physicians in the US, 235857 or 23.9% were aged 25-40 years, 447052 or 45.4% are 40-60 years, 191794 or 19.5% were 60-70 years, and 106121 or 10.8% were 70 years or older. Age was not reported in 4202 or 0.4% of physicians. Overall, 297915 or 30.2% of physicians were 60 years of age or older, 246167 (25.0%) 65 years and older, and 106121 (10.8%) 70 years or older. States in the US reported that a median 5470 licensed physicians (interquartile range [IQR], 2394 to 10108) were 60 years of age or older. Notably, states of North Dakota (n=1180) and Vermont (n = 1215) had the lowest and California (n=50786) and New York (n=31582) the highest number of physicians over the age of 60 years (Figure 1). Across states, the median proportion of physicians aged 60 years and older was 28.9% (IQR, 27.2%, 31.4%), and ranged between 25.9% for Nebraska to 32.6% for New Mexico (Figure 2).\n\nDiscussionOlder physicians represent a large proportion of the US physician workforce, particularly in states with the worst COVID-19 outbreak. Therefore, their exclusion from patient care will be impractical. Optimizing care practices by limiting direct patient contact of physicians vulnerable to adverse outcomes from COVID-19, potentially by expanding their participation in telehealth may be a strategy to protect them.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Rohan Khera",
-        "author_inst": "UT Southwestern Medical Center"
-      },
-      {
-        "author_name": "Lovedeep Singh Dhingra",
-        "author_inst": "All India Institute of Medical Sciences"
-      },
-      {
-        "author_name": "Snigdha Jain",
-        "author_inst": "University of Texas Southwestern Medical Center"
-      },
-      {
-        "author_name": "Harlan Krumholz",
-        "author_inst": "Yale University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "health policy"
-  },
   {
     "rel_doi": "10.1101/2020.03.25.20043331",
     "rel_title": "A Machine Learning Model Reveals Older Age and Delayed Hospitalization as Predictors of Mortality in Patients with COVID-19",
@@ -1571010,6 +1569704,65 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2020.03.26.20043042",
+    "rel_title": "Analysis and Prediction of False Negative Results for SARS-CoV-2 Detection with Pharyngeal Swab Specimen in COVID-19 Patients: A Retrospective Study",
+    "rel_date": "2020-03-30",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20043042",
+    "rel_abs": "BackgroundFalse negative results of SARS-CoV-2 nucleic acid detection pose threats to COVID-19 patients and medical workers alike.\n\nObjectiveTo develop multivariate models to determine clinical characteristics that contribute to false negative results of SARS-CoV-2 nucleic acid detection, and use them to predict false negative results as well as time windows for testing positive.\n\nDesignRetrospective Cohort Study (Ethics number of Tongji Hospital: No. IRBID: TJ-20200320)\n\nSettingA database of outpatients in Tongji Hospital (University Hospital) from 15 January 2020 to 19 February 2020.\n\nPatients1,324 outpatients with COVID-19\n\nMeasurementsClinical information on CT imaging reports, blood routine tests, and clinic symptoms were collected. A multivariate logistic regression was used to explain and predict false negative testing results of SARS-CoV-2 detection. A multivariate accelerated failure model was used to analyze and predict delayed time windows for testing positive.\n\nResultsOf the 1,324 outpatients who diagnosed of COVID-19, 633 patients tested positive in their first SARS-CoV-2 nucleic acid test (47.8%), with a mean age of 51 years (SD=14.9); the rest, which had a mean age of 47 years (SD=15.4), tested negative in the first test. \"Ground glass opacity\" in a CT imaging report was associated with a lower chance of false negatives (aOR, 0.56), and reduced the length of time window for testing positive by 26%. \"Consolidation\" was associated with a higher chance of false negatives (aOR, 1.57), and extended the length of time window for testing positive by 44%. In blood routine tests, basophils (aOR, 1.28) and eosinophils (aOR, 1.29) were associated with a higher chance of false negatives, and were found to extend the time window for testing positive by 23% and 41%, respectively. Age and gender also affected the significantly.\n\nLimitationData were generated in a large single-center study.\n\nConclusionTesting outcome and positive window of SARS-CoV-2 detection for COVID-19 patients were associated with CT imaging results, blood routine tests, and clinical symptoms. Taking into account relevant information in CT imaging reports, blood routine tests, and clinical symptoms helped reduce a false negative testing outcome. The predictive AFT model, what we believe to be one of the first statistical models for predicting time window of SARS-CoV-2 detection, could help clinicians improve the accuracy and efficiency of the diagnosis, and hence, optimizes the timing of nucleic acid detection and alleviates the shortage of nucleic acid detection kits around the world.\n\nPrimary Funding SourceNone.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Hui Xu",
+        "author_inst": "Department of Anesthesiology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China"
+      },
+      {
+        "author_name": "Li Yan",
+        "author_inst": "Department of Emergency, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China"
+      },
+      {
+        "author_name": "Chun (Martin) Qiu",
+        "author_inst": "Lazaridis School, Wilfrid Laurier University, Waterloo, Ontario"
+      },
+      {
+        "author_name": "Bo Jiao",
+        "author_inst": "Department of Anesthesiology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China"
+      },
+      {
+        "author_name": "Yanyan Chen",
+        "author_inst": "Department of Information Management, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Xi Tan",
+        "author_inst": "Department of Anesthesiology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China"
+      },
+      {
+        "author_name": "Zhuo Chen",
+        "author_inst": "Outpatient department office,Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology"
+      },
+      {
+        "author_name": "Ling Ai",
+        "author_inst": "Department of Anesthesiology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China"
+      },
+      {
+        "author_name": "Yaru Xiao",
+        "author_inst": "Department of Emergency, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China"
+      },
+      {
+        "author_name": "Ailin Luo",
+        "author_inst": "Department of Anesthesiology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China"
+      },
+      {
+        "author_name": "Shusheng Li",
+        "author_inst": "Department of Emergency, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.03.29.014415",
     "rel_title": "Flocked swab might be one main reason causing the high false-negative rate in COVID-19 screening----the advantages of a novel silicone swab",
@@ -1571987,25 +1570740,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "public and global health"
   },
-  {
-    "rel_doi": "10.1101/2020.03.26.20044644",
-    "rel_title": "Doubling time tells how effective Covid-19 prevention works",
-    "rel_date": "2020-03-30",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044644",
-    "rel_abs": "Covid-19 (coronavirus disease 2019) is a rapidly spreading pandemic in many countries. The total confirmed cases of Covid-19 are exponentially increasing and many countries are fighting Covid-19 with all strategies. However, there is still lacking consensus for effective strategies. Here, I demonstrate the time dependence of the doubling time in the Covid-19 exponential growths. Tracking the time-dependent doubling time tells how well Covid-19 prevention works, giving an index for successful fighting.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Byung Mook Weon",
-        "author_inst": "Sungkyunkwan University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.03.28.20044578",
     "rel_title": "Government Responses Matter: Predicting Covid-19 cases in US under an empirical Bayesian time series framework",
@@ -1572284,6 +1571018,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "occupational and environmental health"
   },
+  {
+    "rel_doi": "10.1101/2020.03.26.20044214",
+    "rel_title": "Projecting the Spread of COVID19 for Germany",
+    "rel_date": "2020-03-30",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044214",
+    "rel_abs": "We model the evolution of the number of individuals that are reported to be sick with COVID-19 in Germany. Our theoretical framework builds on a continuous time Markov chain with four states: healthy without infection, sick, healthy after recovery or after infection but without symptoms and dead. Our quantitative solution matches the number of sick individuals up to the most recent observation and ends with a share of sick individuals following from infection rates and sickness probabilities. We employ this framework to study inter alia the expected peak of the number of sick individuals in a scenario without public regulation of social contacts. We also study the effects of public regulations. For all scenarios we report the expected end of the CoV-2 epidemic.\n\nWe have four general findings: First, current epidemiological thinking implies that the long-run effects of the epidemic only depend on the aggregate long-run infection rate and on the individual risk to turn sick after an infection. Any measures by individuals and the public therefore only influence the dynamics of spread of CoV-2. Second, predictions about the duration and level of the epidemic must strongly distinguish between the officially reported numbers (Robert Koch Institut, RKI) and actual numbers of sick individuals. Third, given the current (scarce) medical knowledge about long-run infection rate and individual risks to turn sick, any prediction on the length (duration in months) and strength (e.g. maximum numbers of sick individuals on a given day) is subject to a lot of uncertainty. Our predictions therefore offer robustness analyses that provide ranges on how long the epidemic will last and how strong it will be. Fourth, public interventions that are already in place and that are being discussed can lead to more and less severe outcomes of the epidemic. If an intervention takes place too early, the epidemic can actually be stronger than with an intervention that starts later. Interventions should therefore be contingent on current infection rates in regions or countries.\n\nConcerning predictions about COVID-19 in Germany, we find that the long-run number of sick individuals (that are reported to the RKI), once the epidemic is over, will lie between 500 thousand and 5 million individuals. While this seems to be an absurd large range for a precise projection, this reflects the uncertainty about the long-run infection rate in Germany. If we assume that Germany will follow the good scenario of Hubei (and we are even a bit more conservative given discussions about data quality), we will end up with 500 thousand sick individuals over the entire epidemic. If by contrast we believe (as many argue) that once the epidemic is over 70% of the population will have been infected (and thereby immune), we will end up at 5 million cases.\n\nDefining the end of the epidemic by less than 100 newly reported sick individuals per day, we find a large variation depending on the effectiveness of governmental pleas and regulations to reduce social contacts. An epidemic that is not influenced by public health measures would end mid June 2020. With public health measures lasting for few weeks, the end is delayed by around one month or two. The advantage of the delay, however, is to reduce the peak number of individuals that are simultaneously sick. When we believe in long-run infection rates of 70%, this number is equally high for all scenarios we went through and well above 1 million. When we can hope for the Hubei-scenario, the maximum number of sick individuals will be around 200 thousand \"only\".\n\nWhatever value of the range of long-run infection rates we want to assume, the epidemic will last at least until June, with extensive and potentially future public health measures, it will last until July. In the worst case, it will last until end of August.\n\nWe emphasize that all projections are subject to uncertainty and permanent monitoring of observed incidences are taken into account to update the projection. The most recent projections are available at https://www.macro.economics.unimainz.de/corona-blog/.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Jean Roch Donsimoni",
+        "author_inst": "Johannes Gutenberg-University"
+      },
+      {
+        "author_name": "Rene Glawion",
+        "author_inst": "Universitaet Hamburg"
+      },
+      {
+        "author_name": "Bodo Plachter",
+        "author_inst": "Johannes Gutenberg-University"
+      },
+      {
+        "author_name": "Klaus Waelde",
+        "author_inst": "Johannes Gutenberg-University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "health economics"
+  },
   {
     "rel_doi": "10.1101/2020.03.25.20043703",
     "rel_title": "Laboratory findings, signs and symptoms, clinical outcomes of Patients with COVID-19 Infection: an updated systematic review and meta-analysis",
@@ -1573321,25 +1572086,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.03.23.20040279",
-    "rel_title": "Gastrointestinal tract symptoms in coronavirus disease 2019: Analysis of clinical symptoms in adult patients",
-    "rel_date": "2020-03-27",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.23.20040279",
-    "rel_abs": "ObjectiveTo investigate the clinical presentation of coronavirus disease 2019 (COVID-19), particularly the incidence of gastrointestinal tract symptoms.\n\nDesignWe enrolled adult COVID-19 patients from a mobile cabin hospital in Wuhan with a definitive diagnosis by SARS-CoV-2 nucleic acid testing. Face-to-face interviews were conducted in which the patient selected COVID-19-related symptoms and report the time of onset and duration of symptoms.\n\nResultsA total of 212 adults were enrolled in this study, of which 127 (59.9%) were females, mean age was 48.50 {+/-}13.15 (range: 17-79) years, and mean disease course was 26.78{+/-}9.16 (3-60) days. Fever and cough were the most common and earliest clinical symptoms of COVID-19.\n\nDiarrhoea occurred in 43.8% (93/212) of patients, of which 86.0% (80/93) had mushy stools. Nausea and vomiting were also common (20.7%). Diarrhoea lasted for 4.00(2.00-8.85) days and mostly occurred 5.00(0.25-11.00) days after the emergence of the first symptoms. Multiple logistic regression analysis found that diarrhoea was significantly correlated with fatigue [OR2.900,95%CI (1.629-5.164), p<0.0001].\n\nConclusionsGastrointestinal tract symptoms are common in COVID-19 and most occur during the middle stage of the disease and lasts for a short period of time. Clinicians need to pay greater attention to gastrointestinal tract symptoms of COVID-19.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Yong Zhang",
-        "author_inst": "Renmin Hospital of Wuhan University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "gastroenterology"
-  },
   {
     "rel_doi": "10.1101/2020.03.22.20040923",
     "rel_title": "Scarce COVID-19 Testing Capabilities at Urgent Care Centers in States with Greatest Disease Burden",
@@ -1573630,6 +1572376,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.03.23.20040998",
+    "rel_title": "A demographic adjustment to improve measurement of COVID-19 severity at the developing stage of the pandemic",
+    "rel_date": "2020-03-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.23.20040998",
+    "rel_abs": "The need for accurate statistics has never been felt so deeply as the novel COVID-19 pathogen spreads around the world and quantifying its severity is a primary clinical and public health issue. In Italy, the magnitude and increasing trend of the case-fatality risk (CFR) is fueling the already high levels of public alarm. In this paper, we highlight that the widely used crude CFR is an inaccurate measure of the disease severity since the pandemic is still unfolding. With the goal to improve its comparability over time and across countries at this stage, we then propose a demographic adjustment of the CFR that addresses the bias arising from differential case ascertainment by age. When applied to publicly released data for Italy, we show that until March 16 our adjusted CFR was similar to that of Wuhan - the most affected Chinese region, where COVID-19 has now been contained. This indicates that our adjusted CFR improves its comparability over time, making an important tool to chart the course of the COVID-19 pandemic across countries. Since March 16, the Italian COVID-19 outbreak has entered a new phase, with the northern and southern regions following different trajectories. As a result, our adjusted CFR has been increasing between March 16 and March 20. Data at the subnational level are needed to correctly assess the disease severity in the country at this stage.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Simona Bignami",
+        "author_inst": "Universite de Montreal"
+      },
+      {
+        "author_name": "Daniela Ghio",
+        "author_inst": "Joint Research Center European Commission"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.03.24.20041020",
     "rel_title": "Systematic review and critical appraisal of prediction models for diagnosis and prognosis of COVID-19 infection",
@@ -1574931,81 +1573700,6 @@
     "type": "new results",
     "category": "biophysics"
   },
-  {
-    "rel_doi": "10.1101/2020.03.24.005900",
-    "rel_title": "Topoisomerase III-beta is required for efficient replication of positive-sense RNA viruses",
-    "rel_date": "2020-03-27",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.24.005900",
-    "rel_abs": "Based on genome-scale loss-of-function screens we discovered that Topoisomerase III-{beta} (TOP3B), a human topoisomerase that acts on DNA and RNA, is required for yellow fever virus and dengue virus-2 replication. Remarkably, we found that TOP3B is required for efficient replication of all positive-sense-single stranded RNA viruses tested, including SARS-CoV-2. While there are no drugs that specifically inhibit this topoisomerase, we posit that TOP3B is an attractive anti-viral target.",
-    "rel_num_authors": 15,
-    "rel_authors": [
-      {
-        "author_name": "K. Reddisiva Prasanth",
-        "author_inst": "UTMB"
-      },
-      {
-        "author_name": "Minato Hirano",
-        "author_inst": "UTMB"
-      },
-      {
-        "author_name": "W. Samuel Fagg",
-        "author_inst": "UTMB"
-      },
-      {
-        "author_name": "Eileen McAnarney",
-        "author_inst": "UTMB"
-      },
-      {
-        "author_name": "Shao Chan",
-        "author_inst": "UTMB"
-      },
-      {
-        "author_name": "Xuping Xie",
-        "author_inst": "UTMB"
-      },
-      {
-        "author_name": "Adam Hage",
-        "author_inst": "UTMB"
-      },
-      {
-        "author_name": "Colette Pietzsch",
-        "author_inst": "UTMB"
-      },
-      {
-        "author_name": "Alexander Bukreyev",
-        "author_inst": "University of Texas Medical Branch at Galveston"
-      },
-      {
-        "author_name": "Ricardo Rajsbaum",
-        "author_inst": "University of Texas Medical Branch"
-      },
-      {
-        "author_name": "Pei-Yong Shi",
-        "author_inst": "UTMB"
-      },
-      {
-        "author_name": "Mark Bedford",
-        "author_inst": "MD Anderson Cancer Center"
-      },
-      {
-        "author_name": "Shelton Bradrick",
-        "author_inst": "UTMB"
-      },
-      {
-        "author_name": "Vineet D Menachery",
-        "author_inst": "University of Texas Medical Branch"
-      },
-      {
-        "author_name": "Mariano A Garcia-Blanco",
-        "author_inst": "University of Texas Medical Branch"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.03.24.006007",
     "rel_title": "Automatic Identification of SARS Coronavirus using Compression-Complexity Measures",
@@ -1575268,6 +1573962,89 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health informatics"
   },
+  {
+    "rel_doi": "10.1101/2020.03.23.20039362",
+    "rel_title": "Immune Cell Profiling of COVID-19 Patients in the Recovery Stage by Single-Cell Sequencing",
+    "rel_date": "2020-03-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.23.20039362",
+    "rel_abs": "COVID-19, caused by SARS-CoV-2, has recently affected over 300,000 people and killed more than 10,000. The manner in which the key immune cell subsets change and their states during the course of COVID-19 remain unclear. Here, we applied single-cell technology to comprehensively characterize transcriptional changes in peripheral blood mononuclear cells during the recovery stage of COVID-19. Compared with healthy controls, in patients in the early recovery stage (ERS) of COVID-19, T cells decreased remarkably, whereas monocytes increased. A detailed analysis of the monocytes revealed that there was an increased ratio of classical CD14++ monocytes with high inflammatory gene expression as well as a greater abundance of CD14++IL1B+ monocytes in the ERS. CD4+ and CD8+ T cells decreased significantly and expressed high levels of inflammatory genes in the ERS. Among the B cells, the plasma cells increased remarkably, whereas the naive B cells decreased. Our study identified several novel B cell-receptor (BCR) changes, such as IGHV3-23 and IGHV3-7, and confirmed isotypes (IGHV3-15, IGHV3-30, and IGKV3-11) previously used for virus vaccine development. The strongest pairing frequencies, IGHV3-23-IGHJ4, indicated a monoclonal state associated with SARS-CoV-2 specificity. Furthermore, integrated analysis predicted that IL-1{beta} and M-CSF may be novel candidate target genes for inflammatory storm and that TNFSF13, IL-18, IL-2 and IL-4 may be beneficial for the recovery of COVID-19 patients. Our study provides the first evidence of an inflammatory immune signature in the ERS, suggesting that COVID-19 patients are still vulnerable after hospital discharge. Our identification of novel BCR signaling may lead to the development of vaccines and antibodies for the treatment of COVID-19.\n\nHighlights- The immune response was sustained for more than 7 days in the early recovery stage of COVID-19, suggesting that COVID-19 patients are still vulnerable after hospital discharge.\n- Single-cell analysis revealed a predominant subset of CD14++ IL1{beta}+ monocytes in patients in the ERS of COVID-19.\n- Newly identified virus-specific B cell-receptor changes, such as IGHV3-23, IGHV3-7, IGHV3-15, IGHV3-30, and IGKV3-11, could be helpful in the development of vaccines and antibodies against SARS-CoV-2.\n- IL-1{beta} and M-CSF were discovered as novel mediators of inflammatory cytokine storm, and TNFSF13, IL-2, IL-4, and IL-18 may be beneficial for recovery.",
+    "rel_num_authors": 17,
+    "rel_authors": [
+      {
+        "author_name": "Wen Wen",
+        "author_inst": "National Center for Liver Cancer, Second Military Medical University, Shanghai, China"
+      },
+      {
+        "author_name": "Wenru Su",
+        "author_inst": "State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China"
+      },
+      {
+        "author_name": "Hao Tang",
+        "author_inst": "Department of Respiratory and Critical Care Medicine Changzheng Hospital, Second Military Medical University, Shanghai, China"
+      },
+      {
+        "author_name": "Wenqing Le",
+        "author_inst": "Department of Critical Care,Wuhan Hankou Hospital, Hubei, China"
+      },
+      {
+        "author_name": "Xiaopeng Zhang",
+        "author_inst": "Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China"
+      },
+      {
+        "author_name": "Yingfeng Zheng",
+        "author_inst": "State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China"
+      },
+      {
+        "author_name": "XiuXing Liu",
+        "author_inst": "State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China"
+      },
+      {
+        "author_name": "Lihui Xie",
+        "author_inst": "State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China"
+      },
+      {
+        "author_name": "Jianmin Li",
+        "author_inst": "Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China"
+      },
+      {
+        "author_name": "Jinguo Ye",
+        "author_inst": "State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China"
+      },
+      {
+        "author_name": "Xiuliang Cui",
+        "author_inst": "National Center for Liver Cancer Second Military Medical University, Shanghai, China"
+      },
+      {
+        "author_name": "Yushan Miao",
+        "author_inst": "Department of Respiratory and Critical Care Medicine Changzheng Hospital, Second Military Medical University, Shanghai, China"
+      },
+      {
+        "author_name": "Depeng Wang",
+        "author_inst": "GrandOmics Diagnosis Co. Ltd. Wuhan, Hubei, China"
+      },
+      {
+        "author_name": "Jiantao Dong",
+        "author_inst": "Berry Genomics Co. Ltd, Beijing, China"
+      },
+      {
+        "author_name": "Chuan-Le Xiao",
+        "author_inst": "State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China"
+      },
+      {
+        "author_name": "Wei Chen",
+        "author_inst": "Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing, China"
+      },
+      {
+        "author_name": "Hongyang Wang",
+        "author_inst": "National Center for Liver Cancer, Second Military Medical University, Shanghai, China"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.03.25.20043877",
     "rel_title": "The current state of COVID-19 in Australia: importation and spread",
@@ -1576265,85 +1575042,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
-  {
-    "rel_doi": "10.1101/2020.03.23.20041533",
-    "rel_title": "Core Outcome Set for Traditional Chinese and Western Medicine Clinical Trials of COVID-19",
-    "rel_date": "2020-03-27",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.23.20041533",
-    "rel_abs": "BackgroundDevelopment of a core outcome set (COS) for clinical trials for COVID-19 is urgent because of the pandemic wreaking havoc worldwide and the heterogeneity of outcomes in clinical trials.\n\nMethodsA preliminary list of outcomes were developed after a systematic review of protocols of clinical trials for COVID-19. Then, two rounds of the Delphi survey were conducted. Stakeholders were traditional Chinese medicine (TCM) experts, Western medicine (WM) experts, nurses and the public. Patients with confirmed COVID-19 were also invited to participate in a questionnaire written in understandable language. Frontline clinicians, as well as nurse, methodologist, evidence based-medicine researcher, and staff from the Chinese Clinical Trials Registry participated by video conference to vote.\n\nResultsNinety-seven eligible study protocols were identified from 160 clinical trials. Seventy-six outcomes were identified from TCM clinical trials and 126 outcomes were identified from WM clinical trials. Finally, 145 outcomes were included in the first round of the Delphi survey. Then, a COS for clinical trials of TCM and WM was developed. The COS include clinical outcomes (recovery/improvement/progression/death), etiology (SARS-CoV-2 nucleic-acid tests, viral load), inflammatory factor (C-reactive protein), vital signs (temperature, respiration), blood and lymphatic-system parameters (lymphocytes, virus antibody), respiratory outcomes (Pulmonary imaging, blood oxygen saturation, PaO2/FiO2 ratio, arterial blood gas analysis, mechanical ventilation, oxygen intake, pneumonia severity index), clinical efficacy (prevalence of preventing patients with mild-to-moderate disease progressing to severe disease), symptoms (clinical symptom score). Outcomes were recommended according to different types of disease. Outcome measurement instrument/definition were also recommended.\n\nConclusionA COS for COVID-19 may improve consistency of outcome reporting in clinical trials.",
-    "rel_num_authors": 16,
-    "rel_authors": [
-      {
-        "author_name": "Ruijin Qiu",
-        "author_inst": "Dongzhimen Hospital, Beijing University of Chinese Medicine"
-      },
-      {
-        "author_name": "Chen Zhao",
-        "author_inst": "Institute of Basic Research In Clinical Medicine, China Academy of Chinese Medical Sciences"
-      },
-      {
-        "author_name": "Tengxiao Liang",
-        "author_inst": "Emergency Department, Dongzhimen Hospital, Beijing University of Chinese Medicine."
-      },
-      {
-        "author_name": "Xuezeng Hao",
-        "author_inst": "Cardiology Department, Dongzhimen Hospital, Beijing University of Chinese Medicine."
-      },
-      {
-        "author_name": "Ya Huang",
-        "author_inst": "Key Laboratory of Chinese Internal Medicine of Ministry of Education and Beijing, Dongzhimen Hospital, Beijing University of Chinese Medicine."
-      },
-      {
-        "author_name": "Xiaoyu Zhang",
-        "author_inst": "Key Laboratory of Chinese Internal Medicine of Ministry of Education and Beijing, Dongzhimen Hospital, Beijing University of Chinese Medicine."
-      },
-      {
-        "author_name": "Zhao Chen",
-        "author_inst": "Key Laboratory of Chinese Internal Medicine of Ministry of Education and Beijing, Dongzhimen Hospital, Beijing University of Chinese Medicine."
-      },
-      {
-        "author_name": "Xuxu Wei",
-        "author_inst": "Key Laboratory of Chinese Internal Medicine of Ministry of Education and Beijing, Dongzhimen Hospital, Beijing University of Chinese Medicine."
-      },
-      {
-        "author_name": "Mengzhu Zhao",
-        "author_inst": "First Teaching Hospital of Tianjin University of Traditional Chinese Medicine."
-      },
-      {
-        "author_name": "Changming Zhong",
-        "author_inst": "Key Laboratory of Chinese Internal Medicine of Ministry of Education and Beijing, Dongzhimen Hospital, Beijing University of Chinese Medicine."
-      },
-      {
-        "author_name": "Jiayuan Hu",
-        "author_inst": "Key Laboratory of Chinese Internal Medicine of Ministry of Education and Beijing, Dongzhimen Hospital, Beijing University of Chinese Medicine."
-      },
-      {
-        "author_name": "Min Li",
-        "author_inst": "Beijing University of Chinese Medicine Third Affiliated Hospital"
-      },
-      {
-        "author_name": "Songjie Han",
-        "author_inst": "Key Laboratory of Chinese Internal Medicine of Ministry of Education and Beijing, Dongzhimen Hospital, Beijing University of Chinese Medicine."
-      },
-      {
-        "author_name": "Tianmai He",
-        "author_inst": "Key Laboratory of Chinese Internal Medicine of Ministry of Education and Beijing, Dongzhimen Hospital, Beijing University of Chinese Medicine."
-      },
-      {
-        "author_name": "Jing Chen",
-        "author_inst": "Baokang Affiliated Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin China."
-      },
-      {
-        "author_name": "Hongcai Shang",
-        "author_inst": "Key Laboratory of Chinese Internal Medicine of Ministry of Education and Beijing, Dongzhimen Hospital, Beijing University of Chinese Medicine."
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.03.26.20039438",
     "rel_title": "Evaluation of COVID-19 RT-qPCR test in multi-sample pools",
@@ -1576758,6 +1575456,29 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.03.21.20040667",
+    "rel_title": "COVID-19 in Canada: Predictions for the future and control lessons from Asia",
+    "rel_date": "2020-03-27",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.21.20040667",
+    "rel_abs": "COVID-19 has spread with unequal efficiency in various parts of the world. In several European countries including Italy, the increase in the number of COVID-19 cases has followed a consistent, exponential pattern of spread. However, some countries, notably Taiwan and Hong Kong, have achieved a different outcome and have managed to bring the COVID-19 outbreak in their countries rapidly under control, without entering the exponential pattern and with very few cases. They have used several different approaches to COVID-19 outbreak control, including the innovative use of smartphone technology and the widespread use of surgical face masks. We show through our models, that Canada has followed the same, consistent COVID-19 exponential growth pattern that is seen in Italy. Both nationally and in its most heavily affected provinces, there is exponential growth of COVID-19 cases, making it possible to make predictions for the future, if no further interventions are made in public health policy. In particular, we argue for the urgent introduction of surgical face masks in health care and other settings and the harnessing of the power of smartphone technology on a national scale.",
+    "rel_num_authors": 2,
+    "rel_authors": [
+      {
+        "author_name": "Cornelius Christian",
+        "author_inst": "Brock University"
+      },
+      {
+        "author_name": "Francis Christian",
+        "author_inst": "University of Saskatchewan"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.03.23.20041913",
     "rel_title": "SARS-CoV-2 infection in 86 healthcare workers in two Dutch hospitals in March 2020",
@@ -1577843,41 +1576564,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.03.23.20034058",
-    "rel_title": "Comparison of the spatiotemporal characteristics of the COVID-19 and SARS outbreaks in mainland China",
-    "rel_date": "2020-03-26",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.23.20034058",
-    "rel_abs": "BackgroundBoth coronavirus disease 2019 (COVID-19) and severe acute respiratory syndrome (SARS) are caused by coronaviruses and have infected people in China and worldwide. We aimed to investigate whether COVID-19 and SARS exhibited similar spatial and temporal features at the provincial level in mainland China.\n\nMethodsThe number of people infected by COVID-19 and SARS were extracted from daily briefings on newly confirmed cases during the epidemics, as of Mar. 4, 2020 and Aug. 3, 2003, respectively. We depicted the spatiotemporal patterns of the COVID-19 and SARS epidemics using spatial statistics such as Morans I and the local indicators of spatial association (LISA).\n\nResultsCompared to SARS, COVID-19 had a higher incidence. We identified 3 clusters (predominantly located in south-central China, highest RR=135.08) for COVID-19 and 4 clusters (mainly in Northern China, highest RR=423.51) for SARS. Fewer secondary clusters were identified after the \"Wuhan lockdown\". The LISA cluster map detected a significantly high-low (Hubei) and low-high spatial clustering (Anhui, Hunan, and Jiangxi, in Central China) for COVID-19. Two significant high-high (Beijing and Tianjin) and low-high (Hebei) clusters were detected for SARS, although the global Morans I value was not significant.\n\nConclusionsThe different spatiotemporal clustering patterns between COVID-19 and SARS could point to changes in social and demographic factors, local government containment strategies or differences in transmission mechanisms between these coronaviruses.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Xi Zhang",
-        "author_inst": "Clinical Research Unit, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China"
-      },
-      {
-        "author_name": "Hua-Xiang Rao",
-        "author_inst": "Department of Public Health and Preventive Medicine, Changzhi Medical College, Changzhi, Shanxi, P.R. China"
-      },
-      {
-        "author_name": "Yuwan Wu",
-        "author_inst": "Department of Pediatrics, Xin Hua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China"
-      },
-      {
-        "author_name": "Yubei Huang",
-        "author_inst": "Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, P.R. China"
-      },
-      {
-        "author_name": "Hongji Dai",
-        "author_inst": "Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, P.R. China"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.03.25.20043828",
     "rel_title": "Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology",
@@ -1578340,6 +1577026,57 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.03.24.20042903",
+    "rel_title": "COVID-19 clinical characteristics, and sex-specific risk of mortality: Systematic Review and Meta-analysis",
+    "rel_date": "2020-03-26",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.24.20042903",
+    "rel_abs": "ObjectivesThe rapidly evolving coronavirus disease 2019 (COVID-19), was declared a pandemic by the World Health Organization on March 11, 2020. It was first detected in the city of Wuhan in China and has spread globally resulting in substantial health and economic crisis in many countries. Observational studies have partially identified the different aspects of this disease. Up to this date, no comprehensive systematic review for the clinical, laboratory, epidemiologic and mortality findings has been published. We conducted this systematic review and meta-analysis for a better understanding of COVID-19.\n\nMethodsWe reviewed the scientific literature published from January 1, 2019 to March 3, 2020. Statistical analyses were performed with STATA (version 14, IC; Stata Corporation, College Station, TX, USA). The pooled frequency with 95% confidence intervals (CI) was assessed using random effect model. Publication bias was assessed and p <0.05 was considered a statistically significant publication bias.\n\nResultsOut of 1102 studies, 32 satisfied the inclusion criteria. A total of 4789 patients with a mean age of 49 years were evaluated. Fever (83.0%, CI 77.5 to 87.6), cough (65.2%, CI 58.6 to 71.2) and myalgia/fatigue (34.7, CI 26.0 to 44.4) were the most common symptoms. The most prevalent comorbidities were hypertension (18.5 %, CI 12.7 to 24.4) and Cardiovascular disease (14.9 %, CI 6.0 to 23.8). Among the laboratory abnormalities, elevated C-Reactive Protein (CRP) (72.0% (CI 54.3 to 84.6) and lymphopenia (50.1%, CI 38.0 to 62.4) were the most common findings. Bilateral ground-glass opacities (66.0%, CI 51.1 to 78.0) was the most common CT-Scan presentation. Pooled mortality rate was 6.6%, with males having significantly higher mortality compared to females (OR 3.4; 95% CI 1.2 to 9.1, P = 0.01).\n\nConclusionCOVID-19 commonly presented with a progressive course of cough and fever with more than half of hospitalized patients showing leukopenia or a high CRP on their laboratory findings. Mortality associated with COVID19 was higher than that reported in studies in China with Males having a 3-fold higher risk of mortality in COVID19 compared to females.\n\nSummary boxO_ST_ABSWhat is already known in this topicC_ST_ABSO_LICOVID-19 was declared a pandemic by the World Health Organization on March 11, 2020.\nC_LIO_LIMany observational studies have separately dealt with different clinical and epidemiologic features of this new and rapidly evolving disease.\nC_LIO_LIVery few systematic reviews about COVID-19 have been done and there was still a need for a systematic review and meta-analysis related to the clinical findings and the mortality of the disease in order to have a better understanding of COVID-19.\nC_LIO_LIPrevious reports have indicated that older age and presence of multiple comorbidities are associated with increased mortality.\nC_LI\n\nWhat this study addsO_LIThe mortality rate in our study for hospitalized COVID-19 patients was 6.6% and males had around 3-fold higher risk of mortality compared to females (OR 3.4; 95% CI 1.2-9.1, P = 0.01).\nC_LIO_LIThese findings could indicate the need for more aggressive treatment of COVID-19 in males.\nC_LI",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Mohammad Javad Nasiri",
+        "author_inst": "Shahid Beheshti University of Medical Sciences"
+      },
+      {
+        "author_name": "Sara Haddadi",
+        "author_inst": "University of Miami Miller School of Medicine"
+      },
+      {
+        "author_name": "Azin Tahvildari",
+        "author_inst": "Shahid Beheshti University of Medical Sciences"
+      },
+      {
+        "author_name": "Yeganeh Farsi",
+        "author_inst": "Shahid Beheshti University of Medical Sciences"
+      },
+      {
+        "author_name": "Mahta Arbabi",
+        "author_inst": "Shahid Beheshti University of Medical Sciences"
+      },
+      {
+        "author_name": "Saba Hasanzadeh",
+        "author_inst": "Shahid Beheshti University of Medical Sciences"
+      },
+      {
+        "author_name": "Parnian Jamshidi",
+        "author_inst": "Shahid Beheshti University of Medical Sciences"
+      },
+      {
+        "author_name": "Mukunthan Murthi",
+        "author_inst": "University of Miami Miller School of Medicine"
+      },
+      {
+        "author_name": "Mehdi Mirsaeidi",
+        "author_inst": "University of Miami Miller School of Medicine"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.03.24.20042382",
     "rel_title": "Viral Kinetics and Antibody Responses in Patients with COVID-19",
@@ -1579565,77 +1578302,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "psychiatry and clinical psychology"
   },
-  {
-    "rel_doi": "10.1101/2020.03.22.20040287",
-    "rel_title": "Estimating excess 1- year mortality from COVID-19 according to underlying conditions and age in England: a rapid analysis using NHS health records in 3.8 million adults",
-    "rel_date": "2020-03-24",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.22.20040287",
-    "rel_abs": "BackgroundThe medical, health service, societal and economic impact of the COVID-19 emergency has unknown effects on overall population mortality. Previous models of population mortality are based on death over days among infected people, nearly all of whom (to date at least) have underlying conditions. Models have not incorporated information on high risk conditions or their longer term background (pre-COVID-19) mortality. We estimated the excess number of deaths over 1 year under different COVID-19 incidence rates and differing mortality impacts.\n\nMethodsUsing population based linked primary and secondary care electronic health records in England (HDR UK - CALIBER), we report the prevalence of underlying conditions defined by UK Public Health England COVID-19 guidelines (16 March 2020) in 3,862,012 individuals aged [&ge;]30 years from 1997-2017. We used previously validated phenotypes, openly available (https://caliberresearch.org/portal), for each condition using ICD-10 diagnosis, Read, procedure and medication codes. We estimated the 1-year mortality in each condition, and developed simple models of excess COVID-19-related deaths assuming relative risk (RR) of the impact of the emergency (compared to background mortality) of 1.2, 1.5 and 2.0.\n\nFindings20.0% of the population are at risk according to current PHE guidelines, of which; 13.7% were age>70 years and 6.3% aged [&le;]70 years with [&ge;]1 underlying condition (cardiovascular disease (2.3%), diabetes (2.2%), steroid therapy (1.9%), severe obesity (0.9%), chronic kidney disease (0.6%) and chronic obstructive pulmonary disease, COPD (0.5%). Multimorbidity (co-occurrence of [&ge;]2 conditions in an individual) was common (10.1%). The 1-year mortality in the at-risk population was 4.46%, and age and underlying conditions combine to influence background risk, varying markedly across conditions (5.9% in age>70 years, 8.6% for COPD and 13.1% in those with [&ge;]3 or more conditions). In a suppression scenario (at SARS CoV2 rates of 0.001% of the UK population), there would be minimal excess deaths (3 and 7 excess deaths at relative risk, RR, 1.5 and 2.0 respectively). At SARS CoV2 rates of 10% of the UK population (mitigation) the model estimates the numbers of excess deaths as: 13791, 34479 and 68957 (at RR 1.2, 1.5 and 2.0 respectively). At SARS CoV2 rates of 80% in the UK population (\"do-nothing\"), the model estimates the number of excess deaths as 110332, 275,830 and 551,659 (at RR 1.2, 1.5 and 2.0) respectively.\n\nInterpretationWe provide the public, researchers and policy makers a simple model to estimate the excess mortality over 1 year from COVID-19, based on underlying conditions at different ages. If the relative mortality impact of COVID-19 were to be about 20% (similar magnitude as the established winter vs summer mortality excess), then the excess deaths would be 0 when 1 in 100 000 (suppression), 13791 when 1 in 10 (mitigation) and 110332 when 8 in 10 are infected (\"do nothing\") scenario. However, the relative impact of COVID-19 is unknown. If the emergency were to double the mortality risk, then we estimate 7, 68957 and 551,659 excess deaths in the same scenarios. These results may inform the need for more stringent suppression measures as well as efforts to target those at highest risk for a range of preventive interventions.",
-    "rel_num_authors": 14,
-    "rel_authors": [
-      {
-        "author_name": "Amitava Banerjee",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Laura Pasea",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Steve Harris",
-        "author_inst": "University College London Hospitals NHS Trust"
-      },
-      {
-        "author_name": "Arturo Gonzalez-Izquierdo",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Ana Torralbo",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Laura Shallcross",
-        "author_inst": "UCL"
-      },
-      {
-        "author_name": "Mahdad Noursadeghi",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Deenan Pillay",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Christina Pagel",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Wai Keong Wong",
-        "author_inst": "University College London Hospitals NHS Trust"
-      },
-      {
-        "author_name": "Claudia Langenberg",
-        "author_inst": "University of Cambridge"
-      },
-      {
-        "author_name": "Bryan Williams",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Spiros Denaxas",
-        "author_inst": "University College London"
-      },
-      {
-        "author_name": "Harry Hemingway",
-        "author_inst": "University College London"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.03.21.20031336",
     "rel_title": "Characterizing occupations that cannot work from home: a means to identify susceptible worker groups during the COVID-19 pandemic",
@@ -1579954,6 +1578620,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.03.22.002204",
+    "rel_title": "Characterisation of the transcriptome and proteome of SARS-CoV-2 using direct RNA sequencing and tandem mass spectrometry reveals evidence for a cell passage induced in-frame deletion in the spike glycoprotein that removes the furin-like cleavage site.",
+    "rel_date": "2020-03-24",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.22.002204",
+    "rel_abs": "Direct RNA sequencing using an Oxford Nanopore MinION characterised the transcriptome of SARS-CoV-2 grown in Vero E6 cells. This cell line is being widely used to propagate the novel coronavirus. The viral transcriptome was analysed using a recently developed ORF-centric pipeline. This revealed the pattern of viral transcripts, (i.e. subgenomic mRNAs), generally fitted the predicted replication and transcription model for coronaviruses. A 24 nt in-frame deletion was detected in subgenomic mRNAs encoding the spike (S) glycoprotein. This feature was identified in over half of the mapped transcripts and was predicted to remove a proposed furin cleavage site from the S glycoprotein. This motif directs cleavage of the S glycoprotein into functional subunits during virus entry or exit. Cleavage of the S glycoprotein can be a barrier to zoonotic coronavirus transmission and affect viral pathogenicity. Allied to this transcriptome analysis, tandem mass spectrometry was used to identify over 500 viral peptides and 44 phosphopeptides, covering almost all of the proteins predicted to be encoded by the SARS-CoV-2 genome, including peptides unique to the deleted variant of the S glycoprotein. Detection of an apparently viable deletion in the furin cleavage site of the S glycoprotein reinforces the point that this and other regions of SARS-CoV-2 proteins may readily mutate. This is of clear significance given the interest in the S glycoprotein as a potential vaccine target and the observation that the furin cleavage site likely contributes strongly to the pathogenesis and zoonosis of this virus. The viral genome sequence should be carefully monitored during the growth of viral stocks for research, animal challenge models and, potentially, in clinical samples. Such variations may result in different levels of virulence, morbidity and mortality.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Andrew D. Davidson",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Maia Kavangh Williamson",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Sebastian Lewis",
+        "author_inst": "Universiry of Bristol"
+      },
+      {
+        "author_name": "Deborah Shoemark",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Miles W Carroll",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Kate Heesom",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Maria Zambon",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Joanna Ellis",
+        "author_inst": "Public Health England"
+      },
+      {
+        "author_name": "Phillip A Lewis",
+        "author_inst": "University of Bristol"
+      },
+      {
+        "author_name": "Julian A Hiscox",
+        "author_inst": "University of Liverpool"
+      },
+      {
+        "author_name": "David A Matthews",
+        "author_inst": "University of Bristol"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2020.03.21.20037267",
     "rel_title": "Effect of SARS-CoV-2 infection upon male gonadal function: A single center-based study",
@@ -1581143,49 +1579868,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.03.20.20039602",
-    "rel_title": "A Tempo-geographic Analysis of Global COVID-19 Epidemic Outside of China",
-    "rel_date": "2020-03-23",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.20.20039602",
-    "rel_abs": "BackgroundUnderstanding the global epidemic trends, geographic distribution, and transmission patterns of COVID-19 contribute to providing timely information for the global response of the epidemic. This study aims to understand the global pandemic geospatial patterns and trends and identify new epicenters requiring urgent attention.\n\nMethodsData on COVID-19 between 31st Dec. 2019 and 14th Mar. 2020 was included. The epidemic trend was analyzed using joinpoint regressions; the growth of affected countries was by descriptive analysis; and the global distribution and transmission trend by spatial analysis. Findings: The number of new cases in the regions outside of China slowly increased before 24th Feb. and rapidly accelerated after 24th Feb. Compared to China, other affected countries experienced a longer duration of a slow increase at the early stage and rapid growth at the latter stages. The first apparent increase in the number of affected countries occurred from 23rd Jan to 1st Feb, and the second apparent increase started from 25th Feb. The fist COVID-19 cases reported by countries from 28th Feb. were mainly imported from Europe. The geographic distribution changed from single-center (13th Jan. - 20th Feb.) to multi-centers pattern (20th Feb. - 14th Mar.). More countries were affected with COVID-19 and developed local transmission.\n\nInterpretationThe joinpoint regression and geospatial analysis indicated a multi-center pandemic of COVID-19. Strategies to prevent the new multiple centers as well as prevent ongoing transmission are needed.\n\nFundingNIH.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Huipeng Liao",
-        "author_inst": "University of North Carolina Project-China"
-      },
-      {
-        "author_name": "Gifty Marley",
-        "author_inst": "School of Public Health of Nanjing Medical University and University of North Carolina Project-China"
-      },
-      {
-        "author_name": "Yafei Si",
-        "author_inst": "University of North Carolina Project-China"
-      },
-      {
-        "author_name": "Zaisheng Wang",
-        "author_inst": "University of North Carolina Project-China"
-      },
-      {
-        "author_name": "Yewei Xie",
-        "author_inst": "University of North Carolina Project-China"
-      },
-      {
-        "author_name": "Cheng Wang",
-        "author_inst": "Dermatology Hospital and the Institute of Global Health and STI Research of Southern Medical"
-      },
-      {
-        "author_name": "Weiming Tang",
-        "author_inst": "Dermatology Hospital, Southern Medical University, and the University of North Carolina at Chapel Hill Project-China"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.03.18.20038455",
     "rel_title": "ACE-2 Expression in the Small Airway Epithelia of Smokers and COPD Patients: Implications for COVID-19",
@@ -1581420,6 +1580102,89 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.03.19.20038315",
+    "rel_title": "Association between Clinical, Laboratory and CT Characteristics and RT-PCR Results in the Follow-up of COVID-19 patients",
+    "rel_date": "2020-03-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.19.20038315",
+    "rel_abs": "BackgroundSince December 2019, more than 100,000 coronavirus disease 2019 (COVID-19) patients have been confirmed globally based on positive viral nucleic acids with real-time reverse transcriptase-polymerase chain reaction (RT-PCR). However, the association between clinical, laboratory and CT characteristics and RT-PCR results is still unclear. We sought to examine this association in detail, especially in recovered patients.\n\nMethodsWe analysed data from 52 confirmed patients who had been discharged with COVID-19. The clinical, laboratory, and radiological data were dynamically recorded and compared with the admission and follow-up RT-PCR results.\n\nResultsIn this cohort, 52 admitted COVID-19 patients who had confirmed positive RT-PCR results were discharged after 2 rounds of consecutively negative RT-PCR results. Compared with admission levels, CRP levels (median 4.93 mg/L [IQR: 1.78-10.20]) decreased significantly (p<0.001). and lymphocyte counts (median 1.50x109/L [IQR: 1.11-1.88]) increased obviously after obtaining negative RT-PCR results (p<0.001). Additionally, substantially improved inflammatory exudation was observed on chest CT except for 2 progressed patients. At the two-week follow-up after discharge, 7 patients had re-positive RT-PCR results, including the abovementioned 2 progressed patients. Among the 7 patients, new GGO was demonstrated in 2 patients. There were no significant differences in CPR levels or lymphocyte counts when comparing the negative and re-positive PCT results (all p >0.05).\n\nConclusionHeterogeneity between CT features and RT-PCR results was found in COVID-19, especially in some recovered patients with negative RT-PCR results. Our study highlights that both RT-PCR and chest CT should be considered as the key determinants for the diagnosis and management of COVID-19 patients.",
+    "rel_num_authors": 17,
+    "rel_authors": [
+      {
+        "author_name": "Hang Fu",
+        "author_inst": "Department of Radiology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospi"
+      },
+      {
+        "author_name": "Huayan Xu",
+        "author_inst": "Department of Radiology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospi"
+      },
+      {
+        "author_name": "Na Zhang",
+        "author_inst": "Department of Radiology, Public Health Clinical Center of Chengdu, Cheng Du, China"
+      },
+      {
+        "author_name": "Hong Xu",
+        "author_inst": "Department of Ultrasonography, West China Second University Hospital, Sichuan University, Chengdu, China"
+      },
+      {
+        "author_name": "Zhenlin Li",
+        "author_inst": "Department of Radiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China"
+      },
+      {
+        "author_name": "Huizhu Chen",
+        "author_inst": "Department of Radiology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospi"
+      },
+      {
+        "author_name": "Rong Xu",
+        "author_inst": "Department of Radiology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospi"
+      },
+      {
+        "author_name": "Ran Sun",
+        "author_inst": "Department of Radiology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospi"
+      },
+      {
+        "author_name": "Lingyi Wen",
+        "author_inst": "Department of Radiology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospi"
+      },
+      {
+        "author_name": "Linjun Xie",
+        "author_inst": "Department of Radiology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospi"
+      },
+      {
+        "author_name": "Hui Liu",
+        "author_inst": "Department of Radiology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospi"
+      },
+      {
+        "author_name": "Kun Zhang",
+        "author_inst": "Department of Radiology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospi"
+      },
+      {
+        "author_name": "Chuan Fu",
+        "author_inst": "Department of Radiology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospi"
+      },
+      {
+        "author_name": "Keke Hou",
+        "author_inst": "Department of Radiology, Public Health Clinical Center of Chengdu, Cheng Du, China"
+      },
+      {
+        "author_name": "Zhigang Yang",
+        "author_inst": "Department of Radiology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China"
+      },
+      {
+        "author_name": "Ming Yang",
+        "author_inst": "Department of Respiratory Medicine, Public Health Clinical Center of Chengdu, Cheng Du, China"
+      },
+      {
+        "author_name": "Yingkun Guo Sr.",
+        "author_inst": "Department of Radiology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospi"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.03.19.20038539",
     "rel_title": "Clinical Characteristics of Coronavirus Disease 2019 in Hainan, China",
@@ -1582557,413 +1581322,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.03.22.002386",
-    "rel_title": "A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing",
-    "rel_date": "2020-03-22",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.22.002386",
-    "rel_abs": "An outbreak of the novel coronavirus SARS-CoV-2, the causative agent of COVID-19 respiratory disease, has infected over 290,000 people since the end of 2019, killed over 12,000, and caused worldwide social and economic disruption1,2. There are currently no antiviral drugs with proven efficacy nor are there vaccines for its prevention. Unfortunately, the scientific community has little knowledge of the molecular details of SARS-CoV-2 infection. To illuminate this, we cloned, tagged and expressed 26 of the 29 viral proteins in human cells and identified the human proteins physically associated with each using affinity-purification mass spectrometry (AP-MS), which identified 332 high confidence SARS-CoV-2-human protein-protein interactions (PPIs). Among these, we identify 66 druggable human proteins or host factors targeted by 69 existing FDA-approved drugs, drugs in clinical trials and/or preclinical compounds, that we are currently evaluating for efficacy in live SARS-CoV-2 infection assays. The identification of host dependency factors mediating virus infection may provide key insights into effective molecular targets for developing broadly acting antiviral therapeutics against SARS-CoV-2 and other deadly coronavirus strains.",
-    "rel_num_authors": 98,
-    "rel_authors": [
-      {
-        "author_name": "David E. Gordon",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Gwendolyn M. Jang",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Mehdi Bouhaddou",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Jiewei Xu",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Kirsten Obernier",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Jeffrey Z. Guo",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Danielle L. Swaney",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Tia A. Tummino",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Ruth Huttenhain",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Robyn M. Kaake",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Alicia L. Richards",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Beril Tutuncuoglu",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Helene Foussard",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Jyoti Batra",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Kelsey Haas",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Maya Modak",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Minkyu Kim",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Paige Haas",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Benjamin J. Polacco",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Hannes Braberg",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Jacqueline M. Fabius",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Manon Eckhardt",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Margaret Soucheray",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Melanie J. Bennett",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Merve Cakir",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Michael J. McGregor",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Qiongyu Li",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Zun Zar Chi Naing",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Yuan Zhou",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Shiming Peng",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Ilsa T. Kirby",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "James E. Melnyk",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "John S Chorba",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Kevin Lou",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Shizhong A. Dai",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Wenqi Shen",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Ying Shi",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Ziyang Zhang",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Inigo Barrio-Hernandez",
-        "author_inst": "EMBL-EBI"
-      },
-      {
-        "author_name": "Danish Memon",
-        "author_inst": "EMBL-EBI"
-      },
-      {
-        "author_name": "Claudia Hernandez-Armenta",
-        "author_inst": "EMBL-EBI"
-      },
-      {
-        "author_name": "Christopher J.P. Mathy",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Tina Perica",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Kala B. Pilla",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Sai J. Ganesan",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Daniel J. Saltzberg",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Rakesh Ramachandran",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Xi Liu",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Sara B. Rosenthal",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Lorenzo Calviello",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Srivats Venkataramanan",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Jose Liboy-Lugo",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Yizhu Lin",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Stephanie A. Wankowicz",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Markus Bohn",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Phillip P. Sharp",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Raphael Trenker",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Janet M. Young",
-        "author_inst": "Fred Hutchinson Cancer Research Center"
-      },
-      {
-        "author_name": "Devin A. Cavero",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Joseph Hiatt",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Theo Roth",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Ujjwal Rathore",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Advait Subramanian",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Julia Noack",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Mathieu Hubert",
-        "author_inst": "Institut Pasteur"
-      },
-      {
-        "author_name": "Ferdinand Roesch",
-        "author_inst": "Institut Pasteur"
-      },
-      {
-        "author_name": "Thomas Vallet",
-        "author_inst": "Institut Pasteur"
-      },
-      {
-        "author_name": "Bj\u00f6rn Meyer",
-        "author_inst": "Institut Pasteur"
-      },
-      {
-        "author_name": "Kris M. White",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Lisa Miorin",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Oren S. Rosenberg",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Kliment A. Verba",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "David Agard",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Melanie Ott",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Michael Emerman",
-        "author_inst": "Fred Hutchinson Cancer Research Center"
-      },
-      {
-        "author_name": "Davide Ruggero",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Adolfo Garc\u00ed-Sastre",
-        "author_inst": "Icahn School of Medicine at Mount Sinai"
-      },
-      {
-        "author_name": "Natalia Jura",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Mark von Zastrow",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Jack Taunton",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Alan Ashworth",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Olivier Schwartz",
-        "author_inst": "Institut Pasteur"
-      },
-      {
-        "author_name": "Marco Vignuzzi",
-        "author_inst": "Institut Pasteur"
-      },
-      {
-        "author_name": "Shaeri Mukherjee",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Matt Jacobson",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Harmit S. Malik",
-        "author_inst": "Fred Hutchinson Cancer Research Center"
-      },
-      {
-        "author_name": "Danica G Fujimori",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Trey Ideker",
-        "author_inst": "University of California San Diego"
-      },
-      {
-        "author_name": "Charles S Craik",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Stephen Floor",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "James S. Fraser",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "John Gross",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Andrej Sali",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Tanja Kortemme",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Pedro Beltrao",
-        "author_inst": "EMBL-EBI"
-      },
-      {
-        "author_name": "Kevan Shokat",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Brian K. Shoichet",
-        "author_inst": "UCSF"
-      },
-      {
-        "author_name": "Nevan J. Krogan",
-        "author_inst": "QBI COVID-19 Research Group (QCRG); University of California San Francisco, Quantitative Biosciences Institute (QBI); J. David Gladstone Institutes"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "systems biology"
-  },
   {
     "rel_doi": "10.1101/2020.03.16.20036723",
     "rel_title": "Building a COVID-19 Vulnerability Index",
@@ -1583266,6 +1581624,89 @@
     "type": "new results",
     "category": "biochemistry"
   },
+  {
+    "rel_doi": "10.1101/2020.03.21.001628",
+    "rel_title": "Respiratory disease and virus shedding in rhesus macaques inoculated with SARS-CoV-2",
+    "rel_date": "2020-03-21",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.21.001628",
+    "rel_abs": "An outbreak of a novel coronavirus, now named SARS-CoV-2, causing respiratory disease and a [~]2% case fatality rate started in Wuhan, China in December 2019. Following unprecedented rapid global spread, the World Health Organization declared COVID-19 a pandemic on March 11, 2020. Although data on disease in humans are emerging at a steady pace, certain aspects of the pathogenesis of SARS-CoV-2 can only be studied in detail in animal models, where repeated sampling and tissue collection is possible. Here, we show that SARS-CoV-2 causes respiratory disease in infected rhesus macaques, with disease lasting 8-16 days. Pulmonary infiltrates, a hallmark of human disease, were visible in lung radiographs of all animals. High viral loads were detected in swabs from the nose and throat of all animals as well as in bronchoalveolar lavages; in one animal we observed prolonged rectal shedding. Taken together, the rhesus macaque recapitulates moderate disease observed in the majority of human cases. The establishment of the rhesus macaque as a model of COVID-19 will increase our understanding of the pathogenesis of this disease and will aid development and testing of medical countermeasures.",
+    "rel_num_authors": 17,
+    "rel_authors": [
+      {
+        "author_name": "Vincent Munster",
+        "author_inst": "NIAID"
+      },
+      {
+        "author_name": "Friederike Feldmann",
+        "author_inst": "NIAID"
+      },
+      {
+        "author_name": "Brandi Williamson",
+        "author_inst": "NIAID"
+      },
+      {
+        "author_name": "Neeltje van Doremalen",
+        "author_inst": "NIAID"
+      },
+      {
+        "author_name": "Lizzette Perez-Perez,",
+        "author_inst": "NIAID"
+      },
+      {
+        "author_name": "Jonathan Schultz",
+        "author_inst": "NIAID"
+      },
+      {
+        "author_name": "Kimberly Meade-White",
+        "author_inst": "NIAID"
+      },
+      {
+        "author_name": "Atsushi Okumura",
+        "author_inst": "NIAID"
+      },
+      {
+        "author_name": "Julie Callison",
+        "author_inst": "NIAID"
+      },
+      {
+        "author_name": "Beniah Brumbaugh",
+        "author_inst": "NIAID"
+      },
+      {
+        "author_name": "Victoria Avanzato",
+        "author_inst": "NIAID"
+      },
+      {
+        "author_name": "Rebecca Rosenke",
+        "author_inst": "NIAID"
+      },
+      {
+        "author_name": "Patrick Hanley",
+        "author_inst": "NIAID"
+      },
+      {
+        "author_name": "Greg Saturday",
+        "author_inst": "NIAID"
+      },
+      {
+        "author_name": "Dana Scott",
+        "author_inst": "NIAID"
+      },
+      {
+        "author_name": "Elizabeth Fischer",
+        "author_inst": "NIAID"
+      },
+      {
+        "author_name": "Emmie de Wit",
+        "author_inst": "NIAID, NIH"
+      }
+    ],
+    "version": "1",
+    "license": "cc0",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2020.03.19.998179",
     "rel_title": "Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino-acid deletion in nsp2 (Asp268Del)",
@@ -1584395,37 +1582836,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.03.18.20036731",
-    "rel_title": "Preliminary evidence that higher temperatures are associated with lower incidence of COVID-19, for cases reported globally up to 29th February 2020",
-    "rel_date": "2020-03-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.18.20036731",
-    "rel_abs": "Seasonal variation in COVID-19 incidence could impact the trajectory of the pandemic. Using global line-list data on COVID-19 cases reported until 29th February 2020 and global gridded temperature data, and after adjusting for surveillance capacity and time since first imported case, higher average temperature was strongly associated with lower COVID-19 incidence for temperatures of 1{degrees}C and higher. However, temperature explained a relatively modest amount of the total variation in COVID-19 incidence. These preliminary findings support stringent containment efforts in Europe and elsewhere.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Melanie Bannister-Tyrrell",
-        "author_inst": "Ausvet"
-      },
-      {
-        "author_name": "Anne Meyer",
-        "author_inst": "Ausvet Europe"
-      },
-      {
-        "author_name": "Celine Faverjon",
-        "author_inst": "Ausvet Europe"
-      },
-      {
-        "author_name": "Angus Cameron",
-        "author_inst": "Ausvet Europe"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.03.16.20034934",
     "rel_title": "Advance of Novel Coronavirus Registration Clinical Trial",
@@ -1584688,6 +1583098,37 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "allergy and immunology"
   },
+  {
+    "rel_doi": "10.1101/2020.03.16.20037176",
+    "rel_title": "Hundreds of severe pediatric COVID-19 infections in Wuhan prior to the lockdown",
+    "rel_date": "2020-03-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.16.20037176",
+    "rel_abs": "Before January 22, 2020, only one pediatric case of COVID-19 was reported in mainland China1,2. However, a retrospective surveillance study3 identified six children who had been hospitalized for COVID-19 in one of three central Wuhan hospitals between January 7th and January 15th. Given that Wuhan has over 395 other hospitals, there may have been far more severe pediatric cases than reported.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Zhanwei Du",
+        "author_inst": "University of Texas at Austin"
+      },
+      {
+        "author_name": "Ciara Nugent",
+        "author_inst": "University of Texas at Austin"
+      },
+      {
+        "author_name": "Benjamin J Cowling",
+        "author_inst": "The University of Hong Kong"
+      },
+      {
+        "author_name": "Lauren Ancel Meyers",
+        "author_inst": "The University of Texas at Austin"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.03.18.20038125",
     "rel_title": "Non-severe vs severe symptomatic COVID-19: 104 cases from the outbreak on the cruise ship \"Diamond Princess\" in Japan",
@@ -1585761,37 +1584202,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.03.17.20037671",
-    "rel_title": "Modeling and Forecasting Trend of COVID-19 Epidemic in Iran",
-    "rel_date": "2020-03-20",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.17.20037671",
-    "rel_abs": "BackgroundCOVID-19 is an emerging disease and precise data are not available in the world and Iran. this study aimed to determine the epidemic trend and prediction of COVID-19 in Iran.\n\nMethodsThis study is a secondary data analysis and modeling. We used the daily reports of definitive COVID-19 patients (sampling of severe cases and hospitalization) released by Iran Ministry of Health and Medical Education. Epidemic projection models of Gompertz, Von Bertalanffy and least squared error (LSE) were used to predict the number of cases at April 3, 2020 until May 13, 2020.\n\nResultsR0 in Iran was estimated to be 4.7 that has now fallen to below 2. Given the three different scenarios, the prediction of the patients on April 3, 2020 by Von Bertalanffy, Gompertz and LSE were estimated at 48200, 52500 and 58000, respectively. The number of deceased COVID-19 patients was also estimated to be 3600 individuals using the Von growth model, 4200 ones by Gompertzs model and 4850 ones according to the LSE method. To predict and estimate the number of patients and deaths in the end of epidemic based on Von and Gompertz models, we will have 87000 cases, 4900 and 11000 deaths until 13 May and 1 June, respectively.\n\nConclusionThe process of controlling the epidemic is tangible. If enforcement and public behavior interventions continue with current trends, the control and reduction of the COVID-19 epidemic in Iran will be flat from April 28, until July, 2020 and new cases are expected to decline from the following Iranian new year.\n\nO_TEXTBOX{uparrow}What is \"already known\" in this topicCOVID-19 is an emerging disease, pandemic and precise data on its epidemic are not available in the world and Iran.\n\n [-&gt;]What this article addsthis study is shown, If enforcement and public behavior interventions continue with current trends, the control and reduction of the COVID-19 epidemic in Iran will be flat from April 28, until July, 2020.\n\nC_TEXTBOX",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Ali Ahmadi",
-        "author_inst": "Modeling in Health Research Center, Shahrekord University of Medical Sciences, Shahrekord"
-      },
-      {
-        "author_name": "Yasin Fadaei",
-        "author_inst": "Ph.D of Applied Mathematics, Researcher at Modeling in Health Research Center, Shahrekord University of Medical Sciences, Shahrekord, Iran"
-      },
-      {
-        "author_name": "Majid Shirani",
-        "author_inst": "Department of Urology, Shahrekord University of Medical Sciences, Shahrekord, Iran."
-      },
-      {
-        "author_name": "Fereydoon Rahmani",
-        "author_inst": "Department of Infectious Disease, School of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran."
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.03.18.20038117",
     "rel_title": "Predicting the epidemic trend of COVID-19 in China and across the world using the machine learning approach",
@@ -1585962,6 +1584372,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health policy"
   },
+  {
+    "rel_doi": "10.1101/2020.03.16.20037291",
+    "rel_title": "Short-range airborne route dominates exposure of respiratory infection during close contact",
+    "rel_date": "2020-03-20",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.16.20037291",
+    "rel_abs": "A susceptible person experiences the highest exposure risk of respiratory infection when he or she is in close proximity with an infected person. The large droplet route has been commonly believed to be dominant for most respiratory infections since the early 20th century, and the associated droplet precaution is widely known and practiced in hospitals and in the community. The mechanism of exposure to droplets expired at close contact, however, remains surprisingly unexplored. In this study, the exposure to exhaled droplets during close contact (< 2 m) via both the short-range airborne and large droplet sub-routes is studied using a simple mathematical model of expired flows and droplet dispersion/deposition/inhalation, which enables the calculation of exposure due to both deposition and inhalation. The short-range airborne route is found to dominate at most distances studied during both talking and coughing. The large droplet route only dominates when the droplets are larger than 100 m and when the subjects are within 0.2 m while talking or 0.5 m while coughing. The smaller the exhaled droplets, the more important the short-range airborne route. The large droplet route contributes less than 10% of exposure when the droplets are smaller than 50 m and when the subjects are more than 0.3 m apart, even while coughing.\n\nPractical implicationsOur simple but novel analysis shows that conventional surgical masks are not effective if most infectious viruses are contained in fine droplets, and non-conventional intervention methods such as personalised ventilation should be considered as infection prevention strategies given the possible dominance of the short-range airborne route, although further clinical evidence is needed.\n\nNomenclatureO_ST_ABSSubscriptC_ST_ABSi Droplets of different diameter groups (i = 1, 2, ..., N)\n\nLD Large droplet route\n\nSR Short-range airborne route\n\nSymbolsA0 Area of source mouth [m2]\n\nAE Aspiration efficiency [-]\n\nAr0 Archimedes number [-]\n\nbg Gaussian half width [m]\n\nbt Top-hat half width [m]\n\nCD Drag coefficient [-]\n\nCI Specific heat of liquid [J*kg-1*K-1]\n\nCs Specific heat of solid [J*kg-1*K-1]\n\nCT Correction factor for diffusion coefficient due to temperature dependence [-]\n\ndd Droplet diameter [m]\n\ndd0 Droplet initial diameter [m]\n\nde1 Major axis of eye ellipse [m]\n\nde2 Minor axis of eye ellipse [m]\n\ndh Characteristic diameter of human head [m]\n\ndm Mouth diameter [m]\n\ndn Nostril diameter [m]\n\nD{infty} Binary diffusion coefficient far from droplet [m2*s-1]\n\nDE Deposition efficiency [-]\n\neLD Exposure due to large droplet route [L]\n\neSR Exposure due to short-range airborne route [L]\n\ng Gravitational acceleration [m*s-2]\n\nIv Mass current [kg*s-1]\n\nIF Inhalation fraction [-]\n\nKc Constant (=0.3) [-]\n\nKg Thermal conductivity of air [W*m-1*K-1]\n\nLS Exposure ratio between large droplet and short-range airborne [-]\n\nLv Latent heat of vaporization [J*kg-1]\n\nmd Droplet mass [kg]\n\nmI Mass of liquid in a droplet [kg]\n\nms Mass of solid in a droplet [kg]\n\nM0 Jet initial momentum [m4*s-2]\n\nMW Molecular weight of H2O [kg*mol-1]\n\nMF Membrane fraction [-]\n\nn Number of droplets [n]\n\nn0 Number of droplets expelled immediately at mouth [n]\n\nNin Number of droplets entering the inhalation zone [n]\n\nNm Number of droplets potentially deposited on mucous membranes [n]\n\nNt Total number of released droplets [n]\n\nNu Nusselt number [-]\n\np Total pressure [Pa]\n\npv{infty} Vapour pressure distant from droplet surface [Pa]\n\npvs Vapour pressure at droplet surface [Pa]\n\nQjet Jet flow rate [m3*s-1]\n\nr Radial distance away from jet centreline [m]\n\nrd Droplet radius [m]\n\nR Radius of jet potential core [m]\n\nRg Universal gas constant [J*K-1*mol-1]\n\ns Jet centreline trajectory length [m]\n\nSin Width of region on sampler enclosed by limiting stream surface [m]\n\nSh Sherwood number [-]\n\nStc Stokes number in convergent part of air stream [-]\n\nSth Stokes number for head [-]\n\nStm Stokes number for mouth [-]\n\nt Time [s]\n\nT0 Initial temperature of jet [K]\n\nT{infty} Ambient temperature [K]\n\nTd Droplet temperature [K]\n\nu0 Initial velocity at mouth outlet [m*s-1]\n\nud Droplet velocity [m*s-1]\n\nug Gaussian velocity [m*s-1]\n\nugas Gas velocity [m*s-1]\n\nugc Gaussian centreline velocity [m*s-1]\n\nuin Inhalation velocity [m*s-1]\n\nut Top-hat velocity [m*s-1]\n\nvp Individual droplet volume considering evaporation [m3]\n\nx Horizontal distance between source and target [m]\n\nz Jet vertical centreline position [m]\n\n{rho}0 Jet initial density [kg*m-3]\n\n{rho}{infty}Ambient air density [kg*m-3]\n\n{rho}d Droplet density [kg*m-3]\n\n{rho}g Gas density [kg*m-3]\n\n{Delta}{rho}Density difference between jet and ambient air [kg*m-3]\n\ng Gas dynamic viscosity [Pa*s]\n\n {varphi}Sampling ratio in axisymmetric flow system [-]\n\nc Impaction efficiency in convergent part of air stream [-]",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Wenzhao Chen",
+        "author_inst": "The University of Hong Kong"
+      },
+      {
+        "author_name": "Nan Zhang",
+        "author_inst": "The University of Hong Kong"
+      },
+      {
+        "author_name": "Jianjian Wei",
+        "author_inst": "Zhejiang University"
+      },
+      {
+        "author_name": "Hui-Ling YEN",
+        "author_inst": "The University of Hong Kong"
+      },
+      {
+        "author_name": "Yuguo Li",
+        "author_inst": "The University of Hong Kong"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.03.17.20037903",
     "rel_title": "Double-Quencher Probes Improved the Detection Sensitivity of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by One-Step RT-PCR",
@@ -1587343,53 +1585788,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "neurology"
   },
-  {
-    "rel_doi": "10.1101/2020.03.15.20036533",
-    "rel_title": "Is a 14-day quarantine period optimal for effectively controlling coronavirus disease 2019 (COVID-19)?",
-    "rel_date": "2020-03-18",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.15.20036533",
-    "rel_abs": "BackgroundThe outbreak of a new coronavirus (SARS-CoV-2) disease (Covid-19) has become pandemic. To be more effectively controlling the disease, it is critical to set up an optimal quarantine period so that about 95% of the cases developing symptoms will be retained for isolation. At the moment, the WHO-established quarantine period is 14 days based on previous reports which had studied small sizes of hospitalized cases (10 and [~]100, respectively), however, over 80% of adult- and 95% of child-cases were not necessary to stay in hospitals, and therefore, had not been hospitalized. Therefore, we are questioning if the current-inferred median incubation time is representative for the whole Covid-19 population, and if the current quarantine period is optimal.\n\nMethodsWe compiled and analyzed the patient-level information of 2015 laboratory-confirmed Covid-19 cases including 99 children in 28 Chinese provinces. This cohort represents a wide-range spectrum of Covid-19 disease with both hospitalized and non-hospitalized cases.\n\nResultsThe full range of incubation periods of the Covid-19 cases ranged from 0 to 33 days among 2015 cases. There were 6 (0.13%) symptom-free cases including 4 females with a median age of 25.5 years and 2 males with a median age of 36 years. The median incubation period of both male and female adults was similar (7-day) but significantly shorter than that (9-day) of child cases (P=0.02). This cohort contained 4 transmission generations, and incubation periods of the cases between generations were not significantly different, suggesting that the virus has not been rapidly adapted to human beings. Interestingly, incubation periods of 233 cases (11.6%) were longer than the WHO-established quarantine period (14 days). Data modeling suggested that if adults take an extra 4-day or 7-day of isolation (i.e., a quarantine period of 18 or 21 days), 96.2% or 98.3%, respectively, of the people who are developing symptoms will be more effectively quarantined. Patients transmitted via lunch/dinner parties (i.e., gastrointestinal tract infection through oral transmission) had a significantly longer incubation period (9-day) than other adults transmitted via respiratory droplets or contaminated surfaces and objects (P<0.004).\n\nConclusionsThe whole Covid-19 population including both hospitalized and non-hospitalized cases had a median incubation period of 7-day for adults, which is 1.8-day longer than the hospitalized cases reported previously. An extension of the adult quarantine period to 18 days or 21 days could be more effective in preventing virus-spreading and controlling the disease. The cases transmitted by lunch/dinner parties could be infected first in the gastrointestinal tract through oral transmission and then infected in the respiratory system so that they had a longer incubation period.",
-    "rel_num_authors": 8,
-    "rel_authors": [
-      {
-        "author_name": "Xue Jiang",
-        "author_inst": "Shanghai Mental Health Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China"
-      },
-      {
-        "author_name": "Yawei Niu",
-        "author_inst": "Cumming School Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada"
-      },
-      {
-        "author_name": "Xiong Li",
-        "author_inst": "Cumming School Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada"
-      },
-      {
-        "author_name": "Lin Li",
-        "author_inst": "Cumming School Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada"
-      },
-      {
-        "author_name": "Wenxiang Cai",
-        "author_inst": "Shanghai Mental Health Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China"
-      },
-      {
-        "author_name": "Yucan Chen",
-        "author_inst": "Shanghai Mental Health Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China"
-      },
-      {
-        "author_name": "Bo Liao",
-        "author_inst": "School of Mathematics and Statistics, Hainan Normal University, Haikou, Hainan, China"
-      },
-      {
-        "author_name": "Edwin Wang",
-        "author_inst": "Cumming School Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.03.13.20035345",
     "rel_title": "Forecasting of COVID-19 Confirmed Cases in Different Countries with ARIMA Models",
@@ -1587640,6 +1586038,109 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.03.16.994152",
+    "rel_title": "Characterization of the SARS-CoV-2 Spike in an Early Prefusion Conformation",
+    "rel_date": "2020-03-17",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.16.994152",
+    "rel_abs": "Pandemic coronavirus disease 2019 (COVID-19) is caused by the emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), for which there are no efficacious vaccines or therapeutics that are urgently needed. We expressed three versions of spike (S) proteins--receptor binding domain (RBD), S1 subunit and S ectodomain--in insect cells. RBD appears monomer in solutions, whereas S1 and S associate into homotrimer with substantial glycosylation. The three proteins confer excellent antigenicity with six convalescent COVID-19 patient sera. Cryo-electron microscopy (cryo-EM) analyses indicate that the SARS-CoV-2 S trimer dominate in a unique conformation distinguished from the classic prefusion conformation of coronaviruses by the upper S1 region at lower position ~15 [A] proximal to viral membrane. Such conformation is proposed as an early prefusion state for the SARS-CoV-2 spike that may broaden the knowledge of coronavirus and facilitate vaccine development.",
+    "rel_num_authors": 22,
+    "rel_authors": [
+      {
+        "author_name": "Tingting Li",
+        "author_inst": "Xiamen University"
+      },
+      {
+        "author_name": "Qingbing Zheng",
+        "author_inst": "Xiamen University"
+      },
+      {
+        "author_name": "Hai Yu",
+        "author_inst": "Xiamen University"
+      },
+      {
+        "author_name": "Dinghui Wu",
+        "author_inst": "The First Affiliated Hospital of Xiamen University"
+      },
+      {
+        "author_name": "Wenhui Xue",
+        "author_inst": "Xiamen University"
+      },
+      {
+        "author_name": "Yuyun Zhang",
+        "author_inst": "Xiamen University"
+      },
+      {
+        "author_name": "Xiaofen Huang",
+        "author_inst": "Xiamen University"
+      },
+      {
+        "author_name": "Lizhi Zhou",
+        "author_inst": "Xiamen University"
+      },
+      {
+        "author_name": "Zhigang Zhang",
+        "author_inst": "Xiamen University"
+      },
+      {
+        "author_name": "Zhenghui Zha",
+        "author_inst": "Xiamen University"
+      },
+      {
+        "author_name": "Tingting Chen",
+        "author_inst": "Xiamen University"
+      },
+      {
+        "author_name": "Zhiping Wang",
+        "author_inst": "Xiamen University"
+      },
+      {
+        "author_name": "Jie Chen",
+        "author_inst": "Xiamen University"
+      },
+      {
+        "author_name": "Hui Sun",
+        "author_inst": "Xiamen University"
+      },
+      {
+        "author_name": "Tingting Deng",
+        "author_inst": "Xiamen University"
+      },
+      {
+        "author_name": "Yingbin Wang",
+        "author_inst": "Xiamen University"
+      },
+      {
+        "author_name": "Yixin Chen",
+        "author_inst": "Xiamen University"
+      },
+      {
+        "author_name": "Qinjian Zhao",
+        "author_inst": "Xiamen University"
+      },
+      {
+        "author_name": "Jun Zhang",
+        "author_inst": "Xiamen University"
+      },
+      {
+        "author_name": "Ying Gu",
+        "author_inst": "Xiamen University"
+      },
+      {
+        "author_name": "Shaowei Li",
+        "author_inst": "Xiamen University"
+      },
+      {
+        "author_name": "Ningshao Xia",
+        "author_inst": "Xiamen University"
+      }
+    ],
+    "version": "1",
+    "license": "",
+    "type": "new results",
+    "category": "molecular biology"
+  },
   {
     "rel_doi": "10.1101/2020.03.13.20035253",
     "rel_title": "Impact of city and residential unit lockdowns on prevention and control of COVID-19",
@@ -1588905,105 +1587406,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.03.17.995639",
-    "rel_title": "Comparative Pathogenesis Of COVID-19, MERS And SARS In A Non-Human Primate Model",
-    "rel_date": "2020-03-17",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.17.995639",
-    "rel_abs": "A novel coronavirus, SARS-CoV-2, was recently identified in patients with an acute respiratory syndrome, COVID-19. To compare its pathogenesis with that of previously emerging coronaviruses, we inoculated cynomolgus macaques with SARS-CoV-2 or MERS-CoV and compared with historical SARS-CoV infections. In SARS-CoV-2-infected macaques, virus was excreted from nose and throat in absence of clinical signs, and detected in type I and II pneumocytes in foci of diffuse alveolar damage and mucous glands of the nasal cavity. In SARS-CoV-infection, lung lesions were typically more severe, while they were milder in MERS-CoV infection, where virus was detected mainly in type II pneumocytes. These data show that SARS-CoV-2 can cause a COVID-19-like disease, and suggest that the severity of SARS-CoV-2 infection is intermediate between that of SARS-CoV and MERS-CoV.\n\nOne Sentence SummarySARS-CoV-2 infection in macaques results in COVID-19-like disease with prolonged virus excretion from nose and throat in absence of clinical signs.",
-    "rel_num_authors": 21,
-    "rel_authors": [
-      {
-        "author_name": "Barry Rockx",
-        "author_inst": "Erasmus MC"
-      },
-      {
-        "author_name": "Thijs Kuiken",
-        "author_inst": "Erasmus MC"
-      },
-      {
-        "author_name": "Sander Herfst",
-        "author_inst": "Erasmus MC"
-      },
-      {
-        "author_name": "Theo Bestebroer",
-        "author_inst": "Erasmus MC"
-      },
-      {
-        "author_name": "Mart Lamers",
-        "author_inst": "Erasmus MC"
-      },
-      {
-        "author_name": "Dennis de Meulder",
-        "author_inst": "Erasmus MC"
-      },
-      {
-        "author_name": "Geert van Amerongen",
-        "author_inst": "Viroclinics Xplore"
-      },
-      {
-        "author_name": "Judith van de Brand",
-        "author_inst": "Erasmus MC"
-      },
-      {
-        "author_name": "Nisreen Okba",
-        "author_inst": "Erasmus MC"
-      },
-      {
-        "author_name": "Debby Schipper",
-        "author_inst": "Erasmus MC"
-      },
-      {
-        "author_name": "Peter van Run",
-        "author_inst": "Erasmus MC"
-      },
-      {
-        "author_name": "Lonneke Leijten",
-        "author_inst": "Erasmus MC"
-      },
-      {
-        "author_name": "Ernst Verschoor",
-        "author_inst": "BPRC"
-      },
-      {
-        "author_name": "Babs Verstrepen",
-        "author_inst": "BPRC"
-      },
-      {
-        "author_name": "Jan Langermans",
-        "author_inst": "BPRC"
-      },
-      {
-        "author_name": "Christian Drosten",
-        "author_inst": "Charite Universitatsmedizin"
-      },
-      {
-        "author_name": "Martje Fentener van Vlissingen",
-        "author_inst": "Erasmus MC"
-      },
-      {
-        "author_name": "Ron Fouchier",
-        "author_inst": "Erasmus MC"
-      },
-      {
-        "author_name": "Rik L. de Swart",
-        "author_inst": "Erasmus MC"
-      },
-      {
-        "author_name": "Marion Koopmans",
-        "author_inst": "Erasmus MC"
-      },
-      {
-        "author_name": "Bart Haagmans",
-        "author_inst": "Erasmus MC"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.03.15.20034199",
     "rel_title": "Temporal relationship between outbound traffic from Wuhan and the 2019 coronavirus disease (COVID-19) incidence in China",
@@ -1589234,6 +1587636,49 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.03.14.20035873",
+    "rel_title": "Expected impact of COVID-19 outbreak in a major metropolitan area in Brazil",
+    "rel_date": "2020-03-17",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.14.20035873",
+    "rel_abs": "In January 2020 China reported to the World Health Organization an outbreak of pneumonia of undetermined origin in the city of Wuhan, Hubei. In January 30, 2020, the World Health Organization declared the outbreak of COVID-19 as a Public Health Emergency of International Interest (PHEI).\n\nObjectivesThe aim of this study is to assess the impact of a COVID-19 epidemic in the metropolitan region of Sao Paulo, Brazil.\n\nMethodsWe used a generalized SEIR (Susceptibles, Exposed, Infectious, Recovered) model, with additional Hospitalized variables (SEIHR model) and age-stratified structure to analyze the expected time evolution during the onset of the epidemic in the metropolitan area of Sao Paulo. The model allows to determine the evolution of the number of cases, the number of patients admitted to hospitals and deaths caused by COVID-19. In order to investigate the sensibility of our results with respect to parameter estimation errors we performed Monte Carlo analysis with 100 000 simulations by sampling parameter values from an uniform distribution in the confidence interval.\n\nResultsWe estimate 1 368 (IQR: 880, 2 407) cases, 301 (22%) in older people ([&ge;]60 years), 81 (50, 143) hospitalizations, and 14 (9, 26) deaths in the first 30 days, and 38 583 (IQR: 16 698, 113, 163) cases, 8 427 (21.8%) in older people ([&ge;]60 years), 2181 (914, 6392) hospitalizations, and 397(166, 1205) deaths in the first 60 days.\n\nLimitationsWe supposed a constant transmission probability Pc among different age-groups, and that every severe and critic case will be hospitalized, as well as that the detection capacity in all the primary healthcare services does not change during the outbreak.\n\nConclusionSupposing the reported parameters in the literature apply in the city of Sao Paulo, our study shows that it is expected that the impact of a COVID-19 outbreak will be important, requiring special planning from the authorities. This is the first study for a major metropolitan center in the south hemisphere, and we believe it can provide policy makers with a prognosis of the burden of the pandemic not only in Brazil, but also in other tropical zones, allowing to estimate total cases, hospitalization and deaths, in support to the management of the public health emergence caused by COVID-19.",
+    "rel_num_authors": 7,
+    "rel_authors": [
+      {
+        "author_name": "Tarcisio M Rocha Filho",
+        "author_inst": "International Center for Condensed Matter Physics and Instituto de Fisica, Universidade de Brasilia, Brasilia, DF, BRAZIL"
+      },
+      {
+        "author_name": "Fabiana S. Ganem dos Santos",
+        "author_inst": "Departamento de Imunizacao e Doencas Transmissiveis (DEIDT/SVS), Ministerio da Saude, Brasilia, DF, BRAZIL"
+      },
+      {
+        "author_name": "Victor B Gomes",
+        "author_inst": "Departamento de Imunizacao e Doencas Transmissiveis (DEIDT/SVS), Ministerio da Saude, Brasilia, DF, BRAZIL"
+      },
+      {
+        "author_name": "Thiago A.H. Rocha",
+        "author_inst": "Organizacao Panamericana de Saude (OPAS), Brasilia, DF, BRAZIL"
+      },
+      {
+        "author_name": "Julio H.R. Croda",
+        "author_inst": "Departamento de Imunizacao e Doencas Transmissiveis (DEIDT/SVS), Ministerio da Saude, Brasilia, DF, BRAZIL"
+      },
+      {
+        "author_name": "Walter M Ramalho",
+        "author_inst": "Faculdade de Ceilandia & Nucleo de Medicina Tropical, Universidade de Brasilia, Brasilia, DF, BRAZIL"
+      },
+      {
+        "author_name": "Wildo N Araujo",
+        "author_inst": "Faculdade de Ceilandia & Nucleo de Medicina Tropical, Universidade de Brasilia, Brasilia, DF, BRAZIL"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.03.14.20035956",
     "rel_title": "Assessment of public attention, risk perception, emotional and behavioural responses to the COVID-19 outbreak: social media surveillance in China",
@@ -1590334,41 +1588779,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.03.11.20033639",
-    "rel_title": "Evaluating the effect of public health intervention on the global-wide spread trajectory of Covid-19",
-    "rel_date": "2020-03-16",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.11.20033639",
-    "rel_abs": "As COVID-19 evolves rapidly, the issues the governments of affected countries facing are whether and when to take public health interventions and what levels of strictness of these interventions should be, as well as when the COVID-19 spread reaches the stopping point after interventions are taken. To help governments with policy-making, we developed modified auto-encoders (MAE) method to forecast spread trajectory of Covid-19 of countries affected, under different levels and timing of intervention strategies. Our analysis showed public health interventions should be executed as soon as possible. Delaying intervention 4 weeks after March 8, 2020 would cause the maximum number of cumulative cases of death increase from 7,174 to 133,608 and the ending points of the epidemic postponed from Jun 25 to Aug 22.",
-    "rel_num_authors": 5,
-    "rel_authors": [
-      {
-        "author_name": "Zixin Hu",
-        "author_inst": "State Key Laboratory of Genetic Engineering and Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China; Human"
-      },
-      {
-        "author_name": "Qiyang Ge",
-        "author_inst": "The School of Mathematic Sciences, Fudan University, Shanghai, China"
-      },
-      {
-        "author_name": "Shudi Li",
-        "author_inst": "Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA"
-      },
-      {
-        "author_name": "Li Jin",
-        "author_inst": "State Key Laboratory of Genetic Engineering and Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China; Human"
-      },
-      {
-        "author_name": "Momiao Xiong",
-        "author_inst": "Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.03.12.20034660",
     "rel_title": "Impact assessment of non-pharmaceutical interventions against COVID-19 and influenza in Hong Kong: an observational study",
@@ -1590787,6 +1589197,129 @@
     "type": "new results",
     "category": "genomics"
   },
+  {
+    "rel_doi": "10.1101/2020.03.13.990226",
+    "rel_title": "Reinfection could not occur in SARS-CoV-2 infected rhesus macaques",
+    "rel_date": "2020-03-14",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.13.990226",
+    "rel_abs": "A global pandemic of Corona Virus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome CoV-2 (SARS-CoV-2) is ongoing spread. It remains unclear whether the convalescing patients have a risk of reinfection. Rhesus macaques were rechallenged with SARS-CoV-2 during an early recovery phase from initial infection characterized by weight loss, interstitial pneumonia and systemic viral dissemination mainly in respiratory and gastrointestinal tracts. The monkeys rechallenged with the identical SARS-CoV-2 strain have failed to produce detectable viral dissemination, clinical manifestations and histopathological changes. A notably enhanced neutralizing antibody response might contribute the protection of rhesus macaques from the reinfection by SARS-CoV-2. Our results indicated that primary SARS-CoV-2 infection protects from subsequent reinfection.\n\nOne Sentence SummaryNeutralizing antibodies against SARS-CoV-2 might protect rhesus macaques which have undergone an initial infection from reinfection during early recovery days.",
+    "rel_num_authors": 27,
+    "rel_authors": [
+      {
+        "author_name": "Linlin Bao",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      },
+      {
+        "author_name": "Wei Deng",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      },
+      {
+        "author_name": "Hong Gao",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      },
+      {
+        "author_name": "Chong Xiao",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      },
+      {
+        "author_name": "Jiayi Liu",
+        "author_inst": "Bejing Anzhen Hospital, Capital Medical University."
+      },
+      {
+        "author_name": "Jing Xue",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      },
+      {
+        "author_name": "Qi Lv",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      },
+      {
+        "author_name": "Jiangning Liu",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      },
+      {
+        "author_name": "Pin Yu",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      },
+      {
+        "author_name": "Yanfeng Xu",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      },
+      {
+        "author_name": "Feifei Qi",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      },
+      {
+        "author_name": "Yajin Qu",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      },
+      {
+        "author_name": "Fengdi Li",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      },
+      {
+        "author_name": "Zhiguang Xiang",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      },
+      {
+        "author_name": "Haisheng Yu",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      },
+      {
+        "author_name": "Shuran Gong",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      },
+      {
+        "author_name": "Mingya Liu",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      },
+      {
+        "author_name": "Guanpeng Wang",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      },
+      {
+        "author_name": "Shunyi Wang",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      },
+      {
+        "author_name": "Zhiqi Song",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      },
+      {
+        "author_name": "Ying Liu",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences"
+      },
+      {
+        "author_name": "Wenjie Zhao",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      },
+      {
+        "author_name": "Yunlin Han",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      },
+      {
+        "author_name": "Linna Zhao",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      },
+      {
+        "author_name": "Xing Liu",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      },
+      {
+        "author_name": "Qiang Wei",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      },
+      {
+        "author_name": "Chuan Qin",
+        "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences."
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2020.03.13.990267",
     "rel_title": "Differential Antibody Recognition by Novel SARS-CoV-2 and SARS-CoV Spike Protein Receptor Binding Domains: Mechanistic Insights",
@@ -1592102,77 +1590635,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.03.09.20033365",
-    "rel_title": "Genomic epidemiology of a densely sampled COVID19 outbreak in China",
-    "rel_date": "2020-03-13",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.09.20033365",
-    "rel_abs": "Analysis of genetic sequence data from the pandemic SARS Coronavirus 2 can provide insights into epidemic origins, worldwide dispersal, and epidemiological history. With few exceptions, genomic epidemiological analysis has focused on geographically distributed data sets with few isolates in any given location. Here we report an analysis of 20 whole SARS-CoV 2 genomes from a single relatively small and geographically constrained outbreak in Weifang, Peoples Republic of China. Using Bayesian model-based phylodynamic methods, we estimate the reproduction number for the outbreak to be 2.6 (95% CI:1.5-5). We further estimate the number of infections through time and compare these estimates to confirmed diagnoses by the Weifang Centers for Disease Control. We find that these estimates are consistent with reported cases and there is unlikely to be a large undiagnosed burden of infection over the period we studied.",
-    "rel_num_authors": 14,
-    "rel_authors": [
-      {
-        "author_name": "Lily Geidelberg",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Han Fu",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Haowei Wang",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Xiauoyue Xi",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Wei Chen",
-        "author_inst": "Department of Microbiology, Weifang Center for Disease Control and Prevention, Weifang 261061, China."
-      },
-      {
-        "author_name": "Dehui Liu",
-        "author_inst": "Department of Microbiology, Weifang Center for Disease Control and Prevention, Weifang 261061, China."
-      },
-      {
-        "author_name": "Yingying Chen",
-        "author_inst": "Department of Microbiology, Weifang Center for Disease Control and Prevention, Weifang 261061, China."
-      },
-      {
-        "author_name": "Mengmeng Tian",
-        "author_inst": "Department of Microbiology, Weifang Center for Disease Control and Prevention, Weifang 261061, China."
-      },
-      {
-        "author_name": "Wei Tan",
-        "author_inst": "Department of Respiratory Medicine, Weifang People's Hospital, Weifang 261061, China."
-      },
-      {
-        "author_name": "Junjie Zai",
-        "author_inst": "Immunology Innovation Team, School of Medicine, Ningbo University, Ningbo 315211, China."
-      },
-      {
-        "author_name": "Wanying Zan",
-        "author_inst": "Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China."
-      },
-      {
-        "author_name": "Erik Volz",
-        "author_inst": "Imperial College London"
-      },
-      {
-        "author_name": "Xinguang Li",
-        "author_inst": "Hubei Engineering Research Center of Viral Vector, Wuhan University of Bioengineering, Wuhan, 430415, China."
-      },
-      {
-        "author_name": "Qing Nie",
-        "author_inst": "Department of Microbiology, Weifang Center for Disease Control and Prevention, Weifang 261061, China."
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.03.09.20033241",
     "rel_title": "The demand for inpatient and ICU beds for COVID-19 in the US: lessons from Chinese cities",
@@ -1592419,6 +1590881,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.03.10.20033738",
+    "rel_title": "Effectiveness of isolation and contact tracing for containment and slowing down a COVID-19 epidemic: a modelling study",
+    "rel_date": "2020-03-13",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.10.20033738",
+    "rel_abs": "BackgroundNovel coronavirus (SARS-CoV-2) has extended its range of transmission in all parts of the world, with substantial variation in rates of transmission and severity of associated disease. Many countries have implemented social distancing as a measure to control further spread.\n\nMethodsWe evaluate whether and under which conditions containment or slowing down COVID-19 epidemics are possible by isolation and contact tracing in settings with various levels of social distancing. We use a stochastic transmission model in which every person generates novel infections according to a probability distribution that is affected by the incubation period distribution (time from infection to symptoms), distribution of the latent period (time from infection to onset of infectiousness), and overall transmissibility. The model distinguishes between close contacts (e.g., within a household) and other contacts in the population. Social distancing affects the number of contacts outside but not within the household.\n\nFindingsThe proportion of asymptomatic or unascertained cases has a strong impact on the controllability of the disease. If the proportion of asymptomatic infections is larger than 30%, contact tracing and isolation cannot achieve containment for an R0 of 2.5. Achieving containment by social distancing requires a reduction of numbers of non-household contacts by around 90%. Depending on the realized level of contact reduction, tracing and isolation of only household contacts, or of household and non-household contacts are necessary to reduce the effective reproduction number to below 1. A combination of social distancing with isolation and contact tracing leads to synergistic effects that increase the prospect of containment.\n\nInterpretationIsolation and contact tracing can be an effective means to slow down epidemics, but only if the majority of cases are ascertained. In a situation with social distancing, contact tracing can act synergistically and tip the scale towards containment, and can therefore be a tool for controlling COVID-19 epidemics as part of an exit strategy from current lockdown measures.\n\nFundingThis research was partly funded by ZonMw project number 91216062.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSAs of 8 April 2020, the novel coronavirus (SARS-CoV-2) has spread to more than 170 countries and has caused near 90,000 deaths of COVID-19 worldwide. In the absence of effective medicines and vaccines, the preventive measures are limited to social distancing, isolation of confirmed and suspected cases, and identification and quarantining of their contacts. Evidence suggests that a substantial portion of transmission may occur before the onset of symptoms and before cases can be isolated, and that many cases remain unascertained. This has potentially important implications for the prospect of containment by combinations of these measures.\n\nAdded value of this studyUsing a stochastic transmission model armed with current best estimates of epidemiological parameters, we evaluated under which conditions containment could be achieved with combinations of social distancing, isolation and contact tracing. We investigated the level of social distancing needed for containment, and how an additional implementation of isolation and contact tracing may likely help to in reducing the effective reproduction number to below 1, the critical threshold. We analyzed what proportion of household and non-household contacts need to be isolated effectively to achieve containment depending on the level of social distancing in the population. We estimated the impact of combinations of these measures on epidemic growth rate and doubling time for the number of infections. We find that under realistic assumptions on the level of social distancing, additional isolation and contact tracing are needed for stopping the epidemic. Whether quarantining only household contacts is sufficient, depends on levels of social distancing and timeliness of tracing and isolation.\n\nImplications of all the available evidenceOur analyses based on best understanding of the epidemiology of COVID-19, highlight that if social distancing is not complete, isolation and contact tracing at least of household contacts can help to delay and lower the epidemic peak. High levels of timely contact tracing of household and non-household contacts may be sufficient to control the epidemic.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Mirjam E Kretzschmar",
+        "author_inst": "University Medical Center Utrecht, Utrecht University"
+      },
+      {
+        "author_name": "Ganna Rozhnova",
+        "author_inst": "University Medical Center Utrecht, Utrecht University"
+      },
+      {
+        "author_name": "Michiel E van Boven",
+        "author_inst": "University Medical Center Utrecht, Utrecht University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.03.10.20033522",
     "rel_title": "Protocol for a randomized controlled trial testing inhaled nitric oxide therapy in spontaneously breathing patients with COVID-19",
@@ -1594379,25 +1592868,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.03.10.985499",
-    "rel_title": "In silico Design of novel Multi-epitope recombinant Vaccine based on Coronavirus surface glycoprotein",
-    "rel_date": "2020-03-10",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.10.985499",
-    "rel_abs": "It is of special significance to find a safe and effective vaccine against coronavirus disease 2019 (COVID-19) that can induce T cell and B cell -mediated immune responses. There is currently no vaccine to prevent COVID-19. In this project, a novel multi-epitope vaccine for COVID-19 virus based on surface glycoprotein was designed through application of bioinformatics methods. At the first, seventeen potent linear B-cell and T-cell binding epitopes from surface glycoprotein were predicted in silico, then the epitopes were joined together via different linkers. The ability of the selected epitopes to induce interferon-gamma was evaluate using IFNepitope web server. One final vaccine was constructed which composed of 398 amino acids and attached to 50S ribosomal protein L7/L12 as adjuvant. Physicochemical properties, as well as antigenicity in the proposed vaccines, were checked for defining the vaccine stability and its ability to induce cell-mediated immune responses. Three-dimensional structure of the mentioned vaccine was subjected to the molecular docking studies with MHC-I and MHC-II molecules. The results proposed that the multi-epitope vaccine with 50S ribosomal protein L7/L12 was a stable construct with high aliphatic content and high antigenicity.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Mandana Behbahani",
-        "author_inst": "uni of esfahan"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "new results",
-    "category": "immunology"
-  },
   {
     "rel_doi": "10.1101/2020.03.06.20032425",
     "rel_title": "Prevalence and Risk Factors of Acute Posttraumatic Stress Symptoms during the COVID-19 Outbreak in Wuhan, China",
@@ -1594724,6 +1593194,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.03.08.20031229",
+    "rel_title": "Mortality of COVID-19 is Associated with Cellular Immune Function Compared to Immune Function in Chinese Han Population",
+    "rel_date": "2020-03-10",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.08.20031229",
+    "rel_abs": "In December 2019, novel coronavirus (SARS-CoV-2) infected pneumonia occurred in Wuhan, China. The number of cases has increased rapidly but information on the clinical characteristics of SARS-CoV-2 pneumonia compared to normal controls in Chinese Han population is limited. Our objective is to describe the clinical characteristics of SARS-CoV-2 pneumonia compared to normal controls in the Chinese Han population. In this case series of 752 patients, the full spectrum of cases is described. Fever was present in 86-90% of the patients. The second most common symptom was cough (49.1-51.0%), fatigue (25.2-27.1%), sputum (20.0-23.1%), and headache (9.8-11.1%). the mortality rate is 4.6% in Wuhan, 1.9% in Beijing, and 0.9% in Shanghai. Our findings showed that the levels of lymphocytes were 0.8(IQR, 0.6-1.1)109/L in Wuhan, 1.0(IQR, 0.7-1.4)109/L in Beijing, and 1.1 (IQR, 0.8-1.5) 109/L in Shanghai before admission to hospitals, respectively, indicating that cellular immune function might relate to the mortality. Based on the reference ranges of normal Chinese Han population and the data of the critically ill patients we have observed, it is recommended that reference ranges of people at high risk of COVID-19 infection are CD3+ lymphocytes below 900 cells/mm3, CD4+ lymphocytes below 500 cells/mm3, and CD8+ lymphocytes below 300 cells/mm3.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Qiang Zeng Sr.",
+        "author_inst": "Chinese PLA General Hospital"
+      },
+      {
+        "author_name": "Yong-zhe Li Sr.",
+        "author_inst": "Peking Union Medical College Hospital"
+      },
+      {
+        "author_name": "Gang Huang Sr.",
+        "author_inst": "Shanghai University of Medicine and Health Sciences"
+      },
+      {
+        "author_name": "Wei Wu Sr.",
+        "author_inst": "Peking Union Medical College and Chinese Academy of Medical Sciences"
+      },
+      {
+        "author_name": "Sheng-yong Dong Sr.",
+        "author_inst": "Chinese PLA General Hospital"
+      },
+      {
+        "author_name": "Yang Xu",
+        "author_inst": "Shanghai University of Medicine and Health Sciences"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.03.08.20029710",
     "rel_title": "A retrospective study of the clinical characteristics of COVID-19 infection in 26 children",
@@ -1595957,45 +1594466,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.03.05.20032003",
-    "rel_title": "The prevalence and influencing factors for anxiety in medical workers fighting COVID-19 in China: A cross-sectional survey",
-    "rel_date": "2020-03-08",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.05.20032003",
-    "rel_abs": "BackgroundThe COVID-19 outbreak caused by the SARS-Cov-2 virus has been sustained in China since December 2019, and could become a pandemic if we do not contain it. The mental health of frontline medical staff is a concern. In this study, we aimed to identify the influencing factors on medical worker anxiety in China during the COVID-19 outbreak.\n\nMethodsWe conducted a cross-sectional study to estimate the prevalence of anxiety among medical staff from 10th February 2020 to 20th February 2020 in China using the Zung Self-rating Anxiety Scale (SAS) to assess anxiety, using the criteria of normal ([&le;]49), mild (50-59), moderate (60- 70) and severe anxiety ([&ge;]70). We used multivariable linear regression to determine the factors (e.g., having direct contact treating infected patients, being a medical staff worker from Hubei province, being a suspect case) for anxiety. We also used adjusted models to confirm independent factors for anxiety after adjusting for gender, age, education and marital status.\n\nResultsOf 512 medical staff from China, 164 healthcare workers (32.03%) had had direct contact by treating infected patients. The prevalence of anxiety was 12.5%, with 53 workers suffering from mild (10.35%), seven workers from moderate (1.36%) and four workers from severe anxiety (0.78%). After adjusting for sociodemographic characteristics (gender, age, education and marital status), medical staff who had had direct contact treating infected patients saw higher anxiety scores than those who had not had direct contact ({beta}value=2.33, CI: 0.65 -4.00; p=0.0068). Similar things were observed in medical staff from Hubei province, compared with those from other parts of China ({beta} value=3.67, CI: 1.44 -5.89; p=0.0013). The most important variable was suspect cases with high anxiety scores, compared to non-suspect cases ({beta}value=4.44, CI: 1.55 -7.33; p=0.0028).\n\nConclusionOur results highlight that government authorities should make early detection of the high risk of anxiety among medical staff a priority, and implement appropriate psychological intervention programs, to prevent medical staff from developing psychological disorders that could potentially exert an adverse effect on combating the COVID-19 epidemic.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Chenyun Liu",
-        "author_inst": "People 's Hospital of Shenzhen Baoan District"
-      },
-      {
-        "author_name": "Yun-zhi Yang",
-        "author_inst": "People's hospital of shenzhen baoan district"
-      },
-      {
-        "author_name": "Xiao Ming Zhang",
-        "author_inst": "people's hospital of shenzhen baoan district"
-      },
-      {
-        "author_name": "Xinying Xu",
-        "author_inst": "People's hospital of shenzhen baoan district"
-      },
-      {
-        "author_name": "Qing-Li Dou",
-        "author_inst": "People's hospital of shenzhen baoan districtP"
-      },
-      {
-        "author_name": "Wen-Wu Zhang",
-        "author_inst": "People's Hospital of Shenzhen Baoan District"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "psychiatry and clinical psychology"
-  },
   {
     "rel_doi": "10.1101/2020.03.05.20031872",
     "rel_title": "Role of temperature and humidity in the modulation of the doubling time of COVID-19 cases",
@@ -1596262,6 +1594732,97 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.03.05.20031591",
+    "rel_title": "Acute Myocardial Injury of Patients with Coronavirus Disease 2019",
+    "rel_date": "2020-03-08",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.05.20031591",
+    "rel_abs": "BackgroundSince the outbreak of the Coronavirus Disease 2019 (COVID-19) in China, respiratory manifestations of the disease have been observed. However, as a fatal comorbidity, acute myocardial injury (AMI) in COVID-19 patients has not been previously investigated in detail. We investigated the clinical characteristics of COVID-19 patients with AMI and determined the risk factors for AMI in them.\n\nMethodsWe analyzed data from 53 consecutive laboratory-confirmed and hospitalized COVID-19 patients (28 men, 25 women; age, 19-81 years). We collected information on epidemiological and demographic characteristics, clinical features, routine laboratory tests (including cardiac injury biomarkers), echocardiography, electrocardiography, imaging findings, management methods, and clinical outcomes.\n\nResultsCardiac complications were found in 42 of the 53 (79.25%) patients: tachycardia (n=15), electrocardiography abnormities (n=11), diastolic dysfunction (n=20), elevated myocardial enzymes (n=30), and AMI (n=6). All the six AMI patients were aged >60 years; five of them had two or more underlying comorbidities (hypertension, diabetes, cardiovascular diseases, and chronic obstructive pulmonary disease). Novel coronavirus pneumonia (NCP) severity was higher in the AMI patients than in patients with non-definite AMI (p<0.001). All the AMI patients required care in intensive care unit; of them, three died, two remain hospitalized. Multivariate analyses showed that C-reactive protein (CRP) levels, NCP severity, and underlying comorbidities were the risk factors for cardiac abnormalities in COVID-19 patients.\n\nConclusionsCardiac complications are common in COVID-19 patients. Elevated CRP levels, underlying comorbidities, and NCP severity are the main risk factors for cardiac complications in COVID-19 patients.",
+    "rel_num_authors": 19,
+    "rel_authors": [
+      {
+        "author_name": "Huayan Xu",
+        "author_inst": "Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University"
+      },
+      {
+        "author_name": "Keke Hou",
+        "author_inst": "Public Health Clinical Center of Chengdu"
+      },
+      {
+        "author_name": "Hong Xu",
+        "author_inst": "West China Second University Hospital, Sichuan University"
+      },
+      {
+        "author_name": "Zhenlin Li",
+        "author_inst": "State Key Laboratory of Biotherapy, West China Hospital, Sichuan University"
+      },
+      {
+        "author_name": "Huizhu Chen",
+        "author_inst": "Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University"
+      },
+      {
+        "author_name": "Na Zhang",
+        "author_inst": "Public Health Clinical Center of Chengdu"
+      },
+      {
+        "author_name": "Rong Xu",
+        "author_inst": "Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University"
+      },
+      {
+        "author_name": "Hang Fu",
+        "author_inst": "Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University"
+      },
+      {
+        "author_name": "Ran Sun",
+        "author_inst": "Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University"
+      },
+      {
+        "author_name": "Lingyi Wen",
+        "author_inst": "Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University"
+      },
+      {
+        "author_name": "Linjun Xie",
+        "author_inst": "Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University"
+      },
+      {
+        "author_name": "Hui Liu",
+        "author_inst": "Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University"
+      },
+      {
+        "author_name": "Kun Zhang",
+        "author_inst": "Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University"
+      },
+      {
+        "author_name": "Joseph B Selvanayagam",
+        "author_inst": "Flinders Medical Centre, Flinders University of South Australia"
+      },
+      {
+        "author_name": "Chuan Fu",
+        "author_inst": "Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University"
+      },
+      {
+        "author_name": "Shihua Zhao",
+        "author_inst": "Cardiac Imaging Center, Fuwai Hospital, National Center for Cardiovascular Diseases of China, Chinese Academy of Medical Sciences and Peking Union Medical Colle"
+      },
+      {
+        "author_name": "Zhigang Yang",
+        "author_inst": "State Key Laboratory of Biotherapy, West China Hospital, Sichuan University"
+      },
+      {
+        "author_name": "Ming Yang",
+        "author_inst": "Public Health Clinical Center of Chengdu"
+      },
+      {
+        "author_name": "Yingkun Guo",
+        "author_inst": "Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, Sichuan university"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "public and global health"
+  },
   {
     "rel_doi": "10.1101/2020.03.04.20031401",
     "rel_title": "Outcome reporting from protocols of clinical trials of Coronavirus Disease 2019 (COVID-19): a review",
@@ -1597490,81 +1596051,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.03.04.20031120",
-    "rel_title": "Human Kidney is a Target for Novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection",
-    "rel_date": "2020-03-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.04.20031120",
-    "rel_abs": "BACKGROUNDThe outbreak of a novel coronavirus (SARS-CoV-2, previously provisionally named 2019 novel coronavirus or 2019-nCoV) since December 2019 in Wuhan, China, has become an emergency of major international concern. Apart from the respiratory system, it is unclear whether SARS-CoV-2 can also directly infect other tissues such as the kidney or induce acute renal failure.\n\nMETHODSWe conducted a retrospective analysis of estimated glomerular filtration rate (eGFR) along with other clinical parameters from 85 patients with laboratory-confirmed COVID-19 admitted to a hospital in Wuhan from January 17, 2020 to March 3, 2020. Kidney tissues from six patients with postmortem examinations were analyzed by Hematoxylin and Eosin (H&E) and in situ expression of viral nucleocaspid protein (NP) antigen, immune cell markers (CD8, CD68 and CD56) and the complement C5b-9 was detected by immunohistochemistry. Moreover, the viral particles in kidneys were also investigated by transmission electronic microscope (EM).\n\nRESULTS27.06% (23/85) patients exhibited acute renal failure (ARF). The eldery patients and cases with comorbidities such as hypertension and heart failure more easily developed ARF (65.22% vs 24.19%, p< 0.001; 69.57% vs 11.29%, p< 0.001, respectively). H&E staining demonstrated kidney tissues from postmortems have severe acute tubular necrosis and lymphocyte infiltration. Immunohistochemistry showed that SARS-CoV-2 NP antigen was accumulated in kidney tubules. EM observation also demonstrated that viruses-like particles are visible in the kidneys. Viral infection not only induces CD68+ macrophages infiltrated into tubulointerstitium, but also enhances complement C5b-9 deposition on tubules.\n\nCONCLUSIONSSARS-CoV-2 induces ARF in COVID-19 patients. Viruses directly infect human kidney tubules to induce acute tubular damage. The viruses not only have direct cytotoxicity, but also initiate CD68+ macrophage together with complement C5b-9 deposition to mediate tubular pathogenesis.",
-    "rel_num_authors": 15,
-    "rel_authors": [
-      {
-        "author_name": "Bo Diao",
-        "author_inst": "Department of Medical Laboratory Center, General Hospital of  Central Theater Command, Wuhan,   China"
-      },
-      {
-        "author_name": "Chenhui Wang",
-        "author_inst": "Institute of Immunology, PLA, Third Military Medical University, Chongqing,China"
-      },
-      {
-        "author_name": "Rongshuai Wang",
-        "author_inst": "Hubei Chongxin Judicial Expertise Center, Wuhan,China"
-      },
-      {
-        "author_name": "Zeqing Feng",
-        "author_inst": "Institute of Immunology, PLA, Third Military Medical University, Chongqing,China"
-      },
-      {
-        "author_name": "Yingjun Tan",
-        "author_inst": "Department of Medical Laboratory Center, General Hospital of  Central Theater Command, Wuhan, Hubei province, China"
-      },
-      {
-        "author_name": "Huiming Wang",
-        "author_inst": "Department of Nephrology, Renmin Hospital of Wuhan University, Wuhan, Hubei province,China"
-      },
-      {
-        "author_name": "Changsong Wang",
-        "author_inst": "Department of Pathology, 989th Hospital of PLA, Luoyang, Henan Province, China"
-      },
-      {
-        "author_name": "Liang Liu",
-        "author_inst": "Hubei Chongxin Judicial Expertise Center, Wuhan, Hubei province,  China"
-      },
-      {
-        "author_name": "Ying Liu",
-        "author_inst": "Department of Medical Laboratory Center, General Hospital of  Central Theater Command, Wuhan,  China"
-      },
-      {
-        "author_name": "Yueping Liu",
-        "author_inst": "Department of Medical Laboratory Center, General Hospital of  Central Theater Command, Wuhan,  China"
-      },
-      {
-        "author_name": "Gang Wang",
-        "author_inst": "Department of Medical Laboratory Center, General Hospital of Central Theater Command, Wuhan, China"
-      },
-      {
-        "author_name": "Zilin Yuan",
-        "author_inst": "Department of Medical Laboratory Center, General Hospital of Central Theater Command, Wuhan, China"
-      },
-      {
-        "author_name": "Liang Ren",
-        "author_inst": "Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, No. 13 Hangkong Road, Wuhan, Hubei province, China"
-      },
-      {
-        "author_name": "Yuzhang Wu",
-        "author_inst": "Institute of Immunology, PLA, Third Military Medical University, Chongqing,China"
-      },
-      {
-        "author_name": "Yongwen Chen",
-        "author_inst": "Institute of Immunology, PLA, Third Military Medical University, Chongqing, China"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.03.04.20031047",
     "rel_title": "How to differentiate COVID-19 pneumonia from heart failure with computed tomography at initial medical contact during epidemic period",
@@ -1597815,6 +1596301,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "radiology and imaging"
   },
+  {
+    "rel_doi": "10.1101/2020.03.03.20030858",
+    "rel_title": "Prediction of New Coronavirus Infection Based on a Modified SEIR Model",
+    "rel_date": "2020-03-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.03.20030858",
+    "rel_abs": "BACKGROUNDThe outbreak of the new coronavirus infection in Wuhan City, Hubei Province in December 2019, poses a huge threat to China and even global public health security. Respiratory droplets and contact transmission are the main routes of transmission of new coronaviruses. Compared with SARS and Ebola viruses, new coronavirus infections are infectious during the incubation period. Traditional SEIR (susceptibility-exposure-infection-Removal) There are some differences in conditions for the prediction of the epidemic trend of new coronavirus infection. The outbreak of the new coronavirus infection coincided with the Spring Festival before and after the Chinese Spring Festival.It is necessary to make appropriate optimization and amendments to the traditional model to meet the actual evolution of the epidemic situation.\n\nMETHODSThe traditional SEIR model assumes that the virus-infected person is not infectious during the incubation period and that the infected person did not take isolation measures during the illness. The transmission of the new coronavirus no longer meets the basic assumptions of the classical kinetic system. Therefore, this article first establishes a modified SEIR model. Predict and analyze the changing trend of the epidemic situation, then estimate the parameters involved in the infection dynamics model, and then use Matlab to simulate the established dynamic equations based on public data and analyze the results. Recommendations for universal prevention and control of infectious diseases.\n\nRESULTSThe first case of new coronavirus infection was confirmed in Wuhan on December 8, 2019. When Wuhan City took no action, assuming the average daily number of contacts per infected person k = 5, the number of infected persons will reach about 2,384,803 people; If wuhan adopts the measures of sealing the city on January 22, 2020, under the premise of k=2, the number of infected people decreases by 19,773 compared with that on January 23, and there is no significant change in the time when the number of infected people reaches the peak. Under the premise of k = 1, the number of infected persons was reduced by 14,330 compared with the closure on January 23, and the time to reach the peak of the number of infected persons was reduced by 2 days. If Wuhan City is closed for one day, the number of infected persons will increase from 106,145 to 130,626 under the premise of k = 2; the number of infected persons will increase from 74,369 to 92,010 under the premise of k = 1.\n\nCONCLUSIONSComparing the number of confirmed diagnoses actually notified by the department with the number of infected people obtained from the simulation of the model, it can be seen that the city closure measures adopted by the Wuhan Municipal Government on January 23 and the first-level response measures adopted by the country are effective for the epidemic Prevention and control play a vital role. Wearing a mask when going out and avoiding close contact with people can effectively reduce the infection rate.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Zhou Tang",
+        "author_inst": "Sichuan Academy of Social Sciences"
+      },
+      {
+        "author_name": "Xianbin Li",
+        "author_inst": "Sichuan Academy of Social Sciences"
+      },
+      {
+        "author_name": "Houqiang Li",
+        "author_inst": "Sichuan Academy of Social Sciences"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.03.04.20030916",
     "rel_title": "Serological detection of 2019-nCoV respond to the epidemic: A useful complement to nucleic acid testing",
@@ -1599100,101 +1597613,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "respiratory medicine"
   },
-  {
-    "rel_doi": "10.1101/2020.03.04.20030395",
-    "rel_title": "Clinical Features of Patients Infected with the 2019 Novel Coronavirus (COVID-19) in Shanghai, China",
-    "rel_date": "2020-03-06",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.04.20030395",
-    "rel_abs": "BackgroundSince mid-December 2019, a cluster of pneumonia-like diseases caused by a novel coronavirus, now designated COVID-19 by the WHO, emerged in Wuhan city and rapidly spread throughout China. Here we identify the clinical characteristics of COVID-19 in a cohort of patients in Shanghai.\n\nMethodsCases were confirmed by real-time RT-PCR and were analysed for demographic, clinical, laboratory and radiological features.\n\nResultsOf 198 patients, the median duration from disease onset to hospital admission was 4 days. The mean age of the patients was 50.1 years, and 51.0% patients were male. The most common symptom was fever. Less than half of the patients presented with respiratory systems including cough, sputum production, itchy or sore throat, shortness of breath, and chest congestion. 5.6% patients had diarrhoea. On admission, T lymphocytes were decreased in 45.8% patients. Ground glass opacity was the most common radiological finding on chest computed tomography. 9.6% were admitted to the ICU because of the development of organ dysfunction. Compared with patients not treated in ICU, patients treated in the ICU were older, had longer waiting time to admission, fever over 38.5{degrees} C, dyspnoea, reduced T lymphocytes, elevated neutrophils and organ failure.\n\nConclusionsIn this single centre cohort of COVID-19 patients, the most common symptom was fever, and the most common laboratory abnormality was decreased blood T cell counts. Older age, male, fever over 38.5{degrees}C, symptoms of dyspnoea, and underlying comorbidity, were the risk factors most associated with severity of disease.",
-    "rel_num_authors": 20,
-    "rel_authors": [
-      {
-        "author_name": "Min Cao",
-        "author_inst": "Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China"
-      },
-      {
-        "author_name": "Dandan Zhang",
-        "author_inst": "Shanghai Public Health Clinical Centre, Shanghai, China"
-      },
-      {
-        "author_name": "Youhua Wang",
-        "author_inst": "Longhua Hospital, Shanghai University of Traditional Chinese Medicine"
-      },
-      {
-        "author_name": "Yunfei Lu",
-        "author_inst": "Shanghai Public Health Clinical Centre, Shanghai, China"
-      },
-      {
-        "author_name": "Xiangdong Zhu",
-        "author_inst": "Department of Emergency Medicine, University of Illinois College of Medicine, Chicago, IL, USA"
-      },
-      {
-        "author_name": "Ying Li",
-        "author_inst": "Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China"
-      },
-      {
-        "author_name": "Honghao Xue",
-        "author_inst": "Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China"
-      },
-      {
-        "author_name": "Yunxiao Lin",
-        "author_inst": "Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China"
-      },
-      {
-        "author_name": "Min Zhang",
-        "author_inst": "Shanghai Public Health Clinical Centre, Shanghai, China"
-      },
-      {
-        "author_name": "Yiguo Sun",
-        "author_inst": "Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China"
-      },
-      {
-        "author_name": "Zongguo Yang",
-        "author_inst": "Shanghai Public Health Clinical Centre, Shanghai, China"
-      },
-      {
-        "author_name": "Jia Shi",
-        "author_inst": "Shanghai Public Health Clinical Centre, Shanghai, China"
-      },
-      {
-        "author_name": "Yi Wang",
-        "author_inst": "Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China"
-      },
-      {
-        "author_name": "Chang Zhou",
-        "author_inst": "Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China"
-      },
-      {
-        "author_name": "Yidan Dong",
-        "author_inst": "Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China"
-      },
-      {
-        "author_name": "Ping Liu",
-        "author_inst": "Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China"
-      },
-      {
-        "author_name": "Steven M Dudek",
-        "author_inst": "Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois College of Medicine, Chicago, IL, USA"
-      },
-      {
-        "author_name": "Zhen Xiao",
-        "author_inst": "Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China"
-      },
-      {
-        "author_name": "Hongzhou Lu",
-        "author_inst": "Shanghai Public Health Clinical Centre, Shanghai, China"
-      },
-      {
-        "author_name": "Longping Peng",
-        "author_inst": "Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "respiratory medicine"
-  },
   {
     "rel_doi": "10.1101/2020.03.01.20028944",
     "rel_title": "Epidemiologic Characteristics of COVID-19 in Guizhou, China",
@@ -1599533,6 +1597951,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.02.29.20029462",
+    "rel_title": "68 Consecutive patients assessed for COVID-19 infection; experience from a UK regional infectious disease unit",
+    "rel_date": "2020-03-06",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.29.20029462",
+    "rel_abs": "Clinical assessment of possible infection with SARS-CoV-2, the novel coronavirus responsible for the outbreak of COVID-19 respiratory illness, has been a major activity of infectious diseases services in the UK and elsewhere since the first report of cases in December 2019. We report our case series of 68 patients, reviewed by Infectious Diseases Consultants at a Regional Infectious Diseases Unit in the UK. We prospectively evaluated our service between the 29th Jan 2020 and 24th Feb 2020.\n\nDemographic, clinical, epidemiological and laboratory data were collected. We have compared clinical features and subsequent diagnosis between well patients not requiring admission for clinical reasons or antimicrobials with those assessed as needing either admission or antimicrobial treatment.\n\nFinal microbiological diagnoses included SARS-CoV-2 (COVID-19), Mycoplasma pneumonia, influenza A, RSV, non SARS/MERS coronaviruses, rhinovirus/enterovirus. 9/68 were treated with antimicrobials, 15/68 were admitted to a negative pressure room of whom 5/68 were admitted solely due to an inability to isolate at home. Patients requiring either admission on clinical grounds or antimicrobials (14/68) were similar to those not requiring admission or antimicrobials, with modestly more fever and shortness of breath in the clinically admitted / antimicrobial group. The most commonly prescribed antimicrobials were doxycycline, moxifloxacin and oseltamivir.\n\nThe majority of patients had mild illness which did not require a clinical intervention to manage. This finding supports a community testing approach supported by clinicians to review the proportion of more unwell patients.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Nicholas Easom",
+        "author_inst": "Department of Infection, Hull University Teaching Hospitals NHS Trust, Hull, East Yorkshire, United Kingdom"
+      },
+      {
+        "author_name": "Peter Moss",
+        "author_inst": "Department of Infection, Hull University Teaching Hospitals NHS Trust, Hull, East Yorkshire, United Kingdom"
+      },
+      {
+        "author_name": "Gavin Barlow",
+        "author_inst": "Department of Infection, Hull University Teaching Hospitals NHS Trust, Hull, East Yorkshire, United Kingdom"
+      },
+      {
+        "author_name": "Anda Samson",
+        "author_inst": "Department of Infection, Hull University Teaching Hospitals NHS Trust, Hull, East Yorkshire, United Kingdom"
+      },
+      {
+        "author_name": "Tom Taynton",
+        "author_inst": "Department of Infection, Hull University Teaching Hospitals NHS Trust, Hull, East Yorkshire, United Kingdom"
+      },
+      {
+        "author_name": "Kate Adams",
+        "author_inst": "Department of Infection, Hull University Teaching Hospitals NHS Trust, Hull, East Yorkshire, United Kingdom"
+      },
+      {
+        "author_name": "Monica Ivan",
+        "author_inst": "Department of Infection, Hull University Teaching Hospitals NHS Trust, Hull, East Yorkshire, United Kingdom"
+      },
+      {
+        "author_name": "Phillipa Burns",
+        "author_inst": "Department of Infection, Hull University Teaching Hospitals NHS Trust, Hull, East Yorkshire, United Kingdom"
+      },
+      {
+        "author_name": "Kavitha Gajee",
+        "author_inst": "Department of Infection, Hull University Teaching Hospitals NHS Trust, Hull, East Yorkshire, United Kingdom"
+      },
+      {
+        "author_name": "Kirstine Eastick",
+        "author_inst": "Department of Infection, Hull University Teaching Hospitals NHS Trust, Hull, East Yorkshire, United Kingdom"
+      },
+      {
+        "author_name": "Patrick Lillie",
+        "author_inst": "Department of Infection, Hull University Teaching Hospitals NHS Trust, Hull, East Yorkshire, United Kingdom"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.03.04.20029538",
     "rel_title": "Nanopore target sequencing for accurate and comprehensive detection of SARS-CoV-2 and other respiratory viruses",
@@ -1600821,105 +1599298,6 @@
     "type": "new results",
     "category": "microbiology"
   },
-  {
-    "rel_doi": "10.1101/2020.02.29.20029603",
-    "rel_title": "Machine learning-based CT radiomics model for predicting hospital stay in patients with pneumonia associated with SARS-CoV-2 infection: A multicenter study",
-    "rel_date": "2020-03-03",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.29.20029603",
-    "rel_abs": "ObjectivesTo develop and test machine learning-based CT radiomics models for predicting hospital stay in patients with pneumonia associated with SARS-CoV-2 infection.\n\nDesignCross-sectional\n\nSettingMulticenter\n\nParticipantsA total of 52 patients with laboratory-confirmed SARS-CoV-2 infection and their initial CT images were enrolled from 5 designated hospitals in Ankang, Lishui, Zhenjiang, Lanzhou, and Linxia between January 23, 2020 and February 8, 2020. As of February 20, patients remained in hospital or with non-findings in CT were excluded. Therefore, 31 patients with 72 lesion segments were included in the final analysis.\n\nInterventionCT radiomics models based on logistic regression (LR) and random forest (RF) were developed on features extracted from pneumonia lesions in training and inter-validation datasets. The predictive performance was further evaluated in test dataset on lung lobe- and patients-level.\n\nMain outcomesShort-term hospital stay ([&le;]10 days) and long-term hospital stay (>10 days).\n\nResultsThe CT radiomics models based on 6 second-order features were effective in discriminating short- and long-term hospital stay in patients with pneumonia associated with SARS-CoV-2 infection, with areas under the curves of 0.97 (95%CI 0.83-1.0) and 0.92 (95%CI 0.67-1.0) by LR and RF, respectively, in the test dataset. The LR model showed a sensitivity and specificity of 1.0 and 0.89, and the RF model showed similar performance with sensitivity and specificity of 0.75 and 1.0 in test dataset.\n\nConclusionsThe machine learning-based CT radiomics models showed feasibility and accuracy for predicting hospital stay in patients with pneumonia associated with SARS-CoV-2 infection.",
-    "rel_num_authors": 21,
-    "rel_authors": [
-      {
-        "author_name": "Xiaolong Qi",
-        "author_inst": "CHESS-COVID-19 center, The First Hospital of Lanzhou University, Lanzhou, China"
-      },
-      {
-        "author_name": "Zicheng Jiang",
-        "author_inst": "CHESS-COVID-19 center, Ankang Central Hospital, Ankang, China"
-      },
-      {
-        "author_name": "QIAN YU",
-        "author_inst": "Department of Radiology, Jiangsu Key Laboratory of Molecular and Functional Imaging, Zhongda Hospital, Medical School, Southeast University, Nanjing, China"
-      },
-      {
-        "author_name": "Chuxiao Shao",
-        "author_inst": "CHESS-COVID-19 center, Zhejiang University Lishui Hospital & Lishui Central Hospital, Lishui, China"
-      },
-      {
-        "author_name": "Hongguang Zhang",
-        "author_inst": "Department of Infectious Diseases and Critical Care Medicine, The Affiliated Third Hospital of Jiangsu University, Zhenjiang, China"
-      },
-      {
-        "author_name": "Hongmei Yue",
-        "author_inst": "CHESS-COVID-19 center, The First Hospital of Lanzhou University, Lanzhou, China"
-      },
-      {
-        "author_name": "Baoyi Ma",
-        "author_inst": "Department of Respiratory Medicine, The People Hospital of LinXia Hui Prefecture, Linxia, China"
-      },
-      {
-        "author_name": "Yuancheng Wang",
-        "author_inst": "3.\tDepartment of Radiology, Jiangsu Key Laboratory of Molecular and Functional Imaging, Zhongda Hospital, Medical School, Southeast University, Nanjing, China"
-      },
-      {
-        "author_name": "Chuan Liu",
-        "author_inst": "CHESS-COVID-19 center, The First Hospital of Lanzhou University, Lanzhou, China"
-      },
-      {
-        "author_name": "Xiangpan Meng",
-        "author_inst": "Department of Radiology, Jiangsu Key Laboratory of Molecular and Functional Imaging, Zhongda Hospital, Medical School, Southeast University, Nanjing, China"
-      },
-      {
-        "author_name": "Shan Huang",
-        "author_inst": "Department of Radiology, Jiangsu Key Laboratory of Molecular and Functional Imaging, Zhongda Hospital, Medical School, Southeast University, Nanjing, China"
-      },
-      {
-        "author_name": "Jitao Wang",
-        "author_inst": "CHESS-COVID-19 center, The First Hospital of Lanzhou University, Lanzhou, China"
-      },
-      {
-        "author_name": "Dan Xu",
-        "author_inst": "CHESS-COVID-19 center, The First Hospital of Lanzhou University, Lanzhou, China"
-      },
-      {
-        "author_name": "Junqiang Lei",
-        "author_inst": "CHESS-COVID-19 center, The First Hospital of Lanzhou University, Lanzhou, China"
-      },
-      {
-        "author_name": "Guanghang Xie",
-        "author_inst": "CHESS-COVID-19 center, The First Hospital of Lanzhou University, Lanzhou, China"
-      },
-      {
-        "author_name": "Huihong Huang",
-        "author_inst": "CHESS-COVID-19 center, Ankang Central Hospital, Ankang, China"
-      },
-      {
-        "author_name": "Jie Yang",
-        "author_inst": "CHESS-COVID-19 center, Zhejiang University Lishui Hospital & Lishui Central Hospital, Lishui, China"
-      },
-      {
-        "author_name": "Jiansong Ji",
-        "author_inst": "CHESS-COVID-19 center, Zhejiang University Lishui Hospital & Lishui Central Hospital, Lishui, China"
-      },
-      {
-        "author_name": "Hongqiu Pan",
-        "author_inst": "Department of Infectious Diseases and Critical Care Medicine, The Affiliated Third Hospital of Jiangsu University, Zhenjiang, China"
-      },
-      {
-        "author_name": "Shengqiang Zou",
-        "author_inst": "Department of Infectious Diseases and Critical Care Medicine, The Affiliated Third Hospital of Jiangsu University, Zhenjiang, China"
-      },
-      {
-        "author_name": "Shenghong Ju",
-        "author_inst": "Department of Radiology, Jiangsu Key Laboratory of Molecular and Functional Imaging, Zhongda Hospital, Medical School, Southeast University, Nanjing, China"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.02.29.20029520",
     "rel_title": "Detectable serum SARS-CoV-2 viral load (RNAaemia) is closely associated with drastically elevated interleukin 6 (IL-6) level in critically ill COVID-19 patients",
@@ -1601454,6 +1599832,41 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.03.02.20030064",
+    "rel_title": "Forecasting the Cumulative Number of COVID-19 Deaths in China: Can More Lives Be Saved?",
+    "rel_date": "2020-03-03",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.02.20030064",
+    "rel_abs": "The COVID-19 outbreak is on-going in China. Here we estimated the potential total numbers of COVID-19 deaths in China, outside Hubei (in China), Hubei Province, Wuhan City and outside Wuhan (in Hubei) by Boltzmann function-based analyses, which are 3342 (95% CI, 3214, 3527), 111 (109, 114), 3245 (3100, 3423), 2613 (2498, 2767) and 627 (603, 654), respectively. The results may help to evaluate the severity of COVID-19 outbreaks and facilitate timely mental service for the families of passed patients.",
+    "rel_num_authors": 5,
+    "rel_authors": [
+      {
+        "author_name": "Cheng Long",
+        "author_inst": "West China Hospital of Sichuan University"
+      },
+      {
+        "author_name": "Qi Ying",
+        "author_inst": "Texas A&M University College Station"
+      },
+      {
+        "author_name": "Xinmiao Fu",
+        "author_inst": "Fujian Normal University"
+      },
+      {
+        "author_name": "Zhongyan Li",
+        "author_inst": "Fujian Normal University"
+      },
+      {
+        "author_name": "Yuanyuan Gao",
+        "author_inst": "Fujian Normal University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.02.28.20028555",
     "rel_title": "Analysis of epidemiological characteristics of coronavirus 2019 infection and preventive measures in Shenzhen China: a heavy population city",
@@ -1602586,49 +1600999,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.02.27.20028787",
-    "rel_title": "Evaluation of Enzyme-Linked Immunoassay and Colloidal Gold- Immunochromatographic Assay Kit for Detection of Novel Coronavirus (SARS-Cov-2) Causing an Outbreak of Pneumonia (COVID-19)",
-    "rel_date": "2020-03-01",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.27.20028787",
-    "rel_abs": "BACKGROUNDIn December 2019, a novel coronavirus (SARS-CoV-2)-infected pneumonia (COVID-19) occurred in Wuhan, China. Travel-associated cases have also been reported in other countries. The number of cases has increased rapidly but laboratory diagnosis is limited.\n\nMETHODSWe collect two groups of cases diagnosed with COVID-19 for experiments. One group collected 63 samples for Enzyme-linked immunosorbent assay (ELISA) IgG and IgM antibodies. The other group collected 91 plasma samples for colloidal gold-immunochromatographic assay (GICA).\n\nRESULTSThe sensitivity of the combined ELISA IgM and ELISA IgG detection was 55/63 ( 87.3%), The sensitivity of the combined GICA IgM and GICA IgG detection was 75/91 ( 82.4%), Both methods are negative for healthy controls, specificity of 100%. There is no significant difference between the sensitivity of between ELISA and GICA (IgM+ IgG).\n\nCONCLUSIONSELISA and GICA for specific IgM and IgG antibodies are conventional serological assays, they are simple, fast, and safe, the results can be used for clinical reference, and the huge clinical diagnosis and treatment pressure can be greatly relieved.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Jie Xiang",
-        "author_inst": "Department of Clinical laboratory, Wuhan Jinyintan Hospital, Wuhan, China."
-      },
-      {
-        "author_name": "Mingzhe Yan",
-        "author_inst": "Department of Clinical laboratory, Wuhan Jinyintan Hospital, Wuhan, China."
-      },
-      {
-        "author_name": "Hongze Li",
-        "author_inst": "Department of Clinical laboratory, Wuhan Jinyintan Hospital, Wuhan, China."
-      },
-      {
-        "author_name": "Ting Liu",
-        "author_inst": "Department of Clinical laboratory, Wuhan Jinyintan Hospital, Wuhan, China."
-      },
-      {
-        "author_name": "Chenyao Lin",
-        "author_inst": "Department of Blood Transfusion, ZhongNan hospital of Wuhan University, China"
-      },
-      {
-        "author_name": "Shuang Huang",
-        "author_inst": "Department of Blood Transfusion, ZhongNan hospital of Wuhan University, China"
-      },
-      {
-        "author_name": "Changxin Shen",
-        "author_inst": "Department of Blood Transfusion, ZhongNan hospital of Wuhan University, China"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.02.26.20028431",
     "rel_title": "Transmission characteristics of the COVID-19 outbreak in China: a study driven by data",
@@ -1602803,6 +1601173,65 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.02.27.20027524",
+    "rel_title": "Sex differences in clinical findings among patients with coronavirus disease 2019 (COVID-19) and severe condition",
+    "rel_date": "2020-02-29",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.27.20027524",
+    "rel_abs": "ObjectiveTo compare the sex differences in the clinical findings among patients with severe coronavirus disease 2019 (COVID-19).\n\nMethodsWe retrospectively collected data of 47 patients diagnosed as severe type of COVID-19 from February 8 to 22, 2020, including demographics, illness history, physical examination, laboratory test, management, and compared differences between men and women.\n\nResultsOf the 47 patients, 28 (59.6%) were men. The median age was 62 years, and 30 (63.8%) had comorbidities. The initial symptoms were mainly fever (34 [72.3%]), cough (36 [76.6%]), myalgia (5 [10.6%]) and fatigue (7 [14.9%]). Procalcitonin level was higher in men than in women (0.08 vs. 0.04ng/ml, p=0.002). N-terminal-pro brain natriuretic peptide increased in 16 (57.1%) men and 5 (26.3%) women (p=0.037). Five men (17.9%) had detected positive influenza A antibody, but no women. During 2-week admission, 5 (17.9%) men and 1 (5.3%) woman were reclassified into the critical type due to deterioration. Mortality was 3.6% in men and 0 in women respectively. Four (21.1%) women and one man (3.6%) recovered and discharged from hospital.\n\nConclusionSex differences may exist in COVID-19 patients of severe type. Men are likely to have more complicated clinical condition and worse in-hospital outcomes as compared to women.",
+    "rel_num_authors": 11,
+    "rel_authors": [
+      {
+        "author_name": "Jing Li",
+        "author_inst": "Division of Cardiology, Beijing Hospital, Beijing 100730, China"
+      },
+      {
+        "author_name": "Yinghua Zhang",
+        "author_inst": "Division of Cardiology, Xuanwu Hospital Capital Medical University, Beijing 100053, China"
+      },
+      {
+        "author_name": "Fang Wang",
+        "author_inst": "Division of Cardiology, Beijing Hospital, Beijing 100730, China"
+      },
+      {
+        "author_name": "Bing Liu",
+        "author_inst": "Division of Cardiology, Beijing Hospital, Beijing 100730, China"
+      },
+      {
+        "author_name": "Hui Li",
+        "author_inst": "Division of Cardiology, Beijing Hospital, Beijing 100730, China"
+      },
+      {
+        "author_name": "Guodong Tang",
+        "author_inst": "Division of Cardiology, Beijing Hospital, Beijing 100730, China"
+      },
+      {
+        "author_name": "Zhigang Chang",
+        "author_inst": "Division of Intensive Care Unit, Beijing Hospital, Beijing 100730, China"
+      },
+      {
+        "author_name": "Aihua Liu",
+        "author_inst": "Division of Rheumatology and Immunology, Beijing Hospital, Beijing 100730, China"
+      },
+      {
+        "author_name": "Chunyi Fu",
+        "author_inst": "Division of Emergency, Beijing Hospital, Beijing 100730, China"
+      },
+      {
+        "author_name": "Jing Gao",
+        "author_inst": "Division of Cardiology, Xuanwu Hospital Capital Medical University, Beijing 100053, China"
+      },
+      {
+        "author_name": "Jing Li",
+        "author_inst": "Division of Cardiology, Xuanwu Hospital Capital Medical University, Beijing 100053, China"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "respiratory medicine"
+  },
   {
     "rel_doi": "10.1101/2020.02.26.20028589",
     "rel_title": "Heart injury signs are associated with higher and earlier mortality in coronavirus disease 2019 (COVID-19)",
@@ -1604220,49 +1602649,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.02.26.20026989",
-    "rel_title": "The definition and risks of Cytokine Release Syndrome-Like in 11 COVID-19-Infected Pneumonia critically ill patients: Disease Characteristics and Retrospective Analysis",
-    "rel_date": "2020-02-27",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.26.20026989",
-    "rel_abs": "IMPORTANCECOVID-19-infected pneumonia patients with severe immune abnormalities and risk of cytokine release syndrome. The definition, prevention, and treatment of COVID-19-infected pneumonia in critically ill patients with cytokine release syndrome symptoms is an important problem.\n\nOBJECTIVETo define the cytokine release syndrome-like (CRSL) in COVID-19-infected pneumonia in critically ill patients and study the risk factors and therapeutic strategies.\n\nDESIGN, SETTING, AND PARTICIPANTSThis is a retrospective, single center case study of 11 COVID-19-infected pneumonia patients with acute respiratory distress syndrome (ARDS) from The First Affiliated Hospital of Guangzhou Medical University in China from January 26, 2020 to February 18, 2020. The follow-up termination date was February 19, 2020.\n\nEXPOSERESEleven COVID-19-infected pneumonia patients with ARDS in the ICU. Some of these patients also had cytokine release syndrome-like (CRSL). Immunologic detection, clinical characteristics, and clinical treatment analysis were carried out to define the CRSL in these COVID-19-infected pneumonia patients.\n\nMAIN OUTCOMES AND MEASURESClinical, radiological, immunology (including immune cell subsets and cytokines analysis), laboratory, and clinical treatment data were collected and analyzed. The critically ill patients with CRSL were defined. Prevention and control strategies were studied.\n\nRESULTSOf 11 critically ill patients in the ICU, the median age was 58 (Inter-Quartile Range{IQR}, 49-72; range, 26-72 years), and 10 (83.3%) were males. Ten (83.3%) patients had extensive pulmonary inflammation and ARDS (the median time from the first symptom to ARDS was 10.0 d), fever, and hypoxia; four (28.6%) patients experienced shock. The lymphocyte subpopulations including CD3 (CD3 + CD45+), CD4 (CD3 + CD4+), CD8 (CD3 + CD8+), NK (CD3-CD16 + CD56 +), Tregs (CD4 + CD25 + CD127 low), B lymphocyte (CD3-CD19 +) cells; and cytokines including IL-2, IL-4, IL-6, IL-10, TNF-, IFN-{gamma} were detected at different time points. All of the patients had a decrease of CD3 (IQR,169-335; range, 50-635 cells/L), CD4 (IQR,101-303; range, 27-350 cells/L), CD8 (IQR, 33-141; range, 21-277 cells/L); ten (90.9%) patients have a decrease in NK immune cells (IQR,8-72; range, 5-170 cells/L); both of Tregs (IQR,3.3-7.8;rang,2.3-9.4%) and B immune cells (IQR,61-146; rang,44-222 cells/L)were decreased in two (18.2%) patients. And nine patients were increase in CD4 / CD8 (IQR,3.3-7.8%; range, 2.3-9.7%). All patients had a significant increase of IL-6 (IQR,14.26-92.2; range, 4.58-1182.91ng/L). Eight (72.7%) patients were determined to have CRSL characteristics, including pulmonary inflammation, fever, a decrease of CD4, CD8, and NK cells; an increase of CD4/CD8, a significant increase of IL-6, and the dysfunction of non-pulmonary organs. The numbers of CD4, CD8, and NK cells and the level of IL-6 in peripheral blood were correlated with the area of pulmonary inflammation in CT images (P<0.05). Mechanical-ventilation used to increase blood oxygen concentration could increased the numbers of CD4 (after Vs before ventilation=259{+/-}53 VS 507{+/-}101; P=0.013, and CD8 (after Vs before ventilation=193{+/-}38 VS 279{+/-}63; P=0.048), while decreasing the level of IL-6 (after Vs before ventilation=223.2{+/-} 89.9 VS 26.8{+/-}10; P=0.041). The increased of IL-6 was occurred earlier than the decrease of CD4{middle dot}, CD8 in the patients with rapidly worsened after ICU.\n\nCONCLUSIONS AND RELEVANCEIn this retrospective analysis of 11 critically ill pneumonia patients infected with COVID-19, we defined and identified eight patients (72.7%) with cytokine release syndrome-like (CRSL). We found that a large area of lung injury ([&ge;]50%) with an decrease of CD4, CD8 (Lower than 50% minimum normal range) and increase of IL-6 in peripheral blood was the highest risk factor of CRSL. IL-6 was a early indicators of CRSL in COVID-19-infected pneumonia. We also found that reduce injury to the lung is a useful method to prevent and improve COVID-19-infected pneumonia-related CRSL in critically ill pneumonia patients.",
-    "rel_num_authors": 7,
-    "rel_authors": [
-      {
-        "author_name": "Wenjun Wang Jr.",
-        "author_inst": "The First Affiliated Hospital of Guangzhou Medical University"
-      },
-      {
-        "author_name": "Jianxing He",
-        "author_inst": "The First Affiliated Hospital of Guangzhou Medical University"
-      },
-      {
-        "author_name": "puyi Lie",
-        "author_inst": "The First Affiliated Hospital of Guangzhou Medical University"
-      },
-      {
-        "author_name": "liyan Huang",
-        "author_inst": "The First Affiliated Hospital of Guangzhou Medical University"
-      },
-      {
-        "author_name": "Sipei Wu",
-        "author_inst": "Guangdong Lung Cancer Research Institute"
-      },
-      {
-        "author_name": "yongping lin",
-        "author_inst": "The First Affiliated Hospital of Guangzhou Medical University"
-      },
-      {
-        "author_name": "xiaoqing liu",
-        "author_inst": "The First Affiliated Hospital of Guangzhou Medical University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "intensive care and critical care medicine"
-  },
   {
     "rel_doi": "10.1101/2020.02.24.20027052",
     "rel_title": "Clinical and radiographic features of cardiac injury in patients with 2019 novel coronavirus pneumonia",
@@ -1604589,6 +1602975,45 @@
     "type": "new results",
     "category": "bioinformatics"
   },
+  {
+    "rel_doi": "10.1101/2020.02.22.961268",
+    "rel_title": "A simple magnetic nanoparticles-based viral RNA extraction method for efficient detection of SARS-CoV-2",
+    "rel_date": "2020-02-27",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.22.961268",
+    "rel_abs": "1The ongoing outbreak of the novel coronavirus disease 2019 (COVID-19) originating from Wuhan, China, draws worldwide concerns due to its long incubation period and strong infectivity. Although RT-PCR-based molecular diagnosis techniques are being widely applied for clinical diagnosis currently, timely and accurate diagnosis are still limited due to labour intensive and time-consuming operations of these techniques. To address the issue, herein we report the synthesis of poly (amino ester) with carboxyl groups (PC)-coated magnetic nanoparticles (pcMNPs), and the development of pcMNPs-based viral RNA extraction method for the sensitive detection of COVID-19 causing virus, the SARS-CoV-2. This method combines the lysis and binding steps into one step, and the pcMNPs-RNA complexes can be directly introduced into subsequent RT-PCR reactions. The simplified process can purify viral RNA from multiple samples within 20 min using a simple manual method or an automated high-throughput approach. By identifying two different regions (ORFlab and N gene) of viral RNA, a 10-copy sensitivity and a strong linear correlation between 10 and 105 copies of SARS-CoV-2 pseudovirus particles are achieved. Benefitting from the simplicity and excellent performances, this new extraction method can dramatically reduce the turn-around time and operational requirements in current molecular diagnosis of COVID-19, in particular for the early clinical diagnosis.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Zhen Zhao",
+        "author_inst": "Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Haodong Cui",
+        "author_inst": "Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Wenxing Song",
+        "author_inst": "Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Xiaoling Ru",
+        "author_inst": "Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Wenhua Zhou",
+        "author_inst": "Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences"
+      },
+      {
+        "author_name": "Xuefeng Yu",
+        "author_inst": "Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "molecular biology"
+  },
   {
     "rel_doi": "10.1101/2020.02.25.963546",
     "rel_title": "An Effective CTL Peptide Vaccine for Ebola Zaire Based on Survivors' CD8+ Targeting of a Particular Nucleocapsid Protein Epitope with Potential Implications for COVID-19 Vaccine Design",
@@ -1605858,157 +1604283,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.02.22.20026617",
-    "rel_title": "A Peptide-based Magnetic Chemiluminescence Enzyme Immunoassay for Serological Diagnosis of Corona Virus Disease 2019 (COVID-19)",
-    "rel_date": "2020-02-25",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.22.20026617",
-    "rel_abs": "A respiratory illness has been spreading rapidly in China, since its outbreak in Wuhan city, Hubei province in December 2019. The illness was caused by a novel coronavirus, named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Clinical manifestations related to SARS-CoV-2 infection ranged from no symptom to fatal pneumonia. World Health Organization (WHO) named the diseases associated with SARS-CoV-2 infection as COVID-19. Real time RT-PCR is the only laboratory test available till now to confirm the infection. However, the accuracy of real time RT-PCR depends on many factors, including sampling location and of methods, quality of RNA extraction and training of operators etc.. Variations in these factors might significantly lower the sensitivity of the detection. We developed a peptide-based luminescent immunoassay to detect IgG and IgM. Cut-off value of this assay was determined by the detection of 200 healthy sera and 167 sera from patients infected with other pathogens than SARS-CoV-2. To evaluate the performance of this assay, we detected IgG and IgM in the 276 sera from confirmed patients. The positive rate of IgG and IgM were 71.4% (197/276) and 57.2% (158/276) respectively. By combining with real time RT-PCR detection, this assay might help to enhance the accuracy of diagnosis of SARS-CoV-2 infection.",
-    "rel_num_authors": 34,
-    "rel_authors": [
-      {
-        "author_name": "Xuefei Cai",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Juan Chen",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Jieli Hu",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Quanxin Long",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Haijun Deng",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Kai Fan",
-        "author_inst": "PEG-Bio Biopharm Co. LTD, Chongqing"
-      },
-      {
-        "author_name": "Pu Liao",
-        "author_inst": "Chongqing People Hospital"
-      },
-      {
-        "author_name": "Beizhong Liu",
-        "author_inst": "Yongchuan Hospital Affiliated to Chongqing Medical University"
-      },
-      {
-        "author_name": "Guicheng Wu",
-        "author_inst": "Chongqing Three Gorges Central Hospital"
-      },
-      {
-        "author_name": "Yaokai Chen",
-        "author_inst": "The Public Health Center, Chongqing"
-      },
-      {
-        "author_name": "Zhijie Li",
-        "author_inst": "Chongqing People Hospital"
-      },
-      {
-        "author_name": "Kun Wang",
-        "author_inst": "Chongqing People Hospital"
-      },
-      {
-        "author_name": "Xiaoli Zhang",
-        "author_inst": "Yongchuan Hospital Affiliated to Chongqing Medical University"
-      },
-      {
-        "author_name": "Wenguang Tian",
-        "author_inst": "Yongchuan Hospital Affiliated to Chongqing Medical University"
-      },
-      {
-        "author_name": "Jianglin Xiang",
-        "author_inst": "Chongqing Three Gorges Central Hospital, Chongqing"
-      },
-      {
-        "author_name": "Hongxin Du",
-        "author_inst": "Chongqing Three Gorges Central Hospital, Chongqing"
-      },
-      {
-        "author_name": "Jing Wang",
-        "author_inst": "The Public Health Center, Chongqing"
-      },
-      {
-        "author_name": "Yuan Hu",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Ni Tang",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Yong Lin",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Jihua Ren",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Luyi Huang",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Jie Wei",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Chunyang Gan",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Yanmeng Chen",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Qingzhu Gao",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Amei Chen",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Changlong He",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Daoxin Wang",
-        "author_inst": "The Second Affiliated Hospital, Chongqing Medical University"
-      },
-      {
-        "author_name": "Peng Hu",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Fachun Zhou",
-        "author_inst": "The First Affiliated Hospital, Chongqing Medical University"
-      },
-      {
-        "author_name": "Ailong Huang",
-        "author_inst": "Chongqing Medical University"
-      },
-      {
-        "author_name": "Ping Liu",
-        "author_inst": "BioScience Co. LTD, Tianjin"
-      },
-      {
-        "author_name": "Deqiang Wang",
-        "author_inst": "Chongqing Medical University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.02.23.20026856",
     "rel_title": "Epidemiologic and Clinical Characteristics of 91 Hospitalized Patients with COVID-19 in Zhejiang, China: A retrospective, multi-centre case series",
@@ -1606271,6 +1604545,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.02.24.20026773",
+    "rel_title": "Characterizing the transmission and identifying the control strategy for COVID-19 through epidemiological modeling",
+    "rel_date": "2020-02-25",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.24.20026773",
+    "rel_abs": "The outbreak of the novel coronavirus disease, COVID-19, originating from Wuhan, China in early December, has infected more than 70,000 people in China and other countries and has caused more than 2,000 deaths. As the disease continues to spread, the biomedical society urgently began identifying effective approaches to prevent further outbreaks. Through rigorous epidemiological analysis, we characterized the fast transmission of COVID-19 with a basic reproductive number 5.6 and proved a sole zoonotic source to originate in Wuhan. No changes in transmission have been noted across generations. By evaluating different control strategies through predictive modeling and Monte carlo simulations, a comprehensive quarantine in hospitals and quarantine stations has been found to be the most effective approach. Government action to immediately enforce this quarantine is highly recommended.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Ke K. Zhang",
+        "author_inst": "TEXAS A&M UNIVERSITY HEALTH SCIENCE CTR"
+      },
+      {
+        "author_name": "Linglin Xie",
+        "author_inst": "Texas A&M University"
+      },
+      {
+        "author_name": "Lauren Lawless",
+        "author_inst": "Texas A&M University"
+      },
+      {
+        "author_name": "Huijuan Zhou",
+        "author_inst": "Texas A&M University"
+      },
+      {
+        "author_name": "Guannan Gao",
+        "author_inst": "Texas A&M University"
+      },
+      {
+        "author_name": "Chengbin Xue",
+        "author_inst": "Huazhong University of Science and Technology"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.02.21.20026468",
     "rel_title": "Trends in Transmissibility of 2019 Novel Coronavirus-infected Pneumonia in Wuhan and 29 Provinces in China",
@@ -1607576,61 +1605889,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.02.20.20025593",
-    "rel_title": "The efficacy of convalescent plasma for the treatment of severe influenza",
-    "rel_date": "2020-02-23",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.20.20025593",
-    "rel_abs": "BackgroundAdministration of convalescent plasma may be of clinical benefit for treatment of severe acute viral respiratory infections. However, no clear evidence exists to support or oppose convalescent plasma use in clinical practice. We conducted a systematic review and meta-analysis to assess the evidence of randomized controlled trials (RCTs) in the convalescent plasma for the treatment of severe influenza.\n\nMethodsHealthcare databases were searched in February 2020. All records were screened against the eligibility criteria. Data extraction and risk of bias assessments were undertaken. The primary outcome was case-fatality rates by influenza.\n\nResultsWe identified 5 RCTs of severe influenza. The pooled analyses showed no evidence for a reduction in mortality (Odds Ratio (OR) 1.06; 95% confidence interval (CI) 0.51-2.23; p = 0.87; I2 = 35%). We also found non-significant reductions in days in ICU and hospital, and days on mechanical ventilation. There seemed to have a biological benefit of increasing HAI titer levels and decreasing influenza B virus loads and cytokines after convalescent plasma treatment. No serious adverse events was reported between two groups. Studies were commonly of low risk of bias with high quality.\n\nConclusionsConvalescent plasma appears safe but may not reduce mortality in severe influenza. This therapy should be studied within the context of a well-designed clinical trial for treatment of SARS-Cov-2 infection.",
-    "rel_num_authors": 10,
-    "rel_authors": [
-      {
-        "author_name": "Zhiheng Xu",
-        "author_inst": "State Key Lab of Respiratory Diseases, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Chin"
-      },
-      {
-        "author_name": "Jianmeng Zhou",
-        "author_inst": "State Key Lab of Respiratory Diseases, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Chin"
-      },
-      {
-        "author_name": "Yongbo Huang",
-        "author_inst": "State Key Lab of Respiratory Diseases, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Chin"
-      },
-      {
-        "author_name": "Xuesong Liu",
-        "author_inst": "State Key Lab of Respiratory Diseases, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Chin"
-      },
-      {
-        "author_name": "Yonghao Xu",
-        "author_inst": "State Key Lab of Respiratory Diseases, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Chin"
-      },
-      {
-        "author_name": "Sibei Chen",
-        "author_inst": "State Key Lab of Respiratory Diseases, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Chin"
-      },
-      {
-        "author_name": "Dongdong Liu",
-        "author_inst": "State Key Lab of Respiratory Diseases, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Chin"
-      },
-      {
-        "author_name": "Zhimin Lin",
-        "author_inst": "State Key Lab of Respiratory Diseases, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Chin"
-      },
-      {
-        "author_name": "Xiaoqing Liu",
-        "author_inst": "State Key Lab of Respiratory Diseases, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Chin"
-      },
-      {
-        "author_name": "Yimin Li",
-        "author_inst": "State Key Lab of Respiratory Diseases, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Chin"
-      }
-    ],
-    "version": "1",
-    "license": "cc_no",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "infectious diseases"
-  },
   {
     "rel_doi": "10.1101/2020.02.20.20025973",
     "rel_title": "Assessing the impact of a symptom-based mass screening and testing intervention during a novel infectious disease outbreak: The case of COVID-19",
@@ -1608025,6 +1606283,81 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.02.18.20024281",
+    "rel_title": "Phase adjusted estimation of the number of 2019 novel coronavirus cases in Wuhan, China",
+    "rel_date": "2020-02-23",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.18.20024281",
+    "rel_abs": "An outbreak of clusters of viral pneumonia due to a novel coronavirus (2019-nCoV / SARS-CoV-2) happened in Wuhan, Hubei Province in China in December 2019. Since the outbreak, several groups reported estimated R0 of Coronavirus Disease 2019 (COVID-19) and generated valuable prediction for the early phase of this outbreak. After implementation of strict prevention and control measures in China, new estimation is needed. An infectious disease dynamics SEIR (Susceptible, Exposed, Infectious and Removed) model was applied to estimate the epidemic trend in Wuhan, China under two assumptions of Rt. In the first assumption, Rt was assumed to maintain over 1. The estimated number of infections would continue to increase throughout February without any indication of dropping with Rt = 1.9, 2.6 or 3.1. The number of infections would reach 11,044, 70,258 and 227,989, respectively, by 29 February 2020. In the second assumption, Rt was assumed to gradually decrease at different phases from high level of transmission (Rt = 3.1, 2.6 and 1.9) to below 1 (Rt = 0.9 or 0.5) owing to increasingly implemented public heath intervention. Several phases were divided by the dates when various levels of prevention and control measures were taken in effect in Wuhan. The estimated number of infections would reach the peak in late February, which is 58,077-84,520 or 55,869-81,393. Whether or not the peak of the number of infections would occur in February 2020 may be an important index for evaluating the sufficiency of the current measures taken in China. Regardless of the occurrence of the peak, the currently strict measures in Wuhan should be continuously implemented and necessary strict public health measures should be applied in other locations in China with high number of COVID-19 cases, in order to reduce Rt to an ideal level and control the infection.",
+    "rel_num_authors": 15,
+    "rel_authors": [
+      {
+        "author_name": "Huwen Wang",
+        "author_inst": "School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China"
+      },
+      {
+        "author_name": "Zezhou Wang",
+        "author_inst": "Department of Cancer Prevention, Shanghai Cancer Center, Fudan University; Department of oncology, Shanghai Medical College, Fudan University, Shanghai 200025, "
+      },
+      {
+        "author_name": "Yinqiao Dong",
+        "author_inst": "Department of Environmental and Occupational Health, School of Public Health, China Medical University, Shenyang 110122, China"
+      },
+      {
+        "author_name": "Ruijie Chang",
+        "author_inst": "School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China"
+      },
+      {
+        "author_name": "Chen Xu",
+        "author_inst": "School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China"
+      },
+      {
+        "author_name": "Xiaoyue Yu",
+        "author_inst": "School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China"
+      },
+      {
+        "author_name": "Shuxian Zhang",
+        "author_inst": "School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China"
+      },
+      {
+        "author_name": "Lhakpa Tsamlag",
+        "author_inst": "School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China"
+      },
+      {
+        "author_name": "Meili Shang",
+        "author_inst": "Sanlin Community Health Service Center, Shanghai 200124, China"
+      },
+      {
+        "author_name": "Jinyan Huang",
+        "author_inst": "State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine (Shanghai), Rui-Jin Hospital, Sh"
+      },
+      {
+        "author_name": "Ying Wang",
+        "author_inst": "School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China"
+      },
+      {
+        "author_name": "Gang Xu",
+        "author_inst": "School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China"
+      },
+      {
+        "author_name": "Tian Shen",
+        "author_inst": "School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China"
+      },
+      {
+        "author_name": "Xinxin Zhang",
+        "author_inst": "Research Laboratory of Clinical Virology, National Research Center for Translational Medicine (Shanghai)c, Rui-Jin Hospital, and Rui-Jin Hospital North, Shangha"
+      },
+      {
+        "author_name": "Yong Cai",
+        "author_inst": "School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.02.19.20025148",
     "rel_title": "Trends and prediction in daily incidence of novel coronavirus infection in China, Hubei Province and Wuhan City: an application of Farr law",
@@ -1609161,37 +1607494,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "health systems and quality improvement"
   },
-  {
-    "rel_doi": "10.1101/2020.02.15.950568",
-    "rel_title": "Multivariate Analyses of Codon Usage in 2019 Novel Coronavirus on the Genomic Landscape of Betacoronavirus",
-    "rel_date": "2020-02-20",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.15.950568",
-    "rel_abs": "Coronavirus disease 2019 (COVID-19) is a global health concern as it continues to spread within China and beyond. The causative agent of this disease, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), belongs to the genus Betacoronavirus which also includes severe acute respiratory syndrome related coronavirus (SARSr-CoV) and Middle East respiratory syndrome related coronavirus (MERSr-CoV). Codon usage of viral genes are believed to be subjected to different selection pressures in different host environments. Previous studies on codon usage of influenza A viruses can help identify viral host origins and evolution trends, however, similar studies on coronaviruses are lacking. In this study, global correspondence analysis (CA), within-group correspondence analysis (WCA) and between-group correspondence analysis (BCA) were performed among different genes in coronavirus viral sequences. The amino acid usage pattern of SARS-CoV-2 was generally found similar to bat and human SARSr-CoVs. However, we found greater synonymous codon usage differences between SARS-CoV-2 and its phylogenetic relatives on spike and membrane genes, suggesting these two genes of SARS-CoV-2 are subjected to different evolutionary pressures.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Haogao Gu",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Daniel K W Chu",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Joseph Sriyal Malik Peiris",
-        "author_inst": "The University of Hong Kong"
-      },
-      {
-        "author_name": "Leo L M Poon",
-        "author_inst": "The University of Hong Kong"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "evolutionary biology"
-  },
   {
     "rel_doi": "10.1101/2020.02.12.946087",
     "rel_title": "Candidate targets for immune responses to 2019-Novel Coronavirus (nCoV): sequence homology- and bioinformatic-based predictions",
@@ -1609554,6 +1607856,33 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2020.02.19.950253",
+    "rel_title": "Pangolin homology associated with 2019-nCoV",
+    "rel_date": "2020-02-20",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.19.950253",
+    "rel_abs": "To explore potential intermediate host of a novel coronavirus is vital to rapidly control continuous COVID-19 spread. We found genomic and evolutionary evidences of the occurrence of 2019-nCoV-like coronavirus (named as Pangolin-CoV) from dead Malayan Pangolins. Pangolin-CoV is 91.02% and 90.55% identical at the whole genome level to 2019-nCoV and BatCoV RaTG13, respectively. Pangolin-CoV is the lowest common ancestor of 2019-nCoV and RaTG13. The S1 protein of Pangolin-CoV is much more closely related to 2019-nCoV than RaTG13. Five key amino-acid residues involved in the interaction with human ACE2 are completely consistent between Pangolin-CoV and 2019-nCoV but four amino-acid mutations occur in RaTG13. It indicates Pangolin-CoV has similar pathogenic potential to 2019-nCoV, and would be helpful to trace the origin and probable intermediate host of 2019-nCoV.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Zhigang Zhang",
+        "author_inst": "Yunnan University"
+      },
+      {
+        "author_name": "Qunfu Wu",
+        "author_inst": "Yunnan University"
+      },
+      {
+        "author_name": "Tao Zhang",
+        "author_inst": "Yunnan University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "pathology"
+  },
   {
     "rel_doi": "10.1101/2020.02.16.951723",
     "rel_title": "SARS-CoV-2 and SARS-CoV Spike-RBD Structure and Receptor Binding Comparison and Potential Implications on Neutralizing Antibody and Vaccine Development",
@@ -1610659,37 +1608988,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.02.15.20023234",
-    "rel_title": "The estimate of infected individuals of the 2019-Novel Coronavirus in South Korea by incoming international students from the countries of risk of 2019-Novel Coronavirus: a simulation study",
-    "rel_date": "2020-02-19",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.15.20023234",
-    "rel_abs": "BackgroundIn March 2020, overall, 37,000 international students from the country at risk of the 2019-novel coronavirus (COVID-19) infection will arrive in Seoul, South Korea. Individuals from the country at risk of COVID-19 infection have been included in a home-quarantine program, but the efficacy of the program is uncertain.\n\nMethodsTo estimate the possible number of infected individuals within the large influx of international students, we used a deterministic compartmental model for epidemic and perform a simulation-based search of different rates of compliance with home-quarantine.\n\nResultsUnder the home-quarantine program, the total number of the infected individuals would reach 24-53 from March 17-March 20, 50-86 from March 18- March 16, and 234- 343 from March 4- March 23 with the arrival of 0.1%, 0.2%, and 1% of pre-infectious individuals, in Seoul, South Korea, respectively. Our findings indicated when incoming international students showed strict compliance with quarantine, epidemics were less likely to occur in Seoul, South Korea.\n\nConclusionTo mitigate possible epidemics, additional efforts to improve the compliance of home-quarantine are warranted along with other containment policies.",
-    "rel_num_authors": 4,
-    "rel_authors": [
-      {
-        "author_name": "Sukhyun Ryu",
-        "author_inst": "Department of Preventive Medicine, College of Medicine, Konyang University, Daejeon"
-      },
-      {
-        "author_name": "Sheikh Taslim Ali",
-        "author_inst": "3WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong"
-      },
-      {
-        "author_name": "Jun-sik Lim",
-        "author_inst": "Department of Public Health Science, Graduate School of Public Health, Seoul National University, Seoul"
-      },
-      {
-        "author_name": "Byung Chul Chun",
-        "author_inst": "Department of Preventive Medicine, Korea University College of Medicine, Seoul, Republic of Korea"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.02.17.20024018",
     "rel_title": "COVID-19 in a Designated Infectious Diseases HospitalOutside Hubei Province,China",
@@ -1611016,6 +1609314,37 @@
     "type": "new results",
     "category": "evolutionary biology"
   },
+  {
+    "rel_doi": "10.1101/2020.02.10.942185",
+    "rel_title": "Structural modeling of 2019-novel coronavirus (nCoV) spike protein reveals a proteolytically-sensitive activation loop as a distinguishing feature compared to SARS-CoV and related SARS-like coronaviruses",
+    "rel_date": "2020-02-18",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.10.942185",
+    "rel_abs": "The 2019 novel coronavirus (2019-nCoV) is currently causing a widespread outbreak centered on Hubei province, China and is a major public health concern. Taxonomically 2019-nCoV is closely related to SARS-CoV and SARS-related bat coronaviruses, and it appears to share a common receptor with SARS-CoV (ACE-2). Here, we perform structural modeling of the 2019-nCoV spike glycoprotein. Our data provide support for the similar receptor utilization between 2019-nCoV and SARS-CoV, despite a relatively low amino acid similarity in the receptor binding module. Compared to SARS-CoV, we identify an extended structural loop containing basic amino acids at the interface of the receptor binding (S1) and fusion (S2) domains, which we predict to be proteolytically-sensitive. We suggest this loop confers fusion activation and entry properties more in line with MERS-CoV and other coronaviruses, and that the presence of this structural loop in 2019-nCoV may affect virus stability and transmission.",
+    "rel_num_authors": 4,
+    "rel_authors": [
+      {
+        "author_name": "Javier A. Jaimes",
+        "author_inst": "Cornell University"
+      },
+      {
+        "author_name": "Nicole M Andre",
+        "author_inst": "Cornell University"
+      },
+      {
+        "author_name": "Jean K Millet",
+        "author_inst": "INRAE"
+      },
+      {
+        "author_name": "Gary R. Whittaker",
+        "author_inst": "Cornell University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "microbiology"
+  },
   {
     "rel_doi": "10.1101/2020.02.13.20022715",
     "rel_title": "Analysis of meteorological conditions and prediction of epidemic trend of 2019-nCoV infection in 2020",
@@ -1612041,33 +1610370,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
-  {
-    "rel_doi": "10.1101/2020.02.14.20023036",
-    "rel_title": "The Efficacy of Contact Tracing for the Containment of the 2019 Novel Coronavirus (COVID-19).",
-    "rel_date": "2020-02-17",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.14.20023036",
-    "rel_abs": "Contact tracing is a central public health response to infectious disease outbreaks, especially in the early stages of an outbreak when specific treatments are limited. Importation of novel Coronavirus (COVID-19) from China and elsewhere into the United Kingdom highlights the need to understand the impact of contact tracing as a control measure. Using detailed survey information on social encounters coupled to predictive models, we investigate the likely efficacy of the current UK definition of a close contact (within 2 meters for 15 minutes or more) and the distribution of secondary cases that may go untraced. Taking recent estimates for COVID-19 transmission, we show that less than 1 in 5 cases will generate any subsequent untraced cases, although this comes at a high logistical burden with an average of 36.1 individuals (95th percentiles 0-182) traced per case. Changes to the definition of a close contact can reduce this burden, but with increased risk of untraced cases; we estimate that any definition where close contact requires more than 4 hours of contact is likely to lead to uncontrolled spread.",
-    "rel_num_authors": 3,
-    "rel_authors": [
-      {
-        "author_name": "Matt J Keeling",
-        "author_inst": "University of Warwick"
-      },
-      {
-        "author_name": "T. Deirdre Hollingsworth",
-        "author_inst": "Oxford University"
-      },
-      {
-        "author_name": "Jonathan M Read",
-        "author_inst": "Lancaster University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "public and global health"
-  },
   {
     "rel_doi": "10.1101/2020.02.14.20023127",
     "rel_title": "Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (COVID-19)",
@@ -1612302,6 +1610604,53 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.02.12.20021386",
+    "rel_title": "Long-Term Persistence of IgG Antibodies in SARS-CoV Infected Healthcare Workers",
+    "rel_date": "2020-02-14",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.12.20021386",
+    "rel_abs": "BACKGROUNDThe ongoing worldwide outbreak of the 2019-nCoV is markedly similar to the severe acute respiratory syndrome (SARS) outbreak 17 years ago. During the 2002-2003 SARS outbreak, healthcare workers formed a special population of patients. Although virus-specific IgG play important roles in virus neutralization and prevention against future infection, limited information is available regarding the long term persistence of IgG after infection with SARS-like coronavirus.\n\nMETHODSA long-term prospective cohort study followed 34 SARS-CoV-infected healthcare workers from a hospital with clustered infected cases during the 2002-2003 SARS outbreak in Guangzhou, China, with a 13-year follow-up. Serum samples were collected annually from 2003-2015. Twenty SARS-CoV-infected and 40 non-infected healthcare workers were enrolled in 2015, and their serum samples were collected. All sera were tested for IgG antibodies with ELISA using whole virus and a recombinant nucleocapsid protein of SARS-CoV, as a diagnostic antigen.\n\nRESULTSAnti SARS-CoV IgG was found to persist for up to 12 years. IgG titers typically peaked in 2004, declining rapidly from 2004-2006, and then continued to decline at a slower rate. IgG titers in SARS-CoV-infected healthcare workers remained at a significantly high level until 2015. Patients treated with corticosteroids at the time of infection were found to have lower IgG titers than those without.\n\nCONCLUSIONSIgG antibodies against SARS-CoV can persist for at least 12 years. The presence of SARS-CoV IgG might provide protection against SARS-CoV and other betacoronavirus. This study provides valuable information regarding humoral immune responses against SARS-CoV and the 2019-nCoV.",
+    "rel_num_authors": 8,
+    "rel_authors": [
+      {
+        "author_name": "Xiaoqin Guo",
+        "author_inst": "Sun Yat-sen University"
+      },
+      {
+        "author_name": "Zhongmin Guo",
+        "author_inst": "Sun Yat-sen University"
+      },
+      {
+        "author_name": "Chaohui Duan",
+        "author_inst": "Sun Yat-sen University"
+      },
+      {
+        "author_name": "Zeliang chen",
+        "author_inst": "Sun Yat-Sen University - North Campus Library"
+      },
+      {
+        "author_name": "Guoling Wang",
+        "author_inst": "Sun Yat-sen University"
+      },
+      {
+        "author_name": "Yi Lu",
+        "author_inst": "Boston University"
+      },
+      {
+        "author_name": "Mengfeng Li",
+        "author_inst": "Sun Yat-sen University"
+      },
+      {
+        "author_name": "Jiahai Lu",
+        "author_inst": "Sun Yat-sen University"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nd",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.02.12.20022566",
     "rel_title": "A spatial model of CoVID-19 transmission in England and Wales: early spread and peak timing",
@@ -1613327,77 +1611676,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "ophthalmology"
   },
-  {
-    "rel_doi": "10.1101/2020.02.10.20021832",
-    "rel_title": "Characteristics of lymphocyte subsets and cytokines in peripheral blood of 123 hospitalized patients with 2019 novel coronavirus pneumonia (NCP)",
-    "rel_date": "2020-02-12",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.10.20021832",
-    "rel_abs": "BackgroundTo explore the cellular immunity and cytokines status of NCP patients and to predict the correlation between the cellular immunity levels, cytokines and the severity of patients.\n\nMethods123 NCP patients were divided into mild and severe groups. Peripheral blood was collected, lymphocyte subsets and cytokines were detected. Correlation analysis was performed on the lymphocyte subsets and cytokines, and the differences between the indexes of the two groups were analyzed.\n\nResults102 mild and 21 severe patients were included. Lymphocyte subsets were reduced in two groups. The proportion of CD8 + T reduction in the mild and severe group was 28.43% and 61.9%, respectively; The proportion of B cell reduction was 25.49% and 28.57%; The proportion of NK cell reduction was 34.31% and 47.62%; The detection value of IL-6 was 0 in 55.88% of the mild group, mild group has a significantly lower proportion of patients with IL-6 higher than normal than severe group; There was no significant linear correlation between the lymphocyte subsets and cytokines, while significant differences were noticed between the two groups in CD4 + T, CD8 + T, IL-6 and IL-10.\n\nConclusionsLow levels of CD4+T and CD8+T are common in severe NCP. IL-6 and IL-10 levels were higher in severe patients. T cell subsets and cytokines can be used as one of the basis for predicting the transition from mild to severe. Large number of samples are still needed to confirm the \"warning value\" of CD4 + T, CD8 + T IL-6 and IL-10.",
-    "rel_num_authors": 14,
-    "rel_authors": [
-      {
-        "author_name": "Suxin Wan",
-        "author_inst": "Chongqing University Three Gorges Hospital"
-      },
-      {
-        "author_name": "Qingjie Yi",
-        "author_inst": "Chongqing University Three Gorges Hospital"
-      },
-      {
-        "author_name": "Shibing Fan",
-        "author_inst": "Chongqing University Three Gorges Hospital"
-      },
-      {
-        "author_name": "Jinglong Lv",
-        "author_inst": "Chongqing Three Gorges Central Hospital"
-      },
-      {
-        "author_name": "Xianxiang Zhang",
-        "author_inst": "Chongqing University Three Gorges Hospital"
-      },
-      {
-        "author_name": "Lian Guo",
-        "author_inst": "Chongqing University Three Gorges Hospital"
-      },
-      {
-        "author_name": "Chunhui Lang",
-        "author_inst": "Chongqing University Three Gorges Hospital"
-      },
-      {
-        "author_name": "Qing Xiao",
-        "author_inst": "the First Affiliated Hospital of Chongqing Medical University"
-      },
-      {
-        "author_name": "Kaihu Xiao",
-        "author_inst": "Chongqing University Three Gorges Hospital"
-      },
-      {
-        "author_name": "Zhengjun Yi",
-        "author_inst": "School of mathematics and statistics, Chongqing University"
-      },
-      {
-        "author_name": "Mao Qiang",
-        "author_inst": "Basic College of Qingdao University, Qingdao"
-      },
-      {
-        "author_name": "Jianglin Xiang",
-        "author_inst": "Chongqing University Three Gorges Hospital"
-      },
-      {
-        "author_name": "Bangshuo Zhang",
-        "author_inst": "Chongqing University Three Gorges Hospital"
-      },
-      {
-        "author_name": "Yongping Chen",
-        "author_inst": "Chongqing University Three Gorges Hospital"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "hematology"
-  },
   {
     "rel_doi": "10.1101/2020.02.10.20021824",
     "rel_title": "Distribution of the 2019-nCoV Epidemic and Correlation with Population Emigration from Wuhan, China",
@@ -1613704,6 +1611982,33 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
+  {
+    "rel_doi": "10.1101/2020.02.07.20021196",
+    "rel_title": "Tracking the spread of novel coronavirus (2019-nCoV) based on big data",
+    "rel_date": "2020-02-11",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.07.20021196",
+    "rel_abs": "The novel coronavirus (2019-nCoV) appeared in Wuhan in late 2019 have infected 34,598 people, and killed 723 among them until 8th February 2020. The new virus has spread to at least 316 cities (until 1st February 2020) in China. We used the traffic flow data from Baidu Map, and number of air passengers who left Wuhan from 1st January to 26th January, to quantify the potential infectious people. We developed multiple linear models with local population and air passengers as predicted variables to explain the variance of confirmed cases in every city across China. We found the contribution of air passengers from Wuhan was decreasing gradually, but the effect of local population was increasing, indicating the trend of local transmission. However, the increase of local transmission is slow during the early stage of novel coronavirus, due to the super strict control measures carried out by government agents and communities.",
+    "rel_num_authors": 3,
+    "rel_authors": [
+      {
+        "author_name": "Xumao Zhao",
+        "author_inst": "Lanzhou University"
+      },
+      {
+        "author_name": "Xiang Liu",
+        "author_inst": "Lanzhou University"
+      },
+      {
+        "author_name": "Xinhai Li",
+        "author_inst": "Institute of Zoology, Chinese Academy of Sciences"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "epidemiology"
+  },
   {
     "rel_doi": "10.1101/2020.02.07.20021154",
     "rel_title": "The Novel Coronavirus, 2019-nCoV, is Highly Contagious and More Infectious Than Initially Estimated",
@@ -1615053,45 +1613358,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "respiratory medicine"
   },
-  {
-    "rel_doi": "10.1101/2020.02.04.933135",
-    "rel_title": "Protein structure and sequence re-analysis of 2019-nCoV genome does not indicate snakes as its intermediate host or the unique similarity between its spike protein insertions and HIV-1",
-    "rel_date": "2020-02-08",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.04.933135",
-    "rel_abs": "As the infection of 2019-nCoV coronavirus is quickly developing into a global pneumonia epidemic, careful analysis of its transmission and cellular mechanisms is sorely needed. In this report, we re-analyzed the computational approaches and findings presented in two recent manuscripts by Ji et al. (https://doi.org/10.1002/jmv.25682) and by Pradhan et al. (https://doi.org/10.1101/2020.01.30.927871), which concluded that snakes are the intermediate hosts of 2019-nCoV and that the 2019-nCoV spike protein insertions shared a unique similarity to HIV-1. Results from our re-implementation of the analyses, built on larger-scale datasets using state-of-the-art bioinformatics methods and databases, do not support the conclusions proposed by these manuscripts. Based on our analyses and existing data of coronaviruses, we concluded that the intermediate hosts of 2019-nCoV are more likely to be mammals and birds than snakes, and that the \"novel insertions\" observed in the spike protein are naturally evolved from bat coronaviruses.",
-    "rel_num_authors": 6,
-    "rel_authors": [
-      {
-        "author_name": "Chengxin Zhang",
-        "author_inst": "Department of Computational Medicine and Bioinformatics, University of Michigan"
-      },
-      {
-        "author_name": "Wei Zheng",
-        "author_inst": "Department of Computational Medicine and Bioinformatics, University of Michigan"
-      },
-      {
-        "author_name": "Xiaoqiang Huang",
-        "author_inst": "Department of Computational Medicine and Bioinformatics, University of Michigan"
-      },
-      {
-        "author_name": "Eric W Bell",
-        "author_inst": "Department of Computational Medicine and Bioinformatics, University of Michigan"
-      },
-      {
-        "author_name": "Xiaogen Zhou",
-        "author_inst": "Department of Computational Medicine and Bioinformatics, University of Michigan"
-      },
-      {
-        "author_name": "Yang Zhang",
-        "author_inst": "Department of Computational Medicine and Bioinformatics, University of Michigan"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by",
-    "type": "contradictory results",
-    "category": "bioinformatics"
-  },
   {
     "rel_doi": "10.1101/2020.02.05.20020792",
     "rel_title": "Preparedness and vulnerability of African countries against introductions of 2019-nCoV",
@@ -1615410,6 +1613676,45 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "epidemiology"
   },
+  {
+    "rel_doi": "10.1101/2020.02.03.20020263",
+    "rel_title": "Network-based Drug Repurposing for Human Coronavirus",
+    "rel_date": "2020-02-05",
+    "rel_site": "medRxiv",
+    "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.03.20020263",
+    "rel_abs": "Human Coronaviruses (HCoVs), including severe acute respiratory syndrome coronavirus (SARS-CoV), Middle east respiratory syndrome coronavirus (MERS-CoV), and 2019 novel coronavirus (2019-nCoV), lead global epidemics with high morbidity and mortality. However, there are currently no effective drugs targeting 2019-nCoV. Drug repurposing, represented as an effective drug discovery strategy from existing drugs, could shorten the time and reduce the cost compared to de novo drug discovery. In this study, we present an integrative, antiviral drug repurposing methodology implementing a systems pharmacology-based network medicine platform, quantifying the interplay between the HCoV-host interactome and drug targets in the human protein-protein interaction network. Phylogenetic analyses of 15 HCoV whole genomes reveal that 2019-nCoV has the highest nucleotide sequence identity with SARS-CoV (79.7%) among the six other known pathogenic HCoVs. Specifically, the envelope and nucleocapsid proteins of 2019-nCoV are two evolutionarily conserved regions, having the sequence identities of 96% and 89.6%, respectively, compared to SARS-CoV. Using network proximity analyses of drug targets and known HCoV-host interactions in the human protein-protein interactome, we computationally identified 135 putative repurposable drugs for the potential prevention and treatment of HCoVs. In addition, we prioritized 16 potential anti-HCoV repurposable drugs (including melatonin, mercaptopurine, and sirolimus) that were further validated by enrichment analyses of drug-gene signatures and HCoV-induced transcriptomics data in human cell lines. Finally, we showcased three potential drug combinations (including sirolimus plus dactinomycin, mercaptopurine plus melatonin, and toremifene plus emodin) captured by the  Complementary Exposure pattern: the targets of the drugs both hit the HCoV-host subnetwork, but target separate neighborhoods in the human protein-protein interactome network. In summary, this study offers powerful network-based methodologies for rapid identification of candidate repurposable drugs and potential drug combinations toward future clinical trials for HCoVs.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Yadi Zhou",
+        "author_inst": "Cleveland Clinic"
+      },
+      {
+        "author_name": "Yuan Hou",
+        "author_inst": "Cleveland Clinic"
+      },
+      {
+        "author_name": "Jiayu Shen",
+        "author_inst": "Cleveland Clinic"
+      },
+      {
+        "author_name": "Yin Huang",
+        "author_inst": "Cleveland Clinic"
+      },
+      {
+        "author_name": "William Martin",
+        "author_inst": "Cleveland Clinic"
+      },
+      {
+        "author_name": "Feixiong Cheng",
+        "author_inst": "Cleveland Clinic"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc",
+    "type": "PUBLISHAHEADOFPRINT",
+    "category": "infectious diseases"
+  },
   {
     "rel_doi": "10.1101/2020.02.04.20020438",
     "rel_title": "The impact of traffic isolation in Wuhan on the spread of 2019-nCov",
@@ -1616439,25 +1614744,6 @@
     "type": "PUBLISHAHEADOFPRINT",
     "category": "infectious diseases"
   },
-  {
-    "rel_doi": "10.1101/2020.01.30.20019828",
-    "rel_title": "Modelling the epidemic trend of the 2019-nCOV outbreak in Hubei Province, China",
-    "rel_date": "2020-02-02",
-    "rel_site": "medRxiv",
-    "rel_link": "https://medrxiv.org/cgi/content/short/2020.01.30.20019828",
-    "rel_abs": "As of 8am 30th January (Beijing Time) 2020, Approximate 8000 cases across the world have been confirmed. Its necessary to simulate epidemic trend of the 2019-nCOV outbreak in Hubei Province, the hardest-hit area. By SEIR simulation, the predicted epidemic peak in Hubei will be within 28th January 2020 to 7th February 2020, up to 7000-9000 infectious cases in total. The estimate above was based on some assumptions and limitations exited.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Lizhe Ai",
-        "author_inst": "Changchun Jilin Province"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "PUBLISHAHEADOFPRINT",
-    "category": "epidemiology"
-  },
   {
     "rel_doi": "10.1101/2020.01.29.20019547",
     "rel_title": "Real time estimation of the risk of death from novel coronavirus (2019-nCoV) infection: Inference using exported cases",
@@ -1616712,6 +1614998,45 @@
     "type": "new results",
     "category": "genetics"
   },
+  {
+    "rel_doi": "10.1101/2020.01.30.926881",
+    "rel_title": "Engineered unnatural ubiquitin for optimal detection of deubiquitinating enzymes",
+    "rel_date": "2020-01-31",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.01.30.926881",
+    "rel_abs": "Deubiquitinating enzymes (DUBs) are responsible for removing ubiquitin (Ub) from its protein conjugates. DUBs have been implicated as attractive therapeutic targets in the treatment of viral diseases, neurodegenerative disorders and cancer. The lack of selective chemical tools for the exploration of these enzymes significantly impairs the determination of their roles in both normal and pathological states. Commercially available fluorogenic substrates are based on the C-terminal Ub motif or contain Ub coupled to a fluorophore (Z-LRGG-AMC, Ub-AMC); therefore, these substrates suffer from lack of selectivity. By using a hybrid combinatorial substrate library (HyCoSuL) and a defined P2 library containing a wide variety of nonproteinogenic amino acids, we established a full substrate specificity profile for two DUBs--MERS PLpro and human UCH-L3. Based on these results, we designed and synthesized Ub-based substrates and activity-based probes (ABPs) containing selected unnatural amino acids located in the C-terminal Ub motif. Biochemical analysis and cell-based experiments confirmed the activity and selectivity of engineered Ub-based substrates and probes. Using this approach, we propose that for any protease that recognizes Ub and Ub-like substrates, a highly active and selective unnatural substrate or probe can be engineered.",
+    "rel_num_authors": 6,
+    "rel_authors": [
+      {
+        "author_name": "Wioletta Rut",
+        "author_inst": "Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland"
+      },
+      {
+        "author_name": "Mikolaj Zmudzinski",
+        "author_inst": "Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland"
+      },
+      {
+        "author_name": "Scott J. Snipas",
+        "author_inst": "Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA"
+      },
+      {
+        "author_name": "Miklos Bekes",
+        "author_inst": "Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA"
+      },
+      {
+        "author_name": "Tony T. Huang",
+        "author_inst": "Department of Biochemistry & Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA"
+      },
+      {
+        "author_name": "Marcin Drag",
+        "author_inst": "Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland"
+      }
+    ],
+    "version": "1",
+    "license": "cc_no",
+    "type": "new results",
+    "category": "biochemistry"
+  },
   {
     "rel_doi": "10.1101/2020.01.30.927806",
     "rel_title": "The digestive system is a potential route of 2019-nCov infection: a bioinformatics analysis based on single-cell transcriptomes",
@@ -1617624,25 +1615949,6 @@
     "type": "new results",
     "category": "ecology"
   },
-  {
-    "rel_doi": "10.1101/2020.01.23.916726",
-    "rel_title": "Modelling the epidemic trend of the 2019 novel coronavirus outbreak in China",
-    "rel_date": "2020-01-25",
-    "rel_site": "bioRxiv",
-    "rel_link": "https://biorxiv.org/cgi/content/short/2020.01.23.916726",
-    "rel_abs": "We present a timely evaluation of the Chinese 2019-nCov epidemic in its initial phase, where 2019-nCov demonstrates comparable transmissibility but lower fatality rates than SARS and MERS. A quick diagnosis that leads to case isolation and integrated interventions will have a major impact on its future trend. Nevertheless, as China is facing its Spring Festival travel rush and the epidemic has spread beyond its borders, further investigation on its potential spatiotemporal transmission pattern and novel intervention strategies are warranted.",
-    "rel_num_authors": 1,
-    "rel_authors": [
-      {
-        "author_name": "Zhihang Peng",
-        "author_inst": "Nanjing Medical University"
-      }
-    ],
-    "version": "1",
-    "license": "cc_by_nc_nd",
-    "type": "new results",
-    "category": "microbiology"
-  },
   {
     "rel_doi": "10.1101/2020.01.24.919241",
     "rel_title": "From SARS-CoV to Wuhan 2019-nCoV: Will History Repeat Itself?",
@@ -1617953,6 +1616259,57 @@
     "type": "new results",
     "category": "microbiology"
   },
+  {
+    "rel_doi": "10.1101/2020.01.21.914044",
+    "rel_title": "Host and infectivity prediction of Wuhan 2019 novel coronavirus using deep learning algorithm",
+    "rel_date": "2020-01-24",
+    "rel_site": "bioRxiv",
+    "rel_link": "https://biorxiv.org/cgi/content/short/2020.01.21.914044",
+    "rel_abs": "The recent outbreak of pneumonia in Wuhan, China caused by the 2019 Novel Coronavirus (2019-nCoV) emphasizes the importance of detecting novel viruses and predicting their risks of infecting people. In this report, we introduced the VHP (Virus Host Prediction) to predict the potential hosts of viruses using deep learning algorithm. Our prediction suggests that 2019-nCoV has close infectivity with other human coronaviruses, especially the severe acute respiratory syndrome coronavirus (SARS-CoV), Bat SARS-like Coronaviruses and the Middle East respiratory syndrome coronavirus (MERS-CoV). Based on our prediction, compared to the Coronaviruses infecting other vertebrates, bat coronaviruses are assigned with more similar infectivity patterns with 2019-nCoVs. Furthermore, by comparing the infectivity patterns of all viruses hosted on vertebrates, we found mink viruses show a closer infectivity pattern to 2019-nCov. These consequences of infectivity pattern analysis illustrate that bat and mink may be two candidate reservoirs of 2019-nCov.These results warn us to beware of 2019-nCoV and guide us to further explore the properties and reservoir of it.\n\nOne Sentence SummaryIt is of great value to identify whether a newly discovered virus has the risk of infecting human. Guo et al. proposed a virus host prediction method based on deep learning to detect what kind of host a virus can infect with DNA sequence as input. Applied to the Wuhan 2019 Novel Coronavirus, our prediction demonstrated that several vertebrate-infectious coronaviruses have strong potential to infect human. This method will be helpful in future viral analysis and early prevention and control of viral pathogens.",
+    "rel_num_authors": 9,
+    "rel_authors": [
+      {
+        "author_name": "Qian Guo",
+        "author_inst": "State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, and Center for Quantitative Biology, and "
+      },
+      {
+        "author_name": "Mo Li",
+        "author_inst": "State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, and Center for Quantitative Biology, and "
+      },
+      {
+        "author_name": "Chunhui Wang",
+        "author_inst": "State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, and Center for Quantitative Biology, and "
+      },
+      {
+        "author_name": "Zhengcheng Fang",
+        "author_inst": "State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, and Center for Quantitative Biology, and "
+      },
+      {
+        "author_name": "Peihong Wang",
+        "author_inst": "State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, and Center for Quantitative Biology, and "
+      },
+      {
+        "author_name": "Jie Tan",
+        "author_inst": "State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, and Center for Quantitative Biology, and "
+      },
+      {
+        "author_name": "Shufang Wu",
+        "author_inst": "State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, and Center for Quantitative Biology, and "
+      },
+      {
+        "author_name": "Yonghong Xiao",
+        "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University"
+      },
+      {
+        "author_name": "Huaiqiu Zhu",
+        "author_inst": "State Key Laboratory for Turbulence and Complex Systems, Department of Biomedical Engineering, College of Engineering, and Center for Quantitative Biology, Peki"
+      }
+    ],
+    "version": "1",
+    "license": "cc_by_nc_nd",
+    "type": "new results",
+    "category": "systems biology"
+  },
   {
     "rel_doi": "10.1101/2020.01.22.914952",
     "rel_title": "Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin",